PDB Chemical Component M8M

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 M8M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 O2 1.414 1.463
O2 C4 1.516 1.429
C4 C5 1.499 1.529
C5 N2 1.500 1.469
N2 C6 1.483 1.468
N2 C5' 1.500 1.469
C5' C4' 1.522 1.530
C4' O4' 1.473 1.438
C4' C3' 1.516 1.542
O4' C1' 1.365 1.444
C1' N5 1.572 1.466
C1' C2' 1.340 1.549
N5 C11 1.396 1.372
N5 C7 1.383 1.362
C11 N4 1.354 1.329
C11 C12 1.395 1.405
N4 C10 1.343 1.316
C10 N3 1.345 1.320
N3 C9 1.360 1.329
C9 N7 1.334 1.384
C9 C12 1.418 1.405
C12 N6 1.388 1.354
N6 C7 1.315 1.301
C7 C8 1.501 1.508
C2' O2' 1.412 1.429
C2' C3' 1.511 1.548
C3' O3' 1.428 1.429
N1 HN1 1.000 1.008
N1 HN1A 1.000 1.009
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 1.090
C6 H6A 1.100 1.090
C6 H6B 1.100 1.089
C5' H5' 1.100 1.091
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 0.971
N7 HN7A 1.000 0.970
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.968
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.966
C8 H8 1.100 1.090
C8 H8A 1.100 1.090
C8 H8B 1.100 1.090

Bond Angles for M8M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N1 O2 C4 110.1 114.0
O2 N1 HN1 109.5 111.0
O2 N1 HN1A 109.5 111.0
O2 C4 C5 113.5 109.5
O2 C4 H4 108.2 109.5
O2 C4 H4A 107.3 109.5
C4 C5 N2 110.7 109.5
C5 C4 H4 108.2 109.5
C5 C4 H4A 107.2 109.5
C4 C5 H5 109.1 109.5
C4 C5 H5A 108.8 109.5
C5 N2 C6 107.7 111.0
C5 N2 C5' 110.9 111.0
N2 C5 H5 109.1 109.4
N2 C5 H5A 108.8 109.4
C6 N2 C5' 109.3 111.0
N2 C6 H6 109.5 109.5
N2 C6 H6A 109.5 109.5
N2 C6 H6B 109.5 109.5
N2 C5' C4' 112.4 109.4
N2 C5' H5' 108.5 109.5
N2 C5' H5'A 107.8 109.5
C5' C4' O4' 113.5 109.9
C5' C4' C3' 114.7 109.9
C4' C5' H5' 108.5 109.5
C4' C5' H5'A 107.8 109.5
C5' C4' H4' 101.4 109.9
O4' C4' C3' 104.8 107.3
C4' O4' C1' 101.7 106.9
O4' C4' H4' 111.9 109.9
C4' C3' C2' 100.8 104.2
C4' C3' O3' 110.8 110.5
C3' C4' H4' 110.6 110.0
C4' C3' H3' 114.2 110.5
O4' C1' N5 107.0 110.6
O4' C1' C2' 119.2 103.5
O4' C1' H1' 106.3 110.6
N5 C1' C2' 114.3 110.6
C1' N5 C11 118.8 126.3
C1' N5 C7 136.0 126.3
N5 C1' H1' 112.1 110.5
C1' C2' O2' 121.9 110.9
C1' C2' C3' 100.6 102.1
C2' C1' H1' 97.4 110.8
C1' C2' H2' 109.5 110.9
C11 N5 C7 105.3 107.5
N5 C11 N4 128.3 135.0
N5 C11 C12 105.5 106.0
