Therefore, the van der Waals distance of the ovoid can be calculated based on its "radius". The "radius" of the ovoid (i) from the viewpoint of the counterpart (j) varies depending on their relative configuration (Figure ). Therefore, the intersection of the surface of the ovoid and the line connecting the centers of them was determined, and the van der Waals radius of the ovoid was calculated as the distance between the center of the ovoid and the intersection. Then, the van der Waals distance of the ovoid was calculated according to the above equation. The well depth of the ovoid was set to be 0.4 kcal/mol after numerically testing 0-1.0 kcal/mol (see Figure for detail).