Four out of the 8 systems compared have substantially smaller ∆G prot conf values in case of Apo scheme as compared to the Holo scheme, and the remaining four have no statistically significant differences in ∆G prot conf between the two cases (with differences ≤ 0.8 kcal/mol). The latter includes all cases with positive ∆G prot conf values (CDK2 and JNK1) as they are the ones with no significant conformational differences in apo and holo states of the protein, as explained in the Supporting Information. The above observations are consistent with a recent report in the literature which sought to establish the superiority of the NEQ approach over other approaches . Here, we provide a critical aspect of the Apo scheme that has not been discussed hitherto in the literature. Looking carefully at Table , we find that for 2 out of these 4 systems (P38 and PDE2) where a reduction in ∆G prot conf is observed, there is also a decrease in overlap between the forward and reverse work distributions (indicated by an increase in the percentage of zero overlap cases); whereas the remaining two (CMET and TRKA) are irrelevant as they have 100% zero overlap using both Holo and Apo schemes. The number of zero overlap cases increases from 0/38% in the case of the Holo scheme to 95/100% in the case of the Apo scheme for PDE2/P38. This contributes to the overall increase in zero overlap cases from 47% to 77% for the full dataset.