Table 4: Values of Vina score, calculated GROMACS total-energy, and calculated binding free energies using MMPBSA (kJ/mol) of loop and hairpin region truncated from each aptamer. H02a gives the lowest MMPBSA ∆E binding energy compared to other complexes.

Aptamer Binding energy
Vina score (kJ/mol)GROMACS Total energy (kJ/mol)MM/PBSA ∆E binding (kJ/mol)

H01a-27.196-6.32094 x 105-971.119
H01b-31.798-7.73169 x 105-977.181
H02a-24.686-7.73238 x 105-1303.080
H02b-24.686-7.93305 x 105-974.453
H03a-22.175-7.71841 x 105-762.144