This is how I proceed for modified residues.

1. Generate (draw) the desired modified residue in a program such as Chemdraw or MarvinSketch, then copy it as a SMILES string.

2. Generate a cif file with phenix eLBOW, from the SMILES string. Name it as you want with 3 letter code.

4. Modify the cif file, especially the definition as a L-peptide and not as Ligand. Change the corresponding atoms to atom names such as C, N, CA, O and OXT (CB, …) as in common residues (additional atom names can remain as they are).

5. In Coot, import the new cif and the new residue. Remove the OXT atom, then change the residue number to the one to replace. It should make the binding with residues -1 and +1 automatically.

For better refinement you can fix the atom occupancy of the residue (CYS in your case) to 1 and modify the occupancy of the « bound » atoms (as a group).

Hope this way will help you.

Xavier

Le 22 janv. 2022 à 20:12, Sergio A. Sampieri <[email protected]> a écrit :

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

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