PDB Chemical Component DND

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 DND

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O13 PA 1.475 1.481
O14 PA 1.507 1.610
PA O3P 1.605 1.609
PA O5B 1.614 1.610
O11 PN 1.471 1.480
O3P PN 1.608 1.610
O5B C5B 1.477 1.429
PN O12 1.502 1.610
PN O5D 1.572 1.610
C5B C4B 1.537 1.531
N7A C8A 1.342 1.302
N7A C5A 1.379 1.355
C8A N9A 1.371 1.363
N6A C6A 1.344 1.384
O5D C5D 1.422 1.429
C5A C6A 1.426 1.405
C5A C4A 1.391 1.406
O4B C4B 1.464 1.444
O4B C1B 1.343 1.444
C6A N1A 1.383 1.329
C4B C3B 1.534 1.545
N9A C4A 1.360 1.372
N9A C1B 1.458 1.465
C5D C4D 1.487 1.529
C3D O3D 1.469 1.430
C3D C4D 1.540 1.540
C3D C2D 1.513 1.549
C4A N3A 1.351 1.329
C1B C2B 1.542 1.545
N1A C2A 1.378 1.320
C4D O4D 1.430 1.438
C2B C3B 1.532 1.546
C2B O2B 1.437 1.429
C2D O2D 1.448 1.428
C2D C1D 1.532 1.550
C3B O3B 1.450 1.429
N3A C2A 1.323 1.316
O4D C1D 1.409 1.444
C1D N1N 1.468 1.465
C6N N1N 1.431 1.318
C6N C5N 1.349 1.384
N1N C2N 1.400 1.317
C5N C4N 1.531 1.383
C2N C3N 1.443 1.395
C4N C3N 1.492 1.401
C3N C7N 1.480 1.478
C7N O7N 1.347 1.215
C7N O8N 1.216 1.347
O12 H1 0.950 0.967
C5D H2 1.100 1.091
C5D H3 1.100 1.091
C4D H4 1.100 1.090
C3D H5 1.100 1.091
O3D H6 0.950 0.967
C2D H7 1.100 1.090
O2D H8 0.950 0.967
C1D H9 1.100 1.090
C6N H10 1.080 1.080
C5N H11 1.079 1.080
C4N H12 1.080 1.081
C2N H13 1.080 1.080
O8N H14 0.950 0.967
O14 H15 0.950 0.967
C5B H16 1.099 1.090
C5B H17 1.100 1.090
C4B H18 1.100 1.090
C3B H19 1.100 1.090
O3B H20 0.949 0.967
C2B H21 1.100 1.090
O2B H22 0.950 0.967
C1B H23 1.100 1.090
C2A H24 1.080 1.080
C8A H25 1.080 1.080
N6A H26 1.000 0.970
N6A H27 1.000 0.970

Bond Angles for DND

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O13 PA O5B 107.0 109.4
O14 PA O5B 109.1 109.5
PA O5B C5B 120.8 123.0
O11 PN O12 111.5 109.5
O11 PN O5D 110.2 109.5
O3P PN O5D 92.5 109.5
O5B C5B C4B 105.6 109.4
O5B C5B H16 110.4 109.5
O5B C5B H17 110.4 109.5
O12 PN O5D 115.5 109.5
PN O12 H1 109.5 113.9
PN O5D C5D 119.7 123.0
C5B C4B C3B 114.3 110.4
C4B C5B H16 110.4 109.4
C4B C5B H17 110.4 109.5
C5B C4B H18 108.1 110.3
N7A C8A H25 123.0 125.0
O5D C5D C4D 103.5 109.5
