There are two known popular ways to calculate charge transfer based on orbital interaction, the first one is the NBO, the charge transfer is evaluated based on off-diagonal terms of Fock matrix (which reflects coupling strength between NBO pairs) and diagonal terms of Fock matrix (corresponding to NBO energies); the second way is charge decomposition analysis (CDA), which is supported by Multiwfn, see Section 4.16 of Multiwfn manual for example. CDA is employed very commonly for studying charge transfer between transition metal and ligands. The difference in these two ways is that the former is analyzed based on NBO orbitals, while the latter is usually based on molecular orbitals calculated for respective fragments.

Evaluation of charge transfer (delta_q) in terms of these orbital interaction models is able to get deeper insight into the nature and source of charge transfer phenomenon, however, the net amount of delta_q obtained in these ways are never as accurate as the delta_q calculated by summing up atomic charges as fragment charge (and then compare it with the net charge of the fragment at isolated state), because orbital interaction models ignore possible high-order interactions, polarization and coupling between different interacting orbital pairs.

So, both kinds of ways of evaluating delta_q may be used in practical study, they have their own advantages.