PDB Chemical Component U31

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 U31

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.464 1.609
P O2P 1.460 1.480
P O3P 1.665 1.611
P O5' 1.575 1.609
O1P H1P 0.950 0.967
O3P H3P 0.951 0.966
O5' C5' 1.448 1.428
C5' C4' 1.453 1.530
C5' H5'1 1.116 1.089
C5' H5'2 1.114 1.089
C4' O4' 1.435 1.437
C4' C3' 1.536 1.541
C4' H4' 1.115 1.090
O4' C1' 1.405 1.444
C3' O3' 1.468 1.429
C3' C2' 1.556 1.547
C3' H3' 1.115 1.089
O3' HA 0.950 0.966
C2' O2' 1.430 1.429
C2' C1' 1.567 1.549
C2' H2' 1.115 1.090
O2' CA' 1.514 1.428
C1' N1 1.476 1.464
C1' H1' 1.115 1.090
N1 C2 1.372 1.345
N1 C6 1.321 1.368
C2 O2 1.157 1.216
C2 N3 1.389 1.345
N3 C4 1.327 1.348
N3 H3 1.020 0.970
C4 O4 1.236 1.218
C4 C5 1.364 1.415
C5 C6 1.345 1.351
C5 H5 1.103 1.080
C6 H6 1.103 1.080
CA' CB' 1.451 1.530
CA' HA'1 1.115 1.090
CA' HA'2 1.115 1.089
CB' CC 1.408 1.531
CB' HB'1 1.116 1.090
CB' HB'2 1.115 1.089
CC ND' 1.414 1.469
CC HCC1 1.115 1.090
CC HCC2 1.115 1.090
ND' HD'1 1.020 1.009
ND' HD'2 1.020 1.009

Bond Angles for U31

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 118.8 109.5
O1P P O3P 103.8 109.4
O1P P O5' 100.1 109.5
P O1P H1P 118.8 106.8
O2P P O3P 110.9 109.4
O2P P O5' 105.5 109.5
O3P P O5' 117.9 109.5
P O3P H3P 103.8 106.8
P O5' C5' 110.5 106.8
O5' C5' C4' 115.2 109.5
O5' C5' H5'1 110.1 109.5
O5' C5' H5'2 110.1 109.5
C4' C5' H5'1 110.2 109.4
C4' C5' H5'2 110.1 109.5
C5' C4' O4' 106.5 110.0
C5' C4' C3' 108.2 109.9
C5' C4' H4' 112.6 109.9
H5'1 C5' H5'2 100.1 109.5
O4' C4' C3' 103.7 107.2
O4' C4' H4' 112.6 109.9
C4' O4' C1' 112.3 107.0
C3' C4' H4' 112.6 109.9
C4' C3' O3' 102.3 110.5
C4' C3' C2' 100.0 104.2
C4' C3' H3' 114.1 110.5
O4' C1' C2' 102.3 103.5
O4' C1' N1 103.6 110.6
O4' C1' H1' 106.3 110.6
O3' C3' C2' 111.0 110.5
O3' C3' H3' 114.0 110.4
C3' O3' HA 102.3 106.9
C2' C3' H3' 114.0 110.6
C3' C2' O2' 109.1 110.9
C3' C2' C1' 97.4 102.1
C3' C2' H2' 108.8 110.9
O2' C2' C1' 123.0 110.9
O2' C2' H2' 108.8 110.8
C2' O2' CA' 122.9 106.8
C1' C2' H2' 108.7 110.9
C2' C1' N1 130.2 110.8
C2' C1' H1' 106.2 110.6
O2' CA' CB' 125.6 109.5
O2' CA' HA'1 106.5 109.4
O2' CA' HA'2 106.5 109.4
N1 C1' H1' 106.3 110.6
C1' N1 C2 124.2 119.7
C1' N1 C6 118.8 119.7
