The first step of the reaction is the conjugate addition of indole 3 to enone 4 to form intermediate (Int1), via a transition state (TS1) (Scheme S1 ESIb). The second step is the product formation by the protonation reaction via a second transition state (TS2). To investigate the enantioselectivity of the Friedel-Craft alkylation, we looked to prior work using cluster models for metalloenzymes-catalyzed reactions . The same QM-cluster model technique along with density functional theory (DFT) methodology was utilised to study our reaction. Three active site models were created for analysis (Figure ESIb). Model A represents a reaction catalysed by Cu(II)-2,2ꞌ-bipyridine, in the absence of protein, whereas models B and C represent reactions catalysed by Cu(II)-bound SCP_Q111BpyAla and SCP_Q111CBpy, respectively. The computational analysis on Model A (Figure ESIb) showed that the conjugate coupling step is both the rate-determining step as well as the enantioselective step, and the formation of the keto product is most likely. This agrees well with the experimental results (Table ) as well as previous studies , therefore only the first step was modelled going forwards. To create models B and C, the indole 3 and enone 4 substrates, along with Cu(II) ions, were incorporated into the crystal structures of Cu(II)-bound SCP_Q111BpyAla and SCP_Q111CBpy, respectively. The PDB files of the apo SCP_ArMs were prepared as described in the ESIb, and 3 and 4 were docked using AutoDock Vina , with the lowest energy docked poses used for molecular dynamics (MD) simulations (see ESIb for detailed methods and results). Next, the Friedel-Craft (FC) alkylation reaction catalysed by SCP_Q111BpyAla, using ReproS,B and ReproR,B reactants as the starting structures, was calculated. Firstly, the conjugate addition of indole 3 to enone 4, where substrate 3 configuration is either proS or proR was tested. The C-C coupling transition states (TS1proS,B and TS1proR,B) of 3 with 4 leads to an intermediate for each configuration: Int1proS,B and Int1proR,B respectively. The calculated potential energy landscape for the conjugate coupling reaction for Model B is represented, along with the optimized geometric structures of these transition states, in Figure . The energy barrier for TS1proS,B (10.1 kcal mol 1 ) is lower than TS1proR,B (15.5 kcal mol 1 ) (values relative to the stable configuration ReProS,B). The transition states were characterized by an imaginary frequency i308 cm 1 and i319 cm 1 for TS1proS,B and TS1proR,B respectively. Furthermore, in transition state TS1proS,B, indole 3 has strong water bridge interactions with D88 that make it more stable than the TS1proR,B, which has a week hydrogen bonding interaction with M112. Subsequently, the transition states are relaxed to their respective intermediates (Int1proS,B and Int1proR,B), which characterized by lower relative energy values: 1.65 and 7.92 kcal mol 1 , Thus, the proS configuration pathway is energetically favoured over the proR configuration pathway. Taken together these analyses explain the preferred enantioselectivity of SCP_Q111BpyAla (e.r. 14:86, R:S) that we observed experimentally (Table ). In a similar manner, the FC alkylation reaction mechanism catalysed by SCP_Q111CBpy (Model C) was explored. The reactant complexes in both proS and proR configurations were selected as the starting structures. The optimized geometries of these reactant complexes ReproS,C and ReproR,C are represented in Figures and. The free energy of the ReproS,C structure is higher than the ReproR,C by 5.6 kcal mol -1 (∆E + ZPE), indicating that the reactant complex of model C in proR configuration shows the strongest substrate-bound pose and hence signifies the favoured reactant orientation.