The excitation energies of blue- and yellow-fluorescent proteins (BFP and YFP) were evaluated by the method of configuration interaction singles and perturbative doubles CIS(D) in conjunction with the fragment molecular orbital (FMO) scheme. Three amino acid residues were identified to be contributive to the excitation energy by the so-called pairwise procedure. Under the multilayer treatment (MFMO) with these selected residues, the best estimates for BFP and YFP were obtained as 3.36 and 2.53 eV, respectively, where the second-order self-energy shift was utilized to modify the CIS(D) expression [Mochizuki, Chem. Phys. Lett. 472 (2009) 143]. These values were comparable to the respective experimental values of 3.21/3.25 and 2.41 eV. (C) 2011 Elsevier B. V. All rights reserved.