PDB Chemical Component DI

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 DI

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P   1.617
OP3 HOP3   0.981
P OP1 1.459 1.501
P OP2 1.523 1.617
P O5' 1.536 1.619
OP2 HOP2 0.950 0.981
O5' C5' 1.403 1.417
C5' C4' 1.506 1.523
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.091
C4' O4' 1.458 1.443
C4' C3' 1.534 1.525
C4' H4' 1.101 1.095
O4' C1' 1.452 1.439
C3' O3' 1.405 1.425
C3' C2' 1.522 1.512
C3' H3' 1.100 1.093
O3' HO3' 0.950 0.969
C2' C1' 1.531 1.522
C2' H2' 1.100 1.097
C2' H2'' 1.100 1.094
C1' N9 1.439 1.459
C1' H1' 1.100 1.095
N9 C8 1.395 1.376
N9 C4 1.386 1.366
C8 N7 1.329 1.318
C8 H8 1.080 1.082
N7 C5 1.399 1.365
C5 C6 1.405 1.440
C5 C4 1.401 1.377
C6 O6 1.263 1.224
C6 N1 1.388 1.402
N1 C2 1.424 1.400
N1 H1 1.000 1.016
C2 N3 1.385 1.302
C2 H2 1.079 1.101
N3 C4 1.345 1.352

Bond Angles for DI

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3   118.9
OP3 P OP1   115.3
OP3 P OP2   103.3
OP3 P O5'   103.7
OP1 P OP2 120.0 115.0
OP1 P O5' 108.3 115.0
OP2 P O5' 106.5 102.9
P OP2 HOP2 109.5 118.9
P O5' C5' 120.6 118.5
O5' C5' C4' 107.0 108.7
O5' C5' H5' 110.9 109.2
O5' C5' H5'' 110.3 109.2
C4' C5' H5' 110.9 110.1
C4' C5' H5'' 110.3 110.1
C5' C4' O4' 113.7 108.0
C5' C4' C3' 120.0 112.7
C5' C4' H4' 97.4 109.4
H5' C5' H5'' 107.6 109.6
O4' C4' C3' 107.9 106.8
O4' C4' H4' 112.4 107.7
C4' O4' C1' 106.8 108.7
C3' C4' H4' 104.7 112.0
C4' C3' O3' 107.0 109.6
C4' C3' C2' 99.9 103.2
C4' C3' H3' 117.3 114.0
O4' C1' C2' 106.9 106.7
O4' C1' N9 103.0 110.0
O4' C1' H1' 118.8 108.1
O3' C3' C2' 110.5 108.4
O3' C3' H3' 107.8 107.8
C3' O3' HO3' 109.5 106.6
C2' C3' H3' 114.1 113.7
C3' C2' C1' 102.1 101.6
C3' C2' H2' 113.6 110.0
C3' C2' H2'' 112.0 114.2
C1' C2' H2' 113.6 110.5
C1' C2' H2'' 112.0 111.7
C2' C1' N9 118.6 114.3
C2' C1' H1' 103.3 111.7
H2' C2' H2'' 103.9 108.7
N9 C1' H1' 107.2 105.9
C1' N9 C8 123.3 126.2
C1' N9 C4 128.3 127.3
C8 N9 C4 108.4 106.6
N9 C8 N7 111.4 112.6
N9 C8 H8 124.3 121.9
N9 C4 C5 103.8 105.0
N9 C4 N3 127.7 126.2
N7 C8 H8 124.3 125.5
C8 N7 C5 104.7 103.9
N7 C5 C6 128.9 128.6
N7 C5 C4 111.7 112.0