O5D C5D H2 110.9 109.5
O5D C5D H3 110.9 109.5
O4B C4B C3B 105.1 104.8
O4B C4B H18 109.1 110.5
O4B C1B C2B 100.2 104.8
O4B C1B H23 113.9 110.4
C4B C3B O3B 111.1 110.5
C3B C4B H18 108.2 110.4
C4B C3B H19 108.9 110.5
N9A C4A N3A 127.3 134.9
N9A C1B H23 111.9 110.4
C5D C4D O4D 105.5 109.9
C4D C5D H2 110.9 109.5
C4D C5D H3 110.9 109.5
C5D C4D H4 109.8 109.9
O3D C3D C2D 110.6 110.4
O3D C3D H5 111.7 110.4
C3D O3D H6 109.5 114.0
C3D C4D H4 109.1 110.0
C3D C2D O2D 111.7 110.9
C3D C2D C1D 100.7 102.1
C2D C3D H5 111.1 110.6
C3D C2D H7 109.9 110.9
C4A N3A C2A 112.4 120.6
C1B C2B H21 109.0 110.6
N1A C2A H24 116.2 118.8
C4D O4D C1D 109.5 107.0
O4D C4D H4 110.7 109.8
C2B C3B H19 108.9 110.7
O2B C2B H21 110.3 110.5
C2B O2B H22 109.5 114.0
O2D C2D C1D 113.7 110.9
O2D C2D H7 110.8 110.8
C2D O2D H8 109.5 114.0
O4D C1D C2D 105.3 103.5
C2D C1D N1N 111.1 110.6
C1D C2D H7 109.6 111.0
C2D C1D H9 108.5 110.6
O3B C3B H19 110.0 110.4
C3B O3B H20 109.5 114.1
N3A C2A H24 116.2 118.7
O4D C1D N1N 112.5 110.6
O4D C1D H9 110.1 110.6
C1D N1N C2N 117.3 119.0
N1N C1D H9 109.3 110.7
C6N N1N C2N 118.7 121.9
C6N C5N C4N 120.8 119.3
C5N C6N H10 118.3 119.4
C6N C5N H11 119.6 120.4
N1N C2N C3N 122.9 120.5
N1N C2N H13 118.5 119.7
C5N C4N C3N 115.5 118.3
C4N C5N H11 119.6 120.3
C5N C4N H12 122.2 120.9
C2N C3N C7N 115.0 120.6
C4N C3N C7N 126.3 120.5
C3N C4N H12 122.3 120.8
C3N C7N O7N 124.7 120.0
C3N C7N O8N 113.3 120.0
O7N C7N O8N 122.0 120.0
C7N O8N H14 109.5 117.0
H2 C5D H3 109.5 109.4
H16 C5B H17 109.5 109.5
H26 N6A H27 109.5 120.0

Torsion Angles for DND

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O14 PA O13 O5B 120.5 120.0
O13 PA O5B C5B 308.0 55.0
O13 PA O14 O5B 240.7 240.0
O14 PA O5B C5B 184.8 295.0
PA O5B C5B C4B 198.0 180.0
PA O5B C5B H16 317.4 300.0
PA O5B C5B H17 78.6 60.0
O3P PN O11 O5D 103.8 120.0
O12 PN O11 O5D 230.3 240.0
O11 PN O12 H1 360.0 180.0
O11 PN O5D C5D 303.8 305.0
O11 PN O3P O5D 245.8 240.0
O12 PN O3P O5D 118.2 120.0
O3P PN O12 H1 130.5 300.0
O3P PN O5D C5D 184.0 185.0
O5B C5B C4B C3B 68.1 185.0
C4B C5B O5B H16 240.6 240.0
C4B C5B O5B H17 119.4 120.0
O5B C5B C4B H18 188.7 307.3
