Obviously, these comparison must be done with caution because the X-ray structures correspond to the protein-inhibitor covalent complex (E-I in our schemes 2 and 3) while the B3 and B4 structures analyzed at this point correspond to the initial reactant complex E:I. Thus, differences observed in the distances defining the attack of the sulfur atom of C145 to the corresponding carbon atom of the inhibitor (C C=O or Cb for B3 and B4, respectively) are as expected. Anyway, the good overlapping of the X-ray structures and the equilibrated E:I reactant complex support the quality of our initial state structures (see