PDB Chemical Component GNP

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 GNP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PG O1G 1.499 1.479
PG O2G 1.520 1.610
PG O3G 1.481 1.609
PG N3B 1.729 1.684
O2G HOG2 0.950 0.967
O3G HOG3 0.950 0.966
N3B PB 1.683 1.683
N3B HNB3 1.020 1.009
PB O1B 1.464 1.480
PB O2B 1.493 1.609
PB O3A 1.629 1.610
O2B HOB2 0.950 0.968
O3A PA 1.553 1.609
PA O1A 1.478 1.481
PA O2A 1.508 1.609
PA O5' 1.519 1.609
O2A HOA2 0.950 0.966
O5' C5' 1.436 1.429
C5' C4' 1.497 1.529
C5' H5'2 1.115 1.090
C5' H5'1 1.115 1.090
C4' O4' 1.382 1.444
C4' C3' 1.557 1.545
C4' H4' 1.114 1.090
O4' C1' 1.407 1.445
C3' O3' 1.440 1.428
C3' C2' 1.542 1.547
C3' H3' 1.115 1.090
O3' HO3' 0.950 0.967
C2' O2' 1.394 1.429
C2' C1' 1.507 1.544
C2' H2' 1.116 1.090
O2' HO2' 0.950 0.967
C1' N9 1.477 1.463
C1' H1' 1.114 1.091
N9 C8 1.456 1.365
N9 C4 1.353 1.369
C8 N7 1.311 1.301
C8 H8 1.103 1.080
N7 C5 1.492 1.356
C5 C6 1.448 1.415
C5 C4 1.349 1.399
C6 O6 1.177 1.219
C6 N1 1.359 1.351
N1 C2 1.363 1.364
N1 HN1 1.020 0.970
C2 N2 1.434 1.372
C2 N3 1.272 1.314
N2 HN21 1.020 0.970
N2 HN22 1.020 0.970
N3 C4 1.337 1.337

Bond Angles for GNP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G PG O2G 109.7 109.5
O1G PG O3G 115.4 109.5
O1G PG N3B 100.6 109.5
O2G PG O3G 112.2 109.5
O2G PG N3B 108.2 109.4
PG O2G HOG2 109.7 106.7
O3G PG N3B 109.9 109.5
PG O3G HOG3 115.5 106.8
PG N3B PB 121.8 106.7
PG N3B HNB3 107.8 106.7
PB N3B HNB3 107.8 106.7
N3B PB O1B 109.6 109.5
N3B PB O2B 109.5 109.5
N3B PB O3A 100.9 109.5
O1B PB O2B 121.2 109.5
O1B PB O3A 105.9 109.5
O2B PB O3A 107.8 109.5
PB O2B HOB2 109.5 106.8
PB O3A PA 129.7 106.8
O3A PA O1A 110.4 109.4
O3A PA O2A 108.8 109.4
O3A PA O5' 101.4 109.5
O1A PA O2A 122.2 109.5
O1A PA O5' 105.7 109.4
O2A PA O5' 106.2 109.5
PA O2A HOA2 108.8 106.8
PA O5' C5' 121.9 106.8
O5' C5' C4' 109.8 109.5
O5' C5' H5'2 112.1 109.5
O5' C5' H5'1 112.0 109.5
C4' C5' H5'2 112.1 109.5
C4' C5' H5'1 112.1 109.5
C5' C4' O4' 116.8 110.4
C5' C4' C3' 112.1 110.5
C5' C4' H4' 100.9 110.4
H5'2 C5' H5'1 98.3 109.5
O4' C4' C3' 105.0 104.8
O4' C4' H4' 108.7 110.4
C4' O4' C1' 111.4 105.3
C3' C4' H4' 113.7 110.3
C4' C3' O3' 111.0 110.5
C4' C3' C2' 101.6 104.1
C4' C3' H3' 113.4 110.5
