The biological assembly and FASTA sequence for each entry was downloaded from the PDB website. When alternative locations or ANISOU records were available, the first coordinates were used. Co-crystallizing ligands and ions were removed manually except Zn and Mg ions. Mg ions were only kept for catechol O-methyltransferase (COMT) structures. Missing residues were added to each structure using the Modeller python package 41 by treating the incomplete sequence as a template and aligning it to the full sequence provided by the FASTA. All structures were protonated at a pH of 7.0 using the EnzyHTP 34 package and ligands were protonated using the Molecular Operating Environment (MOE) software package. Ligands missing heavy atoms were replaced with idealized models found in the PDB's chemical library.