Unreal conformers obtained after conformer generation and UFF optimization for molecules with -NO2 groups

[longdragoon]

Describe the bug For organic molecules with -NO2 groups, conformer generation and UFF optimization will produce one conformer with O-N-O angle being 0 degree (and two O almost overlapping). And this conformer is lower in energy than all the other ones. Using the MMFF for optimization gives reasonable -NO2 structure

To Reproduce python code: from rdkit import Chem, RDLogger from rdkit.Chem import AllChem,Descriptors smiles='O=C[c]1[cH][cH]cc[cH]1' mol = Chem.MolFromSmiles(smiles) mol = Chem.AddHs(mol) AllChem.EmbedMultipleConfs( mol, numConfs=15, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True, numThreads=0, ) opt_energy = AllChem.UFFOptimizeMoleculeConfs( mol, numThreads=num_threads, maxIters=500 )

Expected behavior A lowest energy conform with O-N-O close two 120 degree should be generated

Configuration (please complete the following information):

• RDKit version: 2024.3.5
• OS: SUSE Linux Enterprise Server 15 SP4
• Python version (if relevant): 3.11
• Are you using conda? Yes, but rdkit installed with pip. Conda yml file as below:

name: rdkit_test channels:

• conda-forge
• defaults dependencies:
• python=3.11
• pip=24.2
• pycairo=1.26.0
• cairosvg=2.7.1
• pip:
  • rdkit
  • matplotlib
  • faiss-cpu

[greglandrum]

I think this was probably fixed in #7729 and should be in the 2024.03.6 release when it is available

[github-actions[bot]]

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