From a set of 47 ligands given to us by our OpenEye Scientific collaborators, we chose to study a smaller subset of 12 ligands (Fig. ). Here, we chose ligands based on the overall size and number of rotatable bonds. Particularly, we were interested in only studying small and rigid fragment molecules as we expected to observe more binding mode transitions during our simulations, due to their size and rigidity. The molecule set ranged from 133.13 to 156.73 Figure : Truncated SEH protein structure (C-domain only) with the the docking site is highlighted (blue) in a mesh representation. We divide the full cavity into two sub-cavities denoted by left and right. The sub-cavity division is best denoted at the two loops marked as A and B in the figure. In the SEH apo protein structure, point A is closest to residue VAL381 and point B is closest to residue VAL499. We treat each sub-cavity separately in our analysis to better resolve binding modes within each sub-cavity.