If not otherwise specified, the QM system consisted of the copper ion, the entire aminoterminal His1 and the neighbouring Thr2 residue, the phenol ring of Tyr164, the imidazole ring of His78 and His147 and the carboxylate and amide side chains of Glu148 and Gln162, respectively. A representative example of the QM system is illustrated in Fig. . It should be noted that histidine residues have three probable protonation states, denoted as HIE (N !2 protonated), HID (N δ1 protonated) or HIP (both nitrogens protonated). His147 takes several different forms during the mechanism and we generally follow the mechanism in ref. 37: when acting as a proton donor we employ the HIP state (HID after the protonation event), while for the initial setup, the HIE state was chosen. When a bond is present between the QM and MM systems, the hydrogen link-atom approach was used. All residues except for the terminal His1 were capped at the C α atom i.e. the C α atom was replaced by a hydrogen atom. Two of the three glucose units of the substrate were included in the QM region as well, while the third glucose ring was described at MM level. In a few cases, also the third glucose ring was included in the QM region. Additionally, the two solvent molecules W498 and W599 close to the active site were part of the QM region. The QM system (with two glucose rings) consisted of 151-153 atoms depending on the intermediate and the protonation state of His147.