- Chimera-users - RBVI Mailing Lists

Linewidth in images
by Dipl.-Ing. Thomas Mitterfellner 22 Dec '09

22 Dec '09

Hello! I am making large images (4096x3072) which use silhouette edges and dashed wire-style bonds. When I increase the width of the silhouette edges, I do see that on the screen, but the output image turns out the same regardless of this setting. The same is true for my dashed bonds. Is this some issue of graphics card (GeForce 6200) or am I missing something? Thank you, Thomas

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selecting zone, minimizing, docking
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 11:30 PM, gytjyb wrote: > hello,Mr meng ! > I have 3 questions. > <1> > I select one residues or animo acid > But how can I made a radius around this residues or animo acid, > I aslo can select neighbor residues or animo acid within some radius. > <2> > If I should add water for model minization and refine, > how can I refine for a new model. > I want to do a mutation,wether I must fix other residues when I do > minization. > <3> > how can I prepare for a docking, dose this software do docking? > thank you for your answer! Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include something meaningful in the "Subject" line. Also, you can use "Help... Search Documentation" in the Chimera menu to look up information by keyword. (1) menu "Select... Zone." You can also specify zones in commands. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones > (2) That is up to your own scientific judgement. As mentioned in an earlier reply, the minimization capabilities in Chimera are rather limited. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > (3) Chimera does not do docking calculations. You can move two structures together by hand... of course that is only approximate. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html> However, Chimera does have tools that are related to docking: "Dock Prep" for preparing structures for docking or other calculations (with other programs outside of Chimera) and "ViewDock" for looking at docking results output by other programs, mainly DOCK. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h… > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> Here is the Web site for DOCK. <http://dock.compbio.ucsf.edu/index.html> They also have tutorials: <http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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identifying residues in a surface
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 5:14 PM, gytjyb wrote: > hello:meng! > thank you for your help! > i want to make a surface about protein. > i want to do lipophilicity and electrostatics surface,we had better > label some amino acid on the surface,how can i do? > or i just use differrent color for different amino acid category. > i think the color must be very different from each. > so i can recognize each other,and find out some important different > between homology protein. > thank you very much! > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include a short description in the "Subject" line. You can show lipophilicity on the surface with menu item "Presets... Interactive 3 (hydrophobicity surface)" where orange is most lipophilic and blue is most hydrophilic. You can show Coulombic electrostatic potential on the surface with "Tools... Surface/Binding Analysis... Coulombic Surface Coloring" The regular labels are not that good when you are showing a surface. They are usually partly inside the surface so you can't read them. If it is for a figure, you can put labels anywhere you want with "2D Labels" (under Tools... Utilities), but those do not move when you rotate the structure. Also, there are pop-ups that say what is under your mouse, but they only show the detailed information when you are not showing the surface. Sometimes I like to use color-coding, a different color for each amino acid type. Of course, you can't have that as the same time as the lipophilicity or electrostatic coloring. There is a command file (rescol.com) linked to the User's Guide that does my favorite residue color-coding: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > You would save that file to your computer as plain text and just open it (file named *.com) in Chimera to apply the residue color-coding. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] hide dashed lines
by Elaine Meng 21 Dec '09

21 Dec '09

Hi Vijay, There are a few ways to hide these "missing segments" pseudobonds. Method 1: Ctrl-click to select one of the dashed lines, click magnifying glass on lower right corner of Chimera window to open Selection Inspector, Inspect "Pseudobond group," change "displayed" to "false" Method 2: open PseudoBond Panel (under Tools... General Controls), choose "missing segments" from the left side and click "hide" on the right side Method 3: "setattr" command, e.g.: setattr g display false but that turns off all pseudobonds, not just missing segment. You could also use the setattr command to only undisplay certain pseudobonds but that would require selecting or naming the endpoint atoms in the command, so if you want to retain other pseudobonds the first two methods will be easier. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 21, 2009, at 10:52 AM, Vijay S. Reddy wrote: > Hello, If the there is break in the structure, it is shown by dahsed > lines in the Chimera, How can I hide them or turn them off. I am > deliberately trying to show different regions that are not > sequentially contiguous. Thanks very much, > Vijay

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center of molecule
by Bala subramanian 18 Dec '09

18 Dec '09

Friends, Is is possible to find the central x,y,z coordinates of a pdb file in chimera. Bala

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[Chimera] #7448: show axes/major ellipses for thermal ellipsoids
by Dipl.-Ing. Thomas Mitterfellner 18 Dec '09

18 Dec '09

Hello! > #7448: show axes/major ellipses for thermal ellipsoids Thanks for the implementation of this feature! There's just one thing: the major ellipses are displayed very thinly. The ellipse size factor does not seem to change the size of the ellipses (I supposed them to become larger than the ellipsoid with increased scaling factor so that they extend beyond the surface). Can the thickness or the size of the major ellipses be altered? Thomas

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price quote for chimera software
by Yong You 18 Dec '09

18 Dec '09

Dear Sir,/ Madam, I am emailing to inquire about a single user/computer license for the Chimera software for Molecular Modeling. Can I get the price quotes for using it in Windows 32-bit OS (Windows XP) and in Linux 64-bit OS? Thanks a lot! Sincerely, Yong You Integrated DNA Technologies, Inc. 1710 Commercial Park, Coralville, IA 52241 (319) 626 -9606

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single-component calculation
by Bala subramanian 17 Dec '09

17 Dec '09

Friends, When i try to show the surface sometimes, i get a chimera warning that ' calculation of some surface components failed, falling back to single component calculation'. The message in reply log is as follows. Kindly enlighten me on what is causing the problem. Calculation of some surface components failed. Falling back to single-component calculation. /home/cbala/chimera/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on RAMANA Copyright M.F. Sanner (March 2000) Compilation flags WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: class_arete2: warning hole in a reentrant face 2119 WARNING: classe_aretes2: No cycle in face 3781 (nba=-6) WARNING: classe_aretes2: No cycle in face 11830 (nba=-4) WARNING: classe_aretes2: No cycle in face 19652 (nba=4) WARNING: classe_aretes2: No cycle in face 19653 (nba=-1) WARNING: classe_aretes2: No cycle in face 19663 (nba=-3) RESTART FROM SES: 1 radius of atom 1220 goes from 1.625000 to 1.725000 radius of atom 1221 goes from 1.000000 to 1.100000 radius of atom 1665 goes from 1.700000 to 1.800000 radius of atom 1666 goes from 1.000000 to 1.100000 radius of atom 3490 goes from 1.500000 to 1.600000 radius of atom 3618 goes from 1.000000 to 1.100000 radius of atom 3620 goes from 1.500000 to 1.600000 radius of atom 3621 goes from 1.000000 to 1.100000 radius of atom 5103 goes from 1.625000 to 1.725000 radius of atom 5106 goes from 1.000000 to 1.100000 Partial mode WARNING: class_arete2: warning hole in a reentrant face 2119 RESTART FROM TRI: 2 radius of atom 470 goes from 1.700000 to 1.800000 radius of atom 4231 goes from 1.700000 to 1.800000 radius of atom 4250 goes from 1.480000 to 1.580000 Partial mode Surface black.pdb, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 16352.1 Total solvent accessible surface area = 17959.3

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error running large iterative script (return code 3)
by Sumitro Harjanto 16 Dec '09

16 Dec '09

Hi, I was trying to run the following script (below), which calculates RMSDs between 39 pdb models. Total iteration will be 741 with about 3000 match commands. After it has run for about 10 mins chimera will crash with an error: Chimera failed abnormally; the exit code was 3. I've printed the debug lines below the script: Any suggestions..? Cheers, Sumitro -------------------------------------------------------- open d:\result\pdb\1B0G.pdb open d:\result\pdb\1DUZ.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1EEY.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1EEZ.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1HHG.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1HHI.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 ... ... ... -------------------------------------------------------- initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions CloneMenu failed inside of MenuAddOrInsert. This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Return code: 3 Press return or enter to to exit --------------------------------------------------------

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size limits on bild geometric primitives?
by Kristina Furse 16 Dec '09

16 Dec '09

Hi- I like to use Chimera as a front end to povray to make high resolution images of molecules. I'm starting to work with other types of data, and was wondering if I could still use it. I have some network data--20,000 nodes with 32,000 connections. I translated the data into drawing instructions in bild format--spheres for the nodes and cylinders for the connections. Small test data sets work (300 nodes with 500 connections or 20,000 spheres with vectors instead of cylinders) but the full data set of spheres and cylinders crashes Chimera. Is there a limit somewhere I could raise or is this a hard wall for bild shapes? Would it be less memory intensive to create a "pdb" of the node locations and create the connections as bonds? Thanks! Kristina Kristina Furse Davis, Ph.D. Visualization Scientist Center for Research Computing University of Notre Dame P.O. Box 539 Room 122 Information Technology Center Notre Dame, IN 46556 kristina.davis(a)nd.edu

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how to create surface from volume tracer path
by jinghua＠ucsd.edu 16 Dec '09

16 Dec '09

When I try to create a tube by tracing two planes, the surface it makes is more like a cone. Do I need connect all the markers from two different planes? Thank you for your help! Jinghua

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Surfnet command line
by Jean Didier Pie Marechal 15 Dec '09

15 Dec '09

Dear All, is there a command line equivalent for surfnet applied to atom selection (not interfase)? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dilluns, Desembre 14, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 80, Issue 14 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. help in installation of chimera-1.4-linux_x86_64.exe > (Dr Muhammad Nadeem Kardar) > 2. Re: help in installation of chimera-1.4-linux_x86_64.exe > (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 14 Dec 2009 10:45:22 +0500 > From: Dr Muhammad Nadeem Kardar <drmnkardar(a)ciitlahore.edu.pk> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] help in installation of > chimera-1.4-linux_x86_64.exe > Message-ID: > <38c1a890912132145o18302b67r6fc153793de8d76d(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > chimera-1.4-linux(2).exe > > chimera-1.4-linux.exe > chimera-1.4-linux_x86_64.exe > > I have three files of chimera but unable to execute chimera kindly > help > Kardar > > -- > M. Nadeem Kardar, PhD > Assistant Professor > Department of Chemical Engineering > COMSATS Institute of Information Technology > Defence Road Off Raiwind Road, Lahore, Pakistan > Cell# +92-300-2414231 > Email: drmnkardar(a)ciitlahore.edu.pk > Website: > http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html--- > ----------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://www.cgl.ucsf.edu/pipermail/chimera- > users/attachments/20091214/5abbdcee/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Mon, 14 Dec 2009 08:45:21 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Dr Muhammad Nadeem Kardar <drmnkardar(a)ciitlahore.edu.pk> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] help in installation of > chimera-1.4-linux_x86_64.exe > Message-ID: <92B97B1E-8164-4CC4-AD10-6161D911791F(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Kardar, > The *exe file is not Chimera itself but an installer. Please click > > the appropriate "Instructions" link on the download page to see how > to > install Chimera from the *exe file. > > <http://www.cgl.ucsf.edu/chimera/download.html> > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 13, 2009, at 9:45 PM, Dr Muhammad Nadeem Kardar wrote: > > > chimera-1.4-linux(2).exe > > > > chimera-1.4-linux.exe > > chimera-1.4-linux_x86_64.exe > > > > I have three files of chimera but unable to execute chimera > kindly > > help > > > > Kardar > > > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 80, Issue 14 > ********************************************* >

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thank you ,thank you very much!
by gytjyb 15 Dec '09

15 Dec '09

Thank you very much for you answer. My english is not very well,Because I just come from china. My major subject is gene structure,So I am not good at protein structure. But ,I think this is very useful for me to analyze protein structure and asure their structure. So,I must thank for you first! You means: If I get a homologous model structure from swissmodel which I just align with PDB stucture,i must minimize structure ,at first。 But before i do minimization,I should add water or not.so this is a question.Which condition should I add water? Secondly,I get a stable structure after minimization.If I want to do mutation, I should do minimization for every time mutation about this structure. Thank you very much! Thank you very much! BEST WISHES FOR YOU!

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Programmer's Guide feedback....
by Will Moore 15 Dec '09

15 Dec '09

Hi, I am just trying to get started coding some plugins to Chimera, by following the Programmer's Guide 1.3. I have limited programming experience, and the points below were where I got stuck... Not sure if the guide is generally aimed at those with more or less developer skills? Starting with the examples (writeMol2.py) it isn't clear that all these commands should be typed in the IDLE window. I see that it is mentioned previously in the text, but it would be helpful to make clear that this is not in the command line or python prompt. When you've downloaded 4fun.pdb and saved it somewhere, does it matter where you save it, and how should you specify this in commands like opened = chimera.openModels.open('4fun.pdb') E.g. this would have made it more clear that you don't just put the file in a particular place that Chimera knows were to look: opened = chimera.openModels.open('Users/username/Downloads/4fun.pdb') Actually, this point was more relevant to the command: execfile("backbone.py") which I was working on earlier. I was trying to save backbone.py in one of the Chimera.app/Contents/Resources folders, and hoping that Chimera would find it with the above command: When really the command should be more like: execfile("Users/username/Desktop/backbone.py") Running chimera from the command line: A note that it is necessary to add the Chimera bin to the PATH variable would have been handy, especially for novice developers. export PATH=$PATH:/Applications/Chimera.app/Contents/Resources/bin/ ToolbarButton.py I got errors when running this script unless I put the import statements in the mainchain function like this import os import chimera def mainchain(): import re import chimera MAINCHAIN = re.compile("^(N|CA|C)$", re.I) for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: a.display = MAINCHAIN.match(a.name) != None chimera.tkgui.app.toolbar.add('ToolbarButton.tiff', mainchain, 'Show Main Chain', None) Otherwise I got errors like: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 434, in init tkgui.eventLoop() File "/Applications/Chimera.app/Contents/Resources/share/chimera/ tkgui.py", line 2885, in eventLoop app.mainloop() File "/Applications/Chimera.app/Contents/Frameworks/ Python.framework/Versions/2.5/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop self.tk.mainloop(n) File "/Applications/Chimera.app/Contents/Frameworks/ Python.framework/Versions/2.5/lib/python2.5/site-packages/Pmw/Pmw_1_3/ lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/ toolbar.py", line 191, in <lambda> command=lambda func=callback: _guard(func)) File "/Applications/Chimera.app/Contents/Resources/share/chimera/ toolbar.py", line 28, in _guard func() File "ToolbarButton.py", line 8, in mainchain MAINCHAIN = re.compile("^(N|CA|C)$", re.I) NameError: global name 're' is not defined Error in toolbar callback: NameError: global name 're' is not defined (see reply log for Python traceback info) This is just my feedback, which I hope is useful Cheers, Will.

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(no subject)
by Bala subramanian 15 Dec '09

15 Dec '09

Friends, I have a RNA structure. I want to calculate hydrogen bonds between the bases (for which i used findhbond menu). Then i want to show the ladder representation for those base-pairs which form atleast two hydrogen bonds. How can i do the same. Hope i am clear. Cheers, Bala

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Re: [Chimera-users] matching peptides with altenate locations
by Elaine Meng 15 Dec '09

15 Dec '09

Hi Sumitro, I work on a Mac and cannot open the winmail.dat file. Can you just send the two PDB files as attachments, or if they are in the public database, tell me what the PDB ID codes are? Thanks, Elaine

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FindHBond
by Greg Friedland 14 Dec '09

14 Dec '09

Hello, I'm new to Chimera and just discovered the FindHBond tool. This tool seems very useful, but unfortunately it draws hbonds between the heavy atoms even when I have hydrogens added. Is there a way to configure this behavior? I'd like the hydrogen bonds to be drawn between the hydrogen and the acceptor atom. It looks rather strange now, especially for the hbonds with relaxed constraints that deviate significantly from the angle made by the hydrogen. See the attached tiff for an example. Also, I'm curious what cutoffs are used. I looked at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… but I was hoping for more details. I.e what numbers from the paper are used for the proton-acceptor distances, donor-proton-acceptor angle and the corresponding dihedral angle. Thanks! Greg Friedland Postdoc Joint BioEnergy Instute Sandia National Lab Formerly of Tanja Kortemme's lab at UCSF

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hello!
by gytjyb 14 Dec '09

14 Dec '09

hello! i am a fleshman for this software! can you tell me about this software ,if all the thing is free? how can i minimize a energy and refine for a protein structure? i also want to do a mutation,how can i do? thank you very much!

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help in installation of chimera-1.4-linux_x86_64.exe
by Dr Muhammad Nadeem Kardar 14 Dec '09

14 Dec '09

chimera-1.4-linux(2).exe chimera-1.4-linux.exe chimera-1.4-linux_x86_64.exe I have three files of chimera but unable to execute chimera kindly help Kardar -- M. Nadeem Kardar, PhD Assistant Professor Department of Chemical Engineering COMSATS Institute of Information Technology Defence Road Off Raiwind Road, Lahore, Pakistan Cell# +92-300-2414231 Email: drmnkardar(a)ciitlahore.edu.pk Website: http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html

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File conversion question
by Miriam Gochin 12 Dec '09

12 Dec '09

I have a series of docked ligands produced by AutoDock (as .dlg files, containing more than one conformer per ligand) and I would love to be able to view these ligands using the ViewDock utility in Chimera. Is there a file conversion protocol? Thanks so much, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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image size
by Bala subramanian 11 Dec '09

11 Dec '09

Friends, What is the best way to generate an image of fixed size. Say i want to create an image of 4,4 (width, height) at 300dpi. I tried the following windowsize 1200 1200 When i go to save image--> I saw the pixel width and height changed as *1200, 618* ( I dnt understand why this changes although i set as 1200 1200). So i set the print unit as 'inches', then i entered width and height as 4,4. The final image that it produced has different width and height (4, 6.13). Thanks, Bala

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Problem solved! Sorry, but it seems all I needed to do was show the atoms and bonds. Chimera is reading the file it just doesn't show anything until you tell it to show atoms and bonds. Another surprise with the new Chimera version is that it automatically displays my nucleic acid files with slab bases, filled sugars, and a backbone ribbon. Is there anyway to shut this off so I don't have to go in and manually do it each time I open a nucleic acid structure? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Hi! I have been using a program called Curves for analyzing nucleic acid crystal structures for quite a while and I have always used Chimera to visualize the output pdb. One file shows the backbone splines and the vectors defining the nucleic acid groove widths (r+bdna_b.pdb) and the other file shows the nucleic acid helical axis (r+bdna_X.pdb). Chimera has always been able to read both of these files until the recent production release where it is no longer able to read the r+bdna_b.pdb file. I have attached the two files and the actual DNA pdb file. Can you please help me fix the problem with reading the r+bdna_b.pdb file in the new production release? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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creating additional coordinates to save from BIOMT records
by Irene Newhouse 09 Dec '09

09 Dec '09

I'm working with a pdb structure that's icosahedral. The surface is tiled with hexamers and pentamers of its single chain. The unit cell contains 4 chains, 3 from a hexamer and 1 from a pentamer. I need to compare the pentamer inter-chain contacts to those in the hexamer, so I immediately thought of Chimera. I can generate a pretty picture of hexamers & pentamers on screen, but what I can't seem to figure out how to do is to save additional coordinates for the other units of the pentamer, analogous to saving additional coordinates when you fill out a unit cell using the "Higher-order Structure" utilities. Thanks for your help! Irene Newhouse Res. Corp. U of Hawaii _________________________________________________________________ Windows 7: Unclutter your desktop. Learn more. http://www.microsoft.com/windows/windows-7/videos-tours.aspx?h=7sec&slideid…

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isosurface
by Bala subramanian 09 Dec '09

09 Dec '09

Friends, I have calculated the electrostatic-potential map using APBS program. I can use the 'electrostatic colouring' to colour my protein but i want to display the +ve and -ve isosurface. Kindly write me how to do the same. Thanks, Bala

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chimera help - calmodulin
by roach a.p.l. (aplr1g08) 07 Dec '09

07 Dec '09

Hi, I am a student trying to do a project on the protein calmodulin. I have just started using chimera and have gone though your tutorials and understood everything as it is very clear but i don't know how i would select the protein calmodulin and put it in the chimera display to make my images. I realise this is probably a simple step but this is all new to me and i would much appreciate your help. Thank you Annabel Roach

2 1

Maximizing performance with large volume data maps
by Ryan Rochat 07 Dec '09

07 Dec '09

Hello, I was wondering how much video memory Chimera is capable of accessing. I currently have a 898Mb videocard that begins to slow down with a 550x550x550 map (at step size 1). This map is actually a downsample of the true 1100x1100x1100 map coming in at 5GB. I was contemplating going for a much larger video card at 4GB, however I was curious to what extent I could expect to see acceleration using Chimera with such a massive dataset (600+MB) and video card. Thank you, Ryan H. Rochat MS MD/PhD Candidate (Baylor College of Medicine) Graduate Student SCBMB (Baylor College of Medicine) Chiu Lab One Baylor Plaza N420 Alkek Houston Texas 77030

2 1

Re: [Chimera-users] To consult the Morph conformation
by Elaine Meng 07 Dec '09

07 Dec '09

Dear Jiraporn, Sorry, Morph Conformations only includes parts that are in both structures in the morphing trajectory. In your situation, I suggest text-editing one of the input PDB files (more details below). Morph Conformations maps residues in the starting structure to residues in the ending structure by creating a sequence alignment. Where the residue in the starting structure is aligned with the same type of residue in the ending structure, the whole residue will be included. Where the residue in the starting structure is aligned with a different type of residue, only the parts that are the same will be included, which will include the backbone and sometimes part of the sidechain. Where there are backbone atoms, you can show a ribbon. If the residue is aligned with a gap, it will not be included. Here is the explanation in the manual: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p… > Currently Morph Conformations will only use the sequence alignment it figures out itself. A future improvement will be to allow the user to provide the sequence alignment (perhaps avoiding some of the gaps), but that is not available yet. I took a look at your proteins, 3DRR and 3DRS. They are the same protein, and the only difference is that the 3DRR crystal structure has more residues at the C-terminal end, forming a helix. 3DRR ends at 557 and 3DRS ends at 548. I guess you want that end part shown in the morphing trajectory. The structures look nearly the same in the residues before the difference, so to do this I would just use a text- editor and add the end residues from 3DRR onto the 3DRS structure. For example, make a copy of the 3DRR PDB file, then edit it to replace 543-end with 543-end from the 3DRS PDB file. Then you would just open the new edited 3DRR with the longer tail and then morph from that to 3DRS. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 5, 2009, at 1:29 AM, Nok :p wrote: > Dear Chimera teme, > > First of all, I would like to introduce myself. My name is Jiraporn > Yongpisanphop. Now, I am a master student of KMUTT university in > Bioinformatics field. > > My thesis topic involve in drug design. A part of my work is > concerning about overaly binding pocket of single mutant enzymes > (PDB file: 3DRR and 3DRS). And, I > > use Morph Conformation method. It is good but it not complete for my > work. Because the intermedate structure was generate from compare of > same amino acid > > of both structures. However, the difference amino acid was kept only > reference model. Therefore, I would like to consult you how I will > keep amino acid that > > differece of both structures into intermediate structure. > > Thank you very much for your kind. > > Best regards, > > Jiraporn

1 0

Movie spinning and slicing a density map
by Thomas Goddard 06 Dec '09

06 Dec '09

Hi Andy, I've added an example movie spinning and slicing a virus EM density map to the Chimera Animations page. See the bacteriophage phi6 entry. There is also a link to the movie script. http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom -------- Original Message -------- Subject: making a movie From: Anindito Sen To: Thomas Goddard Date: 12/2/09 5:50 PM > Hi Tom > > I am not sure if this email can be out on the general Chimera wiki. THe > following movie is from a published work of mine. Can you help me > getting the script for generating such a movie. There is a Chimera session in the > webpage but I think its a bit too much for me to understand. > > Please feel free to reframe the question and put it in the Chimera wiki > email list which may prove helpful to others. > > Thanks for your help. > > Best > > Andy > > > > http://emnavi.protein.osaka-u.ac.jp/emnavi_detail.php?id=1500 > > Dr. Anindito Sen (Ph.D) > >

2 1

drawing elipsolids
by Keren Lasker 03 Dec '09

03 Dec '09

Dear Chimera team, Is there a way to draw ellipsoids in Chimera. The ellipsoid is defined by its center and 3 radii. Thanks for your help. Best, Keren.

3 6

How to clip surface using mclip
by Marhoefer, R (Richard) 03 Dec '09

03 Dec '09

Dear Chimera Team and Users, I like to clip the surface of a model (but not the model itself) using the command mclip. Unfortunately, this command apparently is waiting for a model number and therefore works on the surface as well as the model itself. On the other hand, the interactive tool "Per Model Clipping" allows to clip the surface only. Because I like to use clipping in a movie, using the interactive interface is not an option. Does anybody know how this could be acomplished using the command line? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

3 2

Re: [Chimera-users] missing ribbon loop
by klumpler＠sci.muni.cz 03 Dec '09

03 Dec '09

Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas > Hello, > My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 27, 2009, at 2:16 AM, klumpler(a)sci.muni.cz wrote: > >> Hallo, >> please, can you tell me how to create missing part of ribbon >> representation of loop? >> >> Using "ball and stick" representation is peptide chain complete without >> gap, but in "ribbon" representation is one residue missing and forms the >> gap. >> >> Thank you very much >

2 2

keyboard input gone
by Zhou, Wei 02 Dec '09

02 Dec '09

Hi, Yesterday I installed the latest 1.4 32bit linux version of chimera into my opensuse 11.1. Soon after I fetched some pdb files and started to use it, at some point, I can no longer input any text into the program, such as typing another pdb id, or typing a command line, or type a file name to save it. I can still use mouse. Please help. I'm here at mission bay, rock hall. My extension is 60421. Thanks, Wei Zhou

2 1

phenix map not reading in chimera
by Geoffrey Feld 02 Dec '09

02 Dec '09

Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

3 2

Chimera question with Mac
by Durga Velukumar 30 Nov '09

30 Nov '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

5 6

Bond change
by Bruno Cramer 30 Nov '09

30 Nov '09

Hi After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process. Question: How can this arbitrary bond change be avoided? Attached zip file with *.mol2 examples of one compound after splitting process. Thank you Regards Bruno

2 1

missing ribbon loop
by klumpler＠sci.muni.cz 30 Nov '09

30 Nov '09

Hallo, please, can you tell me how to create missing part of ribbon representation of loop? Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap. Thank you very much

2 1

structure manupulation
by Haixin Sui 24 Nov '09

24 Nov '09

Tom and Elaine, Is there a simple way to manipulate part of a protein structure in Chimera? What I would like to do is the following. Let's say I have a molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly but one short helix is off probably owing to conformational change. I would like to move the short helix into the density map manually. The difficult part is how to make a smooth transition for loop regions at both ends of the helix. Would you please give me some advice on this? Thanks! Haixin -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

3 2

Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

5 7

Display of double-bond in Chimera
by J H 24 Nov '09

24 Nov '09

Dear Chimera, Is there a way to display a molecule's double bond as double-bond (i.e., two lines between the atoms instead of one) in chimera? Thanks a lot. Best, Jules.

2 1

Moving PDB between 3 orientations
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Chris, To show a molecular model moving between three orientations you would use Chimera commands savepos and reset and matrixcopy. Here's how I'd go about it. First put copies of the molecular model at all 3 positions. If you have saved these in 3 Chimera session files I would open all 3 sessions telling Chimera not to close the previous session when I open each new session. Now open a 4th copy of the molecule. Suppose the original 3 copies are model numbers #0, #1, #2 and the 4th copy is model #5. To align the 4th copy with #0 use matrixcopy #0 #5 (The matrix being copied is the positioning matrix, the rotation and shift that places the molecule in the scene.) Record the positions of all the models now with savepos p0 The name p0 could be anything. We'll use it later with the reset command. Also save positions with the 4th model in the other 2 states: matrixcopy #1 #5 savepos p1 matrixcopy #2 #5 savepos p2 Now to move the 4th model pack to position 0: reset p0 and to move it from position 0 to 1 over 50 frames reset p1 50 and then from 1 to 2 reset p2 50 In a movie recording command script remember to put a "wait 50" between these two commands so they don't both try to run simultaneously. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html There is a movie making tutorial that explains some of this: http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] how to link three EM confirmations in morph map From: Chris Arthur To: Thomas Goddard Date: 11/23/09 1:40 PM > Hi Tom, > I have one other question. I have a pdb (the same pdb loaded into > chimera 3 times), that I have docked into three distinct EM maps. I > would like to make a movie showing the rotation of the pdb as it goes > from one docked state to the next, to the next. I guess this would be > similar to the morph command but for pdb's instead of EM maps. Any > suggestions? > Thanks, > Chris > > > The Scripps Research Institute

1 0

Make volume have mean 0, standard deviation 1
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Terry, Chimera does not automatically scale density maps. You can use a command like vop scale #0 shift -8.0 factor 0.2 to shift map #0 values by -8.0 and then scale by 0.2. If the mean were 8.0 and standard deviation were 5.0 then this would normalize to mean 0 and SD 1.0. This creates a new volume data set. There is no capability to shift and scale an existing map without making a new volume data set. The Volume Filter dialog (menu Tools / Volume Data) can do the same thing. Python code to do the shift/scale is in chimera/share/VolumeFilter/scale.py There is a menu entry Tools / Volume Data / Volume mean, SD, RMS that reports the mean and SD and RMS about zero of the highlighted map in the volume dialog. There is no command equivalent (I should make the measure command do this). The Python code that does this is in chimera/share/VolumeStatistics/__init__.py Tom -------- Original Message -------- Subject: question about ccp4 formatted map density From: Terry Lang To: Tom Goddard Date: 11/23/09 11:39 AM > Hey Tom, > > I am looking into some new schemes for scaling electron map > density. I know you said that the scaling to a mean of zero and > standard deviation of 1.0 is implemented in the current release. > However, I can't seem to find where the code is located. I am really > interested in figuring out where exactly scaling happens and if it's > automatic or needs to be requested. Any input you can provide would be > greatly appreciated! > > Sincerely, > Terry >

1 0

Re: [Chimera-users] [chimera-dev] Rotation about the axis of symmetry
by Elaine Meng 23 Nov '09

23 Nov '09

On Nov 23, 2009, at 2:06 AM, Liam Browne wrote: > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > > Many thanks, > Liam Hi Liam, You can just use the reported values -- the tricky part is remembering to indicate that they are in the coordinate system of the first model in the "measure rotation" command, and also using the reported axis point as the center of rotation. Let's say you used the command "measure rotation #0 #1". Then the values in the Reply Log are for the transformation of #1 relative to #0 expressed in the coordinate system of #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > Now you can use the values in the Reply Log to rotate #1 further. Keep in mind that this transformation will be applied on top of any existing transformations. If you want only the new rotation and not prior transformations, you would need to "reset default" first. To rotate model #1 90 degrees about the reported axis and use the reported axis point as the center, the command would be: turn -.55288898,.77167664,-.31437070 90 center -56.22800779,0,25.47389901 mod #1 coord #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

question
by Laura Packer 20 Nov '09

20 Nov '09

To whom it may concern: I am not sure if I am sending this inquiry to the correct e-mail address. If not, I apologize for any inconvenience. I am looking to acquire a list of atoms that are within a certain distance of a set other atoms. I have googled this question and have learned how to select these atoms: bfsdjf select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 What I would like to know is how to get a list of these results. It is not appearing in my reply log as I thought it might. Thank you for your time. Sincerely, Laura Packer packer(a)bu.edu

2 1

how to link three EM confirmations in morph map
by Chris Arthur 19 Nov '09

19 Nov '09

I am wondering what would be the best way to link three EM maps using Morph Map? I have three sequential conformations of a protein and I would like to show a movie morphing from 1 to 2 to 3 if possible. Thanks in advance for any tips. Regards, Chris Christopher Arthur Ph.D. Staff Scientist Milligan/Unwin Lab The Scripps Research Institute carthur(a)scripps.edu 858-784-7073

2 1

<< Versions to download >>
by Hatuey Hack 18 Nov '09

18 Nov '09

Hello, I would like to know if it is possible to put the version number of Chimera in the download or to add it to the file name. Regards and keep the good work!, Hatuey ___ Mike Ditka <http://www.brainyquote.com/quotes/authors/m/mike_ditka.html> - "If God had wanted man to play soccer, he wouldn't have given us arms."

3 3

control of scale in STL output files
by Jonathan Schaefer 18 Nov '09

18 Nov '09

Hi- I've got a question about controlling the scale of protein models in .stl files generated by Chimera under File/Export Scene in the GUI. I'm trying to print a 3D model of two interacting proteins with a rapid prototyping machine that takes .stl files as input. The two proteins are co-crystalized and contained in one .pdb file (1nbf). I want the two proteins to be printed at the same scale so that I could fit them together like legos. Can I achieve this by getting a scale set, then showing just the first chain and exporting the data to a .stl file, followed by showing just the other chain and exporting the data to a second .stl file? I'm a novice to Chimera, so I might be missing something obvious. Any help you offer will be appreciated. Jonathan Schaefer Morgan Lab UCSF

2 2

making a movie in Chimera
by Victor Padilla-Sanchez 18 Nov '09

18 Nov '09

Hi, my name is Victor and I would have a question about a problem that I have making movies. I record the movie in MPEG 4 format and everything seems fine but when I want to play the movie in Quicktime I obtain just a black screen playing just that. Could you help me with this problem. Thank you very much Victor

2 1

capping surface with a VRML model
by Damien Larivière 18 Nov '09

18 Nov '09

Dear all, It is possible in Chimera to cap the clipped surface of an isosurface made with the Multiscale Model tool. However, if the isosurface is exported in VRML and then reopened in Chimera, it is no more possible to cap the clipped surface. This function (surface capping) is very interesting in particular when the scene is crowded by many proteins. Is it a way to cap VRML model? Many thanks for your help! Damien

4 4

down arrow goes all the way to empty selection
by Eric Pettersen 17 Nov '09

17 Nov '09

> On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote: > > > (4) It is great to have the down and up arrow to narrow and broaden > > selection, would be great if a final down arrow would lead to > > clearing the selection. > > After some discussion we have decided to do this, though it won't make > it into the next release since we are already in a feature freeze / > debugging mode for that. > > --Eric This is implemented now and will be in tomorrow's daily build and the eventual 1.5 release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

residue label
by Bala subramanian 17 Nov '09

17 Nov '09

Friends, I would like to know how to use our own strings with 3D label. suppose if i give 'rlabel :3', residue 3 is labelled as LEU 3. But i want to pass a string that should replace LEU 3. Hope i am clear. I know 2D label can use a string but i wish to use string especially with 3D label. Thanks, Bala

3 2

suggestion/stereo
by Dougherty, Matthew T. 16 Nov '09

16 Nov '09

I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands. Thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

2 1

help with raytrace
by Corey Fugate 16 Nov '09

16 Nov '09

I am trying to improve image quality using the raytrace option. The script is below - reset view_1 movie record directory /Users/fugate/Desktop pattern partA_* fformat png raytrace true wait 15 delete :.B move x 1.25 15;wait wait 15 movie stop Everything works fine without "raytrace true". I should note that I do not have the movie encode command because I want to have the individual images ( for a larger Flash project). When I compare the raytrace true images produced from the script to an image generated using the "save image" option under the File menu setting "raytrace with POV" to true. Am I missing something? Corey

2 1

Apply rotation with precision
by Damien Larivière 15 Nov '09

15 Nov '09

Dear Chimera team, Once two pdb structures are opened, the command measure rot #1 #0 give the orientation of one structure with respect to the other one under the form of: Position of 1Wxx_chB1.pdb (#0) relative to 1Wxx_chB1.pdb (#1) coordinates: Matrix rotation and translation 0.99727151 0.01713873 0.07180395 46.50921950 -0.01715871 0.99985272 -0.00033862 3.66357812 -0.07179918 -0.00089436 0.99741871 15.01300748 Axis -0.00376406 0.97263698 -0.23229967 Axis point 231.74603365 0.00000000 -638.91369622 Rotation angle (degrees) 4.23351417 Shift along axis -0.09924878 Let's suppose that I want to decrease the rotation angle from 4.233° to 0.5°: I can use "Movement" and select the model to be rotated in order to do that with the mouse but I will not be accurate. Is there way to do such rotation with precision? Thank for your help Damien

4 5

Re: [Chimera-users] help with raytrace
by Corey Fugate 13 Nov '09

13 Nov '09

Doh! Sorry lack of sleep results in incomplete sentences. The raytrace option in the script looks exactly like the chimera window quality and nothing like an image made using raytrace. Corey On Nov 13, 2009, at 4:12 PM, Thomas Goddard wrote: > You didn't say what was wrong with the raytraced image. So we are > missing something. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] help with raytrace > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-users(a)cgl.ucsf.edu > Date: 11/13/09 1:12 PM > >> I am trying to improve image quality using the raytrace option. >> The script is below - >> reset view_1 >> movie record directory /Users/fugate/Desktop pattern partA_* >> fformat png raytrace true >> wait 15 >> delete :.B >> move x 1.25 15;wait >> wait 15 >> movie stop >> Everything works fine without "raytrace true". I should note that >> I do not have the movie encode command because I want to have the >> individual images ( for a larger Flash project). When I compare >> the raytrace true images produced from the script to an image >> generated using the "save image" option under the File menu setting >> "raytrace with POV" to true. >> Am I missing something? >> Corey >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Re: [Chimera-users] Fields in dms format
by Elaine Meng 12 Nov '09

12 Nov '09

No -- that would overcount the area, because it would overlap for neighboring dots. The area is an *estimate* for the piece of surface around the dot that is not assigned to any other dot. If you added up the areas for all the dots for one atom, it would *approximately* equal the surface area for that atom. However, to get the total area for an atom, residue, etc., don't do that -- just use the already existing areaSES (and areaSAS) attributes of atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > Elaine On Nov 12, 2009, at 10:34 AM, Yasser Almeida Hernández wrote: > Thanks for your help... > About the estimated surface area in the 8th field, i view this > number as the area enclosed by the neighboring dots, where the > guessing dot is the center of a square formed by this dots. What do > you think about that? > > *-----* > | | > | * | > | <-|-- Area > *-----* >

1 0

Fields in dms format
by Yasser Almeida Hernández 12 Nov '09

12 Nov '09

Hi all... In the .dms format: 1 - What's the meaning of the digit (allways 0) after the SR (or SC, SC)? 2 - What's the meaning of the number in the 8th field? I've read the help of this format, but i don't understand the meaning of these numbers Thanks... -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

2 1

nmrclust: linux terminal
by Austin B. Yongye 12 Nov '09

12 Nov '09

Hi everyone, I am trying to use nmrclust to cluster a set of about 5K conformers with the chimera gui. It is been ~5hrs now, and still running. I was wondering whether the algorithm can be run via the linux terminal. I found this posting: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003195.html Could some one please let me know how to use this python code to run the clustering in the linux terminal invoking the python environment? Thanks, Austin-

2 1

Select / Structure / secondary structure / turn broken
by Tom Goddard 12 Nov '09

12 Nov '09

Hi Haixin, I suspect "turn" doesn't just mean not helix and not sheet but I don't know. Others in my lab will know so I've forwarded your question to the Chimera mailing list so they can answer. If you want to select all residues that are neither helix nor sheet you can use the command: select ~ :/isHelix :/isSheet Tom -------- Original Message -------- From: Haixin Sui To: 'Thomas Goddard' Date: 11/6/09 2:27 PM > Tom, > > How have you been? > > This email is to report a small bug I experienced. The "select"-> > "structure"->"secondary structure" -> "turn" function is not working. It > worked for selection of "helix" and "strand". Selection of "turn" is the > only one does not work. I am using chimera alpha version 1.3( build 2577) > 2008/12/09 00:54:36 on a laptop PC running Windows XP. > > While I have a lot of different molecules aligned in a map, this selection > function is very useful for me. Any suggestion? > > Best regards from > > Haixin > > -- > Haixin Sui > Research Scientist IV > Wadsworth Center > Empire State Plaza > P.O. Box 509 > Albany, NY 12201-0509 > > Assistant Professor > SUNY-Albany > School of Public Health > Department of Biomedical Sciences >

