PDB Chemical Component VRT

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 VRT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C O 1.236 1.212
C CA 1.542 1.508
C N10 1.340 1.347
N CA 1.511 1.469
N1 C2 1.366 1.320
N1 C6 1.383 1.329
C2 N3 1.383 1.317
N3 C4 1.409 1.329
C4 C5 1.414 1.405
C4 N9 1.377 1.371
C5 C6 1.522 1.405
C5 N7 1.394 1.355
C6 N6 1.338 1.385
N7 C8 1.355 1.302
C8 N9 1.382 1.364
N9 C1' 1.522 1.465
CA CB 1.546 1.530
CB CG 1.544 1.531
CD CG 1.518 1.530
C1' C2' 1.568 1.550
C1' O4' 1.444 1.443
N10 C2' 1.467 1.466
C2' C3' 1.565 1.548
C3' O3' 1.482 1.429
C3' C4' 1.554 1.542
C4' O4' 1.434 1.437
C4' C5' 1.529 1.530
C5' O5' 1.438 1.430
N HN 1.000 1.009
N HNA 1.000 1.009
C2 H2 1.080 1.081
N6 HN6 1.000 0.969
N6 HN6A 0.999 0.971
C8 H8 1.080 1.079
CA HA 1.100 1.090
CB HB 1.100 1.089
CB HBA 1.100 1.089
CD HD 1.100 1.090
CD HDA 1.100 1.090
CD HDB 1.100 1.090
CG HG 1.099 1.089
CG HGA 1.100 1.089
C1' H1' 1.100 1.091
N10 HN10 1.000 0.970
C2' H2' 1.100 1.089
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C4' H4' 1.100 1.090
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
O5' HO5' 0.949 0.967

Bond Angles for VRT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O C CA 121.3 120.0
O C N10 125.6 120.0
CA C N10 112.9 120.0
C CA N 123.9 109.5
C CA CB 118.0 109.4
C CA HA 92.5 109.5
C N10 C2' 131.5 120.0
C N10 HN10 114.3 120.0
N CA CB 117.6 109.5
CA N HN 109.5 111.0
CA N HNA 109.5 111.1
N CA HA 92.6 109.5
C2 N1 C6 118.2 121.2
N1 C2 N3 122.0 122.4
N1 C2 H2 119.0 118.8
N1 C6 C5 122.0 118.5
N1 C6 N6 123.2 120.8
C2 N3 C4 123.4 120.7
N3 C2 H2 119.0 118.8
N3 C4 C5 118.1 119.1
N3 C4 N9 136.4 134.9
C5 C4 N9 105.5 106.0
C4 C5 C6 116.3 118.2
C4 C5 N7 109.4 107.1
C4 N9 C8 108.7 107.5
C4 N9 C1' 124.3 126.3
C6 C5 N7 134.4 134.7
C5 C6 N6 114.8 120.8
C5 N7 C8 106.2 109.4
C6 N6 HN6 109.5 120.0
C6 N6 HN6A 109.5 120.0
N7 C8 N9 110.3 109.9
N7 C8 H8 124.9 125.0
C8 N9 C1' 127.0 126.2
N9 C8 H8 124.9 125.0
N9 C1' C2' 116.0 110.6
N9 C1' O4' 114.8 110.6
N9 C1' H1' 105.9 110.5
CA CB CG 110.2 109.4
CB CA HA 92.5 109.5
CA CB HB 109.3 109.5
CA CB HBA 109.3 109.4
CB CG CD 114.0 109.4
CG CB HB 109.3 109.4
CG CB HBA 109.3 109.5
CB CG HG 108.3 109.4
CB CG HGA 108.3 109.5
CG CD HD 109.5 109.5
CG CD HDA 109.5 109.5
CG CD HDB 109.5 109.4
CD CG HG 108.4 109.5
CD CG HGA 108.4 109.5
C2' C1' O4' 107.1 103.5
