The structure of the covalent photosynthetic model system N,N,N＇,N＇-tetraalkyl-p-phenylenediamine-zinc porphyrin-naphthoquinone (TAPD-ZnP-NQ) has been explored by using a combination of theoretical and experimental techniques. Structural information is extracted from high-level quantum-chemical ab initio calculations, which is a nontrivial task for a large molecule like TAPD-ZnP-NQ. We tackle this problem by dividing the model system into smaller molecular fragments, whose geometries can be optimized separately. The fragments are subsequently fitted together, thus providing an approximate structure of the entire model system. To verify this structure, time-resolved Q-band electron paramagnetic resonance (EPR) experiments on the light-induced radical pair TAPD(+) NQ(-) have been carried out. The time evolution of the transverse magnetization of TAPD(+) NQ(-) is monitored at various static magnetic fields. Quantum beat oscillations are observed at early times after the laser pulse. These quantum beats are highly sensitive probes for the geometry of the underlying radical pair. From the good agreement between observed and simulated EPR time profiles we conclude that the ab initio calculations predict the correct geometry within the experimental precision.