PDB Chemical Component TM1

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 TM1

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.390 1.321
N1 C6 1.426 1.329
C2 N3 1.377 1.317
C2 H2 1.080 1.080
N3 C4 1.405 1.329
C4 C5 1.405 1.405
C4 N9 1.326 1.373
C5 C6 1.455 1.405
C5 N7 1.319 1.354
C6 N6 1.331 1.384
N6 HN6 1.000 0.970
N6 HN6A 1.000 0.970
N7 C8 1.336 1.301
C8 N9 1.364 1.363
C8 H8 1.080 1.080
N9 C1' 1.596 1.465
PA O1A 1.574 1.610
PA O2A 1.510 1.480
PA O3A 1.584 1.610
PA O5' 1.651 1.610
C1' C2' 1.577 1.548
C1' O4' 1.423 1.443
C1' H1' 1.100 1.090
O1A HO1A 0.950 0.967
C1F O2' 1.511 1.436
C1F C2F 1.554 1.499
C1F O3' 1.500 1.442
C1F C6F 1.534 1.499
C2' O2' 1.459 1.436
C2' C3' 1.505 1.557
C2' H2' 1.100 1.090
C2F N2F 1.483 1.479
C2F C3F 1.398 1.299
N2F O2F 1.217 1.218
N2F O3F 1.245 1.218
C3' O3' 1.451 1.446
C3' C4' 1.439 1.539
C3' H3' 1.100 1.090
O3A HO3A 0.950 0.966
C3F C4F 1.387 1.498
C3F H3F 1.080 1.080
C4' O4' 1.436 1.437
C4' C5' 1.618 1.530
C4' H4' 1.100 1.091
C4F N4F 1.326 1.465
C4F C5F 1.416 1.499
C4F H4F 1.100 1.090
N4F O4F 1.208 1.219
N4F O5F 1.189 1.218
C5' O5' 1.491 1.429
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.091
C5F C6F 1.508 1.299
C5F H5F 1.080 1.080
C6F N6F 1.416 1.480
N6F O6F 1.215 1.219
N6F O7F 1.162 1.217

Bond Angles for TM1

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 118.8 121.2
N1 C2 N3 121.0 122.5
N1 C2 H2 119.5 118.8
N1 C6 C5 119.5 118.5
N1 C6 N6 121.1 120.8
N3 C2 H2 119.5 118.8
C2 N3 C4 123.1 120.6
N3 C4 C5 117.7 119.1
N3 C4 N9 136.9 134.9
C5 C4 N9 105.4 106.0
C4 C5 C6 120.0 118.2
C4 C5 N7 110.6 107.2
C4 N9 C8 107.7 107.4
C4 N9 C1' 126.3 126.3
C6 C5 N7 129.5 134.7
C5 C6 N6 119.4 120.8
C5 N7 C8 105.6 109.5
C6 N6 HN6 109.5 120.0
C6 N6 HN6A 109.4 120.0
HN6 N6 HN6A 109.4 120.0
N7 C8 N9 110.7 110.0
N7 C8 H8 124.6 125.0
N9 C8 H8 124.6 125.0
C8 N9 C1' 126.0 126.3
N9 C1' C2' 114.3 110.6
N9 C1' O4' 110.1 110.5
N9 C1' H1' 103.1 110.5
O1A PA O2A 109.3 109.5
O1A PA O3A 108.1 109.5
O1A PA O5' 107.6 109.4
PA O1A HO1A 109.5 114.0
O2A PA O3A 110.6 109.5
O2A PA O5' 110.7 109.5
O3A PA O5' 110.3 109.5
PA O3A HO3A 109.5 114.0
PA O5' C5' 127.5 123.0
C2' C1' O4' 99.3 103.8
