- Chimera-users - RBVI Mailing Lists

Structural alignment of a protein-ligand complex with other ligands only
by N.R. Jena 09 Jul '10

09 Jul '10

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?

2 1

Best density map contour level
by Thomas Goddard 08 Jul '10

08 Jul '10

Hi Maria, Unfortunately I don't think your procedure for setting the contour level will work very well. The problem is that the isosurface is not just the outside surface of the capsid. Usually the virus genome has lower density then the protein capsid so there contour surface may show the virus as hollow, or maybe layers of RNA/DNA will appear. So the expected volume is not going to be the volume of a solid ball. There are no well accepted standards for how to set the contour level when showing EM maps. On the other hand there probably is no "right" answer. A good level for looking at the protein capsid will be different from a good level for looking at the genome packing. If a capsid feature of an icosahedral virus does not appear at all 60-fold symmetric locations then symmetry averaged maps will show lower density and you will need a lower contour level to see such features. In practice I believe people analyzing map primarily choose the contour level by eye that best suits their analysis. Tom > Hi Tom, > > Thank you very much for your help. > I'll measure the radius of my 2 d images afterwards I'll use the radius to calculate the volume of my virus and finally > set the contour level so that this volume is enclosed. > > Thanks a lot, > Maria > > >> Hi Maria, >> >> Chimera shows the volume data as an "isosurface" meaning all points >> on the surface are at a specific map value. That map value is called >> "level" in the volume viewer dialog. The values in a map (volume data >> file) determined by electron microscopy are often not normalized in any >> way -- useful values could be 10000 or 0.1 depending on the map. For >> x-ray maps it is common to normalize so that standard deviation over the >> unit cell is 1.0. In EM there no unit cell so the standard deviation >> would depend on how big a box surrounded the virus density -- so this is >> not as useful a normalization. There is no standard accepted EM map >> normalization that I know of. If you knew the expected volume occupied >> by the structure you could set a contour level so that the surface >> encloses that volume. Here's an explanation of how to do that in Chimera >> >> >> http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… >> >> More often you just visually choose a level that you believe gives a >> surface matching the envelope of the proteins in the structure. The map >> mean, standard deviation and root mean square value can be calculated >> with menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> Tom >> >> >> >>> Dear Chimera users, >>> >>> I'm using Chimera to inspect my calculated density maps of viruses. In >>> order to compare different tree d reconstructions I would like to know >>> what the 'Level' value in Volume Viewer dialog means. At present I'm using >>> the level value 1 but I'm not sure if this is correct. >>> >>> Could you please give me some advice how to define the right contouring >>> threshold to present my data in order to inspect it? >>> >>> Thank you for your help, >>> >>> Maria L. >>> >>

1 0

Alternative to the model panel
by Varela, Lawrence Rocco 07 Jul '10

07 Jul '10

Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more). I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets. Is there an alternative to using the model panel? Like for example writing to file all the info that displays in the model panel including most importantly the model ids? Thanks in advanced, --Rocco

2 1

structural alignment
by Bala subramanian 07 Jul '10

07 Jul '10

Friends, I have 10 conformations of the same RNA molecule obtained from 5 separate MD simulations. Now to compare the conformations, I want to make a structural alignment of these conformations and make an alignment map ( something like multiple seq. alignment for protein ) so as to show residues (or residue positions) that higher flexibility among these ten conformations. What is the best way to do it in Chimera. Thanks, Bala

2 4

Parameters choice for match->align and quality assessment
by compchem compchems 06 Jul '10

06 Jul '10

Dear Chimera developers, great thanks to you for possibility to work with your very useful program. I am new in structural alignment studies and have some questions about parameters in match->align. My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues. First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case. Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me. Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure). I am sorry for long letter and thanks for your attention to my problem. D. Yegorov.

2 3

(no subject)
by Maria Ingrid Liebl 06 Jul '10

06 Jul '10

Dear Chimera users, I'm using Chimera to inspect my calculated density maps of viruses. In order to compare different tree d reconstructions I would like to know what the 'Level' value in Volume Viewer dialog means. At present I'm using the level value 1 but I'm not sure if this is correct. Could you please give me some advice how to define the right contouring threshold to present my data in order to inspect it? Thank you for your help, Maria L.

