#
#   nucleic acid base pairs. Some of the base pairs may not be standard. But they appear in some structures
pairs  monomer A group RNA monomer T group RNA label A:T grouplabel basepair
bond atom N6 A atom O4 T value 2.94 sigma 0.15
bond atom N1 A atom N3 T value 2.84 sigma 0.1
chiral atom N1 A atom C2 A atom C6 A atom N3 T value 0.0 sigma 0.5
chiral atom N3 T atom C2 T atom C4 T atom N1 A value 0.0 sigma 0.5
torsion atom C2 A atom N1 A atom N3 T atom C4 T value 180.0 sigma 15.0

pairs monomer DA group DNA monomer DT group DNA label DA:DT grouplabel basepair
bond atom N6 DA atom O4 DT value 2.94 sigma 0.15
bond atom N1 DA atom N3 DT value 2.84 sigma 0.1
chiral atom N1 DA atom C2 DA atom C6 DA atom N3 DT value 0.0 sigma 0.5
chiral atom N3 DT atom C2 DT atom C4 DT atom N1 DA value 0.0 sigma 0.5
torsion atom C2 DA atom N1 DA atom N3 DT atom C4 DT value 180.0 sigma 15.0

pairs monomer A group RNA monomer U group RNA label A:U grouplabel basepair
bond atom N6 A atom O4 U value 2.94 sigma 0.15
bond atom N1 A atom N3 U value 2.84 sigma 0.1
chiral atom N1 A atom C2 A atom C6 A atom N3 U value 0.0 sigma 0.5
chiral atom N3 U atom C2 U atom C4 U atom N1 A value 0.0 sigma 0.5
torsion atom C2 A atom N1 A atom N3 U atom C4 U value 180.0 sigma 15.0

pairs monomer DA group DNA monomer DU group DNA label DA:DU grouplabel basepair
bond atom N6 DA atom O4 DU value 2.94 sigma 0.15
bond atom N1 DA atom N3 DU value 2.84 sigma 0.1
chiral atom N1 DA atom C2 DA atom C6 DA atom N3 DU value 0.0 sigma 0.5
chiral atom N3 DU atom C2 DU atom C4 DU atom N1 DA value 0.0 sigma 0.5
torsion atom C2 DA atom N1 DA atom N3 DU atom C4 DU value 180.0 sigma 15.0

pairs monomer C group RNA monomer G group RNA label C:G grouplabel basepair
bond atom N4 C atom O6 G value 2.91 sigma 0.15
bond atom N3 C atom N1 G value 2.95 sigma 0.1
bond atom O2 C atom N2 G value 2.86 sigma 0.15
chiral atom N1 G atom C6 G atom C2 G atom N3 C value 0.0 sigma 0.5
chiral atom N3 C atom C4 C atom C2 C atom N1 G value 0.0 sigma 0.5
torsion atom C4 C atom N3 C atom N1 G atom C2 G value 180.0 sigma 15.0

pairs monomer DC group DNA monomer DG group DNA label DC:DG grouplabel basepair
bond atom N4 DC atom O6 DG value 2.91 sigma 0.1
bond atom N3 DC atom N1 DG value 2.95 sigma 0.1
bond atom O2 DC atom N2 DG value 2.86 sigma 0.1
chiral atom N1 DG atom C6 DG atom C2 DG atom N3 DC value 0.0 sigma 0.5
chiral atom N3 DC atom C4 DC atom C2 DC atom N1 DG value 0.0 sigma 0.5
torsion atom C4 DC atom N3 DC atom N1 DG atom C2 DG value 180.0 sigma 15.0

pairs monomer G group RNA monomer U group RNA label G:U grouplabel basepair
bond atom O6 G atom N3 U value 2.94 sigma 0.1
bond atom N1 G atom O4 U value 2.94 sigma 0.1
chiral atom N1 G atom C6 G atom C2 G atom O4 U value 0.0 sigma 0.5
chiral atom N3 U atom C2 U atom C4 U atom O6 G value 0.0 sigma 0.5
torsion atom C2 U atom N3 U atom O6 G atom C6 G value 180.0 sigma 15.0
torsion atom C2 G atom N1 G atom O4 U atom C4 U value 180.0 sigma 15.0
bond atom O6 G atom N3 U value 2.94 sigma 0.1
bond atom N1 G atom O2 U value 2.94 sigma 0.1
chiral atom N1 G atom C6 G atom C2 G atom O2 U value 0.0 sigma 0.5
chiral atom N3 U atom C2 U atom C4 U atom O6 G value 0.0 sigma 0.5
torsion atom C4 U atom N3 U atom O6 G atom C6 G value 180.0 sigma 15.0
bond atom N2 G atom O2 U value 2.94 sigma 0.1
bond atom N3 G atom N3 U value 2.84 sigma 0.1
chiral atom N3 G atom C2 G atom C4 G atom N3 U value 0.0 sigma 0.5
chiral atom N3 U atom C2 U atom C4 U atom N3 G value 0.0 sigma 0.5
torsion atom C4 U atom N3 U atom N3 G atom C2 G value 180.0 sigma 15.0

#Sugar and back-bone related restraints(torsions)
puckers monomer . group DNA label C2'-endo grouplabel DNA
torsion atom C4' atom O4' atom C1' atom C2'   value -19.3  sigma 6.3
torsion atom O4' atom C1' atom C2' atom C3'   value  32.8  sigma 4.9
torsion atom C1' atom C2' atom C3' atom C4'   value -33.1  sigma 3.6
torsion atom C2' atom C3' atom C4' atom O4'   value  22.6  sigma 4.4
torsion atom C3' atom C4' atom O4'  atom C1'  value  -2.3  sigma 5.7

puckers monomer . group RNA label C2'-endo  grouplabel RNA
torsion atom C4' atom O4' atom C1' atom C2'   value -20.8  sigma 10
torsion atom O4' atom C1' atom C2' atom C3'   value  35.2  sigma 10
torsion atom C1' atom C2' atom C3' atom C4'   value -35.4  sigma 10
torsion atom C2' atom C3' atom C4' atom O4'   value  24.2  sigma 10
torsion atom C3' atom C4' atom O4'  atom C1'  value  -2.3  sigma 10

puckers monomer . group DNA label C3'-endo  grouplabel DNA
torsion atom C4' atom O4' atom C1' atom C2'   value   6.6  sigma 10
torsion atom O4' atom C1' atom C2' atom C3'   value -26.7  sigma 10
torsion atom C1' atom C2' atom C3' atom C4'   value  35.6  sigma 10
torsion atom C2' atom C3' atom C4' atom O4'   value -32.3  sigma 10
torsion atom C3' atom C4' atom O4'  atom C1'  value  16.4  sigma 10

puckers monomer . group RNA label C3'-endo grouplabel RNA
torsion atom C4' atom O4' atom C1' atom C2'   value   2.8  sigma 10
torsion atom O4' atom C1' atom C2' atom C3'   value -24.6  sigma 10
torsion atom C1' atom C2' atom C3' atom C4'   value  35.9  sigma 10
torsion atom C2' atom C3' atom C4' atom O4'   value -35.3  sigma 10
torsion atom C3' atom C4' atom O4' atom C1'   value  20.5  sigma 10

#Back-bone related restraints(torsions)