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Jungfraujoch/image_analysis/structure_refinement/monomers/NDP.cif
T
leonarski_f 00662c4110 Refinement: common cofactors and modified RNA nucleotides in the embedded dictionary; heme iron restrained from LINK records 
The embedded CCP4 Monomer Library subset grows from 62 to 84 compounds:
- the modified tRNA/rRNA nucleotides PSU, 5MC, 1MA, OMG, OMC, OMU, H2U, M2G, 7MG, 2MG, 5MU (RNA group,
  joined by the library's backbone link "p");
- the cofactors NAD, NAI, NAP, NDP, FAD, FMN, HEM, HEC, SAM, SAH, and dioxygen (OXY). CMO is left out:
  its dictionary has C-O at 1.25 A, where bound CO is near 1.15 A.
links_and_mods.cif gains the links these compounds use: HEC-CYS1/HEC-CYS2 (heme C thioethers),
CYS-HEMB/CYS-HEMC, CYS-FAD and HIS-FAD1/2, with their modifications.

AddMetalLinks now takes a metal atom of any residue, not only a one-atom ion, so a heme iron's LINK records
to His NE2 / Met SD / water become bonds at the library's metal-site distances; the site's coordination counts
the metal's bonds in its own dictionary (a heme's four pyrrole N) as well as the records. A metal within a
ligand is also a metal for the repulsions (1.9 A to N, O, S) and its dictionary bonds are kept with the metal
bonds. Note HEC.cif's own Fe-N(pyrrole) ideal is 1.90 A (HEM: 2.04 A), so a cytochrome c reports a metal-bond
rmsd near 0.1 A.

Test RefinementRestraints_deposited_ligands builds the topology of eleven deposited models cut down to the
ligand and its surroundings (tests/test_data/ligands, 66 KB, from PDB 1EHZ, 8BKH, 6K9I, 2W3V, 5VML, 6F3P,
8CON, 3TK0, 7TCD, 6W4H, 5EPE): every ligand restrained, bond rmsd < 0.03 A, the RNA backbone bonded to each
modified nucleotide, the heme Fe-His bonds, and the HEC thioethers. rugnux --mode refine on the full entries
against their deposited structure factors: R-free within +-0.003 of the build where these were held fixed,
ligand bond rmsd vs the dictionary from 0.004-0.058 A down to 0.002-0.042 A. rugnux grows by 425 KiB.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit f4d407c8de6cb462320edb21a70665350e436d28)
2026-10-26 13:56:29 +01:00

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#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
NDP NDP "NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE" NON-POLYMER 74 48 .
#
data_comp_NDP
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
NDP PA P P 0 14.746 11.568 81.367
NDP O1A O O 0 14.846 12.116 82.752
NDP O2A O OP -1 15.219 10.173 81.123
NDP O5B O O2 0 15.480 12.564 80.346
NDP C5B C CH2 0 15.269 13.993 80.484
NDP C4B C CH1 0 15.682 14.683 79.207
NDP O4B O O2 0 15.216 16.056 79.244
NDP C3B C CH1 0 17.194 14.748 78.938
NDP O3B O OH1 0 17.492 14.414 77.587
NDP C2B C CH1 0 17.556 16.184 79.308
NDP O2B O O2 0 18.652 16.694 78.540
NDP C1B C CH1 0 16.277 16.931 78.947
NDP N9A N NR5 0 16.067 18.164 79.699
NDP C8A C CR15 0 16.031 18.293 81.065
NDP N7A N NRD5 0 15.816 19.519 81.470
NDP C5A C CR56 0 15.691 20.250 80.299
NDP C6A C CR6 0 15.449 21.620 80.056
NDP N6A N NH2 0 15.287 22.522 81.021
NDP N1A N NRD6 0 15.382 22.028 78.762
NDP C2A C CR16 0 15.546 21.113 77.794
NDP N3A N NRD6 0 15.777 19.804 77.905
NDP C4A C CR56 0 15.840 19.425 79.196
NDP O3 O O2 0 13.226 11.692 80.871
NDP PN P P 0 12.518 11.379 79.466
