[BUG] Conformer generation struggles with organometallics like HEM

[ljarosch]

Describe the bug
Inference queries that use organometallics such as HEM groups will run into conformer timeout problems. This is because RDKit by default cannot seem to properly handle conformer generation for such compounds.

To Reproduce

from openfold3.core.data.primitives.structure.query import structure_with_ref_mol_from_ccd_code

structure_with_ref_mol_from_ccd_code("HEM", chain_id="A")

> ConformerGenerationError: Failed to generate 3D coordinates

Expected behavior
A conformer should be generated without failure.

Additional context
Our training pipeline makes use of input sanitization by pdbeccdutils, which solves these conformer generation issues. Because of that, this issue is inference-specific.