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coarse-grained MD
by Francesco Pietra 11 Nov '09

11 Nov '09

I know that questions about coarse-grained MD wit amber have already been raised. However, I wonder whether any plan is going on - if feasible at all - to implement in the ambertools something like the cg builder of vmd. Or ask chimera software if a conjoint effort may allow us amber users to approach cd md "at home", benefitting of the amber's secure code. thanks francesco pietra

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Re: [Chimera-users] Coloring range for residues
by Eric Pettersen 10 Nov '09

10 Nov '09

Hi Ibrahim, I'm glad it helped. I've opened a Trac ticket for your request for restricted rainbow coloring, so you'll get a notification when it gets implemented. It could be quite some time before I get to it, though if others request it also it could happen sooner. --Eric On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote: > Hi Eric, > > Thank you very much, as usual, I got the help I expected from > chimera team. > > Actually, the conformational change for the structure I have is > dramatic and involves wide range of residues. It is really painful > for the eye to follow the structural change for a certain element. > Coloring the residues in few colors did the job; however, the > rainbow coloring using the script you sent did a much better job. > It would be useful if this command can be added to the chimera!. > > Many thanks, > Ibrahim > > -------------------------------------------------------------------------------------------------------------------------- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, November 09, 2009 7:29 PM > To: Ibrahim Moustafa > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring range for residues > > Hi Ibrahim, > I'm not 100% sure why you want to rainbow the > highlighted part of your structure, rather than use a single color, > or color the rest of the structure dark gray, or make the rest of > the structure semi-transparent, or many other possible highlighting > schemes. > Anyway, there's no way to do it without resorting to > (simple) Python. Put the following in a file that ends in ".py": > > import chimera > residues = chimera.selection.currentResidues() > residues.sort() > for i, r in enumerate(residues): > r.highlightNum = i+1 > > Then select the residues you want highlighted in > Chimera. Run the Python script by opening it with the "open" > command or with the File->Open dialog. Then run this Chimera command: > > rangecolor highlightNum,r min blue mid white max red sel > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote: > > > Dear Chimera team, > > I wonder if there is a way to color a certain range of residues > using rainbow. > I tried to use the rainbow command with atom_spec but it applied for > the whole chain. > > What I want to do is to color part of the structure as a rainbow > (from blue-white-red) with an increasing order of residues number. > I just wanted to highlight a region of conformational change so the > eye can follow which part of the structure has changed dramatically. > > > Thanks in advance for your help. > > Ibrahim > > -- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park, > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] Coloring range for residues
by Elaine Meng 10 Nov '09

10 Nov '09

Hi Ibrahim, Just thought I would mention that there are some other interesting ways to show conformational changes or conformational variability in a single picture. Some images are attached at the bottom. You can assign attributes to residues, and then show those attribute values on one or more structures with color and/or "worms". If two or more structures are associated with an alignment and you show the alignment "RMSD" header, that automatically creates the residue attribute named mavRMSD, where the values are the alpha-carbon RMSDs for residues in the same column of the alignment. If you only have two structures it boils down to the CA-CA distance between the two residues in each column of the alignment. You are probably thinking "but I don't have an alignment!" -- however, in Chimera it is easy to make one. If you have > 2 structures already superimposed, you can use Match->Align (under Tools... Structure Comparison) to create and display the sequence alignment. If you have 2 structures, you can use MatchMaker to both create the pairwise sequence alignment and superimpose the structures. Here is an example with a G protein in the "on" and "off" conformations, using the command version of MatchMaker: open 1tad open 1tnd del ~ :.a mm #0 #1 show true That will create the pairwise sequence alignment with RMSD header shown. Then in the alignment window, choosing "Structure... Render by Conservation" brings up the dialog for mapping colors and/or worm fatness onto the structures. In that dialog, change the attribute from "mavConservation" to "mavRMSD" to see the histogram of values. Then use the Colors or Worms section in the dialog to map the values. You can do it for either or both structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > I attached images for the example above, where mavRMSD is shown with: (a) worms for both structures (b) color on one structure (c) both color and worms on one structure You could also do the coloring with command "rangecolor" instead of with the dialog <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> The example uses two conformations of the same protein, but it will also work with different proteins along as they are similar enough for Matchmaker to create a good alignment. Or instead of using an alignment, you can create your own attribute in a text file and then use "rangecolor" or the "Render by Attribute" tool (under Tools... Depiction), actually the same dialog used above for showing mavRMSD, to show your custom attribute on the structure. There is a description of the file format <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > and example files <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Probably more information than you wanted 8-) Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

It would be nice that Chimera also compute and save the SAS (like a grid), since there're a few softwares to do this task spacifically. I hope this will avaible in the future... Anywere, thanks a lot for your helps -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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Re: [Chimera-users] problem with surface representation
by Miriam Gochin 10 Nov '09

10 Nov '09

Outstanding! That worked perfectly! Thank you so much, Tom. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463 ________________________________________ From: Tom Goddard [goddard(a)cgl.ucsf.edu] Sent: Monday, November 09, 2009 10:07 PM To: Miriam Gochin Subject: Re: [Chimera-users] problem with surface representation Hi Miriam, I think the cusps (two points) are just parts of the surface. The surface is obtained by rolling a sphere of a 1.4A radius over the molecule and the surface is all points reached by that rolling sphere. The cusps happen because that sphere does not fit between the residue 36 and 104 HE2 atoms. If you reduce the probe radius to 1.2 A then you get rid of the cusp but the surface is slightly different. You would change probe radius in the same dialog where you changed vertex density. Tom -------- Original Message -------- Subject: Re: [Chimera-users] problem with surface representation From: Miriam Gochin <miriam.gochin(a)tu.edu> To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 11/9/09 9:31 PM > Hi Tom, > > Thanks for the suggestions. That does improve things a bit, but not completely. Maybe I just have bad geometry at that position? I attach the pdb file. The residues involved are #36 and #104, if you have time to take a look at it. > > Best, > > Miriam > Touro University - CA > miriam.gochin(a)tu.edu > 707-638-5463 > ________________________________________ > From: Tom Goddard [goddard(a)cgl.ucsf.edu] > Sent: Monday, November 09, 2009 8:50 PM > To: Miriam Gochin > Cc: Chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem with surface representation > > Hi Miriam, > > I guess the surface is being divided into two few triangles. You can > increase the number of triangles by increasing the "vertex density" > parameter. To do this, select the surface (ctrl-click it), use > inspection selector (menu Actions / Inspect), set the "Inspect" menu in > the inspector dialog to MSMS Surface, increase the "vertex density" > parameter, say from 2 to 5, and press the Enter key after typing in the > new number. That should give a smoother surface. > > Another step that can improve the lighting of the surface is to enable > glossy lighting in the Lighting panel. Menu Tools / Viewing Controls / > Lighting, quality -> glossy. Some old graphics cards don't support this. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] problem with surface representation > From: Miriam Gochin > To: Chimera-users > Date: 11/9/09 8:07 PM > >> I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. >> >> Thanks, >> Miriam Gochin >> Touro University - CA >> miriam.gochin(a)tu.edu >> >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

Hi Tom... I'm actually interested in compute and save the accesible surface as a grid (like DMS). If Chimera doesn't compute the SAS surface (with MSMS code), why it ask for the probe radius in Favorites > Preferences > New Surfaces? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

2 1

problem with surface representation
by Miriam Gochin 09 Nov '09

09 Nov '09

I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. Thanks, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

2 1

Coloring range for residues
by Ibrahim Moustafa 09 Nov '09

09 Nov '09

Dear Chimera team, I wonder if there is a way to color a certain range of residues using rainbow. I tried to use the rainbow command with atom_spec but it applied for the whole chain. What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number. I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically. Thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

2 2

External SAS calculation
by Yasser Almeida Hernández 09 Nov '09

09 Nov '09

Hi all.. In the Chimera source where is located the sources files for the calculation of SAS. I'm writing a python script for calculate the SAS and i want to call the Chimera's routines to do this task... Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

2 1

access rotation and translation matrices
by Lori Nyland 05 Nov '09

05 Nov '09

Hello, I have been trying to rotate a large volume relative to a reference volume using the vop resample command. The problem is that both volumes are nearly 2GB. However, If I were to bin the volumes (by n) and had access to the rotation R(alpha, beta, gamma) and translation T(x,y,z) matrices I could perform the rotation in an alternate program via R and nT. Thanks! Lori

2 2

How to increase h bond width
by Kshatresh Dutta Dubey 01 Nov '09

01 Nov '09

Dear Users, I want to increase the hydrogen bond width and change bond color. How can i do this ? Any help is heartily appreciated. Regards Kshatresh

2 1

classifying contact interactions
by M. Shahid 31 Oct '09

31 Oct '09

Dear All, I have a question regarding the contact interactions between a protein-ligand complex. I can retrieve the contacts by the findclash command in --nogui mode as below: chimera --nogui protligcomplex.pdb clash.com and similarly I can find the hbonds. The output I am getting is as below: -------------------------------------------------------------------------------- 32 contacts atom1 atom2 overlap distance LIG 1 H ALA 265.A O 1.045 1.435 LIG 1 O ALA 265.A O 0.550 2.430 LIG 1 N GLU 169.A OE2 0.439 2.666 LIG 1 H GLU 169.A CD 0.116 2.584 LIG 1 O ASN 253.A 1HD2 0.094 2.386 LIG 1 H ALA 265.A C 0.090 2.610 LIG 1 C ALA 265.A O 0.059 3.121 LIG 1 N ASN 253.A OD1 -0.037 3.142 LIG 1 C ALA 265.A O -0.039 3.219 LIG 1 N GLU 169.A HG3 -0.072 2.697 LIG 1 C PHE 168.A HB2 -0.081 2.781 LIG 1 N GLU 169.A CG -0.113 3.438 LIG 1 N GLU 169.A CD -0.125 3.450 LIG 1 N GLU 169.A CD -0.128 3.453 LIG 1 C MET 270.A HG2 -0.140 2.840 LIG 1 N PHE 168.A CD2 -0.163 3.488 .......... .... ... .. . -------------------------------------------------------------------------------- Now I want to further classify these contact interactions into more other types: Aromatic and Ionic (anion < - > cation). Is there any way in Chimera to achieve this? Or if I want to do it with some scripting, which atoms I would say are involved in ionic and aromatic interactions considering the distance value as well? I would be very much grateful if someone suggest me a way to do this. Thanks, Best regards, -- Shahid.

3 6

Help Installing Chimera
by Muhammad Ahmad Chaudary 30 Oct '09

30 Oct '09

Hi, I am trying to install chimera on Fedora 11 and i am running into problems. After config i tried running make and got the following error. #first i got the error evp.h not found Even though yum said openssl was installed. Anyway i downloaded openssl and tried to install it manually. But i still got the same error. So then i copied the openssl header files folder to /usr/include This got me past this error. #Next i got this error gcc -g -O2 -o sha1_keygen sha1_keygen.o -L/home/ahmad/chimera/src -lchimera -lpthread -lcrypto /usr/bin/ld: cannot find -lcrypto collect2: ld returned 1 exit status make[1]: *** [sha1_keygen] Error 1 I just installed openssl with the default options. Any ideas what i am doing wrong here! Ahmad

3 2

binning large volumes
by Lori Nyland 28 Oct '09

28 Oct '09

Hello, I have two volumes with the same dimensions and each are nearly 2GB. I can use the vop resample command in a 64 bit Chimera for Linux and reassign one volumes coordinates relative to the other. However, it is slow to execute, but it does work. In order to speed things up is there a way to bin the volumes (to use less space), place it through the vop resample command, and then un-bin the volume without losing information? Thanks! Lori

2 1

script for
by lorenzo 28 Oct '09

28 Oct '09

Dear all, I'm trying to write a script to interpolate between two structures and save the intermediate conformations as pdb files. I need a script since I have to repeat this procedure several times. As far as importing the structures and interpolating is concerned I have no problem: open A.pdb open B.pdb morph start #0 morph interpolate #1 frames 6 (I need 5 intermediates) What I don't manage to figure out is how to save the intermediate configurations. Figuring out that morph interpolate was generating a trajectory stored as the model #2 I tried write format pdb trajectory #2 out.pdb but it didn't write anything I also unsuccessfully tried with perframe write format pdb out.pdb but I still got no output. Does anybody have any suggestion? Regards Lorenzo Bongini

2 2

problems display a mrc or ccp4 file
by maillist＠dejung.net 27 Oct '09

27 Oct '09

Hi all, I have problems diplaying a 3D map in chimera. I recognized this problems with .mrc and .ccp4 maps. And only at my system. When I load a map, I get an image like this: http://download.dejung.net/chimera.png My version of chimera is: $ chimera --version chimera snapshot version 1.4 (build 28596) 2009-08-20 19:46:50 GMT I tried also other versions (chimera alpha version 1.3 (build 2577)) but they will not start at all. Tell me there is a segmentation fault at the beginning without any molecule, map or other things. Just exits directly at start up. Friends of mine told me, it will be maybe the wrong graphic driver, but I all ready tried different ones. At the Moment I use nvidia drivers 185.18.14 on a Linux 64 bit system. I have no idea now, so hope someone can help me at this point... Best regards! Mario

3 4

problem with SAXS profile
by Stefan Jehle 27 Oct '09

27 Oct '09

Hi, I have to finish very urgently a model of a big oligomer and the SAXS curve utility would be extremely helpfull for me if working properly. Here my problem: I get the following error message after pressing the "Profile" button: Wrote /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb Executing command: /Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat Error 512 executing command "/Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat" First I thought this may be because I have encrypted my cache (using MacOSX Leopard) but the same problem occurs using Win Vista or Windows XP or Windows Vista. I would appreciate your help, if you could provide me a saxs.py file working. Thanks a lot Best Regards Stefan __________________________________ Dr. Stefan Jehle Structural Biology Unit Leibniz Institute for Molecular Pharmacology, FMP Robert-Rössle-Str. 10 13125 Berlin Germany jehle(a)fmp-berlin.de Phone +49 30 94793232 Fax +49 30 94793169

2 1

Error during PDB Fetch
by Bryan Krantz 27 Oct '09

27 Oct '09

Dear Chimera Users: Does anyone know how to resolve this bug. I tried to load a PDB file from the web using the ID 3hvd. Got this error back: Error reading 3hvd: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') I am running this Chimera : Linux 64-bitchimera-1.4-linux_x86_64.exe<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux_x86_64/chimera-1…> Size: 77850528 bytes MD5: 1e05f4607699c88467e81cc249aa4ad1 My OS is Debian Lenny AMD64. Thanks in advance for your help. Yours, bryan -- Bryan Krantz University of California, Berkeley Department of Molecular & Cell Biology Department of Chemistry 476 Stanley Hall #3220 Berkeley, CA 94720-3220 Phone: (510) 666-2788 Email: bakrantz(a)berkeley.edu Lab: 492 Stanley Hall Lab phone: (510) 666-2789 URL: http://mcb.berkeley.edu/labs/krantz/

2 1

Re: [Chimera-users] Terminating Match-align without loosing reply log
by Eric Pettersen 27 Oct '09

27 Oct '09

Hi Mario, There is no guaranteed way. On the Mac or on Linux you may be able to stop the computation by sending Chimera's Python interpreter an INT signal (terminal interrupt) [I don't know of any such option on Windows]. Open a terminal window (on Mac: /Applications/Utilities/ Terminal.app). Find Chimera's Python process via: ps augxww | grep python You'll see something along the lines of: pett 86576 98.7 13.4 1218088 562256 ?? R 11:58AM 2:17.97 /Users/pett/Applications/Chimera-daily-x11.app/Contents/ Resources/bin/python2.5 /Users/pett/Applications/Chimera-daily-x11.app/ Contents/Resources/share/__main__.py The first number (86576) is the process ID of Chimera's Python interpreter. Send it an interrupt signal by: kill -INT 86576 If all goes well, Chimera will bring up an error dialog saying something about KeyboardInterrupt. The Match->Align computation will have stopped with the structures in the same position as they were at the end of the last iteration, the last alignment window will be up, and the Reply Log will be available. On Linux, if you started Chimera yourself from the command line you may be able to just hit control-C (or whatever your interrupt character is) instead of the rigamarole above. --Eric On Oct 27, 2009, at 11:46 AM, Mario Borgnia wrote: > Hi Eric, > > Thanks for the fast response. My other question is how to terminate > the process > in progress without compromising the output of previous iterations. > Thanks!!! > > Mario > > Eric Pettersen wrote: >> Hi Mario, >> The iterations are independent. So you could iterate twice, save a >> session, and then iterate further later. You could use the 'Save' >> button on the Reply Log to save info as needed. >> >> --Eric >> >> P.S. Sorry it's slow. It's all in Python and given how complex it >> is >> it's unlikely it's going to be recoded in C++ anytime soon. >> >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >> >> On Oct 27, 2009, at 7:47 AM, Mario Borgnia wrote: >> >>> Hi, >>> I launched a massive match-align procedure with five iterations >>> without knowing >>> that it would take so long to complete. Is it possible to stop it at >>> iteration 2 >>> without loosing the information computed to that point? Also, is it >>> possible to >>> continue from that point on in a subsequent round? >>> Thanks! >>> >>> Mario

1 0

Chimera slow on Win 7 64-bit system
by Thomas Goddard 27 Oct '09

27 Oct '09

Hi Wen, The slow ribbon and atom rendering must be a graphics driver issue. Surfaces use different OpenGL calls for rendering allowing them to be fast. You can try updating your graphics driver. If you have the most recent you could try poking around with graphics driver settings that trade of speed and quality. We don't have a 64-bit Windows Chimera. Only 64-bit Linux Chimera is available. We'll probably put out a 64-bit Mac Chimera in about 6 months and 64-bit Windows Chimera in about 1 year. Tom -------- Original Message -------- Subject: chimera question From: Wen Jiang To: Tom Goddard Date: 10/15/09 7:54 PM > Hi Tom. > I recently set up a Windows 7 64bit system for Nvision stereo display > and ran into some problems with Chimera. First, the performance for > pdb molecules (ribbon and atoms) is very slow. It seems fine with > volume data (surface). Do you have any clue? Second, there is only > 32bit version for Chimera and it cannot deal with large map. Do you > have a 64bit version for Windows? > Thanks, > > Wen > > Wen Jiang, Ph.D. > Assistant Professor > Department of Biological Sciences > Lilly Hall, B-402A > Purdue University > West Lafayette, IN 47907

4 3

Terminating Match-align without loosing reply log
by Mario Borgnia 27 Oct '09

27 Oct '09

Hi, I launched a massive match-align procedure with five iterations without knowing that it would take so long to complete. Is it possible to stop it at iteration 2 without loosing the information computed to that point? Also, is it possible to continue from that point on in a subsequent round? Thanks! Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

2 1

[Fwd: creating more memory]
by Lori Nyland 24 Oct '09

24 Oct '09

Ooops forgot attachment. Here it is.

3 2

problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

Hi everyone, I'm using chimera 1.4 since few days on Fedora 11 (leonidas) with a nvidia card (8600 gts), and it's working very fine. but just one problem, when we have more than one model displaying, every informations like distances, H-bond, labels, doesn't move with models during rotation or translation. this problem don't exist with just one model. best regards, ____________________________________ Mr NAUTON Lionel Ingénieur d'étude CNRS Laboratoire SEESIB UMR6504 Université Blaise Pascal Campus des Cézeaux Bâtiment Chimie 4 et Chimie 3 RDC 24 avenue des Landais 63177 AUBIERE Cedex France Tel : 0473405506 http://seesib.univ-bpclermont.fr/Nouveau_site/pages/

4 3

creating more memory
by Lori Nyland 23 Oct '09

23 Oct '09

Hello, I have attached an image that shows the command line and the command where I am trying to save an image map of one volume relative to another. I received an error when the operation was executed. The error code is in the image. I noticed that there was an error in memory allocation (toward bottom of error script). So I think I need to allocate more memory. How do I do that? Thanks so much! Lori

1 0

problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

thank's for your answer Victor Sure that the Action Mark is active, my problem is for the distance, label or H-bond printing, they stay fixed when the models are moving.

1 0

trying to process 1000 proteins via Chimera
by Bisn 21 Oct '09

21 Oct '09

Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen

3 2

Calculation of RMSD between 2 PDB structures automatically
by Sumitro Harjanto 21 Oct '09

21 Oct '09

Hi, I have about 150 peptide structures in PDB format. I would like to compare each of them with a Template Structure (also in PDB format) and obtain an RMSD measurement for each comparison. These peptides are similar in structures to the template but may have very low sequence similarity/conservation. So my question is: 1. what is the command I should use given this scenario..? I was quite confused with the many different commands such as: rmsd, match, ensemblematch, matchmaker,... can anyone enlighten me on the differences among them. I would like to find one which can align/superimpose 2 peptides and calculate RMSD (Ca or backbone) 2. Is there a way to automate the process through scripting..? I'm still young with CHIMERA so please pardon my ignorance. =] Cheers, Sum

2 1

Re: [Chimera-users] using CHIMERA to measure RMSD for large number of short peptides against a template structure
by Elaine Meng 21 Oct '09

21 Oct '09

On Oct 21, 2009, at 6:45 AM, Sumitro Harjanto wrote: > > Background: > Basically I would like to compare peptide to peptide and obtain the > RMSD between the two peptides using CHIMERA. These peptides may > have different lengths (eg 9-mer vs 10-mer) and they are not > conserved at all, in fact, they can be quite different in sequence. > They however have similar structures. > > Problem: > I have a dilemma in choosing which alignment method to use. If I > use matchmaker, which is based on sequence alignment, only selected > amino acid pairs will be measured (since the peptides are not > conserved); if I use match instead, the peptides have to be of > equal length, but they are not. Is there way to get around this > dilemma..? > I need the RMSD value to be exported from CHIMERA. I understand > that CHIMERA kept a log (replylog) for each session. Is there a way > for me to extract the content of this file? Or is there any other > way to keep a record of the RMSD values (since I would need to > automate this process to calculate RMSD for many pairs of peptides. > Thanks, > Sumitro Hi Sumitro, Matchmaker does not require the sequences to be identical, but generally it is intended for homologous proteins with at least partly conserved sequences and secondary structures. If you are working with short peptides, I agree that matchmaker will probably not give the matches that you want, so "match" would be the way to go. The "match" command does not require that the overall structures have the same number of atoms, only that you tell it to use equal numbers of atoms from the two models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> For example, model 0 could be some protein with residues 1-500 in chain A and residues 1-250 in chain B, while model 1 is your peptide that only has 10 residues. In the match command you just say exactly which atoms and residues should be used. When the residues are of different types, you would normally just use their backbone atoms instead of the whole residues, which could have different numbers of atoms. Examples: match #1:1-10@ca #0:1-10.a@ca match #1:1-10@n,ca,c,o #0:425-434.b@n,ca,c,o match #1:2-9@ca #0:4.a,6-9.a,8-10.b@ca The RMSD values will be reported in the Reply Log (under Favorites menu). You can copy the text in it and paste to a file. Or, if you are running Chimera in "nogui" mode, this information can be redirected to a file as described in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/ 003064.html> For more about scripting to process multiple structures, see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003261.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003262.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera 1.4 release candidate
by Elaine Meng 21 Oct '09

21 Oct '09

Hi everybody, Candidate builds for the Chimera 1.4 production release are now available. <http://www.cgl.ucsf.edu/chimera/download.html> As detailed in the release notes, <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> many new features have been added since the 1.3 release. Please try the candidate and report any problems. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Incompatibility between --nogui and viewdock scripting ?
by Aurelien Grosdidier 20 Oct '09

20 Oct '09

Dear all, I'm trying to create a minimal chimera script that loads a PDB structure, then loads docking results (Dock format), saves the result and exits, as follows: open mystructure.pdb viewdock myresult.dock4 "Dock 4, 5 or 6" save result.py stop This works perfectly, when I launch Chimera (1.4rc 32-bits on Kubuntu 9.04 AMD64) : chimera --script mkview.com However, when I try to get rid of the display by adding the --nogui switch, chimera crashes with the following stack trace: ...Traceback (most recent call last): File "CHIMERA/share/chimeraInit.py", line 425, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1439, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 32, in func File "CHIMERA/share/Midas/midas_text.py", line 101, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 132, in _processFile File "CHIMERA/share/Midas/midas_text.py", line 64, in makeCommand File "CHIMERA/share/ViewDock/ChimeraExtension.py", line 42, in cmdViewdock File "CHIMERA/share/ViewDock/base.py", line 97, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 523, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 244, in __init__ File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI TclError: invalid command name "tix" Error while processing mkview.com: TclError: invalid command name "tix" File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI See reply log for Python traceback. Any idea / workaround ? Cheers, -- Aurélien Grosdidier Molecular Modeling Group Swiss Institute of Bioinformatics PS: I already tried Xvfb with no luck (segfault, this might be a *buntu bug, though).

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minimize without addh and without GUI
by richardbonnet 19 Oct '09

19 Oct '09

Dear users Would you give me the best way to minimize the hydrogens in ligands with chimera used without GUI and without addh? I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py here is script.py : from chimera import runCommand runCommand("select @H=") runCommand("minimize freeze unselected nsteps 1000") runCommand("write format mol2 0 out.mol2") However, chimera add wrong hydrogen because of the load of addh with minimize. I have a lot of ligands to process and I can not use GUI. thank you much for your help, Richard Bonnet Universite Auvergne

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Running chimera in Intel Core 2
by Dimitrios Evangelopoulos 19 Oct '09

19 Oct '09

Hi everyone, Just a question regarding running chimera on a Intel Core 2 cpu. Do you know if it is running propeprly? I just show that you mention that Chimera uses the Intel Pentium instruction set so wondering before download it. Thanks in advance. Best regards, Dimitrios Evangelopoulos, PhD student

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chimera 1.4 and Windows 7
by Boaz Shaanan 19 Oct '09

19 Oct '09

Hi, Has the latest production release (1.4) been also tested under Windows 7 ? Does it work OK ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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bond order
by Dan Gurnon 19 Oct '09

19 Oct '09

I was wondering if there are plans to enable the display of bond order in ball and stick mode? -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] 3D-glassen
by Dan Gurnon 16 Oct '09

16 Oct '09

Thomas, I've been using the Quadro fx 380 for a couple weeks now, and I would say that the results are marginally better than with the fx 4500. There is still some occasional flickering, and for some reason, the card has trouble resetting to the normal windows aero after I close chimera with the view set to sequential stereo. I also have occasional issues when using stereoplayer or Pymol, so it looks like Nvidia still has to work out some driver issues with their 3Dvision. On Fri, Oct 2, 2009 at 4:23 PM, Thomas Classen < Thomas.Classen(a)uni-duesseldorf.de> wrote: > Thank you for your help. > > > > > > > > --------------------------------- > > Thomas Classen, M. Sc. Biochemie > > Thomas.Classen(a)uni-duesseldorf.de > > > ------------------------------ > > *Von:* doublehelix00(a)gmail.com [mailto:doublehelix00@gmail.com] *Im > Auftrag von *Dan Gurnon > *Gesendet:* Freitag, 2. Oktober 2009 16:28 > *An:* Thomas Classen > *Cc:* chimera-users(a)cgl.ucsf.edu > *Betreff:* Re: [Chimera-users] 3D-glassen > > > > Tom, > I use the 3D vision system with Chimera. Note that in order for the > 3Dvision to work you'll either need a 100Hz or better CRT or a 3D-ready > 120Hz LCD from Samsung or Viewsonic. It won't work with standard LCDs. > You'll also need to be running Vista or Windows 7. > http://www.nvidia.com/object/3D_Vision_Requirements.html > > You're also going to want a Quadro card, not the GTX285 geforce card you > have listed below. The Geforce cards can't do sequential stereo in windowed > mode, and I'm not sure if Chimera would even allow sequential stereo even in > full screen mode with a geforce (but I haven't tested it with a geforce > card). > > In my experience, the sequential stereo with the Nvidia hardware has been > just "ok"...its nice when it works, but it hasn't always worked. I really > think my issue has been my hardware...I have a Quadro FX 4500, which is an > older (albeit expensive!) card with an onboard DIN-connector. I just found > out that its not supported by the 3D vision drivers, so thats hopefully why > I'm having occasional display problems. Here's a list of compatible quadro > cards: > > http://www.nvidia.com/object/quadro_pro_graphics_boards.html > > The nice thing about Nvidia's 3D vision is that you don't need to buy one > of the very expensive Quadro cards with stereo output through an onboard > DIN-connector (the fx 3000 series and up). In fact, I just ordered a Quadro > Fx 380 for about $125, which I hope will solve the issues I'm having with > the fx 4500. It should be here next week- I'll let you know how it goes. > > > Dan > > On Fri, Oct 2, 2009 at 4:12 AM, Thomas Classen < > Thomas.Classen(a)uni-duesseldorf.de> wrote: > > Dear colleaques; > > > > I want to use 3D-glasses of nVidia for the sequential stereo view in > chimera. Are there any experiences with that system in combination with > chimera? > > Or are there some problems with that kind of technology known? > > > > Wanted hardware > > - nVidia GF 3D Vision 3D-Glasses > > -nVidia graphicboard; GTX285 Series min. 1024MB > > > > Additional hardware: > > - Intel 2 Duo Quad Prozessor; Q9650; boxed > > - 8GB DDR2 RAM PC1066 > > > > > > Thanks for your help from germany > > Tom > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu > -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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questions about volume tracer
by Jean-Francois Menetret 16 Oct '09

16 Oct '09

I have a few questions about *volume tracer*: Is it possible to add marker(s) in an existing marker set ? Is it possible to change the marker note of an existing markers ?

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Re: [Chimera-users] Hydrodynamic radius
by Tom Goddard 14 Oct '09

14 Oct '09

Hi Sudheer, I don't know if the theoretical hydrodynamic radius Rhyd defined on the wikipedia page http://en.wikipedia.org/wiki/Hydrodynamic_radius is a good approximation to the Stokes' radius. The Stokes' radius depends on both shape and hydration details. I've added a request for this calculation in Chimera to our feature request page (item 220). http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests This is much more specialized than typical Chimera features and I would not expect it to be implemented any time soon. If you wished to implement it I could probably show you how to get out of Chimera a list of grid points within a displayed contour level that would be the input to the calculation. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Hydrodynamic radius From: Sudheer To: goddard(a)cgl.ucsf.edu Date: 10/14/09 2:03 PM > Hi Tom, > > Im interested in the optical properties of a protein. Yes, "the > hydrodynamic radius for a uniform solid bounded by a contour surface > of your map would be useful". Yes, Stocks radius. Actually I'm running > Dynamic light Scattering experiment to find the variation in the size > distribution of a protein with change in Temperature. (I mean im > trying to find at what temperature the protein forms monomer and > dimer...!) I already have Cryo-EM map of the dimer and so just thought > of comparing the Hydrodynamic radius between the cryo-map and the DLS > result. > > I hope you got my interest in finding the Hydrodynamic radius of my > protein. > > Thank you very much for your help, > Sudheer. > > > Date: Wed, 14 Oct 2009 13:54:03 -0700 > > From: goddard > > To: Sudheer > > CC: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] Hydrodynamic radius > > > > Hi Sudheer, > > > > Chimera isn't able to compute hydrodynamic radius of maps or > > molecules. Are you primarily interested in diffusion properties or > > optical properties of your structure? Do you think the hydrodynamic > > radius for a uniform solid bounded by a contour surface of your map > > would be useful? Do you mean Stokes' radius or the R_H defined on the > > wikipedia page? > > > > http://en.wikipedia.org/wiki/Hydrodynamic_radius > > > > The latter looks like a pretty simple calculation. > > > > Tom > > > > -------- Original Message -------- > > Subject: [Chimera-users] Hydrodynamic radius > > From: Sudheer > > To: chimera users > > Date: 10/14/09 1:05 PM > > > Hi, > > > > > > Can I measure the Hydrodynamic radius a Cryo-EM density map using > Chimera? > > > > > > Thank you, > > > Sudheer Molugu. > > > > ------------------------------------------------------------------------

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Hydrodynamic radius
by skmolugu＠miners.utep.edu 14 Oct '09

14 Oct '09

Hi, Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera? Thank you, Sudheer Molugu.

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Running Chimera on Ubuntu
by Claudio Saracini 12 Oct '09

12 Oct '09

Hello, I installed Chimera on my MacBook Pro with Unix OS (Ubuntu). When I try to run the program from the bash I get: Bash: Chimera: Command not found I'm a newbie of Linux. I guess I forgot to do something after having installed Chimera. I would appreciate your help. Claudio *************************************************** Claudio Saracini Kenneth D. Karlin Research Group Department of Chemistry The Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 E-Mail: claudio.saracini(a)jhu.edu Group Website: http://www.jhu.edu/~chem/karlin/ ****************************************************

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Protein secondary structure
by Beale, John 08 Oct '09

08 Oct '09

I realize that this is probably simple, but I haven't been able to work this problem out. Is there a way to read a single pdb file into Chimera and then have the program show me what amino acid sequences of the protein are alpha helices, what are beta sheets, and what are 3,10 helices, etc? Thanks! John John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Re: [Chimera-users] Displaying Surface For Selected Residues
by Eric Pettersen 07 Oct '09

07 Oct '09

On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote: > Thanks Eric, but just to follow up on the surf sel command, > > It displays the surface for the selected residues, > > does it assign solvent-excluded and solvent-accessible surface areas > per atom and residue to attributes named areaSES and areaSAS to the > selected residues or to the whole protein?. > > after I do "surf sel" I have select:/areaSAS > 50 , looks like it > selects for the whole protein. Shouldn't it show only for the > selected surface region. > Hi Thiru, Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need: sel :/areaSAS > 50 & @/surfaceDisplay --Eric > Thanks > > -Thiru > > --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: Displaying Surface For Selected Residues > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Date: Wednesday, October 7, 2009, 5:14 PM > > Yes, most commands work on everything if you don't specify what to > work on. For instance "color red" colors everything red whereas > "color red sel" colors the selection red. > > --Eric > > On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote: > >> Worked fine, Thanks, Eric >> >> -Thiru >> >> --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: Displaying Surface For Selected Residues >> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >> Date: Wednesday, October 7, 2009, 5:04 PM >> >> "surface sel" >> >> --Eric >> >> On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote: >> >>> Hi Eric, >>> >>> I have a protein with a few residues selected, and I wanted to >>> show surface only on the selected residues, when I go to Actions - >>> Surface -Show , it shows surface only for the selected residues, >>> but when I use the command surface on the command line it shows >>> the surface for the entire protein. Is there a command line >>> option to show surface only for the selected residues on the >>> protein. >>> >>> Thanks >>> >>> Thiru >>> >>> --- On Thu, 10/1/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Solvent Accessible Surface Area >>> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >>> Cc: "UCSF Chimera Mailing List" <chimera-users(a)cgl.ucsf.edu> >>> Date: Thursday, October 1, 2009, 3:38 PM >>> >>> Oops, spotted a bug in the script. This line: >>> >>> out = open(os.path.expanduser("~/out", "w")) >>> >>> should be: >>> >>> out = open(os.path.expanduser("~/out"), "w") >>> >>> --Eric >>> >>> >>> >> >> > >

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Re: [Chimera-users] Chimera pov-tracing question
by Tom Goddard 07 Oct '09

07 Oct '09

Hi Maya, Your mesh is transparent in the povray image (zoom in on the image and look at the mesh lines) but I guess is much less transparent than in the Chimera window. I ran some test images with the current Chimera 1.4 daily build which also showed the povray mesh looked much different (darker, thicker and less transparent) than in the Chimera window. While we have improved the match between povray images and what you see in the Chimera window it is still very bad. Dozens of messages on the chimera-users mailing list relate to the poor quality of Chimera Povray images. http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpiper… As suggested in the following message, with these poor quality povray results a better presentation can almost always be obtained by not using povray: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html Attached are 5 test images showing some of the problems. 1mwm chain A, molmap 6 angstroms. test.png - povray transparent mesh 0.24, appears very dark test2.png - povray transparent mesh 0.04, black specks all over the mesh test4.png - povray transparent surface 0.24, ugly multilayer mosaic test5.png - no povray, transparent surf 0.24, glossy lighting, silhouette edges test6.png - no povray, same as test5 but mesh. Tom -------- Original Message -------- Subject: Chimera pov-tracing question From: maya shcushan To: 'Thomas Goddard' Date: 10/7/09 9:59 AM > > Dear Dr Goddard, > > > > You previously assisted me with other problems with Chimera, so now I > am asking your help again. > > I have a density map and a structure mapped on it. I showed the map as > transparent mesh, and tried to pov-ray the image. However, the picture > came up with the map not transparent (attached). Do you have any idea > how to resolve this issue, making the map transparent in the image as > it is in the main window > > > > Thanks, > > Best, > > *Maya Schushan* > > Department of Biochemistry > > George S. Wise Faculty of Life Sciences > Tel Aviv University >

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Movies in Chimera
by Anindito Sen 07 Oct '09

07 Oct '09

Dear All These questions may have been answered in the past ( and I must have missed it)- 1. I have 3 movies (.mov) made in Chimera. I want to add them all together to make a single movie. How can I do that? 2. How can I build a movie where I "zoom"-inside a crystal structure or an EM density map showing the regions of interest. Thank you Andy Dr. Anindito Sen (Ph.D)

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(no subject)
by Cathy Lawson 06 Oct '09

06 Oct '09

Dear Chimera Team, I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11). (1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection. cheers, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

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Re: [Chimera-users] SAS values for single atoms and residues
by Elaine Meng 06 Oct '09

06 Oct '09

Hi Dave, It is not clear to me what you did to list values in the Reply Log. After you display surface to create those surface area attributes, then start "Render by Attribute" (for example, from under Tools... Depiction) and in that dialog, choose "File... Save Attributes." In the resulting file-save dialog you can specify not only which attribute you want to save, but there is a checkbox "Restrict save to current selection" that you will want to activate before saving the file. For example, you could select all the LYS and then this would be used to write a file listing the areaSAS of each of those residues. Alternatively you could select all the :lys@nz and then write the areas of the selected atoms. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 6, 2009, at 9:23 AM, David Chenoweth wrote: > Hi Elaine, > > I'm trying to calculate the solvent accessible surface area for > several lysine residues in a protein to evaluate which are most > likely to be free on the surface for functionalization. My thought > was to just calculate the SAS area and rank order them. When I > select just the primary amine of all the lysine residues and go to > the reply log I get several numbers in a row under SAS and I'm not > sure which are correct. These numbers don't seem to change if I > select different residues so I'm not sure how to get the SAS values > just for my lysine amines. > > Thanks, > Dave

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SAS values for single atoms and residues
by David Chenoweth 06 Oct '09

06 Oct '09

Hi Elaine, I'm trying to calculate the solvent accessible surface area for several lysine residues in a protein to evaluate which are most likely to be free on the surface for functionalization. My thought was to just calculate the SAS area and rank order them. When I select just the primary amine of all the lysine residues and go to the reply log I get several numbers in a row under SAS and I'm not sure which are correct. These numbers don't seem to change if I select different residues so I'm not sure how to get the SAS values just for my lysine amines. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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citation
by Abeer Shokeer 06 Oct '09

06 Oct '09

Hello I have used Chimera to prepare very nice figure in my manuscript and I would like to cite the Chimera. which reference that should be cited? Best wishes Abeer

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python scripting for multiscale model
by Pat Weinkam 05 Oct '09

05 Oct '09

Hi, I am a new postdoc with Andrej Sali. I am looking to use the multiscale model tool to recreate a 3x3x3 set of unit cells around my pdb file. I can use the GUI to do this just fine but I would like to incorporate this into a python script. Is such a thing available? It would be greatly appreciated. Thanks! Pat

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mouse selection not working
by lorenzo 05 Oct '09

