The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do
your PDB atom names match the CCD?
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You can make molecule in chemdraw or chemdraw 3d with proper bond order and
save it in sdf or .mol format or any other format compatible with schrodinger.
Schrodinger should be able to read .sdf or .mol format.
Dhiraj
From: CCP4 bulletin board on behalf of
Joel
You'll need to be more specific than ".cif" files. CIF can be used for
models, data and restraints. Read more here.
http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6
If you are referring to the restraints CIF, it is possible but I'm not sure
Does the Schrodinger software read a .cif file? The bond order should be
embedded in there.
From: CCP4 bulletin board On Behalf Of Nigel Moriarty
Sent: Friday, 8 July 2022 7:47 am
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Missing double bonds in the ligand
Further reading
Further reading
https://en.wikipedia.org/wiki/The_Treachery_of_Images
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National
Dear Anil,Bond orders are not captured in PDB files explicitly. The way bonds are shown depends on the program and possibly additional information sources (i.e. molecular restraint or topology files). So this is just a "problem" with Schrödinger.Cheers,RobbieOn 7 Jul 2022 21:00, "Dr. Anil Kumar
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