O4' C1' C2' 106.8 104.9
O4' C1' N9 108.7 110.4
O4' C1' H1' 112.1 110.3
O3' C3' C2' 109.1 110.6
O3' C3' H3' 106.5 110.5
C3' O3' HO3' 110.9 106.8
C2' C3' H3' 115.1 110.6
C3' C2' O2' 112.8 110.5
C3' C2' C1' 98.6 104.0
C3' C2' H2' 114.4 110.5
O2' C2' C1' 109.4 110.8
O2' C2' H2' 104.4 110.5
C2' O2' HO2' 112.8 106.8
C1' C2' H2' 117.5 110.4
C2' C1' N9 110.6 110.4
C2' C1' H1' 110.3 110.4
N9 C1' H1' 108.4 110.3
C1' N9 C8 123.5 126.3
C1' N9 C4 128.7 126.3
C8 N9 C4 107.8 107.5
N9 C8 N7 109.7 109.8
N9 C8 H8 129.4 125.1
N9 C4 C5 108.1 106.1
N9 C4 N3 124.1 134.2
N7 C8 H8 120.9 125.1
C8 N7 C5 104.4 109.3
N7 C5 C6 128.3 134.1
N7 C5 C4 109.1 107.3
C6 C5 C4 121.7 118.6
C5 C6 O6 129.9 120.8
C5 C6 N1 109.7 118.3
C5 C4 N3 127.8 119.7
O6 C6 N1 119.8 120.8
C6 N1 C2 118.6 120.3
C6 N1 HN1 120.5 119.8
C2 N1 HN1 120.9 119.8
N1 C2 N2 108.4 119.0
N1 C2 N3 135.3 121.9
N2 C2 N3 116.3 119.1
C2 N2 HN21 108.4 119.9
C2 N2 HN22 112.6 120.0
C2 N3 C4 105.8 121.1
HN21 N2 HN22 112.7 120.0

Torsion Angles for GNP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G PG O1G O3G 128.0 120.0
O2G PG O1G N3B 246.1 240.0
O1G PG O2G HOG2 180.0 300.0
O3G PG O1G N3B 118.1 120.0
O1G PG O3G HOG3 179.9 180.0
O1G PG N3B PB 189.8 60.0
O1G PG N3B HNB3 64.5 306.2
O1G PG O2G O3G 230.3 239.9
O1G PG O2G N3B 108.9 120.0
O3G PG O2G N3B 238.6 240.0
O2G PG O3G HOG3 53.2 60.0
O2G PG N3B PB 304.8 180.0
O2G PG N3B HNB3 179.6 66.2
O1G PG O3G O2G 126.7 120.0
O1G PG O3G N3B 247.2 240.0
O2G PG O3G N3B 120.4 119.9
O3G PG O2G HOG2 309.8 60.0
O3G PG N3B PB 67.6 299.9
O3G PG N3B HNB3 302.4 186.2
O1G PG N3B O2G 245.0 240.0
O1G PG N3B O3G 122.2 120.1
O2G PG N3B O3G 237.2 240.0
N3B PG O2G HOG2 71.2 180.0
N3B PG O3G HOG3 292.8 300.0
PB N3B PG HNB3 125.2 113.8
PG N3B PB O1B 278.4 300.0
PG N3B PB O2B 53.6 60.0
PG N3B PB O3A 167.0 180.0
HOG2 O2G PG O3G 309.8 60.0
HOG2 O2G PG N3B 71.2 180.0
HOG3 O3G PG N3B 292.8 300.0
PG N3B PB HNB3 234.8 246.3
O1B PB N3B O2B 224.8 240.0
O1B PB N3B O3A 111.4 120.0
O2B PB N3B O3A 246.6 240.0
N3B PB O2B HOB2 180.1 60.0
N3B PB O3A PA 261.9 180.0
PG N3B HNB3 PB 133.2 113.7
HNB3 N3B PB O1B 43.7 53.8
HNB3 N3B PB O2B 178.9 173.7
HNB3 N3B PB O3A 292.3 293.7
O1B PB N3B HNB3 43.7 53.8
N3B PB O1B O2B 129.1 120.0
N3B PB O1B O3A 252.0 240.0
