The coordinates of the last simulation frame were used as starting points for the subsequent stage of the ABFE calculation, unless the ligand had moved too far from the binding site's key residues, indicating an unstable pose. In particular, a pose was considered unstable if, in the final snapshot of the MD equilibration simulation, no ligand atom was within 4.5 Å of a selected atom in the parent co-crystal structure. For BACE1, this is the nitrogen of the 6WUP ligand that is closest to the two catalytic Asp residues. For CDK2, this is the nitrogen of the 3DDQ ligand closest to the molecular fork formed by Glu81 and Leu83. For thrombin, this is the amide nitrogen of the 5JZY ligand near His57 of thrombin's catalytic triad. The best-scoring 5 poses that passed the filter were sent to the next stage, free energy simulation.