Re: [ccp4bb] Missing double bonds in the ligand

[Robbie Joosten]

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,

Robbie

On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" <anilmarap...@gmail.com> wrote:

Dear CCP4 Users,

We are working on a ligand-bound structure and would like to look at protein-ligand interactions using Schrodinger.

Molecule structure is: 

When we load the ligand-fitted PDB file into Schrodinger, the molecule appears to be flat like it should be in the structure but it removed all the double bonds in the ligand where the above shown original molecular structure has double bonds in it.

When we load the same PDB file into pymol and look at the ligand it shows correctly

We would appreciate if any insight or suggestions for why this may be happening and how to ensure the ligand shows properly when the PDB is loaded into Schrodinger. Would this be an issue with Schrodinger software or with the PDB file?

I can be available by direct email for troubleshooting at amara...@purdue.edu.

--

Anil Kumar Marapaka, Ph.D.
Post-Doctoral Research Associate 

Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),

Purdue University, West lafayette,

Indiana-47907, USA.

Mobile 1: +1-765-409-6245 (USA)

Mobile 2: +91-995-998-5571 (India)

Email 1: amara...@purdue.edu

Email 2: anilmarap...@gmail.com

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