PDB Chemical Component A8M

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 A8M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.411 1.469
C2 C4 1.515 1.530
C4 C5 1.497 1.530
C5 N2 1.421 1.469
N2 C6 1.485 1.469
N2 C5' 1.424 1.469
C5' C4' 1.521 1.530
C4' O4' 1.476 1.437
C4' C3' 1.512 1.542
O4' C1' 1.371 1.443
C1' N5 1.578 1.465
C1' C2' 1.366 1.551
N5 C11 1.406 1.372
N5 C7 1.387 1.363
C11 N4 1.360 1.329
C11 C12 1.402 1.406
N4 C10 1.350 1.317
C10 N3 1.351 1.320
N3 C9 1.366 1.329
C9 N7 1.338 1.385
C9 C12 1.425 1.405
C12 N6 1.382 1.354
N6 C7 1.311 1.302
C7 C8 1.498 1.506
C2' O2' 1.406 1.429
C2' C3' 1.509 1.548
C3' O3' 1.433 1.429
N1 HN1 1.000 1.009
N1 HN1A 1.001 1.010
C2 H2 1.100 1.090
C2 H2A 1.100 1.090
C4 H4 1.100 1.090
C4 H4A 1.100 1.090
C5 H5 1.100 1.090
C5 H5A 1.100 1.090
C6 H6 1.100 1.089
C6 H6A 1.100 1.090
C6 H6B 1.100 1.091
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
C4' H4' 1.100 1.089
C1' H1' 1.100 1.090
C10 H10 1.080 1.080
N7 HN7 1.000 0.970
N7 HN7A 1.000 0.970
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.967
C3' H3' 1.100 1.089
O3' HO3' 0.950 0.967
C8 H8 1.100 1.090
C8 H8A 1.100 1.090
C8 H8B 1.100 1.090

Bond Angles for A8M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N1 C2 C4 111.0 109.5
C2 N1 HN1 109.5 111.0
C2 N1 HN1A 109.5 111.0
N1 C2 H2 109.0 109.5
N1 C2 H2A 108.6 109.5
C2 C4 C5 111.3 109.5
C4 C2 H2 109.0 109.5
C4 C2 H2A 108.6 109.5
C2 C4 H4 108.9 109.5
C2 C4 H4A 108.4 109.5
C4 C5 N2 113.4 109.5
C5 C4 H4 108.8 109.5
C5 C4 H4A 108.4 109.4
C4 C5 H5 108.2 109.5
C4 C5 H5A 107.3 109.4
C5 N2 C6 109.0 111.1
C5 N2 C5' 110.9 111.0
N2 C5 H5 108.2 109.5
N2 C5 H5A 107.3 109.4
C6 N2 C5' 109.9 111.0
N2 C6 H6 109.5 109.5
N2 C6 H6A 109.5 109.5
N2 C6 H6B 109.4 109.4
N2 C5' C4' 111.8 109.4
N2 C5' H5' 108.7 109.5
N2 C5' H5'A 108.2 109.4
C5' C4' O4' 114.2 109.9
C5' C4' C3' 115.3 109.8
C4' C5' H5' 108.7 109.5
C4' C5' H5'A 108.2 109.5
C5' C4' H4' 100.2 109.9
O4' C4' C3' 103.9 107.3
C4' O4' C1' 103.2 107.0
O4' C4' H4' 112.4 109.9
C4' C3' C2' 99.7 104.2
C4' C3' O3' 110.8 110.4
