Table 5.

The effect of gHBfix potential for base pairing on structural dynamics of r(GACC) TN. Populations (in %) of two major conformations, i.e., RNA A-major (the first number) and A-minor (the second number), are displayed for each gHBfix combination at the reference replica (T = 298 K). See Figure S6 in Supporting Information for examples of the other populated conformations from the REST2 simulations. The number in parentheses displays the χ², which further validates the simulations against the data from experiments.^a,b

(–NH…N–) interaction bias (kcal/mol)	(–NH…O–) interaction bias (kcal/mol)
	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +0.0\end{array}\right)$	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +0.5\end{array}\right)$	$\left(\begin{array}{c}\text{NH}\dots \text{O}\\ +1.0\end{array}\right)$
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +1.0\end{array}\right)$	46.2/9.7 (0.32 c)	35.1/6.0 (0.78)	13.5/2.4 (1.98)
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +0.5\end{array}\right)$	56.8/5.6 (0.11)	55.9/9.0 (0.23)	33.2/5.7 (0.95)
$\left(\begin{array}{c}\text{NH}\dots \text{N}\\ +0.0\end{array}\right)$	58.7/7.4 (0.15) d	57.6/9.8 (0.15)	54.1/9.3 (0.42)

^a$\text{gHBfix}\left(\begin{array}{c}2-\text{OH}\dots \text{nbO}/\text{bO}\\ -0.5\end{array}\right)$ weakening SPh interactions is applied in all simulations.

^bCluster analysis performed for the last 7 out of 10 μs-long trajectory at 298 K.

^cχ² values were obtained by calculating and comparing backbone ³J scalar couplings, sugar ³J scalar couplings, NOEs and uNOEs (see Table 3 for details).

^dREST2 simulation with the $\text{gHBfix}\left(\begin{array}{c}2-\text{OH}\dots \text{nbO}/\text{bO}\\ -0.5\end{array}\right)$ potential only (Table 3, last column).