. Author manuscript; available in PMC: 2019 Dec 15.

Published in final edited form as: J Comput Chem. 2018 Dec 15;39(32):2624–2646. doi: 10.1002/jcc.25709

Table 15.

Hydrogen bonding distances in the 2KOC stem-loop simulation. Error bars for the MD data are the RMS fluctuations over the entire time series.

Hydrogen Bond	Reference Distance (Å)^a	Drude-2017 Distance (Å)^b	% H-Bond Formation^c
Ura6(O2) – Gua9(N1)	2.77	2.9 ± 0.1	99.7
Ura6(O2’) – Gua9(O6)	2.66	3.0 ± 0.3	94.5
Ura7(O2’) – Gua9(N7)	2.76	3.2 ± 0.3	87.2
Cyt8(N4) – Ura7(O2P)	2.76	3.7 ± 1.1	60.5

The distance measured in the first model of the 2KOC NMR ensemble.

The average and RMS fluctuation from the 1-μs MD simulation.

The percentage of time frames in which the donor-acceptor distance was ≤ 3.5 Å.