In vacuum or organic solvents, the Q y excitation energies of the Chl-c molecules are blue-shifted compared to those of the Chl-a molecules. Hence, one could expect a similar trend within the FCP complex leading to an exclusive energy transfer from the Chl-c to the Chl-a molecules but not in the reverse direction. In fact, this trend has been proposed based on two-dimensional and pump-probe spectroscopy for the FCP complex of the diatom C. meneghiniana . However, in the present study, an atomistic structure-based analysis of the FCP complex from the diatom P. tricornutum questions the associated energetic ordering within FCP complexes. Based on a variety of quantum chemical approaches for single conformations as well as a long QM/MM MD trajectories, we found that the Chl-c2 pigment 403 has the lowest excitation energy in P. tricornutum. We found that electric fields in specific directions within the FCP matrix can substantially reduce the excitation energies of Chl-c molecules, about five times more than in Chl-a molecules. This electric field effect on Chl-c2 is the largest concerning the excitation energy as well as the density difference between ground and Q y excited state. Thus, the peculiar properties of Chl-c molecules are the main reason behind the counter-intuitive energy ladder in the studied FCP complex. Furthermore, we have determined the linear absorption spectrum based on atomistic simulations and found a good agreement with the experimental measurement. Surprisingly, the contribution of the Chl-c molecules to the absorption is small compared to that of the Chl-a molecules and their Q y excitation energies cannot be directly determined from the absorption spectrum of the FCP complex. Previous assignments of the experimental Q y excitation energies of the Chl-c pigments in FCP complexes might need to be reconsidered .