We have developed a three-dimensional (3D) extension of the reference interaction site model-self-consistent field (RISM-SCF) method to treat the electronic structure of a solvated molecule. The site-site treatment of the solute-solvent correlations involving the approximation of radial averaging constitutes a bottleneck of the RISM-SCF method, and thus lacks a 3D picture of the solvation structure for complex solutes. To resolve this problem, we devised out a 3D generalization of the RISM integral equations which yields the 3D correlation functions of interaction sites of solvent molecules around a solute of arbitrary shape. In the present article, we propose a SCF combination of the ab initio molecular orbital (MO) methods and 3D-RISM approach. A benchmark result for carbon monoxide in ambient water is also presented.