C6 C5 C4 119.4 119.4
C5 C6 O6 124.8 123.8
C5 C6 N1 113.3 110.9
C5 C4 N3 128.4 128.8
O6 C6 N1 121.9 125.4
C6 N1 C2 125.1 123.6
C6 N1 H1 117.5 118.2
C2 N1 H1 117.4 118.2
N1 C2 N3 120.8 125.8
N1 C2 H2 119.6 112.7
N3 C2 H2 119.6 121.5
C2 N3 C4 113.1 111.5

Torsion Angles for DI

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2   126.3
OP1 P OP3 O5'   233.4
OP2 P OP3 O5'   107.1
OP3 P OP2 HOP2   78.5
OP3 P O5' C5'   53.2
HOP3 OP3 P OP1   48.8
HOP3 OP3 P OP2   282.5
HOP3 OP3 P O5'   175.4
OP1 P OP3 HOP3   48.8
OP3 P OP1 OP2   239.9
OP3 P OP1 O5'   120.6
OP2 P OP1 O5' 122.3 240.7
OP1 P OP2 HOP2 121.3 312.0
OP1 P O5' C5' 288.6 180.0
OP2 P OP3 HOP3   282.5
OP3 P OP2 OP1   126.5
OP3 P OP2 O5'   252.3
OP1 P OP2 O5' 236.8 125.8
OP2 P O5' C5' 158.4 305.8
O5' P OP3 HOP3   175.4
OP3 P O5' OP1   233.2
OP3 P O5' OP2   107.4
OP1 P O5' OP2 130.2 234.2
O5' P OP2 HOP2 244.5 186.1
P O5' C5' C4' 144.8 180.0
P O5' C5' H5' 23.8 300.1
P O5' C5' H5'' 264.8 59.9
HOP2 OP2 P O5' 244.5 186.1
C4' C5' O5' H5' 121.0 239.9
C4' C5' O5' H5'' 240.0 120.1
O5' C5' C4' O4' 169.2 61.8
O5' C5' C4' C3' 299.0 179.5
O5' C5' C4' H4' 50.7 304.8
H5' C5' O5' H5'' 119.0 240.2
O5' C5' C4' H5' 239.0 119.6
O5' C5' C4' H5'' 120.0 240.5
H5' C5' C4' H5'' 241.0 120.9
O4' C4' C5' C3' 230.2 242.3
O4' C4' C5' H4' 118.5 117.0
C5' C4' O4' C1' 121.9 116.0
C3' C4' C5' H4' 248.3 234.7
C5' C4' C3' O3' 146.3 152.1
C5' C4' C3' C2' 261.4 267.4
C5' C4' C3' H3' 25.2 31.2
O5' C5' H5' C4' 118.6 240.8
O5' C5' H5' H5'' 239.3 119.6
C4' C5' H5' H5'' 120.7 238.8
H5' C5' C4' O4' 290.1 302.2
H5' C5' C4' C3' 59.9 60.0
H5' C5' C4' H4' 171.6 185.3
O5' C5' H5'' C4' 242.1 119.2
O5' C5' H5'' H5' 121.0 240.4
C4' C5' H5'' H5' 239.0 121.2
H5'' C5' C4' O4' 49.2 181.3
H5'' C5' C4' C3' 179.0 299.1
H5'' C5' C4' H4' 290.7 64.3
O4' C4' C5' H5' 290.1 302.2
O4' C4' C5' H5'' 49.2 181.3
C5' C4' O4' C3' 135.6 121.5
C5' C4' O4' H4' 250.5 242.0
C3' C4' O4' H4' 114.9 120.5
O4' C4' C3' O3' 278.6 270.6
O4' C4' C3' C2' 33.8 25.9
O4' C4' C3' H3' 157.6 149.7
C4' O4' C1' C2' 347.7 342.7
C4' O4' C1' N9 222.0 218.2
C4' O4' C1' H1' 103.9 103.1
C3' C4' C5' H5' 59.9 60.0
