We use the constrained random phase approximation (cRPA) to derive from first principles the Ru-$t_{2g}$ Wannier function based model for the Kitaev spin-liquid candidate material $alpha$-RuCl$_3$. We find the non-local Coulomb repulsion to be sizable compared to the local one. In addition we obtain the contribution to the Hamiltonian from the spin-orbit coupling and find it to also contain non-negligible non-local terms. We invoke strong coupling perturbation theory to investigate the influence of these non-local elements of the Coulomb repulsion and the spin-orbit coupling on the magnetic interactions. We find that the non-local Coulomb repulsions cause a strong enhancement of the magnetic interactions, which deviate from experimental fits reported in the literature. Our results contribute to the understanding and design of quantum spin liquid materials via first principles calculations.