Geometry optimization and calculation of molecular vibrational frequency
In order to calculate molecular vibrational frequency, the structure of a chemical must first be geometrically optimized. Since each provided theoretical 3-D conformer SDF is not at an energy minimum and may not represent the lowest energetic form in a vacuum, solvent, or a binding pocket, each SDF file of a ligand molecule underwent conversion to a single low-energy conformation using the general atomic and molecular electronic structure system (GAMESS) program package [14]. Restricted Hartree-Fock (RHF) calculations using Becke's exchange and Lee-Yang-Parr's correlation functionals (BLYP) density functional theory (DFT) method with 6-31G basis set were performed to optimize the geometries of the molecules. Each result was taken as the representative conformation of the molecule, although the calculation of molecular vibrational frequency has some dependence on conformation. Each geometry optimization result was subjected to the calculation step for the vibrational frequency with RUNTYP of HESSIAN in the GAMESS program.