PDB Chemical Component O8M

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 O8M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2 C4 1.208 1.213
C4 C5 1.500 1.507
C4 N1 1.301 1.347
C5 N2 1.495 1.469
N2 C6 1.429 1.469
N2 C5' 1.435 1.469
C5' C4' 1.552 1.530
C4' O4' 1.465 1.437
C4' C3' 1.581 1.542
O4' C1' 1.318 1.444
C1' N5 1.431 1.464
C1' C2' 1.582 1.549
N5 C11 1.292 1.373
N5 C7 1.320 1.364
C11 N4 1.287 1.329
C11 C12 1.308 1.406
N4 C10 1.249 1.316
C10 N3 1.287 1.320
N3 C9 1.298 1.330
C9 N7 1.378 1.383
C9 C12 1.360 1.405
C12 N6 1.293 1.354
N6 C7 1.235 1.301
C7 C8 1.371 1.506
C2' O2' 1.223 1.429
C2' C3' 1.485 1.548
C3' O3' 1.255 1.429
C5 H5 1.100 1.090
C5 H5A 1.100 1.090
C6 H6 1.100 1.090
C6 H6A 1.100 1.090
C6 H6B 1.100 1.090
C5' H5' 1.100 1.089
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' 1.099 1.090
O3' HO3' 0.949 0.967
C8 H8 1.100 1.090
C8 H8A 1.100 1.090
C8 H8B 1.100 1.090
N1 HN1 1.000 0.970
N1 HN1A 1.000 0.970

Bond Angles for O8M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O2 C4 C5 120.4 120.0
O2 C4 N1 120.4 120.0
C5 C4 N1 119.2 120.0
C4 C5 N2 104.8 109.5
C4 C5 H5 111.1 109.4
C4 C5 H5A 112.1 109.5
C4 N1 HN1 110.3 120.1
C4 N1 HN1A 124.9 120.0
C5 N2 C6 115.8 111.0
C5 N2 C5' 112.5 110.9
N2 C5 H5 111.1 109.5
N2 C5 H5A 112.0 109.5
C6 N2 C5' 112.6 111.0
N2 C6 H6 109.5 109.4
N2 C6 H6A 109.4 109.4
N2 C6 H6B 109.5 109.5
N2 C5' C4' 114.4 109.4
N2 C5' H5' 107.8 109.5
N2 C5' H5'A 106.7 109.5
C5' C4' O4' 121.0 109.9
C5' C4' C3' 123.5 109.9
C4' C5' H5' 107.9 109.5
C4' C5' H5'A 106.7 109.4
C5' C4' H4' 82.8 109.9
O4' C4' C3' 107.1 107.3
C4' O4' C1' 111.7 107.0
O4' C4' H4' 111.2 109.9
C4' C3' C2' 95.9 104.2
C4' C3' O3' 106.3 110.5
C3' C4' H4' 106.9 110.0
C4' C3' H3' 121.8 110.4
O4' C1' N5 102.5 110.6
O4' C1' C2' 103.5 103.5
O4' C1' H1' 119.5 110.6
N5 C1' C2' 115.3 110.7
C1' N5 C11 124.8 126.3
C1' N5 C7 129.5 126.3
N5 C1' H1' 108.6 110.6
C1' C2' O2' 110.9 111.0
C1' C2' C3' 105.5 102.1
C2' C1' H1' 107.6 110.7
C1' C2' H2' 110.9 110.9
C11 N5 C7 105.7 107.4
N5 C11 N4 135.9 134.9
N5 C11 C12 106.8 106.0
N5 C7 N6 111.5 110.0
N5 C7 C8 133.2 125.0
