To gain better insight into how the fluctuating protein environment influences the site energy ordering of the chromophores in PE545 light-harvesting antenna system, we carried out quantum mechanics/molecular mechanics (QM/MM) calculations along the molecular dynamics (MD) trajectory. The Polarized Protein-Specific Charge (PPC) scheme was adopted in both the MD simulation and the QM/MM calculations for a more realistic description of the protein environment. The deduced site energy ladder calculated using ZINDO/S-CIS agrees well with the best model extracted from experiments by a simultaneous fit of the steady-state spectra and transient absorption spectra. Three combinations of charge schemes were compared to elucidate how the protein environment modulates the site energy of chromophores. The result indicates that the multiroles that the protein environment is playing, for instance, by fine-tuning of the conformation of chromophores or by specific pigment-protein interactions, are both crucial for site energy arrangement. Furthermore, we investigated the effects of individual environments and found that the polar residues and water molecules contribute most to the energy shifts.