The fluorescence dynamics of isoalloxazine (Iso) in AppA were analyzed in order to elucidate the mechanism of photoinduced electron transfer (ET) in a photosensing flavoprotein, blue-light sensing using flavin (BLUF) of AppA. The ET parameters contained in Kakitani and Mataga ET theory (KM theory) were determined by a non-linear least squares method using atomic coordinates obtained by molecular dynamic simulation (MD). The ET rate from Tyr21 to the excited state of isoalloxazine (Iso*) was slightly slower than that from Trp104 to Iso*. It was found that frequency factor ν₀ in the ET process from Tyr21 to Iso* was 16 times higher than the one from Tyr35 in a non-photosensing flavoprotein, flavin mononucleotide binding protein (FBP). Transferred charges and interaction energies in the systems of Iso*-Gln63-Trp104 and Iso*-Gln63-Tyr21 were obtained by a semi-empirical molecular orbital method (MO). Forty configurations of these systems by MD structures at 50 ps time intervals were geometrically optimized with the PM3 method. The mean charges at Iso* over 40 configurations were -0.254 ± 0.057 in the Iso*-Gln63-Trp104 system and 0.016 ± 0.002 in the Iso*-Gln63-Tyr21 system. Mean interaction energies among Iso*, Gln63 and Trp104 or Tyr21 were -11.7 ± 1.02 kcal/mol in the Iso*-Gln63-Trp104 system. The extraordinarily high ν₀ value in ET from Tyr21 to Iso* was elucidated by the H bond chain from Tyr21 to Iso* through Gln63, though MO results by PM3 could not elucidate it.