O2B PB O1B O3A 122.9 120.0
O1B PB O2B HOB2 309.1 180.0
O1B PB O3A PA 147.7 60.0
O2B PB N3B HNB3 178.9 173.7
N3B PB O2B O1B 230.9 240.0
N3B PB O2B O3A 108.9 120.0
O1B PB O2B O3A 238.0 240.0
O2B PB O3A PA 16.6 300.0
O3A PB N3B HNB3 292.3 293.7
N3B PB O3A O1B 114.2 120.0
N3B PB O3A O2B 245.3 240.0
O1B PB O3A O2B 131.1 120.0
O3A PB O2B HOB2 71.2 300.0
PB O3A PA O1A 289.9 300.0
PB O3A PA O2A 66.6 60.0
PB O3A PA O5' 178.2 180.0
HOB2 O2B PB O3A 71.2 300.0
O1A PA O3A O2A 223.3 240.0
O1A PA O3A O5' 111.7 120.0
O2A PA O3A O5' 248.4 239.9
O3A PA O2A HOA2 180.0 60.0
O3A PA O5' C5' 299.0 180.0
O3A PA O1A O2A 129.9 120.0
O3A PA O1A O5' 251.1 240.0
O2A PA O1A O5' 121.2 120.0
O1A PA O2A HOA2 310.6 180.0
O1A PA O5' C5' 183.7 60.0
O3A PA O2A O1A 229.4 240.0
O3A PA O2A O5' 108.4 120.1
O1A PA O2A O5' 239.0 240.0
O2A PA O5' C5' 52.6 300.0
O3A PA O5' O1A 115.3 120.0
O3A PA O5' O2A 246.4 240.0
O1A PA O5' O2A 131.1 120.0
O5' PA O2A HOA2 71.6 300.0
PA O5' C5' C4' 198.4 180.0
PA O5' C5' H5'2 323.7 300.0
PA O5' C5' H5'1 73.1 59.9
HOA2 O2A PA O5' 71.6 300.0
C4' C5' O5' H5'2 234.7 240.0
C4' C5' O5' H5'1 125.3 120.0
O5' C5' C4' O4' 298.4 61.5
O5' C5' C4' C3' 59.5 176.9
O5' C5' C4' H4' 180.8 299.1
H5'2 C5' O5' H5'1 250.6 240.0
O5' C5' C4' H5'2 125.2 120.0
O5' C5' C4' H5'1 234.8 240.0
H5'2 C5' C4' H5'1 109.5 120.0
O4' C4' C5' C3' 238.8 244.6
O4' C4' C5' H4' 117.5 122.3
C5' C4' O4' C1' 119.1 159.4
C3' C4' C5' H4' 238.7 237.8
C5' C4' C3' O3' 145.0 98.3
C5' C4' C3' C2' 260.9 217.1
C5' C4' C3' H3' 25.1 335.8
O5' C5' H5'2 C4' 236.0 240.0
O5' C5' H5'2 H5'1 117.9 120.0
C4' C5' H5'2 H5'1 241.9 240.0
H5'2 C5' C4' O4' 173.1 301.5
H5'2 C5' C4' C3' 294.3 56.9
H5'2 C5' C4' H4' 55.6 179.2
O5' C5' H5'1 C4' 124.0 120.0
O5' C5' H5'1 H5'2 242.0 240.0
C4' C5' H5'1 H5'2 118.1 120.0
H5'1 C5' C4' O4' 63.6 181.5
H5'1 C5' C4' C3' 184.7 296.9
H5'1 C5' C4' H4' 306.1 59.2
O4' C4' C5' H5'2 173.1 301.5
O4' C4' C5' H5'1 63.6 181.5
C5' C4' O4' C3' 124.9 118.9
C5' C4' O4' H4' 246.8 237.7
C3' C4' O4' H4' 121.9 118.8
O4' C4' C3' O3' 272.7 217.2
O4' C4' C3' C2' 28.7 335.9
O4' C4' C3' H3' 152.9 94.7
C4' O4' C1' C2' 339.5 319.6
C4' O4' C1' N9 220.2 200.6
C4' O4' C1' H1' 100.4 78.4
C3' C4' C5' H5'2 294.3 56.9
C3' C4' C5' H5'1 184.7 296.9
