To elucidate the energy transfer mechanism of the PE545 light-harvesting complex, an exciton model is constructed with the full Hamiltonian obtained from structure-based calculations. The electronic couplings and spectral densities are evaluated on the basis of the site energies and transition dipole moments obtained from our recent Molecular Dynamics–Quantum Mechanical/Molecular Mechanical (MD–QM/MM) study [Tong et al., J. Phys. Chem. B 123, 2040–2049 (2019)]. The polarized protein-specific charge model is employed both in the MD simulation and in the QM/MM calculations to account for the environmental fluctuation of the protein scaffold. The energy transfer pathways are, thus, derived, which agree well with the phenomenological models based on the spatial organization of the chromophores and the experimental observations. Moreover, the simulated linear absorption spectra using the dissipaton equation of motion approach agree well with the experimental ones, and the resulting population dynamics indicates that an optimal energy transfer efficiency is reproduced.

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