The overall charge on this QM model is -1 but the system contains 9 fragments with non-zero charge. Small anions in the gas phase are sometimes inherently unstable (or metastable), as in the case of SO 2- 4 , and delocalization errors in DFT can exacerbate this problem. To avoid artifacts, charged residues are often neutralized in fragment-based calculations on proteins. This is not always a viable or realistic option, however, as charged side chains may be directly involved in stabilizing the protein structure or binding to a ligand (as in the present example), or may be vital to a reaction mechanism. A general procedure for enzymatic thermochemistry must admit the possibility of fragments with non-zero charge.