PDB Chemical Component UPE

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for UPE

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP1 P 1.514 1.480
O5' P 1.616 1.610
OP3 P 1.584 1.610
P OP2 1.511 1.610
C1' N1 1.471 1.464
C2 N1 1.415 1.342
N1 C6 1.334 1.359
O2 C2 1.244 1.216
C2 N3 1.341 1.344
N3 C4 1.337 1.350
N3 HN3 1.000 0.970
C4 O4 1.248 1.217
C4 C5 1.489 1.471
C6 C5 1.392 1.381
C5 C21 1.505 1.470
C6 H6 1.080 1.080
C2' C1' 1.522 1.545
C1' O4' 1.427 1.444
C1' H1' 1.100 1.090
C2' C3' 1.512 1.545
C2' H2' 1.100 1.091
C2' H2'A 1.100 1.090
C21 O22 1.232 1.217
C21 N23 1.337 1.348
N23 C24 1.464 1.465
N23 HN23 1.000 0.971
C24 C25 1.518 1.530
C24 H24 1.100 1.090
C24 H24A 1.100 1.090
C25 C26 1.506 1.507
C25 H25 1.100 1.090
C25 H25A 1.100 1.090
C31 C26 1.388 1.382
C26 C27 1.405 1.383
C27 C28 1.394 1.382
C27 H27 1.080 1.080
C29 C28 1.394 1.382
C28 H28 1.080 1.080
C30 C29 1.403 1.382
C29 H29 1.080 1.080
O3' C3' 1.429 1.430
C3' C4' 1.518 1.544
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.966
C31 C30 1.395 1.383
C30 H30 1.080 1.080
C31 H31 1.079 1.080
C4' O4' 1.439 1.444
C4' C5' 1.530 1.530
C4' H4' 1.100 1.089
C5' O5' 1.427 1.428
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.968

Bond Angles for UPE

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 118.1 109.5
O5' P OP2 109.6 109.5
P OP2 HOP2 109.5 114.0
C2 N1 C6 119.5 121.5
N1 C6 C5 120.8 119.4
N1 C6 H6 119.6 120.3
O2 C2 N3 118.1 118.9
C2 N3 C4 121.0 120.4
C2 N3 HN3 119.5 119.8
C4 N3 HN3 119.5 119.8
N3 C4 O4 119.3 120.7
N3 C4 C5 118.5 118.5
O4 C4 C5 122.1 120.7
C4 C5 C21 124.4 121.0
C6 C5 C21 117.5 121.0
C5 C21 O22 117.0 120.0
C5 C21 N23 122.4 120.0
C2' C1' O4' 105.2 104.8
C2' C1' H1' 108.4 110.5
O4' C1' H1' 109.7 110.4
C1' O4' C4' 110.1 105.3
C3' C2' H2' 110.8 110.5
C3' C2' H2'A 110.7 110.5
C2' C3' C4' 105.6 104.1
C2' C3' H3' 111.6 110.5
H2' C2' H2'A 109.5 110.6
O22 C21 N23 120.5 120.0
C21 N23 C24 120.2 120.0
C21 N23 HN23 119.9 119.9
C24 N23 HN23 119.9 120.0
N23 C24 C25 108.4 109.5
N23 C24 H24 109.7 109.5
N23 C24 H24A 109.7 109.5
C25 C24 H24 109.7 109.4
C25 C24 H24A 109.7 109.5
C24 C25 C26 114.5 109.5
C24 C25 H25 108.2 109.4
C24 C25 H25A 108.2 109.5