C2' C1' H1' 113.3 110.5
C1' C2' O2' 114.8 108.9
C1' C2' C3' 105.6 102.2
C1' C2' H2' 109.9 113.0
O4' C1' H1' 117.2 110.7
C1' O4' C4' 121.6 106.9
O2' C1F C2F 101.0 109.9
O2' C1F O3' 114.2 106.2
O2' C1F C6F 112.1 110.0
C1F O2' C2' 100.3 107.2
C2F C1F O3' 115.2 109.6
C2F C1F C6F 113.5 111.5
C1F C2F N2F 123.9 118.6
C1F C2F C3F 120.8 122.7
O3' C1F C6F 101.4 109.6
C1F O3' C3' 103.8 103.6
C1F C6F C5F 118.0 122.7
C1F C6F N6F 127.4 118.6
O2' C2' C3' 113.0 105.0
O2' C2' H2' 101.9 113.0
C3' C2' H2' 111.8 113.9
C2' C3' O3' 107.8 102.9
C2' C3' C4' 112.9 104.1
C2' C3' H3' 107.7 113.4
N2F C2F C3F 115.4 118.7
C2F N2F O2F 126.5 120.0
C2F N2F O3F 122.2 120.0
C2F C3F C4F 126.8 122.9
C2F C3F H3F 116.6 118.6
O2F N2F O3F 111.3 120.0
O3' C3' C4' 107.6 108.6
O3' C3' H3' 113.0 113.2
C4' C3' H3' 107.9 113.7
C3' C4' O4' 100.6 107.4
C3' C4' C5' 116.0 109.9
C3' C4' H4' 112.8 109.8
C4F C3F H3F 116.6 118.6
C3F C4F N4F 125.9 109.1
C3F C4F C5F 116.5 111.3
C3F C4F H4F 68.8 109.1
O4' C4' C5' 113.9 109.9
O4' C4' H4' 115.0 109.9
C5' C4' H4' 99.3 109.9
C4' C5' O5' 125.8 109.5
C4' C5' H5' 104.4 109.5
C4' C5' H5'A 104.3 109.4
N4F C4F C5F 117.6 109.1
N4F C4F H4F 57.1 109.1
C4F N4F O4F 123.4 120.0
C4F N4F O5F 121.8 120.0
C5F C4F H4F 174.7 109.0
C4F C5F C6F 124.4 122.8
C4F C5F H5F 117.8 118.6
O4F N4F O5F 114.8 120.0
O5' C5' H5' 104.3 109.5
O5' C5' H5'A 104.4 109.5
H5' C5' H5'A 114.1 109.4
C6F C5F H5F 117.8 118.6
C5F C6F N6F 114.7 118.7
C6F N6F O6F 122.4 120.0
C6F N6F O7F 126.5 120.1
O6F N6F O7F 111.1 120.0

Torsion Angles for TM1

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 C5 360.0 360.0
C2 N1 C6 N6 180.1 179.9
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 0.0 0.0
C6 N1 C2 N3 0.0 0.0
C6 N1 C2 H2 180.0 180.0
C4 C5 C6 N1 360.0 360.0
N1 C6 C5 N7 180.1 180.0
C5 C6 N1 N6 179.9 180.0
N1 C6 N6 HN6 0.0 0.1
N1 C6 N6 HN6A 120.0 180.0
N3 C2 N1 C6 0.0 0.0
N1 C2 N3 H2 180.0 179.9
C2 N3 C4 C5 360.0 359.9
C2 N3 C4 N9 180.0 180.0
H2 C2 N1 C6 180.0 180.0
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 180.0 180.1
C4 N3 C2 H2 180.0 180.1
C5 C4 N3 N9 179.9 180.0
N3 C4 C5 C6 0.1 0.1
N3 C4 C5 N7 180.0 180.0
N3 C4 N9 C8 180.0 180.0
N3 C4 N9 C1' 359.7 359.9
