1. A method for controlling a molecular information providing apparatus that is an information processing unit including a database for retrieving a characteristic decided depending on a molecular structure on a basis of said molecular structure, said method comprising: using a processor to perform steps comprising: calculating principal axes of inertia from an atomic arrangement notation specifying said molecular structure, and registering said principal axes of inertia in a memory; determining a proximity of a moment of inertia to said principal axes of inertia; reading out data of the principal axes of inertia from said memory, and registering in said database an intermediate representation that is a coordinate transformation of atomic coordinates into a coordinate system in directions of said principal axes of inertia; and retrieving the molecular structure from said database, employing said intermediate representation, and registering the molecular structure in the memory.