Positions of the active site residues and the Gln substrate are highly conserved in crystallographic models except for the HisFH dimer conformation composed of chains E and F from PDB 7ac8 (Figure ). There are four distinct geometric differences observed in this conformation: 1) an interfacial residue, fGln123, interacts with the bound Gln as a result of subunit closure; 2) the hVal51 amide N-H points toward the substrate carbonyl; 3) the oxyanion strand is positioned above the catalytic thiol; and 4) the reactive carboxamide of Gln is preorganized for acylation. Two truncated active site models were created from the 7ac8 14 crystallized unit of IGPS using atomic positions from chains E/F and chains C/D; the deposition authors refer to these complexes as active and inactive conformations, respectively. Residue hAla84 in chains F and D was reverted back to wild-type hCys84 with PyMol 50 by selecting the backbone-dependent side chain rotamer with the least steric clash. We will refer to these truncated models as Active and Inactive. The size and residue components of the QM model are important to consider, and informed decisions based on selection criteria remain an active area of development. Residues were selected based on interactions (Fig. ) with the substrate and biochemical relevance indicated in the literature. The ligand interaction diagrams in Figure illustrate how the C/D and E/F conformations yield different interactions with the glutamine substrate. Since the main objective of this work is to evaluate the catalytic impact of active site structural changes, we focused on building models suitable for direct comparison. Therefore, the same atoms were included in each model from the following residues: fGly121, fSer122, fGln123 and fAla124 from the HisF subunit, hGly50, hVal51, hGly52, hHis53, hCys84, hLeu85, hGln88, hGlu96, hVal140, hHis141, hThr142, hTyr143, hHis178 and hGlu180 from the HisH subunit, the Gln substrate in zwitterionic form and two conserved crystallographic waters. Hereon, all residues without a prefix are assumed to be from the HisH monomer since they are the model majority, but the HisF prefix will be kept for clarity. Amino acid side and main chains were truncated according to potential involvement in the elementary reaction steps and interactions with the substrate (see Table and text for a detailed list of included atoms, truncation scheme, and geometry optimization constraints). Each model contains 237 atoms, an overall charge of -2 and 12 constrained carbon atoms (Figure ). Geometry optimizations were performed with the rangeseparated, dispersion-corrected ωB97X-D 64 functional using the 6-31G* basis set for all C, H, and N atoms and the 6-31+G* 66 basis set for S and O atoms. Stationary point electronic energies were further refined at the B3LYP-D3(BJ)/6-311+G(2d,2p) level of theory and the default IEF-PCM implicit solvent method with internal parameters for diethyl ether (ε=4.24). Additional information is presented in the Computational Details section.