  Spin-orbit coupling in crystals is known to lead to unusual direction
dependent exchange interactions, however understanding of the consequeces of
such effects in molecular crystals is incomplete. Here we perform four
component relativistic density functional theory computations on the
multi-nuclear molecular crystal {Mo$_3$S$_7$(dmit)$_3$} and show that both
intra- and inter-molecular spin-orbit coupling are significant. We determine a
long-range relativistic single electron Hamiltonian from first principles by
constructing Wannier spin-orbitals. We analyse the various contributions
through the lens of group theory. Intermolecular spin-orbit couplings like
those found here are known to lead to quantum spin-Hall and topological
insulator phases on the 2D lattice formed by the tight-binding model predicted
for a single layer of {Mo$_3$S$_7$(dmit)$_3$}.
