TABLE 3.

Free energies (G total taken from MM-PBSA analysis, last 2-ns snapshots average) were calculated for the whole system (TOTAL) and various combinations of guanine stem (S) and both loops (L1 and L2) to distinguish upper and lower loop contributions

Simulation	G(TOTAL)	G(S + L1)	G(S + L2)	G(S)	G(L1)*	G(L2)*
Lateral
K-M	−5167	−4521	−4518	−3871	−650	−647
K-M(K+)	−5148	−4504	−4498	−3854	−650	−644
C1-M	−5120	−4479	−4489	−3848	−631	−641
C2-M	−5168	−4523	−4520	−3874	−649	−646
C3-M	−5168	−4511	−4511	−3853	−658	−658
C1-L-M	−5202	−4544	−4541	−3882	−662	−659
C4-M	−5167	−4524	−4523	−3880	−644	−643
K-M-L-M	−5196	−4538	−4548	−3888	−650	−660
Diagonal
Fdiag-L-M	−5203	−4541	−4549	−3886	−655	−663
Fdiag-M†	−5183	−4533	−4532	−3881	−652	−651
Ndiag-M	−5188	−4534	−4536	−3882	−652	−654

^*Contributions of L1 and L2 are extracted from the preceding four columns as specified in the text. Solute entropy term is not included in this table.

^†8.0–10.0 ns.