The present study can be seen as a detailed structure-based analysis of the FCP complex of the diatom P. tricornutum which questions the interpretation of experimental results regarding the Chl-c pigments in FCP complexes, especially the proposed order in the energy ladder. The present outcomes further trigger the question whether Chl-c pigments in FCP complexes from other organisms have also the lowest Q y excitation energies, or if the energetical ordering might be different due to varying protein environments. From an evolutionary point of view, it seems unlikely that the specific electric fields near to the Chl-c pigments are not present in the FCP complexes from different organism, but switched on and off depending on the conditions (environment). Interestingly, performing a computational experiment by removing the QM/MM coupling to the environment in the excited state calculations, the Chl-c2 pigment is found to have the highest excitation energy shift compared to the rest of the Chl both for the QM/MM-minimized geometry and for the average value determined along the QM/MM MD trajectory. This fact signifies the strong and peculiar effect of the FCP protein matrix on Chl-c properties for the diatom P. tricornutum. Due to the earlier belief that Chl-c molecules have a higher excitation energies than Chl-a pigments also within protein complexes, there is a risk that two-dimensional spectroscopy signals have been misinterpreted in earlier studies . For this reason, experimental investigations of the FCP complex of P. tricornutum would be highly desired, while the results need to be compared to those of other organisms. In this context, a recent experimental study on the FCP of P. tricornutum has been carried out to investigate the energy transfer from the Fx carotenoid to the Chl-a pool which possibly could be extended to investigate the energy transfer dynamics from Chl-c to Ch-a molecules. At the same time, a crystallographic structure of the FCP complex from the diatom C. meneghiniana is also sought-after in order to understand whether the FCP matrices from different organisms contain similar electrostatic effects on the Chl-c pigments. Moreover, the proposed crystal structure of the FCP from C. meneghiniana in Ref. 5 together with the estimated energy transfer rates from Chl-c to Chl-a might need to be revisited. Finally, it is also necessary to understand the structure-function relationship in the FCP complex from P. tricornutum especially concerning the flow of the excitation energy within the complex and how the energy would be transferred from the energetically low-lying Chl-c2 pigments towards the reaction center. To this end, a structure of the complete PSII supercomplex of the diatom P. tricornutum would be highly beneficial.