diff --git a/gufe/components/smallmoleculecomponent.py b/gufe/components/smallmoleculecomponent.py index 560287b1..4cdce660 100644 --- a/gufe/components/smallmoleculecomponent.py +++ b/gufe/components/smallmoleculecomponent.py @@ -175,8 +175,13 @@ def _from_sdf_supplier(cls, supp): def to_openff(self): """OpenFF Toolkit representation of this molecule""" from openff.toolkit.topology import Molecule as OFFMolecule + m = self.to_rdkit() - m = OFFMolecule(self._rdkit, allow_undefined_stereo=True) + # see openfe #278 / openff tk #1563 + Chem.Kekulize(m) + Chem.SetAromaticity(m, Chem.AromaticityModel.AROMATICITY_MDL) + + m = OFFMolecule(m, allow_undefined_stereo=True) m.name = self.name return m