The stability of the binding site in the presence of water and hydroxide was investigated with QM/MM MD simulations and compared to the starting crystal structure of VIM-2 with ligand 16 (see Fig. ). While it is clear that the phosphonate group of the inhibitor should be fully deprotonated when found near two positively charged zinc ions at neutral pH, the protonation state of the catalytic water is less obvious. Our simulations suggested that there should be one water molecule near the phosphate group which was confirmed by obtaining a stable geometry of the active site during 100 ps of QM/MM simulation that closely resembled the crystal structure (Fig. ).