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According to Castiel https://www.youtube.com/watch?v=62cMMy0cf1U  (min 1:15) Rahpael destroyed him at a subatomic level.

Low end (destroying the nucleus of each atom)

According to this 201_Elements_of_the_Human_Body-01.jpg

Human body is 65 % Oxygen

18.5 % Carbon

9.5 % Hydrogen

Assuming that Castiel weighs around 70 kg

Mass of Oxygen = 45.5 kg

Mass of Carbon 13 kg

won't count hydrogen since it has a single proton

According to this page http://periodictable.com/Isotopes/008.16/index.html

Nuclear Binding energy of O2 = 7.97 MeV

Nuclear Binding energy of C = 7.6 MeV

For oxygen Mr = 32 g/mol

n = m / Mr = 45500 / 32 = 1421 mols of O2

n = N / NA (NA = avogadro's number = 6.022e23) => N = n*NA = 1421*6.022e23 = 8.5e26 molecules of Oxygen = 1.7e27 atoms

Binding energy = number of atoms * binding energy of each atom = 2.16e15 Joules

For Carbon Mr = 12

n= m/Mr = 13000 / 12 = 1083 mols of C

N = n*NA = 6.5e26 Carbon atoms 

E = binding energy of each atom * number of atoms = 7.8e14 Joules

Total energy = 2.95e15 Joules ( 703 Kilotons of TNT ) or Large Town level

High end (destroying the protons and neutrons)

According to wikipedia https://en.wikipedia.org/wiki/Quark%E2%80%93gluon_plasma#How_the_QGP_is_studied_theoretically

the energy needed to do that is 175 MeV per particle

Atoms of oxygen = 1.7e27

Each atom has 16 protons and neutrons

Number of Hadrons = 1.7e27 * 16 = 2.72e28

Carbon atoms = 6.5e26

Each atom has 12 Hadrons 

Number of Hadrons = 7.8e27

Hydrogen = 9.5 % of human body => mass = 6.65 kg

n = m / Mr = 6650 / 2 = 3325 mols

N = n*NA = 2e27 molecules -> 4e27 Hadrons

Total number of hadrons = 3.9e28

Energy = 6.825e30 MeV = 1.09e18 Joules = 261 Megatons of TNT (Mountain level)