Figure : Initial ligand conformations from docking and for the two independent runs of BACE1 active compound CHEMBL1090542. The same initial ligand pose (left) from docking relaxes to two different conformations during the MD equilibration step. In the run that yields the more favorable BFE (middle), the ligand stays close to the initial pose, whereas in the less favorable run (right) the ligand drifts away and loses interaction with the catalytic Asp residues, resulting in much less favorable binding free energy. BACE1 is shown in ribbon representation, the two catalytic Asp residues in ball and stick representation, and the ligand in licorice representation.