After adding missing heavy and hydrogen atoms, the FCP structure from P. tricornutum (pdb:6A2W) was considered as a rigid model in a first step. Then, a QM/MM optimization was performed on an equilibrated FCP model that included the thylakoid membrane and aqueous phases as designed at neutral pH in our previous study . We have determined the Q y excitation energies for the individual Chl molecules based on the crystal structure conformation and the QM/MM-optimized geometry. The chlorin ring of the Chl-a molecules contains three unsaturated and a saturated pyrrole ring, whereas in the case of Chl-c molecules the chlorin ring includes four unsaturated pyrrole rings. Moreover, the so-called "phytyl tail", which is commonly found in chlorophyll molecules of plants and bacteria, is not present in Chl-c molecules. In addition, an acrylic group is connected to the chlorin ring of the Chl-c molecules. These structural differences between Chl-a and Chl-c molecules are depicted in Fig. . Chl-c than for Chl-a molecules . In our calculations, the Q y states have been identified based on their transition dipole moment orientation and direction. In case of Chl-a molecules, the NB-ND direction was considered as the direction of the transition dipole moment (see Fig. ), whereas for Chl-c molecules the NA-ND direction was considered in accordance with the DFT/MRCI results as shown in the SI (see Fig. ). The selected Q y state had the highest transition dipole moment strength as well as oscillatory strength along the timedependent trajectory in line with the expected properties of the Q y state. The Q y state is usually the first excited state (S 1 ) for the Chl-a pigments. For the Chl-c molecules, however, the Q y state jumps between the first (S 1 ) and second (S 2 ) excited states. An example for the behavior of the Q y state for Chl-a and Chl-c molecules is shown in Fig. . Fig. depicts the Q y excitation energies based on the QM-MM optimized geometry which form the energy ladder in the FCP complex of the diatom P. tricornutum calculated at different levels of theory (see details in Materials and Methods in the SI). The DFT/MRCI calculations are computationally more demanding than the LC-DFT formalism and have been shown to produce quite accurate excitation energies for Chl molecules while the TD-LC-DFTB scheme has been tested and used earlier for Chl molecules of bacterial LH complexes . The results clearly show that the numerically efficient TD-LC-DFTB formalism yields energies that are as accurate as the numerically much more expensive TD-DFT schemes. Therefore, they enable us to calculate excitation energies along a QM/MM MD trajectory sampling diverse conformations. All calculations have been performed also for the crystal structure geometry without lipids and solvents as a reference. The resulting energy ladder is presented in Fig. . The relative excitation energies show a similar trend for both the QM/MM-minimized and the crystal structure.