Hi all, hope this message finds you well.

As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand.

The link shall be made between a carbon atom that is double bonded to an oxigen

“SMILES C1=CC=C(C=C1)C=O” and the SG group of a Cys residue.

I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different aproaches during refinement, (Automatic Linking parameters, Atom selection,  acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”).

I readed in the phenixbb that this was solved by changing the nature of the ligand (http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html), but is not the way I would like to follow.

Any suggestions or ideas would be greately appreciated, thanks a lot for your time. Stay safe.