We report a molecular-mechanics (AMBER*) study on the Henry–Michaelis complex and the corresponding acyl–enzyme adduct formed between imipenem (1), a transient inhibitor of β-lactamases, and Enterobacter cloacae P99, a class C-β-lactamase. We have examined the influence of the structural configuration of the functional groups in the substrate on their three-dimensional (3D) arrangement at the active site, which was compared with those adopted by typical penicillins and cephalosporins. Our results confirm that the carboxy group of the antibiotic plays a prominent role in the binding of the substrate to the active site, and that it activates Ser64 through interaction with the phenolic OH group of Tyr150. The binding of imipenem to E. cloacae P99 increases the distance between Tyr150 and Ser64 due to the presence of a hydrophobic Me group in the (R)-1-hydroxyethyl substituent at C(6). This, together with the 3D arrangement of its carboxy group, leads to an interaction with the active site in a manner that hinders H+ exchange between the nucleophile in Ser64 and its basic activator, the phenolic group of Tyr150.