The key in molecular design of pharmaceutical products for drug discovery is in designing a compound that more selectively and more strongly binds to the target protein of the drug. Until recently, drug design has been mainly based on docking simulation using mostly classical force field and empirical scoring functions. However, expectations have been shifting to drug design based on quantum chemical calculation of proteins using the fragment molecular orbital (FMO) method. We will develop a bio molecule interaction simulator that contributes to “process innovation” in FMO-based drug discovery, using the ABINIT-MP/BioStation system, which was developed through the Revolutionary Simulation Software Project and the FMO-based Biomolecule Computing System Project.