An unusual intermolecular carbon-carbon short contact, observed previously in the crystal structure of the copper complex of pyridoxal-5-phosphate-pyridoxamine-5-phospate Schiff base, was investigated from a standpoint of quantum chemistry by DFT calculations with plane wave basis sets. The DFT-optimized structure qualitatively reproduced the short contact (2.6-2.8 angstrom) of the intermolecular carbon-carbon pairs for the dimer of the copper complexes in the unit cell, compared to that (similar to 2.3 angstrom) of the X-ray diffraction data. By the occupied and unoccupied orbitals, the dimer showed the in-phase and out-of-phase interactions along the direction of the intermolecular distance. The dimer of the copper complexes was confirmed as the stable intermediate between nonbonding and sigma-covalent bonding by the electronic energy curve along the distance of the monomers.