2 1

movie panel
by Susan Tsutakawa 02 Jul '10

02 Jul '10

Dear Users List, I apologize for these novice questions. I looked in the archives and could not find it. How do I get a MD molecular movement panel if I accidentally close it or I start a new session? I made a morph and I can see it on the model panel. Another very novice question is how do I delete a pdb in my model panel. Thank you in advance. Sincerely, Susan

2 2

Chimera Installation - NOVELL SUSE Enterprise Linux Desktop 11 (64bit)
by Madhumita Pattanayak 01 Jul '10

01 Jul '10

Request you let me know, whether the following specification will support the installation of Chimera: Operating System Novell SUSE Enterprise Linux 11 (64 bit) Processor Intel® Core?2 Duo Processor E8400 Chipset Intel® Q43 Express Memory (RAM) 4 GB PC-3-10600 (1333 MHz) DDR3 SDRAM Memory Graphics ATI Radeon HD 3470 256MB Appreciate an early reply in this regard. Many thanks for your help. Regards, Madhumita Senior Research Fellow CCMB, Hyderabad India "The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium."

2 1

renumber model IDs
by Dougherty, Matthew T 24 Jun '10

24 Jun '10

There are a number of times I would like to change the model ID numbers. Sometimes it is because a researcher gives me a session file that has sequences like monomer-b, monomer-d, monomer-a, monomer-c; or sometimes when I got an easy sequence to memorize (monomer-a, monomer-b, monomer-c, monomer-d), I do a colorzone split map that causes sequence names to comeback in a different order (monomer-b, monomer-d, monomer-a, monomer-c). Is there a way using commands to maintain better ID order?

1 0

Re: [Chimera-users] structure based sequence alignment
by Eric Pettersen 24 Jun '10

24 Jun '10

Hi Sonya, On Jun 24, 2010, at 7:39 AM, Sona Vasudevan wrote: > Hello Eric, > > Thanks for all the great features you have added in the last couple > of years since I was last in touch with you. This is a fantastic tool! Thanks! Glad you like it. > I need some help with the alignment editor. > > I am trying to import an alignment in fasta format (fasta aligned) > (see attached). The alignment as you can see has three structures. I > use Load structures from the sequence > window and it brings in all the chains corresponding to teh > structures. It does, but there's a subtlety here that I should point out. The first two sequences in the alignment are for 1XVA, chain A and chain B. Chimera opens two copies of 1XVA and associates one copy with each sequence, but it associates chain A in both, since the sequences of the two chains are identical. It doesn't really look at the sequence name to try to figure out which chain to associate, just how well the sequences match and in this case they both match perfectly. By hovering the mouse over the sequence name you can see which structure/ chain it is associated with. To change the association of the second sequence to use chain B, you need to go to the alignment's Structure menu and choose "Associations...". Thus will bring up a panel showing the association of each structure to a sequence. Change the association of "1xva (#1)" from "chain A" to "chain B" and then click OK. > I then use Matchmaker to align them. I have a few questions: > > 1. Does the match maker use the info from the imported alignment > since the structures are already aligned? In other words is the > structural alignment I am seeing the saem as that was imported. No. MatchMaker is its own tool and doesn't use any open alignments. After all, you could have several alignments involving those structures open. If you want to superimpose the structures based on your alignment, use the alignment's own "Structure->Match" menu item. That brings up a dialog offering a variety of options as to how to carry out the match. I like using the "Iterate" option, but it's totally up to you. > 2. Is there a way to just output the superposed co-ordinates without > the chains that are not being used? There are probably several ways. One that comes to mind is to click on one of the alignment's "Consensus" letters to select all the residues in that column. Then click into the graphics window and hit the up-arrow key to expand the selection to the entire chain. Then either choose Select->Invert or hit right-arrow to invert the selection -- now the unused chains are selected. Actions->Atoms/Bonds- >delete will delete them. You can then write out what's left. Keep in mind that if you want to get model 2's coordinates as superimposed with model 0's original coordinates (for instance) then make sure to use the "relative 0" option in the "write" command or check the "Save relative to" option in the Write PDB dialog and choose model 0. Or you could just write out all models current coordinates. They will all differ from their originals, but they will be superimposed. > 3. Looks like I can add sequences to the alignement. Can I add a > fasta file with many sequences? No. It is on my to-do list but I haven't gotten to it yet. I'll open a feature-request ticket in our Trac database with you on the recipient list so you'll know when it gets implemented. Sorry! > Thanks so much! I have alignment files for 100 families which are > high-qualityas they were manually aligned with Cn3d and I would like > to import them into chimera for further analysis. > > Thanks so much for your time! You're welcome! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Paint a pseudobond....
by Yasser Almeida Hernández 24 Jun '10