C1' C2' N10 107.2 110.9
C1' C2' C3' 106.2 102.1
C2' C1' H1' 105.4 110.6
C1' C2' H2' 110.4 110.9
C1' O4' C4' 111.9 107.0
O4' C1' H1' 106.8 110.8
N10 C2' C3' 110.5 110.9
C2' N10 HN10 114.3 120.0
N10 C2' H2' 111.9 110.8
C2' C3' O3' 117.3 110.5
C2' C3' C4' 104.1 104.2
C3' C2' H2' 110.5 110.9
C2' C3' H3' 107.0 110.5
O3' C3' C4' 112.7 110.5
O3' C3' H3' 108.0 110.4
C3' O3' HO3' 109.5 114.0
C3' C4' O4' 109.7 107.3
C3' C4' C5' 121.5 109.8
C4' C3' H3' 107.1 110.7
C3' C4' H4' 108.2 109.9
O4' C4' C5' 98.4 109.9
O4' C4' H4' 109.8 109.9
C4' C5' O5' 109.6 109.4
C5' C4' H4' 108.5 110.0
C4' C5' H5' 109.5 109.5
C4' C5' H5'A 109.4 109.5
O5' C5' H5' 109.5 109.4
O5' C5' H5'A 109.5 109.5
C5' O5' HO5' 109.5 114.0
HN N HNA 109.5 111.0
HN6 N6 HN6A 109.5 120.0
HB CB HBA 109.5 109.5
HD CD HDA 109.5 109.5
HD CD HDB 109.5 109.5
HDA CD HDB 109.5 109.5
HG CG HGA 109.5 109.5
H5' C5' H5'A 109.4 109.5

Torsion Angles for VRT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
CA C O N10 185.8 180.3
O C CA N 185.8 340.0
O C CA CB 356.8 100.0
O C CA HA 91.0 220.0
O C N10 C2' 2.0 360.0
O C N10 HN10 182.0 180.0
O C CA N10 174.9 179.7
CA C N10 C2' 176.7 179.7
CA C N10 HN10 356.6 359.8
N CA C CB 189.0 240.0
C CA N HN 180.0 296.0
C CA N HNA 300.0 60.0
N CA C HA 94.8 120.0
C CA CB CG 63.4 175.0
CB CA C HA 265.8 240.0
C CA CB HB 183.5 295.0
C CA CB HBA 303.3 55.0
O C N10 CA 185.3 180.3
N10 C CA N 10.9 160.3
N10 C CA CB 181.9 280.3
N10 C CA HA 276.1 40.3
C1' C2' N10 C 151.9 155.0
C N10 C2' C3' 267.3 267.7
C2' N10 C HN10 180.0 180.0
C N10 C2' H2' 30.8 31.4
N CA C N10 10.9 160.3
C CA N CB 171.0 120.0
C CA N HA 265.2 240.0
N CA CB CG 235.0 295.0
CB CA N HA 94.2 120.1
N CA CB HB 355.1 54.9
N CA CB HBA 114.9 175.0
HN N CA HNA 240.0 236.0
C2 N1 C6 C5 357.6 360.0
C2 N1 C6 N6 177.8 180.0
N1 C2 N3 C4 359.0 359.9
N3 C2 N1 H2 180.0 180.1
C6 N1 C2 N3 2.0 0.1
C6 N1 C2 H2 182.1 180.0
C4 C5 C6 N1 1.8 360.0
N1 C6 C5 N7 181.6 180.1
C5 C6 N1 N6 179.7 180.0
N1 C6 N6 HN6 0.0 359.9
N1 C6 N6 HN6A 120.0 180.0
N3 C2 N1 C6 2.0 0.1
N1 C2 N3 H2 180.0 179.9
C2 N3 C4 C5 0.4 360.0
C2 N3 C4 N9 180.5 180.0
C4 N3 C2 H2 178.9 180.1
C5 C4 N3 N9 179.9 180.0
N3 C4 C5 C6 359.2 0.0
N3 C4 C5 N7 179.4 180.0
N3 C4 N9 C8 180.2 180.0
N3 C4 N9 C1' 1.5 0.0
N1 C6 C5 C4 1.8 360.0
N3 C4 C5 N9 180.1 180.0
C5 C4 N9 C8 0.3 0.0
C5 C4 N9 C1' 181.6 180.0
C6 C5 C4 N7 179.9 180.1
C4 C5 C6 N6 181.6 180.0
