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How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

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How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Giovanni Cincilla
Hi everybody,
Starting from a certain molecule with possibly undefined sp3 stereocenters (R/S) is it possible to enumerate with OpenBabel all the possible stereisomers as different molecules?
Any help is appreciated. Thanks
Gio
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Re: How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Noel O'Boyle
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I think it's possible to write some code to do this using Open Babel.

On 8 September 2016 at 08:48, Giovanni Cincilla <[hidden email]> wrote:

> Hi everybody,
> Starting from a certain molecule with possibly undefined sp3 stereocenters
> (R/S) is it possible to enumerate with OpenBabel all the possible
> stereisomers as different molecules?
> Any help is appreciated. Thanks
> Gio
>
>
>
> --
> View this message in context: http://forums.openbabel.org/How-to-enumerate-all-possible-stereoisomers-of-a-molecule-with-a-not-defined-stereocenter-tp4659459.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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Re: How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Stefano Forli
In reply to this post by Giovanni Cincilla
Hi Giovanni,
I while ago I wrote this code in Python to enumerate all/undefined chiral centers in a
given molecule.

It works fairly well, although, you may want to check your structures if you're generating
3D coordinates, since at least the stable version of OpenBabel (2.3.2) has some issues
with chiral centers in (multiple?)rings.


S

On 09/08/2016 12:48 AM, Giovanni Cincilla wrote:

> Hi everybody,
> Starting from a certain molecule with possibly undefined sp3 stereocenters
> (R/S) is it possible to enumerate with OpenBabel all the possible
> stereisomers as different molecules?
> Any help is appreciated. Thanks
> Gio
>
>
>
> --
> View this message in context: http://forums.openbabel.org/How-to-enumerate-all-possible-stereoisomers-of-a-molecule-with-a-not-defined-stereocenter-tp4659459.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--

  Stefano Forli, PhD

  Assistant Professor of ISCB
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     fax: +1 (858)784-2860
     email: [hidden email]
     http://www.scripps.edu/~forli/

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Re: How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Giovanni Cincilla
Thank you so much Stefano. You are very kind.
I will give a try to the script, keeping an eye on the structures as you suggested.
I appreciated it very much.
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