The photochemistry of heterocyclic molecules plays a decisive role for processes and applications like DNA photo-protection from UV damage and organic photocatalysis. The photochemical reactivity of heterocycles is determined by the redistribution of photoenergy into electronic and nuclear degrees of freedom, initially involving ultrafast internal conversion. Most heterocycles are planar in their ground state and internal conversion requires symmetry breaking. To lower the symmetry, the molecule must undergo an out-of-plane motion, which has not yet been observed directly. Here we show using the example of 2-thiouracil, how Coulomb explosion imaging can be utilized to extract comprehensive information on this molecular deformation, linking the extracted deplanarization of the molecular geometry to the previously studied temporal evolution of its electronic properties. Particularly, the protons of the exploded molecule are well-suited messengers carrying rich information on its geometry at distinct times after electronic excitation. We expect that our new analysis approach centered on these peripheral protons can be adapted as a general concept for future time-resolved studies of complex molecules in the gas phase.