05 Oct '09

Hi everybody, I just installed chimera-1.3-linux.exe on an atom netbook. The OS is ubuntu 9.04. My problem is that the mouse selection tool does not work. To complete the scenario I add a few details 1) I don't have the green outline and setting Fill mode for selection highlighting in Preferences does not work around the problem (probably just a screen setting problem). 2) Other forms of selections work. For example by Select -> Chemistry -> Element -> H and then by Actions -> Atoms/Bonds -> Delete I can delete hydrogens. 3) I cannot delete anything that I select by ctrl + mouse left button. 4) libgl1-mesa-glx and libgl1-mesa-dri are installed. Thanks for your attention Lorenzo Bongini

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CA-only shown as ribbons
by Andrei Neamtu 05 Oct '09

05 Oct '09

Hello, Just a quick question: I have downloaded the latest daily build of CHIMERA and I want to make a ribbon picture only fom the alpha-Carbon trace. On the site it is said in the Appearance and Image-Saving section that "CA-only and P-only structures can be shown as ribbons and worms " I tried but didn't succeded . Does anybody know what are the steps in displayng such a structure? Andrei

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comparing protein structures
by Beale, John 03 Oct '09

03 Oct '09

Hello, I am trying to compare a protein structure generated through molecular dynamics to a reference structure that is the starting pdb file. I was using MATCHMAKER. I get the rms value and the residue matches, but when I do this I don't get the overlaid reference and MD structure in the viewing window. Can someone tell me what I need to do to get the overlaid structures? Thanks! John

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Saving ligand and protein as a single PDB
by Nancy 03 Oct '09

03 Oct '09

Hello, I am planning to run a docking simulation in a different program, and I need to have a "reference ligand" included in the PDB file. The particular PDB I am working on does not have a ligand included. So I am trying to position one using Chimera. I started with the protein file and a ligand file (ligand is in .mol2 format). I loaded both into Chimera, and I correctly positioned the ligand relative to the PDB. I then saved both using File -> Save PDB... I choose to save the file relative to the protein, and I select "save multiple models: in a single file". However, when I load the file into the docking program, it does not show the ligand. Additionally, there are a few structural errors in the output PDB file. Please advise. Thanks, Nancy

2 3

zone command
by Francesco Pietra 02 Oct '09

02 Oct '09

Hi: I prepared with the zone command a model (#0) of a protein partly immersed into a hydrated lipidic bilayer (cut-and-paste from the two models from the zone command). Now I would like to solvate with water the part of protein which protrudes out of the bilayer. Water is single-point (coarse-grain simulations) indicated in model #0 as ATOM 2724 W W 2060 45.420 3.750 23.380 1.00 0.00 W and in the pdb file of the water block (model #1) to be added ATOM 27558 W W 5018 84.320 142.862 11.262 1.00 0.00 Once model #0 and model #1 are superimposed, clearly the zone command does not distinguish W from the two models. How could the zone command be made working now? I renamed W to WAT in model #1 but the zone command does not recognizes WAT under such circumstances. Not yet found a way out, which should be simple. Thanks for suggestions. (solvating model #0 with programs from the MD suite also solvates what it should not; this is why I am trying with CHIMERA) francesco pietra

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3D-glassen
by Thomas Classen 02 Oct '09

02 Oct '09

Dear colleaques; I want to use 3D-glasses of nVidia for the sequential stereo view in chimera. Are there any experiences with that system in combination with chimera? Or are there some problems with that kind of technology known? Wanted hardware - nVidia GF 3D Vision 3D-Glasses -nVidia graphicboard; GTX285 Series min. 1024MB Additional hardware: - Intel 2 Duo Quad Prozessor; Q9650; boxed - 8GB DDR2 RAM PC1066 Thanks for your help from germany Tom

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licensing
by Schulz-Gasch, Tanja 02 Oct '09

02 Oct '09

Hi there, I have a single-user license for Chimera at Roche. Meanwhile others are interested in using Chimera as well. Could you please send me an update on licensing scemes and costs? Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

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segmentation fault
by Francesco Pietra 01 Oct '09

01 Oct '09

Hi: On Debian Linux i386 squeeze I had the X system broken while attempting to install the gnome cd burner "brasero". I purged everything about that bad code, installed and reconfigured the X system, however something is still broken. Attempts at launching CHIMERA returned "segmentation fault". That also sitting in the directory where chimera is installed ( /usr/local/chimera/bin). As I had an old version, I reinstalled chimera-1.3-linux.exe, while that did not solve the above problem. I do not remember where to put the hands in such cases. Thankful for reminding me about that. francesco@deb32:~$ gcc --version gcc (Debian 4.3.4-2) 4.3.4 francesco pietra

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Re: [Chimera-users] Solvent Accessible Surface Area
by Elaine Meng 01 Oct '09

01 Oct '09

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am using Chimera for identifying the surface residues. > > I select areaSAS > 0.05 square angstroms, is this same as saying > areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq > angstroms have these been switched some how or are they curiously > the same in the following statement? > > I just need some help in understanding. > Thank You > Sincerely > -Thiru Ramaraj Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html> However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say select :/areaSAS>10 but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Transparent Spheres
by Waight, Andrew 30 Sep '09

30 Sep '09

Hello everyone again. I apologize for a potentially embarassing question but is it possible to display sidechains as transparent spheres with solid stick representation inside. Seeing as I also can't find an image in the Chimera gallery where it is represented as such, I am wondering if it is possible to individually color (and set opacity) on spheres. I am also aware that vdw will create dots of varying density, but is it alternatively possible to display vdw as solid surface with opacity. Thanks to all for your patience. Drew ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
by vamsi krishna 30 Sep '09

30 Sep '09

Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding . Thank you vamsi chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Solvent Accessible Surface Area (Elaine Meng) > 2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj) > 3. Re: Solvent Accessible Surface Area (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Sep 2009 12:14:48 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying >> areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq >> angstroms have these been switched some how or are they curiously >> the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area > value in square angstroms. Some other programs give % exposed for a > residue, which is a ratio of the area of that residue in your > structure to the area of the same type of residue in some theoretical > unfolded state. See for example the GetArea server, which gives > "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or > residue in your structure. To choose surface residues, I'd probably > use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results. You can > try different values and see what looks reasonable. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT) > From: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <842106.2825.qm(a)web53905.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks,? Elaine for the information. > > Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. > > Is there anyway I could resolve this problem. > > Thank You > > -Thiru Ramaraj > > --- On Mon, 9/28/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Solvent Accessible Surface Area > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Date: Monday, September 28, 2009, 1:14 PM > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > >

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Using Chimera to read SMILES string into structure
by Miriam Gochin 29 Sep '09

29 Sep '09

I have downloaded the latest build (Aug 30, 2009) and don't seem to be able to input a SMILES string. I have tried both the Utilities -> Structure Diagram and the Structure Editing -> Build Structure tool, and in both cases I can see a box to input the SMILES string, but the copy and paste mechanism won't work. I can enter text in the box, but cannot paste it in, which I need to do. Thanks for your help. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Zoom factor for model when first opened
by Tom Goddard 25 Sep '09

25 Sep '09

Hi Kevin, The camera settings (position, amount of zoom, angular field of view) all contribute to how much of the Chimera window is filled when you open a map. How those are initially set when you start Chimera and open a map has changed a few times over the last year or two so if you run different Chimera versions (Help / About Chimera... to check version number) you may see different initial sizes. Tom -------- Original Message -------- Subject: chimera question From: Kevin Koehntop To: goddard Date: 9/24/09 6:34 PM > Hi Tom, > > I have a quick chimera question. When I open the same EM map in two > different chimera sessions, even though the scale factor, origin, > voxel size, and isosurface threshold level are exactly the same, the > map appears much smaller in one of the windows and I can't determine > why. Is there another parameter that I need to check? Thank you > > Kevin

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Re: [Chimera-users] [chimera-dev] select opt
by Eric Pettersen 23 Sep '09

23 Sep '09

On Sep 21, 2009, at 7:27 AM, Victor MuÃ±oz wrote: > I'd like to know if there's a way to select the select mode "append" > using the > command line instead of the visual interface. Hi Victor, There isn't a way to do that, but it typically isn't necessary. The "|" and "&" characters perform union and intersection operations respectively. So for example you can add all LYS residues to the current selection with: sel sel | : LYS or you could intersect the current selection with LYS residues with: sel sel & :LYS If you really need to change the mode for some reason, let me know what that reason is and maybe we can add something. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. The "|" character is a vertical bar, not a capital i, in case that's not clear in the font you're using.

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Re: [Chimera-users] question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: 吴雪<wuxue(a)nankai.edu.cn> >Subject: Re: [Chimera-users] question about Chimera >Date: Tue, 22 Sep 2009 11:00:11 -0700 > >Dear Wu Xue, >There are several different distance and angle cutoffs that depend on >the donor and acceptor atom types. For example, the distance and >angle cutoffs for finding a H-bond donated from hydroxyl -OH to >carbonyl =O will be different than from amine -NH3 to carbonyl =O. >The cutoff values are taken from tables in this paper: > > Three-dimensional hydrogen-bond geometry and probability >information from a crystal survey. Mills JE, Dean PM. J Comput Aided >Mol Des. 1996 Dec;10(6):607-22. > >As discussed in the FindHBond documentation, > findhbond.html#criteria> > >the criteria in this paper were based on very high resolution crystal >structures of small molecules. Typically the structures in the PDB >are not so high resolution and so the criteria are relaxed. For >example, if a strict criterion from the paper is 2.8 Angstroms >cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. >We set the default relaxation amounts to what we felt gives >reasonable results on most PDB structures. However, we made them >user-adjustable so that if you don't like them, you can change the >values to whatever you want. > >I hope this helps, >ELaine >----- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > >On Sep 22, 2009, at 4:18 AM, 吴雪 wrote: > >> Dear colleague: >> I have a question about the "find hydrongen bond" in Chimera. >> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". >> I don't understand the meaning of the parameter. 20 degree may >> means the angle bias the line,but I can't figure out what is the >> 0.04nm. >> The cutoff of the hydrogen is 0.4nm, and the angle is about 90 >> degree or some other parameters depending on the strength of the >> hydrogen bond. >> If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds >> are found. I don't know the criteria. Can you give me some advice >> so that I can follow your instruction? >> Sincerly Yours >> WU Xue > >

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.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
by Xarana 22 Sep '09

22 Sep '09

Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie

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question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue

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Write out phi/psi angles
by David Belnap 21 Sep '09

21 Sep '09

I've read on the archived lists that Chimera does not have a Ramachandran plot viewer. I found phi/psi angles by selecting "Actions", "Inspect", then inspecting "Residue". Can I output the phi/ psi angles to a text file? If so, how do I write out that information? Thanks. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David.Belnap(a)byu.edu ============================================

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Zooming and orthographic projection mode
by James Conway 21 Sep '09

21 Sep '09

I am struggling a bit and would be interested in any pointers from the knowledgeable folk here. It seems that I cannot use the mouse to get arbitrarily close to a surface in orthographic mode, but I can in perspective mode. In orthographic mode (Viewing -> Camera -> Projection) if I try to zoom in, the camera instead moves in until the front surface clips, but without much actually zooming. (True for the different "Center of Rotation" methods). In the Viewing -> Side View panel, the width of the field is represented by red lines that I cannot control but which I really want to move close together. According to the help for the Viewing -> Camera panel: horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window. In fact, with the nightly builds of 1.4 this parameter *does* affect the orthographic projection, and does zoom in (or out) without clipping. Is there an updated explanation of how this works, and if it has changed since 1.3 as I seem to find? Am I looking in the wrong place for help on nightly builds? Thanks, James Conway

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Fit MAP to MODEL
by Michael Schmid 21 Sep '09

21 Sep '09

HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.

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select many atoms by serial number
by Stefano Meliga 21 Sep '09

21 Sep '09

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster. I would like to plot the clusters in different colours. I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano

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measurements to planes
by Elaine Meng 18 Sep '09

18 Sep '09

Hi Serge, Dave, Jim, et al., In recent daily builds of Chimera, you can now define planes and measure distances and angles to these objects. The planes are shown as disks, and you can perform plane-plane, axis-plane, and atom-plane measurements, in addition to the axis-axis and atom-axis measurements we had earlier. The tool formerly known as Axes is now "Axes/Planes," and we anticipate it will eventually include centroids. The updated documentation isn't there today but should show up tomorrow at <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > and the interface is mostly self-explanatory anyway. Each of you had asked about planes at some point (possibly a while ago), in case you are wondering why I addressed this message to you. 8-) Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Cannot open pdb files with older versions of Chimera
by Hiroshi Nikaido 17 Sep '09

17 Sep '09

Hello, I sometimes have to use older versions of Chimera (1.2350 or 1.2422) because the more recent versions refuse to calculate surfaces for my protein. They used to work fine in my old computer running windows xp, but with my new computer (still running xp) an attempt to try any pdb files on my hard disk produces an error message (TypeError: argument 1 should be a str.). How could this problem be fixed? Your help will be greatly appreciated. Hiroshi

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 16
by Gaël McGill 16 Sep '09

16 Sep '09

Hi Andrew, You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience importing PDB data into Blender. Here is her site: http://www.scivis.ifc.cnr.it/ Her e-mail: Monica Zoppè <mzoppe(a)ifc.cnr.it> Hope this is helpful, -Gael. ------------------------- Gaël McGill, Ph.D. Director of Molecular Visualization Center for Molecular & Cellular Dynamics Harvard Medical School www.molecularmovies.org President & CEO Digizyme, Inc. P.O. Box 1921 Brookline, MA 02446-1921 (617) 232-7676 (phone) (617) 232-5623 (fax) mcgill(a)digizyme.com www.digizyme.com On 9/16/09 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Exporting from Chimera to Blender - basic questions. > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Sep 2009 23:03:03 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > To: "Waight, Andrew" <Andrew.Waight(a)med.nyu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4AB07F97.6080108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Andrew, > > Chimera exports the surface vertex and individual atom and ribbon > residue colors in the X3D and VRML output. If you raytrace a scene > with Chimera File / Save Image... it first exports X3D and then converts > that X3D to input for POVray which does get all the colors right. So I > think your question calls for some expertise with Blender, to find out > what color information it can handle when importing those files. I > don't know anything about Blender. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > From: Waight, Andrew <Andrew.Waight(a)med.nyu.edu> > To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Date: 9/15/09 10:31 AM >> Hello all, >> >> I have recently solved the structure of a novel membrane protein, and >> have been using chimera quite a bit for my figures and analysis. In my free >> time I have been playing around with the 3D animation package Blender which I >> must say is a total blast, and makes fantastic movies and animations. However >> exporting from Chimera to Blender is a little tricky, in that when using >> VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, >> the colors are not imported, and imported items such as cartoon helices seem >> to have totally random materials assigned to nonsensical segments (instead of >> materials assigned by chain for example) . Ideally I would like to perform >> and export the coloring operations using chimera because it's obviously an >> order of magnitude easier to select residues, chains and monomers with >> chimera. Or at least have the grouping of objects imported correctly. This is >> really just for fun so I'd thought I'd ask if anyone here has any experienc! > e ! >> with importing Chimera models into Blender. Of course I have no idea how >> VRML2 actually works. Thanks all. >> >> Andrew Waight >> Wang Lab >> Skirball Institute of Biomedical Sciences >> NYU School of Medicine >> >> P.S. Extra Credit: Does anyone have any idea how to export the calculated >> electrostatic surface into UV mapping for a Blender Object (the surface mesh >> obviously)? >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check this >> email and any attachments for the presence of viruses. The organization >> accepts no liability for any damage caused by any virus transmitted by this >> email. >> ================================= >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 77, Issue 16 > *********************************************

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RMSD supports symmetry?
by Kevin Wu 11 Sep '09

11 Sep '09

Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin

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Zalman 3D
by Miles Pufall 11 Sep '09

11 Sep '09

Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall

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Re: [Chimera-users] [chimera-dev] suggestion for feature addition to chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote: > Hello, > > I have a small suggestion for an additional feature for Chimera that > I think would be useful. I often look at structures of multiple > small molecules, some artificial and some real, and I noticed > something interesting with the way Chimera writes mol2 files. > > Here is Scenario 1: > > 1) I open a mol2 file that contains multiple molecules flagged as > "separate" MOLECULEs. > > 2) I save the loaded file as mol2 and select "a single file > [combined @MOLECULE section]" for the "Save multiple models in" > option. > > > 3) After saving and reloading this new mol2 file that now has a > single MOLECULE section, all the "names" of the previous molecules > have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the > SUBSTRUCTURE section "UNK0" is used. > > It would useful if Chimera could name the components of the new > single molecule with the proper names. I could easily write a > script to fix this after the fact but I thought it might be a useful > option for other people too? Okay, I changed the Mol2 writer to use the model name instead of the residue type under the following conditions (only): 1) Combining models into a single @MOLECULE 2) All models are a single residue 3) Model names are unique and residue types are not This change will be in tonight's build. > Scenario 2: > > 1) Same as 1 above. > 2) Now I want to save all the MOLECULEs in the file as separate mol2 > files but with the proper "names" that are listed in the original > file loaded. Currently the only option is to provide a common name > and to append the "model number". It would be nice if we were > allowed to NOT provide a common name and allow it to name all the > files according to the molecule "names" not model numbers. This seems like a reasonable enough request. I will open a ticket in our Trac database for it, with you on the recipient list so you'll know when it gets done. It's a tad more work than the preceding change because aside from adding code to support it, the interface has to be changed to allow for the option and the documentation has to be updated to describe it -- whereas the other change can sneak in under the radar. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Can you morph a ligand
by Walter Fast 09 Sep '09

09 Sep '09

Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question: We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well? Thanks, Walt -- Walter Fast, Ph.D. Associate Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

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Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Jean Didier Pie Marechal 09 Sep '09

09 Sep '09

Hi Eric, "binding site" was an idea more than anything else but I realize from your e-mail that we don't really need. Strangely, though using @/display frequently I never thought about using it for selecting. Think I can do without the shortcut... Sorry! Cheers JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Setembre 9, 2009 8:46 pm Assumpte: Re: [chimera-dev] Suggestion: define selection name for startup chimera > On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > > > In the new builts of chimera, you have change the initial > > representation of the protein so that binding sites immediately > > appear and the rest of the protein is in ribbon (which is a > great > > idea by the way). That means that you have a automatic analysis > of > > binding site recognition. I wonder if you couldn't include a > > selection named "binding site" (or something similar), that > would > > appear as a named selection and that we could call at the early > > beginning of the session. > > Hi JD, > I could. I definitely wouldn't want to call it "binding site" > since > it includes waters and residues not necessarily involved in > binding, > not to mention the entire structure for small-molecule structures. > > It's also a misleading name for structures without ligand present - > - > since their binding sites won't be selected by it. FInally, it's > also > somewhat confusing as to what should happen if you open multiple > structures over the course of a session. > So it could be called "smart display atoms" I suppose. If some > other > users thought it'd be useful I'd do that (anyone?). In the > interim, > you can pretty easily create the selection yourself with these > commands after opening the structure: > > sel @/display; namesel smart atoms; ~sel > > You could alias that to something snappier. :-) > > --Eric > >

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Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > In the new builts of chimera, you have change the initial > representation of the protein so that binding sites immediately > appear and the rest of the protein is in ribbon (which is a great > idea by the way). That means that you have a automatic analysis of > binding site recognition. I wonder if you couldn't include a > selection named "binding site" (or something similar), that would > appear as a named selection and that we could call at the early > beginning of the session. Hi JD, I could. I definitely wouldn't want to call it "binding site" since it includes waters and residues not necessarily involved in binding, not to mention the entire structure for small-molecule structures. It's also a misleading name for structures without ligand present -- since their binding sites won't be selected by it. FInally, it's also somewhat confusing as to what should happen if you open multiple structures over the course of a session. So it could be called "smart display atoms" I suppose. If some other users thought it'd be useful I'd do that (anyone?). In the interim, you can pretty easily create the selection yourself with these commands after opening the structure: sel @/display; namesel smart atoms; ~sel You could alias that to something snappier. :-) --Eric

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label
by Bala subramanian 09 Sep '09

09 Sep '09

Friends, Is there any possiblity to move a 3D label along a particular axis in chimera 1.4. I labelled the residues of a DNA molecule using rlabel command. Some residue labels are displayed behind the base of the DNA. I tried to change the lighting also but it vain. Thanks, Bala

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Problem with benzenes split across crystal unit cell
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, The Chimera unit cell dialog is behaving as expected in the cases where the asymmetric unit contains half of a benzene ring. First, parts of the asymmetric unit are not moved relative to other parts of the asymmetric unit, so as you observe the half benzenes in asymmetric unit copies sometimes lie outside the unit cell. All unit cell dialog just puts the center of the asymmetric unit in the unit cell box. A second problem is that a half benzene ring from one asymmetric unit will not be joined to a half benzene ring from another asymmetric unit. They will line up perfectly but Chimera does not see bonds between the two halfs so for instance, selecting aromatic rings won't pick those up. I guess the first problem could be handled by moving each connected group of atoms so its center lies in the unit cell. I think it could lead to undesired results. For example a protein with a bound ligand might have the ligand outside the unit cell causing it to be moved to some other asymmetric unit's binding site. The trouble with that is that the protein and ligand are part of one molecule model in Chimera, so now you have taken the ligand in that molecule and placed it with the protein of another copy of the molecule. That may not be what you want. Another answer to the first problem, is that I added to the unit cell dialog the ability to make multiple asymmetric unit copies to fill multiple unit cells. If you make several unit cells, then the half benzenes lying outside one unit cell do join up with the half benzenes from a different unit cell. If you were trying to make a figure and you didn't want half-benzenes floating around -- you could simply select them and delete them (Actions / Atoms / Delete). The second problem is harder. Chimera could guess that the half-benzenes should be joined since they have exactly coincident atoms. (This relies on the strange inconsistency that the half-benzenes in the PDB files you sent contain 4 atoms instead of the expected 3 atoms. So it doesn't actually represent an asymmetric unit since there is an extra atom that will be duplicated in other asymmetric units.) But Chimera can't join them because covalent bonds can't be formed between different molecule objects -- it would require making a new molecule to contain all the atoms. Creating extra molecule models to join the half benzenes is possible but weird. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > Thanks. It looks like the issue is mostly resolved. > > The is a problem with molecular units sitting at symmetry element in > non-primitive cells, for now I've found it in C2/c (iat03.pdb) and > Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is not > unique to chimera, some programs handle this okay, many don't. You'll > see that in these two cases benzene molecules land outside of the cell > or fail to complete a pair. > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>> > > On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote: > > Hi Mike, > > I've fixed the unit cell dialog to handle inverting symmetries. It > was a simple change. Will be in tonight's daily builds. > > We could have Unit Cell work with CIF files but that is an > enhancement that will have to compete for time with the hundreds of > other feature requests we're looking at. My list of requests is here > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests > > and Eric and other developer maintain their own off-line lists. So > you need to make a good case. It could be an easy task if our > third-party CIF file reader already parses the needed symmetry > operators. If it does not provide those then it could be a > significant bit of work. > > Tom > > > -------- Original Message -------- > Subject: Re: [Chimera-users] Centro-symmetric space groups > From: Michael Day > To: Thomas Goddard > Date: 9/1/09 1:19 PM >> Hi Tom, >> >> Thanks. >> >> Another option you might consider is to have the Unit Cell tool work >> also with CIF files then only coordinate transformations are needed >> as the symmetry operators are included. An advantage is that if >> someone uses a non-standard setting of a space group the symmetry >> operators are still valid for the coordinates. >> >> Thanks for all your work. All of you on the Chimera team (Elaine, >> Eric and Greg) set the bar pretty high! My hats off to you. >> >> Cheers, >> Mike >> >> <<< >> ------------------------------------------------------------------------>>> >> Dr. Michael W. Day >> Director - X-ray Crystallography Lab & Molecular Observatory >> California Institute of Technology >> Mail Code 139-74 >> Pasadena, CA 91125 >> >> <<< >> ------------------------------------------------------------------------>>> >> >> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote: >> >> Hi Mike, >> >> Thanks for the suggestions. The coordinate transformations are >> routine. The trouble is that the Chimera Molecule C++ code takes the >> transformation matrix and orthonormalizes it to a proper rotation. >> So the inversion operator of "P -1" gets changed to inverting x and >> y axes but not the z axis. The orthonormalization is supposed to >> just fix tiny round-off transformation problems, like matrices read >> from a PDB file that have only 5 digits of precision. Really we >> should be warning if a transformation is very far from a proper rotation. >> >> I'll let you know when the problem is fixed in the daily builds. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Centro-symmetric space groups >> From: Michael Day >> To: Thomas Goddard >> Date: 8/31/09 7:54 PM >> >>> Tom, >>> Thanks again. Awesome! >>> I suspect mirrors and therefore glide planes could be an issue as >>> you don't see them in proteins. >>> I don't know what your overall strategy is for applying space group >>> operators but to avoid issues I would suggest; >>> 1) deorthogonalize into crystallographic coordinates as fractions of >>> cell edge >>> 2) apply symmetry operators in turn to the original set (x,y,z) to >>> get (x',y',z') for each operator >>> 3) calculate the centroid for each equivalent set of coordinates >>> (x',y',z') >>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1 >>> and z=0,1 >>> I suspect you already know this but it never hurts to say it. My >>> students think I overstate the basics at times but it sure helps all >>> of us get on the same page. >>> Cheers, >>> Mike >>> <<< >>> ------------------------------------------------------------------------>>> >>> Dr. Michael W. Day >>> Director - X-ray Crystallography Lab & Molecular Observatory >>> California Institute of Technology >>> Mail Code 139-74 >>> Pasadena, CA 91125 >>> > >>> <<< >>> ------------------------------------------------------------------------>>> >>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote: >>>> Hi Mike, >>>> >>>> Oops. The symmetries that invert coordinates don't work in the Unit >>>> Cell tool. This is because it sets the transformation matrix >>>> (rotation and shift) for the asymmetric unit copies but it can only >>>> handle proper rotations. Chimera is generally used for proteins >>>> which are handed (not symmetric under inversion) so such space >>>> groups generally don't occur for proteins. But of course for small >>>> molecules they can. >>>> >>>> I'll fix this soon, maybe later this week. I'll have to change >>>> atom coordinates instead of setting the transform matrix for the >>>> asymmetric unit copies. >>>> >>>> Tom

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Computing xray density from structure factors
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, If it is just a matter of computing a Fourier transform that is easy. Chimera already has libraries that does that. The trouble will be parsing the CIF file. Chimera reads molecular structure CIF and mmCIF files using a third party library called mmLib. I don't know if mmLib will read the structure factors. If you send me an example CIF file with structure factors I'll give it a try. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > ... > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>>

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hydrogen bond representation
by Bala subramanian 04 Sep '09

04 Sep '09

Friends, Is there any way to represent hydrogen bonds as dotted lines instead of a solid line in Chimera. Sometimes hbond analysis in chimera shows same atom to be involved in two hydrogen bonds, why is it so ? Thanks, Bala

2 1

2D projections
by Ana Luiza 03 Sep '09

03 Sep '09

Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza.

3 3

wglMakeCurrent failed
by Stefano Marzi 03 Sep '09

03 Sep '09

Hi, With the new production releases, from 1.2540 to the very last one 1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure. This happens when I try to make a movie. I have searched in the Chimera-user mailing list archive but I have found only a thread by Greg Couch saying that this bug has been fixed already one year ago, September 2008. Could anyone please help me with that? Thank you, Best Stefano Marzi

2 1

Rendering with nogui
by Kevin Wu 02 Sep '09

02 Sep '09

Hi, It seems like it's not possible to render figures or models in Chimera when using the nogui option. Is there anyway around this? I'd like to use Chimera in a program to render models to display. Regards, Kevin

2 1

chimera latest build
by Bala subramanian 01 Sep '09

01 Sep '09

Friends, 1) I downloaded the chimera's today's build and tried to change the nucleic acid representation using..Depiction in Tools. I get the following error. Kindly write me what is going wrong ? TclError: unknown option -width TclError: unknown option -width File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ See reply log for Python traceback. Thanks, Bala

4 3

substitute single residue
by Andrew P. Hinck 01 Sep '09

01 Sep '09

Dear all, I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions. Andy Hinck Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck(a)uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu

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Chimera works on Snow Leopard
by Thomas Goddard 31 Aug '09

31 Aug '09

Hi John, I tested Chimera 1.3 and 1.4 daily builds on Mac OS 10.6 (Snow Leopard). All the tests worked fine. I ran our test suite using the Aqua Mac Chimera 1.4 snapshot and it all passed. I tested Chimera 1.3 production releases Mac Aqua and Mac X11 by hand opening a few data sets (molecules and volume data) and doing some coloring and encountered no problems. Tom -------- Original Message -------- Subject: Re: Snow Leopard ? From: Elaine Meng To: John Gerlt Date: 8/27/09 9:12 AM > Hi John, > I don't know for certain, so I'm turning over the question to the rest > of the staff (cc'd on this message). To whomever answers: could > include response on chimera-users list if you think others will have the > same question... thanks! > Best, > Elaine > > > On Aug 27, 2009, at 9:08 AM, John Gerlt wrote: > >> Elaine, >> >> Apple is issuing OS 10.6 tomorrow. For reasons I don't understand, I >> like to be current. But, as I recall from the past, when I tried to >> be current and install a new OS (10.5?), Chimera would not work. Do >> you know if Chimera will work with 10.6? >> >> Thanks. >> >> John

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Centro-symmetric space groups
by Michael Day 31 Aug '09

31 Aug '09

How do you get Chimera to recognize centrosymmetric space groups. If I include the space group on the CRYST1 card of the PDB file all is well for non-centrosymmetric groups but when a center of symmetry enters the picture all bets are off. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Re: [Chimera-users] Problem building 3D structure from smile text ...(Solved. Thanks)
by Sergio Garay 29 Aug '09

29 Aug '09

Thank tou Alaine. The new chimera version works perfect! On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Sergio, > Normally if you want to report an error it is best to use "Help... Report a > Bug" in the Chimera menu since that would automatically include information > about your computer and Chimera version, and let you attach files. > > However, in this case I can immediately see the problem: you need a newer > version of Chimera! > > You would need a version from July 3 or later, for example the August 20 > snapshot: > <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> > > Explanation: The SMILES -> 3D structure conversion is done by a Web server > provided by a group at Indiana University, and a few months ago they changed > how this service is accessed. It was necessary to change Chimera to use the > new, updated service. > > I tested the following command in the snapshot version just now, and it > worked fine: > > open smiles:N[C@@H](C)C(=O)O > > Using this command is the same as entering the SMILES in the Build > Structure dialog. I also checked doing it that way. > > I think you will be pleasantly surprised to see the many improvements we > have made in Build Structure and in other tools, and the many new features > that have been added to Chimera! > > Improvements between 1.3 and the snapshot (and you were using a version > older than 1.3): > <http://www.cgl.ucsf.edu/chimera/1.4_b28596/docs/relnotes/snapshot.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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movie image resolution
by Anastasia A Aksyuk 28 Aug '09

28 Aug '09

Hi, It is very easy to specify resolution for a saved image, but not for the images used to create a movie. Is there a way to generate a movie or a stack of images with higher resolution then a display screen? I seem to be limited to 1273x870. Thanks a lot, Anastasia

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Problem building 3D structure from smile text ...
by Sergio Garay 28 Aug '09

28 Aug '09

Hi all I'm trying to build a 3D structure from this smile text: N[C@@H](C)C(=O)O But the program stops and doesn't respond to any key. The log window shows the next message: <type 'exceptions.KeyboardInterrupt'> Exception in Tk callback Function: <bound method BuildStructureDialog._placeAtoms of <BuildStructure.gui.BuildStructureDialog instance at 0x31ca3b0>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/BuildStructure/gui.py", line 632, in _placeAtoms None File "CHIMERA/share/BuildStructure/Smiles.py", line 15, in openSmiles None File "CHIMERA/share/BuildStructure/Smiles.py", line 21, in smiles2mol None File "CHIMERA/share/BuildStructure/SOAPpy/WSDL.py", line 61, in __init__ None File "CHIMERA/lib/python2.5/urllib.py", line 82, in urlopen return opener.open(url) File "CHIMERA/lib/python2.5/urllib.py", line 190, in open return getattr(self, name)(url) File "CHIMERA/lib/python2.5/urllib.py", line 325, in open_http h.endheaders() File "CHIMERA/lib/python2.5/httplib.py", line 860, in endheaders self._send_output() File "CHIMERA/lib/python2.5/httplib.py", line 732, in _send_output self.send(msg) File "CHIMERA/lib/python2.5/httplib.py", line 699, in send self.connect() File "CHIMERA/lib/python2.5/httplib.py", line 673, in connect self.sock.connect(sa) File "<string>", line 1, in connect None <type 'exceptions.KeyboardInterrupt'>: Am I doing something wrong? I am working with this chimera version: alpha version, build 2577, 2008/12/09 -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Exporting surfaces as vrml
by Christian Hesketh 28 Aug '09

28 Aug '09

Hi there, I am trying to export molecular surfaces with varying transparencies to vrml, but the resultant model has a completely opaque surface. Is there anyway to export surfaces with transparent features to a 3D model? I would rather not work with x3d files as there don't seem to be any good 3D modeling programs that can accept this format. Thanks in advance, Christian

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Enabling silhouette edges in a nogui script
by Thomas Goddard 27 Aug '09

27 Aug '09

Hi Davide, There is a new command in Chimera 1.4 daily builds that lets you turn on silhouette edges and set their width set silhouette set silhouette_width 2 and to turn off silhouette edges ~set silhouette Here's the documentation http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html You're right that the "ac" command to run keyboard shortcuts doesn't work in nogui mode. That is because of some sloppy code that tries to create the keyboard shortcut dialog if you use the "ac" command and dialogs cannot be created in nogui mode. I've added an entry to the Chimera request list to fix that. http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests Tom -------- Original Message -------- Subject: Re: [chimera-dev] Generating images in chimera with the --nogui option From: Davide Baú To: Tom Goddard Date: 8/27/09 7:22 AM > Tom, > > how are you? > > I'm just back from (good) holidays! Hope you had good holidays too :-) > > I've tried out the "shape tube" command and it works great. Just one > question. From the sample image you attached to your last email, it > seems to me that silhouettes are toggled on ('ac se'). Is that > true/possible via a command script? Chimera Keyboard Shortcuts > (Accelerators) do not work when called form within a script (Error while > sourcing chimera.cmd: Unrecognized command: "'ac") and I haven't found a > different way (maybe using the set command?) to toggle silhouettes on. > > Thanks againg for your support, > Davide >

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Image not appearing
by MIKALS,KYLE A 27 Aug '09

27 Aug '09

I made a code to make movie and two of the molecules are not appearing in the saved output images. I put in the code where to save them so if something went wrong. This is the code I made and models 18 and 14 display in the window while the code is running, but not in the saved images. I have no idea what is going wrong. Any ideas? Here is my code below. # start capturing frames, in .png format movie record fformat png raytrace true directory /msg/users/kmikals/Chimera_Files #Created Label saying AAV Capsid Assembly 2dlabels create lab1 text 'AAV Capsid Assembly' color khaki size 28 xpos .2 ypos .94 visibility show scale 1.008 50 #Starts action once previous command is complete wait modeldisplay#0 wait 5 turn y -1 35 wait 30 modeldisplay#17 turn y -.6 20 wait 30 modeldisplay#18 wait 30 turn y +1.4 35 wait 30 modeldisplay#3 ~modeldisplay#0 ~modeldisplay#17 ~modeldisplay#18 wait 30 scale 0.992 50 wait 15 turn y -1 65 wait 9 modeldisplay#4 wait 9 turn y -1 35 modeldisplay#5 wait 9 turn y -1 65 modeldisplay#10 wait 9 modeldisplay#9 wait 9 turn y -1 65 modeldisplay#14 wait 9 modeldisplay#11 wait 9 turn y -0.5 30 modeldisplay#12 wait 9 turn y -1 65 modeldisplay#13 wait 9 modeldisplay#6 turn y -1 65 wait 9 modeldisplay#7 wait 9 modeldisplay#8 2dlabels delete lab1 #hide_all_molecules ~modeldisplay#3 ~modeldisplay#4 ~modeldisplay#5 ~modeldisplay#6 ~modeldisplay#7 ~modeldisplay#8 ~modeldisplay#9 ~modeldisplay#10 ~modeldisplay#11 ~modeldisplay#12 ~modeldisplay#13 ~modeldisplay#14 wait 20 scale 0.987 modeldisplay#16 turn y -.3 20 wait turn x -.75 35 wait 30 turn x .75 35 wait 30 turn x -.38 35 wait turn y -1 35 wait 30 turn y 2 180 wait turn x 2 180 wait # stop recording frames movie stop # write status information to reply log movie status # encode a movie in mp4 format from recorded frames movie encode mformat mp4 output /msg/users/kmikals/Chimera_Files -- MIKALS,KYLE A Biochemistry University of Florida

2 1

extending DNA for a figure
by Elaine Meng 27 Aug '09

27 Aug '09

On Aug 13, 2009, at 12:00 AM, Janet G Yang wrote: > Hi Elaine, > > I'm a grad student in Geeta Narlikar's lab, and I've been to a few > of your Chimera tutorials at UCSF and found them very helpful. I > have a less analytical and more aesthetic structural task, and I'm > wondering if you might have any insight. I would like to make a > figure showing the structure of the nucleosome with some extra DNA > docked in at the edges. The crystal structure of the nucleosome > contains 147 bp wrapped around the histone octamer, and I would like > to extend out the DNA on one side. I think I could just take the > structure of the nucleosome, and that of some B form DNA, and > somehow align them together. Is there a good way to do this? > > Thanks a bunch > janet Hi Janet, My guess is that lots of people run across similar aesthetic issues -- making a figure is partly art, after all! Everything you say sounds reasonable. First you would need to get the extra B-form DNA, then position it relative to the nucleosome structure. (1) Getting the extra DNA. This could be from another PDB structure, or built using standard B-form parameters. The NDB atlas <http://ndbserver.rutgers.edu/atlas/xray/index.html > lists nucleic acid structures in categories such as B-DNA; you can use "File...Fetch by ID" in Chimera to fetch using NDB identifiers. Those structures might be shorter or less regular than what you need. Here is a server that will build canonical structures to order: <http://structure.usc.edu/make-na/server.html > (I admit I haven't actually tried using it, but it looks promising) (2) Positioning the extra DNA relative to the nucleosome structure. You could position it by hand and/or by matching overlapping sets of atoms. Positioning by hand requires activating/deactivating models for motion so that they can be moved relative to one another -- you would do that with the checkboxes below the Command Line, or with the "A(ctive)" checkboxes in the Model Panel. Matching would be done with the "match" command. It may be tedious to figure out the atom naming in the two structures and then figure out which sets of atoms to match to get the best result, but I don't really see any way around that trial and error process, unless you are really skilled at just positioning the structures by hand. I would probably do some matching and then maybe make slight manual adjustments depending on how it looked. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> My answer was based on the understanding that you just want the DNA to trail away in a somewhat straight path, rather than continuing on curling as in the nucleosome. If you wanted that continued curling, there might be some fancy ways to do it with several copies of a curved segment and symmetry operators, but that is beyond my skill set! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

2 1

is there a way...
by Connie Oshiro 26 Aug '09

26 Aug '09

Elaine, et al-- I have a chimera session that was saved a while back (xxx.py). I can open it and view it in chimera. Question: Is there a way to extract/recontruct the commands that were used to create the view that I have? In this case, all commands were executed on the command line. The history file doesn't go back far enough. I took a look at the python file and didn't find midas/chimera commands. For example, I know I used "rainbow", with some options for the colors, but I don't see "rainbow" in the .py file. thanks for any info. connie

2 1

pause during a fly-by?
by Daniel Gurnon 24 Aug '09

24 Aug '09

Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in? Thanks Dan ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

