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Thanks a lot for this detailed analysis. In the end we excluded molecules with undefined stereocenters (might not have been necessary according to your work here) and averaged the PMI by Median over the generated conformations (pmi.py).
Variability of PMI descriptors | RDKit blog
Which is more important, stereochemistry or conformational variability
https://greglandrum.github.io/rdkit-blog/3d/questions/2022/06/22/variability-of-pmi-descriptors.html
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