The SMILES of the "Charge Matched DUDE" set were downloaded from dudez.docking.org. The DUDE-Z set is a 43-target, enhanced version of the DUD-E set that aims to correct charge imbalance that could artificially increase active compound enrichment. This set contains 2,312 unique ligands and 69,994 unique charge and property-matched decoy molecules. These SMILES were prepared as 3D molecules using RDKit, without changing protonation or tautomeric states. For each compound, we generated 60 conformers using the ETKDGv3 26 followed by an energy minimization using the MMF94s force field, with energy cutoff=30 kcal/mol and rms cutoff=0.1 Å. When stereochmeistry was specified in the SMILES file, each stereoisomer was treated as a unique molecule. Otherwise, RDKit enumerated unspecified stereocenters, but only the top-scoring aligned stereoisomer was kept. Near-identical molecules with differences only in protonation or tautomeric states were treated as unique molecules. Molecules that failed conformer generation or minimization were discarded. This was often due to highly distorted and energetically unfavorable 3D poses, typically due to unusual specified chirality on fused ring and/or spirocylic compounds. This led to a final set of 2,267 unique ligands and 66,581 unique decoy molecules. These conformers were fed into both ROSHAMBO and Shape-it, aligning both the decoys and the ligands to the crystallographically-resolved ligand pose.