Table 1.

List of simulations

Simulated systema	Number of simulations × length [μs]
2n0j_wt	1 × 10 μsb, 5 × 1 μs
2n0j_RIO_wt	1 × 10 μsb, 3 × 1 μs
2n0j_RIO_wt_CaseP_OPCc	1 × 1 μs
2n0j_RIO_wt_HBfix_Ad	1 × 1 μs
2n0j_RIO_wt_HBfix_Bd	3 × 1 μs
2n0j_RIO_wt_HBfix_Cd	1 × 1 μs
2n0j_C14+	1 × 10 μsb, 5 × 1 μs
2n0j_RIO_C14+	1 × 10 μsb, 3 × 1 μs
2n0j_RIO_wt_Nae	4 × 1 μs
free_RIOf	1 × 1 μs
1bvjg	1 × 1 μs
3rg5g	1 × 0.5 μs

^aThe abbreviations ‘wt’, ‘C14+’, and ‘RIO’ in the simulation names refer to systems containing the wild-type uracil 14, protonated cytosine 14, and the ribostamycin ligand, respectively.

^bOnly the first microsecond of the ten-microsecond simulations, along with all the one-microsecond simulations, is included in the analyses presented in the main text. The rest of the ten-microsecond simulations (i.e. time interval of 1–10 μs) is described in the Supplementary Data.

^cThe Case et al. parameters for RNA phosphates (59) in combination with OPC waters (60) were used.

^dThe U14(O2′)/A16(N7) H-bond interaction was stabilized using 1 kcal/mol (variant A) or 2 kcal/mol (variant B) HBfix potential function (61). In variant C, we used 1 kcal/mol repulsive HBfix potential to destabilize the spurious U14(O2′)/U15(O5′) interaction, in addition to the HBfix potential used in variant A. All HBfix potentials were applied in the 2–3 Å hydrogen-acceptor distance range (61).

^eNa⁺ ions were used instead of K⁺.

^fSimulation of a free ribostamycin.

^gControl simulations of other U-turn-containing RNA molecules—HIV-1 RNA A-Rich Hairpin Loop (PDB: 1bvj) (62) and a fragment (residues 47–47K) of the Mouse tRNA(Sec) (PDB: 3rg5) (63).