Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bimetallic Mg(II)/Zn(II) enzyme, isopentenyl diphosphate isomerase, to an inhibitor built up of a trianionic diphosphate and of a cationic ethyldimethylammonium (EDMA) moiety. The analyses are performed on the protein recognition site, which totals 13 residues, as well as on some 'mutants' in which one selected residue is removed at a time. They are also carried out for the individual recognition sites, namely, EDMA, Mg(II), and Zn(II). Comparisons are done with ab initio quantum chemistry (QC) results on all considered sites, with different basis sets and at different levels of correlation. The SIBFA computations reproduce the evolutions of the QC interaction energies in the recognition site and its 'mutants'. For such sites, small (<2-3%) relative errors are found after the BSSE correction is done. Such close agreements can conceal, however, some shortcomings found in the individual binding sites, which QC energy decomposition analyses can identify.