Complex sentence: However, a proton and neutron will have lower energy when their spins are parallel, not anti-parallel, since this parallel spin alignment does not infringe upon the Pauli Exclusion Principle, but instead it has to do with the quark structure of these two nucleons.
Split into simpler sentences: However, a proton and neutron will have lower energy when their spins are parallel, not anti-parallel. The lowering of energy for parallel spins has to do with the quark structure of these two nucleons.