To prepare the parameters for covalently linked 3, the ligand and C197 (atoms SG, CA, CB, HB1-3) residues were obtained from PDB ID 6B95. CA in C197 was changed to a hydrogen, and the CYS was renamed to CYX. The PDB file was converted to mol2 format using antechamber and the AM1-BCC charge method, with a neutral charge. The atom types in the mol2 file were set as follows: SB was set to S, CB to CT and HB1-3 to ha. The force field modification file was generated using parmchk2 and the parameter file was generated using tLeAP. The information corresponding to the Cys197 residue was removed from the parameter file, also modifying connectivity and atom number entries.