PDB Chemical Component C8M

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 C8M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C1 1.353 1.348
C1 C4 1.429 1.507
C1 O1 1.190 1.212
C4 C5 1.446 1.530
C5 N2 1.354 1.469
N2 C6 1.378 1.469
N2 C5' 1.417 1.468
C5' C4' 1.511 1.530
C4' O4' 1.134 1.437
C4' C3' 1.536 1.540
O4' C1' 1.294 1.443
C1' N5 1.383 1.465
C1' C2' 1.526 1.550
N5 C11 1.319 1.372
N5 C7 1.279 1.363
C11 N4 1.258 1.329
C11 C12 1.345 1.405
N4 C10 1.206 1.316
C10 N3 1.339 1.321
N3 C9 1.335 1.328
C9 N7 1.403 1.383
C9 C12 1.429 1.406
C12 N6 1.283 1.355
N6 C7 1.194 1.301
C7 C8 1.399 1.507
C2' O2' 1.216 1.429
C2' C3' 1.565 1.548
C3' O3' 1.254 1.429
N1 HN1 1.000 0.970
N1 HN1A 1.000 0.970
C4 H4 1.100 1.090
C4 H4A 1.100 1.091
C5 H5 1.100 1.090
C5 H5A 1.100 1.091
C6 H6 1.100 1.090
C6 H6A 1.101 1.091
C6 H6B 1.100 1.090
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
C4' H4' 1.100 1.090
C1' H1' 1.100 1.090
C10 H10 1.080 1.080
N7 HN7 1.000 0.970
N7 HN7A 1.000 0.971
C2' H2' 1.100 1.089
O2' HO2' 0.950 0.967
C3' H3' 1.101 1.091
O3' HO3' 0.950 0.967
C8 H8 1.100 1.089
C8 H8A 1.100 1.089
C8 H8B 1.100 1.090

Bond Angles for C8M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N1 C1 C4 126.9 120.0
N1 C1 O1 116.4 120.0
C1 N1 HN1 110.5 120.0
C1 N1 HN1A 124.8 119.9
C4 C1 O1 116.7 120.0
C1 C4 C5 115.5 109.5
C1 C4 H4 107.5 109.5
C1 C4 H4A 106.2 109.5
C4 C5 N2 119.3 109.5
C5 C4 H4 107.5 109.5
C5 C4 H4A 106.1 109.4
C4 C5 H5 106.3 109.5
C4 C5 H5A 104.0 109.4
C5 N2 C6 119.7 111.0
C5 N2 C5' 113.8 111.0
N2 C5 H5 106.3 109.4
N2 C5 H5A 104.0 109.5
C6 N2 C5' 107.7 111.0
N2 C6 H6 109.5 109.5
N2 C6 H6A 109.5 109.5
N2 C6 H6B 109.5 109.5
N2 C5' C4' 120.7 109.5
N2 C5' H5' 105.9 109.5
N2 C5' H5'A 103.3 109.5
C5' C4' O4' 129.5 109.9
C5' C4' C3' 102.4 109.9
C4' C5' H5' 105.9 109.4
C4' C5' H5'A 103.3 109.5
C5' C4' H4' 101.9 109.8
O4' C4' C3' 112.8 107.3
C4' O4' C1' 116.4 107.0
O4' C4' H4' 88.2 109.9
C4' C3' C2' 91.1 104.2
C4' C3' O3' 113.7 110.5
C3' C4' H4' 123.4 110.0
C4' C3' H3' 118.6 110.5
O4' C1' N5 118.4 110.6
O4' C1' C2' 103.8 103.5
O4' C1' H1' 109.4 110.6
N5 C1' C2' 114.6 110.6
C1' N5 C11 122.8 126.3
C1' N5 C7 134.4 126.3
N5 C1' H1' 97.2 110.5
C1' C2' O2' 122.7 110.9
C1' C2' C3' 101.1 102.1
C2' C1' H1' 113.7 110.8
C1' C2' H2' 108.1 110.9
C11 N5 C7 102.7 107.4
