Using a quantum chemical approach, we report the dependence of the wavelength of chlorophyll a (ChM), namely the Qy absorption band, on the location of a negatively charged group. Among 14 chlorophyll molecules, the energy difference between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained using the density functional theory (DFT) method (Delta EHOMO-LUMO) correlates strongly with the experimentally measured absorption wavelength. A negative charge being located along the Qx transition dipole moment makes the Chla absorption wavelength longer, because it destabilizes the HOMO and decreases Delta EHOMO-LUMO. Based on the analysis presented here, it seems most likely that in the water-oxidizing enzyme photosystem II, polar and charged groups, D1-Met172, D1-Thr179, and Cl-1, which exist along the Qx transition dipole moment of the accessory Chl(D1), increase the absorption wavelength of Chl(D1) with respect to that of Chl(D2). Not only the distance between Chl(D1) and charged/polar groups but also the orientation of the groups with respect to Chl(D1) plays a key role in increasing the Chl(D1) absorption wavelength.