N5 C7 N6 114.2 110.0
N5 C7 C8 119.7 125.0
N4 C11 C12 126.1 119.1
C11 N4 C10 111.4 120.7
C11 C12 C9 116.9 118.2
C11 C12 N6 110.9 107.2
N4 C10 N3 129.0 122.4
N4 C10 H10 115.5 118.8
C10 N3 C9 118.4 121.2
N3 C10 H10 115.5 118.8
N3 C9 N7 118.6 120.8
N3 C9 C12 118.2 118.4
N7 C9 C12 123.2 120.8
C9 N7 HN7 109.5 120.0
C9 N7 HN7A 109.4 120.0
C9 C12 N6 132.2 134.7
C12 N6 C7 104.1 109.4
N6 C7 C8 126.1 125.0
C7 C8 H8 109.5 109.4
C7 C8 H8A 109.5 109.5
C7 C8 H8B 109.5 109.5
O2' C2' C3' 114.6 110.9
O2' C2' H2' 93.7 110.8
C2' O2' HO2' 109.5 114.0
C2' C3' O3' 109.4 110.5
C3' C2' H2' 117.6 111.0
C2' C3' H3' 115.4 110.5
O3' C3' H3' 106.2 110.5
C3' O3' HO3' 109.5 114.0
HN1 N1 HN1A 109.5 111.0
H4 C4 H4A 112.6 109.5
H5 C5 H5A 110.4 109.4
H6 C6 H6A 109.4 109.4
H6 C6 H6B 109.5 109.4
H6A C6 H6B 109.5 109.5
H5' C5' H5'A 111.8 109.5
HN7 N7 HN7A 109.5 120.0
H8 C8 H8A 109.4 109.4
H8 C8 H8B 109.4 109.5
H8A C8 H8B 109.5 109.5

Torsion Angles for M8M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N1 O2 C4 C5 179.8 180.0
N1 O2 C4 H4 299.8 300.0
N1 O2 C4 H4A 61.5 60.0
HN1 N1 O2 HN1A 240.0 236.1
C4 O2 N1 HN1 189.8 56.1
C4 O2 N1 HN1A 309.8 180.0
O2 C4 C5 N2 166.9 64.7
C5 C4 O2 H4 240.0 240.0
C5 C4 O2 H4A 118.3 120.0
O2 C4 C5 H5 286.9 184.7
O2 C4 C5 H5A 47.4 304.7
H4 C4 O2 H4A 238.3 240.0
O2 C4 C5 H4 120.0 120.0
O2 C4 C5 H4A 241.7 240.0
C4 C5 N2 C6 277.5 195.6
C4 C5 N2 C5' 157.9 71.6
N2 C5 C4 H5 240.0 240.0
N2 C5 C4 H5A 119.5 120.0
H4 C4 C5 H4A 121.7 120.0
H5 C5 C4 H5A 239.5 240.0
N2 C5 C4 H4 46.9 304.7
N2 C5 C4 H4A 285.1 184.7
C4 C5 N2 H5 120.0 120.0
C4 C5 N2 H5A 240.5 239.9
C6 N2 C5 C5' 119.6 124.0
C5 N2 C6 H6 152.1 63.2
C5 N2 C6 H6A 272.1 183.2
C5 N2 C6 H6B 32.0 303.2
C5 N2 C5' C4' 178.9 190.0
C5 N2 C5' H5' 298.9 310.0
C5 N2 C5' H5'A 60.2 70.1
H5 C5 N2 H5A 120.5 119.9
C5 N2 C6 C5' 239.4 236.0
C6 N2 C5 H5 157.5 75.5
C6 N2 C5 H5A 37.0 315.6
C6 N2 C5' C4' 60.3 66.1
C6 N2 C5' H5' 180.3 186.0
C6 N2 C5' H5'A 301.5 306.1
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 118.6 124.0
C5' N2 C5 H5 38.0 311.5
C5' N2 C5 H5A 277.5 191.6
C5' N2 C6 H6 272.6 187.2
C5' N2 C6 H6A 32.6 307.2
C5' N2 C6 H6B 152.6 67.2
N2 C5' C4' O4' 59.3 66.5
N2 C5' C4' C3' 179.8 184.3
C4' C5' N2 H5' 240.0 240.0
C4' C5' N2 H5'A 118.7 120.0
