PDB Chemical Component NB8

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 NB8

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2P P 1.506 1.610
P O1P 1.503 1.480
P O3P 1.636 1.610
P O5' 1.601 1.610
O3P C 1.474 1.342
C O 1.235 1.208
C CA 1.516 1.507
CA N 1.448 1.469
CA CB 1.517 1.529
CB CG 1.529 1.508
CG OD1 1.225 1.212
CG ND2 1.331 1.348
ND2 OAJ 1.390 1.416
O5' C5' 1.418 1.429
C5' C4' 1.520 1.530
C4' C3' 1.507 1.545
C4' O4' 1.419 1.444
C3' O3' 1.423 1.429
C3' C2' 1.490 1.545
C2' O2' 1.422 1.430
C2' C1' 1.507 1.545
C1' O4' 1.411 1.444
C1' N9 1.474 1.465
N9 C4 1.328 1.372
N9 C8 1.328 1.363
C4 N3 1.360 1.330
C4 C5 1.372 1.405
N3 C2 1.344 1.316
C2 N1 1.327 1.320
N1 C6 1.319 1.328
C6 N6 1.349 1.384
C6 C5 1.469 1.406
C5 N7 1.340 1.354
O2P H2P 0.950 0.967
CA HA 1.100 1.091
N HN1 1.000 1.010
N HN2 1.000 1.009
CB HB1C 1.100 1.090
CB HB2C 1.100 1.090
ND2 HD2 1.000 0.970
OAJ HAJ 0.950 0.967
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.089
C4' H4' 1.100 1.090
C3' H3' 1.100 1.090
O3' HB 0.950 0.967
C2' H2' 1.100 1.090
O2' HC 0.949 0.966
C1' H1' 1.100 1.090
C8 H8 1.080 1.080
C2 H2 1.080 1.079
N6 H61N 1.000 0.970
N6 H62N 1.000 0.970
N7 C8 1.361 1.301

Bond Angles for NB8

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P 116.0 109.5
O2P P O3P 113.3 109.5
O2P P O5' 107.1 109.4
P O2P H2P 109.5 114.0
O1P P O3P 103.8 109.5
O1P P O5' 116.8 109.5
O3P P O5' 98.5 109.4
P O3P C 124.0 117.0
P O5' C5' 120.4 123.0
O3P C O 119.6 120.0
O3P C CA 118.7 120.0
O C CA 121.7 120.0
C CA N 112.3 109.5
C CA CB 110.0 109.5
C CA HA 107.2 109.4
N CA CB 109.5 109.5
N CA HA 107.7 109.4
CA N HN1 109.5 111.0
CA N HN2 109.5 111.0
CA CB CG 110.9 109.5
CB CA HA 110.1 109.5
CA CB HB1C 109.0 109.4
CA CB HB2C 108.7 109.5
CB CG OD1 121.4 120.0
CB CG ND2 116.8 120.0
CG CB HB1C 109.0 109.4
CG CB HB2C 108.7 109.5
OD1 CG ND2 121.8 120.1
CG ND2 OAJ 119.9 120.0
CG ND2 HD2 120.1 120.0
OAJ ND2 HD2 120.1 120.0
ND2 OAJ HAJ 109.5 114.0
O5' C5' C4' 110.7 109.4
O5' C5' H5'1 109.1 109.5
O5' C5' H5'2 108.8 109.5
C5' C4' C3' 113.1 110.3
C5' C4' O4' 111.9 110.4
C4' C5' H5'1 109.1 109.5
C4' C5' H5'2 108.8 109.5
C5' C4' H4' 103.9 110.4
C3' C4' O4' 105.0 104.8
C4' C3' O3' 110.6 110.5
C4' C3' C2' 101.2 104.0
C3' C4' H4' 111.0 110.3
C4' C3' H3' 114.5 110.5
C4' O4' C1' 110.4 105.3
O4' C4' H4' 112.1 110.5