24 Jun '10

Hi... I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera? If it does, how would be the Python API code? Thanks ;) -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 1

Question about attribute assignment file
by Peng Ni 24 Jun '10

24 Jun '10

Hi, I am trying to use the define attribute function. However, the attribute assignment sheet I generated cannot be read. It reports: "Line 1 of file is either not 'name: value' or is missing initial tab". I cannot spot anything wrong in my txt file, which is also attached in the e-mail. I'd greatly appreciate it if you could help me fix this problem. Regards Peng

2 1

Lost hydrogens when saving mol2 file
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera. Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers. Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option. When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed. How do a save multiple models in a combined MOLECULE section without loosing any hydrogen atoms? Thanks :-) Rocco

2 3

PDB
by Dougherty, Matthew T 23 Jun '10

23 Jun '10

Hi, When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera. Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed? Matthew

2 4

Grouping Molecules
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

Is there a way of grouping molecules in Chimera? Here is my situation. I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation. Rocco

2 1

Fwd: Chimera 3-D viewing
by Eric Pettersen 21 Jun '10

21 Jun '10

Forwarding Ed Pate's question (below) to this list, in the hope that someone who actually knows the answer can chime in! --Eric Begin forwarded message: > From: Edward Pate <edpate(a)hotmail.com> > Date: June 19, 2010 2:39:09 PM PDT > To: <pett(a)cgl.ucsf.edu> > Subject: Chimera 3-D viewing > > Hi Eric: > > I am looking into getting a new workstation for Chimera. In the > past, we have gotten CRT displays in order to do 3-D visualization. > Could you recommend other display options that are available now and > that users have been happy with? Is a CRT still the best option? > > Thanks for the help. > > Ed

3 2

vop binning
by Katrina Lexa 21 Jun '10

21 Jun '10

Hello - Is the volume data (vop) code available somewhere? Particulary the code for binning electron densities? I'm interested in looking at how chimera handles xplor files since I want to find the density of solvent at the edges of my grid. I would love to try to play with the volume code in order see if it can be done through chimera. Thank you, Katrina

2 3

Re: [Chimera-users] Chimera -RMSD
by Eric Pettersen 21 Jun '10

21 Jun '10

On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote: > Dear Eric, > > I am using Chimera v1.4. When aligning 2 or more structures, it > gives the > RMSD as a bar graph. Is it possible to get the RMSD value for each > residue? > > Thanks > Raj Hi Raj, I'm guessing the "RMSD as a bar graph" is the RMSD header at the top of the Multalign Viewer tool. You can save the header values to a file with the "Headers->Save..." menu entry at the top of the tool. This will save the RMSD value for each alignment position to a file. This may or may not be useful for you since the residues associated with each alignment position aren't indicated in the file. Alternatively, each residue involved in the Multalign Viewer RMSD header calculation gets a "mavRMSD" attribute assigned to it. You can save these attributes to a file by using the "File->Save Attributes..." menu of the Render By Attribute tool (available in the Depiction and Structure Analysis tools menus). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Error running chimera
by Christian Hesketh 21 Jun '10

21 Jun '10

Hi there, I have been able to use Chimera many times in the past, but now when I try to run it, a dialog box pops up and I get get any further. In fact, it seems to be spawned infinitely and I cannot close it. Here is the message: "Class DBPuppet.AC_KEY_ERROR'> Can't open web info file for reading". I don't know what has changed on my system to cause this, it was working fine a week ago. Does anyone have any ideas? I am using the most stable production version right now. My operating system is Windows Vista. Thanks in advance, Christian

2 1

total sum of a map
by Mario Dejung 21 Jun '10

21 Jun '10

Hi all, I try to multiply two maps in chimera. At the moment my workflow is the following: *open my two maps in chimera and try to fit map into map... *then I use "vop resample #1 inGrid #2" to set the same orientation *after this step, I convert the mrc files to Imagic and do a total-sum *what I get is one volume. Isn't there a way to do this in chimera? Thanks to all for any suggestions. Kind regards Mario

2 1

Rendering solid objects and POVRAY
by Mario J. Borgnia 16 Jun '10

16 Jun '10

Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks -- +---------------------------------+ | 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 | +---------------------------------+

4 3

Open dialog box
by Rocco Varela 15 Jun '10

15 Jun '10

Is there a way to change the look-and-feel of the GUI open dialog box? Every time I try to open a file using the File>Open option in the GUI menu I'm faced with the problem of not being able to see the entire file names in the file navigator window. Enlarging the size of the open dialog box doesn't seem to resolve the issue. -Rocco