C5' C4' C3' O4' 232.3 241.1
C5' C4' C3' H4' 113.6 122.3
O4' C4' C3' H4' 241.4 241.2
C3' C4' O4' C1' 354.2 40.5
O3' C3' C4' C2' 244.1 241.3
O3' C3' C4' H3' 119.9 122.6
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 235.8 241.3
C4' C3' C2' O2' 206.3 241.2
C4' C3' C2' C1' 321.6 0.1
C4' C3' C2' H2' 87.1 118.6
H4' C4' C5' H5'2 55.6 179.2
H4' C4' C5' H5'1 306.1 59.2
C5' C4' H4' O4' 123.3 122.3
C5' C4' H4' C3' 239.8 237.7
O4' C4' H4' C3' 116.5 115.4
H4' C4' O4' C1' 232.3 281.7
H4' C4' C3' O3' 31.4 336.1
H4' C4' C3' C2' 147.3 94.8
H4' C4' C3' H3' 271.5 213.5
C1' O4' C4' C3' 354.2 40.5
C1' O4' C4' H4' 232.3 281.7
C3' C2' C1' O4' 36.9 23.8
O2' C2' C1' O4' 154.8 142.6
O4' C1' C2' H2' 273.6 265.3
C2' C1' O4' N9 119.3 119.0
C2' C1' O4' H1' 239.1 241.2
N9 C1' O4' H1' 119.8 122.2
O4' C1' N9 C8 65.4 27.0
O4' C1' N9 C4 244.2 207.0
O3' C3' C4' H4' 31.4 336.1
C4' C3' O3' C2' 111.2 114.7
C4' C3' O3' H3' 236.1 237.4
C2' C3' O3' H3' 124.9 122.8
O3' C3' C2' O2' 323.6 359.9
O3' C3' C2' C1' 78.9 118.8
O3' C3' C2' H2' 204.4 237.3
C2' C3' C4' H4' 147.3 94.8
C4' C3' C2' O3' 242.7 241.3
C4' C3' C2' H3' 123.0 118.6
O4' C1' C2' C3' 36.9 23.8
O3' C3' C2' H3' 240.3 237.3
C2' C3' O3' HO3' 68.8 65.3
O2' C2' C3' C1' 244.7 241.1
O2' C2' C3' H2' 119.2 122.6
C3' C2' O2' HO2' 180.0 298.5
C1' C2' C3' H2' 234.5 241.5
C3' C2' C1' N9 155.0 142.8
C3' C2' C1' H1' 274.8 265.0
H3' C3' C4' H4' 271.5 213.5
C4' C3' H3' O3' 122.4 122.6
C4' C3' H3' C2' 243.5 245.3
O3' C3' H3' C2' 121.1 122.7
H3' C3' O3' HO3' 303.9 302.6
H3' C3' C2' O2' 83.2 122.6
H3' C3' C2' C1' 198.6 241.5
H3' C3' C2' H2' 324.1 360.0
HO3' O3' C3' C2' 68.8 65.3
HO3' O3' C3' H3' 303.9 302.6
O4' C1' C2' O2' 154.8 142.6
O2' C2' C3' H3' 83.2 122.6
C3' C2' O2' C1' 108.6 114.8
C3' C2' O2' H2' 235.2 237.4
C1' C2' O2' H2' 126.6 122.6
O2' C2' C1' N9 272.9 261.5
O2' C2' C1' H1' 32.8 23.8
O4' C1' C2' N9 241.9 241.1
O4' C1' C2' H1' 122.0 118.8
C1' C2' C3' H3' 198.6 241.5
C3' C2' C1' O2' 242.0 241.2
C3' C2' C1' H2' 123.3 118.6
O2' C2' C1' H2' 241.2 237.3
C1' C2' O2' HO2' 71.4 183.8
N9 C1' C2' H1' 240.1 237.8
C2' C1' N9 C8 308.4 271.5
C2' C1' N9 C4 127.2 91.5
H2' C2' C3' H3' 324.1 360.0
C3' C2' H2' O2' 123.8 122.6
C3' C2' H2' C1' 245.2 245.5
O2' C2' H2' C1' 121.4 122.8
