It is often necessary to map chemically meaningful conformational differences to a few coordinates, which may be followed over time and through transitions. Here, we call these reaction coordinates, but other synonyms are often used; e.g., progress coordinates or collective variables. In general, intuition based on one coordinate alone, such as the central torsion angle, can be unreliable; it is preferable to account for all degrees of freedom in the system using methods like MD simulations, and then verify hypotheses about key coordinates through analysis of the resulting trajectories. For the motors in this study, the key conformational features are the rotation of the rotor relative to the stator, the pucker of the stator, the pucker of the rotor, and the pyramidalization of the two central carbons. We found that one well-chosen reaction coordinate suffices to differentiate between the metastable form and the stable form, as in the umbrella sampling calculations; however, at least two coordinates are needed to differentiate all the conformationally distinct and kinetically separated metastable substates. The approach used to define reaction coordinates in this study is detailed in the Appendix B.