In the physical processes of proton interaction in bio-materials, most of the proton energy is transferred to electrons. Ionization and excitation occur most frequently around the Bragg peak region, where nuclear reactions also exist. In this study, we investigated the processes of energy deposition by considering interactions including the nuclear reactions between protons and water molecules by a Monte Carlo simulation for proton therapy. We estimated the number of particles produced by a variety of nuclear reactions, and we focused on the interaction in the low-energy region (below 1 MeV). Furthermore, we considered the charge-changing processes in the low-energy region (less than a few hundred keV). Finally, we evaluated the total dose and the contribution of primary protons and secondary particles through nuclear reactions to the absorbed dose. The results showed that the protons generate numerous neutrons via nuclear reactions. Particularly, neutrons with relatively low energies produce recoil protons by elastic collisions with the hydrogen atoms. Around the Bragg peak, low-energy primary protons (slowed-down protons) are prevalent, whereas recoil (secondary) protons gradually become dominant behind the distal falloff region of the Bragg peak. Therefore, around the Bragg peak, the main contribution to the absorbed dose is that of the primary protons (from 80 to 90%), whereas secondary protons created by primary proton-induced reactions contribute to the dose from 20 to 5%. Behind the distal endpoint of the Bragg peak, the absorbed dose is mainly due to the protons produced by (1)H(n, p), and the contribution of these is about 70%.