A generalization of the Prony method, which fits a set of complex exponentials to a time dependent signal, is presented. This generalized Prony method is applied to analyze rovibrational dynamics of products in a theoretical treatment of molecular collisions. Employing suitable coherent states an a posteriori quantum analysis can be performed on molecular trajectories with classical nuclei obtained with electron nuclear dynamics theory. Illustrative calculations are presented for state resolved cross sections of proton collisions with water molecules and compared to results from crossed beam experiments.