protein_ligand challenge: inconsistent SMILES for structure F62

[iorga]

The current SMILES for structure F62 CC(=O)N1C[C@H]2CC[C@H]1C=3C=CC=CC23 produces a highly strained and geometrically impossible 3D structure, due to in and out of plain configurations at bridgehead atoms (thanks to Christof Schwab from Molecular Networks for help in assessing this issue). Some software refuse to convert into 3D such a structure, some others neglect the stereochemistry and generate randomly one of the two possible diastereomers CC(=O)N1C[C@@H]2CC[C@H]1C=3C=CC=CC23 or CC(=O)N1C[C@H]2CC[C@@H]1C=3C=CC=CC23. Could you please investigate this issue and provide the SMILES string for the correct structure? Thank you in advance.

Best regards,
Bogdan

[davidlmobley]

Checking. @haroldgrosjean ?

[davidlmobley]

OK, so after some e-mails back and forth I have this from Harold:

I check on the database of the library (see attached) and the smile seems correct.

Otherwise, Zinc returns these two pages which correspond to the stereochemistry quoted in the email:
http://zinc.docking.org/substances/ZINC000225784236/ >CC(=O)N1C[C@H]2CC[C@H]1c1ccccc12
http://zinc.docking.org/substances/ZINC000882751699/ >CC(=O)N1C[C@@h]2CC[C@H]1c1ccccc12

But then after an exchange with a chemist at Diamond indicates the SMILES IS incorrect (problems at Enamine) and gives a correction:

The smiles given by Enamine, CC(=O)N1C[C@H]2CC[C@H]1C=3C=CC=CC23. gives an incorrect molecule (unless they have magic chemists)

...

In any case, this is the smiles you want (CC(=O)N1CC2CCC1c1ccccc12), replace the wrong one in the repo.