N1 C6 C5 C4 360.0 360.0
N3 C4 C5 N9 180.1 180.0
C5 C4 N9 C8 0.0 0.0
C5 C4 N9 C1' 179.8 180.0
C6 C5 C4 N7 180.1 180.0
C4 C5 C6 N6 179.9 180.0
C4 C5 N7 C8 0.1 0.0
N3 C4 N9 C5 179.9 180.0
N9 C4 C5 C6 180.0 180.0
N9 C4 C5 N7 359.9 360.0
N7 C8 N9 C4 0.0 360.0
C4 N9 C8 H8 180.0 180.0
C8 N9 C4 C1' 180.2 180.0
C4 N9 C1' C2' 99.0 85.0
C4 N9 C1' O4' 209.7 199.4
C4 N9 C1' H1' 335.5 322.3
N1 C6 C5 N6 180.1 180.0
C6 C5 C4 N9 180.0 180.0
C4 C5 C6 N7 179.9 180.0
C6 C5 N7 C8 180.0 180.0
C5 C6 N6 HN6 180.1 180.0
C5 C6 N6 HN6A 300.1 359.9
N7 C5 C4 N9 359.9 360.0
C4 C5 N7 C6 180.1 180.0
N7 C5 C6 N6 360.0 0.1
C5 N7 C8 N9 359.9 0.0
C5 N7 C8 H8 179.9 180.0
N1 C6 N6 C5 179.9 180.0
N6 C6 C5 N7 360.0 0.1
HN6 N6 C6 HN6A 240.0 180.1
C6 N6 HN6 HN6A 120.0 179.9
C6 N6 HN6A HN6 240.0 180.1
C4 N9 C8 N7 0.0 360.0
N9 C8 N7 H8 180.0 180.1
N7 C8 N9 C1' 180.2 180.0
C4 N9 C8 C1' 179.8 180.0
N7 C8 N9 H8 180.0 179.9
C8 N9 C1' C2' 278.7 265.0
C8 N9 C1' O4' 29.4 19.4
C8 N9 C1' H1' 155.3 142.2
N7 C8 H8 N9 180.0 180.1
H8 C8 N9 C1' 0.3 0.1
C4 N9 C1' C8 180.3 180.0
C1' N9 C8 H8 0.3 0.1
C2' C1' N9 O4' 249.3 245.6
C2' C1' N9 H1' 123.4 122.7
N9 C1' C2' O2' 242.7 265.1
N9 C1' C2' C3' 117.5 154.3
N9 C1' C2' H2' 356.8 31.5
O4' C1' N9 H1' 234.2 237.1
N9 C1' O4' C4' 239.6 201.4
O2A PA O1A O3A 239.5 240.0
O2A PA O1A O5' 120.3 120.0
O3A PA O1A O5' 240.9 240.0
O1A PA O3A HO3A 240.3 300.0
O1A PA O5' C5' 244.2 65.1
O1A PA O2A O3A 119.0 120.0
O1A PA O2A O5' 241.6 240.0
O2A PA O1A HO1A 360.0 180.0
O3A PA O2A O5' 122.6 120.0
O2A PA O3A HO3A 360.0 60.0
O2A PA O5' C5' 124.7 305.1
O1A PA O3A O2A 240.3 240.0
O1A PA O3A O5' 117.4 119.9
O3A PA O1A HO1A 120.5 300.0
O2A PA O3A O5' 237.1 240.0
O3A PA O5' C5' 1.9 185.0
O1A PA O5' O2A 119.4 120.0
O1A PA O5' O3A 242.3 240.0
O5' PA O1A HO1A 239.7 60.0
O2A PA O5' O3A 122.8 120.0
O5' PA O3A HO3A 122.9 180.0
C4' C5' O5' PA 215.4 180.0
PA O5' C5' H5' 95.4 59.9
PA O5' C5' H5'A 335.3 300.0
N9 C1' C2' O4' 117.1 118.5
N9 C1' C2' H1' 242.2 237.2
O4' C1' C2' H1' 125.1 118.7
C2' C1' O4' C4' 359.8 319.9
C1F O2' C2' C1' 242.1 246.9
O2' C2' C1' C3' 125.2 110.7
O2' C2' C1' H2' 245.9 233.6
C3' C2' C1' H2' 120.7 122.8
C1' C2' C3' O3' 118.3 94.3
