[EDIT: As some commentators have suggested, I should conclude that the energy minimize feature is not intended for the purpose of Hydrogen-bonding, and primarily for refining the modelling of molecules.]
Using the Chem3D automatic Huckel charge calculator, I was able to calculate the charges of the atoms in the citrate and borate ion.
Individually, the borate ion's oxygen atoms have a small negative charge, i.e. -0.07. Individually, the citrate ion's oxygen atoms have a large negative charge, i.e. -0.56.
I use the energy minimize function to make the two hydrogen bond. I then do the charge calculation, and I found that some of the citrate's oxygens' charges increased to ~-0.67, while some of them decreased, and the borate ion's increased to ~-0.5. The hydrogen atoms do increase positive charge.
I actually noticed another particular feature, the oxygen atom of the hydroxyl involved in both hbond donating and accepting has a positive charge now. The other charges remain as I've explained above. The highlighted yellow atom was just an oxygen atom that I clicked.
For my own explanation, I would suggest that the hydrogen bonding is the cause of the charges being induced and increased. Yet, due to the size of the molecules, only two or four atoms seem to be involved in the hydrogen bonding. Then, why should the OTHER atoms still increase their charge? The atoms not involved in hydrogen bonding between the two molecules?
Would it be a feature of the calculator, or would this be the scenario in real life?
I am interested in how different ions are compatible with borate in terms of hydrogen bonding and screening, based on their charges. This will aid my experiments.