NDP O1N O O 0 13.514 10.727 78.565
NDP O2N O OP -1 11.231 10.667 79.724
NDP O5D O O2 0 12.213 12.863 78.935
NDP C5D C CH2 0 11.328 13.716 79.706
NDP C4D C CH1 0 11.023 14.974 78.929
NDP O4D O O2 0 12.257 15.648 78.585
NDP C3D C CH1 0 10.306 14.797 77.585
NDP O3D O OH1 0 8.904 14.643 77.770
NDP C2D C CH1 0 10.697 16.089 76.857
NDP O2D O OH1 0 9.719 17.111 76.999
NDP C1D C CH1 0 12.016 16.522 77.506
NDP N1N N NR6 0 13.173 16.451 76.558
NDP C2N C CR16 0 13.593 15.236 76.075
NDP C3N C CR6 0 14.740 15.096 75.322
NDP C7N C C 0 15.161 13.734 74.898
NDP O7N O O 0 15.511 13.557 73.727
NDP N7N N NH2 0 15.161 12.736 75.773
NDP C4N C CH2 0 15.493 16.332 74.936
NDP C5N C CR16 0 14.940 17.593 75.478
NDP C6N C CR16 0 13.806 17.617 76.151
NDP P2B P P 0 20.124 16.448 79.172
NDP O1X O O 0 20.271 14.965 79.456
NDP O2X O OP -1 20.204 17.281 80.438
NDP O3X O OP -1 21.106 16.923 78.118
NDP H51A H H 0 15.806 14.341 81.239
NDP H52A H H 0 14.314 14.177 80.667
NDP H4B H H 0 15.242 14.224 78.463
NDP H3B H H 0 17.664 14.123 79.548
NDP HO3A H H 0 17.093 14.951 77.068
NDP H2B H H 0 17.743 16.245 80.273
NDP H1B H H 0 16.282 17.128 77.984
NDP H8A H H 0 16.159 17.569 81.654
NDP H61A H H 0 14.828 23.253 80.863
NDP H62A H H 0 15.640 22.380 81.812
NDP H2A H H 0 15.491 21.442 76.910
NDP H51N H H 0 11.757 13.954 80.565
NDP H52N H H 0 10.485 13.237 79.901
NDP H4D H H 0 10.493 15.568 79.503
NDP H3D H H 0 10.672 14.015 77.099
NDP HO3N H H 0 8.534 14.576 77.009
NDP H2D H H 0 10.834 15.895 75.897
NDP HO2N H H 0 9.885 17.733 76.446
NDP H1D H H 0 11.933 17.443 77.851
NDP H2N H H 0 13.079 14.471 76.264
NDP H71N H H 0 14.910 12.863 76.612
NDP H72N H H 0 15.415 11.924 75.519
NDP H41N H H 0 15.516 16.397 73.959
NDP H42N H H 0 16.424 16.244 75.229
NDP H5N H H 0 15.417 18.410 75.332
NDP H6N H H 0 13.411 18.445 76.360
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
NDP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122
NDP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122
NDP PA O5B SINGLE n 1.604 0.0133 1.604 0.0133
NDP PA O3 SINGLE n 1.604 0.0133 1.604 0.0133
NDP O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166
NDP C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100
NDP C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100
NDP C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100
NDP O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100
NDP C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100
NDP C3B C2B SINGLE n 1.523 0.0106 1.523 0.0106
NDP C2B O2B SINGLE n 1.425 0.0152 1.425 0.0152
NDP C2B C1B SINGLE n 1.524 0.0100 1.524 0.0100
NDP O2B P2B SINGLE n 1.614 0.0178 1.614 0.0178
NDP C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100
NDP N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100
NDP N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101
NDP C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100
NDP N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100
NDP C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100
NDP C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100
NDP C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100
NDP C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100
NDP N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100
NDP C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100
