PDB Chemical Component TDI

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 TDI

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C2 N1 1.344 1.321
C2 N3 1.343 1.314
C2 H2 1.103 1.080
C4 C5 1.420 1.406
C4 C9 1.452 1.459
C4 N3 1.371 1.336
C5 C6 1.411 1.399
C5 N7 1.372 1.376
C6 N6 1.390 1.385
C6 N1 1.377 1.330
CS5 S 1.827 1.814
CS5 HS51 1.115 1.090
CS5 HS52 1.115 1.089
CS5 HS53 1.115 1.090
S C5' 1.793 1.814
C5' C4' 1.517 1.530
C5' H5'1 1.115 1.090
C5' H5'2 1.115 1.091
C4' C1' 1.532 1.540
C4' C3' 1.560 1.546
C4' H4' 1.115 1.090
C1' N1' 1.497 1.479
C1' H1'1 1.115 1.090
C1' H1'2 1.115 1.090
N1' C10 1.470 1.469
N1' C2' 1.499 1.485
C10 C9 1.505 1.506
C10 H101 1.114 1.090
C10 H102 1.115 1.090
C9 C8 1.352 1.346
C8 N7 1.363 1.364
C8 H8 1.103 1.081
N7 HN7 1.020 0.970
N6 HN61 1.020 0.970
N6 HN62 1.020 0.970
C2' C3' 1.545 1.551
C2' H2'1 1.115 1.090
C2' H2'2 1.115 1.090
C3' O3' 1.446 1.430
C3' H3' 1.115 1.090
O3' H1 0.950 0.966

Bond Angles for TDI

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N1 C2 N3 120.8 122.4
N1 C2 H2 119.6 118.8
C2 N1 C6 121.9 121.3
N3 C2 H2 119.5 118.8
C2 N3 C4 120.8 120.4
C5 C4 C9 105.1 106.0
C5 C4 N3 120.1 119.1
C4 C5 C6 117.5 118.1
C4 C5 N7 107.6 107.3
C9 C4 N3 134.8 134.9
C4 C9 C10 125.5 126.5
C4 C9 C8 107.9 107.0
C6 C5 N7 134.9 134.5
C5 C6 N6 119.7 120.7
C5 C6 N1 118.9 118.6
C5 N7 C8 110.0 109.8
C5 N7 HN7 125.3 125.1
N6 C6 N1 121.4 120.7
C6 N6 HN61 108.5 120.0
C6 N6 HN62 119.7 120.0
S CS5 HS51 121.2 109.5
S CS5 HS52 87.2 109.5
S CS5 HS53 121.2 109.5
CS5 S C5' 87.2 100.0
HS51 CS5 HS52 121.2 109.5
HS51 CS5 HS53 88.6 109.5
HS52 CS5 HS53 121.3 109.5
S C5' C4' 148.9 109.5
S C5' H5'1 99.1 109.5
S C5' H5'2 99.1 109.5
C4' C5' H5'1 99.1 109.4
C4' C5' H5'2 99.1 109.4
C5' C4' C1' 120.6 110.3
C5' C4' C3' 91.3 110.3
C5' C4' H4' 113.4 110.3
H5'1 C5' H5'2 107.5 109.4
C1' C4' C3' 106.0 105.2
C1' C4' H4' 100.5 110.3
C4' C1' N1' 105.0 107.1
C4' C1' H1'1 113.9 109.9
C4' C1' H1'2 113.9 109.9
C3' C4' H4' 126.6 110.3
C4' C3' C2' 104.3 102.9
C4' C3' O3' 94.9 111.0
C4' C3' H3' 118.9 110.7
N1' C1' H1'1 113.9 109.9
N1' C1' H1'2 113.9 109.9
C1' N1' C10 93.8 106.7
C1' N1' C2' 104.4 105.8
H1'1 C1' H1'2 96.6 110.1
C10 N1' C2' 105.8 106.7
N1' C10 C9 141.3 109.5
N1' C10 H101 101.5 109.5
N1' C10 H102 101.5 109.4
N1' C2' C3' 104.0 103.3
N1' C2' H2'1 114.3 110.7
N1' C2' H2'2 114.3 110.7
C9 C10 H101 101.5 109.5
C9 C10 H102 101.5 109.4
C10 C9 C8 126.6 126.5
H101 C10 H102 106.3 109.5
C9 C8 N7 109.4 109.9
C9 C8 H8 125.0 125.0
N7 C8 H8 125.6 125.1
