The algorithm requires the 3D structure of a protein with key residues making up the active site demarcated. The generation starts at the centre of geometry (COG) of the selected residues. Individual atom parameters for the protein are loaded from the CHARMM27 forcefield. No connectivity information or bond data is loaded because protein atom coordinates are only used for non-bonded energy calculations. The main steps in the generation algorithm are given below. Figures and in the supporting information (SI) contain flowcharts for the same.