MD simulations of all systems were performed using the same protocol: each replica for each system was first energy minimized using the steepest descent algorithm for 100 steps, followed by 900 steps of conjugate gradient minimization, with a 100 kcal mol -1 Å -2 restraint applied to all solute (protein and substrate) atoms. The complete system was then heated from 50 to 300 K in an NVT ensemble, using a simulated annealing protocol, in which the system was able to reach 300 K in the first 100 ps of heating. This was continued for a total of 1 ns, using a 1 fs time step, and Langevin temperature control, with a collision frequency of 1 ps -1 . The 100 kcal mol -1 Å -2 restraint applied to all solute atoms was retained until this point in the equilibration, and then reduced from 100 to 10 kcal mol -1 Å -2 in subsequent equilibration steps. Following this heating, a second energy minimization and heating were performed using the prior protocol, with positional restraints applied to just the solute heavy atoms. During the subsequent equilibration steps, the restraints were progressively reduced from 10 to 1 to 0.1 kcal mol -1 Å -2 , until the heavy atom restraints were removed in the final step. The final systems with only this distance restraint applied were then equilibrated for a final 1 ns in an NPT ensemble (300K, 1 atm), using a