NDP N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100
NDP O3 PN SINGLE n 1.604 0.0133 1.604 0.0133
NDP PN O1N DOUBLE n 1.493 0.0122 1.493 0.0122
NDP PN O2N SINGLE n 1.493 0.0122 1.493 0.0122
NDP PN O5D SINGLE n 1.604 0.0133 1.604 0.0133
NDP O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166
NDP C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100
NDP C4D O4D SINGLE n 1.449 0.0100 1.449 0.0100
NDP C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100
NDP O4D C1D SINGLE n 1.407 0.0132 1.407 0.0132
NDP C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100
NDP C3D C2D SINGLE n 1.530 0.0134 1.530 0.0134
NDP C2D O2D SINGLE n 1.420 0.0122 1.420 0.0122
NDP C2D C1D SINGLE n 1.527 0.0119 1.527 0.0119
NDP C1D N1N SINGLE n 1.492 0.0124 1.492 0.0124
NDP N1N C2N SINGLE n 1.367 0.0104 1.367 0.0104
NDP N1N C6N SINGLE n 1.374 0.0156 1.374 0.0156
NDP C2N C3N DOUBLE n 1.365 0.0175 1.365 0.0175
NDP C3N C7N SINGLE n 1.480 0.0169 1.480 0.0169
NDP C3N C4N SINGLE n 1.491 0.0200 1.491 0.0200
NDP C7N O7N DOUBLE n 1.235 0.0110 1.235 0.0110
NDP C7N N7N SINGLE n 1.325 0.0100 1.325 0.0100
NDP C4N C5N SINGLE n 1.477 0.0200 1.477 0.0200
NDP C5N C6N DOUBLE n 1.315 0.0139 1.315 0.0139
NDP P2B O1X DOUBLE n 1.517 0.0192 1.517 0.0192
NDP P2B O2X SINGLE n 1.517 0.0192 1.517 0.0192
NDP P2B O3X SINGLE n 1.517 0.0192 1.517 0.0192
NDP C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200
NDP C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200
NDP C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200
NDP C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200
NDP O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200
NDP C2B H2B SINGLE n 1.089 0.0100 0.985 0.0119
NDP C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200
NDP C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170
NDP N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200
NDP N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200
NDP C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200
NDP C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200
NDP C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200
NDP C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200
NDP C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200
NDP O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200
NDP C2D H2D SINGLE n 1.089 0.0100 0.988 0.0200
NDP O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200
NDP C1D H1D SINGLE n 1.089 0.0100 0.986 0.0200
NDP C2N H2N SINGLE n 1.082 0.0130 0.940 0.0112
NDP N7N H71N SINGLE n 1.016 0.0100 0.887 0.0200
NDP N7N H72N SINGLE n 1.016 0.0100 0.887 0.0200
NDP C4N H41N SINGLE n 1.089 0.0100 0.980 0.0113
NDP C4N H42N SINGLE n 1.089 0.0100 0.980 0.0113
NDP C5N H5N SINGLE n 1.082 0.0130 0.957 0.0130
NDP C6N H6N SINGLE n 1.082 0.0130 0.941 0.0198
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
NDP O1A PA O2A 118.411 2.35
NDP O1A PA O5B 109.410 1.50
NDP O1A PA O3 108.816 2.14
NDP O2A PA O5B 109.410 1.50
NDP O2A PA O3 108.816 2.14
NDP O5B PA O3 101.065 1.97
NDP PA O5B C5B 118.553 2.41
NDP O5B C5B C4B 109.342 1.50
NDP O5B C5B H51A 109.845 1.50
NDP O5B C5B H52A 109.845 1.50
NDP C4B C5B H51A 109.624 1.50
NDP C4B C5B H52A 109.624 1.50
NDP H51A C5B H52A 108.472 1.50
NDP C5B C4B O4B 109.123 1.50
