`AssignBondOrdersFromTemplate` does not copy bond stereochemistry information of terminal imine

[nielskm]

terminal-imine.pdb.txt

Assigning bond orders to the attached PDB with SMILES:[H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[nH]ccc23)C1 removes the stereochemistry of the C=N bond in the terminal imine group.

To Reproduce

from rdkit.Chem import AddHs, MolFromPDBFile, MolFromSmiles
from rdkit.Chem.rdmolfiles import MolToSmiles

smiles = "[H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[nH]ccc23)C1"
mol = MolFromPDBFile("terminal-imine.pdb", removeHs=False)
refmol = AddHs(MolFromSmiles(smiles))

result_mol = AssignBondOrdersFromTemplate(refmol, mol)

result_smiles = MolToSmiles(result_mol)

Expected behavior The result_smiles from the code above should have the stereochemistry information from the original SMILES.

Configuration (please complete the following information):

• RDKit version: 2023.03.2
• OS: Ubuntu 22.04
• Python version: 3.9.18
• Are you using conda? Not for installing RDKit
• If you are not using conda: how did you install the RDKit? PyPI

Additional context I need the stereochemistry information to be assigned in order to use the OpenFF Toolkit Molecule class (constructed with Molecule.from_rdkit). If I add b2.SetStereo(b.GetStereo()) to the AssignBondOrdersFromStereo function, this problem dissapears. But the SMILES produced by RDKit still lack the isomer information.

[mattwthompson]

Are you sure that SMILES fully defines the stereochemistry? OEChem thinks the nitrogen in the non-aromatic ring is a stereocenter

# problematic atom is ..................... *
smiles = "[H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[nH]ccc23)C1"

[Lzh-Function]

I have the same issue. It seems that only E/Z isomerism cannot be assigned.

My Configuration :

• Python version : Python 3.11.9 (using conda)
• OS : Ubuntu 22.04.3 LTS
• RDKit version : 2024.03.5 (from conda-forge)

[radifar]

ui3.pdb.txt

I got the same issue with ligand UI3 from PDB file 1QST. I have already extracted the ligand UI3 and the file is attached.

Using the command

smiles_ui3 = r'[H]/N=C(/c1ccc2ccc(c(c2c1)c3cnn(c3)S(=O)(=O)C)OC)\N'
ui3 = Chem.MolFromSmiles(smiles_ui3)
ui3_manual = Chem.MolFromPDBFile("ui3.pdb")

corrected_ui3 = Chem.AssignBondOrdersFromTemplate(ui3, ui3_manual)

gave me the error message ValueError: No matching found