Highlights•Reaction dynamics modeled within a quantum trajectory (QT) framework.•On-the-fly electronics structure (ES) calculated with DFTB.•Motion of active site nuclei increase rate constants and kinetic isotope effect.•KIE temperature trends agree with experiment.The motion of local substrate nuclei is incorporated into the quantum hydrogen transfer reaction which occurs in the active site of soybean lipoxygenase-1, modeled within a quantum trajectory (QT) framework. Interactions within the active site are obtained from on-the-fly electronic structure (ES) calculations at the density-functional tight-binding (DFTB) level. By selectively constraining substrate nuclei, changes in the rate constants and kinetic isotope effect are computed over a 100 K temperature range. Substrate motion, occurring on the time-scale of the hydrogen transfer, enhances both the rate constants and isotope effect, but does not change trends captured in a constrained substrate environment.Graphical abstract