C8 N7 HN7 124.7 125.1
HN61 N6 HN62 108.6 120.0
C3' C2' H2'1 114.3 110.6
C3' C2' H2'2 114.3 110.7
C2' C3' O3' 102.3 110.7
C2' C3' H3' 113.0 110.7
H2'1 C2' H2'2 96.2 110.7
O3' C3' H3' 120.5 110.6
C3' O3' H1 94.9 106.8

Torsion Angles for TDI

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 0.0 359.6
C5 C6 N1 C2 360.0 0.0
N6 C6 N1 C2 180.0 180.0
N1 C2 N3 H2 180.0 179.9
N3 C2 N1 C6 359.9 0.0
C5 C4 N3 C2 0.2 0.7
C9 C4 N3 C2 180.1 179.6
N1 C2 H2 N3 180.0 180.1
H2 C2 N1 C6 179.9 180.0
H2 C2 N3 C4 180.1 179.7
C2 N3 C4 C5 0.2 0.7
C9 C4 C5 N3 180.0 180.8
C5 C4 C9 C10 180.4 179.8
C5 C4 C9 C8 0.1 359.6
C6 C5 C4 N7 179.8 179.8
C4 C5 C6 N6 180.2 180.3
C4 C5 C6 N1 0.2 0.3
C4 C5 N7 C8 0.0 359.8
C4 C5 N7 HN7 180.0 179.7
C2 N3 C4 C9 180.1 179.6
C5 C4 C9 N3 180.0 179.0
C9 C4 C5 C6 179.7 180.2
C9 C4 C5 N7 359.9 0.4
N1' C10 C9 C4 69.0 79.8
C4 C9 C10 H101 194.3 319.7
C4 C9 C10 H102 303.8 199.7
C10 C9 C4 C8 180.3 180.3
C4 C9 C8 N7 359.9 0.3
C4 C9 C8 H8 180.0 180.2
C4 N3 C2 H2 180.1 179.7
C5 C4 N3 C9 180.0 181.1
N3 C4 C5 C6 359.7 359.4
N3 C4 C5 N7 179.9 179.6
N3 C4 C9 C10 0.4 0.8
N3 C4 C9 C8 180.1 180.6
C2 N1 C6 C5 360.0 0.0
C6 C5 C4 C9 179.7 180.2
C6 C5 C4 N3 359.7 359.4
C4 C5 C6 N7 180.3 180.3
C6 C5 N7 C8 180.3 180.0
C6 C5 N7 HN7 0.3 360.0
N6 C6 C5 N1 180.0 180.0
C5 C6 N6 HN61 54.7 0.0
C5 C6 N6 HN62 180.0 180.0
N7 C5 C4 C9 359.9 0.4
N7 C5 C4 N3 179.9 179.6
C4 C5 N7 C6 179.8 179.7
N7 C5 C6 N6 360.0 0.0
N7 C5 C6 N1 180.0 180.0
C9 C8 N7 C5 0.0 360.0
C5 N7 C8 H8 180.0 180.0
C8 N7 C5 HN7 180.0 180.1
C2 N1 C6 N6 180.0 180.0
N6 C6 C5 N7 360.0 0.0
C5 C6 N6 N1 180.0 180.0
HN61 N6 C6 HN62 234.7 180.0
C6 N1 C2 N3 359.9 0.0
C6 N1 C2 H2 179.9 180.0
N1 C6 C5 N7 180.0 180.0
C5 C6 N1 N6 180.0 180.0
N1 C6 N6 HN61 234.7 180.0
N1 C6 N6 HN62 0.0 0.1
HS51 CS5 S HS52 234.8 240.0
HS51 CS5 S HS53 109.5 120.0
HS52 CS5 S HS53 234.7 240.0
CS5 S C5' C4' 269.7 180.0
CS5 S C5' H5'1 144.4 300.0
CS5 S C5' H5'2 35.0 60.0
S CS5 HS51 HS52 107.5 120.0
S CS5 HS51 HS53 233.7 240.0
HS51 CS5 S C5' 54.8 60.0
HS52 CS5 HS51 HS53 126.3 120.0
S CS5 HS52 HS51 234.8 240.0
S CS5 HS52 HS53 125.3 120.0
HS52 CS5 S C5' 180.0 180.0
HS51 CS5 HS52 HS53 250.5 240.0
S CS5 HS53 HS51 126.2 120.0
S CS5 HS53 HS52 252.5 240.0
HS53 CS5 S C5' 305.3 300.0
HS51 CS5 HS53 HS52 126.2 120.0
C5' S CS5 HS51 54.8 60.0
C5' S CS5 HS52 180.0 180.0
C5' S CS5 HS53 305.3 300.0
C4' C5' S H5'1 125.3 240.0
C4' C5' S H5'2 234.7 120.0
S C5' C4' C1' 195.5 67.8
S C5' C4' C3' 305.0 183.6
S C5' C4' H4' 76.3 305.7
H5'1 C5' S H5'2 109.5 240.0
