I recently did this for a covalently modified Cys. Follow these steps:

Generate a SMILES string for L-cysteine bonded the modification. Yours appears to be C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N. https://pubchem.ncbi.nlm.nih.gov/compound/262741
Input the SMILES string to PHENIX eLBOW using the graphical user interface with quantum optimization enabled to generate restraints (.cif) and coordinates (.pdb).
Use the eLBOW graphical user interface to change the atom names for the backbone atoms of the modified cysteine to the standard ones for amino acids (N, CA, C, O, CB).
Save the new coordinates and restraints.
Move the modified cysteine you saved in step 4 into the density using Coot.
Delete the extra O atom of the cysteine carboxylate and save the coordinates of the modified Cys.
Using a text editor, change the residue number and chain ID of the modified cysteine to those of the Cys in your structure. Save the file.
Using a text editor, replace the Cys coordinates of your structure with the coordinates of the modified Cys save in step 7.

In subsequent refinements, PHENIX refine should automatically incorporate the modified cysteine into the polypeptide chain, assuming you correctly renamed the atoms in step 3 and deleted the correct O atom in step 6.

John J. Tanner

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University of Missouri
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From: [email protected] <[email protected]> on behalf of Sergio A. Sampieri <[email protected]>
Date: Friday, January 21, 2022 at 10:39 PM
To: [email protected] <[email protected]>
Subject: [phenixbb] refining a covalent-bound ligand (part 2)

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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.