Compound design program, compound design apparatus, and compound design method

摘要

A compound design apparatus (100) stably disposes fragments (130, 140) at an active site (121) of a protein (120) disposed on a simulation space. The compound design apparatus (100) disposes a virtual single atom at a position that does not collide with the protein (120), the fragments (130, 140), or a virtual single atom disposed on the simulation space. The compound design apparatus (100) forms a bond when an interatomic distance and an angle formed by the disposed virtual single atom and a virtual single atom in the fragments (130, 140) or another virtual single atom are within predetermined ranges for bond length and bond angle. The compound design apparatus (100) executes a cyclization process when a set of three contiguous atoms including a virtual single atom forming a bond satisfies a cyclization condition under which a chemically proper ring may be formed when a virtual single atom is added to these atoms.