H24 C24 H24A 109.5 109.5
C26 C25 H25 108.2 109.5
C26 C25 H25A 108.2 109.5
C25 C26 C27 117.6 120.0
H25 C25 H25A 109.5 109.5
C26 C27 C28 120.5 120.0
C26 C27 H27 119.7 120.0
C28 C27 H27 119.7 120.0
C27 C28 H28 120.6 120.0
C29 C28 H28 120.5 120.0
C30 C29 H29 119.9 120.0
O3' C3' C4' 107.1 110.5
O3' C3' H3' 112.9 110.5
C4' C3' H3' 111.5 110.6
C3' C4' O4' 106.8 104.8
C3' C4' C5' 112.8 110.4
C3' C4' H4' 107.8 110.4
C31 C30 H30 119.5 120.0
O4' C4' C5' 112.7 110.3
O4' C4' H4' 108.9 110.4
C5' C4' H4' 107.7 110.4
C4' C5' O5' 110.2 109.5
C4' C5' H5' 109.3 109.4
C4' C5' H5'A 109.3 109.4
O5' C5' H5' 109.3 109.5
O5' C5' H5'A 109.3 109.5
H5' C5' H5'A 109.5 109.4

Torsion Angles for UPE

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5' P OP1 OP2 126.3 120.0
OP1 P OP2 HOP2 0.0 180.0
OP1 P O5' OP2 229.0 240.0
O5' P OP2 HOP2 233.7 60.0
OP3 P OP2 HOP2 121.4 300.0
C1' N1 C6 H6 0.7 0.2
C2 N1 C6 C5 359.9 360.0
C2 N1 C6 H6 179.9 180.0
N1 C6 C5 C21 179.2 180.0
O2 C2 N1 C6 179.9 180.0
O2 C2 N3 C4 180.3 180.0
O2 C2 N3 HN3 0.3 360.0
N3 C2 N1 C6 0.2 0.0
C4 N3 C2 HN3 180.0 180.0
C2 N3 C4 O4 180.2 180.0
C2 N3 C4 C5 359.7 0.0
C2 N3 C4 HN3 180.0 180.0
O4 C4 N3 C5 180.5 180.0
N3 C4 C5 C21 181.0 180.0
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 O4 0.2 0.0
HN3 N3 C4 C5 179.7 180.0
O4 C4 N3 HN3 0.2 0.0
N3 C4 O4 C5 179.5 180.0
O4 C4 C5 C21 0.5 360.0
N1 C6 C5 C4 359.8 360.0
C5 C4 N3 HN3 179.7 180.0
N3 C4 C5 O4 180.5 180.0
C6 C5 C4 C21 179.4 180.0
C4 C5 C21 O22 182.1 174.3
C4 C5 C21 N23 3.6 354.3
N1 C6 C5 H6 180.0 180.0
C4 C5 C6 C21 180.6 180.0
C6 C5 C21 O22 2.7 354.3
C6 C5 C21 N23 184.2 174.3
O22 C21 C5 N23 178.5 180.0
C5 C21 N23 C24 179.2 185.1
C5 C21 N23 HN23 359.2 5.1
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C21 359.2 0.0
O4' C1' C2' H1' 117.3 118.9
C2' C1' O4' C4' 333.0 319.5
C2' C1' O4' H1' 243.5 241.1
C3' C4' O4' C1' 14.7 40.6
C1' O4' C4' C5' 139.1 159.4
C1' O4' C4' H4' 258.6 281.7
C2' C1' H1' O4' 114.4 115.4
H1' C1' O4' C4' 89.5 78.4
C3' C2' C1' O4' 28.1 24.0
C3' C2' C1' H1' 270.7 265.1
H2' C2' C3' H2'A 121.7 122.7
O3' C3' C2' C4' 114.2 118.6
O3' C3' C2' H3' 235.5 237.3
C4' C3' C2' H3' 121.3 118.7
C2' C3' C4' O4' 3.7 336.0
