The organic molecule adsorption sites in a Sr2CaCu2Oy (0((Sr))212) half unit cell upon water molecule intercalation were estimated by simulation using Molecular Orbital PACkage (MOPAC) program. For water molecules, the unit cell was elongated with increasing the number of molecules. Upon four water molecules intercalated between the two SrO layers, the upper Sr atom moved along the c-axis by 1.49 A. This value was smaller than but comparable to the experimentally obtained elongation of half of the c-parameter. The primary reason of the elongation is the repulsive force between Sr-H atoms in the two SrO layers. For ethanol and acetone molecules, stable intercalation sites were not found in the 0((Sr))212 crystal. These results coincided to the experimental results, which did not show intercalations. It was concluded that MOPAC can reproduce the organic molecule intercalation phenomena in oxide crystals.