C2 N1 C6 116.9 120.6
N1 C2 O2 123.2 119.5
N1 C2 N3 116.6 121.0
N1 C6 C5 123.8 119.7
N1 C6 H6 118.1 120.1
O2 C2 N3 120.0 119.6
C2 N3 C4 127.2 120.3
C2 N3 H3 116.4 119.9
C4 N3 H3 116.4 119.8
N3 C4 O4 120.8 120.4
N3 C4 C5 112.7 119.4
O4 C4 C5 126.5 120.3
C4 C5 C6 122.3 119.1
C4 C5 H5 118.9 120.5
C6 C5 H5 118.8 120.4
C5 C6 H6 118.1 120.2
CB' CA' HA'1 106.5 109.5
CB' CA' HA'2 106.5 109.5
CA' CB' CC 113.5 109.5
CA' CB' HB'1 110.7 109.5
CA' CB' HB'2 110.7 109.5
HA'1 CA' HA'2 103.0 109.5
CC CB' HB'1 110.7 109.4
CC CB' HB'2 110.7 109.5
CB' CC ND' 114.5 109.5
CB' CC HCC1 110.4 109.5
CB' CC HCC2 110.4 109.5
HB'1 CB' HB'2 99.6 109.5
ND' CC HCC1 110.4 109.5
ND' CC HCC2 110.4 109.5
CC ND' HD'1 115.2 106.7
CC ND' HD'2 115.1 106.7
HCC1 CC HCC2 99.9 109.4
HD'1 ND' HD'2 95.3 106.7

Torsion Angles for U31

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 123.7 240.1
O2P P O1P O5' 245.9 120.0
O3P P O1P O5' 122.2 240.0
O1P P O3P H3P 180.1 60.1
O1P P O5' C5' 309.0 180.0
O1P P O2P O3P 239.8 119.9
O1P P O2P O5' 111.1 239.9
O2P P O1P H1P 180.1 300.0
O3P P O2P O5' 231.3 120.0
O2P P O3P H3P 51.3 180.0
O2P P O5' C5' 72.9 60.0
O1P P O3P O2P 128.8 240.0
O1P P O3P O5' 250.5 120.1
O3P P O1P H1P 56.3 60.0
O2P P O3P O5' 121.7 240.0
O3P P O5' C5' 197.4 300.0
O1P P O5' O2P 236.1 120.0
O1P P O5' O3P 111.6 240.0
O5' P O1P H1P 294.1 180.0
O2P P O5' O3P 235.5 120.0
O5' P O3P H3P 289.6 300.0
P O5' C5' C4' 208.0 180.0
P O5' C5' H5'1 82.7 60.0
P O5' C5' H5'2 333.2 299.9
H1P O1P P O2P 180.1 300.0
H1P O1P P O3P 56.3 60.0
H1P O1P P O5' 294.1 180.0
H3P O3P P O5' 289.6 300.0
C4' C5' O5' H5'1 125.3 120.0
C4' C5' O5' H5'2 234.8 240.0
O5' C5' C4' O4' 142.0 62.1
O5' C5' C4' C3' 253.0 180.0
O5' C5' C4' H4' 18.1 301.0
H5'1 C5' O5' H5'2 109.5 120.1
O5' C5' C4' H5'1 234.7 240.0
O5' C5' C4' H5'2 125.2 120.0
H5'1 C5' C4' H5'2 250.5 240.0
O4' C4' C5' C3' 249.0 242.1
O4' C4' C5' H4' 123.9 121.1
C5' C4' O4' C1' 107.9 146.0
C3' C4' C5' H4' 234.9 238.9
C5' C4' C3' O3' 167.0 119.6
C5' C4' C3' C2' 281.3 238.4
C5' C4' C3' H3' 43.4 357.2
O5' C5' H5'1 C4' 128.1 120.0
O5' C5' H5'1 H5'2 244.0 240.0
C4' C5' H5'1 H5'2 116.0 120.0
H5'1 C5' C4' O4' 267.3 182.1
H5'1 C5' C4' C3' 18.3 300.0
H5'1 C5' C4' H4' 143.4 61.0
O5' C5' H5'2 C4' 231.9 240.0