O3' C3' C2' 110.6 110.5
O3' C3' H3' 105.7 110.5
C3' O3' HB 109.5 114.0
C3' C2' O2' 108.0 110.5
C3' C2' C1' 105.0 104.1
C2' C3' H3' 114.4 110.6
C3' C2' H2' 112.8 110.5
O2' C2' C1' 108.1 110.5
O2' C2' H2' 109.9 110.5
C2' O2' HC 109.5 114.0
C2' C1' O4' 105.6 104.8
C2' C1' N9 110.3 110.4
C1' C2' H2' 112.7 110.6
C2' C1' H1' 111.7 110.4
O4' C1' N9 110.1 110.4
O4' C1' H1' 111.8 110.4
C1' N9 C4 124.2 126.3
C1' N9 C8 126.8 126.3
N9 C1' H1' 107.3 110.4
C4 N9 C8 109.1 107.4
N9 C4 N3 133.2 134.9
N9 C4 C5 107.1 106.0
N9 C8 H8 125.6 125.0
N9 C8 N7 108.8 110.0
N3 C4 C5 119.7 119.1
C4 N3 C2 120.6 120.7
C4 C5 C6 117.5 118.1
C4 C5 N7 108.4 107.1
N3 C2 N1 121.9 122.4
N3 C2 H2 119.0 118.8
C2 N1 C6 121.5 121.2
N1 C2 H2 119.0 118.8
N1 C6 N6 120.5 120.8
N1 C6 C5 118.8 118.5
N6 C6 C5 120.7 120.7
C6 N6 H61N 109.5 120.0
C6 N6 H62N 109.5 120.0
C6 C5 N7 134.1 134.7
C5 N7 C8 106.7 109.5
HN1 N HN2 109.5 111.0
HB1C CB HB2C 110.6 109.5
H5'1 C5' H5'2 110.4 109.5
N7 C8 H8 125.6 125.0
H61N N6 H62N 109.4 120.1

Torsion Angles for NB8

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P O3P 240.0 240.0
O1P P O2P O5' 132.4 120.0
O3P P O2P O5' 252.4 240.1
O2P P O3P C 54.3 294.9
O2P P O5' C5' 180.3 65.1
O2P P O1P O3P 125.0 120.0
O2P P O1P O5' 232.2 240.0
O1P P O2P H2P 95.7 180.1
O3P P O1P O5' 107.2 120.0
O1P P O3P C 181.0 54.9
O1P P O5' C5' 48.3 305.1
O2P P O3P O1P 233.3 240.0
O2P P O3P O5' 112.9 119.9
O3P P O2P H2P 215.7 300.1
O1P P O3P O5' 239.6 240.0
O3P P O5' C5' 298.1 185.0
P O3P C O 352.7 0.1
P O3P C CA 172.9 180.0
O2P P O5' O1P 132.0 120.0
O2P P O5' O3P 242.3 240.1
O5' P O2P H2P 323.2 60.0
O1P P O5' O3P 110.3 120.0
O5' P O3P C 301.4 175.0
P O5' C5' C4' 238.9 180.0
P O5' C5' H5'1 358.9 299.9
P O5' C5' H5'2 119.4 59.9
C O3P P O5' 301.4 175.0
O C O3P CA 179.8 180.1
O3P C CA N 158.0 160.0
O3P C CA CB 280.1 280.1
O3P C CA HA 39.9 40.1
O3P C O CA 180.2 179.9
O C CA N 338.2 340.0
O C CA CB 100.3 100.0
O C CA HA 220.1 220.0
O3P C CA O 179.8 180.1
N CA C CB 237.8 240.0
N CA C HA 118.1 119.9
C CA N HN1 46.3 60.0
C CA N HN2 166.3 184.0
C CA CB CG 193.5 175.0
CB CA C HA 240.3 240.0
C CA CB HB1C 313.5 295.0
C CA CB HB2C 74.1 55.0
C CA N CB 122.4 120.1
C CA N HA 242.2 240.1
N CA CB CG 317.3 295.1
CB CA N HA 119.8 120.0
N CA CB HB1C 77.3 55.0
N CA CB HB2C 197.9 175.0
HN1 N CA HN2 240.0 236.0
