We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.