where d is the distance between the atom of 2 distinct ligands and N is the number of atoms. From a reference docked CS conformation all 500 RMSDs can be generated from the reference viewpoint. The reference of the highest scoring ligand can be used if the grouping is strong at high score. A centroid over a set of docked ligands can be used also. But if there is a diffuse set of states in localization then more care is required. The 5 th highest scoring epitope in P197 is used in this case, and the 10 th highest is used the S197 case due to the much broadening. However, these also represent the potentially longest bound epitope in each case due to the higher scores of each in the modeled interaction. The distributions of these RMSDs for P197 and S197 are given in Figures and. Note the large difference between the 2 in the number at individual RMSD.