[Chimera-users] Create oxime functional group

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 4 10:54:56 PDT 2017

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).

(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 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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