Stacking interaction energies for ten B-DNA base-pair steps are computed with density fitted local second-order Møller–Plesset perturbation theory (DF-LMP2), and with the spin-component scaled (SCS) and spin-component scaled for nucleobases (SCSN) variants of DF-LMP2. Comparison with existing CBS(T) reference data indicates larger than expected energy differences for both SCS variants. After an analysis of the errors involved, an alternative method of producing reference data is proposed where DF-LMP2/aug-cc-pVTZ and DF-LMP2/aug-cc-pVQZ energies for the whole complex are extrapolated to produce interaction energies that do not require many-body correction and show reduced error in estimation of the basis set limit. A literature correction term from coupled cluster theory with perturbative triples is then added to the DF-LMP2 estimated basis set limit. These new reference data are consistently around 1 kcal mol⁻¹ less than previous literature data. DF-SCSN-LMP2/aug-cc-pVTZ is found to reproduce the new reference interaction energies with a root mean square error (RMSE) of 0.71 kcal mol⁻¹, while SCS consistently underestimates the binding energy.