N4 C11 C12 117.3 119.1
C11 N4 C10 124.1 120.6
C11 C12 C9 119.0 118.2
C11 C12 N6 109.5 107.1
N4 C10 N3 120.9 122.5
N4 C10 H10 119.5 118.8
C10 N3 C9 118.9 121.2
N3 C10 H10 119.6 118.7
N3 C9 N7 119.4 120.8
N3 C9 C12 119.5 118.4
N7 C9 C12 121.1 120.8
C9 N7 HN7 109.5 120.0
C9 N7 HN7A 109.5 120.0
C9 C12 N6 131.4 134.7
C12 N6 C7 106.6 109.5
N6 C7 C8 115.4 125.0
C7 C8 H8 109.5 109.5
C7 C8 H8A 109.4 109.5
C7 C8 H8B 109.5 109.5
O2' C2' C3' 108.5 110.9
O2' C2' H2' 107.9 110.8
C2' O2' HO2' 109.5 114.1
C2' C3' O3' 115.4 110.5
C3' C2' H2' 113.2 110.9
C2' C3' H3' 113.5 110.5
O3' C3' H3' 104.3 110.6
C3' O3' HO3' 109.5 114.0
H5 C5 H5A 105.9 109.5
H6 C6 H6A 109.5 109.5
H6 C6 H6B 109.5 109.5
H6A C6 H6B 109.5 109.4
H5' C5' H5'A 113.4 109.5
HN7 N7 HN7A 109.5 120.0
H8 C8 H8A 109.5 109.5
H8 C8 H8B 109.4 109.4
H8A C8 H8B 109.5 109.5
HN1 N1 HN1A 124.8 120.0

Torsion Angles for O8M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5 C4 O2 N1 179.9 180.2
O2 C4 C5 N2 68.0 0.1
O2 C4 C5 H5 188.0 120.1
O2 C4 C5 H5A 306.3 240.0
O2 C4 N1 HN1 360.0 360.0
O2 C4 N1 HN1A 180.0 180.0
O2 C4 C5 N1 180.1 179.8
C5 C4 N1 HN1 180.0 179.8
C5 C4 N1 HN1A 0.0 359.8
C4 C5 N2 C6 49.7 293.9
C4 C5 N2 C5' 278.3 170.0
N2 C5 C4 H5 240.0 240.0
N2 C5 C4 H5A 121.7 120.0
H5 C5 C4 H5A 241.7 240.0
O2 C4 N1 C5 179.9 180.2
N1 C4 C5 N2 248.0 180.2
N1 C4 C5 H5 8.0 300.2
N1 C4 C5 H5A 126.2 60.2
HN1 N1 C4 HN1A 180.0 180.0
N2 C5 C4 N1 248.0 180.2
C4 C5 N2 H5 120.0 119.9
C4 C5 N2 H5A 238.2 240.0
C6 N2 C5 C5' 131.4 123.9
C5 N2 C6 H6 140.0 60.0
C5 N2 C6 H6A 260.0 180.1
C5 N2 C6 H6B 20.0 300.0
C5 N2 C5' C4' 222.9 190.0
C5 N2 C5' H5' 342.9 310.0
C5 N2 C5' H5'A 105.1 70.1
H5 C5 N2 H5A 118.2 120.0
C5 N2 C6 C5' 228.7 236.1
C6 N2 C5 H5 289.7 174.0
C6 N2 C5 H5A 171.4 53.9
C6 N2 C5' C4' 89.9 66.1
C6 N2 C5' H5' 209.9 186.1
C6 N2 C5' H5'A 332.1 306.1
H6 C6 N2 H6A 240.0 240.0
H6 C6 N2 H6B 120.0 120.0
H6A C6 N2 H6B 240.0 240.0
C5 N2 C5' C6 133.0 123.9
C5' N2 C5 H5 158.3 50.0
C5' N2 C5 H5A 40.1 290.0
C5' N2 C6 H6 271.3 183.9
C5' N2 C6 H6A 31.3 303.9
C5' N2 C6 H6B 151.3 63.9
N2 C5' C4' O4' 15.7 66.5
N2 C5' C4' C3' 159.8 184.3
