[phenixbb] refining a covalent-bound ligand (part 2) (try 2)

[Sergio A. Sampieri]

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 approaches 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 greatly appreciated, thanks a lot for
your time. Stay safe.

-- 
“I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of
errors.”
John J. Holland


Biól. Sergio Aguirre Sampieri
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20220122/ede281c7/attachment.htm>