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 <yanyangh...@163.com> 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<maquevedo....@gmail.com> > <maquevedo....@gmail.com> 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 >> >> >> _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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