Table 3.

Interaction energies, in kcal/mol, of the tRNA nine tertiary interactions

Base complex	Interaction	EDef	EInter	ΔEOpt	E3(Opt)	ΔERBI	E3(RBI)
U8–A14–A21	U…A…A	1.7	−25.7	−24.0	−1.5	−19.3	0.1
	(U–A)…A	0.3	−9.3	−9.0		−3.5
A9–U12–A23	A…U…A	2.8	−28.9	−26.1	−1.3	−24.0	−0.4
	A…(U–A)	1.1	−12.8	−11.7		−9.7
G10–C25–G45	G…C…G	5.6	−44.6	−39.0
	(G-C)…G	2.0	−14.4	−12.4
m2G10–C25–G45	m2G…C…G	4.9	−44.8	−39.9	−6.4	−38.7	−0.2
	(m2G–C)…G	2.3	−14.6	−12.3		−8.4
C13–G22–m7G46	C…G…m7G	6.8	−70.5	−63.6	−7.0	−68.7	−2.8
	(C–G)…m7G	0.6	−38.6	−38.0		−38.1
C13–G22–G46	C…G…G	5.8	−52.0	−46.2
	(C–G)…G	1.8	−21.2	−19.4
G15–C48		1.5	−16.1	−14.6		−13.7
G18–Ψ55		0.9	−13.4	−12.5		−13.8
G18–U55		1.7	−14.2	−12.6
G19–C56		3.4	−30.2	−26.8		−29.5
m22G26–A44		1.9	−18.1	−16.2		−13.9
G26–A44		1.5	−18.5	−17.0
T54–A58		1.1	−16.8	−15.7
T54–m1A58		2.1	−24.6	−22.5		−20.7
U54–A58		1.7	−16.7	−15.0
U54–m1A58		2.5	−23.7	−21.2

ΔE^Opt is the stabilization energy of the base pair/triplet starting from the optimized and isolated bases. ΔE^Opt can be decomposed as ΔE^Opt = E^Def + E^Inter, where E^Def is the energy required to deform the isolated bases to the geometry they assume in the base pair/triplet and E^Inter is the interaction energy between the bases in the geometry they assume in the base pair/triplet. ΔE^RBI is the interaction energy of the base pair/triplet with the geometry fixed to the yeast tRNA^Phe 1ehz X-ray structure. For triplets two energy values are reported. In the first approach the X–Y–Z triplet is fragmented into the three bases, X, Y and Z, and the interaction energy reported reflects the X…Y…Z interaction. In the second approach the X–Y–Z triplet is fragmented into the base pair (X–Y) and the base Z, and the interaction energy reported reflects the (X–Y)…Z interaction. E³ is the three-body contribution to the total interaction energy of triplets; it is a measure of the non-additivity of the pairwise base interactions. Further details can be found in Computational details section.