C2' C3' C4' C5' 239.3 217.2
C2' C3' C4' H4' 120.5 94.9
H2' C2' C1' O4' 147.2 142.6
H2' C2' C1' H1' 29.9 23.7
C3' C2' H2' H2'A 237.6 237.3
H2' C2' C3' C4' 221.7 241.4
H2' C2' C3' H3' 100.4 122.7
H2'A C2' C1' O4' 268.9 265.3
H2'A C2' C1' H1' 151.5 146.4
C3' C2' H2'A H2' 122.4 122.7
H2'A C2' C3' C4' 100.0 118.7
H2'A C2' C3' H3' 338.7 360.0
C5 C21 O22 N23 181.5 180.0
O22 C21 N23 C24 0.8 5.1
O22 C21 N23 HN23 180.8 185.1
C5 C21 N23 O22 178.4 180.0
C24 N23 C21 HN23 180.0 180.0
C21 N23 C24 C25 153.9 180.0
C21 N23 C24 H24 273.7 300.0
C21 N23 C24 H24A 34.0 60.0
C21 N23 C24 HN23 180.0 180.0
C25 C24 N23 H24 240.2 240.1
C25 C24 N23 H24A 119.9 120.0
N23 C24 C25 C26 280.1 180.0
N23 C24 C25 H25 40.8 300.0
N23 C24 C25 H25A 159.4 60.0
H24 C24 N23 H24A 239.7 240.0
C21 N23 HN23 C24 180.0 180.0
HN23 N23 C24 C25 333.9 0.0
HN23 N23 C24 H24 93.7 120.0
HN23 N23 C24 H24A 214.0 240.0
C25 C24 N23 HN23 333.9 0.0
N23 C24 C25 H24 119.8 120.0
N23 C24 C25 H24A 240.2 240.0
H24 C24 C25 H24A 120.3 120.0
C26 C25 C24 H25 239.3 240.0
C26 C25 C24 H25A 120.7 120.0
C24 C25 C26 C27 166.6 89.9
H25 C25 C24 H25A 241.4 240.0
H24 C24 N23 HN23 93.7 120.0
N23 C24 H24 C25 240.9 240.0
N23 C24 H24 H24A 120.5 120.0
C25 C24 H24 H24A 239.5 240.0
H24 C24 C25 C26 160.3 60.0
H24 C24 C25 H25 281.0 180.0
H24 C24 C25 H25A 39.6 300.0
H24A C24 N23 HN23 214.0 240.0
N23 C24 H24A C25 119.1 120.0
N23 C24 H24A H24 239.6 240.0
C25 C24 H24A H24 120.5 120.0
H24A C24 C25 C26 39.9 300.0
H24A C24 C25 H25 160.6 60.0
H24A C24 C25 H25A 279.2 180.0
C26 C25 C24 H24 160.3 60.0
C26 C25 C24 H24A 39.9 300.0
C24 C25 C26 H25 120.7 120.0
C24 C25 C26 H25A 239.3 240.0
H25 C25 C26 H25A 118.6 120.0
C25 C26 C27 C28 180.7 180.0
C25 C26 C27 H27 0.7 0.0
H25 C25 C24 H24 281.0 180.0
H25 C25 C24 H24A 160.6 60.0
C24 C25 H25 C26 235.5 240.0
C24 C25 H25 H25A 117.7 120.0
C26 C25 H25 H25A 242.3 240.0
H25 C25 C26 C27 45.9 330.0
H25A C25 C24 H24 39.6 300.0
H25A C25 C24 H24A 279.2 180.0
C24 C25 H25A C26 124.5 120.0
C24 C25 H25A H25 242.3 240.0
C26 C25 H25A H25 117.7 120.0
H25A C25 C26 C27 287.3 210.0
C31 C26 C25 H25 226.4 149.8
C31 C26 C25 H25A 107.9 29.7
C31 C26 C27 H27 180.1 180.3
C27 C26 C25 H25 45.9 330.0
