3J coupling refers to the experimental measurement of the two hydrogens that are bonds away in nuclear magnetic resonance (NMR) spectroscopy. The magnitude of the coupling (Hz) is related to the dihedral angles formed by the three covalent bond, following the Karplus relationshipi.^[1] Likewise, RNA structures generated by molecular dynamic (MD) simulations can be evaluated by extracting the dihedral angle information and converting it into 3J couplings The figure on the left illustrats how the dihedral angles within an RNA are defined.^[2] Particularly:

α = O3'(i-1)-P-O5'-C5'

β = P-O5'-C5'-C4'

γ = O5'-C5'-C4'-C3'

δ = C5′−C4′−C3′−O3′

ε = C4′−C3′−O3′-P(i+1)

ζ = C3′−O3′-P(i+1)-O5'(i+1)

ν1 = O4'−C1′−C2′−C3′

ν2 = C1'-C2′−C3′−C4′

ν3 = C2′−C3′−C4′−O4′

χ = O4′−C1′−N*−C*