[Chimera-users] Create oxime functional group

Wikel, Jim jimwikel at iu.edu
Wed Oct 4 13:40:54 PDT 2017


Thank you Eric and Elaine for the prompt responses.  They were helpful and I am proceeding with my project.    I had entered the structure without going through the smi23d web service.  I had assumed the web service was gated by the IU network and I am working on this off site.  I failed to even try it.  Thanks.

jim
________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, October 4, 2017 1:54 PM
To: Wikel, Jim
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Create oxime functional group

Hi Jim,
If you’re processing the molecule on its own (e.g. not trying to minimize it in a binding site), the short answer is to not minimize it in Chimera.  If you got it via the smi23d web service from Indiana University, e.g. Chimera command

open smiles:CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1

… then the molecule has already been through geometry optimization with MMFF94.  The Chimera Reply Log reports whether the Indiana U web service was used (and when I tried the SMILES string above, it was).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html#fetch>

(MMFF94 is mentioned in the paper linked to the smiles fetch description)

In Chimera, if you minimize that fetch result without adding further hydrogens or changing atom types, the result seems bad (large deviation from planarity).  If you change the atom types to N2 as Eric said, I expect it to be better-behaved.  Nevertheless, I would not minimize it at all unless analyzing it within some larger system.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 4, 2017, at 9:25 AM, Wikel, Jim <jimwikel at iu.edu> wrote:
>
> Hello,
>
> I recently had difficulties with creating a particular structure in Chimera.  The SMILES is depicted below.  The problem is I have not been able to represent the oxime portion of the molecule.  I have tried to reset atomtypes, redrawing the structure, adding and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution.   Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization.  I am puzzled and suspect I may be doing fundamentally wrong.  Any advice would be helpful.
>
> CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1​
>
> Thanks you.
> jim
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