We used two approaches to model the two zinc ions in the active site of VIM-2 to be able to evaluate their accuracy for RBFE calculations. The first approach is a restraint-based hybrid non-bonded model, where the zinc coordination bonds are replaced by harmonic restraints, as described by Li and Merz, while the rest of the protein is parameterized with ff14SB. To avoid adding a bias to the RBFE predictions, the distance between the zinc and the ligand is not restrained.