Binding energy of docked complex

HADDOCK
1

Hello, I would like to compute the interaction energy between two proteins docked with haddock.
I see that each cluster pdb contain the terms: Binding Energy, Desolvation Energy and Internal Energy of isolated and docked molecules.
Although I get haddock score < -2, the binding energy looks always positive (i performed several docking) and also the internal energy difference complex - free molecules looks positive, so in principle the two molecules should not like each other. On the other hand, when I re-compute the binding affinity with prodigy, I get negative values, meaning that the docked conformation i preferred.
For example, the pdb of the best docked conformation have data like these (which units?)
REMARK Desolvation energy: -14.3262
REMARK Internal energy free molecules: -19248.3
REMARK Internal energy complex: -18658.4
REMARK Binding energy: 182.598

while the haddock output is like
HADDOCK score -133.7 +/- 0.6
Cluster size 132
RMSD from the overall lowest-energy structure 2.2 +/- 2.4
Van der Waals energy -77.8 +/- 5.9
Electrostatic energy -297.0 +/- 45.5
Desolvation energy -13.6 +/- 2.6
Restraints violation energy 170.6 +/- 14.7
Buried Surface Area 2013.0 +/- 35.4
Z-Score -2.3

and the prodigy output is like
cluster2_1 -11.2 6.5E-09

They look contradictory to me , but I’m sure there is something I’m getting wrong from these numbers.
Thanks for any help

2

The HADDOCK score is the relevant value to look at.

In this case the score is -133.7

But do remember that docking scores are not equal to binding affinities… Little to zero correlation here!

See for example:

P.L. Kastritis and A.M.J.J. Bonvin On the binding affinity of macromolecular interactions: daring to ask why proteins interact J. R. Soc. Interface, 10, doi: 10.1098/rsif.2012.0835 (2013).

P. Kastritis and A.M.J.J. Bonvin Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Research, 9, 2216-2225 (2010).