C3' C4' H4' 111.2 110.0
C4' C3' H3' 114.7 110.5
O4' C1' N5 109.3 110.6
O4' C1' C2' 115.7 103.5
O4' C1' H1' 106.2 110.7
N5 C1' C2' 112.1 110.6
C1' N5 C11 120.8 126.3
C1' N5 C7 134.5 126.3
N5 C1' H1' 110.2 110.5
C1' C2' O2' 122.0 110.9
C1' C2' C3' 101.4 102.1
C2' C1' H1' 103.0 110.7
C1' C2' H2' 108.9 110.9
C11 N5 C7 104.7 107.5
N5 C11 N4 128.9 134.9
N5 C11 C12 105.3 106.0
N5 C7 N6 114.6 110.0
N5 C7 C8 119.7 125.0
N4 C11 C12 125.8 119.1
C11 N4 C10 111.9 120.6
C11 C12 C9 116.9 118.2
C11 C12 N6 111.1 107.2
N4 C10 N3 128.6 122.5
N4 C10 H10 115.7 118.7
C10 N3 C9 118.4 121.2
N3 C10 H10 115.7 118.8
N3 C9 N7 118.6 120.7
N3 C9 C12 118.3 118.5
N7 C9 C12 123.0 120.8
C9 N7 HN7 109.5 120.0
C9 N7 HN7A 109.5 120.0
C9 C12 N6 132.0 134.7
C12 N6 C7 104.3 109.4
N6 C7 C8 125.7 125.0
C7 C8 H8 109.5 109.5
C7 C8 H8A 109.5 109.5
C7 C8 H8B 109.5 109.5
O2' C2' C3' 114.7 111.0
O2' C2' H2' 93.5 110.8
C2' O2' HO2' 109.5 114.0
C2' C3' O3' 109.0 110.5
C3' C2' H2' 117.1 110.9
C2' C3' H3' 116.3 110.5
O3' C3' H3' 106.3 110.5
C3' O3' HO3' 109.5 114.0
HN1 N1 HN1A 109.5 111.0
H2 C2 H2A 110.6 109.4
H4 C4 H4A 111.0 109.5
H5 C5 H5A 112.6 109.5
H6 C6 H6A 109.5 109.5
H6 C6 H6B 109.4 109.4
H6A C6 H6B 109.5 109.5
H5' C5' H5'A 111.4 109.5
HN7 N7 HN7A 109.4 120.0
H8 C8 H8A 109.4 109.5
H8 C8 H8B 109.4 109.5
H8A C8 H8B 109.5 109.4

Torsion Angles for A8M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N1 C2 C4 C5 180.3 180.0
C4 C2 N1 H2 240.0 240.0
C4 C2 N1 H2A 119.4 120.0
N1 C2 C4 H4 300.3 300.0
N1 C2 C4 H4A 61.1 60.1
HN1 N1 C2 HN1A 240.0 236.0
H2 C2 N1 H2A 239.4 240.0
C4 C2 N1 HN1 267.4 56.0
C4 C2 N1 HN1A 27.5 180.0
N1 C2 C4 H2 120.0 120.0
N1 C2 C4 H2A 240.6 240.0
C2 C4 C5 N2 207.4 180.0
C5 C4 C2 H4 240.0 239.9
C5 C4 C2 H4A 119.2 119.9
C2 C4 C5 H5 327.5 300.0
C2 C4 C5 H5A 89.1 60.1
H2 C2 C4 H2A 120.6 120.0
H4 C4 C2 H4A 239.2 240.0
C5 C4 C2 H2 60.2 59.9
C5 C4 C2 H2A 299.6 300.0
C2 C4 C5 H4 120.0 120.0
C2 C4 C5 H4A 240.8 240.1
C4 C5 N2 C6 49.6 294.0
C4 C5 N2 C5' 288.5 170.0
N2 C5 C4 H5 240.0 239.9
N2 C5 C4 H5A 118.3 119.9
H4 C4 C5 H4A 120.8 120.0
H5 C5 C4 H5A 238.3 240.0