O5' C5' H5'2 H5'1 115.9 120.0
C4' C5' H5'2 H5'1 244.0 240.0
H5'2 C5' C4' O4' 16.8 302.1
H5'2 C5' C4' C3' 127.8 60.0
H5'2 C5' C4' H4' 252.9 181.0
O4' C4' C5' H5'1 267.3 182.1
O4' C4' C5' H5'2 16.8 302.1
C5' C4' O4' C3' 114.1 119.5
C5' C4' O4' H4' 236.1 238.9
C3' C4' O4' H4' 122.1 119.4
O4' C4' C3' O3' 279.8 239.2
O4' C4' C3' C2' 34.1 357.9
O4' C4' C3' H3' 156.2 116.7
C4' O4' C1' C2' 335.7 320.0
C4' O4' C1' N1 198.6 201.3
C4' O4' C1' H1' 86.8 78.4
C3' C4' C5' H5'1 18.3 300.0
C3' C4' C5' H5'2 127.8 60.0
C5' C4' C3' O4' 247.2 240.4
C5' C4' C3' H4' 125.1 121.1
O4' C4' C3' H4' 237.9 240.6
C3' C4' O4' C1' 353.8 26.5
O3' C3' C4' C2' 245.8 241.3
O3' C3' C4' H3' 123.6 122.5
C4' C3' O3' HA 180.0 294.8
C2' C3' C4' H3' 237.8 241.2
C4' C3' C2' O2' 184.7 220.9
C4' C3' C2' C1' 313.5 339.2
C4' C3' C2' H2' 66.2 97.4
H4' C4' C5' H5'1 143.4 61.0
H4' C4' C5' H5'2 252.9 181.0
C5' C4' H4' O4' 120.4 121.2
C5' C4' H4' C3' 237.3 239.0
O4' C4' H4' C3' 116.9 117.8
H4' C4' O4' C1' 231.7 267.1
H4' C4' C3' O3' 41.9 358.6
H4' C4' C3' C2' 156.2 117.3
H4' C4' C3' H3' 278.3 236.1
C1' O4' C4' C3' 353.8 26.5
C1' O4' C4' H4' 231.7 267.1
C3' C2' C1' O4' 43.7 37.0
O2' C2' C1' O4' 162.2 155.2
O4' C1' C2' H2' 290.9 278.8
C2' C1' O4' N1 137.1 118.7
C2' C1' O4' H1' 248.8 241.6
N1 C1' O4' H1' 111.7 122.9
O4' C1' N1 C2 308.0 58.2
O4' C1' N1 C6 124.3 238.5
O3' C3' C4' H4' 41.9 358.6
C4' C3' O3' C2' 105.9 114.8
C4' C3' O3' H3' 236.4 237.4
C2' C3' O3' H3' 130.5 122.6
O3' C3' C2' O2' 292.1 339.7
O3' C3' C2' C1' 60.9 97.9
O3' C3' C2' H2' 173.6 216.1
C2' C3' C4' H4' 156.2 117.3
C4' C3' C2' O3' 252.6 241.2
C4' C3' C2' H3' 122.2 118.7
O4' C1' C2' C3' 43.7 37.0
O3' C3' C2' H3' 229.5 237.5
C2' C3' O3' HA 74.1 180.0
O2' C2' C3' C1' 231.2 241.7
O2' C2' C3' H2' 118.5 123.6
C3' C2' O2' CA' 337.1 265.7
C1' C2' C3' H2' 247.3 241.8
C3' C2' C1' N1 163.6 155.5
C3' C2' C1' H1' 292.4 278.5
H3' C3' C4' H4' 278.3 236.1
C4' C3' H3' O3' 117.0 122.6
C4' C3' H3' C2' 245.9 245.2
O3' C3' H3' C2' 128.9 122.6
H3' C3' O3' HA 303.6 57.4
H3' C3' C2' O2' 62.6 102.2
H3' C3' C2' C1' 191.4 220.4
H3' C3' C2' H2' 304.1 338.6
HA O3' C3' C2' 74.1 180.0
HA O3' C3' H3' 303.6 57.4
O4' C1' C2' O2' 162.2 155.2
O2' C2' C3' H3' 62.6 102.2
C3' C2' O2' C1' 112.8 112.8