2 1

Re: [Chimera-users] dock prep multiple models
by Eric Pettersen 14 Jun '10

14 Jun '10

On Jun 14, 2010, at 1:22 PM, Francesco Pietra wrote: > Eric: > Thanks. Headache adding hydrogen atoms (just as you mentioned addH) > with my present system. Neither CHIMERA nor REDUCE were able to treat > ASH/ASP HIP/HIE etc as I know from experiments, and software for pKa > simulation also dropped. But it may be my fault. As per the AddH documentation you should be able to get the protonation states you want if you specifically know those states beforehand: Protonation States AddH aims to generate protonation states reasonable at physiological pH. For example, hydrogens are not added to the phosphodiester moieties of DNA and RNA. By default, aspartic acid and glutamic acid sidechains are assumed to be negatively charged, while arginine and lysine sidechains are assumed to be positively charged (although other states can be attained). Two chemical moieties are treated as ambiguous at biological pH: imidazoles such as histidine sidechains; histidine protonation states can be specified by the user or guessed by the method terminal phosphates (the third ionization); if one P–O bond is at least 0.05 Å longer than the others around that same phosphorus atom, that oxygen will be protonated Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected as needed. For example, extra hydrogens can be deleted, and atom types can be edited (before hydrogen addition) with setattr or Build Structure. That last part could probably use an example. Let's say you know that the asparagine which is residue 39 in chain A should have atom OD1 protonated. Changing the atom type to O3 (from O2-) [before AddH] would accomplish that: setattr a idatmType O3 :39.a@od1 If you don't know specifically which oxygen should be protonated, this may not be a big help. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > > As to the dockprep with either multiple pdb file, or single files > followed by "cat", it seems to me now that the latter is advantageous, > One can combine single-molecule mol2 files at will, and modify one or > more mol2 files without repeating the whole calculation. > > francesco > > On Mon, Jun 14, 2010 at 8:29 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote: >> >> With the combined pdb file, does dockprep operate on single >> molecules >> one after the other, so that it will not encounter obstacles even for >> many (more complex) ligands? >> >> I think this will be okay. Chimera ignores sibling submodels (e.g. >> #0.2 is >> a "sibling" of #0.1) when adding hydrogens so you will be okay if >> all your >> ligands come from one file. >> --Eric >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >

1 0

dock prep multiple models
by Francesco Pietra 14 Jun '10

14 Jun '10

Hi: I always docked different molecules to the same receptor molecule per molecule, by using dockprep in chimera. Is it possible with dockprep to provide DOCK6.4 a single file containing mol2-type data for a number of different molecules to dock to the same receptor? That is, circumventing submission to the ZINC database server. I tried to get mol2 from a small list of molecules, methane and ethane, getting wrong charge (-1) for methane. If adjusted to zero, antechamber fails. The file was ATOM 1 C MTH 1 -0.370 -0.262 0.000 1.00 0.00 ATOM 2 H MTH 1 0.743 -0.262 0.000 1.00 0.00 ATOM 3 H MTH 1 -0.741 -0.787 0.909 1.00 0.00 ATOM 4 H MTH 1 -0.741 -0.787 -0.909 1.00 0.00 ATOM 5 H MTH 1 -0.742 0.787 0.000 1.00 0.00 MODEL ATOM 1 C ETH 1 -0.757 -0.113 -0.004 1.00 0.00 ATOM 2 C ETH 1 0.757 0.113 0.004 1.00 0.00 ATOM 3 H ETH 1 -0.998 -1.202 -0.006 1.00 0.00 ATOM 4 H ETH 1 -1.234 0.342 0.895 1.00 0.00 ATOM 5 H ETH 1 -1.225 0.343 -0.907 1.00 0.00 ATOM 6 H ETH 1 1.225 -0.343 0.907 1.00 0.00 ATOM 7 H ETH 1 1.234 -0.341 -0.895 1.00 0.00 ATOM 8 H ETH 1 0.998 1.202 0.006 1.00 0.00 ENDMDL Thanks francesco pietra

