Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

[Greg L. <gre...@gm...>]

Hongbin has the answer here completely correct (thanks Hongbin!).

And the reason it's CCW instead of ACW is that I say "counterclockwise" and
not "anticlockwise" :-)

-greg

On Wed, Oct 30, 2019 at 3:07 AM Hongbin Yang <yan...@16...> wrote:

> Hello Alfredo,
>
> The tag "CHI_TETRAHEDRAL_CW" means clockwise and CCW means anti-clockwise
> (I have no idea why it is coded CCW rather than ACW, but whatever ;) ).
> These chiral tags are related but not corresponding to the absolute
> chirality (R/S) defined in organic chemistry.
>
> Look at the SMILES you provided and you will find that both of the chiral
> carbons are [C@@H].
> According to the theory of Smiles in DayLight (
> https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html 3.3.3)
> > The symbol "@" indicates that the following neighbors are listed
> anticlockwise (it is a "visual mnemonic" in that the symbol looks like an
> anticlockwise spiral around a central circle). "@@" indicates that the
> neighbors are listed clockwise (you guessed it, anti-anti-clockwise).
> Then you may have realized that the tags "CHI_TETRAHEDRAL_CW" are
> corresponding to your SMILES but not the real chirality.
>
> I suggest you read the chapter 3.3.3 to understand the meaning of "chiral
> tag", then you will understand why they are not the absolute chirality.
>
> Absolute chirality depends on the chiral tag as well as the CIPRanks of
> the neighbor atoms. That is why the chirality of the two carbons are
> different while their chiral tags are the same.
>
> I am not sure if Lukas had the same question?
>
>
> Best regards,
>
> Hongbin Yang 杨弘宾, Ph.D.
> Research: Toxicophore and Chemoinformatics
> On 10/29/2019 21:14，Alfredo Quevedo<maq...@gm...>
> <maq...@gm...> wrote：
>
> Good morning,
>>
>> I am trying to manually set/change the stereochemistry of a chiral
>> center of a molecule, and I cant understand how to set the
>> CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far my
>> script does the following:
>>
>> -----
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>>
>> molecule='C[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@H](NCc2ccc3c(c2)OCO3)c2ncc[nH]2)nn1'
>>
>> molecule_smiles=Chem.MolFromSmiles(molecule)
>> chiralty=Chem.FindMolChiralCenters(molecule_smiles)
>> centers=len(chiralty)
>>
>> for i in range(centers):
>>          current_center=chiralty[i][1]
>>          print(current_center)
>>          center_to_change=chiralty[i][0]
>>          print(center_to_change)
>>
>>
>> for a in molecule_smiles.GetAtoms():
>>      print(a.GetChiralTag())
>>
>> ----
>>
>> executing the above mentioned script I can see that the molecule has 2
>> chiral centers, the first one on index 1, which is S, and the second
>> one, with index 19, which is R. Both chiral tags are set to:
>> CHI_TETRAHEDRAL_CW. now, I want to manually change the configuration of
>> index 19 to S, so I want to change its tag to CHI_TETRAHEDRAL_CCW.
>>
>> Which would be the command to set this tag and how is the index indicated?
>>
>> thanks in advance for the help,
>>
>> kind regards
>>
>> Alfredo
>>
>>
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