N5 C11 N4 136.6 134.9
N5 C11 C12 109.8 106.0
N5 C7 N6 113.1 110.0
N5 C7 C8 130.1 125.0
N4 C11 C12 113.6 119.1
C11 N4 C10 128.4 120.7
C11 C12 C9 120.6 118.2
C11 C12 N6 102.3 107.1
N4 C10 N3 124.9 122.4
N4 C10 H10 117.6 118.8
C10 N3 C9 113.8 121.2
N3 C10 H10 117.6 118.8
N3 C9 N7 120.5 120.8
N3 C9 C12 118.8 118.4
N7 C9 C12 120.7 120.8
C9 N7 HN7 109.5 120.0
C9 N7 HN7A 109.5 120.0
C9 C12 N6 137.1 134.7
C12 N6 C7 112.1 109.4
N6 C7 C8 116.8 125.0
C7 C8 H8 109.5 109.4
C7 C8 H8A 109.5 109.5
C7 C8 H8B 109.5 109.5
O2' C2' C3' 113.2 110.9
O2' C2' H2' 94.4 110.8
C2' O2' HO2' 109.5 114.0
C2' C3' O3' 110.3 110.5
C3' C2' H2' 118.6 110.9
C2' C3' H3' 121.6 110.5
O3' C3' H3' 102.0 110.5
C3' O3' HO3' 109.5 114.0
HN1 N1 HN1A 124.7 120.1
H4 C4 H4A 114.3 109.4
H5 C5 H5A 117.6 109.5
H6 C6 H6A 109.5 109.5
H6 C6 H6B 109.5 109.5
H6A C6 H6B 109.5 109.5
H5' C5' H5'A 118.8 109.5
HN7 N7 HN7A 109.5 119.9
H8 C8 H8A 109.4 109.5
H8 C8 H8B 109.4 109.5
H8A C8 H8B 109.5 109.5

Torsion Angles for C8M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C4 C1 N1 O1 179.6 180.0
N1 C1 C4 C5 111.4 180.0
N1 C1 C4 H4 231.4 300.0
N1 C1 C4 H4A 354.1 60.0
HN1 N1 C1 HN1A 180.0 180.3
N1 C1 C4 O1 180.4 180.0
C4 C1 N1 HN1 360.0 0.0
C4 C1 N1 HN1A 180.0 179.7
C1 C4 C5 N2 285.1 180.0
C5 C4 C1 H4 240.0 239.9
C5 C4 C1 H4A 117.3 119.9
C1 C4 C5 H5 45.1 300.0
C1 C4 C5 H5A 169.9 60.0
H4 C4 C1 H4A 237.3 240.0
N1 C1 O1 C4 179.6 180.0
O1 C1 N1 HN1 180.4 180.0
O1 C1 N1 HN1A 0.4 359.8
O1 C1 C4 C5 291.0 359.9
O1 C1 C4 H4 51.0 120.0
O1 C1 C4 H4A 173.7 240.0
C5 C4 C1 O1 291.0 359.9
C1 C4 C5 H4 120.0 120.1
C1 C4 C5 H4A 242.7 240.0
C4 C5 N2 C6 314.0 294.0
C4 C5 N2 C5' 184.7 170.0
N2 C5 C4 H5 240.0 240.0
N2 C5 C4 H5A 115.2 120.0
H4 C4 C5 H4A 122.7 120.0
H5 C5 C4 H5A 235.3 240.0
N2 C5 C4 H4 165.1 60.0
N2 C5 C4 H4A 42.4 300.0
C4 C5 N2 H5 120.0 120.0
C4 C5 N2 H5A 244.8 240.0
C6 N2 C5 C5' 129.3 123.9
C5 N2 C6 H6 162.1 60.0
C5 N2 C6 H6A 282.1 180.0
C5 N2 C6 H6B 42.1 300.0
C5 N2 C5' C4' 188.5 190.0
C5 N2 C5' H5' 308.5 310.0
C5 N2 C5' H5'A 74.0 70.0
H5 C5 N2 H5A 124.8 120.0
C5 N2 C6 C5' 228.0 236.1
C6 N2 C5 H5 193.9 173.9
C6 N2 C5 H5A 69.2 53.9
C6 N2 C5' C4' 53.4 66.1
C6 N2 C5' H5' 173.4 186.1
C6 N2 C5' H5'A 298.9 306.1
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 135.1 123.9
C5' N2 C5 H5 64.6 50.0
C5' N2 C5 H5A 299.9 290.0