C CA CB N 236.2 240.0
C CA CB HA 117.9 120.0
N CA CB HA 241.7 240.0
CB CA N HN1 283.8 299.9
CB CA N HN2 43.8 63.9
CA CB CG OD1 286.7 360.0
CA CB CG ND2 107.9 180.0
CG CB CA HB1C 240.0 240.0
CG CB CA HB2C 119.4 120.0
HB1C CB CA HB2C 239.4 240.0
CG CB CA HA 75.6 55.0
CA CB CG HB1C 120.0 120.0
CA CB CG HB2C 240.6 239.9
OD1 CG CB ND2 178.9 180.0
CB CG ND2 OAJ 179.9 180.0
CB CG ND2 HD2 359.9 0.0
HB1C CB CG HB2C 120.6 120.0
CB CG OD1 ND2 181.2 180.0
OD1 CG CB HB1C 166.7 240.0
OD1 CG CB HB2C 46.1 120.0
OD1 CG ND2 OAJ 1.0 360.0
OD1 CG ND2 HD2 181.0 180.0
CB CG ND2 OD1 178.8 180.0
ND2 CG CB HB1C 347.9 60.0
ND2 CG CB HB2C 227.3 300.0
OAJ ND2 CG HD2 180.0 180.0
CG ND2 OAJ HAJ 53.7 180.1
CG ND2 OAJ HD2 180.0 180.0
O5' C5' C4' C3' 68.5 185.0
O5' C5' C4' O4' 310.2 69.6
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 119.5 120.0
O5' C5' C4' H4' 188.9 307.2
H5'1 C5' O5' H5'2 239.5 240.0
O5' C5' C4' H5'1 120.0 119.9
O5' C5' C4' H5'2 240.5 240.0
C3' C4' C5' O4' 118.3 115.4
C5' C4' C3' O3' 85.7 98.5
C5' C4' C3' C2' 202.9 217.2
C3' C4' C5' H4' 239.6 237.8
C5' C4' C3' H3' 326.5 335.9
C5' C4' O4' C1' 147.0 159.3
O4' C4' C5' H4' 121.2 122.5
H5'1 C5' C4' H5'2 120.5 120.0
C5' C4' C3' O4' 237.7 241.2
C3' C4' C5' H5'1 308.5 65.0
C3' C4' C5' H5'2 188.0 305.0
C5' C4' C3' H4' 116.3 122.2
C3' C4' O4' C1' 24.0 40.5
O4' C4' C3' H4' 238.6 241.0
O3' C3' C4' C2' 242.8 241.3
O3' C3' C4' H3' 119.2 122.6
C4' C3' O3' HB 302.3 180.0
C4' C3' C2' O2' 277.6 241.3
C4' C3' C2' C1' 32.9 360.0
C2' C3' C4' H3' 236.4 241.2
C4' C3' C2' H2' 156.0 118.8
C5' C4' O4' C3' 123.0 118.8
O4' C4' C5' H5'1 190.1 309.7
O4' C4' C5' H5'2 69.6 189.6
C5' C4' O4' H4' 243.6 237.6
O4' C4' C3' O3' 208.0 217.4
O4' C4' C3' C2' 325.2 336.0
C3' C4' O4' H4' 120.6 118.8
O4' C4' C3' H3' 88.8 94.8
C2' C1' O4' C4' 357.2 319.5
C4' O4' C1' N9 238.2 200.6
C4' O4' C1' H1' 119.0 78.3
O3' C3' C4' O4' 208.0 217.4
C4' C3' O3' C2' 111.2 114.6
O3' C3' C4' H4' 329.4 336.3
C4' C3' O3' H3' 235.6 237.4
O3' C3' C2' O2' 34.8 360.0
O3' C3' C2' C1' 150.0 118.6
C2' C3' O3' H3' 124.4 122.8
O3' C3' C2' H2' 273.1 237.4
C2' C3' C4' O4' 325.2 336.0
C4' C3' C2' O3' 242.8 241.3
C2' C3' C4' H4' 86.6 95.0
C4' C3' C2' H3' 123.6 118.7
O3' C3' C2' H3' 240.8 237.3
C2' C3' O3' HB 191.1 65.4
O2' C2' C3' C1' 244.8 241.3
O2' C2' C3' H2' 121.7 122.6