C1' C2' C3' C4' 359.6 341.0
C1' C2' C3' H3' 240.5 217.0
N9 C1' O4' C2' 239.8 241.4
N9 C1' O4' H1' 117.4 122.8
C2' C1' O4' H1' 237.7 241.4
O4' C1' C2' O2' 125.6 146.5
O4' C1' C2' C3' 0.4 35.8
O4' C1' C2' H2' 239.7 273.0
C3' C4' O4' C1' 359.9 27.7
C1' O4' C4' C5' 124.7 147.2
C1' O4' C4' H4' 238.4 268.2
N9 C1' H1' C2' 124.1 122.8
N9 C1' H1' O4' 238.9 237.2
C2' C1' H1' O4' 114.8 114.4
H1' C1' C2' O2' 0.4 27.8
H1' C1' C2' C3' 235.3 277.1
H1' C1' C2' H2' 114.6 154.2
H1' C1' O4' C4' 122.1 78.5
HO1A O1A PA O2A 360.0 180.0
HO1A O1A PA O3A 120.5 300.0
HO1A O1A PA O5' 239.7 60.0
C1' C2' O2' C1F 242.1 246.9
C2F C1F O2' O3' 235.8 241.6
C2F C1F O2' C6F 121.1 123.1
O2' C1F C2F N2F 60.6 38.4
O2' C1F C2F C3F 240.5 218.5
O3' C1F O2' C6F 245.4 241.5
O2' C1F O3' C3' 352.9 320.6
O2' C1F C6F C5F 113.0 141.4
O2' C1F C6F N6F 293.4 321.4
C1F O2' C2' C3' 3.3 355.8
C1F O2' C2' H2' 123.4 120.5
O2' C1F C2F O3' 123.6 116.3
O2' C1F C2F C6F 239.9 237.8
C2F C1F O2' C2' 238.2 268.4
O3' C1F C2F C6F 116.3 121.5
C2F C1F O3' C3' 109.2 79.2
C2F C1F C6F C5F 359.4 19.3
C2F C1F C6F N6F 179.8 199.3
N2F C2F C1F C3F 180.1 180.0
C1F C2F N2F O2F 0.0 276.7
C1F C2F N2F O3F 179.7 96.8
C1F C2F C3F C4F 359.7 359.9
C1F C2F C3F H3F 179.7 180.0
O2' C1F O3' C2F 243.7 241.4
O2' C1F O3' C6F 120.7 118.8
O3' C1F O2' C2' 2.4 26.8
C2F C1F O3' C6F 237.0 237.4
O3' C1F C2F N2F 297.0 282.2
O3' C1F C2F C3F 116.9 102.2
O3' C1F C6F C5F 235.3 257.8
O3' C1F C6F N6F 55.7 77.8
C2' C3' O3' C1F 8.5 35.2
C1F O3' C3' C4' 130.6 145.1
C1F O3' C3' H3' 249.6 272.4
O2' C1F C6F C2F 113.6 122.1
O2' C1F C6F O3' 237.8 243.6
C6F C1F O2' C2' 117.0 145.3
C2F C1F C6F O3' 124.1 121.5
C6F C1F C2F N2F 180.7 160.6
C6F C1F C2F C3F 0.6 340.7
C6F C1F O3' C3' 232.1 201.8
C4F C5F C6F C1F 0.3 0.2
C1F C6F C5F H5F 180.2 180.1
C5F C6F C1F N6F 179.6 180.0
C1F C6F N6F O6F 179.8 180.0
C1F C6F N6F O7F 359.6 360.0
O2' C2' C1' O4' 125.6 146.5
O2' C2' C1' H1' 0.4 27.8
C1' C2' O2' C3' 238.8 251.1
C1' C2' O2' H2' 118.7 126.4
C2' O2' C1F C2F 238.2 268.4
C2' O2' C1F O3' 2.4 26.8
C2' O2' C1F C6F 117.0 145.3
C3' C2' O2' H2' 239.9 235.3
O2' C2' C3' O3' 352.1 340.6
O2' C2' C3' C4' 233.3 227.3
O2' C2' C3' H3' 114.3 103.3
C3' C2' C1' O4' 0.4 35.8