C4' C5' N2 H5' 240.0 240.0
C4' C5' N2 H5'A 117.8 119.9
N2 C5' C4' H4' 265.2 305.4
H5' C5' N2 H5'A 237.8 239.9
N2 C5' C4' H5' 120.0 120.0
N2 C5' C4' H5'A 242.2 240.1
O4' C4' C5' C3' 215.9 242.2
C5' C4' O4' C1' 141.8 145.9
O4' C4' C5' H4' 110.5 121.1
C5' C4' C3' C2' 240.9 238.5
C5' C4' C3' O3' 122.2 119.9
C3' C4' C5' H4' 254.5 238.9
C5' C4' C3' H3' 3.3 357.2
H5' C5' C4' H5'A 122.2 120.1
C5' C4' O4' C3' 149.2 119.4
O4' C4' C5' H5' 255.7 306.5
O4' C4' C5' H5'A 133.5 186.4
C5' C4' O4' H4' 265.7 238.9
O4' C4' C3' C2' 29.1 357.9
O4' C4' C3' O3' 270.4 239.3
C3' C4' O4' H4' 116.5 119.5
O4' C4' C3' H3' 151.5 116.6
C4' O4' C1' N5 222.7 201.4
C4' O4' C1' C2' 343.0 320.0
C4' O4' C1' H1' 102.6 78.6
C5' C4' C3' O4' 211.8 240.6
C3' C4' C5' H5' 39.8 64.3
C3' C4' C5' H5'A 277.6 304.2
C5' C4' C3' H4' 92.5 121.1
C3' C4' O4' C1' 352.6 26.5
O4' C4' C3' H4' 240.7 240.5
C1' C2' C3' C4' 321.8 339.1
O2' C2' C3' C4' 202.9 220.9
C2' C3' C4' O3' 118.7 118.7
C4' C3' C2' H2' 83.1 97.4
C2' C3' C4' H3' 237.6 241.3
O3' C3' C4' H3' 118.9 122.6
C4' C3' O3' HO3' 55.6 180.0
C1' O4' C4' C3' 352.6 26.5
C1' O4' C4' H4' 236.1 267.0
N5 C1' O4' C2' 239.7 241.5
O4' C1' N5 C11 40.9 223.5
O4' C1' N5 C7 218.9 43.3
N5 C1' O4' H1' 120.1 122.8
O4' C1' C2' O2' 154.9 155.2
O4' C1' C2' C3' 37.6 37.0
C2' C1' O4' H1' 240.3 241.4
O4' C1' C2' H2' 274.8 278.8
O4' C1' N5 C2' 111.7 114.1
O4' C1' N5 H1' 232.6 237.2
N5 C1' C2' O2' 266.0 273.7
N5 C1' C2' C3' 148.8 155.5
C2' C1' N5 H1' 120.9 123.1
N5 C1' C2' H2' 25.9 37.3
C11 N5 C1' C7 181.9 180.3
C1' N5 C11 N4 359.0 0.1
C1' N5 C11 C12 180.6 180.0
C1' N5 C7 N6 179.9 179.8
C1' N5 C7 C8 0.1 359.9
C4' C3' C2' C1' 321.8 339.1
O4' C1' C2' N5 248.9 241.5
O4' C1' C2' H1' 127.5 118.5
C2' C1' N5 C11 289.1 109.4
C2' C1' N5 C7 107.2 289.2
N5 C1' C2' H1' 238.6 237.0
O2' C2' C1' C3' 117.2 118.2
O2' C2' C1' H2' 240.1 236.4
C1' C2' O2' HO2' 10.5 180.0
C1' C2' C3' O3' 73.0 97.8
C3' C2' C1' H2' 122.9 118.2
C1' C2' C3' H3' 193.3 220.5
C11 N5 C1' C2' 289.1 109.4
C1' N5 C11 C7 178.5 179.8
C11 N5 C1' H1' 168.2 346.4
C11 N5 C7 N6 358.3 359.6
C11 N5 C7 C8 178.4 179.7
N4 C11 N5 C12 178.4 180.1