N2 C5' C4' H4' 299.0 305.4
H5' C5' N2 H5'A 238.7 240.0
N2 C5' C4' H5' 120.0 120.0
N2 C5' C4' H5'A 241.3 240.0
O4' C4' C5' C3' 239.5 242.2
C5' C4' O4' C1' 105.9 145.9
O4' C4' C5' H4' 120.2 121.1
C5' C4' C3' C2' 268.2 238.6
C5' C4' C3' O3' 152.4 119.9
C3' C4' C5' H4' 240.8 238.9
C5' C4' C3' H3' 32.5 357.2
H5' C5' C4' H5'A 121.3 120.0
C5' C4' O4' C3' 126.0 119.4
O4' C4' C5' H5' 299.2 306.5
O4' C4' C5' H5'A 178.0 186.5
C5' C4' O4' H4' 245.9 238.9
O4' C4' C3' C2' 33.3 358.0
O4' C4' C3' O3' 277.6 239.3
C3' C4' O4' H4' 119.9 119.5
O4' C4' C3' H3' 157.7 116.6
C4' O4' C1' N5 225.3 201.4
C4' O4' C1' C2' 357.0 319.9
C4' O4' C1' H1' 105.4 78.7
C5' C4' C3' O4' 234.8 240.6
C3' C4' C5' H5' 59.8 64.3
C3' C4' C5' H5'A 298.5 304.3
C5' C4' C3' H4' 114.0 121.1
C3' C4' O4' C1' 340.0 26.5
O4' C4' C3' H4' 239.2 240.5
C1' C2' C3' C4' 326.7 339.1
O2' C2' C3' C4' 194.1 220.9
C2' C3' C4' O3' 115.8 118.7
C4' C3' C2' H2' 85.4 97.3
C2' C3' C4' H3' 235.7 241.3
O3' C3' C4' H3' 119.9 122.6
C4' C3' O3' HO3' 56.9 180.0
C1' O4' C4' C3' 340.0 26.5
C1' O4' C4' H4' 220.0 267.0
N5 C1' O4' C2' 228.4 241.5
O4' C1' N5 C11 44.6 223.6
O4' C1' N5 C7 224.6 43.3
N5 C1' O4' H1' 119.9 122.8
O4' C1' C2' O2' 152.3 155.2
O4' C1' C2' C3' 24.3 37.0
C2' C1' O4' H1' 251.6 241.3
O4' C1' C2' H2' 259.8 278.8
O4' C1' N5 C2' 134.2 114.1
O4' C1' N5 H1' 243.9 237.2
N5 C1' C2' O2' 280.6 273.7
N5 C1' C2' C3' 152.7 155.5
C2' C1' N5 H1' 109.6 123.1
N5 C1' C2' H2' 28.2 37.3
C11 N5 C1' C7 180.0 180.3
C1' N5 C11 N4 359.8 0.1
C1' N5 C11 C12 179.8 180.0
C1' N5 C7 N6 180.2 179.8
C1' N5 C7 C8 0.2 360.0
C4' C3' C2' C1' 326.7 339.1
O4' C1' C2' N5 231.6 241.5
O4' C1' C2' H1' 113.3 118.6
C2' C1' N5 C11 270.4 109.5
C2' C1' N5 C7 90.4 289.2
N5 C1' C2' H1' 241.7 237.1
O2' C2' C1' C3' 127.9 118.2
O2' C2' C1' H2' 252.4 236.5
C1' C2' O2' HO2' 153.6 180.0
C1' C2' C3' O3' 83.4 97.8
C3' C2' C1' H2' 124.5 118.3
C1' C2' C3' H3' 203.1 220.4
C11 N5 C1' C2' 270.4 109.5
C1' N5 C11 C7 180.0 179.7
C11 N5 C1' H1' 160.8 346.4
C11 N5 C7 N6 0.2 359.6
C11 N5 C7 C8 180.2 179.7
N4 C11 N5 C12 180.0 180.1
N5 C11 N4 C10 179.9 179.9
N5 C11 C12 C9 180.3 180.0
N5 C11 C12 N6 0.1 0.0
C7 N5 C1' C2' 90.4 289.2
C1' N5 C7 C11 180.0 180.3
C7 N5 C1' H1' 340.8 166.1
C7 N5 C11 N4 179.8 180.3