C5' N2 C6 H6 294.1 183.9
C5' N2 C6 H6A 54.1 303.9
C5' N2 C6 H6B 174.1 63.9
N2 C5' C4' O4' 45.7 66.4
N2 C5' C4' C3' 179.6 184.3
C4' C5' N2 H5' 240.0 240.0
C4' C5' N2 H5'A 114.5 120.0
N2 C5' C4' H4' 308.1 305.4
H5' C5' N2 H5'A 234.5 240.0
N2 C5' C4' H5' 120.0 120.0
N2 C5' C4' H5'A 245.5 239.9
O4' C4' C5' C3' 226.1 242.1
C5' C4' O4' C1' 104.6 146.0
O4' C4' C5' H4' 97.6 121.0
C5' C4' C3' C2' 254.2 238.5
C5' C4' C3' O3' 141.5 119.8
C3' C4' C5' H4' 231.5 238.9
C5' C4' C3' H3' 21.6 357.2
H5' C5' C4' H5'A 125.6 119.9
C5' C4' O4' C3' 130.3 119.5
O4' C4' C5' H5' 285.7 306.4
O4' C4' C5' H5'A 160.1 186.5
C5' C4' O4' H4' 256.0 239.0
O4' C4' C3' C2' 37.2 358.0
O4' C4' C3' O3' 284.4 239.3
C3' C4' O4' H4' 125.7 119.6
O4' C4' C3' H3' 164.6 116.7
C4' O4' C1' N5 230.9 201.5
C4' O4' C1' C2' 359.3 319.9
C4' O4' C1' H1' 121.0 78.6
C5' C4' C3' O4' 217.1 240.5
C3' C4' C5' H5' 59.6 64.3
C3' C4' C5' H5'A 294.0 304.3
C5' C4' C3' H4' 113.4 121.0
C3' C4' O4' C1' 334.3 26.5
O4' C4' C3' H4' 256.4 240.5
C1' C2' C3' C4' 327.9 339.1
O2' C2' C3' C4' 194.8 220.9
C2' C3' C4' O3' 112.8 118.7
C4' C3' C2' H2' 85.7 97.3
C2' C3' C4' H3' 232.6 241.3
O3' C3' C4' H3' 119.8 122.7
C4' C3' O3' HO3' 40.6 180.0
C1' O4' C4' C3' 334.3 26.5
C1' O4' C4' H4' 208.6 266.9
N5 C1' O4' C2' 231.7 241.5
O4' C1' N5 C11 46.1 223.6
O4' C1' N5 C7 226.0 43.2
N5 C1' O4' H1' 110.0 122.8
O4' C1' C2' O2' 151.7 155.2
O4' C1' C2' C3' 24.6 37.0
C2' C1' O4' H1' 238.3 241.3
O4' C1' C2' H2' 259.4 278.8
O4' C1' N5 C2' 123.1 114.1
O4' C1' N5 H1' 243.3 237.1
N5 C1' C2' O2' 282.3 273.7
N5 C1' C2' C3' 155.2 155.5
C2' C1' N5 H1' 120.2 123.0
N5 C1' C2' H2' 30.0 37.3
C11 N5 C1' C7 180.0 180.4
C1' N5 C11 N4 0.1 359.9
C1' N5 C11 C12 180.1 180.0
C1' N5 C7 N6 179.9 179.8
C1' N5 C7 C8 359.8 360.0
C4' C3' C2' C1' 327.9 339.1
O4' C1' C2' N5 229.4 241.5
O4' C1' C2' H1' 118.8 118.6
C2' C1' N5 C11 283.0 109.5
C2' C1' N5 C7 103.0 289.2
N5 C1' C2' H1' 249.4 237.1
O2' C2' C1' C3' 127.1 118.2
O2' C2' C1' H2' 252.3 236.4
C1' C2' O2' HO2' 150.6 180.1
C1' C2' C3' O3' 83.7 97.8
C3' C2' C1' H2' 125.2 118.2
C1' C2' C3' H3' 202.9 220.4
C11 N5 C1' C2' 283.0 109.5
C1' N5 C11 C7 180.0 179.7
C11 N5 C1' H1' 162.8 346.5
C11 N5 C7 N6 359.8 359.5
C11 N5 C7 C8 179.8 179.7
N4 C11 N5 C12 180.0 179.9
N5 C11 N4 C10 179.9 180.0
N5 C11 C12 C9 180.0 180.0