N2 C5 C4 H4 87.4 59.9
N2 C5 C4 H4A 326.6 299.9
C4 C5 N2 H5 120.0 120.1
C4 C5 N2 H5A 241.7 240.1
C6 N2 C5 C5' 121.1 124.0
C5 N2 C6 H6 146.4 59.9
C5 N2 C6 H6A 266.4 180.0
C5 N2 C6 H6B 26.4 300.0
C5 N2 C5' C4' 181.1 190.0
C5 N2 C5' H5' 301.1 310.1
C5 N2 C5' H5'A 62.2 70.1
H5 C5 N2 H5A 121.7 120.0
C5 N2 C6 C5' 238.3 236.0
C6 N2 C5 H5 289.6 174.0
C6 N2 C5 H5A 167.9 53.9
C6 N2 C5' C4' 60.5 66.0
C6 N2 C5' H5' 180.5 186.0
C6 N2 C5' H5'A 301.6 306.0
H6 C6 N2 H6A 240.0 239.9
H6 C6 N2 H6B 120.0 119.9
H6A C6 N2 H6B 240.0 240.0
C5 N2 C5' C6 120.6 124.1
C5' N2 C5 H5 168.5 49.9
C5' N2 C5 H5A 46.8 289.9
C5' N2 C6 H6 268.1 183.9
C5' N2 C6 H6A 28.1 304.0
C5' N2 C6 H6B 148.1 64.0
N2 C5' C4' O4' 58.9 66.5
N2 C5' C4' C3' 179.0 184.3
C4' C5' N2 H5' 240.0 239.9
C4' C5' N2 H5'A 119.0 120.0
N2 C5' C4' H4' 298.5 305.5
H5' C5' N2 H5'A 239.0 240.0
N2 C5' C4' H5' 120.0 120.0
N2 C5' C4' H5'A 241.0 240.1
O4' C4' C5' C3' 239.8 242.2
C5' C4' O4' C1' 103.5 145.9
O4' C4' C5' H4' 120.3 121.1
C5' C4' C3' C2' 271.5 238.6
C5' C4' C3' O3' 156.8 119.9
C3' C4' C5' H4' 240.5 238.8
C5' C4' C3' H3' 36.5 357.3
H5' C5' C4' H5'A 121.0 120.1
C5' C4' O4' C3' 126.4 119.3
O4' C4' C5' H5' 298.9 306.5
O4' C4' C5' H5'A 177.9 186.5
C5' C4' O4' H4' 246.7 238.9
O4' C4' C3' C2' 37.2 357.9
O4' C4' C3' O3' 282.5 239.3
C3' C4' O4' H4' 120.3 119.6
O4' C4' C3' H3' 162.2 116.7
C4' O4' C1' N5 230.0 201.4
C4' O4' C1' C2' 357.6 319.9
C4' O4' C1' H1' 111.1 78.6
C5' C4' C3' O4' 234.3 240.6
C3' C4' C5' H5' 59.1 64.3
C3' C4' C5' H5'A 298.0 304.2
C5' C4' C3' H4' 113.2 121.1
C3' C4' O4' C1' 337.1 26.6
O4' C4' C3' H4' 238.9 240.5
C1' C2' C3' C4' 322.5 339.2
O2' C2' C3' C4' 189.1 220.9
C2' C3' C4' O3' 114.7 118.7
C4' C3' C2' H2' 80.8 97.3
C2' C3' C4' H3' 235.0 241.2
O3' C3' C4' H3' 120.3 122.6
C4' C3' O3' HO3' 54.3 180.0
C1' O4' C4' C3' 337.1 26.6
C1' O4' C4' H4' 216.8 267.0
N5 C1' O4' C2' 232.4 241.5
O4' C1' N5 C11 50.1 223.6
O4' C1' N5 C7 230.2 43.2
N5 C1' O4' H1' 118.9 122.9
O4' C1' C2' O2' 155.4 155.2
O4' C1' C2' C3' 26.4 37.0
C2' C1' O4' H1' 246.5 241.3