C7 N5 C11 C12 359.8 0.2
C12 N6 C7 N5 359.8 0.5
N6 C7 N5 C8 180.0 179.9
N5 C7 C8 H8 137.3 90.0
N5 C7 C8 H8A 257.3 210.0
N5 C7 C8 H8B 17.4 330.0
N4 C11 N5 C7 179.8 180.3
N5 C11 N4 C12 180.0 179.9
N4 C11 C12 C9 0.3 360.0
N4 C11 C12 N6 180.1 179.9
C11 N4 C10 N3 359.9 360.0
C11 N4 C10 H10 179.9 179.9
C12 C11 N5 C7 359.8 0.2
N5 C11 C12 N4 180.0 180.1
C12 C11 N4 C10 359.9 0.0
N3 C9 C12 C11 359.8 0.0
N7 C9 C12 C11 179.8 180.1
C9 C12 C11 N6 180.2 180.0
C11 C12 N6 C7 0.0 359.7
C10 N4 C11 C12 359.9 0.0
N4 C10 N3 C9 0.1 360.0
N3 C10 N4 H10 180.0 180.0
N4 C10 N3 H10 180.0 180.0
C10 N3 C9 N7 180.0 180.0
C10 N3 C9 C12 0.1 360.0
C11 C12 C9 N3 359.8 0.0
C9 N3 C10 H10 180.1 180.0
N7 C9 N3 C12 180.0 180.0
N3 C9 N7 HN7 30.3 0.0
N3 C9 N7 HN7A 150.3 179.9
N3 C9 C12 N6 180.0 180.0
C11 C12 C9 N7 179.8 180.1
N3 C9 N7 C12 180.0 180.0
N7 C9 C12 N6 0.0 0.1
HN7 N7 C9 HN7A 240.0 180.1
C11 C12 C9 N6 179.8 180.0
N3 C9 C12 N7 180.0 180.0
C12 C9 N7 HN7 210.3 180.0
C12 C9 N7 HN7A 330.3 359.9
C9 C12 N6 C7 179.8 179.7
N5 C7 N6 C12 359.8 0.5
C11 C12 N6 C9 180.2 180.0
C12 N6 C7 C8 179.9 180.3
N5 C7 N6 C8 180.0 180.1
N6 C7 C8 H8 317.3 270.2
N6 C7 C8 H8A 77.3 30.1
N6 C7 C8 H8B 197.3 150.2
N5 C7 C8 N6 180.0 179.8
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' 194.1 220.9
C1' C2' O2' C3' 238.5 247.3
O2' C2' C1' H1' 38.9 36.7
C1' C2' O2' H2' 115.8 123.6
O2' C2' C3' O3' 310.9 339.6
C3' C2' O2' H2' 237.3 236.3
O2' C2' C3' H3' 70.6 102.3
C4' C3' C2' O3' 243.2 241.3
C2' C3' C4' H4' 154.2 117.5
C4' C3' C2' H3' 123.5 118.7
C1' C2' C3' O2' 132.5 118.2
C3' C2' C1' H1' 271.0 278.5
C1' C2' C3' H2' 241.2 241.8
O2' C2' C3' H2' 108.7 123.6
C3' C2' O2' HO2' 275.1 292.7
O3' C3' C2' H3' 240.3 237.3
C2' C3' O3' HO3' 306.6 65.3
C4' C3' O3' C2' 110.3 114.8
O3' C3' C4' H4' 38.4 358.7
C4' C3' O3' H3' 235.5 237.4
O3' C3' C2' H2' 202.2 216.0
C2' C3' O3' H3' 125.2 122.6
HN1 N1 O2 C4 189.8 56.1
O2 N1 HN1 HN1A 120.0 123.9
HN1A N1 O2 C4 309.8 180.0
O2 N1 HN1A HN1 240.0 236.1
O2 C4 H4 C5 236.7 240.0
O2 C4 H4 H4A 118.4 120.0
H4 C4 C5 N2 46.9 304.7
C5 C4 H4 H4A 241.7 240.0
H4 C4 C5 H5 166.8 64.7
H4 C4 C5 H5A 287.4 184.7
O2 C4 H4A C5 122.2 120.0
O2 C4 H4A H4 241.1 240.0
H4A C4 C5 N2 285.1 184.7
C5 C4 H4A H4 118.9 120.0
H4A C4 C5 H5 45.1 304.7
