TABLE 4.

Free energies (G total taken from MM-PBSA analysis, last 0.5-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	−4523	−4518	−3872	−651	−646
K-M(K+)	−5146	−4504	−4496	−3853	−651	−643
C1-M	−5122	−4480	−4491	−3849	−631	−642
C2-M	−5176	−4528	−4528	−3878	−650	−650
C3-M	−5174	−4514	−4515	−3856	−658	−659
C1-L-M	−5206	−4550	−4543	−3887	−663	−656
C4-M	−5172	−4528	−4528	−3884	−644	−644
K-M-L-M	−5198	−4539	−4549	−3889	−650	−660
Diagonal
Fdiag-L-M	−5210	−4548	−4553	−3890	−658	−663
Fdiag-M†	−5181	−4532	−4531	−3881	−651	−650
Fdiag-M‡	−5180	−4528	−4528	−3876	−652	−653
Ndiag-M	−5189	−4536	−4536	−3882	−654	−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.

^†9.5–10.0 ns.

^‡2.5–3.0 ns.