N5 C11 C12 N6 359.9 359.9
C7 N5 C1' C2' 103.0 289.2
C1' N5 C7 C11 180.0 180.3
C7 N5 C1' H1' 342.8 166.1
C7 N5 C11 N4 180.1 180.2
C7 N5 C11 C12 0.1 0.3
C12 N6 C7 N5 0.1 0.4
N6 C7 N5 C8 180.0 179.9
N5 C7 C8 H8 137.8 90.0
N5 C7 C8 H8A 257.8 210.0
N5 C7 C8 H8B 17.8 330.0
N4 C11 N5 C7 180.1 180.2
N5 C11 N4 C12 180.0 180.1
N4 C11 C12 C9 360.0 0.1
N4 C11 C12 N6 179.9 180.0
C11 N4 C10 N3 0.0 0.0
C11 N4 C10 H10 180.0 180.0
C12 C11 N5 C7 0.1 0.3
N5 C11 C12 N4 180.0 179.9
C12 C11 N4 C10 360.0 359.9
N3 C9 C12 C11 0.0 359.9
N7 C9 C12 C11 180.1 180.0
C9 C12 C11 N6 180.1 180.1
C11 C12 N6 C7 360.0 359.8
C10 N4 C11 C12 360.0 359.9
N4 C10 N3 C9 360.0 0.0
N3 C10 N4 H10 180.0 180.0
N4 C10 N3 H10 180.0 180.0
C10 N3 C9 N7 179.9 179.9
C10 N3 C9 C12 360.0 360.0
C11 C12 C9 N3 0.0 359.9
C9 N3 C10 H10 180.0 180.0
N7 C9 N3 C12 180.0 179.9
N3 C9 N7 HN7 16.5 0.0
N3 C9 N7 HN7A 136.5 180.0
N3 C9 C12 N6 180.1 180.1
C11 C12 C9 N7 180.1 180.0
N3 C9 N7 C12 180.0 180.1
N7 C9 C12 N6 0.2 0.2
HN7 N7 C9 HN7A 240.0 180.0
C11 C12 C9 N6 179.9 179.8
N3 C9 C12 N7 180.0 179.9
C12 C9 N7 HN7 196.5 180.0
C12 C9 N7 HN7A 316.5 359.9
C9 C12 N6 C7 179.9 179.7
N5 C7 N6 C12 0.1 0.4
C11 C12 N6 C9 180.1 180.2
C12 N6 C7 C8 180.2 180.3
N5 C7 N6 C8 180.0 180.1
N6 C7 C8 H8 317.8 270.1
N6 C7 C8 H8A 77.8 30.2
N6 C7 C8 H8B 197.8 150.2
N5 C7 C8 N6 180.0 179.9
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' 194.8 220.9
C1' C2' O2' C3' 238.4 247.3
O2' C2' C1' H1' 32.9 36.6
C1' C2' O2' H2' 114.7 123.7
O2' C2' C3' O3' 310.7 339.6
C3' C2' O2' H2' 236.3 236.3
O2' C2' C3' H3' 69.8 102.2
C4' C3' C2' O3' 244.1 241.3
C2' C3' C4' H4' 140.8 117.5
C4' C3' C2' H3' 125.0 118.7
C1' C2' C3' O2' 133.0 118.2
C3' C2' C1' H1' 265.8 278.4
C1' C2' C3' H2' 242.2 241.8
O2' C2' C3' H2' 109.1 123.6
C3' C2' O2' HO2' 272.2 292.7
O3' C3' C2' H3' 240.8 237.4
C2' C3' O3' HO3' 300.0 65.2
C4' C3' O3' C2' 100.6 114.8
O3' C3' C4' H4' 28.0 358.8
C4' C3' O3' H3' 231.2 237.4
O3' C3' C2' H2' 201.6 216.0
C2' C3' O3' H3' 130.5 122.6
HN1 N1 C1 C4 360.0 0.0
HN1 N1 C1 O1 180.4 180.0
C1 N1 HN1 HN1A 180.0 179.7
HN1A N1 C1 C4 180.0 179.7
HN1A N1 C1 O1 0.4 359.8
C1 N1 HN1A HN1 180.0 180.3
H4 C4 C1 O1 51.0 120.0
C1 C4 H4 C5 235.1 240.0
C1 C4 H4 H4A 117.5 120.0
H4 C4 C5 N2 165.1 60.0
C5 C4 H4 H4A 242.5 240.0
H4 C4 C5 H5 285.1 179.9
H4 C4 C5 H5A 49.9 300.0