S C5' C4' H5'1 234.7 120.0
S C5' C4' H5'2 125.3 240.0
H5'1 C5' C4' H5'2 250.5 119.9
C1' C4' C5' C3' 250.5 244.2
C1' C4' C5' H4' 119.2 122.1
C5' C4' C1' N1' 120.5 117.7
C5' C4' C1' H1'1 355.3 237.0
C5' C4' C1' H1'2 245.8 358.4
C3' C4' C5' H4' 228.7 237.9
C5' C4' C3' C2' 242.9 219.2
C5' C4' C3' O3' 138.8 100.7
C5' C4' C3' H3' 9.8 337.5
S C5' H5'1 C4' 154.7 240.0
S C5' H5'1 H5'2 257.4 120.1
C4' C5' H5'1 H5'2 102.6 240.1
H5'1 C5' C4' C1' 320.8 307.7
H5'1 C5' C4' C3' 70.3 63.5
H5'1 C5' C4' H4' 201.6 185.7
S C5' H5'2 C4' 205.3 120.0
S C5' H5'2 H5'1 102.6 239.9
C4' C5' H5'2 H5'1 257.4 119.9
H5'2 C5' C4' C1' 70.3 187.8
H5'2 C5' C4' C3' 179.8 303.6
H5'2 C5' C4' H4' 311.1 65.8
C1' C4' C5' H5'1 320.8 307.7
C1' C4' C5' H5'2 70.3 187.8
C5' C4' C1' C3' 101.4 119.0
C5' C4' C1' H4' 234.6 238.0
C3' C4' C1' H4' 133.2 119.0
C1' C4' C3' C2' 5.3 338.2
C1' C4' C3' O3' 261.3 219.7
C1' C4' C3' H3' 132.3 96.5
N1' C1' C4' H1'1 125.3 240.7
N1' C1' C4' H1'2 234.7 119.3
C4' C1' N1' C10 215.4 138.7
C4' C1' N1' C2' 322.8 25.3
H1'1 C1' C4' H1'2 109.5 238.6
C3' C4' C5' H5'1 70.3 63.5
C3' C4' C5' H5'2 179.8 303.6
C5' C4' C3' C1' 237.5 241.1
C5' C4' C3' H4' 120.8 122.1
C1' C4' C3' H4' 243.3 241.0
C3' C4' C1' N1' 19.1 358.7
C3' C4' C1' H1'1 253.9 118.0
C3' C4' C1' H1'2 144.4 239.4
N1' C2' C3' C4' 332.2 37.3
C4' C3' C2' H2'1 97.5 278.9
C4' C3' C2' H2'2 206.9 155.8
C2' C3' C4' O3' 104.0 118.5
C2' C3' C4' H3' 233.0 241.7
O3' C3' C4' H3' 129.0 123.2
C4' C3' O3' H1 180.0 175.1
H4' C4' C5' H5'1 201.6 185.7
H4' C4' C5' H5'2 311.1 65.8
C5' C4' H4' C1' 130.2 122.0
C5' C4' H4' C3' 249.3 237.9
C1' C4' H4' C3' 119.1 115.8
H4' C4' C1' N1' 246.0 239.7
H4' C4' C1' H1'1 120.7 359.1
H4' C4' C1' H1'2 11.2 120.4
H4' C4' C3' C2' 122.0 97.1
H4' C4' C3' O3' 18.0 338.7
H4' C4' C3' H3' 249.0 215.4
N1' C1' C4' C3' 19.1 358.7
N1' C1' C4' H4' 246.0 239.7
C4' C1' N1' H1'1 234.7 119.4
C4' C1' N1' H1'2 125.2 240.7
H1'1 C1' N1' H1'2 250.5 121.3
C10 N1' C1' C2' 252.6 113.4
C1' N1' C10 C9 46.6 170.0
C1' N1' C10 H101 281.3 290.0
C1' N1' C10 H102 171.8 50.1
C1' N1' C2' C3' 40.6 320.9
C1' N1' C2' H2'1 275.3 79.2
C1' N1' C2' H2'2 165.9 202.3
H1'1 C1' C4' C3' 253.9 118.0
H1'1 C1' C4' H4' 120.7 359.1
C4' C1' H1'1 N1' 120.4 242.4
C4' C1' H1'1 H1'2 240.2 121.2
N1' C1' H1'1 H1'2 119.8 238.8
H1'1 C1' N1' C10 340.6 19.3
H1'1 C1' N1' C2' 88.1 266.0
H1'2 C1' C4' C3' 144.4 239.4
H1'2 C1' C4' H4' 11.2 120.4
C4' C1' H1'2 N1' 239.6 117.6
C4' C1' H1'2 H1'1 119.8 238.8
N1' C1' H1'2 H1'1 240.2 121.2
H1'2 C1' N1' C10 90.1 258.0