C3' C2' C1' H1' 235.3 277.1
C1' C2' C3' O2' 126.3 113.7
C1' C2' C3' H2' 240.5 237.8
C1F O3' C3' C2' 8.5 35.2
O2' C2' C3' H2' 114.3 124.1
O3' C3' C2' C4' 118.8 113.3
O3' C3' C2' H3' 237.8 237.4
C4' C3' C2' H3' 119.0 124.0
C2' C3' C4' O4' 0.3 356.0
C2' C3' C4' C5' 237.0 236.5
C2' C3' C4' H4' 123.4 115.5
H2' C2' C1' O4' 239.7 273.0
H2' C2' C1' H1' 114.6 154.2
C1' C2' H2' O2' 237.9 235.8
C1' C2' H2' C3' 116.9 116.1
O2' C2' H2' C3' 239.0 240.3
H2' C2' C3' O3' 237.8 216.6
H2' C2' C3' C4' 119.0 103.2
H2' C2' C3' H3' 0.0 339.2
N2F C2F C1F O3' 297.0 282.2
N2F C2F C1F C6F 180.7 160.6
C1F C2F N2F C3F 179.9 180.0
N2F C2F C3F C4F 179.6 180.0
N2F C2F C3F H3F 359.6 0.0
O2F N2F C2F O3F 180.3 180.0
C3F C2F C1F O3' 116.9 102.2
C3F C2F C1F C6F 0.6 340.7
C1F C2F C3F N2F 180.1 180.0
C3F C2F N2F O2F 180.1 96.7
C3F C2F N2F O3F 359.8 276.8
C4F C3F C2F H3F 180.0 180.0
C2F C3F C4F N4F 179.9 258.9
C2F C3F C4F C5F 359.9 19.5
C2F C3F C4F H4F 179.8 139.8
O2F N2F C2F C3F 180.1 96.7
C2F N2F O2F O3F 179.7 180.0
O3F N2F C2F C3F 359.8 276.8
C2F N2F O3F O2F 180.3 180.0
C3' O3' C1F C6F 232.1 201.8
O3' C3' C2' H2' 237.8 216.6
C2' C3' O3' C4' 237.9 250.1
C2' C3' O3' H3' 118.9 122.8
C4' C3' O3' H3' 241.0 232.7
O3' C3' C4' O4' 241.4 246.9
O3' C3' C4' C5' 118.1 127.4
O3' C3' C4' H4' 4.5 6.3
C1' O4' C4' C3' 359.9 27.7
C4' C3' C2' H2' 119.0 103.2
C2' C3' C4' O3' 118.9 109.2
C2' C3' C4' H3' 241.1 236.1
O3' C3' C4' H3' 122.2 127.0
O4' C4' C3' C5' 123.3 119.5
O4' C4' C3' H4' 236.9 240.5
C5' C4' C3' H4' 113.6 121.1
C3' C4' C5' O5' 181.6 185.0
C3' C4' C5' H5' 301.6 305.1
C3' C4' C5' H5'A 61.6 65.0
H3' C3' C2' H2' 0.0 339.2
C2' C3' H3' O3' 241.0 243.2
C2' C3' H3' C4' 122.2 118.6
O3' C3' H3' C4' 241.2 235.4
H3' C3' C4' O4' 119.2 119.9
H3' C3' C4' C5' 355.9 0.4
H3' C3' C4' H4' 242.3 239.3
HO3A O3A PA O5' 122.9 180.0
C2F C3F C4F H3F 180.0 180.0
N4F C4F C3F C5F 180.0 239.5
N4F C4F C3F H4F 0.1 119.1
C3F C4F N4F O4F 257.2 60.0
C3F C4F N4F O5F 77.4 240.0
C5F C4F C3F H4F 180.0 239.7
C3F C4F C5F C6F 0.1 340.5
C3F C4F C5F H5F 180.2 160.6
C2F C3F H3F C4F 180.0 180.0
H3F C3F C4F N4F 359.9 78.9
H3F C3F C4F C5F 179.9 199.4
H3F C3F C4F H4F 359.8 319.8