N5 C11 N4 C10 181.8 180.0
N5 C11 C12 C9 182.4 180.0
N5 C11 C12 N6 358.2 0.0
C7 N5 C1' C2' 107.2 289.2
C1' N5 C7 C11 181.6 180.2
C7 N5 C1' H1' 346.3 166.1
C7 N5 C11 N4 180.5 180.3
C7 N5 C11 C12 2.1 0.2
C12 N6 C7 N5 0.6 0.4
N6 C7 N5 C8 179.8 179.9
N5 C7 C8 H8 144.5 90.0
N5 C7 C8 H8A 264.5 210.0
N5 C7 C8 H8B 24.6 330.0
N4 C11 N5 C7 180.5 180.3
N5 C11 N4 C12 181.7 179.9
N4 C11 C12 C9 3.7 360.0
N4 C11 C12 N6 179.4 180.0
C11 N4 C10 N3 355.4 360.0
C11 N4 C10 H10 175.4 179.9
C12 C11 N5 C7 2.1 0.2
N5 C11 C12 N4 178.7 180.1
C12 C11 N4 C10 0.0 0.0
N3 C9 C12 C11 356.9 0.0
N7 C9 C12 C11 179.1 180.0
C9 C12 C11 N6 184.2 180.0
C11 C12 N6 C7 0.7 359.7
C10 N4 C11 C12 0.0 0.0
N4 C10 N3 C9 5.0 0.0
N3 C10 N4 H10 180.0 180.0
N4 C10 N3 H10 180.0 180.0
C10 N3 C9 N7 176.6 180.0
C10 N3 C9 C12 358.7 360.0
C11 C12 C9 N3 356.9 0.0
C9 N3 C10 H10 185.0 180.0
N7 C9 N3 C12 177.8 180.0
N3 C9 N7 HN7 13.5 360.0
N3 C9 N7 HN7A 133.6 180.0
N3 C9 C12 N6 182.2 180.0
C11 C12 C9 N7 179.1 180.0
N3 C9 N7 C12 182.2 180.0
N7 C9 C12 N6 4.5 0.0
HN7 N7 C9 HN7A 240.0 180.0
C11 C12 C9 N6 174.7 180.0
N3 C9 C12 N7 177.8 180.0
C12 C9 N7 HN7 191.3 180.0
C12 C9 N7 HN7A 311.4 0.0
C9 C12 N6 C7 175.8 179.7
N5 C7 N6 C12 0.6 0.4
C11 C12 N6 C9 184.9 180.0
C12 N6 C7 C8 180.5 180.3
N5 C7 N6 C8 180.1 180.1
N6 C7 C8 H8 324.7 270.1
N6 C7 C8 H8A 84.7 30.2
N6 C7 C8 H8B 204.8 150.2
N5 C7 C8 N6 179.8 179.9
H8 C8 C7 H8A 240.0 240.0
H8 C8 C7 H8B 120.0 120.0
H8A C8 C7 H8B 240.0 240.0
C4' C3' C2' O2' 202.9 220.9
C1' C2' O2' C3' 244.6 247.2
O2' C2' C1' H1' 27.4 36.7
C1' C2' O2' H2' 121.6 123.7
O2' C2' C3' O3' 314.1 339.5
C3' C2' O2' H2' 237.0 236.4
O2' C2' C3' H3' 74.4 102.2
C4' C3' C2' O3' 248.8 241.4
C2' C3' C4' H4' 148.4 117.5
C4' C3' C2' H3' 128.4 118.6
C1' C2' C3' O2' 118.9 118.3
C3' C2' C1' H1' 270.1 278.5
C1' C2' C3' H2' 238.6 241.8
O2' C2' C3' H2' 119.8 123.5
C3' C2' O2' HO2' 125.9 292.7
O3' C3' C2' H3' 239.6 237.3
C2' C3' O3' HO3' 310.7 65.3
C4' C3' O3' C2' 104.9 114.7
O3' C3' C4' H4' 29.7 358.8
C4' C3' O3' H3' 230.2 237.4
O3' C3' C2' H2' 194.3 216.0
C2' C3' O3' H3' 125.3 122.7
H5 C5 C4 N1 8.0 300.2