C3' C4' C5' H5'' 179.0 299.1
C5' C4' C3' O4' 227.7 241.5
C5' C4' C3' H4' 107.7 123.8
O4' C4' C3' H4' 240.1 242.3
C3' C4' O4' C1' 346.2 354.5
O3' C3' C4' C2' 244.9 244.7
O3' C3' C4' H3' 121.1 120.9
C4' C3' O3' HO3' 161.4 46.6
C2' C3' C4' H3' 236.2 236.3
C4' C3' C2' C1' 320.6 325.2
C4' C3' C2' H2' 198.0 82.2
C4' C3' C2' H2'' 80.7 204.8
H4' C4' C5' H5' 171.6 185.3
H4' C4' C5' H5'' 290.7 64.3
C5' C4' H4' O4' 119.5 117.2
C5' C4' H4' C3' 236.3 234.3
O4' C4' H4' C3' 116.8 117.2
H4' C4' O4' C1' 231.3 234.0
H4' C4' C3' O3' 38.6 28.3
H4' C4' C3' C2' 153.7 143.6
H4' C4' C3' H3' 277.5 267.4
C1' O4' C4' C3' 346.2 354.5
C1' O4' C4' H4' 231.3 234.0
C3' C2' C1' O4' 33.5 32.7
O4' C1' C2' H2' 156.1 276.0
O4' C1' C2' H2'' 273.4 154.9
C2' C1' O4' N9 125.6 124.5
C2' C1' O4' H1' 243.8 239.7
N9 C1' O4' H1' 118.2 115.2
O4' C1' N9 C8 250.6 33.5
O4' C1' N9 C4 67.5 213.5
O3' C3' C4' H4' 38.6 28.3
C4' C3' O3' C2' 107.8 111.9
C4' C3' O3' H3' 233.1 235.4
C2' C3' O3' H3' 125.3 123.5
O3' C3' C2' C1' 73.1 81.3
O3' C3' C2' H2' 310.4 198.4
O3' C3' C2' H2'' 193.1 320.9
C2' C3' C4' H4' 153.7 143.6
C4' C3' C2' O3' 247.6 243.8
C4' C3' C2' H3' 125.9 123.9
O4' C1' C2' C3' 33.5 32.7
O3' C3' C2' H3' 238.4 240.1
C2' C3' O3' HO3' 53.6 294.7
C1' C2' C3' H2' 122.7 243.0
C1' C2' C3' H2'' 240.0 120.4
C3' C2' C1' N9 149.1 154.5
C3' C2' C1' H1' 267.4 274.8
H2' C2' C3' H2'' 117.3 237.5
H3' C3' C4' H4' 277.5 267.4
C4' C3' H3' O3' 120.7 121.9
C4' C3' H3' C2' 243.8 242.1
O3' C3' H3' C2' 123.1 120.2
H3' C3' O3' HO3' 288.3 171.2
H3' C3' C2' C1' 194.7 201.2
H3' C3' C2' H2' 72.0 318.3
H3' C3' C2' H2'' 314.7 80.8
HO3' O3' C3' C2' 53.6 294.7
HO3' O3' C3' H3' 288.3 171.2
O4' C1' C2' N9 244.4 238.2
O4' C1' C2' H1' 126.1 117.9
C1' C2' C3' H3' 194.7 201.2
C3' C2' C1' H2' 237.3 116.7
C3' C2' C1' H2'' 120.0 237.8
H2' C2' C1' H2'' 242.7 121.1
N9 C1' C2' H1' 241.7 239.7
C2' C1' N9 C8 132.9 273.4
C2' C1' N9 C4 309.8 93.5
H2' C2' C3' H3' 72.0 318.3
C3' C2' H2' C1' 116.1 248.6
C3' C2' H2' H2'' 238.0 125.7
C1' C2' H2' H2'' 121.9 237.1
H2' C2' C1' N9 271.7 37.8
H2' C2' C1' H1' 30.1 158.1
H2'' C2' C3' H3' 314.7 80.8