NDP C5B C4B C3B 116.008 1.52
NDP C5B C4B H4B 108.268 1.50
NDP O4B C4B C3B 105.388 1.50
NDP O4B C4B H4B 108.947 1.50
NDP C3B C4B H4B 109.363 1.86
NDP C4B O4B C1B 109.903 1.50
NDP C4B C3B O3B 111.281 2.46
NDP C4B C3B C2B 102.352 1.50
NDP C4B C3B H3B 110.452 2.54
NDP O3B C3B C2B 112.463 2.73
NDP O3B C3B H3B 110.380 1.67
NDP C2B C3B H3B 110.255 2.04
NDP C3B O3B HO3A 108.744 3.00
NDP C3B C2B O2B 110.766 3.00
NDP C3B C2B C1B 101.388 1.50
NDP C3B C2B H2B 110.255 2.04
NDP O2B C2B C1B 110.738 2.44
NDP O2B C2B H2B 110.343 1.64
NDP C1B C2B H2B 111.050 1.62
NDP C2B O2B P2B 109.471 3.00
NDP O4B C1B C2B 106.416 1.50
NDP O4B C1B N9A 108.477 1.50
NDP O4B C1B H1B 109.807 1.50
NDP C2B C1B N9A 113.659 1.50
NDP C2B C1B H1B 109.319 1.50
NDP N9A C1B H1B 109.561 1.50
NDP C1B N9A C8A 126.848 1.91
NDP C1B N9A C4A 127.459 1.80
NDP C8A N9A C4A 105.693 1.50
NDP N9A C8A N7A 113.469 1.50
NDP N9A C8A H8A 123.206 1.50
NDP N7A C8A H8A 123.326 1.50
NDP C8A N7A C5A 104.739 1.50
NDP N7A C5A C6A 132.250 1.50
NDP N7A C5A C4A 110.483 1.50
NDP C6A C5A C4A 117.267 1.50
NDP C5A C6A N6A 123.792 1.50
NDP C5A C6A N1A 117.409 1.50
NDP N6A C6A N1A 118.799 1.50
NDP C6A N6A H61A 119.723 1.50
NDP C6A N6A H62A 119.723 1.50
NDP H61A N6A H62A 120.554 1.88
NDP C6A N1A C2A 118.521 1.50
NDP N1A C2A N3A 129.332 1.50
NDP N1A C2A H2A 115.313 1.50
NDP N3A C2A H2A 115.355 1.50
NDP C2A N3A C4A 110.982 1.50
NDP N9A C4A C5A 105.616 1.50
NDP N9A C4A N3A 127.895 1.50
NDP C5A C4A N3A 126.489 1.50
NDP PA O3 PN 132.542 3.00
NDP O3 PN O1N 108.816 2.14
NDP O3 PN O2N 108.816 2.14
NDP O3 PN O5D 101.065 1.97
NDP O1N PN O2N 118.411 2.35
NDP O1N PN O5D 109.410 1.50
NDP O2N PN O5D 109.410 1.50
NDP PN O5D C5D 118.553 2.41
NDP O5D C5D C4D 109.342 1.50
NDP O5D C5D H51N 109.845 1.50
NDP O5D C5D H52N 109.845 1.50
NDP C4D C5D H51N 109.624 1.50
NDP C4D C5D H52N 109.624 1.50
NDP H51N C5D H52N 108.472 1.50
NDP C5D C4D O4D 109.123 1.50
NDP C5D C4D C3D 116.008 1.52
NDP C5D C4D H4D 108.268 1.50
NDP O4D C4D C3D 105.508 1.50
NDP O4D C4D H4D 108.642 1.50
NDP C3D C4D H4D 109.363 1.86
NDP C4D O4D C1D 109.926 1.50
NDP C4D C3D O3D 111.281 2.46
NDP C4D C3D C2D 102.352 1.50
NDP C4D C3D H3D 110.452 2.54
NDP O3D C3D C2D 112.463 2.73
NDP O3D C3D H3D 110.380 1.67
NDP C2D C3D H3D 110.255 2.04
NDP C3D O3D HO3N 108.744 3.00
NDP C3D C2D O2D 112.463 2.73
NDP C3D C2D C1D 104.443 2.26
NDP C3D C2D H2D 110.255 2.04
NDP O2D C2D C1D 111.164 2.38
NDP O2D C2D H2D 110.259 1.63
NDP C1D C2D H2D 110.518 1.74
NDP C2D O2D HO2N 109.104 3.00
NDP O4D C1D C2D 106.204 2.50
NDP O4D C1D N1N 108.278 1.50
NDP O4D C1D H1D 109.395 1.50
NDP C2D C1D N1N 112.110 1.66
NDP C2D C1D H1D 109.914 1.68
NDP N1N C1D H1D 109.209 1.50
NDP C1D N1N C2N 120.851 1.78
NDP C1D N1N C6N 120.851 1.78
NDP C2N N1N C6N 118.299 1.80
NDP N1N C2N C3N 121.110 1.66
NDP N1N C2N H2N 119.532 1.52
NDP C3N C2N H2N 119.358 1.50
NDP C2N C3N C7N 117.781 1.96
NDP C2N C3N C4N 118.007 1.50
NDP C7N C3N C4N 124.211 3.00
NDP C3N C7N O7N 119.878 1.50
NDP C3N C7N N7N 118.037 3.00
NDP O7N C7N N7N 122.085 1.50
NDP C7N N7N H71N 120.214 2.13
NDP C7N N7N H72N 120.224 2.13
NDP H71N N7N H72N 119.583 2.34
NDP C3N C4N C5N 114.356 2.46
NDP C3N C4N H41N 108.993 1.50
NDP C3N C4N H42N 108.993 1.50
NDP C5N C4N H41N 108.815 3.00
NDP C5N C4N H42N 108.815 3.00
NDP H41N C4N H42N 106.630 2.58
NDP C4N C5N C6N 121.257 2.14