H1'2 C1' N1' C2' 197.6 144.6
C4 C9 C10 N1' 69.0 79.8
C10 N1' C1' H1'1 340.6 19.3
C10 N1' C1' H1'2 90.1 258.0
C1' N1' C10 C2' 106.2 247.2
C10 N1' C2' C3' 138.8 207.5
C10 N1' C2' H2'1 13.6 325.9
C10 N1' C2' H2'2 264.1 89.0
C9 C10 N1' H101 125.3 240.0
C9 C10 N1' H102 234.7 119.9
N1' C10 C9 C8 249.4 260.1
H101 C10 N1' H102 109.5 240.0
C4' C3' C2' N1' 332.2 37.3
C2' N1' C1' H1'1 88.1 266.0
C2' N1' C1' H1'2 197.6 144.6
C1' N1' C2' C10 261.8 113.4
C2' N1' C10 C9 300.4 282.7
C2' N1' C10 H101 175.1 42.8
C2' N1' C10 H102 65.6 162.8
C3' C2' N1' H2'1 125.3 241.6
C3' C2' N1' H2'2 234.7 118.5
N1' C2' C3' O3' 70.6 156.0
N1' C2' C3' H3' 201.7 279.0
H2'1 C2' N1' H2'2 109.5 236.9
C10 C9 C4 N3 0.4 0.8
C4 C9 C10 C8 179.6 179.7
C9 C10 N1' C2' 300.4 282.7
N1' C10 C9 H101 234.7 120.0
N1' C10 C9 H102 125.3 240.1
H101 C10 C9 H102 250.5 120.1
C10 C9 C8 N7 179.6 180.0
C10 C9 C8 H8 359.7 360.0
H101 C10 N1' C2' 175.1 42.8
N1' C10 H101 C9 148.6 240.0
N1' C10 H101 H102 254.3 120.0
C9 C10 H101 H102 105.7 240.0
H101 C10 C9 C8 14.6 140.0
H102 C10 N1' C2' 65.6 162.8
N1' C10 H102 C9 211.4 119.9
N1' C10 H102 H101 105.7 240.0
C9 C10 H102 H101 254.3 120.1
H102 C10 C9 C8 124.1 20.0
C8 C9 C4 N3 180.1 180.6
C4 C9 C8 C10 180.3 180.3
C5 N7 C8 C9 0.0 360.0
C8 C9 C10 H101 14.6 140.0
C8 C9 C10 H102 124.1 20.0
N7 C8 C9 H8 180.0 180.1
C9 C8 N7 HN7 180.0 180.0
C5 N7 C8 HN7 180.0 179.9
C9 C8 N7 H8 180.0 179.9
C9 C8 H8 N7 180.0 180.1
H8 C8 N7 HN7 360.0 0.1
C5 N7 HN7 C8 180.0 180.1
HN7 N7 C8 H8 360.0 0.1
HN61 N6 C6 N1 234.7 180.0
C6 N6 HN61 HN62 131.6 180.0
HN62 N6 C6 N1 0.0 0.1
C6 N6 HN62 HN61 234.7 180.0
C2' C3' C4' H4' 122.0 97.1
C4' C3' C2' O3' 261.6 241.3
C4' C3' C2' H3' 130.5 118.3
N1' C2' C3' H2'1 234.7 118.4
N1' C2' C3' H2'2 125.3 241.5
H2'1 C2' C3' H2'2 250.6 123.0
O3' C3' C2' H3' 228.9 237.0
C2' C3' O3' H1 74.2 61.5
N1' C2' H2'1 C3' 119.6 246.2
N1' C2' H2'1 H2'2 239.8 123.1
C3' C2' H2'1 H2'2 120.2 237.0
H2'1 C2' C3' O3' 195.9 37.5
H2'1 C2' C3' H3' 327.0 160.6
N1' C2' H2'2 C3' 240.3 113.9
N1' C2' H2'2 H2'1 120.2 236.9
C3' C2' H2'2 H2'1 239.9 123.0
H2'2 C2' C3' O3' 305.3 274.5
H2'2 C2' C3' H3' 76.4 37.5
O3' C3' C4' H4' 18.0 338.7
C4' C3' O3' C2' 105.8 113.6
C4' C3' O3' H3' 232.2 236.7
O3' C3' C2' H2'1 195.9 37.5
O3' C3' C2' H2'2 305.3 274.5
C2' C3' O3' H3' 126.3 123.1
H3' C3' C4' H4' 249.0 215.4
C4' C3' H3' C2' 237.2 246.6
C4' C3' H3' O3' 116.0 123.5
H3' C3' C2' H2'1 327.0 160.6
H3' C3' C2' H2'2 76.4 37.5
C2' C3' H3' O3' 238.8 236.9
H3' C3' O3' H1 307.8 298.3
H1 O3' C3' H3' 307.8 298.3