The final populations are also very sensitive to the AFE protocol. Kaus et al. initially obtained 20:80 population estimates, after which they modified their AFE protocol to obtain a 50:50 estimate for ligand 3. MD/NCMC simulations have previously been able to correctly sample binding modes of rigid fragments 8 and side-chain rotamers. They also correctly sampled the binding mode populations for ligand 1 in this work. Hence, we believe that the population distribution we obtained using MD/NCMC for ligand 3 is correct given the force fields used in this work.