H16 C5B O5B H17 238.8 239.9
O11 PN O12 O5D 126.9 120.0
O3P PN O12 O5D 257.4 240.0
O12 PN O5D C5D 71.3 65.0
O11 PN O5D O12 232.5 240.0
O5D PN O12 H1 233.1 60.0
PN O5D C5D C4D 180.3 180.0
PN O5D C5D H2 299.4 300.0
PN O5D C5D H3 61.3 59.9
O5B C5B C4B H16 119.4 120.0
O5B C5B C4B H17 240.6 240.0
O4B C4B C5B C3B 240.8 244.6
O4B C4B C5B H18 120.2 122.3
C5B C4B C3B O3B 125.9 98.6
C3B C4B C5B H18 239.4 237.7
C5B C4B C3B H19 4.5 336.0
H16 C5B C4B H17 121.2 120.0
C8A N9A C1B H23 184.4 145.6
O5D C5D C4D O4D 149.0 66.4
C4D C5D O5D H2 240.9 240.0
C4D C5D O5D H3 119.0 120.0
O5D C5D C4D H4 29.7 305.5
H2 C5D O5D H3 238.1 240.1
C5B C4B O4B C3B 124.5 118.8
O4B C4B C5B H16 189.5 309.6
O4B C4B C5B H17 68.3 189.6
C5B C4B O4B H18 240.4 237.8
O4B C4B C3B O3B 248.8 217.4
C3B C4B O4B H18 115.9 118.9
O4B C4B C3B H19 127.4 94.8
C1B O4B C4B C3B 17.6 40.5
C1B O4B C4B H18 261.7 281.6
N9A C1B O4B H23 124.1 122.3
O4B C1B C2B H21 291.4 265.3
C6A N1A C2A H24 180.2 179.9
C3B C4B C5B H16 308.7 65.0
C3B C4B C5B H17 187.5 305.0
C5B C4B C3B H18 120.6 122.2
O4B C4B C3B H18 243.5 241.0
C2B C3B C4B H19 245.7 241.2
O3B C3B C4B H19 121.4 122.6
C4B C3B O3B H20 180.0 180.0
C4A N9A C1B H23 4.2 325.8
N9A C4A N3A C2A 179.8 179.9
O4B C1B N9A H23 234.7 237.7
N9A C1B C2B H21 44.6 24.2
O5D C5D C4D H2 119.1 120.0
O5D C5D C4D H3 241.0 239.9
C3D C4D C5D H4 236.5 238.8
C5D C4D O4D C1D 122.3 145.9
O4D C4D C5D H4 119.3 120.9
H2 C5D C4D H3 121.9 119.9
O3D C3D C4D H4 26.7 358.8
O3D C3D C2D O2D 319.4 339.6
O3D C3D C2D C1D 80.4 97.8
C2D C3D O3D H5 124.3 122.6
O3D C3D C2D H7 196.0 216.1
C3D C4D C5D H2 147.1 64.2
C3D C4D C5D H3 25.2 304.3
C5D C4D C3D H4 123.9 121.1
C3D C4D O4D C1D 359.5 26.5
O4D C4D C3D H4 240.5 240.6
O3D C3D C2D H5 235.4 237.5
C2D C3D O3D H6 68.0 65.3
C2D C3D C4D H4 144.2 117.4
O2D C2D C3D C1D 239.0 241.8
O2D C2D C3D H7 123.4 123.5
C3D C2D O2D H8 180.0 298.5
O4D C1D C2D C3D 38.6 37.0
C3D C2D C1D N1N 160.7 155.5
C1D C2D C3D H7 244.4 241.8
C3D C2D C1D H9 280.8 278.5
C4A N3A C2A H24 179.9 180.0
O4B C1B C2B H23 120.5 118.9
C1B C2B C3B H19 210.7 241.3
O2B C2B C1B H21 236.6 237.3
C1B C2B O2B H22 180.0 183.9
N3A C2A N1A H24 180.0 180.1
