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Planar amide nitrogen incorrectly flagged as _ChiralityPossible #7434

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mark-mackey-cresset opened this issue May 10, 2024 · 1 comment
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@mark-mackey-cresset
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mark-mackey-cresset commented May 10, 2024

If you have a molecule with a lactam, where the amide nitrogen is a ring bridgehead, then Chem.AssignStereochemistry incorrectly assigns the amide nitrogen as "_ChiralityPossible" even though it's flat.

To Reproduce

from rdkit import Chem
rdmol=Chem.MolFromSmiles("O=C1CCCCC[C@@H]2CN1CCO2")
Chem.AssignStereochemistry(rdmol, force=True, flagPossibleStereoCenters=True)
for atom_idx, atom in enumerate(rdmol.GetAtoms()):
   if atom.GetChiralTag() == Chem.ChiralType.CHI_UNSPECIFIED and atom.HasProp(
                "_ChiralityPossible"
            ):
       print(atom_idx)

Expected behavior
The nitrogen is not marked as potentially chiral, as it's flat.

Configuration (please complete the following information):

  • RDKit version: 2022.09.03

Additional context
This is causing issues in OpenFF, which checks that the chirality of the molecule is fully specified and refused to proceed unless it is.

@greglandrum
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confirmed

@greglandrum greglandrum changed the title Molecule has planar amide nitrogen incorrectly flagged as _ChiralityPossible Planar amide nitrogen incorrectly flagged as _ChiralityPossible May 16, 2024
@greglandrum greglandrum added this to the 2024_03_3 milestone May 16, 2024
greglandrum added a commit to greglandrum/rdkit that referenced this issue May 16, 2024
greglandrum added a commit that referenced this issue May 30, 2024
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