In this paper, we examine how bond strain and rotation carry heat in the molecular crystal alpha-RDX. We calculate anharmonic lifetimes and then rank order the phonons and their distortions to the lattice by their importance as carriers of thermal energy. The motions of the atoms that constitute the strain and rotation are determined using the phonon mode energy and mode shapes under the harmonic approximation. To draw the distinction between propagating and diffusive carriers, we additionally compare the thermal conductivity estimates from three microscale models: phonon gas model, Cahill-Watson-Pohl formula and Allen-Feldman harmonic theory. We found that the modes that contribute substantially to the thermal conductivity are also the dominant contributors to the strain and rotation of all bonds in alpha-RDX, among which N-N and N-O bonds were found to exhibit the largest strains and rotations. We also found that on average, the N-N bonds exhibit the largest deformation, similar to 35% more strain and similar to 6% more rotation than N-O bonds. Our calculations confirm that large straining of the N-N and N-O bonds results from relatively larger displacement of the nitrogen atom in the nitro group -NO2.