O4D C4D C5D H2 29.9 306.4
O4D C4D C5D H3 268.0 186.5
C5D C4D O4D H4 241.3 239.0
C3D C4D O4D H4 118.5 119.6
C4D O4D C1D C2D 336.1 320.0
C4D O4D C1D N1N 215.0 201.5
C4D O4D C1D H9 92.8 78.5
O4B C1B C2B C3B 46.6 24.0
C2B C3B C4B H18 129.7 95.0
C4B C3B C2B H19 114.3 118.7
O3B C3B C2B H19 234.5 237.4
C2B C3B O3B H20 65.7 65.4
O4B C1B C2B O2B 168.0 142.6
C1B C2B O2B H21 122.7 122.8
O2B C2B C3B H19 88.6 122.6
C3D C2D O2D C1D 113.2 112.7
O2D C2D C3D H5 84.0 102.1
C3D C2D O2D H7 237.1 236.4
O4D C1D C2D O2D 158.2 155.2
O2D C2D C1D N1N 280.2 273.7
C1D C2D O2D H7 124.0 123.7
O2D C2D C1D H9 40.4 36.7
C3D C2D C1D O2D 240.4 241.8
C1D C2D C3D H5 205.0 220.4
C3D C2D C1D H7 115.8 118.2
O2D C2D C1D H7 235.4 236.4
C1D C2D O2D H8 66.8 185.8
O4D C1D C2D N1N 238.0 241.5
O4D C1D C2D H9 117.8 118.5
C2D C1D N1N C2N 106.5 104.4
N1N C1D C2D H9 239.9 237.0
O3B C3B C4B H18 5.3 336.4
C4B C3B O3B H19 239.3 237.4
C2B C3B O3B H19 124.9 122.8
N1A C2A N3A H24 180.0 179.9
C3D C2D C1D O4D 38.6 37.0
C1D O4D C4D H4 241.0 266.9
O2D C2D C1D O4D 158.2 155.2
C2D C1D O4D N1N 121.1 118.5
O4D C1D C2D H7 282.8 278.8
C2D C1D O4D H9 243.3 241.5
O4D C1D N1N C2N 224.2 218.5
N1N C1D O4D H9 122.2 123.0
O4D C1D N1N C2D 117.7 114.1
N1N C1D C2D H7 44.9 37.3
C2D C1D N1N H9 119.6 123.0
O4D C1D N1N H9 237.4 237.1
C6N N1N C1D C2N 181.2 180.3
C1D N1N C2N C3N 181.7 179.8
C1D N1N C2N H13 1.7 0.0
C1D N1N C6N C2N 178.7 179.7
C6N N1N C1D H9 168.1 161.7
C6N N1N C2N C3N 0.5 359.5
C6N N1N C2N H13 180.5 179.8
C5N C6N N1N C2N 360.0 0.3
C6N C5N C4N C3N 0.6 360.0
C4N C5N C6N H11 180.0 180.0
C6N C5N C4N H12 180.6 179.9
C2N N1N C1D H9 346.9 341.5
N1N C2N C3N C7N 179.2 180.3
C4N C5N C6N H10 179.5 180.0
C6N C5N C4N H11 180.0 180.0
C5N C4N C3N C7N 180.3 180.0
C3N C4N C5N H12 180.0 180.1
N1N C2N C3N H13 180.0 180.3
C4N C3N C2N C7N 180.4 180.2
C2N C3N C4N H12 179.9 179.8
C2N C3N C7N O7N 0.9 0.2
C2N C3N C7N O8N 181.1 180.2
N1N C2N C3N C4N 359.6 0.5
C3N C4N C5N H11 180.6 180.0
C5N C4N C3N H12 180.0 179.9
C2N C3N C4N C7N 179.5 179.8
C4N C3N C7N O7N 180.4 180.0
C4N C3N C7N O8N 0.6 360.0
C7N C3N C4N H12 0.3 0.0
O7N C7N C3N O8N 179.8 180.0
