The value of -13.6 eV, which is the Hydrogen atom ground state energy cannot be accurately obtained from the molecular energy spectrum, which reports the eigenvalues of the Kohn-Sham hamiltonian. The total energy in DFT includes the Kohn-Sham eigenvalues, but there are additional contributions. Therefore, what you really need to calculate is the total energy (TotalEnergy analysis object) which will give you a value close to -13.6 eV.