H2' C2' O2' HO2' 304.8 61.2
H2' C2' C1' N9 31.7 24.2
H2' C2' C1' H1' 151.6 146.4
HO2' O2' C2' C1' 71.4 183.8
HO2' O2' C2' H2' 304.8 61.2
O4' C1' N9 C2' 116.9 115.5
O4' C1' N9 H1' 237.9 237.8
N9 C1' C2' H2' 31.7 24.2
C2' C1' N9 H1' 121.0 122.3
C8 N9 C1' C4 181.2 180.0
C1' N9 C8 N7 184.7 180.0
C1' N9 C8 H8 4.7 0.0
C1' N9 C4 C5 182.1 180.0
C1' N9 C4 N3 3.2 0.0
O4' C1' H1' C2' 241.1 244.6
O4' C1' H1' N9 120.0 122.2
H1' C1' C2' H2' 151.6 146.4
C2' C1' H1' N9 238.8 237.7
H1' C1' N9 C8 187.4 149.3
H1' C1' N9 C4 6.2 329.2
C8 N9 C1' H1' 187.4 149.3
C1' N9 C8 C4 179.0 180.0
C8 N9 C4 C5 1.0 360.0
C8 N9 C4 N3 182.2 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 350.9 0.0
C4 N9 C1' H1' 6.2 329.2
C1' N9 C4 C8 181.1 180.0
C4 N9 C8 N7 5.7 0.0
C4 N9 C8 H8 185.6 180.0
N7 C5 C4 N9 353.5 0.0
C6 C5 C4 N9 183.7 180.0
C5 C4 N9 N3 178.8 180.0
C2 N3 C4 N9 182.6 180.0
N7 C8 N9 C4 5.7 0.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 178.8 180.0
C8 N7 C5 C4 9.9 360.0
H8 C8 N9 C4 185.6 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 171.0 180.0
N9 C4 C5 N7 353.5 0.0
C5 N7 C8 H8 171.0 180.0
C6 C5 N7 C4 168.9 180.0
N7 C5 C6 O6 11.4 360.0
N7 C5 C6 N1 182.0 179.7
N7 C5 C4 N3 172.2 180.0
N9 C4 C5 C6 183.7 180.0
N7 C5 C6 C4 192.4 180.0
C6 C5 C4 N3 2.5 0.0
O6 C6 C5 N1 189.4 180.3
C5 C6 N1 C2 11.5 0.6
C5 C6 N1 HN1 191.5 180.0
N9 C4 C5 N3 181.2 180.0
N7 C5 C4 C6 169.8 180.0
C4 C5 C6 O6 179.1 180.0
C4 C5 C6 N1 349.7 359.7
C2 N3 C4 C5 4.0 360.0
O6 C6 C5 C4 179.1 180.0
C5 C6 O6 N1 169.8 179.7
O6 C6 N1 C2 183.2 180.3
O6 C6 N1 HN1 3.3 359.7
N1 C6 C5 C4 349.7 359.7
C5 C6 N1 O6 188.3 180.3
C2 N1 C6 HN1 180.0 180.7
C6 N1 C2 N2 176.4 179.7
C6 N1 C2 N3 353.6 359.4
C6 N1 C2 HN1 180.0 179.3
N2 C2 N1 N3 182.9 180.3
N1 C2 N2 HN21 180.0 179.8
N1 C2 N2 HN22 54.7 359.4
N1 C2 N3 C4 357.8 0.3
C6 N1 HN1 C2 180.0 180.7
HN1 N1 C2 N2 356.4 0.3
HN1 N1 C2 N3 173.6 180.0
N2 C2 N1 HN1 356.4 0.3
N1 C2 N2 N3 177.7 179.7
N2 C2 N3 C4 174.7 180.0
HN21 N2 C2 HN22 125.3 180.3
N9 C4 N3 C2 182.6 180.0
C5 C4 N3 C2 4.0 360.0
N3 C2 N1 HN1 173.6 180.0
N1 C2 N3 N2 183.1 180.3
N3 C2 N2 HN21 2.3 0.1
N3 C2 N2 HN22 237.0 179.7
HN21 N2 C2 N3 2.3 0.1
C2 N2 HN21 HN22 234.8 179.7
HN22 N2 C2 N3 237.0 179.7
C2 N2 HN22 HN21 122.9 180.3
N9 C4 N3 C5 178.6 180.0