General Idea
In general, binding energy represents the mechanical work which must be done against the forces which hold an object together, disassembling the object into component parts separated by sufficient distance that further separation requires negligible additional work.
At the atomic level the atomic binding energy of the atom derives from electromagnetic interaction and is the energy required to disassemble an atom into free electrons and a nucleus. Electron binding energy is a measure of the energy required to free electrons from their atomic orbits. This is more commonly known as ionization energy.
At the nuclear level, binding energy is also equal to the energy liberated when a nucleus is created from other nucleons or nuclei. This nuclear binding energy (binding energy of nucleons into a nuclide) is derived from the nuclear force (residual strong interaction and is the energy required to disassemble a nucleus into the same number of free, unbound neutrons and protons it is composed of, so that the nucleons are far/distant enough from each other so that the nuclear force can no longer cause the particles to interact.
In astrophysics, gravitational binding energy of a celestial body is the energy required to expand the material to infinity. This quantity is not to be confused with the gravitational potential energy, which is the energy required to separate two bodies, such as a celestial body and a satellite, to infinite distance, keeping each intact (the latter energy is lower).
In bound systems, if the binding energy is removed from the system, it must be subtracted from the mass of the unbound system, simply because this energy has mass. Thus, if energy is removed (or emitted) from the system at the time it is bound, the loss of energy from the system will also result in the loss of the mass of the energy, from the system. System mass is not conserved in this process because the system is "open" (i.e., is not an isolated system to mass or energy input or loss) during the binding process.
Read more about this topic: Binding Energy
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