On 17/09/2022 15:48, Marion Schuller wrote: > > > > Dear CCP4bb community, > > > > I am writing regarding a problem with the refinement of an isomer > ligand. I try to refine a structure which has the ligand “Carba-NAD” > (as beta isomer) bound. This ligand is already in the pdb database as > “CNA”. Although the ligand is in its beta-Carba-NAD form in the > database, it is loaded into WinCoot as alpha isomer. When generating > the restraints of Carba-NAD (via the grade server, calling it also > “CNA”), I can load and refine the correct beta isomer ligand as long > as I provide the grade-generated .cif file otherwise it would refine > it back to the alpha isomer. Yet, in the preliminary preparation of > the wwPDB X-ray validation report for structure deposition, the > message flags up that the ligand “could not be matched to an existing > wwPDB Chemical Component Dictionary definition”. With an older ccp4 > version in the background, I noticed that WinCoot would however load > the beta isomer and I am now wondering if this problem lies in the > .cif file of the new ccp4 library. Is there a possibility to > check/correct the CNA file in the current ccp4 library or would there > be a different way for solving this problem? I would be very grateful > for support and help! > > > Dear Marion,
As a rule, if a molecule has a different anomericity it has a different ligand-id (three-letter-code) in the CCD. It seems to me that you need a new entry in the CCD. It is a good thing that the wwPDB X-ray validation flags this up as a ligand that matched with and existing entry. So take the entry for CNA: https://files.rcsb.org/ligands/view/CNA.cif change the stereo_config from S to an R for C2D (I am guessing that that is the anomeric carbon atom) in the atom table. Then feed that to Acedrg. (I'd chop off the _pdbx_chem_comp_descriptor block so that that Acedrg doesn't get distracted by the out of date SMILES). Using that dictionary your refinement should be smooth sailing. Upon deposition, the wwPDB will then reward you with one of the last ever three letter codes - hooray! Paul ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