3 4

problem with the scripting of rms deviations
by Sebastian Kruggel 24 Aug '09

24 Aug '09

Dear Chimera team and users, I tried to write a small chimera / python script to calculate rmsd to the crystal structure for a bunch of docked ligands and transform the values in a nice csv - because fred22 doesn't do this for me... The core function rms2ref is the one calculating the rmsd, than I save the reply log and afterwards transform this text file. Things worked out fine BUT than I started the script several times, and I got different orders in my list every time. Because I want to assign rmsd values to scores etc it is essential to keep the order provided in the sdf/mol2. I thought about problems with the format but the problem exists with mol2 and sdf files. Than I thought, chimera would change the order in opening the multimolecule files - but saving the #1.1 molecule and opening it in a new session showed - even more strange - that the molecule is exactly the same every time. So there is only the possibility that either the calculation of the rmsd or the order of the list (extraction of the replyLog.txt) doesn't work - which I *really* don't understand at all... Here is a small example where the rmsds-list has different orders every time I start the script... ############################## from chimera import runCommand from chimera.tkgui import saveReplyLog def rms2ref(ref, pose, no): runCommand('open %s; open %s' % (ref, pose)) i = 1 while i <= no: # only hetatms are included --> ~@/element=h runCommand('sel #1.%i & ~@/element=h' % i) runCommand('rmsd #0 sel') i += 1 rms2ref('lig_cryst.pdb', 'poses.sdf', 10) # generate output from replyLog.txt saveReplyLog('replyLog.txt') rmsds = [] for i in open('replyLog.txt').readlines(): if i.startswith('RMSD between'): rmsds.append(i.split()[-2]) print rmsds ############################## Maybe anybody can help me and tell me about the probably stupid mistake I am making - would be really great! I attached the lig_cryst.pdb and poses.sdf files just in case that anybody wants to try out ;-) Best regards and thanks in advance, Sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel: +49 (0)40 42838-3626 (-3484) mail: kruggel(a)chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html #import os, sys, string from chimera import runCommand from chimera.tkgui import saveReplyLog def rms2ref(ref, pose, no): runCommand('open %s; open %s' % (ref, pose)) i = 1 while i <= no: # only hetatms are included --> ~@/element=h runCommand('sel #1.%i & ~@/element=h' % i) runCommand('rmsd #0 sel') i += 1 rms2ref('lig_cryst.pdb', 'poses.sdf', 10) # generate output from replyLog.txt saveReplyLog('replyLog.txt') rmsds = [] for i in open('replyLog.txt').readlines(): if i.startswith('RMSD between'): rmsds.append(i.split()[-2]) print rmsds #csv = open('rmsd2ref.csv', 'w') #string.join(rmsds[(i-1)*10:(i*10)], ',') + '\n' # adapt no #csv.write(line) #csv.close() lig -OEChem-08130912163D 44 46 0 1 0 0 0 0 0999 V2000 22.8829 20.6473 -6.7698 C 0 0 0 0 0 0 0 0 0 0 0 0 23.0122 20.0364 -7.9677 N 0 0 0 0 0 0 0 0 0 0 0 0 22.0250 19.1465 -8.1492 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9921 18.8499 -7.2742 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9675 19.5477 -6.0707 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9346 20.4627 -5.8198 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9556 19.3108 -5.1243 N 0 0 0 0 0 0 0 0 0 0 0 0 19.2194 18.6661 -5.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9291 19.8574 -4.2846 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1710 17.8850 -7.8012 N 0 0 0 0 0 0 0 0 0 0 0 0 20.6949 17.6004 -8.9752 C 0 0 0 0 0 0 0 0 0 0 0 0 21.8199 18.3386 -9.2311 N 0 0 0 0 0 0 0 0 0 0 0 0 22.6384 18.2679 -10.4394 C 0 0 1 0 0 0 0 0 0 0 0 0 23.7073 17.1863 -10.4017 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9207 16.9216 -11.8790 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5072 17.0452 -12.4391 C 0 0 2 0 0 0 0 0 0 0 0 0 21.8040 17.9675 -11.5747 O 0 0 0 0 0 0 0 0 0 0 0 0 21.7533 15.7228 -12.4446 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4556 15.9427 -12.9692 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4195 14.6822 -13.0918 P 0 0 2 0 0 0 0 0 0 0 0 0 18.2575 15.1052 -13.9642 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1778 14.0963 -11.7174 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3527 13.6434 -13.9405 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0478 12.1315 -14.4800 P 0 0 1 0 0 0 0 0 0 0 0 0 19.1566 11.4702 -13.4504 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1036 12.4686 -15.9226 N 0 0 0 0 0 0 0 0 0 0 0 0 17.7718 11.3494 -16.3218 P 0 0 0 0 0 0 0 0 0 0 0 0 17.8288 11.2312 -17.8416 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1286 10.0644 -15.5812 O 0 5 0 0 0 0 0 0 0 0 0 0 16.5333 12.0631 -15.7891 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2894 13.2896 -16.5112 H 0 0 0 0 0 0 0 0 0 0 0 0 21.3520 11.4846 -14.8947 O 0 5 0 0 0 0 0 0 0 0 0 0 21.6680 15.3356 -11.4282 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2744 14.9965 -13.0700 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5057 17.4743 -13.4503 H 0 0 0 0 0 0 0 0 0 0 0 0 24.7290 17.9580 -12.4363 O 0 0 0 0 0 0 0 0 0 0 0 0 24.8367 17.7458 -13.3757 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4099 15.9650 -12.0891 H 0 0 0 0 0 0 0 0 0 0 0 0 24.8780 17.6253 -9.7433 O 0 0 0 0 0 0 0 0 0 0 0 0 24.6471 17.7685 -8.8086 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3372 16.2832 -9.8999 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0710 19.2864 -10.5717 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3079 16.8747 -9.6779 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6406 21.3876 -6.5362 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -60.581470 > <Chemgauss3 Steric> -60.009632 > <Chemgauss3 Desolvation> 33.049973 > <Chemgauss3 Acc> -26.153376 > <Chemgauss3 Donor> -7.468445 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.0123 20.4839 -6.9528 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1416 19.8729 -8.1507 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1544 18.9830 -8.3322 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1215 18.6865 -7.4572 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0969 19.3842 -6.2538 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0640 20.2992 -6.0029 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0850 19.1473 -5.3074 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3488 18.5026 -5.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0585 19.6939 -4.4676 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3004 17.7215 -7.9842 N 0 0 0 0 0 0 0 0 0 0 0 0 20.8244 17.4369 -9.1582 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9493 18.1752 -9.4142 N 0 0 0 0 0 0 0 0 0 0 0 0 22.7678 18.1044 -10.6225 C 0 0 1 0 0 0 0 0 0 0 0 0 23.8367 17.0229 -10.5847 C 0 0 1 0 0 0 0 0 0 0 0 0 24.0502 16.7581 -12.0620 C 0 0 1 0 0 0 0 0 0 0 0 0 22.6366 16.8818 -12.6221 C 0 0 2 0 0 0 0 0 0 0 0 0 21.9334 17.8040 -11.7578 O 0 0 0 0 0 0 0 0 0 0 0 0 21.8827 15.5594 -12.6276 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5850 15.7792 -13.1523 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5490 14.5187 -13.2748 P 0 0 2 0 0 0 0 0 0 0 0 0 18.3869 14.9417 -14.1472 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3072 13.9329 -11.9004 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4821 13.4800 -14.1235 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1772 11.9680 -14.6630 P 0 0 1 0 0 0 0 0 0 0 0 0 19.2860 11.3067 -13.6334 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2330 12.3051 -16.1056 N 0 0 0 0 0 0 0 0 0 0 0 0 17.9012 11.1860 -16.5048 P 0 0 0 0 0 0 0 0 0 0 0 0 17.9582 11.0677 -18.0246 O 0 0 0 0 0 0 0 0 0 0 0 0 18.2580 9.9009 -15.7642 O 0 5 0 0 0 0 0 0 0 0 0 0 16.6627 11.8997 -15.9721 O 0 5 0 0 0 0 0 0 0 0 0 0 19.4188 13.1261 -16.6942 H 0 0 0 0 0 0 0 0 0 0 0 0 21.4814 11.3211 -15.0777 O 0 5 0 0 0 0 0 0 0 0 0 0 21.7974 15.1721 -11.6112 H 0 0 0 0 0 0 0 0 0 0 0 0 22.4038 14.8330 -13.2531 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6352 17.3108 -13.6333 H 0 0 0 0 0 0 0 0 0 0 0 0 24.8584 17.7945 -12.6193 O 0 0 0 0 0 0 0 0 0 0 0 0 24.9661 17.5824 -13.5587 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5394 15.8015 -12.2722 H 0 0 0 0 0 0 0 0 0 0 0 0 25.0074 17.4618 -9.9263 O 0 0 0 0 0 0 0 0 0 0 0 0 24.7765 17.6050 -8.9916 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4666 16.1197 -10.0829 H 0 0 0 0 0 0 0 0 0 0 0 0 23.2004 19.1229 -10.7547 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4373 16.7113 -9.8609 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7700 21.2242 -6.7192 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -61.100990 > <Chemgauss3 Steric> -55.512741 > <Chemgauss3 Desolvation> 31.886629 > <Chemgauss3 Acc> -31.031534 > <Chemgauss3 Donor> -6.443346 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.0464 20.5179 -6.5868 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1757 19.9070 -7.7847 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1884 19.0171 -7.9662 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1556 18.7205 -7.0912 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1310 19.4183 -5.8877 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0980 20.3333 -5.6368 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1191 19.1814 -4.9413 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3829 18.5367 -5.1581 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0925 19.7279 -4.1015 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3345 17.7556 -7.6182 N 0 0 0 0 0 0 0 0 0 0 0 0 20.8584 17.4709 -8.7922 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9834 18.2092 -9.0481 N 0 0 0 0 0 0 0 0 0 0 0 0 22.8019 18.1385 -10.2564 C 0 0 1 0 0 0 0 0 0 0 0 0 23.8708 17.0569 -10.2186 C 0 0 1 0 0 0 0 0 0 0 0 0 24.0842 16.7922 -11.6959 C 0 0 1 0 0 0 0 0 0 0 0 0 22.6707 16.9158 -12.2561 C 0 0 2 0 0 0 0 0 0 0 0 0 21.9675 17.8381 -11.3917 O 0 0 0 0 0 0 0 0 0 0 0 0 21.9168 15.5934 -12.2616 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6191 15.8133 -12.7862 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5830 14.5528 -12.9088 P 0 0 2 0 0 0 0 0 0 0 0 0 18.4210 14.9758 -13.7812 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3413 13.9669 -11.5344 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5162 13.5140 -13.7575 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2113 12.0021 -14.2970 P 0 0 1 0 0 0 0 0 0 0 0 0 19.3201 11.3408 -13.2674 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2671 12.3392 -15.7396 N 0 0 0 0 0 0 0 0 0 0 0 0 17.9353 11.2200 -16.1388 P 0 0 0 0 0 0 0 0 0 0 0 0 17.9923 11.1018 -17.6586 O 0 0 0 0 0 0 0 0 0 0 0 0 18.2921 9.9350 -15.3982 O 0 5 0 0 0 0 0 0 0 0 0 0 16.6967 11.9337 -15.6061 O 0 5 0 0 0 0 0 0 0 0 0 0 19.4529 13.1602 -16.3282 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5155 11.3552 -14.7117 O 0 5 0 0 0 0 0 0 0 0 0 0 21.8315 15.2062 -11.2452 H 0 0 0 0 0 0 0 0 0 0 0 0 22.4379 14.8671 -12.8870 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6692 17.3449 -13.2673 H 0 0 0 0 0 0 0 0 0 0 0 0 24.8925 17.8286 -12.2533 O 0 0 0 0 0 0 0 0 0 0 0 0 25.0002 17.6164 -13.1927 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5734 15.8356 -11.9061 H 0 0 0 0 0 0 0 0 0 0 0 0 25.0415 17.4959 -9.5603 O 0 0 0 0 0 0 0 0 0 0 0 0 24.8106 17.6391 -8.6256 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5007 16.1538 -9.7169 H 0 0 0 0 0 0 0 0 0 0 0 0 23.2344 19.1570 -10.3887 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4714 16.7453 -9.4949 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8041 21.2582 -6.3532 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -57.862740 > <Chemgauss3 Steric> -55.774300 > <Chemgauss3 Desolvation> 33.089848 > <Chemgauss3 Acc> -28.135231 > <Chemgauss3 Donor> -7.043065 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.5324 20.5433 -6.7965 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6374 19.8798 -7.9685 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6729 18.9532 -8.0708 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6822 18.6683 -7.1447 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6791 19.4219 -5.9751 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6253 20.3763 -5.8039 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7101 19.2006 -4.9813 N 0 0 0 0 0 0 0 0 0 0 0 0 18.9873 18.5245 -5.1397 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6968 19.7857 -4.1676 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8734 17.6552 -7.5947 N 0 0 0 0 0 0 0 0 0 0 0 0 20.3633 17.3303 -8.7729 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4543 18.0887 -9.1053 N 0 0 0 0 0 0 0 0 0 0 0 0 22.2304 17.9845 -10.3389 C 0 0 1 0 0 0 0 0 0 0 0 0 23.3336 16.9383 -10.2908 C 0 0 1 0 0 0 0 0 0 0 0 0 23.5017 16.6095 -11.7611 C 0 0 1 0 0 0 0 0 0 0 0 0 22.0656 16.6640 -12.2728 C 0 0 2 0 0 0 0 0 0 0 0 0 21.3654 17.6053 -11.4267 O 0 0 0 0 0 0 0 0 0 0 0 0 21.3541 15.3210 -12.1881 C 0 0 0 0 0 0 0 0 0 0 0 0 20.0320 15.4767 -12.6732 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8434 14.5265 -12.0717 P 0 0 2 0 0 0 0 0 0 0 0 0 17.5216 15.0090 -12.6286 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0377 14.3646 -10.5795 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2276 13.1150 -12.7999 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3326 12.7249 -14.3832 P 0 0 1 0 0 0 0 0 0 0 0 0 20.4874 13.5195 -14.9547 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7941 11.0326 -14.2871 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9247 10.4104 -15.5200 P 0 0 0 0 0 0 0 0 0 0 0 0 20.4035 9.0105 -15.8294 O 0 0 0 0 0 0 0 0 0 0 0 0 20.7949 11.3956 -16.6774 O 0 5 0 0 0 0 0 0 0 0 0 0 22.2762 10.4400 -14.8131 O 0 5 0 0 0 0 0 0 0 0 0 0 19.4478 10.4190 -13.5396 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9556 12.8171 -15.0051 O 0 5 0 0 0 0 0 0 0 0 0 0 21.3179 14.9805 -11.1522 H 0 0 0 0 0 0 0 0 0 0 0 0 21.8749 14.5814 -12.7980 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0140 17.0439 -13.3022 H 0 0 0 0 0 0 0 0 0 0 0 0 24.2562 17.6416 -12.3964 O 0 0 0 0 0 0 0 0 0 0 0 0 24.3365 17.3880 -13.3282 H 0 0 0 0 0 0 0 0 0 0 0 0 24.0129 15.6590 -11.9445 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5130 17.4430 -9.6982 O 0 0 0 0 0 0 0 0 0 0 0 0 24.3116 17.6239 -8.7633 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0106 16.0497 -9.7338 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6256 19.0079 -10.5349 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9741 16.5606 -9.4258 H 0 0 0 0 0 0 0 0 0 0 0 0 23.2743 21.3162 -6.6265 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.795750 > <Chemgauss3 Steric> -64.465843 > <Chemgauss3 Desolvation> 31.438301 > <Chemgauss3 Acc> -16.462120 > <Chemgauss3 Donor> -6.306088 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.1931 20.4030 -6.5176 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4105 19.8375 -7.7251 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4994 18.8832 -7.9670 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4605 18.4869 -7.1399 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3407 19.1463 -5.9206 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2274 20.1223 -5.6096 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3157 18.8090 -5.0199 N 0 0 0 0 0 0 0 0 0 0 0 0 18.6379 18.1184 -5.2810 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2184 19.3279 -4.1679 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7330 17.4797 -7.7225 N 0 0 0 0 0 0 0 0 0 0 0 0 20.3186 17.2679 -8.8826 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3941 18.0937 -9.0764 N 0 0 0 0 0 0 0 0 0 0 0 0 22.2586 18.1177 -10.2541 C 0 0 1 0 0 0 0 0 0 0 0 0 23.4029 17.1168 -10.2035 C 0 0 1 0 0 0 0 0 0 0 0 0 23.6886 16.9106 -11.6780 C 0 0 1 0 0 0 0 0 0 0 0 0 22.2909 16.9462 -12.2881 C 0 0 2 0 0 0 0 0 0 0 0 0 21.4904 17.7894 -11.4277 O 0 0 0 0 0 0 0 0 0 0 0 0 21.6381 15.5728 -12.3565 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3475 15.7118 -12.9243 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4130 14.3827 -13.1187 P 0 0 2 0 0 0 0 0 0 0 0 0 18.2550 14.7441 -14.0235 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1661 13.7417 -11.7701 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4508 13.4398 -13.9578 O 0 0 0 0 0 0 0 0 0 0 0 0 20.6114 11.8146 -14.0112 P 0 0 1 0 0 0 0 0 0 0 0 0 19.3503 11.2703 -14.6475 O 0 0 0 0 0 0 0 0 0 0 0 0 21.9443 11.6411 -15.1424 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9066 10.2508 -16.2609 P 0 0 0 0 0 0 0 0 0 0 0 0 23.3600 9.7930 -16.3337 O 0 0 0 0 0 0 0 0 0 0 0 0 20.9703 9.2533 -15.5860 O 0 5 0 0 0 0 0 0 0 0 0 0 21.3664 10.8484 -17.5563 O 0 5 0 0 0 0 0 0 0 0 0 0 22.7127 12.3216 -15.1816 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0609 11.3195 -12.6532 O 0 5 0 0 0 0 0 0 0 0 0 0 21.5453 15.1515 -11.3544 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2340 14.9047 -12.9801 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2940 17.4027 -13.2873 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4372 18.0190 -12.1772 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5942 17.8422 -13.1170 H 0 0 0 0 0 0 0 0 0 0 0 0 24.2548 15.9989 -11.8940 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5133 17.6214 -9.4899 O 0 0 0 0 0 0 0 0 0 0 0 0 24.2388 17.7206 -8.5614 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0832 16.1750 -9.7397 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6188 19.1685 -10.3435 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0122 16.5362 -9.6180 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8847 21.1899 -6.2364 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -51.976028 > <Chemgauss3 Steric> -61.704735 > <Chemgauss3 Desolvation> 33.137104 > <Chemgauss3 Acc> -17.409328 > <Chemgauss3 Donor> -5.999057 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.6302 20.5423 -6.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7525 19.9688 -7.7770 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7752 19.0710 -7.9727 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7577 18.7344 -7.0942 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7389 19.3958 -5.8703 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6966 20.3164 -5.6043 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7425 19.1170 -4.9190 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0124 18.4687 -5.1457 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7192 19.6380 -4.0631 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9431 17.7740 -7.6395 N 0 0 0 0 0 0 0 0 0 0 0 0 20.4559 17.5315 -8.8278 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5673 18.2927 -9.0756 N 0 0 0 0 0 0 0 0 0 0 0 0 22.3712 18.2691 -10.2954 C 0 0 1 0 0 0 0 0 0 0 0 0 23.4552 17.2020 -10.3030 C 0 0 1 0 0 0 0 0 0 0 0 0 23.6533 16.9840 -11.7900 C 0 0 1 0 0 0 0 0 0 0 0 0 22.2312 17.1044 -12.3287 C 0 0 2 0 0 0 0 0 0 0 0 0 21.5267 17.9908 -11.4288 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4953 15.7723 -12.3643 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1882 15.9894 -12.8661 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1679 14.7188 -13.0133 P 0 0 2 0 0 0 0 0 0 0 0 0 17.9892 15.1511 -13.8583 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9516 14.0892 -11.6540 O 0 5 0 0 0 0 0 0 0 0 0 0 20.1042 13.7187 -13.9039 O 0 0 0 0 0 0 0 0 0 0 0 0 19.8131 12.2192 -14.4843 P 0 0 1 0 0 0 0 0 0 0 0 0 19.1030 12.3926 -15.8100 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4469 11.6456 -14.7807 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7136 10.6017 -16.2036 P 0 0 0 0 0 0 0 0 0 0 0 0 22.7217 9.5643 -15.7196 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3324 10.0335 -16.5145 O 0 5 0 0 0 0 0 0 0 0 0 0 22.2531 11.5642 -17.2570 O 0 5 0 0 0 0 0 0 0 0 0 0 22.2322 11.9125 -14.1749 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1958 11.3782 -13.3875 O 0 5 0 0 0 0 0 0 0 0 0 0 21.4283 15.3540 -11.3589 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0183 15.0721 -13.0174 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2110 17.5630 -13.3267 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4403 18.0476 -12.3263 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5389 17.8648 -13.2728 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1528 16.0409 -12.0346 H 0 0 0 0 0 0 0 0 0 0 0 0 24.6281 17.6376 -9.6464 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4072 17.7499 -8.7051 H 0 0 0 0 0 0 0 0 0 0 0 0 23.1038 16.2793 -9.8238 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7882 19.2971 -10.4027 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0698 16.8217 -9.5469 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3806 21.2859 -6.3139 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -53.372250 > <Chemgauss3 Steric> -60.079601 > <Chemgauss3 Desolvation> 32.019829 > <Chemgauss3 Acc> -17.636133 > <Chemgauss3 Donor> -7.676340 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.1758 20.3544 -6.7698 C 0 0 0 0 0 0 0 0 0 0 0 0 23.3051 19.7435 -7.9677 N 0 0 0 0 0 0 0 0 0 0 0 0 22.3179 18.8536 -8.1492 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2850 18.5571 -7.2742 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2604 19.2548 -6.0707 C 0 0 0 0 0 0 0 0 0 0 0 0 22.2275 20.1698 -5.8198 N 0 0 0 0 0 0 0 0 0 0 0 0 20.2485 19.0179 -5.1243 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5123 18.3732 -5.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2219 19.5645 -4.2846 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4639 17.5921 -7.8012 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9878 17.3075 -8.9752 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1128 18.0458 -9.2311 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9313 17.9750 -10.4394 C 0 0 1 0 0 0 0 0 0 0 0 0 24.0002 16.8935 -10.4017 C 0 0 1 0 0 0 0 0 0 0 0 0 24.2136 16.6287 -11.8790 C 0 0 1 0 0 0 0 0 0 0 0 0 22.8001 16.7523 -12.4391 C 0 0 2 0 0 0 0 0 0 0 0 0 22.0969 17.6746 -11.5747 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0462 15.4299 -12.4446 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7485 15.6498 -12.9692 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7124 14.3893 -13.0918 P 0 0 2 0 0 0 0 0 0 0 0 0 18.5504 14.8123 -13.9642 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4707 13.8034 -11.7174 O 0 5 0 0 0 0 0 0 0 0 0 0 20.6456 13.3506 -13.9405 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3407 11.8386 -14.4800 P 0 0 1 0 0 0 0 0 0 0 0 0 19.4495 11.1773 -13.4504 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3965 12.1757 -15.9226 N 0 0 0 0 0 0 0 0 0 0 0 0 18.0647 11.0566 -16.3218 P 0 0 0 0 0 0 0 0 0 0 0 0 18.1217 10.9383 -17.8416 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4215 9.7715 -15.5812 O 0 5 0 0 0 0 0 0 0 0 0 0 16.8262 11.7703 -15.7891 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5823 12.9967 -16.5112 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6449 11.1917 -14.8947 O 0 5 0 0 0 0 0 0 0 0 0 0 21.9609 15.0427 -11.4282 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5673 14.7036 -13.0700 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7986 17.1814 -13.4503 H 0 0 0 0 0 0 0 0 0 0 0 0 25.0219 17.6651 -12.4363 O 0 0 0 0 0 0 0 0 0 0 0 0 25.1296 17.4529 -13.3757 H 0 0 0 0 0 0 0 0 0 0 0 0 24.7028 15.6721 -12.0891 H 0 0 0 0 0 0 0 0 0 0 0 0 25.1709 17.3324 -9.7433 O 0 0 0 0 0 0 0 0 0 0 0 0 24.9400 17.4756 -8.8086 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6301 15.9903 -9.8999 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3639 18.9935 -10.5717 H 0 0 0 0 0 0 0 0 0 0 0 0 20.6008 16.5819 -9.6779 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9335 21.0948 -6.5362 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -57.754070 > <Chemgauss3 Steric> -50.744411 > <Chemgauss3 Desolvation> 32.443180 > <Chemgauss3 Acc> -33.542538 > <Chemgauss3 Donor> -5.910290 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.0198 20.5212 -6.8826 C 0 0 0 0 0 0 0 0 0 0 0 0 22.9548 19.8591 -8.0584 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8982 19.0328 -8.0735 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9700 18.8401 -7.0627 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1447 19.5816 -5.8986 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1919 20.4370 -5.8133 N 0 0 0 0 0 0 0 0 0 0 0 0 20.2502 19.4496 -4.8224 N 0 0 0 0 0 0 0 0 0 0 0 0 19.4530 18.8492 -4.9152 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3667 20.0272 -4.0116 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0285 17.9149 -7.4378 N 0 0 0 0 0 0 0 0 0 0 0 0 20.3778 17.5520 -8.6544 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5048 18.2016 -9.0833 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1547 18.0306 -10.3807 C 0 0 1 0 0 0 0 0 0 0 0 0 23.1491 16.8806 -10.4291 C 0 0 1 0 0 0 0 0 0 0 0 0 23.1533 16.5476 -11.9081 C 0 0 1 0 0 0 0 0 0 0 0 0 21.6900 16.7471 -12.2905 C 0 0 2 0 0 0 0 0 0 0 0 0 21.1638 17.7465 -11.3870 O 0 0 0 0 0 0 0 0 0 0 0 0 20.8596 15.4801 -12.1411 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5217 15.7688 -12.5073 O 0 0 0 0 0 0 0 0 0 0 0 0 18.3030 14.9359 -11.8014 P 0 0 2 0 0 0 0 0 0 0 0 0 16.9912 15.5503 -12.2396 O 0 0 0 0 0 0 0 0 0 0 0 0 18.6114 14.7447 -10.3321 O 0 5 0 0 0 0 0 0 0 0 0 0 18.4800 13.4988 -12.5588 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4056 13.1119 -14.1446 P 0 0 1 0 0 0 0 0 0 0 0 0 19.5782 13.7931 -14.8174 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7044 11.3817 -14.0874 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6547 10.6603 -15.4148 P 0 0 0 0 0 0 0 0 0 0 0 0 18.9725 9.3209 -15.6748 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5210 11.6619 -16.5576 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0596 10.5514 -14.8306 O 0 5 0 0 0 0 0 0 0 0 0 0 18.3667 10.7997 -13.3113 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9949 13.3439 -14.6421 O 0 5 0 0 0 0 0 0 0 0 0 0 20.8817 15.1372 -11.1056 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2489 14.6972 -12.7937 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5854 17.1377 -13.3118 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9469 17.5051 -12.6092 O 0 0 0 0 0 0 0 0 0 0 0 0 23.9191 17.2516 -13.5441 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5499 15.5527 -12.1348 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4203 17.2623 -9.9442 O 0 0 0 0 0 0 0 0 0 0 0 0 24.3212 17.4553 -8.9953 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7904 16.0240 -9.8444 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6301 19.0116 -10.6124 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8584 16.8292 -9.2691 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8465 21.2160 -6.7802 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -60.291306 > <Chemgauss3 Steric> -63.095200 > <Chemgauss3 Desolvation> 33.013611 > <Chemgauss3 Acc> -23.504499 > <Chemgauss3 Donor> -6.705223 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.9157 19.5400 -6.9090 C 0 0 0 0 0 0 0 0 0 0 0 0 22.8655 18.8004 -8.0384 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6309 18.3094 -8.2229 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5240 18.4967 -7.4105 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7029 19.2799 -6.2745 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9249 19.8088 -6.0248 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6341 19.5227 -5.3945 N 0 0 0 0 0 0 0 0 0 0 0 0 18.7238 19.1654 -5.6145 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7719 20.1279 -4.6075 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4316 17.8401 -7.9190 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8664 17.2643 -9.0204 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1929 17.5191 -9.2471 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9811 17.0326 -10.3771 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5800 15.6504 -10.1659 C 0 0 1 0 0 0 0 0 0 0 0 0 22.7464 15.1723 -11.5948 C 0 0 1 0 0 0 0 0 0 0 0 0 21.5007 15.7342 -12.2728 C 0 0 2 0 0 0 0 0 0 0 0 0 21.1449 16.9329 -11.5459 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3180 14.7770 -12.2284 C 0 0 0 0 0 0 0 0 0 0 0 0 19.2137 15.3903 -12.8700 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6974 15.0166 -12.3814 P 0 0 2 0 0 0 0 0 0 0 0 0 16.7274 15.9253 -13.1050 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6699 14.9058 -10.8723 O 0 5 0 0 0 0 0 0 0 0 0 0 17.5695 13.5150 -13.0131 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6649 12.9961 -14.5596 P 0 0 1 0 0 0 0 0 0 0 0 0 19.0868 13.2418 -15.0173 O 0 0 0 0 0 0 0 0 0 0 0 0 17.4198 11.2686 -14.3549 N 0 0 0 0 0 0 0 0 0 0 0 0 18.3312 10.1694 -15.4257 P 0 0 0 0 0 0 0 0 0 0 0 0 17.3382 9.0572 -15.7483 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7062 11.0387 -16.6219 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5133 9.7321 -14.5666 O 0 5 0 0 0 0 0 0 0 0 0 0 16.7924 10.8929 -13.6336 H 0 0 0 0 0 0 0 0 0 0 0 0 16.4987 13.5618 -15.3414 O 0 5 0 0 0 0 0 0 0 0 0 0 20.0534 14.5556 -11.1933 H 0 0 0 0 0 0 0 0 0 0 0 0 20.5654 13.8504 -12.7486 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6996 16.0259 -13.3131 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9000 15.7852 -12.1705 O 0 0 0 0 0 0 0 0 0 0 0 0 23.9638 15.4506 -13.0777 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8622 14.0874 -11.6859 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8004 15.7078 -9.4558 O 0 0 0 0 0 0 0 0 0 0 0 0 23.5971 16.0221 -8.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 21.8850 14.9982 -9.6219 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7603 17.8085 -10.5587 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2726 16.6556 -9.6890 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8801 19.9800 -6.6785 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.466789 > <Chemgauss3 Steric> -69.126480 > <Chemgauss3 Desolvation> 36.278793 > <Chemgauss3 Acc> -17.038673 > <Chemgauss3 Donor> -5.580438 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.8395 20.1676 -6.9807 C 0 0 0 0 0 0 0 0 0 0 0 0 21.8133 19.3310 -7.2487 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9575 18.7870 -8.4663 C 0 0 0 0 0 0 0 0 0 0 0 0 22.9865 19.0092 -9.3675 C 0 0 0 0 0 0 0 0 0 0 0 0 23.9864 19.8933 -8.9747 C 0 0 0 0 0 0 0 0 0 0 0 0 23.9054 20.4805 -7.7565 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0684 20.1771 -9.8259 N 0 0 0 0 0 0 0 0 0 0 0 0 25.1420 19.7009 -10.7047 H 0 0 0 0 0 0 0 0 0 0 0 0 25.8021 20.7801 -9.5053 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7959 18.2773 -10.5125 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6717 17.6221 -10.3111 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1258 17.8980 -9.0856 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8862 17.3392 -8.5509 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6354 18.1029 -8.9583 C 0 0 1 0 0 0 0 0 0 0 0 0 17.5741 17.0265 -8.8438 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3120 15.7879 -9.3421 C 0 0 2 0 0 0 0 0 0 0 0 0 19.7105 15.9941 -9.0360 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1750 15.5797 -10.8438 C 0 0 0 0 0 0 0 0 0 0 0 0 18.8994 14.4180 -11.2087 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9254 13.9526 -12.7771 P 0 0 2 0 0 0 0 0 0 0 0 0 19.8951 12.7990 -12.9146 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0518 15.1748 -13.6608 O 0 5 0 0 0 0 0 0 0 0 0 0 17.4049 13.3698 -12.9141 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6268 12.7070 -14.1889 P 0 0 1 0 0 0 0 0 0 0 0 0 16.7365 13.6944 -15.3310 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6511 11.3210 -14.5299 N 0 0 0 0 0 0 0 0 0 0 0 0 17.8738 10.8554 -16.2385 P 0 0 0 0 0 0 0 0 0 0 0 0 17.8680 9.3301 -16.2117 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6757 11.4724 -16.9534 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2179 11.4762 -16.6060 O 0 5 0 0 0 0 0 0 0 0 0 0 18.1266 10.8025 -13.7816 H 0 0 0 0 0 0 0 0 0 0 0 0 15.2722 12.2080 -13.7335 O 0 5 0 0 0 0 0 0 0 0 0 0 18.5814 16.4386 -11.3801 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1254 15.4459 -11.1099 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9887 14.8808 -8.8135 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2338 16.8380 -7.4702 O 0 0 0 0 0 0 0 0 0 0 0 0 16.5566 16.1452 -7.4485 H 0 0 0 0 0 0 0 0 0 0 0 0 16.6529 17.2560 -9.3891 H 0 0 0 0 0 0 0 0 0 0 0 0 18.3949 19.2095 -8.1131 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1204 19.8430 -8.2535 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7102 18.4588 -9.9937 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0213 17.3068 -7.4451 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2072 16.9395 -11.0100 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8072 20.6550 -6.0122 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -56.654259 > <Chemgauss3 Steric> -76.621002 > <Chemgauss3 Desolvation> 35.320370 > <Chemgauss3 Acc> -14.346529 > <Chemgauss3 Donor> -1.007106 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.2886 20.1594 -6.8363 C 0 0 0 0 0 0 0 0 0 0 0 0 23.2726 19.5678 -8.0507 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1044 18.9397 -8.2510 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0295 18.8702 -7.3792 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1675 19.5213 -6.1574 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3220 20.1768 -5.8870 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1269 19.5030 -5.2127 N 0 0 0 0 0 0 0 0 0 0 0 0 19.2603 19.0551 -5.4429 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2281 20.0175 -4.3585 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0056 18.1395 -7.9277 N 0 0 0 0 0 0 0 0 0 0 0 0 20.4499 17.7717 -9.1114 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7170 18.2321 -9.3531 N 0 0 0 0 0 0 0 0 0 0 0 0 22.4979 18.0040 -10.5669 C 0 0 1 0 0 0 0 0 0 0 0 0 23.2831 16.7013 -10.5632 C 0 0 1 0 0 0 0 0 0 0 0 0 23.4306 16.4339 -12.0481 C 0 0 1 0 0 0 0 0 0 0 0 0 22.0864 16.9009 -12.5977 C 0 0 2 0 0 0 0 0 0 0 0 0 21.6180 17.9386 -11.7056 O 0 0 0 0 0 0 0 0 0 0 0 0 21.0432 15.7929 -12.6348 C 0 0 0 0 0 0 0 0 0 0 0 0 19.8341 16.3252 -13.1470 O 0 0 0 0 0 0 0 0 0 0 0 0 18.5314 15.3468 -13.2980 P 0 0 2 0 0 0 0 0 0 0 0 0 17.5024 16.0541 -14.1531 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1568 14.7971 -11.9386 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1959 14.1415 -14.1787 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8504 12.5455 -14.2353 P 0 0 1 0 0 0 0 0 0 0 0 0 17.4579 12.4188 -14.8156 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0184 11.9860 -15.4223 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5116 10.6857 -16.5350 P 0 0 0 0 0 0 0 0 0 0 0 0 20.7514 9.8072 -16.6690 O 0 0 0 0 0 0 0 0 0 0 0 0 18.3444 10.0142 -15.8182 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1262 11.4338 -17.8073 O 0 5 0 0 0 0 0 0 0 0 0 0 20.9555 12.4000 -15.4960 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1833 11.9221 -12.8967 O 0 5 0 0 0 0 0 0 0 0 0 0 20.8679 15.4091 -11.6287 H 0 0 0 0 0 0 0 0 0 0 0 0 21.3802 14.9818 -13.2819 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1871 17.3455 -13.5972 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4603 17.2664 -12.5816 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5166 17.0605 -13.5268 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6820 15.3953 -12.2861 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5231 16.8353 -9.8991 O 0 0 0 0 0 0 0 0 0 0 0 0 24.3309 17.0033 -8.9598 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7106 15.8969 -10.0839 H 0 0 0 0 0 0 0 0 0 0 0 0 23.1576 18.8958 -10.6741 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9044 17.1765 -9.8313 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1985 20.6947 -6.5868 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.867493 > <Chemgauss3 Steric> -62.668209 > <Chemgauss3 Desolvation> 34.452843 > <Chemgauss3 Acc> -21.702168 > <Chemgauss3 Donor> -5.949977 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.8179 17.6795 -10.4313 C 0 0 0 0 0 0 0 0 0 0 0 0 22.5708 17.3829 -10.0051 N 0 0 0 0 0 0 0 0 0 0 0 0 22.3042 18.0202 -8.8553 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1429 18.8729 -8.1553 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4039 19.0998 -8.6975 C 0 0 0 0 0 0 0 0 0 0 0 0 24.7418 18.4881 -9.8582 N 0 0 0 0 0 0 0 0 0 0 0 0 25.3192 19.9509 -8.0544 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0410 20.4345 -7.2216 H 0 0 0 0 0 0 0 0 0 0 0 0 26.2045 20.1379 -8.4855 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5264 19.3371 -7.0206 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3348 18.7771 -7.0307 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1529 17.9701 -8.1223 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9480 17.2048 -8.4348 C 0 0 1 0 0 0 0 0 0 0 0 0 18.9788 17.9249 -9.3599 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2395 16.7599 -9.9879 C 0 0 1 0 0 0 0 0 0 0 0 0 19.3466 15.7235 -10.1537 C 0 0 2 0 0 0 0 0 0 0 0 0 20.3092 15.9821 -9.1055 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0587 15.8253 -11.4952 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0701 14.8345 -11.5482 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0010 14.7143 -12.8885 P 0 0 2 0 0 0 0 0 0 0 0 0 23.0956 13.7049 -12.6179 O 0 0 0 0 0 0 0 0 0 0 0 0 22.3391 16.1015 -13.3903 O 0 5 0 0 0 0 0 0 0 0 0 0 20.9192 14.0427 -13.9127 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1022 12.6302 -13.8263 P 0 0 1 0 0 0 0 0 0 0 0 0 19.1592 12.7408 -12.6473 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1685 12.6854 -15.3134 N 0 0 0 0 0 0 0 0 0 0 0 0 17.5195 12.0033 -15.2826 P 0 0 0 0 0 0 0 0 0 0 0 0 17.3804 11.3065 -16.6325 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5295 11.0549 -14.0878 O 0 5 0 0 0 0 0 0 0 0 0 0 16.6286 13.2294 -15.1092 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5409 13.1118 -16.1705 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0882 11.4851 -13.9154 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5157 16.8101 -11.6033 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3513 15.6593 -12.3090 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9716 14.7007 -10.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2726 16.2571 -9.0658 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8290 15.5187 -9.5098 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7168 17.0176 -10.9147 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1280 18.8030 -8.6515 O 0 0 0 0 0 0 0 0 0 0 0 0 18.6852 19.5129 -8.2867 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5165 18.4961 -10.1273 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4870 16.9521 -7.4521 H 0 0 0 0 0 0 0 0 0 0 0 0 20.5674 18.9166 -6.2811 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1216 17.2071 -11.3595 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.934418 > <Chemgauss3 Steric> -63.549084 > <Chemgauss3 Desolvation> 32.847904 > <Chemgauss3 Acc> -24.380148 > <Chemgauss3 Donor> -3.853091 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.5411 17.7419 -7.3873 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5311 18.0119 -8.2659 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3772 18.9187 -7.7548 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3029 19.5283 -6.5126 C 0 0 0 0 0 0 0 0 0 0 0 0 20.2355 19.1660 -5.6971 C 0 0 0 0 0 0 0 0 0 0 0 0 19.3407 18.2546 -6.1492 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0822 19.7343 -4.4207 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7760 20.3717 -4.0786 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3333 19.4250 -3.8306 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3457 20.4030 -6.3376 N 0 0 0 0 0 0 0 0 0 0 0 0 23.0413 20.3264 -7.4529 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4942 19.4404 -8.3428 N 0 0 0 0 0 0 0 0 0 0 0 0 23.0169 19.1203 -9.6691 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9293 17.9036 -9.6988 C 0 0 1 0 0 0 0 0 0 0 0 0 23.7841 17.4528 -11.1389 C 0 0 1 0 0 0 0 0 0 0 0 0 22.3085 17.7223 -11.4168 C 0 0 2 0 0 0 0 0 0 0 0 0 21.9264 18.8256 -10.5631 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4165 16.5324 -11.0915 C 0 0 0 0 0 0 0 0 0 0 0 0 21.8142 15.4346 -11.8940 O 0 0 0 0 0 0 0 0 0 0 0 0 21.0196 14.0114 -11.7509 P 0 0 2 0 0 0 0 0 0 0 0 0 20.8781 13.6920 -10.2784 O 0 0 0 0 0 0 0 0 0 0 0 0 21.6232 13.0021 -12.7036 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5567 14.4565 -12.3269 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1194 15.0505 -13.7850 P 0 0 1 0 0 0 0 0 0 0 0 0 19.3621 13.9509 -14.7968 O 0 0 0 0 0 0 0 0 0 0 0 0 17.3884 15.2539 -13.5646 N 0 0 0 0 0 0 0 0 0 0 0 0 16.3309 14.9310 -14.9657 P 0 0 0 0 0 0 0 0 0 0 0 0 15.2566 16.0104 -14.8768 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2555 15.0674 -16.1713 O 0 5 0 0 0 0 0 0 0 0 0 0 15.8258 13.5139 -14.7133 O 0 5 0 0 0 0 0 0 0 0 0 0 16.9868 15.5283 -12.6600 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7481 16.4151 -13.9692 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3748 16.7749 -11.3068 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5193 16.2630 -10.0393 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1402 18.0355 -12.4561 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5722 18.2929 -11.9823 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4474 17.9674 -12.8865 H 0 0 0 0 0 0 0 0 0 0 0 0 24.0964 16.4177 -11.3103 H 0 0 0 0 0 0 0 0 0 0 0 0 25.2592 18.2337 -9.3536 O 0 0 0 0 0 0 0 0 0 0 0 0 25.2552 18.5091 -8.4200 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5698 17.1241 -9.0150 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5309 20.0438 -10.0226 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9422 20.8835 -7.6723 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8066 17.0148 -7.7166 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.961903 > <Chemgauss3 Steric> -68.297684 > <Chemgauss3 Desolvation> 39.064884 > <Chemgauss3 Acc> -18.067144 > <Chemgauss3 Donor> -11.661962 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.8474 17.7646 -10.0104 C 0 0 0 0 0 0 0 0 0 0 0 0 22.5673 17.5597 -9.6303 N 0 0 0 0 0 0 0 0 0 0 0 0 22.2941 18.2491 -8.5124 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1552 19.0703 -7.8022 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4496 19.2009 -8.2954 C 0 0 0 0 0 0 0 0 0 0 0 0 24.7959 18.5324 -9.4218 N 0 0 0 0 0 0 0 0 0 0 0 0 25.3893 20.0140 -7.6386 N 0 0 0 0 0 0 0 0 0 0 0 0 25.1080 20.5404 -6.8334 H 0 0 0 0 0 0 0 0 0 0 0 0 26.3018 20.1318 -8.0362 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5227 19.6081 -6.7096 N 0 0 0 0 0 0 0 0 0 0 0 0 21.2995 19.1230 -6.7549 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1124 18.2940 -7.8291 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8756 17.5952 -8.1709 C 0 0 1 0 0 0 0 0 0 0 0 0 18.9931 18.3438 -9.1581 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2083 17.2073 -9.7830 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2535 16.0995 -9.8698 C 0 0 2 0 0 0 0 0 0 0 0 0 20.1862 16.3316 -8.7889 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0258 16.1136 -11.1815 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9738 15.0609 -11.1611 O 0 0 0 0 0 0 0 0 0 0 0 0 21.9500 14.8400 -12.4555 P 0 0 2 0 0 0 0 0 0 0 0 0 22.9664 13.7740 -12.1079 O 0 0 0 0 0 0 0 0 0 0 0 0 22.3959 16.1867 -12.9829 O 0 5 0 0 0 0 0 0 0 0 0 0 20.8715 14.2041 -13.5055 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9638 12.8485 -13.4130 P 0 0 1 0 0 0 0 0 0 0 0 0 18.9815 13.0553 -12.2799 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0981 12.9135 -14.9403 N 0 0 0 0 0 0 0 0 0 0 0 0 17.4093 12.3363 -14.9611 P 0 0 0 0 0 0 0 0 0 0 0 0 17.2826 11.6063 -16.2945 O 0 0 0 0 0 0 0 0 0 0 0 0 17.3096 11.4280 -13.7395 O 0 5 0 0 0 0 0 0 0 0 0 0 16.5914 13.6201 -14.8629 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5320 13.2881 -15.7926 H 0 0 0 0 0 0 0 0 0 0 0 0 20.8782 11.6423 -13.4253 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5483 17.0642 -11.2987 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3437 15.9656 -12.0201 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8090 15.1069 -9.7148 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1740 16.7953 -8.8894 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7034 16.0719 -9.3302 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7420 17.4669 -10.7389 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1710 19.2954 -8.5137 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7563 19.9807 -8.1461 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5973 18.8556 -9.9180 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3590 17.4034 -7.2021 H 0 0 0 0 0 0 0 0 0 0 0 0 20.5121 19.3338 -6.0439 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1588 17.2446 -10.9101 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -59.461769 > <Chemgauss3 Steric> -66.395706 > <Chemgauss3 Desolvation> 34.581688 > <Chemgauss3 Acc> -22.694374 > <Chemgauss3 Donor> -4.953379 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.9391 20.3765 -7.5601 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9204 19.5135 -7.7662 N 0 0 0 0 0 0 0 0 0 0 0 0 22.0370 18.9289 -8.9679 C 0 0 0 0 0 0 0 0 0 0 0 0 23.0337 19.1363 -9.9081 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0291 20.0507 -9.5782 C 0 0 0 0 0 0 0 0 0 0 0 0 23.9748 20.6796 -8.3794 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0791 20.3224 -10.4723 N 0 0 0 0 0 0 0 0 0 0 0 0 25.1343 19.8164 -11.3357 H 0 0 0 0 0 0 0 0 0 0 0 0 25.8112 20.9488 -10.1962 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8213 18.3609 -11.0203 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7159 17.6943 -10.7608 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2029 18.0045 -9.5293 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9906 17.4440 -8.9367 C 0 0 1 0 0 0 0 0 0 0 0 0 18.7143 18.1714 -9.3313 C 0 0 1 0 0 0 0 0 0 0 0 0 17.6766 17.0820 -9.1458 C 0 0 1 0 0 0 0 0 0 0 0 0 18.4212 15.8390 -9.6233 C 0 0 2 0 0 0 0 0 0 0 0 0 19.8244 16.0798 -9.3685 O 0 0 0 0 0 0 0 0 0 0 0 0 18.2419 15.5751 -11.1117 C 0 0 0 0 0 0 0 0 0 0 0 0 18.9757 14.4136 -11.4580 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9619 13.8931 -13.0092 P 0 0 2 0 0 0 0 0 0 0 0 0 19.9477 12.7519 -13.1363 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0390 15.0849 -13.9388 O 0 5 0 0 0 0 0 0 0 0 0 0 17.4488 13.2800 -13.0779 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6440 12.5590 -14.3036 P 0 0 1 0 0 0 0 0 0 0 0 0 16.7007 13.5068 -15.4826 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6822 11.1793 -14.6277 N 0 0 0 0 0 0 0 0 0 0 0 0 17.8608 10.6569 -16.3250 P 0 0 0 0 0 0 0 0 0 0 0 0 17.8834 9.1337 -16.2444 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6304 11.2276 -17.0232 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1815 11.2869 -16.7559 O 0 5 0 0 0 0 0 0 0 0 0 0 18.1898 10.6961 -13.8769 H 0 0 0 0 0 0 0 0 0 0 0 0 15.3133 12.0536 -13.7888 O 0 5 0 0 0 0 0 0 0 0 0 0 18.6161 16.4211 -11.6902 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1873 15.4141 -11.3399 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1307 14.9460 -9.0533 H 0 0 0 0 0 0 0 0 0 0 0 0 17.3821 16.9368 -7.7565 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7185 16.2337 -7.6893 H 0 0 0 0 0 0 0 0 0 0 0 0 16.7352 17.2761 -9.6698 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4799 19.3032 -8.5184 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1892 19.9435 -8.7036 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7508 18.4914 -10.3804 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1601 17.4535 -7.8352 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2425 16.9795 -11.4204 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9277 20.8975 -6.6087 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.222118 > <Chemgauss3 Steric> -71.668221 > <Chemgauss3 Desolvation> 35.301819 > <Chemgauss3 Acc> -15.918826 > <Chemgauss3 Donor> -2.936887 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.6784 17.6297 -7.0461 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6091 17.7871 -8.0127 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4261 18.8085 -7.7150 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3765 19.6230 -6.5950 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3709 19.3600 -5.6702 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5084 18.3423 -5.9063 N 0 0 0 0 0 0 0 0 0 0 0 0 20.2465 20.1363 -4.5050 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9188 20.8558 -4.3182 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5449 19.9007 -3.8290 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3756 20.5629 -6.6333 N 0 0 0 0 0 0 0 0 0 0 0 0 23.0209 20.3240 -7.7559 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4829 19.2706 -8.4465 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9595 18.7470 -9.7247 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9364 17.5884 -9.5945 C 0 0 1 0 0 0 0 0 0 0 0 0 23.7488 16.8849 -10.9241 C 0 0 1 0 0 0 0 0 0 0 0 0 22.2489 17.0315 -11.1608 C 0 0 2 0 0 0 0 0 0 0 0 0 21.8462 18.2486 -10.4911 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4415 15.8768 -10.5846 C 0 0 0 0 0 0 0 0 0 0 0 0 20.0683 16.1092 -10.8446 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9624 15.0177 -10.3319 P 0 0 2 0 0 0 0 0 0 0 0 0 17.5823 15.5846 -10.5851 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3501 14.5192 -8.9565 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2373 13.8228 -11.4121 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1303 13.8126 -13.0425 P 0 0 1 0 0 0 0 0 0 0 0 0 19.3582 12.3838 -13.4878 O 0 0 0 0 0 0 0 0 0 0 0 0 17.4378 14.2218 -13.2753 N 0 0 0 0 0 0 0 0 0 0 0 0 16.5766 13.4465 -14.6328 P 0 0 0 0 0 0 0 0 0 0 0 0 15.6791 14.5507 -15.1826 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6889 13.0141 -15.5830 O 0 5 0 0 0 0 0 0 0 0 0 0 15.8279 12.2945 -13.9700 O 0 5 0 0 0 0 0 0 0 0 0 0 16.9456 14.8671 -12.6457 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9809 14.9345 -13.5986 O 0 5 0 0 0 0 0 0 0 0 0 0 21.5963 15.8124 -9.5065 H 0 0 0 0 0 0 0 0 0 0 0 0 21.7413 14.9385 -11.0536 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0143 17.1486 -12.2276 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4476 17.5995 -11.9434 O 0 0 0 0 0 0 0 0 0 0 0 0 24.2987 17.1145 -12.7690 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1103 15.8515 -10.9310 H 0 0 0 0 0 0 0 0 0 0 0 0 25.2605 18.0362 -9.3873 O 0 0 0 0 0 0 0 0 0 0 0 0 25.2852 18.4711 -8.5168 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6540 16.9253 -8.7668 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4035 19.6171 -10.2612 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8777 20.8756 -8.1190 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9712 16.8222 -7.2026 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -62.831017 > <Chemgauss3 Steric> -75.950592 > <Chemgauss3 Desolvation> 37.679874 > <Chemgauss3 Acc> -15.042402 > <Chemgauss3 Donor> -9.517878 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.0929 19.5389 -7.1579 C 0 0 0 0 0 0 0 0 0 0 0 0 22.9343 18.7590 -8.2496 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6871 18.2675 -8.2976 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6629 18.4894 -7.3909 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9503 19.3124 -6.3065 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1912 19.8442 -6.1937 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9705 19.5919 -5.3382 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0430 19.2312 -5.4573 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1835 20.2246 -4.5905 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5262 17.8199 -7.7688 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8533 17.2026 -8.8848 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1525 17.4428 -9.2459 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8289 16.9119 -10.4274 C 0 0 1 0 0 0 0 0 0 0 0 0 22.4434 15.5355 -10.2238 C 0 0 1 0 0 0 0 0 0 0 0 0 22.4722 15.0051 -11.6436 C 0 0 1 0 0 0 0 0 0 0 0 0 21.1683 15.5479 -12.2201 C 0 0 2 0 0 0 0 0 0 0 0 0 20.8849 16.7739 -11.5068 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9940 14.5985 -12.0283 C 0 0 0 0 0 0 0 0 0 0 0 0 18.9760 14.9440 -12.9512 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5860 14.0808 -12.9672 P 0 0 2 0 0 0 0 0 0 0 0 0 16.6181 14.7562 -13.9144 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1769 13.7626 -11.5453 O 0 5 0 0 0 0 0 0 0 0 0 0 18.1253 12.7079 -13.6703 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8075 12.4550 -15.1334 P 0 0 1 0 0 0 0 0 0 0 0 0 19.8579 13.5292 -15.3189 O 0 0 0 0 0 0 0 0 0 0 0 0 19.6061 10.9118 -14.8745 N 0 0 0 0 0 0 0 0 0 0 0 0 21.1783 10.6473 -15.6770 P 0 0 0 0 0 0 0 0 0 0 0 0 21.1293 9.1878 -16.1182 O 0 0 0 0 0 0 0 0 0 0 0 0 21.1836 11.6482 -16.8281 O 0 5 0 0 0 0 0 0 0 0 0 0 22.1946 10.9418 -14.5782 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2017 10.1883 -14.2679 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7122 12.2673 -16.1612 O 0 5 0 0 0 0 0 0 0 0 0 0 19.6027 14.6864 -11.0136 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3093 13.5701 -12.2107 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2675 15.8008 -13.2845 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5665 15.5913 -12.3486 O 0 0 0 0 0 0 0 0 0 0 0 0 23.5431 15.2238 -13.2449 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5775 13.9171 -11.7057 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7260 15.6127 -9.6357 O 0 0 0 0 0 0 0 0 0 0 0 0 23.6096 15.9604 -8.7340 H 0 0 0 0 0 0 0 0 0 0 0 0 21.8026 14.9067 -9.5926 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5881 17.6770 -10.7105 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1978 16.5728 -9.4711 H 0 0 0 0 0 0 0 0 0 0 0 0 24.0754 19.9824 -7.0365 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -57.296555 > <Chemgauss3 Steric> -57.186905 > <Chemgauss3 Desolvation> 33.524109 > <Chemgauss3 Acc> -27.596338 > <Chemgauss3 Donor> -6.037434 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.6842 19.2911 -5.6096 C 0 0 0 0 0 0 0 0 0 0 0 0 20.0575 18.3863 -6.3930 N 0 0 0 0 0 0 0 0 0 0 0 0 20.8302 18.0565 -7.4388 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0966 18.5377 -7.7304 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6355 19.4667 -6.8459 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9100 19.8465 -5.7666 N 0 0 0 0 0 0 0 0 0 0 0 0 23.9146 20.0072 -7.0639 N 0 0 0 0 0 0 0 0 0 0 0 0 24.4606 19.6834 -7.8395 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3036 20.6390 -6.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5774 17.9718 -8.8844 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6209 17.1613 -9.2868 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5414 17.1780 -8.4438 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3164 16.3970 -8.5998 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2698 17.0557 -9.4855 C 0 0 1 0 0 0 0 0 0 0 0 0 17.4829 15.8532 -9.9679 C 0 0 1 0 0 0 0 0 0 0 0 0 18.5746 14.8046 -10.1569 C 0 0 2 0 0 0 0 0 0 0 0 0 19.6224 15.1306 -9.2147 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1694 14.8132 -11.5581 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1753 13.8181 -11.6300 O 0 0 0 0 0 0 0 0 0 0 0 0 20.9888 13.6046 -13.0337 P 0 0 2 0 0 0 0 0 0 0 0 0 19.9833 13.5615 -14.1639 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0027 12.4942 -12.8618 O 0 5 0 0 0 0 0 0 0 0 0 0 21.7875 15.0284 -13.1055 O 0 0 0 0 0 0 0 0 0 0 0 0 23.2332 15.4089 -13.7649 P 0 0 1 0 0 0 0 0 0 0 0 0 24.2498 14.4571 -13.1714 O 0 0 0 0 0 0 0 0 0 0 0 0 22.9631 14.9820 -15.4474 N 0 0 0 0 0 0 0 0 0 0 0 0 24.3323 14.2852 -16.3559 P 0 0 0 0 0 0 0 0 0 0 0 0 24.2142 14.9095 -17.7427 O 0 0 0 0 0 0 0 0 0 0 0 0 25.5645 14.7290 -15.5737 O 0 5 0 0 0 0 0 0 0 0 0 0 24.0629 12.7843 -16.3131 O 0 5 0 0 0 0 0 0 0 0 0 0 22.0477 15.1052 -15.8966 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4379 16.9058 -13.6717 O 0 5 0 0 0 0 0 0 0 0 0 0 19.6128 15.7871 -11.7712 H 0 0 0 0 0 0 0 0 0 0 0 0 18.3956 14.5947 -12.2955 H 0 0 0 0 0 0 0 0 0 0 0 0 18.2160 13.7948 -9.9153 H 0 0 0 0 0 0 0 0 0 0 0 0 16.5996 15.4168 -8.9347 O 0 0 0 0 0 0 0 0 0 0 0 0 16.1217 14.6514 -9.2882 H 0 0 0 0 0 0 0 0 0 0 0 0 16.8823 16.0491 -10.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4802 17.9824 -8.7682 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0644 18.7136 -8.5010 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7385 17.5721 -10.3329 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9416 16.2128 -7.5666 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6521 16.5421 -10.1732 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1318 19.6171 -4.7348 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -44.051826 > <Chemgauss3 Steric> -54.253803 > <Chemgauss3 Desolvation> 29.746668 > <Chemgauss3 Acc> -15.224940 > <Chemgauss3 Donor> -4.319755 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.2924 19.3736 -5.7741 C 0 0 0 0 0 0 0 0 0 0 0 0 19.8449 18.3721 -6.5626 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7765 18.0354 -7.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0349 18.5945 -7.6225 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3800 19.6199 -6.7477 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4869 20.0123 -5.8077 N 0 0 0 0 0 0 0 0 0 0 0 0 23.6366 20.2438 -6.8333 N 0 0 0 0 0 0 0 0 0 0 0 0 24.3064 19.9132 -7.5016 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8834 20.9478 -6.1639 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7097 17.9926 -8.6548 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8768 17.0842 -9.1182 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6919 17.0718 -8.4313 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5574 16.1880 -8.6894 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6013 16.7017 -9.7552 C 0 0 1 0 0 0 0 0 0 0 0 0 17.9741 15.4114 -10.2449 C 0 0 1 0 0 0 0 0 0 0 0 0 19.1513 14.4419 -10.2050 C 0 0 2 0 0 0 0 0 0 0 0 0 20.0327 14.9116 -9.1587 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9334 14.4041 -11.5104 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0058 13.4888 -11.3704 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0195 13.2471 -12.6318 P 0 0 2 0 0 0 0 0 0 0 0 0 23.1570 12.3647 -12.1652 O 0 0 0 0 0 0 0 0 0 0 0 0 22.2997 14.5705 -13.3106 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0437 12.3646 -13.6009 O 0 0 0 0 0 0 0 0 0 0 0 0 21.3091 11.7161 -15.0770 P 0 0 1 0 0 0 0 0 0 0 0 0 22.3691 10.6494 -14.9030 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7639 10.9417 -15.3915 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7785 9.3908 -16.2747 P 0 0 0 0 0 0 0 0 0 0 0 0 18.5648 9.4759 -17.1950 O 0 0 0 0 0 0 0 0 0 0 0 0 21.1177 9.3891 -17.0051 O 0 5 0 0 0 0 0 0 0 0 0 0 19.6606 8.3478 -15.1677 O 0 5 0 0 0 0 0 0 0 0 0 0 18.8788 11.3478 -15.0648 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5032 12.8345 -16.0783 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3339 15.3935 -11.7363 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2868 14.0766 -12.3258 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8330 13.4253 -9.9368 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9878 14.9765 -9.3089 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6178 14.1540 -9.6634 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4919 15.4994 -11.2238 H 0 0 0 0 0 0 0 0 0 0 0 0 17.6575 17.6089 -9.2234 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1470 18.4001 -8.9374 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1467 17.1959 -10.5693 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0560 16.0440 -7.7046 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0738 16.4117 -9.9423 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6024 19.7126 -5.0088 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -49.039917 > <Chemgauss3 Steric> -59.005875 > <Chemgauss3 Desolvation> 32.931259 > <Chemgauss3 Acc> -19.185522 > <Chemgauss3 Donor> -3.779778 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.7271 17.2789 -10.4728 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4813 16.8861 -10.1283 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1017 17.4789 -8.9864 C 0 0 0 0 0 0 0 0 0 0 0 0 22.8337 18.3739 -8.2226 C 0 0 0 0 0 0 0 0 0 0 0 0 24.1053 18.7006 -8.6832 C 0 0 0 0 0 0 0 0 0 0 0 0 24.5547 18.1387 -9.8311 N 0 0 0 0 0 0 0 0 0 0 0 0 24.9172 19.6007 -7.9715 N 0 0 0 0 0 0 0 0 0 0 0 0 24.5559 20.0459 -7.1494 H 0 0 0 0 0 0 0 0 0 0 0 0 25.8109 19.8587 -8.3448 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1191 18.7696 -7.1200 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9735 18.1271 -7.2119 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9153 17.3322 -8.3258 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7892 16.4904 -8.7237 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8276 17.1593 -9.6941 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2126 15.9584 -10.3851 C 0 0 1 0 0 0 0 0 0 0 0 0 19.3991 15.0065 -10.5003 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2765 15.3106 -9.3914 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1808 15.1863 -11.7941 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2620 14.2708 -11.8018 O 0 0 0 0 0 0 0 0 0 0 0 0 22.2773 14.2446 -13.0848 P 0 0 2 0 0 0 0 0 0 0 0 0 23.4235 13.3097 -12.7648 O 0 0 0 0 0 0 0 0 0 0 0 0 22.5443 15.6624 -13.5420 O 0 5 0 0 0 0 0 0 0 0 0 0 21.3095 13.5198 -14.1839 O 0 0 0 0 0 0 0 0 0 0 0 0 21.1004 11.9398 -14.5445 P 0 0 1 0 0 0 0 0 0 0 0 0 20.9601 11.2048 -13.2285 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5388 11.9778 -15.3483 N 0 0 0 0 0 0 0 0 0 0 0 0 18.4366 10.5991 -15.0839 P 0 0 0 0 0 0 0 0 0 0 0 0 17.7886 10.3747 -16.4465 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3551 9.4670 -14.6347 O 0 5 0 0 0 0 0 0 0 0 0 0 17.4832 11.1052 -14.0060 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2515 12.7703 -15.9352 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1524 11.5208 -15.5490 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5715 16.2030 -11.8579 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5368 14.9877 -12.6522 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0909 13.9570 -10.3991 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2311 15.3693 -9.5321 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8689 14.6109 -10.0144 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7289 16.1978 -11.3377 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8754 17.9602 -9.0244 O 0 0 0 0 0 0 0 0 0 0 0 0 18.3574 18.6999 -8.6145 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3677 17.7830 -10.4177 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2898 16.1853 -7.7752 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1548 18.1964 -6.5083 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1186 16.8487 -11.3884 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -52.104725 > <Chemgauss3 Steric> -57.534855 > <Chemgauss3 Desolvation> 32.421551 > <Chemgauss3 Acc> -23.301737 > <Chemgauss3 Donor> -3.689687 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.3610 18.1665 -10.1406 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1535 17.9663 -9.5690 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1218 18.5027 -8.3399 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1449 19.1773 -7.6928 C 0 0 0 0 0 0 0 0 0 0 0 0 24.3422 19.3193 -8.3870 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4457 18.8016 -9.6347 N 0 0 0 0 0 0 0 0 0 0 0 0 25.4330 19.9899 -7.8070 N 0 0 0 0 0 0 0 0 0 0 0 0 25.3291 20.4095 -6.9028 H 0 0 0 0 0 0 0 0 0 0 0 0 26.2703 20.1225 -8.3417 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7455 19.5831 -6.4442 N 0 0 0 0 0 0 0 0 0 0 0 0 21.5025 19.1631 -6.3344 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0795 18.5027 -7.4573 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7581 17.9137 -7.6621 C 0 0 1 0 0 0 0 0 0 0 0 0 18.7732 18.8318 -8.3700 C 0 0 1 0 0 0 0 0 0 0 0 0 17.8184 17.8300 -8.9887 C 0 0 1 0 0 0 0 0 0 0 0 0 18.7561 16.7008 -9.4043 C 0 0 2 0 0 0 0 0 0 0 0 0 19.8727 16.7373 -8.4856 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2930 16.8657 -10.8191 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1571 15.7801 -11.1058 O 0 0 0 0 0 0 0 0 0 0 0 0 20.8816 15.7012 -12.5709 P 0 0 2 0 0 0 0 0 0 0 0 0 21.8677 14.5534 -12.5522 O 0 0 0 0 0 0 0 0 0 0 0 0 21.3213 17.0880 -12.9882 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5994 15.2673 -13.4863 O 0 0 0 0 0 0 0 0 0 0 0 0 18.6311 13.9532 -13.4122 P 0 0 1 0 0 0 0 0 0 0 0 0 17.7072 14.0216 -14.6095 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7934 12.6593 -13.6590 N 0 0 0 0 0 0 0 0 0 0 0 0 19.2632 11.2366 -14.5973 P 0 0 0 0 0 0 0 0 0 0 0 0 19.9073 10.0558 -13.8776 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7411 11.2719 -14.5019 O 0 5 0 0 0 0 0 0 0 0 0 0 19.8155 11.5034 -15.9941 O 0 5 0 0 0 0 0 0 0 0 0 0 20.7534 12.7183 -13.2985 H 0 0 0 0 0 0 0 0 0 0 0 0 18.0661 13.8366 -12.0127 O 0 5 0 0 0 0 0 0 0 0 0 0 19.8511 17.7995 -10.9019 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4697 16.8673 -11.5350 H 0 0 0 0 0 0 0 0 0 0 0 0 18.2783 15.7167 -9.3041 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9258 17.3419 -7.9871 O 0 0 0 0 0 0 0 0 0 0 0 0 16.3391 16.7091 -8.4280 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2148 18.2417 -9.8040 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1391 19.7182 -7.4706 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8235 20.3186 -7.1264 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2725 19.4185 -9.1515 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4022 17.6102 -6.6506 H 0 0 0 0 0 0 0 0 0 0 0 0 20.8636 19.3060 -5.4732 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4788 17.7653 -11.1416 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -54.316120 > <Chemgauss3 Steric> -63.750996 > <Chemgauss3 Desolvation> 35.071918 > <Chemgauss3 Acc> -20.921602 > <Chemgauss3 Donor> -4.715435 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.8110 18.3568 -9.7745 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6928 17.6313 -9.5553 N 0 0 0 0 0 0 0 0 0 0 0 0 21.1395 17.9661 -8.3801 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5985 18.9107 -7.4760 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7622 19.5934 -7.8161 C 0 0 0 0 0 0 0 0 0 0 0 0 23.3754 19.3061 -8.9895 N 0 0 0 0 0 0 0 0 0 0 0 0 23.2988 20.5689 -6.9582 N 0 0 0 0 0 0 0 0 0 0 0 0 22.8108 20.8061 -6.1155 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1112 21.0822 -7.2432 H 0 0 0 0 0 0 0 0 0 0 0 0 20.7717 18.9789 -6.3829 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8273 18.0922 -6.6183 C 0 0 0 0 0 0 0 0 0 0 0 0 20.0067 17.4524 -7.8160 N 0 0 0 0 0 0 0 0 0 0 0 0 19.1411 16.4170 -8.3759 C 0 0 1 0 0 0 0 0 0 0 0 0 18.0749 16.9457 -9.3233 C 0 0 1 0 0 0 0 0 0 0 0 0 17.8034 15.7266 -10.1824 C 0 0 1 0 0 0 0 0 0 0 0 0 19.1936 15.1160 -10.3292 C 0 0 2 0 0 0 0 0 0 0 0 0 19.9300 15.4850 -9.1402 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9473 15.6415 -11.5430 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2231 15.0267 -11.5858 O 0 0 0 0 0 0 0 0 0 0 0 0 22.2541 15.4099 -12.7972 P 0 0 2 0 0 0 0 0 0 0 0 0 22.4014 16.9155 -12.8376 O 0 0 0 0 0 0 0 0 0 0 0 0 21.8726 14.6395 -14.0429 O 0 5 0 0 0 0 0 0 0 0 0 0 23.6322 14.7709 -12.1951 O 0 0 0 0 0 0 0 0 0 0 0 0 25.1463 14.7293 -12.8082 P 0 0 1 0 0 0 0 0 0 0 0 0 25.0428 14.1208 -14.1904 O 0 0 0 0 0 0 0 0 0 0 0 0 25.4984 16.4435 -12.9623 N 0 0 0 0 0 0 0 0 0 0 0 0 26.4738 16.9668 -14.3624 P 0 0 0 0 0 0 0 0 0 0 0 0 27.3805 18.0557 -13.7974 O 0 0 0 0 0 0 0 0 0 0 0 0 27.2103 15.7039 -14.7979 O 0 5 0 0 0 0 0 0 0 0 0 0 25.4312 17.4658 -15.3580 O 0 5 0 0 0 0 0 0 0 0 0 0 25.1429 17.1317 -12.2876 H 0 0 0 0 0 0 0 0 0 0 0 0 26.0792 14.1339 -11.7756 O 0 5 0 0 0 0 0 0 0 0 0 0 20.0728 16.7226 -11.4672 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4022 15.3999 -12.4566 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1549 14.0188 -10.3663 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9733 14.8137 -9.4643 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8286 14.0559 -10.0507 H 0 0 0 0 0 0 0 0 0 0 0 0 17.3067 15.9571 -11.1304 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9309 17.3993 -8.6288 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1986 18.1775 -8.1089 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4649 17.7678 -9.9368 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7032 15.8832 -7.5011 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9947 17.8707 -5.9641 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3277 18.1530 -10.7064 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -50.029724 > <Chemgauss3 Steric> -58.437996 > <Chemgauss3 Desolvation> 26.702433 > <Chemgauss3 Acc> -15.976658 > <Chemgauss3 Donor> -2.317504 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.8508 19.5431 -5.5426 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3174 18.6342 -6.3878 N 0 0 0 0 0 0 0 0 0 0 0 0 21.1805 18.3477 -7.3739 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4499 18.8730 -7.5560 C 0 0 0 0 0 0 0 0 0 0 0 0 22.8871 19.8015 -6.6167 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0667 20.1388 -5.5926 N 0 0 0 0 0 0 0 0 0 0 0 0 24.1614 20.3851 -6.7235 N 0 0 0 0 0 0 0 0 0 0 0 0 24.7771 20.0927 -7.4583 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4753 21.0160 -6.0107 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0384 18.3436 -8.6770 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1433 17.5116 -9.1672 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0005 17.4795 -8.4127 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8174 16.6642 -8.6781 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8235 17.3067 -9.6336 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1162 16.0896 -10.1963 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2526 15.0788 -10.3147 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2116 15.4194 -9.2869 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9557 15.1317 -11.6638 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6538 13.9144 -11.8595 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0219 13.9137 -12.7571 P 0 0 2 0 0 0 0 0 0 0 0 0 21.7584 14.6955 -14.0258 O 0 0 0 0 0 0 0 0 0 0 0 0 22.5796 12.5081 -12.8201 O 0 5 0 0 0 0 0 0 0 0 0 0 22.9849 14.8098 -11.7876 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5395 15.2795 -11.9671 P 0 0 1 0 0 0 0 0 0 0 0 0 25.3501 14.0258 -12.2177 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4452 16.2074 -13.4559 N 0 0 0 0 0 0 0 0 0 0 0 0 25.8307 16.1180 -14.5775 P 0 0 0 0 0 0 0 0 0 0 0 0 25.9705 17.5410 -15.1093 O 0 0 0 0 0 0 0 0 0 0 0 0 26.9926 15.6616 -13.7007 O 0 5 0 0 0 0 0 0 0 0 0 0 25.3835 15.0955 -15.6174 O 0 5 0 0 0 0 0 0 0 0 0 0 23.6178 16.7682 -13.6923 H 0 0 0 0 0 0 0 0 0 0 0 0 24.9047 16.2157 -10.8350 O 0 5 0 0 0 0 0 0 0 0 0 0 20.6661 15.9595 -11.6841 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2243 15.2580 -12.4634 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9086 14.0542 -10.1186 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1685 15.6072 -9.2438 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7449 14.8342 -9.6465 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5822 16.2835 -11.1322 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9502 18.1951 -8.9667 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4877 18.9389 -8.6422 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3408 17.8529 -10.4326 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3683 16.4494 -7.6811 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2643 16.9102 -10.0581 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2208 19.8357 -4.7094 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -47.971436 > <Chemgauss3 Steric> -56.468704 > <Chemgauss3 Desolvation> 34.141125 > <Chemgauss3 Acc> -21.375908 > <Chemgauss3 Donor> -4.267947 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.6601 17.2112 -7.3122 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6078 17.3807 -8.2599 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3800 18.4377 -7.9670 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2738 19.2749 -6.8679 C 0 0 0 0 0 0 0 0 0 0 0 0 20.2560 18.9963 -5.9611 C 0 0 0 0 0 0 0 0 0 0 0 0 19.4367 17.9426 -6.1937 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0753 19.7935 -4.8177 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7165 20.5411 -4.6320 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3663 19.5478 -4.1531 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2390 20.2496 -6.9046 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9197 20.0092 -8.0057 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4370 18.9215 -8.6840 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9632 18.3871 -9.9379 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9777 17.2681 -9.7577 C 0 0 1 0 0 0 0 0 0 0 0 0 23.8481 16.5285 -11.0746 C 0 0 1 0 0 0 0 0 0 0 0 0 22.3501 16.6148 -11.3500 C 0 0 2 0 0 0 0 0 0 0 0 0 21.8876 17.8312 -10.7186 O 0 0 0 0 0 0 0 0 0 0 0 0 21.5710 15.4447 -10.7660 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1971 15.6209 -11.0637 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1190 14.5014 -10.5519 P 0 0 2 0 0 0 0 0 0 0 0 0 17.7259 15.0117 -10.8508 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4906 14.0486 -9.1564 O 0 5 0 0 0 0 0 0 0 0 0 0 19.4630 13.2934 -11.5970 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3963 13.2426 -13.2289 P 0 0 1 0 0 0 0 0 0 0 0 0 19.6862 11.8134 -13.6351 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6963 13.5843 -13.5110 N 0 0 0 0 0 0 0 0 0 0 0 0 16.8970 12.7477 -14.8699 P 0 0 0 0 0 0 0 0 0 0 0 0 15.9741 13.8057 -15.4664 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0471 12.3350 -15.7833 O 0 5 0 0 0 0 0 0 0 0 0 0 16.1743 11.5843 -14.1982 O 0 5 0 0 0 0 0 0 0 0 0 0 17.1660 14.2252 -12.9084 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2193 14.3820 -13.7908 O 0 5 0 0 0 0 0 0 0 0 0 0 21.7016 15.4103 -9.6834 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9158 14.5076 -11.2058 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1376 16.6993 -12.4244 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5455 17.2451 -12.0935 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4343 16.7364 -12.9108 H 0 0 0 0 0 0 0 0 0 0 0 0 24.2466 15.5092 -11.0487 H 0 0 0 0 0 0 0 0 0 0 0 0 25.2794 17.7686 -9.5298 O 0 0 0 0 0 0 0 0 0 0 0 0 25.2671 18.2236 -8.6694 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6993 16.6140 -8.9216 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3886 19.2605 -10.4841 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7647 20.5834 -8.3613 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9863 16.3751 -7.4663 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -57.545662 > <Chemgauss3 Steric> -73.853493 > <Chemgauss3 Desolvation> 36.392467 > <Chemgauss3 Acc> -11.867089 > <Chemgauss3 Donor> -8.217545 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.7074 19.5710 -6.6137 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7204 18.8561 -7.7599 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4871 18.4173 -8.0528 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3264 18.6317 -7.3268 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4427 19.3850 -6.1629 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6597 19.8608 -5.8050 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3166 19.6520 -5.3651 N 0 0 0 0 0 0 0 0 0 0 0 0 18.4143 19.3349 -5.6647 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4135 20.2359 -4.5562 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2545 18.0283 -7.9351 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7544 17.4576 -9.0113 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1034 17.6649 -9.1262 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9610 17.1703 -10.2008 C 0 0 1 0 0 0 0 0 0 0 0 0 22.4890 15.7619 -9.9740 C 0 0 1 0 0 0 0 0 0 0 0 0 22.7514 15.3057 -11.3957 C 0 0 1 0 0 0 0 0 0 0 0 0 21.5860 15.9289 -12.1576 C 0 0 2 0 0 0 0 0 0 0 0 0 21.2180 17.1261 -11.4342 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3686 15.0178 -12.2288 C 0 0 0 0 0 0 0 0 0 0 0 0 19.3429 15.6862 -12.9420 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7795 15.3624 -12.5838 P 0 0 2 0 0 0 0 0 0 0 0 0 16.9051 16.3223 -13.3613 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6270 15.2233 -11.0845 O 0 5 0 0 0 0 0 0 0 0 0 0 17.6466 13.8796 -13.2575 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8463 13.3878 -14.8028 P 0 0 1 0 0 0 0 0 0 0 0 0 19.3085 13.5867 -15.1406 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5212 11.6675 -14.6573 N 0 0 0 0 0 0 0 0 0 0 0 0 18.4739 10.5547 -15.6771 P 0 0 0 0 0 0 0 0 0 0 0 0 17.4692 9.4886 -16.1025 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9758 11.4319 -16.8198 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5662 10.0549 -14.7369 O 0 5 0 0 0 0 0 0 0 0 0 0 16.8245 11.3025 -13.9968 H 0 0 0 0 0 0 0 0 0 0 0 0 16.7684 14.0136 -15.6617 O 0 5 0 0 0 0 0 0 0 0 0 0 20.0138 14.7868 -11.2232 H 0 0 0 0 0 0 0 0 0 0 0 0 20.6222 14.0927 -12.7485 H 0 0 0 0 0 0 0 0 0 0 0 0 21.8783 16.2329 -13.1719 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9695 15.8843 -11.8641 O 0 0 0 0 0 0 0 0 0 0 0 0 24.0933 15.5653 -12.7707 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8336 14.2191 -11.5019 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6498 15.7577 -9.1683 O 0 0 0 0 0 0 0 0 0 0 0 0 23.3870 16.0621 -8.2819 H 0 0 0 0 0 0 0 0 0 0 0 0 21.7287 15.1268 -9.5018 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7806 17.9186 -10.3024 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1938 16.8858 -9.7385 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6660 19.9684 -6.2975 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -51.490845 > <Chemgauss3 Steric> -65.077263 > <Chemgauss3 Desolvation> 36.648796 > <Chemgauss3 Acc> -17.308743 > <Chemgauss3 Donor> -5.753643 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.7704 17.3462 -7.4946 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6982 17.7407 -8.3938 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4334 18.7473 -7.8981 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3099 19.3413 -6.6522 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3157 18.8454 -5.8148 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5342 17.8281 -6.2505 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1200 19.3884 -4.5331 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7346 20.1084 -4.2040 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4298 18.9858 -3.9279 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2367 20.3413 -6.4969 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9113 20.3549 -7.6276 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4615 19.4074 -8.5085 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9909 19.1576 -9.8473 C 0 0 1 0 0 0 0 0 0 0 0 0 24.0497 18.0669 -9.9017 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9308 17.6027 -11.3399 C 0 0 1 0 0 0 0 0 0 0 0 0 22.4271 17.6826 -11.5842 C 0 0 2 0 0 0 0 0 0 0 0 0 21.9270 18.7275 -10.7181 O 0 0 0 0 0 0 0 0 0 0 0 0 21.7011 16.3886 -11.2439 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3176 16.5659 -11.4925 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4145 15.2762 -11.9381 P 0 0 2 0 0 0 0 0 0 0 0 0 17.9627 15.7020 -11.9734 O 0 0 0 0 0 0 0 0 0 0 0 0 19.8426 14.0641 -11.1392 O 0 5 0 0 0 0 0 0 0 0 0 0 19.9381 15.0944 -13.4753 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5203 14.0098 -14.6238 P 0 0 1 0 0 0 0 0 0 0 0 0 20.4450 14.2392 -15.8003 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9551 12.4990 -13.8399 N 0 0 0 0 0 0 0 0 0 0 0 0 20.6165 11.1946 -14.8630 P 0 0 0 0 0 0 0 0 0 0 0 0 19.9963 9.9235 -14.2914 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1402 11.5446 -16.2693 O 0 5 0 0 0 0 0 0 0 0 0 0 22.1239 11.3097 -14.6589 O 0 5 0 0 0 0 0 0 0 0 0 0 19.8560 12.3675 -12.8260 H 0 0 0 0 0 0 0 0 0 0 0 0 18.0185 14.0443 -14.8103 O 0 5 0 0 0 0 0 0 0 0 0 0 21.8473 16.1424 -10.1911 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0755 15.5738 -11.8653 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1972 17.9728 -12.6184 H 0 0 0 0 0 0 0 0 0 0 0 0 24.5867 18.5370 -12.1973 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4841 18.1991 -13.0997 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3683 16.6158 -11.5222 H 0 0 0 0 0 0 0 0 0 0 0 0 25.3342 18.5631 -9.5846 O 0 0 0 0 0 0 0 0 0 0 0 0 25.3161 18.8348 -8.6501 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8076 17.2473 -9.2131 H 0 0 0 0 0 0 0 0 0 0 0 0 23.3753 20.1394 -10.2084 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7289 21.0222 -7.8647 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1271 16.5319 -7.8105 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -57.002838 > <Chemgauss3 Steric> -57.651527 > <Chemgauss3 Desolvation> 33.184734 > <Chemgauss3 Acc> -20.922493 > <Chemgauss3 Donor> -11.613541 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.8708 18.4161 -10.0453 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7766 17.6398 -9.8872 N 0 0 0 0 0 0 0 0 0 0 0 0 21.1302 17.9648 -8.7576 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4815 18.9447 -7.8428 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6310 19.6786 -8.1177 C 0 0 0 0 0 0 0 0 0 0 0 0 23.3348 19.4040 -9.2424 N 0 0 0 0 0 0 0 0 0 0 0 0 23.0613 20.6924 -7.2443 N 0 0 0 0 0 0 0 0 0 0 0 0 22.5070 20.9182 -6.4404 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8652 21.2408 -7.4844 H 0 0 0 0 0 0 0 0 0 0 0 0 20.5809 18.9888 -6.8084 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6982 18.0530 -7.0893 C 0 0 0 0 0 0 0 0 0 0 0 0 19.9881 17.4046 -8.2604 N 0 0 0 0 0 0 0 0 0 0 0 0 19.2130 16.3192 -8.8571 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1886 16.7802 -9.8827 C 0 0 1 0 0 0 0 0 0 0 0 0 18.0344 15.5361 -10.7351 C 0 0 1 0 0 0 0 0 0 0 0 0 19.4591 14.9927 -10.7782 C 0 0 2 0 0 0 0 0 0 0 0 0 20.0954 15.4157 -9.5501 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2663 15.5360 -11.9488 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5703 14.9844 -11.8956 O 0 0 0 0 0 0 0 0 0 0 0 0 22.6605 15.3993 -13.0430 P 0 0 2 0 0 0 0 0 0 0 0 0 24.0014 14.8119 -12.6591 O 0 0 0 0 0 0 0 0 0 0 0 0 22.5260 16.8747 -13.3525 O 0 5 0 0 0 0 0 0 0 0 0 0 22.0653 14.5492 -14.3052 O 0 0 0 0 0 0 0 0 0 0 0 0 22.3802 13.0275 -14.8104 P 0 0 1 0 0 0 0 0 0 0 0 0 22.3476 12.1425 -13.5827 O 0 0 0 0 0 0 0 0 0 0 0 0 20.9629 12.6950 -15.7937 N 0 0 0 0 0 0 0 0 0 0 0 0 20.3116 11.0334 -15.7740 P 0 0 0 0 0 0 0 0 0 0 0 0 19.8923 10.7815 -17.2189 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4844 10.1777 -15.3054 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1534 11.1150 -14.7845 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5046 13.4285 -16.3478 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5986 13.0493 -15.7084 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3342 16.6231 -11.8851 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7960 15.2539 -12.8920 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4760 13.8945 -10.7974 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2029 14.5945 -10.0568 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1346 13.8216 -10.6373 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5918 15.7273 -11.7181 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9800 17.1874 -9.2742 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1744 17.9857 -8.7522 H 0 0 0 0 0 0 0 0 0 0 0 0 18.5788 17.6110 -10.4843 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7436 15.7780 -8.0035 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8353 17.8008 -6.4877 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4579 18.2238 -10.9369 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -44.601654 > <Chemgauss3 Steric> -56.435631 > <Chemgauss3 Desolvation> 24.889746 > <Chemgauss3 Acc> -12.262419 > <Chemgauss3 Donor> -0.793344 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.9229 18.1975 -9.3520 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7574 17.5219 -9.2513 N 0 0 0 0 0 0 0 0 0 0 0 0 21.0584 17.9483 -8.1888 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4229 18.9349 -7.2865 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6485 19.5587 -7.4976 C 0 0 0 0 0 0 0 0 0 0 0 0 23.4084 19.1779 -8.5526 N 0 0 0 0 0 0 0 0 0 0 0 0 23.0973 20.5708 -6.6316 N 0 0 0 0 0 0 0 0 0 0 0 0 22.5057 20.8765 -5.8826 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9610 21.0399 -6.8283 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4544 19.0985 -6.3281 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5183 18.2275 -6.6423 C 0 0 0 0 0 0 0 0 0 0 0 0 19.8385 17.5066 -7.7620 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0201 16.4639 -8.3768 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1188 16.9626 -9.4960 C 0 0 1 0 0 0 0 0 0 0 0 0 17.9228 15.6994 -10.3108 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2950 15.0388 -10.2218 C 0 0 2 0 0 0 0 0 0 0 0 0 19.8714 15.4611 -8.9642 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2312 15.4618 -11.3450 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4754 14.8072 -11.1692 O 0 0 0 0 0 0 0 0 0 0 0 0 22.6802 15.0801 -12.2423 P 0 0 2 0 0 0 0 0 0 0 0 0 23.9332 14.4013 -11.7328 O 0 0 0 0 0 0 0 0 0 0 0 0 22.6961 16.5465 -12.6162 O 0 5 0 0 0 0 0 0 0 0 0 0 22.1106 14.2276 -13.5147 O 0 0 0 0 0 0 0 0 0 0 0 0 21.7530 12.6399 -13.6614 P 0 0 1 0 0 0 0 0 0 0 0 0 20.5766 12.3693 -12.7479 O 0 0 0 0 0 0 0 0 0 0 0 0 21.2104 12.5660 -15.3307 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8771 11.4451 -15.7200 P 0 0 0 0 0 0 0 0 0 0 0 0 20.2633 10.8655 -17.0772 O 0 0 0 0 0 0 0 0 0 0 0 0 19.8954 10.4319 -14.5797 O 0 5 0 0 0 0 0 0 0 0 0 0 18.6472 12.3472 -15.7445 O 0 5 0 0 0 0 0 0 0 0 0 0 21.6246 13.1578 -16.0609 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0277 11.8342 -13.5301 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3871 16.5413 -11.3167 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8105 15.1784 -12.3109 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2190 13.9432 -10.1986 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9652 14.8602 -9.6651 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8746 14.0709 -10.2199 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5732 15.8832 -11.3319 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9074 17.4944 -8.9996 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1297 18.2960 -8.4942 H 0 0 0 0 0 0 0 0 0 0 0 0 18.6227 17.7312 -10.0956 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4435 16.0012 -7.5429 H 0 0 0 0 0 0 0 0 0 0 0 0 18.5943 18.0739 -6.1012 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5566 17.9185 -10.1870 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -49.183449 > <Chemgauss3 Steric> -64.508087 > <Chemgauss3 Desolvation> 29.018906 > <Chemgauss3 Acc> -11.611927 > <Chemgauss3 Donor> -2.082343 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.9597 17.2266 -9.9251 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7054 17.1847 -9.4253 N 0 0 0 0 0 0 0 0 0 0 0 0 22.5564 18.0992 -8.4553 C 0 0 0 0 0 0 0 0 0 0 0 0 23.5109 18.9881 -7.9871 C 0 0 0 0 0 0 0 0 0 0 0 0 24.7668 18.9340 -8.5833 C 0 0 0 0 0 0 0 0 0 0 0 0 24.9890 18.0335 -9.5709 N 0 0 0 0 0 0 0 0 0 0 0 0 25.7949 19.7992 -8.1710 N 0 0 0 0 0 0 0 0 0 0 0 0 25.6049 20.4926 -7.4726 H 0 0 0 0 0 0 0 0 0 0 0 0 26.6777 19.7762 -8.6453 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9947 19.7726 -6.9865 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7492 19.3682 -6.8491 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4364 18.3557 -7.7168 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1432 17.6841 -7.8245 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2233 18.2763 -8.8812 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3359 17.0912 -9.2070 C 0 0 1 0 0 0 0 0 0 0 0 0 19.3147 15.9232 -9.1372 C 0 0 2 0 0 0 0 0 0 0 0 0 20.3407 16.3053 -8.1919 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9800 15.6258 -10.4736 C 0 0 0 0 0 0 0 0 0 0 0 0 18.9759 15.2927 -11.4160 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4107 14.9239 -12.9498 P 0 0 2 0 0 0 0 0 0 0 0 0 20.3972 15.9672 -13.4280 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1722 14.6062 -13.7595 O 0 5 0 0 0 0 0 0 0 0 0 0 20.2216 13.5318 -12.6762 O 0 0 0 0 0 0 0 0 0 0 0 0 20.9806 12.5183 -13.7090 P 0 0 1 0 0 0 0 0 0 0 0 0 21.4228 11.3179 -12.8994 O 0 0 0 0 0 0 0 0 0 0 0 0 19.6535 12.0440 -14.7578 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6352 10.3654 -15.3640 P 0 0 0 0 0 0 0 0 0 0 0 0 19.1441 10.4952 -16.8025 O 0 0 0 0 0 0 0 0 0 0 0 0 21.0844 9.9063 -15.2374 O 0 5 0 0 0 0 0 0 0 0 0 0 18.6632 9.6570 -14.4256 O 0 5 0 0 0 0 0 0 0 0 0 0 18.8983 12.6956 -15.0030 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9841 13.3063 -14.5234 O 0 5 0 0 0 0 0 0 0 0 0 0 20.6682 14.7854 -10.3711 H 0 0 0 0 0 0 0 0 0 0 0 0 20.5246 16.5034 -10.8252 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8353 15.0122 -8.7536 H 0 0 0 0 0 0 0 0 0 0 0 0 17.3568 16.9332 -8.1801 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8174 16.1685 -8.4315 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8085 17.1847 -10.1618 H 0 0 0 0 0 0 0 0 0 0 0 0 18.5031 19.3883 -8.3897 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1491 20.0939 -8.2098 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7898 18.5864 -9.7686 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6965 17.7230 -6.8042 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0322 19.7669 -6.1441 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1725 16.5188 -10.7192 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -56.854340 > <Chemgauss3 Steric> -65.454643 > <Chemgauss3 Desolvation> 35.481754 > <Chemgauss3 Acc> -23.875549 > <Chemgauss3 Donor> -3.005906 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 21.0359 19.5953 -5.5524 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5488 18.6195 -6.3496 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3225 18.4712 -7.4354 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4682 19.1834 -7.7522 C 0 0 0 0 0 0 0 0 0 0 0 0 22.8691 20.1636 -6.8498 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1343 20.3685 -5.7302 N 0 0 0 0 0 0 0 0 0 0 0 0 24.0199 20.9338 -7.0911 N 0 0 0 0 0 0 0 0 0 0 0 0 24.5813 20.7411 -7.8987 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3177 21.6021 -6.4060 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9928 18.7539 -8.9452 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1810 17.7979 -9.3462 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1532 17.5900 -8.4650 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0828 16.6060 -8.6091 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8978 17.0944 -9.4283 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3196 15.7866 -9.9316 C 0 0 1 0 0 0 0 0 0 0 0 0 19.5727 14.9601 -10.2033 C 0 0 2 0 0 0 0 0 0 0 0 0 20.5844 15.4378 -9.2866 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0955 15.1244 -11.6234 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9402 14.0277 -11.9256 O 0 0 0 0 0 0 0 0 0 0 0 0 22.1772 14.2379 -12.9758 P 0 0 2 0 0 0 0 0 0 0 0 0 21.6514 14.9760 -14.1879 O 0 0 0 0 0 0 0 0 0 0 0 0 22.9279 12.9333 -13.1340 O 0 5 0 0 0 0 0 0 0 0 0 0 23.1026 15.2655 -12.1053 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5371 15.9661 -12.4539 P 0 0 1 0 0 0 0 0 0 0 0 0 24.9809 16.7002 -11.2066 O 0 0 0 0 0 0 0 0 0 0 0 0 25.5586 14.5552 -12.6818 N 0 0 0 0 0 0 0 0 0 0 0 0 27.2533 14.6613 -12.1317 P 0 0 0 0 0 0 0 0 0 0 0 0 28.0399 13.9168 -13.2060 O 0 0 0 0 0 0 0 0 0 0 0 0 27.5352 16.1594 -12.0761 O 0 5 0 0 0 0 0 0 0 0 0 0 27.2315 13.9711 -10.7715 O 0 5 0 0 0 0 0 0 0 0 0 0 25.1981 13.6875 -13.0967 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4196 16.6976 -13.7739 O 0 5 0 0 0 0 0 0 0 0 0 0 20.6663 16.0503 -11.7080 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2641 15.1417 -12.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4118 13.8944 -9.9911 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5741 15.1623 -8.8863 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2267 14.3357 -9.2538 H 0 0 0 0 0 0 0 0 0 0 0 0 17.6558 15.9012 -10.7946 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9862 17.8376 -8.6451 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4407 18.6529 -8.3690 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2294 17.7159 -10.2698 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7919 16.3215 -7.5715 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2847 17.2254 -10.2582 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4721 19.7856 -4.6454 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -51.377781 > <Chemgauss3 Steric> -60.085003 > <Chemgauss3 Desolvation> 36.238125 > <Chemgauss3 Acc> -26.166836 > <Chemgauss3 Donor> -1.364068 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.5172 19.4584 -5.3936 C 0 0 0 0 0 0 0 0 0 0 0 0 19.8539 18.5320 -6.1195 N 0 0 0 0 0 0 0 0 0 0 0 0 20.5285 18.2456 -7.2431 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7354 18.7861 -7.6573 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3209 19.7319 -6.8216 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6944 20.0702 -5.6689 N 0 0 0 0 0 0 0 0 0 0 0 0 23.5453 20.3316 -7.1631 N 0 0 0 0 0 0 0 0 0 0 0 0 24.0223 20.0389 -7.9947 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9733 20.9754 -6.5251 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1193 18.2514 -8.8614 N 0 0 0 0 0 0 0 0 0 0 0 0 21.1634 17.4013 -9.1733 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1770 17.3625 -8.2238 N 0 0 0 0 0 0 0 0 0 0 0 0 18.9783 16.5278 -8.2627 C 0 0 1 0 0 0 0 0 0 0 0 0 17.8177 17.1449 -9.0280 C 0 0 1 0 0 0 0 0 0 0 0 0 17.0394 15.9115 -9.4417 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1514 14.9152 -9.7547 C 0 0 2 0 0 0 0 0 0 0 0 0 19.2753 15.2814 -8.9211 O 0 0 0 0 0 0 0 0 0 0 0 0 18.5975 14.9614 -11.2094 C 0 0 0 0 0 0 0 0 0 0 0 0 19.6339 14.0136 -11.3964 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3069 13.8480 -12.8786 P 0 0 2 0 0 0 0 0 0 0 0 0 19.1930 13.7678 -13.9000 O 0 0 0 0 0 0 0 0 0 0 0 0 21.3814 12.7836 -12.8254 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0298 15.3071 -13.0147 O 0 0 0 0 0 0 0 0 0 0 0 0 22.5276 15.8001 -12.5864 P 0 0 1 0 0 0 0 0 0 0 0 0 22.9000 15.0343 -11.3349 O 0 0 0 0 0 0 0 0 0 0 0 0 23.4824 15.1969 -13.9321 N 0 0 0 0 0 0 0 0 0 0 0 0 25.1245 14.5934 -13.5786 P 0 0 0 0 0 0 0 0 0 0 0 0 25.9595 15.0741 -14.7613 O 0 0 0 0 0 0 0 0 0 0 0 0 25.4863 15.2502 -12.2502 O 0 5 0 0 0 0 0 0 0 0 0 0 24.9417 13.0806 -13.5069 O 0 5 0 0 0 0 0 0 0 0 0 0 23.1109 15.1684 -14.8893 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5708 17.3131 -12.6015 O 0 5 0 0 0 0 0 0 0 0 0 0 18.9728 15.9560 -11.4550 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7622 14.7135 -11.8660 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8648 13.8883 -9.4898 H 0 0 0 0 0 0 0 0 0 0 0 0 16.2877 15.4276 -8.3287 O 0 0 0 0 0 0 0 0 0 0 0 0 15.8104 14.6440 -8.6406 H 0 0 0 0 0 0 0 0 0 0 0 0 16.3417 16.0867 -10.2670 H 0 0 0 0 0 0 0 0 0 0 0 0 17.0658 18.0292 -8.2222 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6415 18.7843 -8.0075 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1730 17.6885 -9.9127 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7207 16.3189 -7.1987 H 0 0 0 0 0 0 0 0 0 0 0 0 21.1305 16.7909 -10.0657 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0441 19.7523 -4.4628 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -47.073658 > <Chemgauss3 Steric> -63.381184 > <Chemgauss3 Desolvation> 31.919828 > <Chemgauss3 Acc> -12.645876 > <Chemgauss3 Donor> -2.966434 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.4900 17.1748 -10.2406 C 0 0 0 0 0 0 0 0 0 0 0 0 22.2471 16.8805 -9.8007 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8885 17.7164 -8.8147 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6377 18.7521 -8.2795 C 0 0 0 0 0 0 0 0 0 0 0 0 23.9042 18.9558 -8.8181 C 0 0 0 0 0 0 0 0 0 0 0 0 24.3327 18.1480 -9.8178 N 0 0 0 0 0 0 0 0 0 0 0 0 24.7324 19.9840 -8.3359 N 0 0 0 0 0 0 0 0 0 0 0 0 24.3864 20.6046 -7.6290 H 0 0 0 0 0 0 0 0 0 0 0 0 25.6220 20.1439 -8.7692 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9423 19.3903 -7.2834 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7914 18.7544 -7.2145 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7114 17.7319 -8.1223 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5741 16.8333 -8.3075 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6022 17.2783 -9.3896 C 0 0 1 0 0 0 0 0 0 0 0 0 17.9693 15.9595 -9.7874 C 0 0 1 0 0 0 0 0 0 0 0 0 19.1479 14.9947 -9.7033 C 0 0 2 0 0 0 0 0 0 0 0 0 20.0438 15.5298 -8.7018 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9110 14.8743 -11.0149 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9862 13.9698 -10.8328 O 0 0 0 0 0 0 0 0 0 0 0 0 21.9818 13.6488 -12.0910 P 0 0 2 0 0 0 0 0 0 0 0 0 23.1268 12.7978 -11.5860 O 0 0 0 0 0 0 0 0 0 0 0 0 22.2508 14.9265 -12.8563 O 0 5 0 0 0 0 0 0 0 0 0 0 20.9929 12.7065 -12.9879 O 0 0 0 0 0 0 0 0 0 0 0 0 21.2375 11.9658 -14.4237 P 0 0 1 0 0 0 0 0 0 0 0 0 22.3010 10.9124 -14.1979 O 0 0 0 0 0 0 0 0 0 0 0 0 19.6886 11.1729 -14.6660 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6920 9.5691 -15.4492 P 0 0 0 0 0 0 0 0 0 0 0 0 18.4650 9.5956 -16.3553 O 0 0 0 0 0 0 0 0 0 0 0 0 21.0205 9.5213 -16.1975 O 0 5 0 0 0 0 0 0 0 0 0 0 19.5913 8.5984 -14.2768 O 0 5 0 0 0 0 0 0 0 0 0 0 18.8080 11.5988 -14.3528 H 0 0 0 0 0 0 0 0 0 0 0 0 21.4159 13.0186 -15.4966 O 0 5 0 0 0 0 0 0 0 0 0 0 20.3071 15.8474 -11.3089 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2529 14.4957 -11.7985 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8345 13.9971 -9.3666 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9970 15.5847 -8.8115 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6228 14.7414 -9.1077 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4727 15.9853 -10.7628 H 0 0 0 0 0 0 0 0 0 0 0 0 17.6652 18.2173 -8.9027 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1580 19.0251 -8.6745 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1352 17.7200 -10.2413 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0872 16.7520 -7.3083 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9839 18.9864 -6.5332 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8649 16.5477 -11.0424 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.242352 > <Chemgauss3 Steric> -57.957653 > <Chemgauss3 Desolvation> 32.472023 > <Chemgauss3 Acc> -30.822769 > <Chemgauss3 Donor> -1.933959 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.7723 18.8858 -5.5845 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5272 17.9369 -6.5143 N 0 0 0 0 0 0 0 0 0 0 0 0 20.5202 17.8954 -7.4151 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6595 18.6838 -7.4440 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7981 19.6263 -6.4299 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8321 19.7240 -5.4850 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9226 20.4682 -6.3812 N 0 0 0 0 0 0 0 0 0 0 0 0 23.6528 20.3545 -7.0583 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0262 21.1077 -5.6164 H 0 0 0 0 0 0 0 0 0 0 0 0 22.4501 18.3558 -8.5166 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8034 17.3857 -9.1284 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6282 17.0714 -8.4989 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6769 16.0442 -8.9168 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6629 16.5201 -9.9459 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2879 15.2175 -10.6246 C 0 0 1 0 0 0 0 0 0 0 0 0 19.6200 14.4750 -10.6618 C 0 0 2 0 0 0 0 0 0 0 0 0 20.3832 14.9472 -9.5275 O 0 0 0 0 0 0 0 0 0 0 0 0 20.4191 14.7527 -11.9272 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6365 14.0309 -11.8625 O 0 0 0 0 0 0 0 0 0 0 0 0 22.6995 14.1449 -13.1012 P 0 0 2 0 0 0 0 0 0 0 0 0 23.9692 13.4224 -12.7060 O 0 0 0 0 0 0 0 0 0 0 0 0 22.7480 15.5764 -13.5902 O 0 5 0 0 0 0 0 0 0 0 0 0 21.9166 13.2431 -14.2165 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4532 11.6764 -14.1881 P 0 0 1 0 0 0 0 0 0 0 0 0 20.3970 11.5513 -13.1109 O 0 0 0 0 0 0 0 0 0 0 0 0 20.6878 11.5191 -15.7615 N 0 0 0 0 0 0 0 0 0 0 0 0 19.2529 10.4646 -15.8835 P 0 0 0 0 0 0 0 0 0 0 0 0 19.4197 9.7645 -17.2285 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3670 9.5370 -14.6778 O 0 5 0 0 0 0 0 0 0 0 0 0 18.0840 11.4427 -15.8204 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0328 12.0279 -16.5843 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6863 10.7989 -14.1592 O 0 5 0 0 0 0 0 0 0 0 0 0 20.6382 15.8186 -12.0059 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8569 14.4294 -12.8045 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4859 13.3913 -10.5413 H 0 0 0 0 0 0 0 0 0 0 0 0 17.3799 14.4927 -9.7950 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1710 13.6734 -10.2684 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8151 15.3505 -11.6031 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5613 17.1659 -9.3407 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8947 17.9851 -8.9342 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1243 17.2083 -10.6654 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1923 15.6821 -7.9808 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1333 16.8763 -10.0238 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0189 18.9909 -4.8111 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -49.125511 > <Chemgauss3 Steric> -62.593338 > <Chemgauss3 Desolvation> 33.039288 > <Chemgauss3 Acc> -17.053471 > <Chemgauss3 Donor> -2.517986 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 18.2843 15.4691 -10.7278 C 0 0 0 0 0 0 0 0 0 0 0 0 19.4395 16.1642 -10.6428 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5592 16.7286 -9.4318 C 0 0 0 0 0 0 0 0 0 0 0 0 18.6638 16.6484 -8.3772 C 0 0 0 0 0 0 0 0 0 0 0 0 17.5090 15.9015 -8.5880 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3217 15.3028 -9.7888 N 0 0 0 0 0 0 0 0 0 0 0 0 16.5464 15.7663 -7.5727 N 0 0 0 0 0 0 0 0 0 0 0 0 16.7181 16.1743 -6.6735 H 0 0 0 0 0 0 0 0 0 0 0 0 15.7445 15.1855 -7.7286 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1237 17.3554 -7.2947 N 0 0 0 0 0 0 0 0 0 0 0 0 20.2776 17.8560 -7.6841 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5848 17.5043 -8.9717 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7879 17.8911 -9.7051 C 0 0 1 0 0 0 0 0 0 0 0 0 22.9152 16.8728 -9.6280 C 0 0 1 0 0 0 0 0 0 0 0 0 23.6879 17.1818 -10.8950 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5735 17.5091 -11.8840 C 0 0 2 0 0 0 0 0 0 0 0 0 21.4775 18.0405 -11.1039 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0749 16.2868 -12.6420 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1550 15.7357 -13.3747 O 0 0 0 0 0 0 0 0 0 0 0 0 23.1847 14.1255 -13.6643 P 0 0 2 0 0 0 0 0 0 0 0 0 23.3707 13.4086 -12.3445 O 0 0 0 0 0 0 0 0 0 0 0 0 24.1060 13.8427 -14.8312 O 0 5 0 0 0 0 0 0 0 0 0 0 21.6422 13.9086 -14.1581 O 0 0 0 0 0 0 0 0 0 0 0 0 20.8554 12.5599 -14.6394 P 0 0 1 0 0 0 0 0 0 0 0 0 20.7665 11.6501 -13.4328 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2588 13.2037 -14.9898 N 0 0 0 0 0 0 0 0 0 0 0 0 17.8494 12.1760 -14.6120 P 0 0 0 0 0 0 0 0 0 0 0 0 16.8885 12.4225 -15.7709 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4200 10.7621 -14.5633 O 0 5 0 0 0 0 0 0 0 0 0 0 17.3677 12.7101 -13.2667 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1286 14.1454 -15.3788 H 0 0 0 0 0 0 0 0 0 0 0 0 21.4719 12.0645 -15.9301 O 0 5 0 0 0 0 0 0 0 0 0 0 21.2813 16.5728 -13.3340 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6980 15.5394 -11.9423 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8777 18.2865 -12.5980 H 0 0 0 0 0 0 0 0 0 0 0 0 24.4832 18.3503 -10.6945 O 0 0 0 0 0 0 0 0 0 0 0 0 24.9552 18.5063 -11.5263 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3540 16.3734 -11.2134 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6885 17.0304 -8.4558 O 0 0 0 0 0 0 0 0 0 0 0 0 23.1149 16.8125 -7.7002 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5238 15.8480 -9.6580 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0854 18.8841 -9.2957 H 0 0 0 0 0 0 0 0 0 0 0 0 20.9298 18.4755 -7.0832 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1022 14.9754 -11.6764 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -49.874100 > <Chemgauss3 Steric> -59.653816 > <Chemgauss3 Desolvation> 32.096989 > <Chemgauss3 Acc> -21.855219 > <Chemgauss3 Donor> -0.462057 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.5682 19.7083 -6.9033 C 0 0 0 0 0 0 0 0 0 0 0 0 22.5523 19.1167 -8.1177 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3841 18.4886 -8.3180 C 0 0 0 0 0 0 0 0 0 0 0 0 20.3092 18.4190 -7.4461 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4472 19.0702 -6.2244 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6016 19.7257 -5.9539 N 0 0 0 0 0 0 0 0 0 0 0 0 19.4066 19.0519 -5.2797 N 0 0 0 0 0 0 0 0 0 0 0 0 18.5400 18.6039 -5.5099 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5078 19.5664 -4.4255 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2853 17.6883 -7.9947 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7296 17.3206 -9.1783 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9967 17.7810 -9.4201 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7775 17.5529 -10.6338 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5627 16.2501 -10.6302 C 0 0 1 0 0 0 0 0 0 0 0 0 22.7103 15.9828 -12.1150 C 0 0 1 0 0 0 0 0 0 0 0 0 21.3660 16.4498 -12.6647 C 0 0 2 0 0 0 0 0 0 0 0 0 20.8977 17.4875 -11.7726 O 0 0 0 0 0 0 0 0 0 0 0 0 20.3229 15.3418 -12.7018 C 0 0 0 0 0 0 0 0 0 0 0 0 19.1138 15.8741 -13.2140 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8110 14.8957 -13.3650 P 0 0 2 0 0 0 0 0 0 0 0 0 16.7820 15.6030 -14.2201 O 0 0 0 0 0 0 0 0 0 0 0 0 17.4365 14.3459 -12.0056 O 0 5 0 0 0 0 0 0 0 0 0 0 18.4756 13.6904 -14.2457 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1300 12.0943 -14.3023 P 0 0 1 0 0 0 0 0 0 0 0 0 16.7376 11.9677 -14.8826 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2981 11.5349 -15.4893 N 0 0 0 0 0 0 0 0 0 0 0 0 18.7912 10.2346 -16.6019 P 0 0 0 0 0 0 0 0 0 0 0 0 20.0311 9.3561 -16.7360 O 0 0 0 0 0 0 0 0 0 0 0 0 17.6240 9.5630 -15.8852 O 0 5 0 0 0 0 0 0 0 0 0 0 18.4059 10.9827 -17.8743 O 0 5 0 0 0 0 0 0 0 0 0 0 20.2352 11.9489 -15.5630 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4630 11.4709 -12.9637 O 0 5 0 0 0 0 0 0 0 0 0 0 20.1476 14.9580 -11.6957 H 0 0 0 0 0 0 0 0 0 0 0 0 20.6599 14.5307 -13.3489 H 0 0 0 0 0 0 0 0 0 0 0 0 21.4668 16.8944 -13.6641 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7400 16.8153 -12.6486 O 0 0 0 0 0 0 0 0 0 0 0 0 23.7963 16.6093 -13.5938 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9616 14.9442 -12.3531 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8028 16.3841 -9.9661 O 0 0 0 0 0 0 0 0 0 0 0 0 23.6106 16.5522 -9.0268 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9903 15.4458 -10.1509 H 0 0 0 0 0 0 0 0 0 0 0 0 22.4373 18.4447 -10.7411 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1841 16.7253 -9.8983 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4782 20.2436 -6.6538 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -50.522217 > <Chemgauss3 Steric> -65.991142 > <Chemgauss3 Desolvation> 34.788292 > <Chemgauss3 Acc> -14.870156 > <Chemgauss3 Donor> -4.449219 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.3142 16.4261 -12.6502 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5793 16.4455 -11.5168 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1625 17.2239 -10.5931 C 0 0 0 0 0 0 0 0 0 0 0 0 23.3466 17.9326 -10.7202 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0120 17.8322 -11.9379 C 0 0 0 0 0 0 0 0 0 0 0 0 23.4802 17.0624 -12.9178 N 0 0 0 0 0 0 0 0 0 0 0 0 25.2198 18.5178 -12.1545 N 0 0 0 0 0 0 0 0 0 0 0 0 25.5788 19.1214 -11.4394 H 0 0 0 0 0 0 0 0 0 0 0 0 25.6587 18.4699 -13.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6293 18.6172 -9.5650 N 0 0 0 0 0 0 0 0 0 0 0 0 22.6353 18.3301 -8.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7214 17.4891 -9.3280 N 0 0 0 0 0 0 0 0 0 0 0 0 20.5051 16.9788 -8.6993 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2630 17.8077 -8.9887 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1643 16.7802 -8.8014 C 0 0 1 0 0 0 0 0 0 0 0 0 18.7976 15.5181 -9.3785 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2250 15.6528 -9.1879 O 0 0 0 0 0 0 0 0 0 0 0 0 18.5261 15.3449 -10.8663 C 0 0 0 0 0 0 0 0 0 0 0 0 19.1608 14.1577 -11.3080 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0336 13.7213 -12.8798 P 0 0 2 0 0 0 0 0 0 0 0 0 19.9318 12.5264 -13.1156 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1447 14.9527 -13.7527 O 0 5 0 0 0 0 0 0 0 0 0 0 17.4807 13.2129 -12.8971 O 0 0 0 0 0 0 0 0 0 0 0 0 16.5681 12.6114 -14.1117 P 0 0 1 0 0 0 0 0 0 0 0 0 16.6298 13.6141 -15.2442 O 0 0 0 0 0 0 0 0 0 0 0 0 17.4924 11.1858 -14.5583 N 0 0 0 0 0 0 0 0 0 0 0 0 17.5494 10.7426 -16.2863 P 0 0 0 0 0 0 0 0 0 0 0 0 17.4724 9.2190 -16.2818 O 0 0 0 0 0 0 0 0 0 0 0 0 16.3271 11.4283 -16.8886 O 0 5 0 0 0 0 0 0 0 0 0 0 18.8865 11.3067 -16.7562 O 0 5 0 0 0 0 0 0 0 0 0 0 18.0032 10.6316 -13.8604 H 0 0 0 0 0 0 0 0 0 0 0 0 15.2337 12.1678 -13.5515 O 0 5 0 0 0 0 0 0 0 0 0 0 18.9274 16.1938 -11.4219 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4528 15.2654 -11.0450 H 0 0 0 0 0 0 0 0 0 0 0 0 18.4761 14.6173 -8.8381 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9309 16.5819 -7.4070 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2252 15.9212 -7.3388 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2130 17.0627 -9.2638 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1473 18.9082 -8.1098 O 0 0 0 0 0 0 0 0 0 0 0 0 19.8883 19.5096 -8.3013 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2683 18.1793 -10.0213 H 0 0 0 0 0 0 0 0 0 0 0 0 20.7301 16.9193 -7.6095 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5239 18.6979 -7.7395 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9169 15.8196 -13.4570 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.641106 > <Chemgauss3 Steric> -66.448975 > <Chemgauss3 Desolvation> 28.218323 > <Chemgauss3 Acc> -17.185810 > <Chemgauss3 Donor> -3.224650 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.6079 17.3500 -9.8035 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3424 17.0904 -9.4086 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9744 17.9316 -8.4307 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7346 18.9420 -7.8636 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0246 19.1108 -8.3568 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4636 18.2957 -9.3459 N 0 0 0 0 0 0 0 0 0 0 0 0 24.8653 20.1117 -7.8400 N 0 0 0 0 0 0 0 0 0 0 0 0 24.5134 20.7387 -7.1418 H 0 0 0 0 0 0 0 0 0 0 0 0 25.7738 20.2473 -8.2413 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0240 19.5955 -6.8884 N 0 0 0 0 0 0 0 0 0 0 0 0 20.8532 18.9936 -6.8633 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7748 17.9785 -7.7794 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6188 17.1149 -8.0093 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6986 17.5939 -9.1218 C 0 0 1 0 0 0 0 0 0 0 0 0 18.0414 16.2964 -9.5491 C 0 0 1 0 0 0 0 0 0 0 0 0 19.1875 15.2967 -9.4300 C 0 0 2 0 0 0 0 0 0 0 0 0 20.0634 15.8001 -8.3949 O 0 0 0 0 0 0 0 0 0 0 0 0 19.9919 15.1603 -10.7151 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0331 14.2235 -10.5013 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0620 13.8794 -11.7262 P 0 0 2 0 0 0 0 0 0 0 0 0 23.1632 12.9924 -11.1869 O 0 0 0 0 0 0 0 0 0 0 0 0 22.3949 15.1524 -12.4740 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0777 12.9713 -12.6625 O 0 0 0 0 0 0 0 0 0 0 0 0 21.3501 12.2308 -14.0933 P 0 0 1 0 0 0 0 0 0 0 0 0 22.3737 11.1453 -13.8371 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7880 11.4854 -14.3939 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7715 9.8861 -15.1862 P 0 0 0 0 0 0 0 0 0 0 0 0 18.5782 9.9535 -16.1341 O 0 0 0 0 0 0 0 0 0 0 0 0 21.1233 9.8027 -15.8882 O 0 5 0 0 0 0 0 0 0 0 0 0 19.6015 8.9130 -14.0238 O 0 5 0 0 0 0 0 0 0 0 0 0 18.9099 11.9356 -14.1089 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5967 13.2832 -15.1530 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4265 16.1227 -10.9893 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3507 14.8053 -11.5233 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8334 14.3071 -9.1104 H 0 0 0 0 0 0 0 0 0 0 0 0 17.0252 15.9457 -8.6097 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6369 15.1153 -8.9239 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5801 16.3417 -10.5409 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7733 18.5578 -8.6619 O 0 0 0 0 0 0 0 0 0 0 0 0 18.2814 19.3495 -8.4119 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2737 18.0238 -9.9517 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0952 17.0430 -7.0281 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0297 19.2461 -6.2089 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9919 16.7160 -10.5956 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -56.521282 > <Chemgauss3 Steric> -58.702721 > <Chemgauss3 Desolvation> 33.513321 > <Chemgauss3 Acc> -28.060061 > <Chemgauss3 Donor> -3.271830 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.5441 17.4600 -10.1280 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3706 17.2614 -9.4889 N 0 0 0 0 0 0 0 0 0 0 0 0 22.2276 18.1416 -8.4868 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1172 19.1351 -8.1101 C 0 0 0 0 0 0 0 0 0 0 0 0 24.2925 19.2395 -8.8473 C 0 0 0 0 0 0 0 0 0 0 0 0 24.5040 18.3823 -9.8749 N 0 0 0 0 0 0 0 0 0 0 0 0 25.2510 20.2190 -8.5351 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0623 20.8774 -7.8033 H 0 0 0 0 0 0 0 0 0 0 0 0 26.0689 20.3079 -9.1077 H 0 0 0 0 0 0 0 0 0 0 0 0 22.6313 19.8415 -7.0386 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4675 19.2877 -6.7691 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1788 18.2532 -7.6191 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9713 17.4308 -7.5938 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8704 17.9173 -8.5240 C 0 0 1 0 0 0 0 0 0 0 0 0 18.0990 16.6365 -8.7740 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2116 15.5952 -8.8444 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2878 16.0897 -8.0141 O 0 0 0 0 0 0 0 0 0 0 0 0 19.7473 15.3937 -10.2549 C 0 0 0 0 0 0 0 0 0 0 0 0 18.6872 14.9504 -11.0838 