C3' C2' O2' H2' 241.5 236.4
C1' C2' O2' H2' 128.7 123.6
O2' C2' C1' N1 282.2 273.8
O2' C2' C1' H1' 51.0 36.7
C2' O2' CA' CB' 4.2 180.0
C2' O2' CA' HA'1 238.9 60.0
C2' O2' CA' HA'2 129.5 300.0
O4' C1' C2' N1 240.1 241.4
O4' C1' C2' H1' 111.2 118.5
C1' C2' C3' H3' 191.4 220.4
C3' C2' C1' O2' 241.4 241.8
C3' C2' C1' H2' 112.7 118.2
O2' C2' C1' H2' 231.3 236.4
C1' C2' O2' CA' 224.4 152.9
N1 C1' C2' H1' 231.1 237.0
C2' C1' N1 C2 188.6 304.1
C2' C1' N1 C6 4.9 124.4
H2' C2' C3' H3' 304.1 338.6
C3' C2' H2' O2' 118.7 123.6
C3' C2' H2' C1' 255.0 247.3
O2' C2' H2' C1' 136.3 123.7
H2' C2' O2' CA' 95.7 29.3
H2' C2' C1' N1 50.9 37.4
H2' C2' C1' H1' 179.7 160.3
CA' O2' C2' C1' 224.4 152.9
CA' O2' C2' H2' 95.7 29.3
CB' CA' O2' HA'1 125.3 120.0
CB' CA' O2' HA'2 234.7 240.0
O2' CA' CB' CC 148.1 180.0
O2' CA' CB' HB'1 22.9 60.1
O2' CA' CB' HB'2 273.4 300.0
HA'1 CA' O2' HA'2 109.4 120.0
O4' C1' N1 C2' 119.4 114.1
O4' C1' N1 H1' 248.3 237.1
N1 C1' C2' H2' 50.9 37.4
C2' C1' N1 H1' 128.9 123.0
C2 N1 C1' C6 183.7 179.7
C1' N1 C2 O2 359.2 0.3
C1' N1 C2 N3 183.9 179.7
C1' N1 C6 C5 174.3 180.0
C1' N1 C6 H6 354.3 0.0
O4' C1' H1' C2' 251.6 246.0
O4' C1' H1' N1 109.9 122.9
H1' C1' C2' H2' 179.7 160.3
C2' C1' H1' N1 218.3 236.9
H1' C1' N1 C2 59.7 181.1
H1' C1' N1 C6 236.0 1.4
C2 N1 C1' H1' 59.7 181.1
C1' N1 C2 C6 176.4 180.3
C2 N1 C6 C5 350.9 0.3
C2 N1 C6 H6 170.9 180.3
O2 C2 N1 N3 175.3 180.6
N1 C2 N3 C4 357.6 0.5
N1 C2 N3 H3 177.6 180.3
C6 N1 C1' H1' 236.0 1.4
C1' N1 C6 C2 183.4 179.7
C6 N1 C2 O2 182.8 180.0
C6 N1 C2 N3 7.5 359.5
C4 C5 C6 N1 5.0 0.0
N1 C6 C5 H5 185.0 180.0
C5 C6 N1 H6 180.0 180.0
O2 C2 N1 C6 182.8 180.0
N1 C2 O2 N3 184.9 179.4
O2 C2 N3 C4 182.2 180.0
O2 C2 N3 H3 2.2 359.7
N3 C2 N1 C6 7.5 359.5
N1 C2 N3 O2 175.4 180.6
C4 N3 C2 H3 180.0 180.3
C2 N3 C4 O4 177.8 179.7
C2 N3 C4 C5 358.2 359.7
C2 N3 C4 H3 180.0 179.7
O4 C4 N3 C5 179.6 180.0
N3 C4 C5 C6 0.7 0.0
N3 C4 C5 H5 180.7 180.0
C2 N3 H3 C4 180.0 180.3
H3 N3 C4 O4 357.8 360.0
H3 N3 C4 C5 178.3 180.0
O4 C4 N3 H3 357.8 360.0
N3 C4 O4 C5 180.5 180.0
O4 C4 C5 C6 181.1 180.0
O4 C4 C5 H5 1.1 360.0
N1 C6 C5 C4 5.0 0.0
C5 C4 N3 H3 178.3 180.0
N3 C4 C5 O4 179.5 180.0
C6 C5 C4 H5 180.0 180.0
C4 C5 C6 H6 185.0 180.0
N1 C6 C5 H6 180.0 180.0
