Swapaa only works for standard amino acids, I'm afraid. There is a command in ISOLDE you can use for this, but keep in mind it's a little unpolished and requires some common-sense in the types of situations you should apply it to. Specifically, it doesn't take chirality into account (although it will highlight chiral centres for you to double-check), and isn't always great about choosing the placement of new atoms (I should really rewrite it using the newer ChimeraX structure-building tools). That being said, it works well enough for this case (it does place one of the oxygens in the terminal thiophosphate on top of another, but that settles out easily with energy minimisation). Also incorrectly labels the two phosphodiester phosphorus atoms as chiral (probably because the CCD template has them protonated, in which case they would be), but that's a minor thing. Anyway, once you have the GSP parameters loaded in ISOLDE, select the GTP and do: