The thorough understanding of energy and electron transfer mechanisms in photosynthetic pigmentprotein complexes is essential for the knowledgeguided design of synthetic platforms and devices that will drive the energy transition. Photosystem II (PSII) of oxygenic photosynthesis 1 is one of the most important potential blueprints for artificial light-driven charge-separating devices. The four chlorophyll and two pheophytin molecules that comprise the reaction center (RC) of PSII (Figure ) are able to convert with ultimate efficiency visible light to electron flow, powering water oxidation and plastoquinone reduction. Three main factors need to be elucidated for understanding the function of the PSII RC, each factor representing a substantial challenge for both experiment and theory: a) the electronic structure of the pigments themselves, b) the influence of the protein environment in terms of structure and electrostatics, and c) the role that dynamic motion plays in modulating the electronic structure, absorption properties, and function of RC pigments. Since the initial charge separation is intimately tied to the light absorption process, the electronic structure analysis must encompass the ground state and the spectrum of low-lying excited states. Crucial advances have been made toward a reliable description of the electronic structure of chlorophylls using modern quantum chemical methods, while the influence of the protein environment on the PSII RC properties and function has also began to be reliably quantified in recent studies using hybrid quantum-mechanics/molecular-mechanics (QM/MM) approaches. Initial studies have also begun to consider how the flexibility of the protein environment affects the properties of RC pigments. On the other hand, the flexibility of the geometric structures of the pigments themselves is a crucial factor that remains unexplored, in part because the classical force fields used in typical molecular dynamics studies of PSII are not able to correctly sample the conformation flexibility of the photosynthetic macrocycles. This flexibility however can have important implications for the theoretical description of the primary RC function as well as for the charge separation processes that follow the initial photo-initiation. Methods for characterising excited states are well established. Specifically, the charge-transfer character of an excited state can be conveniently analysed with electron-hole correlation plots or natural transition orbitals. These methods represent both qualitative and quantitative ways to analyze the wavefunction of an excited state. A distinct challenge, however, is how to perform such analysis in an ensemble of distorted geometries, as it will be present in reality due to zero point vibrations, conformational flexibility and other effects. The electronic states will reorder and mix among each other upon distortion of the nuclear coordinates. Each member of the ensemble can thus possess a different set of electronic states. Herein, we present a new way to analyse a thermally populated nuclear ensemble. We solve the issue of reordering and mixing of the electronic states by calculating the electronic properties in a chosen set of reference states. Our method is rooted in the determination of wavefunction overlaps and is exemplified with the Chl D1 Pheo D1 and P D1 P D2 pairs of Photosystem II. We expect the method to be generally applicable to electron transfer chains in enzymes as well as in synthetic charge-separating systems.