Method and apparatus for storing and processing molecular information

To provide a molecular information providing system that allows the molecular information to be shared by providing high precision information without depending on the format of atomic arrangement notation from a terminal unit. The molecular information providing system of the invention has the terminal units 12 to 16 including molecular structure input/output means, and a molecular information providing apparatus 18 connected via a network 10 to the terminal units 12 to 16 and including a database 32 storing a molecular structure, an intermediate representation generated from the molecular structure, and a characteristic decided depending on the molecular structure. The molecular information providing apparatus 18 comprises a coordinate system transforming part 40 for calculating the principal axes of inertia from an atomic arrangement notation specifying the molecular structure, and registering in the database 32 an intermediate representation that is a coordinate transformation of the atomic coordinates into a coordinate system in the directions of the principal axes of inertia, and a retrieval executing part 46 for retrieving the molecular structure stored in the database 32, employing the intermediate representation.