O4' C1' C2' H2' 262.3 278.8
O4' C1' N5 C2' 129.6 114.1
O4' C1' N5 H1' 243.7 237.1
N5 C1' C2' O2' 281.6 273.7
N5 C1' C2' C3' 152.6 155.5
C2' C1' N5 H1' 114.1 123.0
N5 C1' C2' H2' 28.5 37.3
C11 N5 C1' C7 179.9 180.4
C1' N5 C11 N4 0.0 360.0
C1' N5 C11 C12 179.9 180.0
C1' N5 C7 N6 180.1 179.9
C1' N5 C7 C8 359.9 0.0
C4' C3' C2' C1' 322.5 339.2
O4' C1' C2' N5 233.8 241.5
O4' C1' C2' H1' 115.3 118.6
C2' C1' N5 C11 280.5 109.5
C2' C1' N5 C7 100.6 289.1
N5 C1' C2' H1' 241.5 237.1
O2' C2' C1' C3' 129.0 118.2
O2' C2' C1' H2' 253.1 236.4
C1' C2' O2' HO2' 158.0 180.1
C1' C2' C3' O3' 78.6 97.8
C3' C2' C1' H2' 124.1 118.2
C1' C2' C3' H3' 198.6 220.4
C11 N5 C1' C2' 280.5 109.5
C1' N5 C11 C7 180.1 179.7
C11 N5 C1' H1' 166.4 346.5
C11 N5 C7 N6 0.1 359.6
C11 N5 C7 C8 180.0 179.7
N4 C11 N5 C12 180.1 180.0
N5 C11 N4 C10 179.9 180.0
N5 C11 C12 C9 180.2 180.0
N5 C11 C12 N6 0.1 359.9
C7 N5 C1' C2' 100.6 289.1
C1' N5 C7 C11 179.9 180.3
C7 N5 C1' H1' 346.5 166.1
C7 N5 C11 N4 179.9 180.3
C7 N5 C11 C12 359.9 0.3
C12 N6 C7 N5 359.9 0.4
N6 C7 N5 C8 180.2 179.8
N5 C7 C8 H8 137.6 90.0
N5 C7 C8 H8A 257.5 210.0
N5 C7 C8 H8B 17.6 329.9
N4 C11 N5 C7 179.9 180.3
N5 C11 N4 C12 179.9 180.0
N4 C11 C12 C9 0.1 0.0
N4 C11 C12 N6 180.0 179.9
C11 N4 C10 N3 359.9 0.0
C11 N4 C10 H10 179.9 179.9
C12 C11 N5 C7 359.9 0.3
N5 C11 C12 N4 180.1 180.0
C12 C11 N4 C10 360.0 360.0
N3 C9 C12 C11 359.9 359.9
N7 C9 C12 C11 180.0 180.0
C9 C12 C11 N6 180.1 180.1
C11 C12 N6 C7 360.0 359.8
C10 N4 C11 C12 360.0 360.0
N4 C10 N3 C9 0.1 360.0
N3 C10 N4 H10 180.0 180.1
N4 C10 N3 H10 180.0 179.9
C10 N3 C9 N7 180.0 180.0
C10 N3 C9 C12 0.0 0.1
C11 C12 C9 N3 359.9 359.9
C9 N3 C10 H10 180.1 180.0
N7 C9 N3 C12 179.9 179.9
N3 C9 N7 HN7 21.6 0.0
N3 C9 N7 HN7A 141.5 180.0
N3 C9 C12 N6 180.0 180.1
C11 C12 C9 N7 180.0 180.0
N3 C9 N7 C12 180.1 180.1
N7 C9 C12 N6 0.1 0.1
HN7 N7 C9 HN7A 240.0 180.0
C11 C12 C9 N6 179.9 179.9
N3 C9 C12 N7 179.9 179.9
C12 C9 N7 HN7 201.5 180.0
C12 C9 N7 HN7A 321.5 360.0
C9 C12 N6 C7 179.9 179.7
N5 C7 N6 C12 359.9 0.4
C11 C12 N6 C9 180.1 180.1
C12 N6 C7 C8 180.1 180.2