H4A C4 C5 H5A 165.6 64.7
C4 C5 H5 N2 239.0 240.0
H5 C5 C4 H4 166.8 64.7
H5 C5 C4 H4A 45.1 304.7
C4 C5 H5 H5A 119.5 120.0
H5 C5 N2 C6 157.5 75.5
H5 C5 N2 C5' 38.0 311.5
N2 C5 H5 H5A 240.5 240.1
C4 C5 H5A N2 120.7 120.1
H5A C5 C4 H4 287.4 184.7
H5A C5 C4 H4A 165.6 64.7
C4 C5 H5A H5 240.3 240.0
H5A C5 N2 C6 37.0 315.6
H5A C5 N2 C5' 277.5 191.6
N2 C5 H5A H5 119.7 119.9
H6 C6 N2 C5' 272.6 187.2
N2 C6 H6 H6A 120.0 120.0
N2 C6 H6 H6B 240.0 240.0
H6A C6 H6 H6B 120.0 119.9
H6A C6 N2 C5' 32.6 307.2
N2 C6 H6A H6 240.0 239.9
N2 C6 H6A H6B 120.0 120.0
H6 C6 H6A H6B 240.0 240.1
H6B C6 N2 C5' 152.6 67.2
N2 C6 H6B H6 120.0 120.1
N2 C6 H6B H6A 240.0 240.0
H6 C6 H6B H6A 120.0 119.9
N2 C5' H5' C4' 237.6 240.0
N2 C5' H5' H5'A 118.8 120.0
H5' C5' C4' O4' 299.2 306.5
H5' C5' C4' C3' 59.8 64.3
C4' C5' H5' H5'A 241.2 240.0
H5' C5' C4' H4' 179.0 185.4
N2 C5' H5'A C4' 121.6 120.0
N2 C5' H5'A H5' 240.8 240.0
H5'A C5' C4' O4' 178.0 186.5
H5'A C5' C4' C3' 298.5 304.3
C4' C5' H5'A H5' 119.2 120.0
H5'A C5' C4' H4' 57.8 65.4
C5' C4' H4' O4' 121.3 121.0
C5' C4' H4' C3' 237.8 238.9
H4' C4' C5' H5' 179.0 185.4
H4' C4' C5' H5'A 57.8 65.4
O4' C4' H4' C3' 116.5 117.9
H4' C4' O4' C1' 220.0 267.0
H4' C4' C3' C2' 154.2 117.5
H4' C4' C3' O3' 38.4 358.7
H4' C4' C3' H3' 278.5 236.1
O4' C1' H1' N5 116.6 122.8
O4' C1' H1' C2' 236.7 245.8
N5 C1' H1' C2' 120.1 123.0
H1' C1' N5 C11 160.8 346.4
H1' C1' N5 C7 340.8 166.1
H1' C1' C2' O2' 38.9 36.7
H1' C1' C2' C3' 271.0 278.5
H1' C1' C2' H2' 146.5 160.2
N4 C10 H10 N3 180.0 180.0
H10 C10 N3 C9 180.1 180.0
HN7 N7 C9 C12 210.3 180.0
C9 N7 HN7 HN7A 120.0 179.9
HN7A N7 C9 C12 330.3 359.9
C9 N7 HN7A HN7 240.0 180.1
C1' C2' H2' O2' 234.2 236.4
C1' C2' H2' C3' 113.9 112.8
H2' C2' C1' H1' 146.5 160.2
O2' C2' H2' C3' 239.7 236.4
H2' C2' O2' HO2' 37.8 56.4
H2' C2' C3' O3' 202.2 216.0
H2' C2' C3' H3' 321.9 338.7
HO2' O2' C2' C3' 275.1 292.7
HO2' O2' C2' H2' 37.8 56.4
C4' C3' H3' C2' 243.8 245.3
C4' C3' H3' O3' 122.4 122.6
H3' C3' C4' H4' 278.5 236.1
C2' C3' H3' O3' 238.5 237.4
H3' C3' C2' H2' 321.9 338.7
H3' C3' O3' HO3' 181.4 302.6
HO3' O3' C3' H3' 181.4 302.6
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 240.0 240.1
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