C3' C2' H2'' C1' 246.0 114.6
C3' C2' H2'' H2' 123.0 236.7
C1' C2' H2'' H2' 237.0 122.1
H2'' C2' C1' N9 29.1 276.7
H2'' C2' C1' H1' 147.4 37.0
O4' C1' N9 C2' 117.7 120.0
O4' C1' N9 H1' 233.9 243.5
N9 C1' C2' H2' 271.7 37.8
N9 C1' C2' H2'' 29.1 276.7
C2' C1' N9 H1' 116.3 123.5
C8 N9 C1' C4 183.1 180.0
C1' N9 C8 N7 177.7 180.1
C1' N9 C8 H8 357.8 0.1
C1' N9 C4 C5 183.0 179.9
C1' N9 C4 N3 2.1 0.0
O4' C1' H1' C2' 242.0 242.9
O4' C1' H1' N9 116.0 117.8
H1' C1' C2' H2' 30.1 158.1
H1' C1' C2' H2'' 147.4 37.0
C2' C1' H1' N9 234.0 234.9
H1' C1' N9 C8 16.6 150.0
H1' C1' N9 C4 193.5 330.0
C8 N9 C1' H1' 16.6 150.0
C1' N9 C8 C4 177.4 180.0
C8 N9 C4 C5 0.3 359.9
C8 N9 C4 N3 179.4 180.1
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.3 0.0
C4 N9 C1' H1' 193.5 330.0
C1' N9 C4 C8 182.7 180.0
C4 N9 C8 N7 0.3 0.0
C4 N9 C8 H8 180.3 180.0
N7 C5 C4 N9 359.3 0.1
C6 C5 C4 N9 178.9 180.1
C5 C4 N9 N3 180.9 179.9
C2 N3 C4 N9 180.7 179.9
N7 C8 N9 C4 0.3 0.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 181.4 179.9
C8 N7 C5 C4 0.9 359.9
H8 C8 N9 C4 180.3 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 179.3 180.0
N9 C4 C5 N7 359.3 0.1
C5 N7 C8 H8 179.3 180.0
C6 C5 N7 C4 180.5 180.0
N7 C5 C6 O6 0.7 360.0
N7 C5 C6 N1 180.1 180.0
N7 C5 C4 N3 180.2 180.0
N9 C4 C5 C6 178.9 180.1
N7 C5 C6 C4 179.5 180.0
C6 C5 C4 N3 359.8 359.9
O6 C6 C5 N1 180.6 180.0
C5 C6 N1 C2 359.5 0.0
C5 C6 N1 H1 179.5 180.1
N9 C4 C5 N3 179.1 180.1
N7 C5 C4 C6 180.4 180.0
C4 C5 C6 O6 181.2 180.0
C4 C5 C6 N1 0.6 360.0
C2 N3 C4 C5 359.6 0.1
O6 C6 C5 C4 181.2 180.0
C5 C6 O6 N1 179.4 180.0
O6 C6 N1 C2 178.9 180.0
O6 C6 N1 H1 358.9 0.1
N1 C6 C5 C4 0.6 360.0
C5 C6 N1 O6 180.6 180.0
C2 N1 C6 H1 180.0 180.0
C6 N1 C2 N3 359.9 360.0
C6 N1 C2 H2 179.9 179.9
C6 N1 C2 H1 180.0 180.0
N3 C2 N1 H2 180.0 180.0
N1 C2 N3 C4 0.5 360.0
C6 N1 H1 C2 180.0 180.0
H1 N1 C2 N3 179.9 179.9
H1 N1 C2 H2 359.9 359.9
N9 C4 N3 C2 180.7 179.9
C5 C4 N3 C2 359.6 0.1
N3 C2 N1 H1 179.9 179.9
N1 C2 N3 H2 180.0 180.0
H2 C2 N1 H1 359.9 359.9
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 180.6 180.0
N9 C4 N3 C5 181.1 179.8
C4 N3 C2 H2 180.6 180.0