. 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 16.

Hydrogen bonding distances in the holo adenine riboswitch 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
Ade (N7) – Ura22 (O2’)	2.78	3.6 ± 0.8
Ade (N3) – Ura51 (N3)	2.77	2.8 ± 0.1
Ade (N9) – Ura51 (O4)	2.93	3.1 ± 0.2
Ade (N1) – Ura74 (N3)	2.65	2.8 ± 0.2
Ade (N6) – Ura74 (O4)	2.87	2.8 ± 0.3

The distance of each interaction measured in the 1Y26 crystal structure.

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