I have an enzyme with an inhibitor covalently linked to a cysteine. The link is from CYS SG to an atom “CAC” in residue “DRG”. I have a .cif file that contains the geometric parameters of the ligand, AND at the bottom, information to create the link at the end. Hopefully this is self-explanatory... loop_ _chem_link.idhttp://chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name CYS-DRG CYS . . DRG . . CYS-DRG # data_link_CYS-DRG loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd CYS-DRG 1 SG 2 CAC single 1.792 0.010 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd CYS-DRG 1 SG 2 CAC 2 CAA 112.576 2.44 CYS-DRG 1 CB 1 SG 2 CAC 100.595 1.50 CYS-DRG 1 SG 2 CAC 2 HAC 108.861 1.50 CYS-DRG 1 SG 2 CAC 2 HAD 108.861 1.50 loop_ _chem_link_tor.link_id _chem_link_tor.idhttp://chem_link_tor.id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period CYS-DRG sd 1 CB 1 SG 2 CAC 2 CAA 180.00 15.0 3 On 15 Apr 2020, at 8:44 pm, Xavier Brazzolotto mailto:[email protected]> wrote: 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 mailto:[email protected]> 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 Phone: 780-492-4577- e-mail: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] Xavier Brazzolotto, PhD [email protected]mailto:[email protected] Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy. _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]