1. A non-transitory computer-readable storage medium storing a program that causes a computer to perform a procedure comprising: calculating coordinates of a point with reference to structure data that includes coordinates of vertices of a plurality of polygons representing a three-dimensional structure; storing the calculated coordinates of the point in a memory device as a piece of information relating to the structure data; producing a graph including graph nodes corresponding to the point and vertices of the three-dimensional structure, first graph edges corresponding to structure edges connecting the vertices of the three-dimensional structure, and second graph edges corresponding to other edges connecting the point to the vertices of the three-dimensional structure; acquiring characteristic quantities of the structure data based on the produced graph; and searching for a first three-dimensional structure similar to a second three-dimensional structure specified in a search query by comparing first characteristic quantities corresponding to the first three-dimensional structure with second characteristic quantities corresponding to the second three-dimensional structure, wherein the calculating coordinates is performed based on second-degree moment of inertia of the three-dimensional structure, with respect to a center of mass and a principal component direction of the three-dimensional structure.