N5 C7 N6 C8 179.8 180.2
N6 C7 C8 H8 317.4 270.2
N6 C7 C8 H8A 77.4 30.2
N6 C7 C8 H8B 197.4 150.1
N5 C7 C8 N6 180.2 179.8
H8 C8 C7 H8A 240.0 240.0
H8 C8 C7 H8B 120.0 120.1
H8A C8 C7 H8B 239.9 240.1
C4' C3' C2' O2' 189.1 220.9
C1' C2' O2' C3' 237.1 247.3
O2' C2' C1' H1' 40.1 36.6
C1' C2' O2' H2' 114.9 123.6
O2' C2' C3' O3' 305.2 339.6
C3' C2' O2' H2' 237.9 236.3
O2' C2' C3' H3' 65.2 102.2
C4' C3' C2' O3' 243.9 241.4
C2' C3' C4' H4' 158.3 117.4
C4' C3' C2' H3' 123.9 118.8
C1' C2' C3' O2' 133.4 118.2
C3' C2' C1' H1' 271.1 278.4
C1' C2' C3' H2' 241.7 241.8
O2' C2' C3' H2' 108.2 123.6
C3' C2' O2' HO2' 281.0 292.8
O3' C3' C2' H3' 240.0 237.4
C2' C3' O3' HO3' 305.5 65.3
C4' C3' O3' C2' 108.8 114.8
O3' C3' C4' H4' 43.6 358.8
C4' C3' O3' H3' 234.8 237.4
O3' C3' C2' H2' 196.9 216.0
C2' C3' O3' H3' 126.1 122.6
HN1 N1 C2 C4 267.4 56.0
C2 N1 HN1 HN1A 120.0 123.9
HN1 N1 C2 H2 27.5 176.0
HN1 N1 C2 H2A 148.1 296.0
HN1A N1 C2 C4 27.5 180.0
C2 N1 HN1A HN1 240.0 236.0
HN1A N1 C2 H2 147.5 300.0
HN1A N1 C2 H2A 268.1 60.0
N1 C2 H2 C4 238.8 240.0
H2 C2 N1 HN1 27.5 176.0
H2 C2 N1 HN1A 147.5 300.0
N1 C2 H2 H2A 119.4 120.0
H2 C2 C4 C5 60.2 59.9
C4 C2 H2 H2A 240.6 240.0
H2 C2 C4 H4 180.2 180.0
H2 C2 C4 H4A 301.1 300.0
N1 C2 H2A C4 120.8 120.0
H2A C2 N1 HN1 148.1 296.0
H2A C2 N1 HN1A 268.1 60.0
N1 C2 H2A H2 240.4 240.0
H2A C2 C4 C5 299.6 300.0
C4 C2 H2A H2 119.6 120.0
H2A C2 C4 H4 59.6 60.0
H2A C2 C4 H4A 180.4 180.0
C2 C4 H4 C5 238.5 240.0
H4 C4 C2 H2 180.2 180.0
H4 C4 C2 H2A 59.6 60.0
C2 C4 H4 H4A 119.3 120.0
H4 C4 C5 N2 87.4 59.9
C5 C4 H4 H4A 240.8 240.0
H4 C4 C5 H5 207.5 180.0
H4 C4 C5 H5A 329.1 300.0
C2 C4 H4A C5 121.0 120.0
H4A C4 C2 H2 301.1 300.0
H4A C4 C2 H2A 180.4 180.0
C2 C4 H4A H4 240.5 240.0
H4A C4 C5 N2 326.6 299.9
C5 C4 H4A H4 119.5 120.0
H4A C4 C5 H5 86.7 60.0
H4A C4 C5 H5A 208.3 180.0
C4 C5 H5 N2 236.8 240.0
H5 C5 C4 H4 207.5 180.0
H5 C5 C4 H4A 86.7 60.0
C4 C5 H5 H5A 118.4 120.0
H5 C5 N2 C6 289.6 174.0
H5 C5 N2 C5' 168.5 49.9
N2 C5 H5 H5A 241.6 240.0
C4 C5 H5A N2 122.2 119.9
H5A C5 C4 H4 329.1 300.0
H5A C5 C4 H4A 208.3 180.0
