Recent experimental and theoretical studies have revealed that the excitation energy transfer (EET) can exhibit coherent characteristics in various photosynthetic systems. However, how the noisy protein environment helps to maintain the coherence has not been fully elucidated yet. Applying an all-atom nonadiabatic simulation technique will be extremely advantageous for the elucidation, as it can offer detailed views on protein-chromophore interactions. In this presentation, we will discuss the results of semiclassical Poisson bracket mapping equation (PBME) simulations on EET of the Fenna-Matthews-Olson (FMO) protein-chromophore complex. We will show that the chromophore coupling maintained by the protein scaffold is the key factor for governing the coherence. The electrostatic modulations by the protein and the related site energy dispersion have only a limited effect. Limitations and future aspects of our approach will also be discussed, together with prospects on studying other quantum mechanical events around biology.