CT interactions between Iso* and nearby aromatic amino acids in FBP were investigated by a semiempirieal MO method. Atomic coordinates of lumiflavin as Iso, 3-methylindole as Trp, and 4-methylphenol as Tyr, used for MO calculations, were obtained from crystal, 20 NMR structures and 40 MD structures (20 ps time intervals). Geometries of Iso-Trp32, Iso-Trpl06 and Iso-Tyr35 systems were optimized by the PM3 method. The interaction energies (kcal/mol) of crystal structure were -16.9 in the Iso-Trp32 system, -7.4 in the Iso-Trpl06 system and 1.4 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of NMR structures were -16.5 ± 0.28 in the Iso-Trp32 system, -10.6 ± 0.14 in the Iso-Trpl06 system, and 0.97 ± 0.09 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of MD structures were -24.3 ± 0.19 in the Iso-Trp32 system, -10.2 ± 0.49 in the Iso-Trpl06 system, and 0.285 ± 0.037 in the Iso-Tyr35 system. CT interaction from the aromatic amino acids to Iso* was judged from negative charge at Iso*. The charge in the Iso-Trp32 system was -0.490 in crystals, -0.439 ± -0.099 in NMR structures, -0.454 ± 0.048 in MD structures. The charge in the Iso and Trp 106 system was -0.011 ± 0.004 in MD structures, but negligible in other structures. CT interactions in Iso-Tyr35 system were also negligible. The ET rate obtained with Kakitani and Mataga theory and MD decreased as the magnitude of the interaction energy decreased. Correlation between the ET rate and CT interaction in FBP was examined. The interaction energy (Y) was approximated with ln(ET rate) (X) by a function, Y = 0.0036X³ + 0.0306X² -1.7822X - 21.177.