Re: obchiral

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Re: obchiral

Nick England
Florbela Pereira,

The OBchiral tool returns the information which was in the input file.
It does not calculate R/S configuration.

Since no stereochemistry was defined in the input file the chiral
information is only available from the 3D co-ordinates. The
ChiralVolume of is 8 for atom 4, and -8 for atom 6. This depends on
the ordering of the atoms in the file. For a mol file the convention
for stereochemistry is based on the order of the atoms, except for
hydrogens which always count as having the highest number. The
Clockwise/Anti-Clockwise flag is used by the SMILES format, molv3000
etc (CFG=1, @@ etc) but won't be set by an xyz style input file.

Each file format defines chirality in a different way and obchiral
will only report to you how it was recorded in that file. Conversion
of clockwise/anti-clockwise to R/S is not a one-to-one mapping and
will depend on the file format used.

I am not aware of a way of using openbabel to calculate R/S
stereochemistry. If you use babel to convert to the inchi format the
+/- is nearly calculated in the same way as R/S, but not quite in all
cases.

I hope this helps,

Nick England

On 20 January 2010 19:26, Florbela Pereira <[hidden email]> wrote:

> Hello,
>
> I´m using the obchiral tool to assign R/S configuration. However, I had
> doubts in the output of the obchiral. What is the meaning "Atom4refs"? Is
> it the ordered list that is entered into a Molfile based in PLR (Petrarca,
> Lynch and Rush) priorities?
> And the parity value is assign 1, when the four ligands in the ordered
> list are arranged clockwise. Otherwise it is 0. It is true?
>
> Thank you.
> Regards,
>
> Florbela Pereira
> Assistant Researcher
> Chemistry Department
> Faculty of Science and Technology
> New University of Lisbon
> Portugal
> Tel: +351212948300 (ext 10994)
> Fax: +351212948550
>
>
>
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