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9812 14.6520 -12.6655 P 0 0 2 0 0 0 0 0 0 0 0 0 19.7736 15.8118 -13.2287 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7036 14.1943 -13.3354 O 0 5 0 0 0 0 0 0 0 0 0 0 19.9787 13.3660 -12.5198 O 0 0 0 0 0 0 0 0 0 0 0 0 20.7277 12.4621 -13.6564 P 0 0 1 0 0 0 0 0 0 0 0 0 21.4013 11.3164 -12.9315 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3536 11.8406 -14.5573 N 0 0 0 0 0 0 0 0 0 0 0 0 19.4652 10.1781 -15.1970 P 0 0 0 0 0 0 0 0 0 0 0 0 18.7979 10.2613 -16.5663 O 0 0 0 0 0 0 0 0 0 0 0 0 20.9637 9.8970 -15.2481 O 0 5 0 0 0 0 0 0 0 0 0 0 18.7008 9.3479 -14.1706 O 0 5 0 0 0 0 0 0 0 0 0 0 18.5026 12.3981 -14.6989 H 0 0 0 0 0 0 0 0 0 0 0 0 21.5282 13.3739 -14.5614 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5381 14.6420 -10.2518 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1386 16.3342 -10.6456 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8924 14.6292 -8.4302 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2721 16.3510 -7.6457 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8022 15.5289 -7.8518 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4566 16.6746 -9.6596 H 0 0 0 0 0 0 0 0 0 0 0 0 18.0849 18.9289 -7.9270 O 0 0 0 0 0 0 0 0 0 0 0 0 18.6586 19.7059 -7.8056 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2886 18.3024 -9.4627 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6451 17.4053 -6.5285 H 0 0 0 0 0 0 0 0 0 0 0 0 20.7951 19.5896 -5.9774 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7459 16.7910 -10.9577 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -56.926132 > <Chemgauss3 Steric> -64.861855 > <Chemgauss3 Desolvation> 36.346146 > <Chemgauss3 Acc> -26.770651 > <Chemgauss3 Donor> -1.639771 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.3634 19.5310 -7.5362 C 0 0 0 0 0 0 0 0 0 0 0 0 22.2916 18.7284 -7.7148 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1840 18.3694 -9.0028 C 0 0 0 0 0 0 0 0 0 0 0 0 23.0182 18.7343 -10.0475 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0897 19.5654 -9.7358 C 0 0 0 0 0 0 0 0 0 0 0 0 24.2599 19.9679 -8.4534 N 0 0 0 0 0 0 0 0 0 0 0 0 24.9866 19.9848 -10.7335 N 0 0 0 0 0 0 0 0 0 0 0 0 24.8779 19.6426 -11.6692 H 0 0 0 0 0 0 0 0 0 0 0 0 25.7785 20.5446 -10.4800 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5939 18.1744 -11.2263 N 0 0 0 0 0 0 0 0 0 0 0 0 21.5216 17.4816 -10.9041 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2327 17.5689 -9.5681 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1145 16.9213 -8.8860 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8200 17.7192 -8.9229 C 0 0 1 0 0 0 0 0 0 0 0 0 17.7855 16.6233 -8.7586 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3911 15.4805 -9.5676 C 0 0 2 0 0 0 0 0 0 0 0 0 19.8256 15.6590 -9.5171 O 0 0 0 0 0 0 0 0 0 0 0 0 17.9571 15.4912 -11.0266 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1741 14.2025 -11.5739 O 0 0 0 0 0 0 0 0 0 0 0 0 18.5194 14.0590 -13.1668 P 0 0 2 0 0 0 0 0 0 0 0 0 17.5410 14.9128 -13.9440 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7073 12.5969 -13.5095 O 0 5 0 0 0 0 0 0 0 0 0 0 19.9808 14.7896 -13.1962 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4834 14.1789 -12.9986 P 0 0 1 0 0 0 0 0 0 0 0 0 21.4829 13.4308 -11.6825 O 0 0 0 0 0 0 0 0 0 0 0 0 21.5557 13.0193 -14.3163 N 0 0 0 0 0 0 0 0 0 0 0 0 22.4380 11.4943 -14.0308 P 0 0 0 0 0 0 0 0 0 0 0 0 23.1563 11.2281 -15.3500 O 0 0 0 0 0 0 0 0 0 0 0 0 23.3692 11.8135 -12.8655 O 0 5 0 0 0 0 0 0 0 0 0 0 21.3314 10.4974 -13.7012 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0924 13.1935 -15.2163 H 0 0 0 0 0 0 0 0 0 0 0 0 22.4972 15.2723 -13.2592 O 0 5 0 0 0 0 0 0 0 0 0 0 18.5429 16.2217 -11.5866 H 0 0 0 0 0 0 0 0 0 0 0 0 16.8971 15.7383 -11.1009 H 0 0 0 0 0 0 0 0 0 0 0 0 18.1644 14.5018 -9.1231 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7202 16.2322 -7.3871 O 0 0 0 0 0 0 0 0 0 0 0 0 17.0499 15.5345 -7.3330 H 0 0 0 0 0 0 0 0 0 0 0 0 16.7785 16.9171 -9.0719 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7683 18.6875 -7.8951 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4617 19.3445 -8.0825 H 0 0 0 0 0 0 0 0 0 0 0 0 18.6944 18.2230 -9.8897 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4647 16.7302 -7.8454 H 0 0 0 0 0 0 0 0 0 0 0 0 20.9176 16.9018 -11.5891 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5305 19.8718 -6.5200 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -51.319405 > <Chemgauss3 Steric> -72.153114 > <Chemgauss3 Desolvation> 36.436180 > <Chemgauss3 Acc> -12.024536 > <Chemgauss3 Donor> -3.577932 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 27.0460 15.3297 -12.9461 C 0 0 0 0 0 0 0 0 0 0 0 0 26.3624 16.0940 -12.0666 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0635 15.7589 -12.0646 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4489 14.7802 -12.8293 C 0 0 0 0 0 0 0 0 0 0 0 0 25.2611 14.0593 -13.6990 C 0 0 0 0 0 0 0 0 0 0 0 0 26.5844 14.3445 -13.7537 N 0 0 0 0 0 0 0 0 0 0 0 0 24.7217 13.0476 -14.5123 N 0 0 0 0 0 0 0 0 0 0 0 0 23.7507 12.8137 -14.4288 H 0 0 0 0 0 0 0 0 0 0 0 0 25.3316 12.5084 -15.0971 H 0 0 0 0 0 0 0 0 0 0 0 0 23.1051 14.7236 -12.5571 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9065 15.6508 -11.6436 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0631 16.3056 -11.3125 N 0 0 0 0 0 0 0 0 0 0 0 0 24.1910 17.3844 -10.3354 C 0 0 1 0 0 0 0 0 0 0 0 0 23.9098 18.7686 -10.8998 C 0 0 1 0 0 0 0 0 0 0 0 0 23.4914 19.5232 -9.6534 C 0 0 1 0 0 0 0 0 0 0 0 0 22.6963 18.4705 -8.8875 C 0 0 2 0 0 0 0 0 0 0 0 0 23.2449 17.1872 -9.2671 O 0 0 0 0 0 0 0 0 0 0 0 0 21.2136 18.4796 -9.2323 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5673 17.4658 -8.4826 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9549 17.2486 -8.6567 P 0 0 2 0 0 0 0 0 0 0 0 0 18.2829 18.6028 -8.5884 O 0 0 0 0 0 0 0 0 0 0 0 0 18.5015 16.1174 -7.7594 O 0 5 0 0 0 0 0 0 0 0 0 0 18.9153 16.7287 -10.2054 O 0 0 0 0 0 0 0 0 0 0 0 0 19.0048 15.2203 -10.8274 P 0 0 1 0 0 0 0 0 0 0 0 0 17.5981 14.6610 -10.8248 O 0 0 0 0 0 0 0 0 0 0 0 0 19.4818 15.5625 -12.4831 N 0 0 0 0 0 0 0 0 0 0 0 0 18.8163 14.5199 -13.7698 P 0 0 0 0 0 0 0 0 0 0 0 0 19.9796 14.3383 -14.7397 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4048 13.2441 -13.0417 O 0 5 0 0 0 0 0 0 0 0 0 0 17.6522 15.3350 -14.3242 O 0 5 0 0 0 0 0 0 0 0 0 0 20.1046 16.3455 -12.7160 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1293 14.4721 -10.1439 O 0 5 0 0 0 0 0 0 0 0 0 0 21.0749 18.2820 -10.2962 H 0 0 0 0 0 0 0 0 0 0 0 0 20.7756 19.4464 -8.9798 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8224 18.5751 -7.8012 H 0 0 0 0 0 0 0 0 0 0 0 0 24.6502 19.8675 -8.8940 O 0 0 0 0 0 0 0 0 0 0 0 0 24.3334 20.3450 -8.1125 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9401 20.4460 -9.8610 H 0 0 0 0 0 0 0 0 0 0 0 0 25.0482 19.3234 -11.5267 O 0 0 0 0 0 0 0 0 0 0 0 0 25.2408 18.7785 -12.3099 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0863 18.7393 -11.6247 H 0 0 0 0 0 0 0 0 0 0 0 0 25.2223 17.2971 -9.9219 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9554 15.8921 -11.1882 H 0 0 0 0 0 0 0 0 0 0 0 0 28.1097 15.5308 -13.0151 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.242962 > <Chemgauss3 Steric> -58.036083 > <Chemgauss3 Desolvation> 35.045261 > <Chemgauss3 Acc> -25.640659 > <Chemgauss3 Donor> -9.611485 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.8454 17.3943 -9.3907 C 0 0 0 0 0 0 0 0 0 0 0 0 20.6944 16.7730 -10.2382 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9439 17.2308 -10.0696 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3685 18.1988 -9.1735 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3981 18.7650 -8.3528 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1135 18.3502 -8.4687 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7397 19.7541 -7.4144 N 0 0 0 0 0 0 0 0 0 0 0 0 22.7003 20.0187 -7.3051 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0344 20.1151 -6.8005 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7200 18.4073 -9.2879 N 0 0 0 0 0 0 0 0 0 0 0 0 24.1099 17.5810 -10.2359 C 0 0 0 0 0 0 0 0 0 0 0 0 23.0697 16.8467 -10.7408 N 0 0 0 0 0 0 0 0 0 0 0 0 23.1596 15.8424 -11.7983 C 0 0 1 0 0 0 0 0 0 0 0 0 23.3348 14.4199 -11.2890 C 0 0 1 0 0 0 0 0 0 0 0 0 22.7711 13.6148 -12.4432 C 0 0 1 0 0 0 0 0 0 0 0 0 21.5992 14.4779 -12.9001 C 0 0 2 0 0 0 0 0 0 0 0 0 21.9459 15.8439 -12.5742 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2962 14.1318 -12.1933 C 0 0 0 0 0 0 0 0 0 0 0 0 19.2769 14.9899 -12.6751 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7592 14.8385 -12.0828 P 0 0 2 0 0 0 0 0 0 0 0 0 16.9192 15.9708 -12.6328 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8257 14.5821 -10.5927 O 0 5 0 0 0 0 0 0 0 0 0 0 17.3126 13.4539 -12.8269 O 0 0 0 0 0 0 0 0 0 0 0 0 16.5831 13.2039 -14.2675 P 0 0 1 0 0 0 0 0 0 0 0 0 17.2954 14.0786 -15.2771 O 0 0 0 0 0 0 0 0 0 0 0 0 16.9975 11.5241 -14.5721 N 0 0 0 0 0 0 0 0 0 0 0 0 17.3238 11.0437 -16.2598 P 0 0 0 0 0 0 0 0 0 0 0 0 16.6921 9.6605 -16.3810 O 0 0 0 0 0 0 0 0 0 0 0 0 16.6364 12.1199 -17.0943 O 0 5 0 0 0 0 0 0 0 0 0 0 18.8468 11.0532 -16.3462 O 0 5 0 0 0 0 0 0 0 0 0 0 17.0728 10.8388 -13.8107 H 0 0 0 0 0 0 0 0 0 0 0 0 15.0841 13.3077 -14.0847 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4045 14.2731 -11.1169 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0207 13.0966 -12.4002 H 0 0 0 0 0 0 0 0 0 0 0 0 21.4537 14.4248 -13.9876 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7343 13.5522 -13.4950 O 0 0 0 0 0 0 0 0 0 0 0 0 23.3306 13.0310 -14.2052 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5009 12.5885 -12.1743 H 0 0 0 0 0 0 0 0 0 0 0 0 24.6884 14.1212 -11.0149 O 0 0 0 0 0 0 0 0 0 0 0 0 24.9616 14.6804 -10.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7444 14.2510 -10.3794 H 0 0 0 0 0 0 0 0 0 0 0 0 24.0031 16.1654 -12.4511 H 0 0 0 0 0 0 0 0 0 0 0 0 25.1237 17.4706 -10.5969 H 0 0 0 0 0 0 0 0 0 0 0 0 18.8076 17.0855 -9.4558 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -46.117962 > <Chemgauss3 Steric> -59.609386 > <Chemgauss3 Desolvation> 33.510418 > <Chemgauss3 Acc> -17.088673 > <Chemgauss3 Donor> -2.930333 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.8576 20.1463 -6.7082 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7378 19.3999 -7.8279 N 0 0 0 0 0 0 0 0 0 0 0 0 21.5770 18.7277 -7.8213 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5995 18.7520 -6.8393 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8394 19.5609 -5.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9928 20.2691 -5.6724 N 0 0 0 0 0 0 0 0 0 0 0 0 19.9018 19.6462 -4.6893 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0317 19.1547 -4.7673 H 0 0 0 0 0 0 0 0 0 0 0 0 20.0723 20.2705 -3.9240 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5501 17.9353 -7.1782 N 0 0 0 0 0 0 0 0 0 0 0 0 19.8834 17.4240 -8.3448 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1032 17.8737 -8.7761 N 0 0 0 0 0 0 0 0 0 0 0 0 21.7634 17.5036 -10.0259 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5881 16.2286 -9.9374 C 0 0 1 0 0 0 0 0 0 0 0 0 22.5924 15.7712 -11.3827 C 0 0 1 0 0 0 0 0 0 0 0 0 21.1842 16.1350 -11.8431 C 0 0 2 0 0 0 0 0 0 0 0 0 20.7747 17.2715 -11.0476 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1804 15.0112 -11.6270 C 0 0 0 0 0 0 0 0 0 0 0 0 19.0584 15.2385 -12.4618 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8140 14.1763 -12.4342 P 0 0 2 0 0 0 0 0 0 0 0 0 16.6908 14.7381 -13.2786 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5605 13.7380 -11.0079 O 0 5 0 0 0 0 0 0 0 0 0 0 18.4985 12.9330 -13.2440 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1029 12.8505 -14.7599 P 0 0 1 0 0 0 0 0 0 0 0 0 19.9665 14.0784 -14.9548 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1379 11.4363 -14.6372 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6697 11.4482 -15.5533 P 0 0 0 0 0 0 0 0 0 0 0 0 21.8055 10.0189 -16.0686 O 0 0 0 0 0 0 0 0 0 0 0 0 21.4434 12.4878 -16.6465 O 0 5 0 0 0 0 0 0 0 0 0 0 22.7080 11.8450 -14.5085 O 0 5 0 0 0 0 0 0 0 0 0 0 19.8900 10.6341 -14.0456 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9760 12.5442 -15.7230 O 0 5 0 0 0 0 0 0 0 0 0 0 19.8548 14.9943 -10.5858 H 0 0 0 0 0 0 0 0 0 0 0 0 20.6305 14.0514 -11.8849 H 0 0 0 0 0 0 0 0 0 0 0 0 21.1676 16.4462 -12.8964 H 0 0 0 0 0 0 0 0 0 0 0 0 23.5339 16.5467 -12.1246 O 0 0 0 0 0 0 0 0 0 0 0 0 23.5004 16.2194 -13.0360 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8528 14.7155 -11.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8842 16.4734 -9.4306 O 0 0 0 0 0 0 0 0 0 0 0 0 23.7832 16.7597 -8.5058 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0948 15.4830 -9.3009 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3785 18.3865 -10.3160 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2877 16.7285 -8.9206 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7698 20.7277 -6.6271 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -58.331234 > <Chemgauss3 Steric> -56.244030 > <Chemgauss3 Desolvation> 32.473732 > <Chemgauss3 Acc> -28.082676 > <Chemgauss3 Donor> -6.478258 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.0807 18.6734 -5.7663 C 0 0 0 0 0 0 0 0 0 0 0 0 19.7740 17.7766 -6.7290 N 0 0 0 0 0 0 0 0 0 0 0 0 20.7625 17.7022 -7.6327 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9512 18.4145 -7.6356 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1512 19.3087 -6.5887 C 0 0 0 0 0 0 0 0 0 0 0 0 21.1934 19.4359 -5.6389 N 0 0 0 0 0 0 0 0 0 0 0 0 23.3287 20.0725 -6.5121 N 0 0 0 0 0 0 0 0 0 0 0 0 24.0501 19.9354 -7.1943 H 0 0 0 0 0 0 0 0 0 0 0 0 23.4739 20.6759 -5.7251 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7189 18.0738 -8.7208 N 0 0 0 0 0 0 0 0 0 0 0 0 22.0099 17.1709 -9.3657 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8164 16.9123 -8.7455 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7996 15.9656 -9.1980 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8195 16.5439 -10.2073 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3598 15.2940 -10.9316 C 0 0 1 0 0 0 0 0 0 0 0 0 19.6400 14.4672 -10.9980 C 0 0 2 0 0 0 0 0 0 0 0 0 20.4323 14.8471 -9.8491 O 0 0 0 0 0 0 0 0 0 0 0 0 20.4562 14.7370 -12.2543 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6234 13.9347 -12.2179 O 0 0 0 0 0 0 0 0 0 0 0 0 22.6921 14.0229 -13.4539 P 0 0 2 0 0 0 0 0 0 0 0 0 21.9217 13.9491 -14.7544 O 0 0 0 0 0 0 0 0 0 0 0 0 23.8459 13.0804 -13.1874 O 0 5 0 0 0 0 0 0 0 0 0 0 23.2186 15.5564 -13.2505 O 0 0 0 0 0 0 0 0 0 0 0 0 24.4605 16.1505 -12.3704 P 0 0 1 0 0 0 0 0 0 0 0 0 24.5773 15.2824 -11.1357 O 0 0 0 0 0 0 0 0 0 0 0 0 25.8197 15.8202 -13.4332 N 0 0 0 0 0 0 0 0 0 0 0 0 27.3690 15.3567 -12.6778 P 0 0 0 0 0 0 0 0 0 0 0 0 28.4219 16.0636 -13.5257 O 0 0 0 0 0 0 0 0 0 0 0 0 27.2607 15.8822 -11.2498 O 0 5 0 0 0 0 0 0 0 0 0 0 27.3817 13.8356 -12.7926 O 0 5 0 0 0 0 0 0 0 0 0 0 25.7315 15.8688 -14.4554 H 0 0 0 0 0 0 0 0 0 0 0 0 24.2993 17.6501 -12.2415 O 0 5 0 0 0 0 0 0 0 0 0 0 20.7450 15.7883 -12.2952 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8742 14.4830 -13.1415 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4348 13.3911 -10.9161 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4057 14.6013 -10.1266 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1434 13.8150 -10.6287 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8971 15.4928 -11.9037 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7626 17.2387 -9.5772 O 0 0 0 0 0 0 0 0 0 0 0 0 18.1491 18.0191 -9.1423 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3255 17.2256 -10.9027 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2919 15.6028 -8.2746 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3059 16.6734 -10.2795 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3356 18.8000 -4.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -46.082470 > <Chemgauss3 Steric> -53.433170 > <Chemgauss3 Desolvation> 35.425697 > <Chemgauss3 Acc> -23.779299 > <Chemgauss3 Donor> -4.295708 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 21.5995 19.9092 -6.0179 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8348 18.9414 -6.5688 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3870 18.4992 -7.7085 C 0 0 0 0 0 0 0 0 0 0 0 0 22.5684 18.9306 -8.2903 C 0 0 0 0 0 0 0 0 0 0 0 0 23.2670 19.9337 -7.6259 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7675 20.4283 -6.4677 N 0 0 0 0 0 0 0 0 0 0 0 0 24.4752 20.4312 -8.1442 N 0 0 0 0 0 0 0 0 0 0 0 0 24.8586 20.0249 -8.9764 H 0 0 0 0 0 0 0 0 0 0 0 0 24.9866 21.1202 -7.6262 H 0 0 0 0 0 0 0 0 0 0 0 0 22.8143 18.2473 -9.4546 N 0 0 0 0 0 0 0 0 0 0 0 0 21.8011 17.4155 -9.5782 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9095 17.5308 -8.5449 N 0 0 0 0 0 0 0 0 0 0 0 0 19.6817 16.7565 -8.3781 C 0 0 1 0 0 0 0 0 0 0 0 0 18.4774 17.3407 -9.1007 C 0 0 1 0 0 0 0 0 0 0 0 0 17.6165 16.1085 -9.2970 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6544 15.0303 -9.5929 C 0 0 2 0 0 0 0 0 0 0 0 0 19.8662 15.4316 -8.9127 O 0 0 0 0 0 0 0 0 0 0 0 0 18.9604 14.8928 -11.0777 C 0 0 0 0 0 0 0 0 0 0 0 0 17.7671 14.5419 -11.7561 O 0 0 0 0 0 0 0 0 0 0 0 0 17.8038 14.3274 -13.3778 P 0 0 2 0 0 0 0 0 0 0 0 0 18.5566 15.4869 -13.9937 O 0 0 0 0 0 0 0 0 0 0 0 0 16.4191 13.9613 -13.8668 O 0 5 0 0 0 0 0 0 0 0 0 0 18.7490 12.9968 -13.4557 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2733 12.1338 -14.7404 P 0 0 1 0 0 0 0 0 0 0 0 0 19.9930 10.9212 -14.1896 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7505 11.6219 -15.4512 N 0 0 0 0 0 0 0 0 0 0 0 0 17.6842 9.9976 -16.1879 P 0 0 0 0 0 0 0 0 0 0 0 0 16.8223 10.1888 -17.4320 O 0 0 0 0 0 0 0 0 0 0 0 0 19.1425 9.6614 -16.4836 O 0 5 0 0 0 0 0 0 0 0 0 0 17.0449 9.1381 -15.1018 O 0 5 0 0 0 0 0 0 0 0 0 0 16.9157 12.2199 -15.4304 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9706 13.0660 -15.7080 O 0 5 0 0 0 0 0 0 0 0 0 0 19.7056 14.1118 -11.2361 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3327 15.8389 -11.4733 H 0 0 0 0 0 0 0 0 0 0 0 0 18.3555 14.0545 -9.1864 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9570 15.7886 -8.0719 O 0 0 0 0 0 0 0 0 0 0 0 0 16.4225 14.9995 -8.2467 H 0 0 0 0 0 0 0 0 0 0 0 0 16.8501 16.2248 -10.0700 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8407 18.3448 -8.3372 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4627 19.0900 -8.2643 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7668 17.7646 -10.0708 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5195 16.6800 -7.2782 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6595 16.7120 -10.3876 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2294 20.3275 -5.0880 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -43.554287 > <Chemgauss3 Steric> -71.840912 > <Chemgauss3 Desolvation> 36.856087 > <Chemgauss3 Acc> -7.611148 > <Chemgauss3 Donor> -0.958317 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 22.7393 19.3428 -6.6887 C 0 0 0 0 0 0 0 0 0 0 0 0 22.5878 18.6367 -7.8304 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3093 18.2604 -7.9829 C 0 0 0 0 0 0 0 0 0 0 0 0 20.2498 18.5254 -7.1299 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5335 19.2635 -5.9851 C 0 0 0 0 0 0 0 0 0 0 0 0 21.8049 19.6772 -5.7662 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5190 19.5789 -5.0648 N 0 0 0 0 0 0 0 0 0 0 0 0 18.5741 19.3081 -5.2610 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7349 20.1514 -4.2708 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0879 17.9791 -7.6143 N 0 0 0 0 0 0 0 0 0 0 0 0 19.4346 17.3929 -8.7411 C 0 0 0 0 0 0 0 0 0 0 0 0 20.7706 17.5355 -9.0074 N 0 0 0 0 0 0 0 0 0 0 0 0 21.4762 17.0078 -10.1730 C 0 0 1 0 0 0 0 0 0 0 0 0 21.9568 15.5738 -10.0100 C 0 0 1 0 0 0 0 0 0 0 0 0 22.0345 15.1159 -11.4530 C 0 0 1 0 0 0 0 0 0 0 0 0 20.8225 15.8005 -12.0772 C 0 0 2 0 0 0 0 0 0 0 0 0 20.5976 17.0088 -11.3146 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5617 14.9501 -12.0120 C 0 0 0 0 0 0 0 0 0 0 0 0 18.4961 15.6727 -12.6035 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2878 14.8527 -13.3416 P 0 0 2 0 0 0 0 0 0 0 0 0 16.2109 15.8420 -13.7313 O 0 0 0 0 0 0 0 0 0 0 0 0 16.9463 13.6229 -12.5282 O 0 5 0 0 0 0 0 0 0 0 0 0 18.0684 14.3771 -14.6961 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5514 13.4986 -15.9732 P 0 0 1 0 0 0 0 0 0 0 0 0 18.7588 13.2504 -16.8520 O 0 0 0 0 0 0 0 0 0 0 0 0 17.0949 11.9942 -15.1892 N 0 0 0 0 0 0 0 0 0 0 0 0 17.3929 10.4740 -16.0755 P 0 0 0 0 0 0 0 0 0 0 0 0 16.1734 9.6140 -15.7586 O 0 0 0 0 0 0 0 0 0 0 0 0 17.4910 10.9054 -17.5354 O 0 5 0 0 0 0 0 0 0 0 0 0 18.7000 9.9621 -15.4783 O 0 5 0 0 0 0 0 0 0 0 0 0 16.6895 11.9772 -14.2456 H 0 0 0 0 0 0 0 0 0 0 0 0 16.3071 14.1448 -16.5436 O 0 5 0 0 0 0 0 0 0 0 0 0 19.3118 14.7291 -10.9733 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7095 14.0176 -12.5588 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0132 16.0975 -13.1174 H 0 0 0 0 0 0 0 0 0 0 0 0 23.2190 15.6383 -12.0550 O 0 0 0 0 0 0 0 0 0 0 0 0 23.2239 15.3204 -12.9704 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0509 14.0275 -11.5699 H 0 0 0 0 0 0 0 0 0 0 0 0 23.1995 15.5074 -9.3406 O 0 0 0 0 0 0 0 0 0 0 0 0 23.0536 15.8176 -8.4296 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2245 14.9728 -9.4560 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3148 17.7162 -10.3652 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7683 16.8543 -9.4014 H 0 0 0 0 0 0 0 0 0 0 0 0 23.7457 19.6910 -6.4821 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.048962 > <Chemgauss3 Steric> -49.288399 > <Chemgauss3 Desolvation> 36.490986 > <Chemgauss3 Acc> -34.310555 > <Chemgauss3 Donor> -7.940979 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.6843 16.9592 -10.8540 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4386 16.5885 -10.4857 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1248 17.1183 -9.2939 C 0 0 0 0 0 0 0 0 0 0 0 0 22.9182 17.9353 -8.5044 C 0 0 0 0 0 0 0 0 0 0 0 0 24.1829 18.2467 -8.9937 C 0 0 0 0 0 0 0 0 0 0 0 0 24.5672 17.7457 -10.1924 N 0 0 0 0 0 0 0 0 0 0 0 0 25.0542 19.0693 -8.2590 N 0 0 0 0 0 0 0 0 0 0 0 0 24.7412 19.4722 -7.3963 H 0 0 0 0 0 0 0 0 0 0 0 0 25.9422 19.3199 -8.6506 H 0 0 0 0 0 0 0 0 0 0 0 0 22.2610 18.2827 -7.3510 N 0 0 0 0 0 0 0 0 0 0 0 0 21.0895 17.6881 -7.4378 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9595 16.9703 -8.5971 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7885 16.1962 -9.0025 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8167 16.9603 -9.8887 C 0 0 1 0 0 0 0 0 0 0 0 0 18.1314 15.8294 -10.6301 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2762 14.8462 -10.8534 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2057 15.0462 -9.7634 O 0 0 0 0 0 0 0 0 0 0 0 0 20.0146 15.0829 -12.1634 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0598 14.1326 -12.2730 O 0 0 0 0 0 0 0 0 0 0 0 0 22.0242 14.1549 -13.5947 P 0 0 2 0 0 0 0 0 0 0 0 0 23.1458 13.1615 -13.3814 O 0 0 0 0 0 0 0 0 0 0 0 0 22.3267 15.5894 -13.9706 O 0 5 0 0 0 0 0 0 0 0 0 0 20.9891 13.5378 -14.6983 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2184 12.0979 -14.7505 P 0 0 1 0 0 0 0 0 0 0 0 0 19.2457 12.0791 -13.5906 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3172 12.2483 -16.2510 N 0 0 0 0 0 0 0 0 0 0 0 0 17.6918 11.5141 -16.3188 P 0 0 0 0 0 0 0 0 0 0 0 0 17.6067 10.9291 -17.7250 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7067 10.4694 -15.2072 O 0 5 0 0 0 0 0 0 0 0 0 0 16.7564 12.6924 -16.0665 O 0 5 0 0 0 0 0 0 0 0 0 0 19.6942 12.7567 -17.0599 H 0 0 0 0 0 0 0 0 0 0 0 0 21.2441 10.9962 -14.9096 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4406 16.0872 -12.1775 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3318 14.9635 -13.0058 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9329 13.8038 -10.8073 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1614 15.2205 -9.7778 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7531 14.5084 -10.2928 H 0 0 0 0 0 0 0 0 0 0 0 0 17.6214 16.1474 -11.5451 H 0 0 0 0 0 0 0 0 0 0 0 0 17.9211 17.7485 -9.1315 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4456 18.4425 -8.6948 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3520 17.6108 -10.5921 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3142 15.8473 -8.0563 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3011 17.7397 -6.6989 H 0 0 0 0 0 0 0 0 0 0 0 0 24.0246 16.5764 -11.8103 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -55.196194 > <Chemgauss3 Steric> -50.258354 > <Chemgauss3 Desolvation> 30.171638 > <Chemgauss3 Acc> -33.380890 > <Chemgauss3 Donor> -1.728590 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 20.7532 19.2414 -5.7144 C 0 0 0 0 0 0 0 0 0 0 0 0 20.1307 18.3175 -6.4785 N 0 0 0 0 0 0 0 0 0 0 0 0 20.8861 18.0017 -7.5410 C 0 0 0 0 0 0 0 0 0 0 0 0 22.1328 18.5126 -7.8651 C 0 0 0 0 0 0 0 0 0 0 0 0 22.6694 19.4591 -6.9979 C 0 0 0 0 0 0 0 0 0 0 0 0 21.9608 19.8262 -5.9032 N 0 0 0 0 0 0 0 0 0 0 0 0 23.9291 20.0300 -7.2489 N 0 0 0 0 0 0 0 0 0 0 0 0 24.4643 19.7160 -8.0360 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3183 20.6746 -6.5874 H 0 0 0 0 0 0 0 0 0 0 0 0 22.5998 17.9530 -9.0278 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6545 17.1171 -9.4035 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5954 17.1113 -8.5350 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3868 16.2994 -8.6581 C 0 0 1 0 0 0 0 0 0 0 0 0 18.3033 16.9276 -9.5212 C 0 0 1 0 0 0 0 0 0 0 0 0 17.5352 15.7035 -9.9793 C 0 0 1 0 0 0 0 0 0 0 0 0 18.6478 14.6814 -10.1899 C 0 0 2 0 0 0 0 0 0 0 0 0 19.7094 15.0380 -9.2745 O 0 0 0 0 0 0 0 0 0 0 0 0 19.2086 14.6977 -11.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1630 14.3915 -12.5108 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4850 14.3394 -14.1142 P 0 0 2 0 0 0 0 0 0 0 0 0 19.2885 15.5692 -14.4778 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2191 13.9952 -14.8690 O 0 5 0 0 0 0 0 0 0 0 0 0 19.4785 13.0425 -14.1510 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2469 12.3219 -15.4001 P 0 0 1 0 0 0 0 0 0 0 0 0 20.9062 11.0757 -14.8488 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8885 11.8518 -16.4100 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0099 10.3074 -17.2964 P 0 0 0 0 0 0 0 0 0 0 0 0 18.3674 10.6033 -18.6480 O 0 0 0 0 0 0 0 0 0 0 0 0 20.5088 10.0320 -17.3639 O 0 5 0 0 0 0 0 0 0 0 0 0 18.2264 9.3318 -16.4238 O 0 5 0 0 0 0 0 0 0 0 0 0 18.0407 12.4277 -16.4789 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0644 13.3593 -16.1395 O 0 5 0 0 0 0 0 0 0 0 0 0 19.9984 13.9516 -11.7039 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6077 15.6858 -11.8390 H 0 0 0 0 0 0 0 0 0 0 0 0 18.3203 13.6642 -9.9352 H 0 0 0 0 0 0 0 0 0 0 0 0 16.6879 15.2506 -8.9232 O 0 0 0 0 0 0 0 0 0 0 0 0 16.2210 14.4718 -9.2618 H 0 0 0 0 0 0 0 0 0 0 0 0 16.9087 15.8801 -10.8596 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5082 17.8380 -8.7893 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0803 18.5848 -8.5395 H 0 0 0 0 0 0 0 0 0 0 0 0 18.7385 17.4512 -10.3819 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0415 16.1111 -7.6153 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6799 16.4944 -10.2877 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2140 19.5580 -4.8280 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -50.562405 > <Chemgauss3 Steric> -56.866371 > <Chemgauss3 Desolvation> 32.686768 > <Chemgauss3 Acc> -22.550596 > <Chemgauss3 Donor> -3.832204 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.3114 19.5971 -6.7297 C 0 0 0 0 0 0 0 0 0 0 0 0 23.1832 18.9000 -7.8797 N 0 0 0 0 0 0 0 0 0 0 0 0 21.9118 18.5081 -8.0512 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8387 18.7506 -7.2087 C 0 0 0 0 0 0 0 0 0 0 0 0 21.0986 19.4814 -6.0536 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3616 19.9099 -5.8154 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0690 19.7741 -5.1426 N 0 0 0 0 0 0 0 0 0 0 0 0 19.1303 19.4926 -5.3529 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2676 20.3418 -4.3408 H 0 0 0 0 0 0 0 0 0 0 0 0 19.6902 18.1935 -7.7123 N 0 0 0 0 0 0 0 0 0 0 0 0 20.0583 17.6229 -8.8403 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3953 17.7859 -9.0891 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1219 17.2791 -10.2510 C 0 0 1 0 0 0 0 0 0 0 0 0 22.6199 15.8502 -10.0958 C 0 0 1 0 0 0 0 0 0 0 0 0 22.7211 15.4074 -11.5421 C 0 0 1 0 0 0 0 0 0 0 0 0 21.5075 16.0816 -12.1743 C 0 0 2 0 0 0 0 0 0 0 0 0 21.2571 17.2794 -11.4031 O 0 0 0 0 0 0 0 0 0 0 0 0 20.2576 15.2137 -12.1325 C 0 0 0 0 0 0 0 0 0 0 0 0 19.1895 15.9276 -12.7299 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7134 15.2275 -12.8219 P 0 0 2 0 0 0 0 0 0 0 0 0 16.8606 16.0395 -13.7723 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2218 14.9087 -11.4264 O 0 5 0 0 0 0 0 0 0 0 0 0 18.1210 13.8275 -13.5595 O 0 0 0 0 0 0 0 0 0 0 0 0 17.2028 12.5557 -14.0172 P 0 0 1 0 0 0 0 0 0 0 0 0 16.6615 12.8787 -15.3935 O 0 0 0 0 0 0 0 0 0 0 0 0 18.4165 11.2937 -14.1610 N 0 0 0 0 0 0 0 0 0 0 0 0 18.2117 10.0914 -15.4641 P 0 0 0 0 0 0 0 0 0 0 0 0 18.6483 8.7756 -14.8276 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7262 10.1584 -15.8046 O 0 5 0 0 0 0 0 0 0 0 0 0 19.1365 10.5980 -16.5664 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2303 11.2520 -13.5358 H 0 0 0 0 0 0 0 0 0 0 0 0 16.2616 12.1963 -12.8875 O 0 5 0 0 0 0 0 0 0 0 0 0 19.9983 14.9794 -11.0990 H 0 0 0 0 0 0 0 0 0 0 0 0 20.4245 14.2887 -12.6863 H 0 0 0 0 0 0 0 0 0 0 0 0 21.7065 16.3912 -13.2094 H 0 0 0 0 0 0 0 0 0 0 0 0 23.9054 15.9514 -12.1247 O 0 0 0 0 0 0 0 0 0 0 0 0 23.9256 15.6424 -13.0430 H 0 0 0 0 0 0 0 0 0 0 0 0 22.7536 14.3204 -11.6691 H 0 0 0 0 0 0 0 0 0 0 0 0 23.8553 15.7940 -9.4121 O 0 0 0 0 0 0 0 0 0 0 0 0 23.6943 16.0934 -8.5000 H 0 0 0 0 0 0 0 0 0 0 0 0 21.8892 15.2341 -9.5565 H 0 0 0 0 0 0 0 0 0 0 0 0 22.9531 18.0005 -10.4262 H 0 0 0 0 0 0 0 0 0 0 0 0 19.4072 17.0818 -9.5137 H 0 0 0 0 0 0 0 0 0 0 0 0 24.3104 19.9567 -6.5076 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -53.391632 > <Chemgauss3 Steric> -60.143772 > <Chemgauss3 Desolvation> 38.709145 > <Chemgauss3 Acc> -24.990257 > <Chemgauss3 Donor> -6.966747 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 19.7089 18.6796 -5.8507 C 0 0 0 0 0 0 0 0 0 0 0 0 19.4202 17.7695 -6.8064 N 0 0 0 0 0 0 0 0 0 0 0 0 20.4109 17.7068 -7.7087 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5858 18.4415 -7.7164 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7676 19.3478 -6.6765 C 0 0 0 0 0 0 0 0 0 0 0 0 20.8067 19.4643 -5.7286 N 0 0 0 0 0 0 0 0 0 0 0 0 22.9303 20.1345 -6.6051 N 0 0 0 0 0 0 0 0 0 0 0 0 23.6548 20.0057 -7.2855 H 0 0 0 0 0 0 0 0 0 0 0 0 23.0632 20.7469 -5.8228 H 0 0 0 0 0 0 0 0 0 0 0 0 22.3609 18.1069 -8.7982 N 0 0 0 0 0 0 0 0 0 0 0 0 21.6699 17.1855 -9.4364 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4809 16.9092 -8.8152 N 0 0 0 0 0 0 0 0 0 0 0 0 19.4828 15.9396 -9.2609 C 0 0 1 0 0 0 0 0 0 0 0 0 18.4928 16.4910 -10.2756 C 0 0 1 0 0 0 0 0 0 0 0 0 18.0578 15.2268 -10.9902 C 0 0 1 0 0 0 0 0 0 0 0 0 19.3537 14.4241 -11.0489 C 0 0 2 0 0 0 0 0 0 0 0 0 20.1374 14.8282 -9.9024 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1657 14.6993 -12.3067 C 0 0 0 0 0 0 0 0 0 0 0 0 21.3480 13.9198 -12.2629 O 0 0 0 0 0 0 0 0 0 0 0 0 22.4160 14.0185 -13.4986 P 0 0 2 0 0 0 0 0 0 0 0 0 21.6484 13.9195 -14.7992 O 0 0 0 0 0 0 0 0 0 0 0 0 23.5873 13.1004 -13.2237 O 0 5 0 0 0 0 0 0 0 0 0 0 22.9130 15.5633 -13.3072 O 0 0 0 0 0 0 0 0 0 0 0 0 23.9929 16.4498 -14.1544 P 0 0 1 0 0 0 0 0 0 0 0 0 24.1505 17.7654 -13.4223 O 0 0 0 0 0 0 0 0 0 0 0 0 25.4546 15.4984 -13.9434 N 0 0 0 0 0 0 0 0 0 0 0 0 26.9999 16.3773 -13.7847 P 0 0 0 0 0 0 0 0 0 0 0 0 27.9941 15.5252 -14.5673 O 0 0 0 0 0 0 0 0 0 0 0 0 26.7199 17.7414 -14.4076 O 0 5 0 0 0 0 0 0 0 0 0 0 27.2411 16.4074 -12.2787 O 0 5 0 0 0 0 0 0 0 0 0 0 25.4299 14.4730 -13.8908 H 0 0 0 0 0 0 0 0 0 0 0 0 23.6074 16.4276 -15.6181 O 0 5 0 0 0 0 0 0 0 0 0 0 20.4345 15.7556 -12.3557 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5896 14.4272 -13.1923 H 0 0 0 0 0 0 0 0 0 0 0 0 19.1689 13.3450 -10.9586 H 0 0 0 0 0 0 0 0 0 0 0 0 17.1163 14.5224 -10.1805 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8696 13.7273 -10.6764 H 0 0 0 0 0 0 0 0 0 0 0 0 17.5924 15.4089 -11.9643 H 0 0 0 0 0 0 0 0 0 0 0 0 17.4223 17.1705 -9.6520 O 0 0 0 0 0 0 0 0 0 0 0 0 17.7934 17.9616 -9.2230 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9865 17.1767 -10.9760 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9812 15.5746 -8.3350 H 0 0 0 0 0 0 0 0 0 0 0 0 21.9762 16.6864 -10.3459 H 0 0 0 0 0 0 0 0 0 0 0 0 18.9607 18.7982 -5.0742 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -45.522896 > <Chemgauss3 Steric> -50.178940 > <Chemgauss3 Desolvation> 31.247393 > <Chemgauss3 Acc> -23.879171 > <Chemgauss3 Donor> -2.712178 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 17.5341 15.1434 -13.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 17.8825 15.8319 -12.1251 N 0 0 0 0 0 0 0 0 0 0 0 0 19.0798 15.4249 -11.6774 C 0 0 0 0 0 0 0 0 0 0 0 0 19.8919 14.4457 -12.2269 C 0 0 0 0 0 0 0 0 0 0 0 0 19.4221 13.8078 -13.3706 C 0 0 0 0 0 0 0 0 0 0 0 0 18.2191 14.1684 -13.8789 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1807 12.8025 -13.9947 N 0 0 0 0 0 0 0 0 0 0 0 0 21.0896 12.5775 -13.6370 H 0 0 0 0 0 0 0 0 0 0 0 0 19.8460 12.3886 -14.8440 H 0 0 0 0 0 0 0 0 0 0 0 0 21.0434 14.3023 -11.4944 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9334 15.1784 -10.5177 C 0 0 0 0 0 0 0 0 0 0 0 0 19.7606 15.8827 -10.5855 N 0 0 0 0 0 0 0 0 0 0 0 0 19.3297 16.9268 -9.6587 C 0 0 1 0 0 0 0 0 0 0 0 0 19.2863 16.4850 -8.2038 C 0 0 1 0 0 0 0 0 0 0 0 0 19.4526 17.8075 -7.4819 C 0 0 1 0 0 0 0 0 0 0 0 0 20.4483 18.5421 -8.3741 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2485 18.0350 -9.7139 O 0 0 0 0 0 0 0 0 0 0 0 0 21.8967 18.2928 -7.9775 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7394 19.0048 -8.8666 O 0 0 0 0 0 0 0 0 0 0 0 0 24.2292 18.4155 -9.1992 P 0 0 2 0 0 0 0 0 0 0 0 0 24.8863 18.0208 -7.8943 O 0 0 0 0 0 0 0 0 0 0 0 0 24.9317 19.3446 -10.1655 O 0 5 0 0 0 0 0 0 0 0 0 0 23.8115 17.0542 -10.0009 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5793 16.2379 -11.1900 P 0 0 1 0 0 0 0 0 0 0 0 0 23.9081 14.8852 -11.2970 O 0 0 0 0 0 0 0 0 0 0 0 0 24.1521 17.2016 -12.5954 N 0 0 0 0 0 0 0 0 0 0 0 0 23.8689 16.3431 -14.1342 P 0 0 0 0 0 0 0 0 0 0 0 0 24.4858 17.2569 -15.1885 O 0 0 0 0 0 0 0 0 0 0 0 0 24.5941 15.0125 -13.9590 O 0 5 0 0 0 0 0 0 0 0 0 0 22.3493 16.2302 -14.2063 O 0 5 0 0 0 0 0 0 0 0 0 0 24.0459 18.2217 -12.5398 H 0 0 0 0 0 0 0 0 0 0 0 0 26.0736 16.3377 -10.9700 O 0 5 0 0 0 0 0 0 0 0 0 0 22.1252 17.2280 -8.0424 H 0 0 0 0 0 0 0 0 0 0 0 0 22.0725 18.6430 -6.9593 H 0 0 0 0 0 0 0 0 0 0 0 0 20.2538 19.6230 -8.3979 H 0 0 0 0 0 0 0 0 0 0 0 0 18.2132 18.5160 -7.4948 O 0 0 0 0 0 0 0 0 0 0 0 0 18.3691 19.3489 -7.0247 H 0 0 0 0 0 0 0 0 0 0 0 0 19.7687 17.7037 -6.4389 H 0 0 0 0 0 0 0 0 0 0 0 0 18.0744 15.8305 -7.8878 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0554 14.9987 -8.3929 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1220 15.8131 -7.9704 H 0 0 0 0 0 0 0 0 0 0 0 0 18.3348 17.2671 -10.0278 H 0 0 0 0 0 0 0 0 0 0 0 0 21.6641 15.3469 -9.7381 H 0 0 0 0 0 0 0 0 0 0 0 0 16.5759 15.4074 -13.6687 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -47.817589 > <Chemgauss3 Steric> -60.447186 > <Chemgauss3 Desolvation> 35.237095 > <Chemgauss3 Acc> -22.516800 > <Chemgauss3 Donor> -0.090703 > <Chemgauss3 Metal> 0.000000 $$$$ lig -OEChem-08130912162D 44 46 0 1 0 0 0 0 0999 V2000 23.7271 16.6619 -11.1514 C 0 0 0 0 0 0 0 0 0 0 0 0 22.4813 16.2691 -10.8069 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1017 16.8619 -9.6650 C 0 0 0 0 0 0 0 0 0 0 0 0 22.8337 17.7570 -8.9013 C 0 0 0 0 0 0 0 0 0 0 0 0 24.1053 18.0836 -9.3618 C 0 0 0 0 0 0 0 0 0 0 0 0 24.5547 17.5217 -10.5097 N 0 0 0 0 0 0 0 0 0 0 0 0 24.9172 18.9837 -8.6501 N 0 0 0 0 0 0 0 0 0 0 0 0 24.5559 19.4289 -7.8280 H 0 0 0 0 0 0 0 0 0 0 0 0 25.8109 19.2418 -9.0234 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1191 18.1527 -7.7986 N 0 0 0 0 0 0 0 0 0 0 0 0 20.9735 17.5102 -7.8905 C 0 0 0 0 0 0 0 0 0 0 0 0 20.9153 16.7152 -9.0045 N 0 0 0 0 0 0 0 0 0 0 0 0 19.7892 15.8734 -9.4023 C 0 0 1 0 0 0 0 0 0 0 0 0 18.8276 16.5423 -10.3727 C 0 0 1 0 0 0 0 0 0 0 0 0 18.2126 15.3414 -11.0638 C 0 0 1 0 0 0 0 0 0 0 0 0 19.3991 14.3895 -11.1789 C 0 0 2 0 0 0 0 0 0 0 0 0 20.2765 14.6936 -10.0700 O 0 0 0 0 0 0 0 0 0 0 0 0 20.1808 14.5693 -12.4727 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2620 13.6538 -12.4804 O 0 0 0 0 0 0 0 0 0 0 0 0 22.2773 13.6276 -13.7634 P 0 0 2 0 0 0 0 0 0 0 0 0 23.4235 12.6927 -13.4434 O 0 0 0 0 0 0 0 0 0 0 0 0 22.5443 15.0454 -14.2206 O 0 5 0 0 0 0 0 0 0 0 0 0 21.3095 12.9028 -14.8625 O 0 0 0 0 0 0 0 0 0 0 0 0 21.1004 11.3228 -15.2231 P 0 0 1 0 0 0 0 0 0 0 0 0 20.9601 10.5878 -13.9071 O 0 0 0 0 0 0 0 0 0 0 0 0 19.5388 11.3608 -16.0270 N 0 0 0 0 0 0 0 0 0 0 0 0 18.4366 9.9821 -15.7625 P 0 0 0 0 0 0 0 0 0 0 0 0 17.7886 9.7578 -17.1251 O 0 0 0 0 0 0 0 0 0 0 0 0 19.3551 8.8500 -15.3133 O 0 5 0 0 0 0 0 0 0 0 0 0 17.4832 10.4882 -14.6846 O 0 5 0 0 0 0 0 0 0 0 0 0 19.2515 12.1533 -16.6138 H 0 0 0 0 0 0 0 0 0 0 0 0 22.1524 10.9038 -16.2276 O 0 5 0 0 0 0 0 0 0 0 0 0 20.5715 15.5860 -12.5365 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5368 14.3708 -13.3308 H 0 0 0 0 0 0 0 0 0 0 0 0 19.0909 13.3400 -11.0777 H 0 0 0 0 0 0 0 0 0 0 0 0 17.2311 14.7523 -10.2107 O 0 0 0 0 0 0 0 0 0 0 0 0 16.8689 13.9939 -10.6930 H 0 0 0 0 0 0 0 0 0 0 0 0 17.7289 15.5808 -12.0163 H 0 0 0 0 0 0 0 0 0 0 0 0 17.8754 17.3432 -9.7030 O 0 0 0 0 0 0 0 0 0 0 0 0 18.3574 18.0829 -9.2931 H 0 0 0 0 0 0 0 0 0 0 0 0 19.3677 17.1661 -11.0963 H 0 0 0 0 0 0 0 0 0 0 0 0 19.2898 15.5683 -8.4538 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1548 17.5794 -7.1869 H 0 0 0 0 0 0 0 0 0 0 0 0 24.1186 16.2317 -12.0670 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 4 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 26 31 1 0 0 0 0 24 32 1 0 0 0 0 18 33 1 0 0 0 0 18 34 1 0 0 0 0 16 35 1 0 0 0 0 15 36 1 0 0 0 0 36 37 1 0 0 0 0 15 38 1 0 0 0 0 14 39 1 0 0 0 0 39 40 1 0 0 0 0 14 41 1 0 0 0 0 13 42 1 0 0 0 0 11 43 1 0 0 0 0 1 44 1 0 0 0 0 M CHG 4 22 -1 29 -1 30 -1 32 -1 M END > <Chemgauss3> -47.468628 > <Chemgauss3 Steric> -47.913109 > <Chemgauss3 Desolvation> 29.329695 > <Chemgauss3 Acc> -28.113005 > <Chemgauss3 Donor> -0.772210 > <Chemgauss3 Metal> 0.000000 $$$$