C4 C5 N7 C8 0.9 0.0
N3 C4 N9 C5 179.9 180.0
N9 C4 C5 C6 179.2 180.0
N9 C4 C5 N7 359.3 360.0
N7 C8 N9 C4 0.3 360.0
C8 N9 C4 C1' 178.6 180.0
C4 N9 C8 H8 180.2 180.0
C4 N9 C1' C2' 152.2 85.0
C4 N9 C1' O4' 278.1 199.1
C4 N9 C1' H1' 35.6 322.1
N1 C6 C5 N6 180.2 180.0
C6 C5 C4 N9 179.2 180.0
C4 C5 C6 N7 180.2 179.9
C6 C5 N7 C8 181.0 179.9
C5 C6 N6 HN6 180.2 180.0
C5 C6 N6 HN6A 300.3 360.0
N7 C5 C4 N9 359.3 360.0
C4 C5 N7 C6 179.8 180.1
N7 C5 C6 N6 1.4 0.1
C5 N7 C8 N9 359.3 360.0
C5 N7 C8 H8 179.3 180.0
N1 C6 N6 C5 179.8 180.0
N6 C6 C5 N7 1.4 0.1
HN6 N6 C6 HN6A 240.0 180.0
C4 N9 C8 N7 0.3 360.0
N7 C8 N9 C1' 178.9 180.0
N9 C8 N7 H8 180.0 180.0
C4 N9 C8 C1' 181.4 180.0
N7 C8 N9 H8 180.0 180.0
C8 N9 C1' C2' 333.8 265.0
C8 N9 C1' O4' 99.7 19.1
C8 N9 C1' H1' 217.2 142.2
C4 N9 C1' C8 178.4 180.0
C1' N9 C8 H8 358.8 360.0
C2' C1' N9 O4' 234.1 245.9
N9 C1' C2' N10 238.8 273.8
N9 C1' C2' C3' 120.7 155.6
C2' C1' N9 H1' 116.6 122.8
N9 C1' C2' H2' 0.9 37.3
N9 C1' O4' C4' 239.9 201.4
O4' C1' N9 H1' 242.5 236.9
CB CA C N10 181.9 280.3
C CA CB N 188.4 240.0
C CA CB HA 94.2 120.0
CB CA N HN 8.9 176.0
CB CA N HNA 129.0 300.1
N CA CB HA 265.8 240.0
CA CB CG CD 62.2 180.0
CG CB CA HB 239.9 240.1
CG CB CA HBA 120.1 120.0
CA CB CG HG 182.9 300.0
CA CB CG HGA 301.5 60.0
HB CB CA HBA 240.2 240.0
CG CB CA HA 329.2 55.0
CA CB CG HB 120.1 120.0
CA CB CG HBA 239.9 240.0
CB CG CD HD 180.0 300.0
CB CG CD HDA 300.0 60.0
CB CG CD HDB 60.0 180.0
CD CG CB HG 239.3 240.0
CD CG CB HGA 120.7 120.0
HB CB CG HBA 119.8 120.1
HG CG CB HGA 241.4 240.0
CD CG CB HB 302.1 60.0
CD CG CB HBA 182.3 300.0
CB CG CD HG 120.7 119.9
CB CG CD HGA 239.3 240.0
HD CD CG HDA 240.0 240.0
HD CD CG HDB 120.0 120.0
HDA CD CG HDB 240.0 240.0
HG CG CD HGA 118.7 120.0
C N10 C2' C1' 151.9 155.0
N9 C1' C2' O4' 129.7 118.5
N9 C1' C2' H1' 243.2 237.2
C2' C1' O4' C4' 10.3 319.9
O4' C1' C2' H1' 113.5 118.7
N10 C2' C1' C3' 118.1 118.2
C1' C2' N10 HN10 332.0 335.0
N10 C2' C1' H2' 237.9 236.4
C1' C2' C3' O3' 129.9 97.8
C1' C2' C3' C4' 4.6 339.1
C3' C2' C1' H2' 119.8 118.2
C1' C2' C3' H3' 251.4 220.3
N9 C1' O4' C2' 229.6 241.5
N9 C1' O4' H1' 117.0 122.9
O4' C1' C2' N10 109.1 155.2
O4' C1' C2' C3' 351.0 37.0
C2' C1' O4' H1' 247.4 241.4
O4' C1' C2' H2' 231.2 278.8
C3' C4' O4' C1' 352.5 26.5
C1' O4' C4' C5' 120.5 145.9
C1' O4' C4' H4' 233.7 267.1
C N10 C2' HN10 180.0 180.0