C3' C2' O2' HC 4.9 298.6
C3' C2' C1' O4' 340.2 24.0
C3' C2' C1' N9 99.2 142.8
C1' C2' C3' H2' 236.9 241.2
C3' C2' C1' H1' 218.4 265.1
C3' C2' O2' C1' 113.1 114.6
O2' C2' C3' H3' 154.0 122.7
C3' C2' O2' H2' 236.5 237.4
O2' C2' C1' O4' 95.4 142.6
O2' C2' C1' N9 214.3 261.4
C1' C2' O2' H2' 123.4 122.8
O2' C2' C1' H1' 333.5 23.7
C4' O4' C1' C2' 357.2 319.5
C3' C2' C1' O2' 244.9 241.4
C1' C2' C3' H3' 269.3 241.3
C3' C2' C1' H2' 123.2 118.7
O2' C2' C1' H2' 238.3 237.3
C1' C2' O2' HC 251.8 183.9
O4' C1' C2' N9 241.1 241.2
O4' C1' C2' H1' 121.8 118.9
C2' C1' N9 C4 110.1 85.0
C2' C1' N9 C8 291.7 264.7
N9 C1' C2' H1' 240.8 237.7
C1' O4' C4' H4' 263.4 281.7
C2' C1' O4' N9 119.0 118.8
O4' C1' C2' H2' 217.1 265.3
C2' C1' O4' H1' 238.2 241.1
O4' C1' N9 C4 226.2 200.3
O4' C1' N9 C8 47.9 20.1
N9 C1' O4' H1' 119.2 122.3
C2' C1' N9 O4' 243.9 244.6
N9 C1' C2' H2' 336.0 24.1
C2' C1' N9 H1' 121.9 122.3
O4' C1' N9 H1' 238.1 237.7
C4 N9 C1' C8 178.4 180.3
C1' N9 C4 N3 0.4 0.0
C1' N9 C4 C5 180.4 180.0
C1' N9 C8 H8 359.7 0.1
C1' N9 C8 N7 179.7 179.8
C1' N9 C4 C8 181.4 179.8
C4 N9 C1' H1' 348.2 322.7
C4 N9 C8 H8 181.1 179.8
C4 N9 C8 N7 1.1 359.6
N3 C4 N9 C5 180.0 180.0
N9 C4 N3 C2 180.0 179.9
N9 C4 C5 C6 181.2 180.0
N9 C4 C5 N7 0.4 0.0
C1' N9 C8 C4 178.6 180.2
C8 N9 C1' H1' 169.8 142.4
C8 N9 C4 N3 179.1 180.3
C8 N9 C4 C5 359.1 0.2
C5 N7 C8 N9 359.1 0.4
N7 C8 N9 H8 180.0 179.7
N3 C4 N9 C8 179.1 180.3
N9 C4 N3 C5 180.0 179.9
N3 C4 C5 C6 1.2 360.0
N3 C4 C5 N7 180.4 180.0
C4 N3 C2 N1 359.5 0.1
C4 N3 C2 H2 179.5 180.0
C5 C4 N9 C8 359.1 0.2
N9 C4 C5 N3 180.0 180.0
C5 C4 N3 C2 0.0 360.0
N1 C6 C5 C4 358.0 0.0
N6 C6 C5 C4 180.2 180.0
C6 C5 C4 N7 180.8 180.0
C4 C5 N7 C8 0.3 359.7
C2 N3 C4 C5 0.0 360.0
N3 C2 N1 C6 359.7 359.9
N1 C2 N3 H2 180.0 180.1
N3 C2 N1 H2 180.0 179.9
C2 N1 C6 N6 179.4 180.0
C2 N1 C6 C5 1.6 0.0
C4 C5 C6 N1 358.0 0.0
C6 N1 C2 H2 179.6 180.1
N6 C6 N1 C5 177.8 180.0
N1 C6 N6 H61N 353.6 0.0
N1 C6 N6 H62N 113.5 180.0
N1 C6 C5 N7 179.1 180.0
C4 C5 C6 N6 180.2 180.0
N1 C6 N6 C5 182.2 180.0
N6 C6 C5 N7 1.2 0.0
H61N N6 C6 H62N 240.0 180.1
C4 C5 C6 N7 178.9 180.0
N1 C6 C5 N6 177.8 180.0
C5 C6 N6 H61N 171.4 180.0
C5 C6 N6 H62N 291.3 360.0
C6 C5 N7 C8 179.3 179.7
N9 C8 N7 C5 359.1 0.4
C4 C5 N7 C6 181.0 180.0
C5 N7 C8 H8 179.1 180.2
H2P O2P P O1P 95.7 180.1
H2P O2P P O3P 215.7 300.1
