TABLE 4.

Free energies (kcal/mol) calculated using MM-PBSA methodology (last 5 ns) for the whole system (total) and subsegments including individual loops and TTA linker loops

G	Model 145-mer	Model 245-mer (EBS)*	Model 345-mer (+ BSU6039)	Model 493-mer
Total	−7853.68	−7813.73	−8033.61	−15,623.70
Quadruplex 1 (A)	−2413.17	−2399.86	−2392.24	−2415.63
Loops 1
LA1	−371.66	−374.13	−367.74	−368.35
LA2	−372.36	−368.44	−371.52	−371.84
LA3	−369.49	−367.42	−370.04	−369.33
TTA Linker Loop 1	−369.67	−308.11	−365.31	−366.58
Quadruplex 2 (B)	−2439.23	−2447.22	−2434.97	−2435.41
Loops 2
LB1	−370.71	−371.36	−370.40	−371.42
LB2	−372.14	−366.43	−370.58	−368.67
LB3	−368.33	−371.20	−368.55	−371.45
TTA Linker Loop 2	–	–	–	−365.74
Quadruplex 3 (C)	–	–	–	−2441.07
Loops 3
LC1	–	–	–	−372.15
LC2	–	–	–	−375.09
LC3	–	–	–	−367.63
TTA Linker Loop 3	–	–	–	−364.10
Quadruplex 4 (D)	–	–	–	−2437.93
Loops 4	–	–	–	−372.22
LD1	–	–	–	−373.58
LD2	–	–	–	−371.40

Free energy values do not include the solute entropy.

^*Empty binding site.