N10 C2' C1' O4' 109.1 155.2
C1' C2' N10 C3' 244.7 247.3
N10 C2' C1' H1' 355.6 36.5
C1' C2' N10 H2' 121.2 123.6
N10 C2' C3' O3' 14.0 339.6
N10 C2' C3' C4' 248.7 220.9
C3' C2' N10 H2' 236.5 236.3
N10 C2' C3' H3' 135.5 102.1
C3' C2' C1' O4' 351.0 37.0
C1' C2' C3' N10 116.0 118.2
C3' C2' C1' H1' 237.5 278.3
C1' C2' C3' H2' 240.3 241.8
C3' C2' N10 HN10 87.3 87.7
N10 C2' C3' H2' 124.3 123.6
O3' C3' C2' C4' 125.3 118.7
O3' C3' C2' H3' 238.5 237.5
C2' C3' O3' HO3' 180.0 180.0
C2' C3' C4' O4' 1.3 357.9
C2' C3' C4' C5' 247.5 238.5
C4' C3' C2' H3' 113.2 118.9
C2' C3' C4' H4' 121.1 117.4
C2' C3' O3' C4' 239.1 245.2
O3' C3' C2' H2' 249.7 216.0
C2' C3' O3' H3' 121.0 122.5
O3' C3' C4' O4' 233.1 239.3
O3' C3' C4' C5' 119.4 119.9
C4' C3' O3' H3' 241.8 237.3
O3' C3' C4' H4' 352.9 358.7
C1' O4' C4' C3' 352.5 26.5
C2' C3' C4' O3' 128.2 118.7
C4' C3' C2' H2' 124.4 97.3
C2' C3' C4' H3' 246.9 241.3
O3' C3' C4' H3' 118.7 122.6
C4' C3' O3' HO3' 300.9 294.8
O4' C4' C3' C5' 113.8 119.4
O4' C4' C3' H4' 240.2 240.5
C3' C4' C5' O5' 181.0 185.0
C5' C4' C3' H4' 126.4 121.1
C3' C4' C5' H5' 301.1 305.0
C3' C4' C5' H5'A 61.0 65.0
C4' O4' C1' H1' 122.9 78.5
C3' C4' O4' C5' 232.1 240.7
O4' C4' C3' H3' 114.4 116.7
C3' C4' O4' H4' 118.8 119.4
O4' C4' C5' O5' 61.6 67.2
C5' C4' O4' H4' 246.8 238.8
O4' C4' C5' H5' 181.7 187.2
O4' C4' C5' H5'A 301.6 307.3
C3' C4' C5' O4' 119.4 117.8
C5' C4' C3' H3' 0.7 357.3
C3' C4' C5' H4' 233.7 239.0
O4' C4' C5' H4' 114.3 121.2
O5' C5' C4' H5' 240.0 240.1
O5' C5' C4' H5'A 120.0 120.0
C4' C5' O5' HO5' 180.0 180.0
H5' C5' C4' H5'A 240.1 239.9
O5' C5' C4' H4' 307.4 306.1
C4' C5' O5' H5' 120.0 120.0
C4' C5' O5' H5'A 240.0 240.0
H5' C5' O5' H5'A 119.9 120.0
HN N CA CB 8.9 176.0
CA N HN HNA 120.0 124.0
HN N CA HA 274.8 56.0
HNA N CA CB 129.0 300.1
CA N HNA HN 239.9 236.0
HNA N CA HA 34.8 180.0
H2 C2 N1 C6 182.1 180.0
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 178.9 180.1
C6 N6 HN6 HN6A 120.0 180.0
C6 N6 HN6A HN6 240.0 180.0
N7 C8 H8 N9 180.0 180.0
H8 C8 N9 C1' 358.8 360.0
HA CA C N10 276.1 40.3
C CA HA N 124.1 120.0
C CA HA CB 241.8 240.0
N CA HA CB 117.8 120.0
HA CA N HN 274.8 56.0
HA CA N HNA 34.8 180.0
HA CA CB CG 329.2 55.0
HA CA CB HB 89.3 175.0
HA CA CB HBA 209.1 295.0
CA CB HB CG 239.3 240.1
HB CB CA HA 89.3 175.0
CA CB HB HBA 119.7 120.0
HB CB CG CD 302.1 60.0
CG CB HB HBA 240.3 239.9
