[phenixbb] covalently linked ligand

Xavier Brazzolotto xavier.brazzolotto at chemdef.fr
Wed Apr 15 03:44:42 PDT 2020

2 solutions that I use

A first one consists in designing your residue linked to your ligand (under ChemDraw / MarvinSketch) then prepare the restraints under eLBOW (from smiles for examples). You will have to modify some atom names into the generated cif file (C, O, CA, N, CB, etc… depending of the modified residue) and above all change the nature of this molecule to L-peptide. Then you can use it in coot as a modified residue and use the modified cif file in Phenix. You can adjust the modification by tuning the occupancy of the atoms corresponding to the ligand and keep the occupancy to 1 for the atoms of the residue. Here you will have a nice covalent bond.

The second solution would be to restrain the distance between the atom of your residue and the atom of the ligand to a covalent bond (C-C distance or whatever it is). Certainly, angles should be restraint too.

> Le 15 avr. 2020 à 00:59, Muhammad Bashir Khan <mbk at ualberta.ca> a écrit :
> Hi All;
> I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix.
>  I used the 
> "  phenix.ligand_linking pdb_file_name"   commond
> It creates 
> apply_link.def
> and 
> data_link.cif
> I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand.
> Thanks for your help
> Bashir
> -- 
> ------------------------------------------------------
> Muhammad Bashir Khan, Ph.D.
> Research Associate
> Department of Biochemistry
> Medical Science Bldg.
> Lab 3-27
> University of Alberta
> Edmonton AB, T6G 2H7
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> e-mail: mbk at ualberta.ca <mailto:cbrooks1 at ualberta.ca>
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Xavier Brazzolotto, PhD
xavier.brazzolotto at chemdef.fr

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