H4A C4 C1 O1 173.7 240.0
C1 C4 H4A C5 123.4 120.0
C1 C4 H4A H4 241.7 240.0
H4A C4 C5 N2 42.4 300.0
C5 C4 H4A H4 118.3 120.0
H4A C4 C5 H5 162.4 60.0
H4A C4 C5 H5A 287.2 180.0
C4 C5 H5 N2 231.9 240.0
H5 C5 C4 H4 285.1 179.9
H5 C5 C4 H4A 162.4 60.0
C4 C5 H5 H5A 115.9 120.0
H5 C5 N2 C6 193.9 173.9
H5 C5 N2 C5' 64.6 50.0
N2 C5 H5 H5A 244.1 240.0
C4 C5 H5A N2 125.6 120.0
H5A C5 C4 H4 49.9 300.0
H5A C5 C4 H4A 287.2 180.0
C4 C5 H5A H5 242.8 240.0
H5A C5 N2 C6 69.2 53.9
H5A C5 N2 C5' 299.9 290.0
N2 C5 H5A H5 117.2 120.0
H6 C6 N2 C5' 294.1 183.9
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' 54.1 303.9
N2 C6 H6A H6 240.0 240.0
N2 C6 H6A H6B 120.0 120.0
H6 C6 H6A H6B 240.0 240.0
H6B C6 N2 C5' 174.1 63.9
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' 230.8 240.0
N2 C5' H5' H5'A 115.4 120.1
H5' C5' C4' O4' 285.7 306.4
H5' C5' C4' C3' 59.6 64.3
C4' C5' H5' H5'A 244.6 240.1
H5' C5' C4' H4' 188.1 185.4
N2 C5' H5'A C4' 126.5 120.0
N2 C5' H5'A H5' 243.3 240.0
H5'A C5' C4' O4' 160.1 186.5
H5'A C5' C4' C3' 294.0 304.3
C4' C5' H5'A H5' 116.8 119.9
H5'A C5' C4' H4' 62.5 65.5
C5' C4' H4' O4' 130.1 121.0
C5' C4' H4' C3' 246.4 238.9
H4' C4' C5' H5' 188.1 185.4
H4' C4' C5' H5'A 62.5 65.5
O4' C4' H4' C3' 116.3 117.9
H4' C4' O4' C1' 208.6 266.9
H4' C4' C3' C2' 140.8 117.5
H4' C4' C3' O3' 28.0 358.8
H4' C4' C3' H3' 268.2 236.2
O4' C1' H1' N5 123.5 122.9
O4' C1' H1' C2' 244.5 245.8
N5 C1' H1' C2' 120.9 122.9
H1' C1' N5 C11 162.8 346.5
H1' C1' N5 C7 342.8 166.1
H1' C1' C2' O2' 32.9 36.6
H1' C1' C2' C3' 265.8 278.4
H1' C1' C2' H2' 140.6 160.2
N4 C10 H10 N3 180.0 180.0
H10 C10 N3 C9 180.0 180.0
HN7 N7 C9 C12 196.5 180.0
C9 N7 HN7 HN7A 120.0 180.0
HN7A N7 C9 C12 316.5 359.9
C9 N7 HN7A HN7 240.0 180.0
C1' C2' H2' O2' 233.5 236.3
C1' C2' H2' C3' 114.1 112.7
H2' C2' C1' H1' 140.6 160.2
O2' C2' H2' C3' 240.5 236.4
H2' C2' O2' HO2' 35.8 56.4
H2' C2' C3' O3' 201.6 216.0
H2' C2' C3' H3' 320.7 338.6
HO2' O2' C2' C3' 272.2 292.7
HO2' O2' C2' H2' 35.8 56.4
C4' C3' H3' C2' 248.9 245.2
C4' C3' H3' O3' 125.7 122.6
H3' C3' C4' H4' 268.2 236.2
C2' C3' H3' O3' 236.9 237.4
H3' C3' C2' H2' 320.7 338.6
H3' C3' O3' HO3' 169.4 302.7
HO3' O3' C3' H3' 169.4 302.7
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 120.0 119.9
C7 C8 H8B H8A 240.0 240.0
H8 C8 H8B H8A 120.0 120.1