C3N C7N O8N H14 179.8 180.0
C3N C7N O7N O8N 180.2 180.0
O7N C7N O8N H14 360.0 360.0
C3N C7N O8N O7N 179.8 180.0
H1 O12 PN O5D 233.1 60.0
O5D C5D H2 C4D 245.5 240.0
O5D C5D H2 H3 122.7 120.0
H2 C5D C4D O4D 29.9 306.4
C4D C5D H2 H3 237.3 240.0
H2 C5D C4D H4 270.6 185.5
O5D C5D H3 C4D 114.5 120.1
O5D C5D H3 H2 237.2 240.0
H3 C5D C4D O4D 268.0 186.5
C4D C5D H3 H2 122.8 120.0
H3 C5D C4D H4 148.7 65.5
C5D C4D H4 O4D 116.1 121.0
H4 C4D C5D H2 270.6 185.5
H4 C4D C5D H3 148.7 65.5
H4 C4D O4D C1D 241.0 266.9
O3D C3D H5 C2D 124.0 122.5
H5 C3D O3D H6 303.8 302.6
H5 C3D C4D H4 262.3 236.3
H5 C3D C2D O2D 84.0 102.1
H5 C3D C2D C1D 205.0 220.4
H5 C3D C2D H7 320.6 338.6
H6 O3D C3D C2D 68.0 65.3
H6 O3D C3D H5 303.8 302.6
C3D C2D H7 O2D 123.9 123.6
C3D C2D H7 C1D 250.2 247.3
H7 C2D C3D H5 320.6 338.6
O2D C2D H7 C1D 126.3 123.7
H7 C2D O2D H8 302.9 62.1
H7 C2D C1D N1N 44.9 37.3
H7 C2D C1D H9 165.0 160.3
H8 O2D C2D C1D 66.8 185.8
H8 O2D C2D H7 302.9 62.1
O4D C1D H9 C2D 245.3 245.9
C2D C1D H9 N1N 238.8 237.0
H9 C1D C2D H7 165.0 160.3
O4D C1D H9 N1N 124.1 122.9
H9 C1D N1N C2N 346.9 341.5
H10 C6N N1N C2N 179.9 180.3
H10 C6N C5N C4N 179.5 180.0
H10 C6N C5N H11 359.5 360.0
C6N C5N H11 C4N 180.0 180.0
H11 C5N C6N H10 359.5 360.0
H11 C5N C4N C3N 180.6 180.0
H11 C5N C4N H12 0.6 360.0
C5N C4N H12 C3N 180.0 180.1
H12 C4N C5N H11 0.6 360.0
H12 C4N C3N C7N 0.3 0.0
N1N C2N H13 C3N 180.0 179.7
H13 C2N C3N C7N 359.2 0.0
H15 O14 PA O5B 119.3 299.9
O5B C5B H16 C4B 243.6 240.0
O5B C5B H16 H17 121.8 120.1
H16 C5B C4B C3B 308.7 65.0
C4B C5B H16 H17 238.2 240.0
H16 C5B C4B H18 69.3 187.3
O5B C5B H17 C4B 116.4 120.0
O5B C5B H17 H16 238.2 239.9
H17 C5B C4B C3B 187.5 305.0
C4B C5B H17 H16 121.8 119.9
H17 C5B C4B H18 308.1 67.3
C5B C4B H18 C3B 235.7 237.8
H18 C4B C5B H16 69.3 187.3
H18 C4B C5B H17 308.1 67.3
O4B C4B H18 C3B 113.9 115.5
H18 C4B C3B O3B 5.3 336.4
H18 C4B C3B H19 243.9 213.8
C4B C3B H19 O3B 122.0 122.6
H19 C3B C4B H18 243.9 213.8
H19 C3B O3B H20 300.7 302.6
H20 O3B C3B H19 300.7 302.6
H21 C2B C3B H19 325.7 0.0
H21 C2B O2B H22 57.3 61.1
H22 O2B C2B H21 57.3 61.1
O4B C1B H23 C2B 248.0 244.6
H23 C1B C2B H21 170.9 146.5