C27 C26 C25 H25A 287.3 210.0
C28 C27 C26 H27 180.0 180.0
C26 C27 C28 H28 179.7 180.0
C26 C27 C28 H27 180.0 180.0
C29 C28 C27 H28 180.0 180.0
C26 C27 H27 C28 180.0 180.0
H27 C27 C28 H28 359.7 0.0
C29 C28 C27 H27 179.7 180.0
C27 C28 C29 H28 180.0 180.0
H28 C28 C27 H27 359.7 0.0
C30 C29 C28 H28 180.7 180.0
H29 C29 C28 H28 0.7 359.9
O3' C3' C2' H2' 335.9 0.1
O3' C3' C2' H2'A 214.2 237.3
C2' C3' O3' C4' 246.8 245.4
C2' C3' O3' H3' 123.7 122.7
C4' C3' O3' H3' 236.9 237.3
O3' C3' C4' O4' 249.0 217.3
O3' C3' C4' C5' 124.6 98.6
O3' C3' C4' H4' 5.8 336.2
C1' O4' C4' C3' 14.7 40.6
C4' C3' C2' H2' 221.7 241.4
C4' C3' C2' H2'A 100.0 118.7
C2' C3' C4' H3' 238.6 241.3
O3' C3' C4' H3' 123.9 122.7
O4' C4' C3' C5' 124.4 118.8
O4' C4' C3' H4' 243.2 241.1
C5' C4' C3' H4' 118.8 122.3
C3' C4' C5' O5' 158.7 185.0
C3' C4' C5' H5' 278.8 305.0
C3' C4' C5' H5'A 38.5 64.9
H3' C3' C2' H2' 100.4 122.7
H3' C3' C2' H2'A 338.7 360.0
C2' C3' H3' C4' 117.8 114.7
O3' C3' H3' C4' 239.4 237.3
H3' C3' C4' O4' 125.0 94.7
H3' C3' C4' C5' 0.7 335.9
H3' C3' C4' H4' 241.9 213.5
HO3' O3' C3' C4' 293.2 176.1
HO3' O3' C3' H3' 56.2 298.8
C31 C30 C29 H29 179.0 179.8
H30 C30 C29 H29 359.0 360.0
H31 C31 C30 H30 0.8 0.1
C4' O4' C1' H1' 89.5 78.4
O4' C4' C3' H3' 125.0 94.7
C3' C4' O4' C5' 235.6 241.2
C3' C4' O4' H4' 116.2 118.9
C5' C4' O4' H4' 240.5 237.7
O4' C4' C5' O5' 37.6 69.6
O4' C4' C5' H5' 157.7 189.7
O4' C4' C5' H5'A 277.5 309.6
C5' C4' C3' H3' 0.7 335.9
C3' C4' C5' O4' 121.0 115.3
C3' C4' C5' H4' 241.1 237.7
O4' C4' C5' H4' 120.1 122.3
O5' C5' C4' H5' 239.9 240.0
O5' C5' C4' H5'A 120.1 120.0
H5' C5' C4' H5'A 240.2 240.1
H4' C4' C3' H3' 241.9 213.5
C3' C4' H4' O4' 244.5 244.6
C3' C4' H4' C5' 122.0 122.3
O4' C4' H4' C5' 237.5 237.7
H4' C4' C5' O5' 277.5 307.3
H4' C4' C5' H5' 37.6 67.4
H4' C4' C5' H5'A 157.4 187.3
C5' O5' P OP2 134.8 65.0
O5' C5' C4' H4' 277.5 307.3
C4' C5' O5' H5' 120.1 120.0
C4' C5' O5' H5'A 239.9 240.0
H5' C5' O5' H5'A 119.8 120.0
H5' C5' C4' H4' 37.6 67.4
C4' C5' H5' O5' 239.3 239.9
C4' C5' H5' H5'A 119.7 119.9
O5' C5' H5' H5'A 240.3 240.0
H5'A C5' C4' H4' 157.4 187.3
C4' C5' H5'A O5' 120.7 120.1
C4' C5' H5'A H5' 240.4 240.1
O5' C5' H5'A H5' 119.7 120.0