The reliability of protein structure is a critical concern to grasp the insights with respect to residue-residue and residue-ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Møller-Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree-Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure.