Comment by duality

Not sure exactly what you're linking the Wikipedia article on quantum states, but if you like it as a reference, check out https://en.wikipedia.org/wiki/Quantum_state#Mixed_states. The operation of "projecting out" the E&M field in my previous comment would be realized on the density matrix as a partial trace over the electromagnetic field. You can also take the partial trace of this field of the Hamiltonian operator to see the effective dynamics of the atom when "ignoring" the E&M field. This is a fully quantum description of the state, so I stand by the statement that your claim "An atom can be described by its quantum state only if it's isolated and in that case its energy is constant." is incorrect.