Nic,

We encountered this situation – see PDB ID 7MYB. We assigned the two stereoisomers to have unique residue names, unique residue numbers, and different alternate location identifiers (the A and B before the residue name below). They can have the same chain ID. The A and B alternative location IDs prevent the molecules from clashing with each other. Here is how we set it up in our case:

HETATM18364 C02AUJM B1301 -4.302 21.083 108.824 0.50 33.60 C

HETATM18365 C04AUJM B1301 -5.200 19.877 108.429 0.50 32.58 C

HETATM18366 C06AUJM B1301 -5.027 17.825 110.133 0.50 31.64 C

HETATM18367 C07AUJM B1301 -6.136 18.797 110.502 0.50 32.44 C

HETATM18368 C08AUJM B1301 -6.405 19.771 109.357 0.50 34.12 C

HETATM18369 O01AUJM B1301 -4.772 22.201 108.497 0.50 30.85 O

HETATM18370 O03AUJM B1301 -3.216 20.883 109.410 0.50 35.44 O1-

HETATM18371 S05AUJM B1301 -4.377 18.249 108.495 0.50 29.52 S

HETATM18372 C02BUJP B1302 -4.324 21.167 108.876 0.31 33.43 C

HETATM18373 C04BUJP B1302 -5.334 20.003 108.712 0.31 32.97 C

HETATM18374 C06BUJP B1302 -5.399 17.805 110.268 0.31 31.16 C

HETATM18375 C07BUJP B1302 -4.356 17.742 109.183 0.31 32.66 C

HETATM18376 C08BUJP B1302 -4.618 18.801 108.125 0.31 30.79 C

HETATM18377 O01BUJP B1302 -4.720 22.265 108.413 0.31 30.37 O

HETATM18378 O03BUJP B1302 -3.227 20.957 109.434 0.31 34.00 O1-

HETATM18379 S05BUJP B1302 -6.135 19.451 110.283 0.31 35.84 S

-----------------------

John J. Tanner 

Professor of Biochemistry and Chemistry

Associate Chair of Biochemistry

Department of Biochemistry

University of Missouri
117 Schweitzer Hall

503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280

Email: [email protected]
https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A

From: [email protected] <[email protected]> on behalf of Pavel Afonine <[email protected]>
Date: Thursday, September 14, 2023 at 10:47 PM
To: Calvin N Steussy <[email protected]>, [email protected] <[email protected]>
Subject: Re: [phenixbb] racemic ligand refinement

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On 9/14/23 21:09, Calvin N Steussy wrote:

All,

I need to refine a ligand that consists of two stereoisomers in my active site.  I have decent density and have created models for the r and s forms of the guest with separate cif files.  They have been fit independently into the active site density.  My questions are;

How to show these in the pdb file.  Separate chains?  Separate amino acids in a given chain?

How do I keep them from interacting with one another during refinement?

Creating an alt-position seems obvious but I'm not certain how to apply the different stereo restraints in that case.

I'm sure someone has solved this before but I can't seem to find that information. 

Thanks,

Nic Steussy

Purdue University.

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