The large number of carotenoid molecules within FCP complexes suggests their crucial role in the photosynthetic process of the diatoms, or its regulation on the turbulent ocean surface. The down-regulatory mechanisms of photosynthesis in diatoms are triggered by an enhanced proton gradient across the thylakoid membrane . Moreover, the presence of LHCX class proteins and xanthophyll-cycle carotenoids can potentially lead to an aggregation of FCP complexes that regulates their transition between light-harvesting and photo-protective states (down-regulation of photosynthesis). Based on classical molecular dynamics (MD) simulations, we have recently identified a remarkable flexibility in the FCP scaffold of the diatom P. tricornutum with the Chl-a 409/Fx-301 pigment pair therein to become a possible key player in the transition between different states of the FCP complex . This was later confirmed by experimental spectroscopy The present study focuses on the diatom P. tricornutum and the impact of the FCP protein matrix on the excitation energy distributions of the different Chl molecules therein. The lowest excitation energies, i.e., the Q y excitation energies, are often also termed site energies in so-called tight-binding models of the Chl network. A structural overview of the FCP complex from P. tricornutum is shown in Fig. along with its Chl network. Only very recently, an exciton Hamiltonian for this system was determined, but with the stark difference that the excitation energies were determined without taking the protein environment into account . As will be shown in this study, the effects of the protein environment on the excitation energies are, however, surprisingly large in the FCP complex and cannot be neglected. Another study looked at the shift in excitation energies upon changing the protonation state of the acrylate group in Chl-c using a QM/MM scheme . The focus of that study was rather narrow on this specific topic. None of these studies looked at the Q y excitation energies for all pigments in the FCP complex in a QM/MM fashion in comparison and the associated energy funnel. In vacuum and in organic solvents, the Q y excitation energies of the Chl-c molecules are known to be blue-shifted compared to those of the Chl-a molecules . Hence, at first sight, a fast energy transfer is expected from the Chl-c to the Chl-a pigments inside the FCP protein. This assumption agrees with earlier experimental studies where an extremely fast energy transfer from the Chl-c to the Chl-a molecules was reported to have been observed in pump-probe and two-dimensional spectroscopy experiments for the FCP complex of the diatom C. meneghiniana at low and at room temperatures .