The dynamics of the dihydrogen molecule when confined in carbon nanotubes with different chiral- ities and diameters are studied by using a 5 dimensional model considering the most relevant degrees of freedom of the system. The nuclear eigenstates are calculated for an (8,0) and a (5,0) carbon nanotubes by the State-Average Multiconfigurational Time-dependent Hartree, and then studied using qualitative tools (mapping of the total wave functions onto given subspaces) and more rigorous analysis (different kinds of overlaps with reference functions). The qualitative analysis is seen to fail due to a strong coupling between the internal and translational degrees of freedom. Using more accurate tools allows us to gain a deeper insight into the behaviour of confined species.