Dear all,
I have a structure where CYS is bound to OCA (octanoic acid). I
started with Jligand and created a CYS-OCA covalent link. It then
output a CIF file (verified looks OK). Add the LINK record to PDB
file:
LINK SG CYS A 161 C1 OCA A 902 CYS-OCA
Place OCA to the model using Coot. When I now use RealSpaceRefinement,
the OCA is placed on top of CYS itself. Coot does not recognise that
OCA-CYS link but why? therefore, I just place OCA at Place it in
*reasonable* position without any overlaps.
All files are located at
https://gist.github.com/ort163/e6b8411f45e5224f7d46fc36c3324e6f
Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After
refinement, I find that the oxygen in the OCA is pointing wrongly. The
thioester bond is also NOT ideal distance (though density is good).
Is there anything wrong with my procedure? *Shouldnt* the refinement
optimise everything in OCA-CYS link?
Best
Markus
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