3 5

Adding Partial Charges
by Nancy 14 Jun '10

14 Jun '10

Hi All, I am trying to add charges to nicotinamide adenine dinucleotide (NAD+) using UCSF Chimera; the total charge on this molecule should be -1 (assuming the ionization of NAD+ at pH ~7.0, see attached figure). When I add Gasteiger charges, the total charge sums up incorrectly to 0, even though the net charge specified in the drop-down box is -1. However, using the "AM1-BCC" method, the net charge correctly sums up to -1. The charge model used is "Amber ff99SB". I have also noticed that the partial charges on individual atoms assigned when using the "AM1-BCC" method are generally of greater magnitude compared to charges assigned using the Gasteiger method. I am wondering why the Gasteiger method assigns an incorrect net charge in the case of NAD+. The mol2 structure code (with incorrect Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy ============================================================================ @<TRIPOS>MOLECULE NAD.mol2 70 74 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C1 -1.4117 5.8700 -3.4377 C.2 1 LIG1 -0.0471 2 C2 -0.2808 5.1989 -2.9922 C.2 1 LIG1 -0.0472 3 C3 0.0698 5.2540 -1.6463 C.2 1 LIG1 -0.0021 4 N1 -0.7125 5.8930 -0.7233 N.2 1 LIG1 -0.2845 5 C4 -1.7621 6.6431 -1.1880 C.2 1 LIG1 0.0105 6 C5 -2.1590 6.6215 -2.5315 C.2 1 LIG1 0.0510 7 C6 -3.3433 7.3892 -2.9991 C.2 1 LIG1 0.2416 8 O1 -3.7255 7.3875 -4.2002 O.2 1 LIG1 -0.2721 9 N2 -4.0978 8.1475 -2.0847 N.3 1 LIG1 -0.3250 10 O2 0.0324 4.4339 0.9916 O.3 1 LIG1 -0.3484 11 C7 -1.0355 3.6965 1.6402 C.3 1 LIG1 0.1165 12 C8 -1.4243 2.4599 0.8071 C.3 1 LIG1 0.1276 13 O3 -0.4100 1.4351 0.9207 O.3 1 LIG1 -0.1602 14 P1 0.8613 1.4216 -0.0633 P.3 1 LIG1 0.5624 15 O4 2.0180 2.1020 0.5580 O.2 1 LIG1 -0.3429 16 O5 0.5634 2.0116 -1.3891 O.3 1 LIG1 -0.3429 17 O6 1.1223 -0.1529 -0.1877 O.3 1 LIG1 0.0575 18 P2 0.0541 -1.2893 -0.5527 P.3 1 LIG1 0.5624 19 O7 -1.1823 -1.2052 0.2607 O.3 1 LIG1 -0.3429 20 O8 0.6340 -2.6390 -0.3765 O.2 1 LIG1 -0.3429 21 O9 -0.2208 -1.0077 -2.1109 O.3 1 LIG1 -0.1602 22 O10 -2.0844 -2.0838 -4.0533 O.3 1 LIG1 -0.3483 23 C9 -1.7580 -0.6726 -3.9721 C.3 1 LIG1 0.1165 24 C10 -1.4291 -0.3206 -2.5098 C.3 1 LIG1 0.1276 25 N3 -5.5165 -1.9977 -1.1853 N.2 1 LIG1 -0.2341 26 C11 -5.3009 -1.7637 -2.4944 C.2 1 LIG1 0.0912 27 N4 -4.1259 -2.3733 -2.8716 N.3 1 LIG1 -0.2445 28 C12 -3.5825 -3.0679 -1.8327 C.2 1 LIG1 0.1583 29 C13 -4.4622 -2.7976 -0.7674 C.2 1 LIG1 0.1418 30 N5 -2.5159 -3.8010 -1.6563 N.2 1 LIG1 -0.2186 31 C14 -2.2518 -4.3018 -0.4707 C.2 1 LIG1 0.1192 32 N6 -3.0604 -4.0697 0.5431 N.2 1 LIG1 -0.2228 33 C15 -4.1365 -3.3442 0.4336 C.2 1 LIG1 0.1340 34 N7 -4.8438 -3.2010 1.5627 N.3 1 LIG1 -0.2849 35 C16 -2.1891 4.7099 1.7524 C.3 1 LIG1 0.1128 36 C17 -1.4568 6.0605 1.7533 C.3 1 LIG1 0.1256 37 C18 -0.3444 5.8071 0.7094 C.3 1 LIG1 0.1560 38 C19 -3.0362 0.0509 -4.4501 C.3 1 LIG1 0.1128 39 C20 -3.9053 -1.0632 -5.0633 C.3 1 LIG1 0.1257 40 C21 -3.5098 -2.2874 -4.2107 C.3 1 LIG1 0.1588 41 O11 -2.9991 4.5200 2.9209 O.3 1 LIG1 -0.3874 42 O12 -0.8413 6.3227 3.0256 O.3 1 LIG1 -0.3858 43 O13 -3.5425 -1.3145 -6.4282 O.3 1 LIG1 -0.3858 44 O14 -2.7472 1.1126 -5.3700 O.3 1 LIG1 -0.3874 45 H1 -1.6809 5.8357 -4.4909 H 1 LIG1 0.0632 46 H2 0.3396 4.6461 -3.6934 H 1 LIG1 0.0636 47 H3 0.9656 4.7572 -1.2733 H 1 LIG1 0.0793 48 H4 -2.2796 7.2615 -0.4632 H 1 LIG1 0.0801 49 H5 -4.8503 8.7190 -2.4374 H 1 LIG1 0.1458 50 H6 -3.7587 8.2854 -1.1465 H 1 LIG1 0.1458 51 H7 -0.6981 3.4004 2.6380 H 1 LIG1 0.0660 52 H8 -1.5845 2.7299 -0.2407 H 1 LIG1 0.0645 53 H9 -2.3510 2.0430 1.2095 H 1 LIG1 0.0645 54 H10 -0.9095 -0.4615 -4.6296 H 1 LIG1 0.0660 55 H11 -1.2870 0.7565 -2.4090 H 1 LIG1 0.0645 56 H12 -2.2603 -0.6329 -1.8739 H 1 LIG1 0.0645 57 H13 -5.9324 -1.1833 -3.1491 H 1 LIG1 0.1018 58 H14 -1.3609 -4.8928 -0.3242 H 1 LIG1 0.1064 59 H15 -4.6910 -3.8437 2.3366 H 1 LIG1 0.1259 60 H16 -5.8375 -2.9879 1.5154 H 1 LIG1 0.1259 61 H17 -2.8150 4.6581 0.8568 H 1 LIG1 0.0659 62 H18 -2.1232 6.8857 1.5028 H 1 LIG1 0.0675 63 H19 0.5295 6.4594 0.8618 H 1 LIG1 0.0853 64 H20 -3.5627 0.4623 -3.5840 H 1 LIG1 0.0659 65 H21 -4.9700 -0.8302 -5.0011 H 1 LIG1 0.0675 66 H22 -3.6913 -3.2429 -4.7274 H 1 LIG1 0.0854 67 H23 -3.4491 3.6578 2.8683 H 1 LIG1 0.2107 68 H24 -0.3142 7.1392 2.9619 H 1 LIG1 0.2108 69 H25 -3.3167 -0.4612 -6.8446 H 1 LIG1 0.2108 70 H26 -3.5789 1.5634 -5.6077 H 1 LIG1 0.2107 @<TRIPOS>BOND 1 1 45 1 2 1 2 ar 3 1 6 ar 4 2 46 1 5 2 3 ar 6 3 47 1 7 3 4 ar 8 4 5 ar 9 5 48 1 10 5 6 ar 11 6 7 1 12 7 9 am 13 7 8 2 14 9 50 1 15 9 49 1 16 10 11 1 17 10 37 1 18 11 35 1 19 11 51 1 20 11 12 1 21 12 53 1 22 12 52 1 23 12 13 1 24 13 14 1 25 14 17 1 26 14 16 1 27 14 15 1 28 17 18 1 29 18 21 1 30 18 20 1 31 18 19 1 32 22 40 1 33 22 23 1 34 23 24 1 35 23 54 1 36 23 38 1 37 24 21 1 38 24 56 1 39 24 55 1 40 25 29 ar 41 25 26 ar 42 26 57 1 43 26 27 ar 44 27 28 ar 45 28 30 ar 46 29 33 ar 47 29 28 ar 48 30 31 ar 49 31 58 1 50 31 32 ar 51 32 33 ar 52 33 34 1 53 34 60 1 54 34 59 1 55 35 36 1 56 35 61 1 57 35 41 1 58 36 37 1 59 36 62 1 60 36 42 1 61 37 4 1 62 37 63 1 63 38 64 1 64 38 44 1 65 38 39 1 66 39 65 1 67 39 43 1 68 39 40 1 69 40 27 1 70 40 66 1 71 41 67 1 72 42 68 1 73 43 69 1 74 44 70 1 @<TRIPOS>SUBSTRUCTURE 1 LIG1 1 GROUP 1 LIG 1 ============================================================================

2 1