C4' O4' C1' H1' 122.1 78.5
O4' C4' C3' H3' 119.2 119.9
C3' C4' O4' C5' 235.3 240.5
C3' C4' O4' H4' 121.6 119.4
C5' C4' O4' H4' 246.3 238.9
O4' C4' C5' O5' 65.6 67.0
O4' C4' C5' H5' 185.6 187.1
O4' C4' C5' H5'A 305.6 307.0
PA O5' C5' C4' 215.4 180.0
C5' C4' C3' H3' 355.9 0.4
C3' C4' C5' O4' 116.0 118.0
C3' C4' C5' H4' 238.8 239.0
O4' C4' C5' H4' 122.8 121.0
O5' C5' C4' H5' 240.0 239.9
O5' C5' C4' H5'A 120.0 120.0
H5' C5' C4' H5'A 240.0 240.1
H4' C4' C3' H3' 242.3 239.3
C3' C4' H4' O4' 245.4 242.0
C3' C4' H4' C5' 123.4 121.0
O4' C4' H4' C5' 238.0 239.0
H4' C4' C5' O5' 302.8 306.0
H4' C4' C5' H5' 62.8 66.1
H4' C4' C5' H5'A 182.8 186.0
N4F C4F C3F H3F 359.9 78.9
C3F C4F N4F C5F 180.0 121.9
C3F C4F N4F H4F 359.9 240.9
C5F C4F N4F H4F 179.9 119.0
N4F C4F C5F C6F 180.1 101.0
N4F C4F C5F H5F 0.2 281.1
O4F N4F C4F O5F 179.8 180.0
C1F C6F C5F C4F 0.3 0.2
C5F C4F C3F H3F 179.9 199.4
C3F C4F C5F N4F 180.0 239.5
C3F C4F C5F H4F 179.5 120.4
N4F C4F C5F H4F 359.5 240.9
C5F C4F N4F O4F 77.2 298.1
C5F C4F N4F O5F 257.5 118.2
C6F C5F C4F H5F 180.0 179.9
C4F C5F C6F N6F 179.9 180.2
H4F C4F C3F H3F 359.8 319.8
C3F C4F H4F N4F 179.9 119.1
C3F C4F H4F C5F 180.5 238.3
N4F C4F H4F C5F 0.5 119.1
H4F C4F N4F O4F 257.3 179.1
H4F C4F N4F O5F 77.5 359.1
H4F C4F C5F C6F 180.6 220.1
H4F C4F C5F H5F 0.6 40.2
O4F N4F C4F C5F 77.2 298.1
O4F N4F C4F H4F 257.3 179.1
C4F N4F O4F O5F 180.2 180.0
O5F N4F C4F C5F 257.5 118.2
O5F N4F C4F H4F 77.5 359.1
C4F N4F O5F O4F 179.8 180.0
O5' C5' C4' H4' 302.8 306.0
C4' C5' O5' H5' 120.0 120.1
C4' C5' O5' H5'A 240.0 240.0
H5' C5' O5' H5'A 120.0 119.9
H5' C5' C4' H4' 62.8 66.1
C4' C5' H5' O5' 226.5 239.9
C4' C5' H5' H5'A 113.2 119.9
O5' C5' H5' H5'A 246.8 240.0
H5'A C5' C4' H4' 182.8 186.0
C4' C5' H5'A O5' 133.5 120.0
C4' C5' H5'A H5' 246.8 240.0
O5' C5' H5'A H5' 113.2 120.0
C1F C6F C5F N6F 180.3 180.0
C6F C5F C4F H4F 180.6 220.1
C4F C5F C6F H5F 180.0 180.1
C5F C6F N6F O6F 0.1 360.0
C5F C6F N6F O7F 180.0 180.0
H5F C5F C4F H4F 0.6 40.2
C4F C5F H5F C6F 180.0 179.9
H5F C5F C6F N6F 359.9 0.1
C1F C6F N6F C5F 179.7 180.0
N6F C6F C5F H5F 359.9 0.1
O6F N6F C6F O7F 180.1 180.0
C6F N6F O6F O7F 179.9 180.0
C6F N6F O7F O6F 180.1 180.0