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

摘要

The compound design apparatus (100) stably arranges the fragments (130, 140) in the active site (121) of the protein (120) arranged on the simulation space. The compound design apparatus (100) arranges a virtual single atom at a position where it does not collide with the protein (120), the fragment (130, 140) and the virtual single atom arranged on the simulation space. In the compound design apparatus (100), the interatomic distance and angle that the arranged virtual single atom forms with the virtual single atom in the fragment (130, 140) or another virtual single atom are within a predetermined range as the bond length and bond angle. If within, a bond is formed. When a virtual single atom is added to a set of three consecutive atoms including a virtual single atom in which a bond is formed, the compound design device (100) can form a chemically reasonable ring. The ring closing process is performed when the ring closing condition is satisfied.