In this work, we have calculated several physical quantities related to two interacting semiconductor organic molecules to reveal the significance and the role of the side-chains. The molecular systems of our target are the geometry-optimized dimer systems: that consisting of two [6,6]-phenyl-C-butyric acid methyl ester molecules and that consisting of two peryline diimide-related molecules. The physical quantities shown in the present work are their relative molecular geometries, optimized energies, barycentric distances, angles between the two molecular planes, dipole moments, and electronic couplings. We have found that these physical quantities show quite different tendencies among the systems, which results from the absence/presence of the side-chains in these molecular species. It is emphasized that the presence of side-chains brings about the diversity of molecular characteristics in interacting molecules. This may point out the importance of side-chains in the various organic materials in general.