If I understood you well. the such criterion is energy minimum. In other words, you can choose any available configuration, but the most stable one will be those with the lowest total energy. Additionally, there can be quite few configurations that have the same energy...
The binding energy criteria can be used, but with caution. The total 'molecule' energy in respect to the 'free atoms' energy will be in most cases lower (unless one want to bring together atoms that normally not bind at all). The total energy of specific structure will be more convenient. In addition you should always compare energies of the same number/type of atoms in your system, when you only want to change its organisation (strucure).
Sorry for chiming in late....
Usually one calculates the transfer integrals for all dimers in a crystalline organic material. For amorphous crystals you can do some sort of Monte Carlo sampling, e.g. with a distance-based criterion.
If you average over all hopping rates, you can calculate the mobility in all directions and anistropicity and plot them in a polar plot (http://pubs.acs.org/doi/abs/10.1021/jp900512s).
For a guided example on how to calculate the transfer integrals and hopping rate for each dimer configuration in ADF: https://www.scm.com/adf-modeling-suite/wizard/organic-electronics/electron-and-hole-mobilities-in-organic-electronics/
This can be easily scripted over the set of dimers you want to calculate.
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