2 1

Help about install Chimera
by Fang, Shunming (NIH/NIDDK) [C] 24 Aug '09

24 Aug '09

Hello, There, I just install the latest version of Chimera in my Fedora 11 machine. When I tested it after I installed it, it just show segmentation fault. I don't know why. The chimera version is chimera-1.3-linux.exe (32bit). my mahchine is 64bit. When I install this 32bit chimera, I also install all package it required. I really appreciate your help, Shunming

2 1

Chimera --send command
by cdlau＠ucsd.edu 24 Aug '09

24 Aug '09

Hi, I am currently running chimera remotely on a computer using "ssh" commands. I have been using the "chimera --send" command to send cmd and python scripts to a computer running chimera. I was wondering if it were possible for me to run 2 or more instances of Chimera on a computer and control which instance of Chimera the "--send" script is executed by. Thanks for your help, Chris

5 5

Script
by Damien Larivière 20 Aug '09

20 Aug '09

Dear all, Sorry for this simple question : Is there an example of how to use a command in a script ? For example, the command "open" is described in the documentation but I confess (i'm not a programmer) that I do not understand how to use it for opening a pdb file in a specific directory : C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb I would like to create a script that does : 1/ Open a PDB file (dock0001.pdb) 2/ open Tools - Structure analysis - Sequence 3/ select residues 203 to 227 chain A 4/ Actions Color Red 5/ open Tools - Structure analysis - Sequence 6/ select residues 54 to 87 chain A 7/ Actions Color Magenta Many thanks for your help Damien

3 4

surftransparency
by Tom Guu 20 Aug '09

20 Aug '09

Hi, I am trying to use the surftransparecy function on a EM-map (surface), and don't seem to be able to get it to work. I read on the documentation page, is this command specific for atoms and not for an entire EM map? I know I can use show or hide for displaying EM map, just wonder what other command can make the EM map gradually disappear or appear. Thanks a bunch. Regards, Tom

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Moving atom labels
by Michael Day 19 Aug '09

19 Aug '09

How does one change the position of atom labels? For small coordination complexes the default atom labels land on the atom and it would be nice to move them as a whole or individually so they are alongside the atom ball or anisotropic ellipsoid. While I'm on the ellipsoid topic; has there been progress on overlaying axis on the ellipsoids? I know I originally asked about axis and shaded octants but after using the anisotropic option for the last month or so I notice tat there is a tremendous amount of information conveyed with just the color and shape and shaded octants may not add much information (in fact it may just confuse the issue). Your implementation of thermal ellipsoids is very, very useful! Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Problems open Amber trajectory
by Koch, O (Oliver) 19 Aug '09

19 Aug '09

Dear Chimera Team, I have a problem opening an AMBER trajectory using chimera v1.3 (2000/12/09). When I look at the frames, they show this "spider web" phenomenon: Connections between atoms that should not be there. Furthermore, I got errors throughout the whole file: "Error: line too long in:" I have a topology file and a coordinate file created using leap/ptraj from the Amber Tools 1.2. I could look at the files using vmd with the options "Amber 7 parm" for the topology file and "Amber coordinates with periodic box" for the coordinate file. Therefore, the files should not be corrupt, but, of course, I would prefer to use Chimera for visualizing... Can you give me any advice how to open the files correctly? Thanks in advance. Kind regards, Oliver Dr. Oliver Koch BioChemInformatics Postdoctoral-Fellow Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: oliver.koch(a)sp.intervet.com Phone: +49 (6130) 948 396 Fax: +49 (6130) 948 517 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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erase octant question
by Kristin Parent 18 Aug '09

18 Aug '09

Hello, I was wondering if you could help me. I am trying to visualize a 3D density map from a cryo-TEM reconstruction of a virus (ccp4 format). I would like to use the "erase octant" function (link below), but actually erase a full quarter of the map to see inside the interior. I would like to do it accurately, and not by dragging the subregions box by hand. Can you help me understand how to set the command line function in order to do this? Thanks in advance. Kristin http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

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Re: [Chimera-users] Chimera frame storage director
by Elaine Meng 14 Aug '09

14 Aug '09

On Aug 14, 2009, at 12:34 PM, Tom Guu wrote: > Dear Dr. Meng, > > This is Tom Guu from Rice University. I am using chimera to make > some animation for my virus structure, that I would like to present > at my defense ten days from today. I encountered a problem with > Chimera with the image storage issues. > > I am able to make movies, but they are generally very short, last > for a few seconds, and the frames are generally stored at a /tmp > folder. Since the /tmp folder in our computer server has quite > limited spaces, once I perform a more complex animation, errors > messages would pop up (each ppm is about 4MB and sometime that's > over 300 frames will fill up the tmp dictory). I am thinking about > storing frame files onto an external hard drive (200-300GB), which > can handle many more frames. So I go into 'movie recorder" under > which there is a "frame options". I specified the dictory for > frames to my external dirve (also clicked on "Set Input > Location"). Then re-execute my command (Open, click on cmd file > which cotains the script), well... the frames seemed to be stored > at the same /tmp location (nothing was written onto my external > drive). Is there a way that I can do to make the frames stored at > the external drive? If the frames are stored on the external > drive, is it going to affect the encoding process? > > In addition, I am also trying Chimera on my windows system > (Vista). I was able to excute the command (cmd files) without any > problem. The molecule is spinning as it should in the chimera. > However, when I opened up the encoded movie, it is just a blank > screen (with no molecule in sight). I check the directory (also > another /tmp directory), and I can see the ppm files were being > written. Then a screen popped up on my computer, C:\Program Files > \Chimera\bin\ffmpeg.exe The screen was on for at lesat 20-30 secs, > then the movie is made. However, as I said, I didn't see any movie > on my computer screen though I did find the "help command" and I > am currently don't seem to be able to find the answers to my > problems. Any suggestion? > > Thanks for such a long email. I much appreciate your help. > > Regards, > Tom Hi Tom, If you are using the movie command to record the movie, you should use the movie command options to specify the directory (for example, a command something like "movie record directory my-directory-path"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> The "frame options" in the Movie Recorder graphical interface only affect recording with that graphical interface, not with the command. However, if you *are* using the Movie Recorder to record and it seems to be ignoring your setting, please use "Help... Report a Bug" in the Chimera menu to send us a problem report. Include a description, and if you want feedback, your email address. I am not sure I understand your second issue. All I can say is that even though a movie file may appear, it takes a while for the ffmpeg program to fully create it, so you have to be patient and wait until ffmpeg is done before you can open the movie and play it back. Was the movie OK after ffmpeg was done? If not, again you may want to use "Help... Report a Bug" and include any relevant information. This mechanism also allows files to be attached to the report. Besides "help command" for commands (for example, "help movie" to see your local copy of the URL given above), the Chimera Help menu provides several routes into the documentation (including "Help... Search documentation") and you can click the Help button on most dialogs to see the corresponding manual pages. For future reference, it is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu than to me personally, unless you are including private data. This allows others to benefit from the information, and other staff to answer your question if I am unavailable or don't know the answer. Best wishes for success and triumph at your defense! Elaine ===== Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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displaying two surfaces
by Marcus Carr 14 Aug '09

14 Aug '09

I am trying to create a figure that encloses three residues in a protein in one surface and the rest of the protein in another. I put the three residues into one group using surfcat and the rest of the protein in another. When I try adjust the surface transparency, the three-residue surface all but disappears. If I set transparency to 0%, I appears normal. If I increase it even to just 1%, it almost completely disappears. It looks like wherever this three-residue surface is inside the protein surface, it only shows if the transparency of three-residue is set to 0%. All this is with the protein surface set to 50%. I'm not sure whether this list accepts attachments, but I put in screen shots of what it looks like. marcus

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Scripting with Chimera
by Lockwood, Svetlana 13 Aug '09

13 Aug '09

Hi All, Here's my problem: I need to calculate hydrogen bonds for several thousand PDB files. Chimera has nice hbonds command line command - sweet! Since Chimera was vanishing from Ubuntu, I had to switch to other available tools, i.e. Windows. After I got my python up and running and communicating with Chimera modules. Here's my very simple pseudo-idea: foreach file in the list: open PDB file construct output filename from input filename calculate & and write out hydrogen bonds using hbonds command close file end foreach Short and sweet. Except that one cannot use a command line command within python code. Command files don't work either because they do not understand python commands. Someone must have run into the same problem before me :-) Is there a way around this problem? Thank you, Svetlana

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Dr. Simon Sauve is out of the office.
by Simon Sauve 13 Aug '09

13 Aug '09

I will be out of the office starting 2009-08-07 and will not return until 2009-08-24. You can reach me at simsauve(a)yahoo.ca & 819-776-2134 (cell: 819-923-2143). In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155

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Saving session with IMOD model
by Bui Khanh Huy 13 Aug '09

13 Aug '09

Hi all, I opened an IMOD model in Chimera. After I opened a saved session with Chimera, the IMOD model disappeared. Is this because of my version (alpha 1.4 (build 26844))? Best, Huy -------------------------------- Huy K. Bui Institute of Molecular Biology and Biophysics Swiss Federal Institute of Technology (ETH Zürich) ETH Hönggerberg, HPK F7 CH-8093 Zürich, Switzerland phone: +41 1-633-2462 fax: : +41 1-633-1073 e-mail: huy.bui(a)mol.biol.ethz.ch <mailto:huy.bui@mol.biol.ethz.ch>

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command 'buriedArea'
by Harinathachari Bahudhanapati 12 Aug '09

12 Aug '09

Hi all, Could you explain the command 'measure buriedArea' ? I am trying yesterday's daily build. Could you give me an example how to use this command? I think I am mangling the command, somehow. Could you help me? Thank you very much. Sincerely, Hari

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Orientation and quaternion
by Damien Larivière 06 Aug '09

06 Aug '09

Dear all, In the attached image, two copies of the FtsZ protein (pdb 1FSZ) are displayed in Chimera. I would like to know the orientation of one copy with respect to the other one. Is there a way to get this information ? Is it possible to get a quaternion instead of a set of Euler angles ? My best regards Damien

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Q about opening two structures in the same window
by Farhana F Syed 06 Aug '09

06 Aug '09

Hello, I recently downloaded chimera and have been using to view my protein homology model - mainly to show the 2 residues that could be involved in binding to a molecule inside the cell. For that purpose, I need to be able to open the small molecule (citrate or phosphate) in the same window with protein; so I can show the small molecule binds to the specific amino acid residues. But even if I open the two together, how do I pick the small molecule and move it around where I need it? Please help. Thanks, Farhana

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loading atomic coordinates without drawing or calculating bonds
by Veysel Berk 05 Aug '09

05 Aug '09

Hello, I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms. Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations? Thanks in advance, Bests, Veysel Berk

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Re: [Chimera-users] movie making
by Eric Pettersen 05 Aug '09

05 Aug '09

On Aug 5, 2009, at 2:32 AM, Schulz-Gasch, Tanja wrote: > Dear Eric, > > your movie making recommendations were indeed very helpful. Thanks > again! Hi Tanja -- glad I could help! > I am currently preparing a show for visitors at Roche that are > interested in 3D modelling and I want to do this with > Chimera. I have alreday started scripting. However, I would like to > have breaks in the scripts in case that there are > questions. So my question is, is there a possibility to implement a > prompt in the Chimera script that waits only > the users presses 'return' or whatever and then Chimera is running > further through the script? The daily build has a few things that will help here. First, there is a "pause" command that will cause a script to pause until any key other than Escape or End is pressed. Those two keys will cause the script to abort instead of continuing. Secondly, even without an explicit "pause" command any script can be paused by hitting Shift-Escape. A second Shift-Escape will continue the script. Also, plain Escape (no Shift) will cause any script to abort. I hope the presentation goes well! --Eric Eric Pettersen UCSF Computer Graphics Lab

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Stereo 3D on 120 Hz displays
by Daniel Gurnon 04 Aug '09

04 Aug '09

Just wanted to let everyone know that its finally possible to view sequential stereo in Chimera with 120 Hz LCD displays. I just confirmed that it works with my system- here's what you'll need: An appropriate Quadro card (I have a FX 4500), with the recent 190-series driver A 120Hz 3D ready LCD screen (I have the samsung 2233RZ. The other choice is a Viewsonic model) The Nvidia 3Dvision glasses kit, which includes a USB IR emitter The latest beta driver for 3Dvision, version 1.10, found here: http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.html Note that this only works for Vista. The 3Dvision software is supposed to only support Geforce cards, but it worked for my quadro fx 4500. After installing the drivers and the hardware I opened the Nvidia control panel 3D settings and set the following options: Stereo-Display mode: "Generic active stereo (with NVIDIA IR emitter)" Stereo-enable: "Yes" Then restart your computer, and enable sequential stereo from within Chimera. The only issue so far is that the accessory software (photo viewer and 3D preview pack) that installs with the drivers won't load; instead you get a message saying your hardware isn't compatible. ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Minimize
by Alex Gawronski 04 Aug '09

04 Aug '09

Hello, I'm preparing proteins for Delphi analysis using Chimera's minimize function (from a script). However this process is very time consuming. Is using minimize necessary to get accurate results from Delphi? If not, what is necessary? I've played around with the "spec" and "freeze" parameters and they either seem to have no affect or throw an error (which I submitted as a bug). What do you suggest I do? Thanks, Alex Gawronski Carleton University

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Chimera pH
by Peter Baker 03 Aug '09

03 Aug '09

I am trying to generate models of my protein at different pH. Any suggestions as to run how to accomplish this? I do have PBD2PQR files for the different pH but I am not sure how to apply them. Thanks -pjb

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transparent ring fill, color by attribute
by Elaine Meng 03 Aug '09

03 Aug '09

On Aug 3, 2009, at 2:29 PM, Alexey V. Cherepanov wrote: > Dear Elaine, > > I have another question. On the structure, I color the atoms > according to > their attribute (in my case the chemical shift differences between the > solution and the solid state NMR). I show the residues as balls & > sticks and > fill the rings of riboses & bases. Can I show the filling (i) > semitransparent, and (ii) that it keeps the colors of the atoms > (e.g. if C1' > is blue, C2' is white and C3' is red in the ribose ring, then the > filling > should be blue close to C1, white close to C2' and red close to C3' > with the > gradient in between)? > > Many thanks in advance. > Warm regards, > > Alexey Dear Alexey, The answer to your question is mostly yes, except the color in the fill is not smoothly blended. Currently it shows a "pie slice" or wedge for each ring atom. Some tricky things: (1) the ring fill automatically matches the ring atoms, so that you cannot make the fill transparent unless the atoms are also transparent. However, you can get around that problem by opening another copy of the same structure in which the atoms/bonds are opaque. (2) the transparent ring fill must not be thick. Either it must be in the "thin" style, or if in the "thick" style, the atoms and bonds in that copy must be in the wire representation (which forces it to really be thin). Why? Because some mysterious extra bonds become visible through the transparent fill when it is thick. Example: - open your structure twice - assign your attribute (e.g. use bfactor column, or Add Charge, or Define Attribute to read your own arbitrary attribute values) --- for my example, I opened 6bna twice and will use bfactor -- - use one model to make the transparent rings and the other for whatever atom/bond display you want --- I used commands: delete solvent; rep stick -- - start Render by Attribute, move the color bars as you like; for each, click the square color well, and in the Color Editor turn on "Opacity" and adjust the "A" row (transparency). There is a "Keep opaque" option, and keep that turned on and only click Apply to test the coloring. When the coloring is how you like it, then in the "Models" list at the top of the dialog, only choose one of the models. Now do not move the coloring bars, only uncheck "Keep opaque" and click Apply again. You won't be able to see any change, but now the two models are colored the same except one has the transparency and the other does not. --- I made #0 my transparent model and #1 opaque. I colored blue->red- >yellow for increasing bfactor. - now, add thin ring fill to the transparent model, command: fill thin #0 Here is the documentation for the fillring command. Today it is only at my site (tomorrow it should show up on the "real" Chimera web site). <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/fillring.html> The fillring command (or "fill" for short) is brand new and a couple things still need fixing: - to turn off filling, use ~fill ("fill off" and "fill unfilled" are not working today) - saving a session with ring fill should be available in the next daily build Here is a picture of the result:

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Using Command Line
by cdlau＠ucsd.edu 30 Jul '09

30 Jul '09

Hi, I was wondering there was a command similar to the --geometry (feature in the system command line option (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#script)) but for the Command Line. I know there is a command "windowsize" in which the user can specify the dimensions of the chimera instance, however where the chimera instance is located cannot be specified with this command. I want to be able to use a feature similar to --geometry where I can specify X and Y offsets of the top left corner of the window from the top left corner of the screen. Thanks, Chris

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projection view for publication
by Tom Duncan 30 Jul '09

30 Jul '09

I have seen some good recent comments on settings for saving publication-quality images, but I wonder if there is a general preference (by users or or journals) for use of perspective versus orthographic projection when generating images for publication. Thanks, Tom Duncan ----------------------------------------------------- Thomas M. Duncan, Ph.D. Research Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY

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Re: [Chimera-users] domains as ellipsoids?
by Elaine Meng 30 Jul '09

30 Jul '09

On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote: > Hello Elaine, > I am writing to ask you the following: I need to define the > relative orientation of two domains of a protein, and I am not sure > about how to do it. I was thinking of approximating the domains as > ellipsoids and then calculate the angles between the axes of the > ellipsoids. I wonder if you have a better way to define the > orientation, or if Chimera can do things like calculate ellipsoids > axes and their orientation. > Regards > Stefano Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes> or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently. Please send chimera questions to chimera-users(a)cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Display all rotamers
by Eric Pettersen 29 Jul '09

29 Jul '09

In the daily build the Rotamers tool will now allow you to add multiple rotamers to a residue, using alt locs to distinguish them. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > On Dec 6, 2008, at 9:35 AM, daniel.hilger at lrz.uni-muenchen.de > wrote: > > > > I´m really sorry for my imprecise question. I will concretize it. I > > know > > the rotamer tool, but I don´t want to replace only one rotamer into > > another. I will have them all in the structure and in the according > > pdb-file. With the rotamer tool, it is only allowed to choose one > > rotamer > > out of the rotamer list before clicking "Apply". This is my problem, > > and I > > didn´t found an appropriate answer in the manual and help menu. > > Hi Daniel, > I'm sorry for misunderstanding - > > It's true that Apply only puts one copy in the structure, but if you > don't Apply and simply keep the Rotamer list dialog and choose all of > its lines, that displays all of the rotamers at the same time. Maybe > that would allow you to do what you want. The Rotamer list dialog > allows calculating clashes and H-bonds, plus selecting the rotamer > atoms so you can control their appearance with the Actions menu. > > The issue is that the structure can't have multiple indistinguishable > atoms (with the same name and residue number). We have talked about > allowing multiple rotamers to be applied to the structure by giving > them different "alternate location" ID codes, but that has not been > implemented yet. Also, some residues may have more rotamers than the > number of possible alternate location ID codes. Nevertheless we will > make sure it is on one of our requested features lists. > > So currently you can't save PDB with multiple rotamers, but you can > save/restore the session in the state where all of the rotamers are > displayed. > I hope this helps, > Elaine

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Convert the structure
by Abeer Shokeer 29 Jul '09

29 Jul '09

Hello I would like to convert the model structure that I have prepared 90 degree or in different position. Can I do that with Chimera? Thanks Abeer

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fusion proteins
by Brennal Pierre 28 Jul '09

28 Jul '09

Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren. _________________________________________________________________ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TXT_…

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FindClashes: iterative input feeding
by Anna Feldman-Salit 27 Jul '09

27 Jul '09

Dear Users and Developers, I'm interested in using a FindClashes option for a large set of files. It is about finding clashes between a small ligand and enzyme which are found at different conformational stages (more than 10000 each). How can one do it iteratively? I understand this is a scripting or could it be that such an application already exists? Thanks in advance. Regards, Anna

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Removing buried substructures
by Brian & Lanie Grech 27 Jul '09

27 Jul '09

Hi everyone The EM map I am currently working on contains hidden buried substructures and I want to remove these substructures from the map, leaving only the outer layer. Because the map I am working on is very complex, I am finding it difficult to remove the buried substructures using the Volume-eraser Tool. Consequently, I would greatly appreciate any advice on how to remove the buried substructures, without removing the outer layer. Thanks Brian

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wrl to spider or mrc format
by Pierre-Damien COUREUX 23 Jul '09

23 Jul '09

Hello everyone, I'm trying to use this skeleton hand (http://www.cc.gatech.edu/projects/large_models/hand.html) as a teaching tool in electron microscopy. I'm only able to open the file in the wrl format and I was wondering if there is an easy way in chimera to convert that file into a density spider or mrc format. So I can import it and make projections in spider for example. I tried to find on the web a free procedure to convert that wrl, without any success. If you have a clear protocol about how to do that, that would be great Thank you in advance for your help Pierre-Damien COUREUX

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Re: [Chimera-users] [chimera-dev] small suggestion regarding savepos
by Eric Pettersen 23 Jul '09

23 Jul '09

Hi JD, I think you're right: closing a session should clear saved positions. In tomorrow's build that's what will happen. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote: > Dear all, > > I see that when I close a session, the savepos list continues > containing the poses I defined for my anterior session. May be that > is something you want to have this way, but I was wondering if the > savepos (with an option for example) could list only the poses for > the working session. > > All the best, > JD > > > > > Dr. Jean-Didier Maréchal > Lecturer > Computational Biotechnological Chemistry @ Transmet > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Matlab script for reading volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, The matlab script on the MRC file format specification web page at http://ami.scripps.edu/software/mrctools/mrc_specification.php was not written by us. But that appears not to be the script you are referring to since it merely reads MRC grid size and data values and does not read the origin, cell size, or cell angles. The Chimera code that reads an MRC map is in Python and included in the distributions: chimera/share/VolumeData/mrc/mrc_format.py It uses other Chimera modules (Matrix and VolumeData) so it can't be used on its own. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard Date: 7/23/09 8:22 AM > Dear Tom, > > It seems Voxel information in Volume Viewer is different from that by reading > .mrc map data. > > For example, > I opened "emd_1080.map" and saved it as "emd_1080.mrc". > > In volume viewer, > Origin index = 50, Voxel size = 2.7, Cell angles = 90. > > But if I use matlab script you linked, > Origin = -1022951423, Cell size = 1132920833, Cell angle = 1119092736 > > Could you let me know how to convert values from .mrc data to those shown in > volume viewer? > > Thank you. > > Best regards, > Do-Nyun Kim. > >> -------- Original Message -------- >> Subject: Re: [Chimera-users] save map as ascii >> From: Do-Nyun Kim >> To: Thomas Goddard >> Date: 7/21/09 7:24 AM >>> Dear Tom, >>> >>> Thank you for your nice reply. >>> Can I get some example code in python? >>> I don't need to write it down as text files, but I want to read values in >>> density map. >>> >>> Thank you for your help. >>> >>> Best regards, >>> Do-Nyun Kim. >>> >>> >>> Quoting Thomas Goddard <goddard(a)cgl.ucsf.edu>: >>> >>>> Hi Do-Nyun, >>>> >>>> Chimera does not write volume data in any ascii file format. >>>> Text formats are much slower to read the files are much larger so >>>> EM maps are almost always in binary. It is not hard to read the >>>> MRC/CCP4 binary formats. Here is the specification. >>>> >>>> http://ami.scripps.edu/software/mrctools/mrc_specification.php >>>> >>>> You can use some Python code in Chimera to dump maps as text files. >>>> If there is a strong reason for doing that let me know and I'll >>>> provide some example code. >>>> >>>> Tom >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [Chimera-users] save map as ascii >>>> From: Do-Nyun Kim >>>> To: chimera-users(a)cgl.ucsf.edu >>>> Date: 7/20/09 1:33 PM >>>> >>>>> Dear Chimera staff, >>>>> >>>>> I'm trying to get the map density data like voxel coordinates and >>>>> density values >>>>> at each voxel from .map files in EM database. >>>>> >>>>> Is there any way to get these data using Chimera? >>>>> >>>>> Or can I save it as an ascii file such that I can read it? All map >>>>> files seem to >>>>> be saved as binary files. >>>>> >>>>> Thank you for your consideration. >>>>> >>>>> Best regards, >>>>> Do-Nyun Kim. >>>>>

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Finding specific voxels in volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, Do you mean you want to find grid indices of volume data points inside a surface? or on (near) a surface? If it is a contour surface the problem is simpler since that just amounts to values above or near the contour level. Chimera doesn't have any capabilities to export lists of volume grid indices so this will require writing some code. It may be quite simple using a Python script in Chimera, but I'd have to know precisely what you need. Export Scene includes surfaces but not values at volume data grid points. The exported file is for graphical rendering -- it does not dump the underlying data. Please direct future questions to chimera-users(a)cgl.ucsf.edu instead of directly to me unless confidential information is included. This will allow others to benefit from the answer. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 7/23/09 7:37 AM > Dear Tom, > > So, now I can easily read and right maps, but I have one more question. > > When I "Export Scene" the surface mesh from a map, how are coordinates > determined? It seems the density map itself does not have coordinate > information. > What I actually want to know is coordinates of voxels in density map "in > current > scene" such that I can figure out which voxel of the density map contains a > point in the surface mesh. > > Thank you for your help. > > Best regards, > Do-Nyun Kim. > > > Quoting Tom Goddard >> Hi Do-Nyun, >> >> The interpolate.py script on the Chimera Python scripts web page >> >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts >> >> shows how to get volume data values interpolated at specific points in >> a volume data set. It uses trilinear interpolation from 8 nearest >> grid points. >> >> More details about the volume data objects are in the Python code >> distributed with Chimera: >> >> chimera/share/VolumeViewer/volume.py >> >> >> Tom

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hydrogen bonds
by Bala subramanian 22 Jul '09

22 Jul '09

Friends, I want to see the hydrogen bond between only side chains & only main chain. 1) I want to know if there is any easy way to do this in chimera 2) What is the default distance and angle used in chimera for calculating the hbond. I see that distance tolerance is 0.4 and angle tolerance is 20. Do these values mean default distance and angle. Thanks, Bala

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mmaker - superposing two structures based on a subset of a chain
by Andrea Rossi 21 Jul '09

21 Jul '09

Dear Chimera Team, I was wondering if it is possible to superpose two structures based on a subset of a chain (a domain for example). I tried the command: mmaker #0:1-100.H #2:1-100.h but Chimera doesn't seem to take into account the residue selection. Superposing according to a subset of a chain is particularly useful when the chain is formed by two or more domains and the domains are connected by a flexible linker (as in the case of antibodies). I can provide more specific examples if needed. Andrea

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save map as ascii
by Do-Nyun Kim 21 Jul '09

21 Jul '09

Dear Chimera staff, I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database. Is there any way to get these data using Chimera? Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files. Thank you for your consideration. Best regards, Do-Nyun Kim. -- Do-Nyun Kim, Ph.D. Laboratory for Computational Cell Biology & Biophysics Department of Biological Engineering Massachusetts Institute of Technology

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depth cueing
by Gabor Papai 21 Jul '09

21 Jul '09

Dear all, I am using Chimera alpha verion 1.4 (build 28110). Whenever I want to save an image on white background with white (or no color) depth cueing and I push the save as button (with supersample 3x3) the depth cueing changes to black. I can change it back to white, but it happens again when I try to save the image. How can I save image with white depth cueing? Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.fr

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icosahedral cage
by Kristin Parent 17 Jul '09

17 Jul '09

does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

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chimera crash in windows vista
by justin oppenheim 17 Jul '09

17 Jul '09

Hello: When I invoke chimera, it crashes with the message: "chimera failed abnormally; the exit code was 1. Use the --debug ...." Then when I execute the "chimera debug" from the list of all the installed progems, I get (in a prompt windows): Traceback (most recent call last): File "C:\Program Files\chimera\share\_main_.py, line 65, in (module) value=chimeraInit.init(sys.argv) File "C:\Program Files\chimera\share\chimeraInit.py", line 361 in init tkgui.initializeGUI(exitonquit,debug_opengl) TypeError:initializeGUI() takes exactly 1 argument (2 given) Return code: 1Press return or enter to to exit What can I do now. Please help! Thanks,JO

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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