C4 C5 H5A H5 241.1 240.0
H5A C5 N2 C6 167.9 53.9
H5A C5 N2 C5' 46.8 289.9
N2 C5 H5A H5 118.9 120.0
H6 C6 N2 C5' 268.1 183.9
N2 C6 H6 H6A 120.0 120.1
N2 C6 H6 H6B 240.0 240.1
H6A C6 H6 H6B 120.0 120.0
H6A C6 N2 C5' 28.1 304.0
N2 C6 H6A H6 239.9 239.9
N2 C6 H6A H6B 120.0 120.0
H6 C6 H6A H6B 240.0 240.1
H6B C6 N2 C5' 148.1 64.0
N2 C6 H6B H6 120.0 120.0
N2 C6 H6B H6A 240.0 240.0
H6 C6 H6B H6A 120.0 120.0
N2 C5' H5' C4' 238.1 240.0
N2 C5' H5' H5'A 119.0 120.0
H5' C5' C4' O4' 298.9 306.5
H5' C5' C4' C3' 59.1 64.3
C4' C5' H5' H5'A 241.0 240.0
H5' C5' C4' H4' 178.5 185.4
N2 C5' H5'A C4' 121.3 119.9
N2 C5' H5'A H5' 240.6 240.0
H5'A C5' C4' O4' 177.9 186.5
H5'A C5' C4' C3' 298.0 304.2
C4' C5' H5'A H5' 119.4 120.1
H5'A C5' C4' H4' 57.5 65.4
C5' C4' H4' O4' 121.7 121.0
C5' C4' H4' C3' 237.6 238.9
H4' C4' C5' H5' 178.5 185.4
H4' C4' C5' H5'A 57.5 65.4
O4' C4' H4' C3' 116.0 117.9
H4' C4' O4' C1' 216.8 267.0
H4' C4' C3' C2' 158.3 117.4
H4' C4' C3' O3' 43.6 358.8
H4' C4' C3' H3' 283.3 236.2
O4' C1' H1' N5 118.2 122.9
O4' C1' H1' C2' 238.0 245.8
N5 C1' H1' C2' 119.8 122.9
H1' C1' N5 C11 166.4 346.5
H1' C1' N5 C7 346.5 166.1
H1' C1' C2' O2' 40.1 36.6
H1' C1' C2' C3' 271.1 278.4
H1' C1' C2' H2' 147.0 160.2
N4 C10 H10 N3 180.0 180.1
H10 C10 N3 C9 180.1 180.0
HN7 N7 C9 C12 201.5 180.0
C9 N7 HN7 HN7A 120.0 180.0
HN7A N7 C9 C12 321.5 360.0
C9 N7 HN7A HN7 240.0 180.0
C1' C2' H2' O2' 234.4 236.4
C1' C2' H2' C3' 114.2 112.7
H2' C2' C1' H1' 147.0 160.2
O2' C2' H2' C3' 239.8 236.3
H2' C2' O2' HO2' 43.1 56.4
H2' C2' C3' O3' 196.9 216.0
H2' C2' C3' H3' 317.0 338.6
HO2' O2' C2' C3' 281.0 292.8
HO2' O2' C2' H2' 43.1 56.4
C4' C3' H3' C2' 244.3 245.2
C4' C3' H3' O3' 122.8 122.6
H3' C3' C4' H4' 283.3 236.2
C2' C3' H3' O3' 238.5 237.4
H3' C3' C2' H2' 317.0 338.6
H3' C3' O3' HO3' 179.5 302.6
HO3' O3' C3' H3' 179.5 302.6
C7 C8 H8 H8A 120.0 120.0
C7 C8 H8 H8B 240.0 240.0
H8A C8 H8 H8B 120.0 120.0
C7 C8 H8A H8 240.0 240.0
C7 C8 H8A H8B 120.0 120.0
H8 C8 H8A H8B 240.0 240.0
C7 C8 H8B H8 120.0 120.0
C7 C8 H8B H8A 240.0 240.0
H8 C8 H8B H8A 120.0 120.0