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a proton has a mass of approximately 938 MeV/c2, of which the rest mass of its three valence quarks only contributes about 9 MeV/c2; much of the remainder can be attributed to the field energy of the gluons.
I've been looking at hydrogen atom and molecule ionizing energies. They are in electron volts rather than mega electron volts. So orders of magnitude less than nucleon separation energies. Nothing seems to mesh together.