C4 C5 C6 H5 180.0 180.0
C4 C5 H5 C6 180.0 180.0
H5 C5 C6 H6 5.0 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 H5 5.0 360.0
O2' CA' CB' HA'1 234.7 240.1
O2' CA' CB' HA'2 125.3 120.0
HA'1 CA' CB' HA'2 250.5 239.9
CC CB' CA' HB'1 125.3 119.9
CC CB' CA' HB'2 234.8 240.0
CA' CB' CC ND' 217.2 180.0
CA' CB' CC HCC1 91.9 60.0
CA' CB' CC HCC2 342.5 300.0
HB'1 CB' CA' HB'2 109.5 120.1
O2' CA' HA'1 CB' 136.2 120.0
O2' CA' HA'1 HA'2 248.1 240.0
CB' CA' HA'1 HA'2 111.9 120.1
HA'1 CA' CB' CC 273.4 299.9
HA'1 CA' CB' HB'1 148.1 180.0
HA'1 CA' CB' HB'2 38.6 59.9
O2' CA' HA'2 CB' 223.8 240.0
O2' CA' HA'2 HA'1 111.9 120.0
CB' CA' HA'2 HA'1 248.1 240.0
HA'2 CA' CB' CC 22.9 60.0
HA'2 CA' CB' HB'1 257.6 300.1
HA'2 CA' CB' HB'2 148.1 180.0
CC CB' CA' HA'1 273.4 299.9
CC CB' CA' HA'2 22.9 60.0
CA' CB' CC HB'1 234.7 240.0
CA' CB' CC HB'2 125.2 120.0
HB'1 CB' CC HB'2 250.5 240.0
ND' CC CB' HCC1 125.3 120.0
ND' CC CB' HCC2 234.7 240.0
CB' CC ND' HD'1 32.5 180.0
CB' CC ND' HD'2 283.1 293.8
HCC1 CC CB' HCC2 109.4 120.0
HB'1 CB' CA' HA'1 148.1 180.0
HB'1 CB' CA' HA'2 257.6 300.1
CA' CB' HB'1 CC 126.8 120.0
CA' CB' HB'1 HB'2 243.4 239.9
CC CB' HB'1 HB'2 116.6 120.0
HB'1 CB' CC ND' 342.5 300.0
HB'1 CB' CC HCC1 217.2 180.0
HB'1 CB' CC HCC2 107.8 60.0
HB'2 CB' CA' HA'1 38.6 59.9
HB'2 CB' CA' HA'2 148.1 180.0
CA' CB' HB'2 CC 233.2 240.0
CA' CB' HB'2 HB'1 116.6 120.0
CC CB' HB'2 HB'1 243.4 240.0
HB'2 CB' CC ND' 92.0 60.0
HB'2 CB' CC HCC1 326.7 300.0
HB'2 CB' CC HCC2 217.2 180.0
ND' CC CB' HB'1 342.5 300.0
ND' CC CB' HB'2 92.0 60.0
CB' CC ND' HCC1 234.7 240.0
CB' CC ND' HCC2 125.3 120.0
HCC1 CC ND' HCC2 250.5 240.0
HD'1 ND' CC HD'2 109.4 246.2
HCC1 CC CB' HB'1 217.2 180.0
HCC1 CC CB' HB'2 326.7 300.0
CB' CC HCC1 ND' 127.6 120.0
CB' CC HCC1 HCC2 243.8 240.0
ND' CC HCC1 HCC2 116.2 120.0
HCC1 CC ND' HD'1 157.8 300.0
HCC1 CC ND' HD'2 48.4 53.8
HCC2 CC CB' HB'1 107.8 60.0
HCC2 CC CB' HB'2 217.2 180.0
CB' CC HCC2 ND' 232.4 240.0
CB' CC HCC2 HCC1 116.2 120.0
ND' CC HCC2 HCC1 243.8 240.0
HCC2 CC ND' HD'1 267.3 60.0
HCC2 CC ND' HD'2 157.8 173.7
HD'1 ND' CC HCC1 157.8 300.0
HD'1 ND' CC HCC2 267.3 60.0
CC ND' HD'1 HD'2 239.0 113.8
HD'2 ND' CC HCC1 48.4 53.8
HD'2 ND' CC HCC2 157.8 173.7
CC ND' HD'2 HD'1 121.0 246.3