C4 C5 H5 N2 243.8 240.0
C4 C5 H5 H5A 121.9 120.0
H5 C5 N2 C6 289.7 174.0
H5 C5 N2 C5' 158.3 50.0
N2 C5 H5 H5A 238.1 239.9
H5A C5 C4 N1 126.2 60.2
C4 C5 H5A N2 117.5 120.0
C4 C5 H5A H5 238.7 240.1
H5A C5 N2 C6 171.4 53.9
H5A C5 N2 C5' 40.1 290.0
N2 C5 H5A H5 121.2 120.0
H6 C6 N2 C5' 271.3 183.9
N2 C6 H6 H6A 120.0 120.0
N2 C6 H6 H6B 240.0 240.0
H6A C6 H6 H6B 120.0 120.0
H6A C6 N2 C5' 31.3 303.9
N2 C6 H6A H6 240.0 240.1
N2 C6 H6A H6B 120.0 120.0
H6 C6 H6A H6B 240.0 239.9
H6B C6 N2 C5' 151.3 63.9
N2 C6 H6B H6 120.0 120.0
N2 C6 H6B H6A 240.0 240.1
H6 C6 H6B H6A 120.0 120.1
N2 C5' H5' C4' 235.9 240.0
N2 C5' H5' H5'A 118.0 120.0
H5' C5' C4' O4' 255.7 306.5
H5' C5' C4' C3' 39.8 64.3
C4' C5' H5' H5'A 242.0 240.0
H5' C5' C4' H4' 145.2 185.4
N2 C5' H5'A C4' 122.8 119.9
N2 C5' H5'A H5' 241.4 239.9
H5'A C5' C4' O4' 133.5 186.4
H5'A C5' C4' C3' 277.6 304.2
C4' C5' H5'A H5' 118.6 120.0
H5'A C5' C4' H4' 23.0 65.4
C5' C4' H4' O4' 120.5 121.1
C5' C4' H4' C3' 237.1 238.9
H4' C4' C5' H5' 145.2 185.4
H4' C4' C5' H5'A 23.0 65.4
O4' C4' H4' C3' 116.6 117.9
H4' C4' O4' C1' 236.1 267.0
H4' C4' C3' C2' 148.4 117.5
H4' C4' C3' O3' 29.7 358.8
H4' C4' C3' H3' 270.8 236.1
O4' C1' H1' N5 116.9 122.9
O4' C1' H1' C2' 242.4 245.9
N5 C1' H1' C2' 125.5 123.0
H1' C1' N5 C11 168.2 346.4
H1' C1' N5 C7 346.3 166.1
H1' C1' C2' O2' 27.4 36.7
H1' C1' C2' C3' 270.1 278.5
H1' C1' C2' H2' 147.3 160.3
N4 C10 H10 N3 180.0 180.0
H10 C10 N3 C9 185.0 180.0
HN7 N7 C9 C12 191.3 180.0
C9 N7 HN7 HN7A 120.0 180.0
HN7A N7 C9 C12 311.4 0.0
C9 N7 HN7A HN7 240.0 180.0
C1' C2' H2' O2' 238.3 236.3
C1' C2' H2' C3' 118.3 112.7
H2' C2' C1' H1' 147.3 160.3
O2' C2' H2' C3' 239.9 236.4
H2' C2' O2' HO2' 248.9 56.3
H2' C2' C3' O3' 194.3 216.0
H2' C2' C3' H3' 314.7 338.7
HO2' O2' C2' C3' 125.9 292.7
HO2' O2' C2' H2' 248.9 56.3
C4' C3' H3' C2' 246.4 245.3
C4' C3' H3' O3' 119.9 122.6
H3' C3' C4' H4' 270.8 236.1
C2' C3' H3' O3' 233.5 237.3
H3' C3' C2' H2' 314.7 338.7
H3' C3' O3' HO3' 185.4 302.6
HO3' O3' C3' H3' 185.4 302.6
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
C4 N1 HN1 HN1A 180.0 180.0
C4 N1 HN1A HN1 180.0 180.0