H2P O2P P O5' 323.2 60.0
C CA HA N 121.0 120.0
C CA HA CB 240.4 240.0
N CA HA CB 119.4 120.0
HA CA N HN1 164.1 179.9
HA CA N HN2 284.1 303.9
HA CA CB CG 75.6 55.0
HA CA CB HB1C 195.6 175.0
HA CA CB HB2C 316.1 295.0
HN1 N CA CB 283.8 299.9
HN1 N CA HA 164.1 179.9
CA N HN1 HN2 120.0 124.0
HN2 N CA CB 43.8 63.9
HN2 N CA HA 284.1 303.9
CA N HN2 HN1 240.0 236.0
CA CB HB1C CG 238.8 240.0
HB1C CB CA HA 195.6 175.0
CA CB HB1C HB2C 119.4 120.0
HB1C CB CG OD1 166.7 240.0
HB1C CB CG ND2 347.9 60.0
CG CB HB1C HB2C 240.6 240.0
CA CB HB2C CG 120.8 120.0
HB2C CB CA HA 316.1 295.0
CA CB HB2C HB1C 240.4 240.0
HB2C CB CG OD1 46.1 120.0
HB2C CB CG ND2 227.3 300.0
CG CB HB2C HB1C 119.6 120.0
CG ND2 HD2 OAJ 180.0 180.0
HD2 ND2 OAJ HAJ 233.7 0.1
HAJ OAJ ND2 HD2 233.7 0.1
O5' C5' H5'1 C4' 239.0 240.1
O5' C5' H5'1 H5'2 119.5 120.1
H5'1 C5' C4' C3' 308.5 65.0
H5'1 C5' C4' O4' 190.1 309.7
C4' C5' H5'1 H5'2 240.5 240.0
H5'1 C5' C4' H4' 68.9 187.2
O5' C5' H5'2 C4' 120.6 120.0
O5' C5' H5'2 H5'1 240.3 240.0
H5'2 C5' C4' C3' 188.0 305.0
H5'2 C5' C4' O4' 69.6 189.6
C4' C5' H5'2 H5'1 119.7 120.0
H5'2 C5' C4' H4' 308.4 67.2
C5' C4' H4' C3' 238.2 237.8
C5' C4' H4' O4' 121.1 122.4
H4' C4' C5' H5'1 68.9 187.2
H4' C4' C5' H5'2 308.4 67.2
C3' C4' H4' O4' 242.9 244.6
H4' C4' C3' O3' 329.4 336.3
H4' C4' C3' C2' 86.6 95.0
H4' C4' C3' H3' 210.2 213.7
H4' C4' O4' C1' 263.4 281.7
H3' C3' C4' O4' 88.8 94.8
C4' C3' H3' O3' 121.9 122.6
C4' C3' H3' C2' 243.9 245.3
H3' C3' C4' H4' 210.2 213.7
O3' C3' H3' C2' 122.0 122.7
H3' C3' O3' HB 66.7 302.6
H3' C3' C2' O2' 154.0 122.7
H3' C3' C2' C1' 269.3 241.3
H3' C3' C2' H2' 32.4 0.1
HB O3' C3' C2' 191.1 65.4
HB O3' C3' H3' 66.7 302.6
C3' C2' H2' O2' 120.6 122.6
C3' C2' H2' C1' 241.3 245.3
H2' C2' C3' H3' 32.4 0.1
O2' C2' H2' C1' 120.7 122.7
H2' C2' O2' HC 128.4 61.1
H2' C2' C1' O4' 217.1 265.3
H2' C2' C1' N9 336.0 24.1
H2' C2' C1' H1' 95.3 146.4
HC O2' C2' C1' 251.8 183.9
HC O2' C2' H2' 128.4 61.1
C2' C1' H1' O4' 118.2 115.4
C2' C1' H1' N9 239.0 237.7
H1' C1' C2' H2' 95.3 146.4
O4' C1' H1' N9 120.9 122.3
H1' C1' N9 C4 348.2 322.7
H1' C1' N9 C8 169.8 142.4
N9 C8 H8 N7 180.0 179.7
N3 C2 H2 N1 180.0 180.1
H2 C2 N1 C6 179.6 180.1
H61N N6 C6 C5 171.4 180.0
C6 N6 H61N H62N 120.0 179.9
H62N N6 C6 C5 291.3 360.0
C6 N6 H62N H61N 240.0 180.1
N9 C8 N7 H8 180.0 180.3