Minimum I-RMSD and L-RMSD of native-like binding modes.

I-RMSD is calculated over all heavy atoms within 5 Å of the small molecule in X-ray crystal structure. L-RMSD is calculated over heavy atoms in the small molecule. Cluster Rank is the rank order of the cluster from lowest binding energy to highest binding energy. Error describes the spatial orientation to the native binding mode if the rank 1 cluster is non-native. I = inverted binding mode, W = wrong conformation of ligand, T = Translation in Å, R = Rotation, C = Cofactors present in native which may influence binding mode. Lines in bold indicate lowest energy binding mode is native-like. Lines in italics indicate binding mode in top 10 lowest energy modes is native like. The chemical structures can be found in Figure S1.