HB CB CG HG 62.8 180.0
HB CB CG HGA 181.4 300.0
CA CB HBA CG 120.6 120.0
HBA CB CA HA 209.1 295.0
CA CB HBA HB 240.3 240.0
HBA CB CG CD 182.3 300.0
CG CB HBA HB 119.7 120.0
HBA CB CG HG 302.9 59.9
HBA CB CG HGA 61.6 180.0
CG CD HD HDA 120.0 120.0
CG CD HD HDB 240.0 240.0
HD CD CG HG 59.4 180.0
HD CD CG HGA 300.7 60.0
HDA CD HD HDB 120.0 120.0
CG CD HDA HD 240.0 240.0
CG CD HDA HDB 120.0 119.9
HDA CD CG HG 179.3 300.1
HDA CD CG HGA 60.7 180.0
HD CD HDA HDB 240.0 239.9
CG CD HDB HD 120.0 120.0
CG CD HDB HDA 240.0 240.1
HDB CD CG HG 299.3 60.0
HDB CD CG HGA 180.7 300.0
HD CD HDB HDA 120.0 120.1
CB CG HG CD 235.9 240.1
HG CG CB HB 62.8 180.0
HG CG CB HBA 302.9 59.9
CB CG HG HGA 117.9 120.0
HG CG CD HD 59.4 180.0
HG CG CD HDA 179.3 300.1
HG CG CD HDB 299.3 60.0
CD CG HG HGA 242.0 240.0
CB CG HGA CD 124.1 120.0
HGA CG CB HB 181.4 300.0
HGA CG CB HBA 61.6 180.0
CB CG HGA HG 242.1 240.0
HGA CG CD HD 300.7 60.0
HGA CG CD HDA 60.7 180.0
HGA CG CD HDB 180.7 300.0
CD CG HGA HG 118.0 120.0
N9 C1' H1' C2' 123.5 122.8
N9 C1' H1' O4' 237.2 237.0
C2' C1' H1' O4' 113.7 114.2
H1' C1' C2' N10 355.6 36.5
H1' C1' C2' C3' 237.5 278.3
H1' C1' C2' H2' 117.7 160.1
H1' C1' O4' C4' 122.9 78.5
C N10 HN10 C2' 180.0 180.0
HN10 N10 C2' C3' 87.3 87.7
HN10 N10 C2' H2' 210.8 211.4
H2' C2' C1' O4' 231.2 278.8
C1' C2' H2' N10 240.7 236.4
C1' C2' H2' C3' 117.2 112.7
H2' C2' C1' H1' 117.7 160.1
N10 C2' H2' C3' 236.5 236.3
H2' C2' N10 HN10 210.8 211.4
H2' C2' C3' O3' 249.7 216.0
H2' C2' C3' C4' 124.4 97.3
H2' C2' C3' H3' 11.2 338.5
C2' C3' H3' O3' 232.8 237.5
C2' C3' H3' C4' 111.1 114.8
H3' C3' C2' H2' 11.2 338.5
O3' C3' H3' C4' 238.3 237.4
H3' C3' O3' HO3' 59.1 57.5
H3' C3' C4' O4' 114.4 116.7
H3' C3' C4' C5' 0.7 357.3
H3' C3' C4' H4' 234.2 236.2
HO3' O3' C3' C4' 300.9 294.8
HO3' O3' C3' H3' 59.1 57.5
C3' C4' H4' O4' 240.3 242.2
C3' C4' H4' C5' 133.7 121.0
H4' C4' C3' H3' 234.2 236.2
O4' C4' H4' C5' 253.4 238.8
H4' C4' C5' O5' 307.4 306.1
H4' C4' C5' H5' 67.4 66.0
H4' C4' C5' H5'A 187.3 186.1
C4' C5' H5' O5' 239.9 240.1
H5' C5' C4' H4' 67.4 66.0
C4' C5' H5' H5'A 119.9 120.1
O5' C5' H5' H5'A 240.0 240.0
H5' C5' O5' HO5' 60.0 60.0
C4' C5' H5'A O5' 120.1 119.9
H5'A C5' C4' H4' 187.3 186.1
C4' C5' H5'A H5' 240.1 239.9
O5' C5' H5'A H5' 120.0 120.0
H5'A C5' O5' HO5' 300.0 300.0
HO5' O5' C5' H5' 60.0 60.0
HO5' O5' C5' H5'A 300.0 300.0