NDP C4N C5N H5N 119.218 1.70
NDP C6N C5N H5N 119.525 1.50
NDP N1N C6N C5N 120.771 1.66
NDP N1N C6N H6N 119.193 1.52
NDP C5N C6N H6N 120.036 1.50
NDP O2B P2B O1X 106.518 3.00
NDP O2B P2B O2X 106.518 3.00
NDP O2B P2B O3X 106.518 3.00
NDP O1X P2B O2X 112.139 1.52
NDP O1X P2B O3X 112.139 1.52
NDP O2X P2B O3X 112.139 1.52
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
NDP sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3
NDP sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3
NDP sp3_sp3_82 C2B O2B P2B O1X 180.000 10.0 3
NDP sp2_sp3_13 C8A N9A C1B O4B 150.000 10.0 6
NDP const_14 N7A C8A N9A C1B 180.000 10.0 2
NDP const_26 C5A C4A N9A C1B 180.000 10.0 2
NDP const_17 N9A C8A N7A C5A 0.000 10.0 2
NDP const_20 C6A C5A N7A C8A 180.000 10.0 2
NDP const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2
NDP const_21 N9A C4A C5A N7A 0.000 10.0 2
NDP sp2_sp2_13 C5A C6A N6A H61A 180.000 5.0 2
NDP const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2
NDP const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2
NDP const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2
NDP const_12 N9A C4A N3A C2A 180.000 10.0 2
NDP sp3_sp3_87 PA O3 PN O1N 60.000 10.0 3
NDP sp3_sp3_88 C5D O5D PN O3 180.000 10.0 3
NDP sp3_sp3_91 C4D C5D O5D PN 180.000 10.0 3
NDP sp3_sp3_94 O4D C4D C5D O5D 180.000 10.0 3
NDP sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3
NDP sp3_sp3_107 O3D C3D C4D C5D 180.000 10.0 3
NDP sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3
NDP sp3_sp3_112 C4D C3D O3D HO3N 180.000 10.0 3
NDP sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3
NDP sp3_sp3_115 C3D C2D O2D HO2N 180.000 10.0 3
NDP sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3
NDP sp2_sp3_19 C2N N1N C1D O4D 150.000 10.0 6
NDP sp2_sp2_2 C3N C2N N1N C1D 180.000 5.0 2
NDP sp2_sp2_18 C5N C6N N1N C1D 180.000 5.0 2
NDP sp2_sp2_6 N1N C2N C3N C7N 180.000 5.0 2
NDP sp2_sp2_24 C2N C3N C7N O7N 180.000 5.0 2
NDP sp2_sp3_4 C7N C3N C4N C5N 180.000 10.0 6
NDP sp2_sp2_27 O7N C7N N7N H71N 0.000 5.0 2
NDP sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3
NDP sp2_sp3_7 C6N C5N C4N C3N 0.000 10.0 6
NDP sp2_sp2_9 C4N C5N C6N N1N 0.000 5.0 2
NDP sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3
NDP sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3
NDP sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3
NDP sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3
NDP sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3
NDP sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3
NDP sp3_sp3_79 C3B C2B O2B P2B 180.000 10.0 3
NDP sp3_sp3_8 O4B C1B C2B O2B 180.000 10.0 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
NDP chir_1 PA O3 O5B O2A both
NDP chir_2 C4B O4B C3B C5B negative
NDP chir_3 C3B O3B C2B C4B negative
NDP chir_4 C2B O2B C1B C3B negative
NDP chir_5 C1B O4B N9A C2B negative
NDP chir_6 PN O3 O5D O2N both
NDP chir_7 C4D O4D C3D C5D negative
NDP chir_8 C3D O3D C4D C2D positive
NDP chir_9 C2D O2D C1D C3D negative
NDP chir_10 C1D O4D N1N C2D negative
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
NDP plan-1 C1B 0.020
NDP plan-1 C2A 0.020
NDP plan-1 C4A 0.020
NDP plan-1 C5A 0.020
NDP plan-1 C6A 0.020
NDP plan-1 C8A 0.020
NDP plan-1 H2A 0.020
NDP plan-1 H8A 0.020
NDP plan-1 N1A 0.020
NDP plan-1 N3A 0.020
NDP plan-1 N6A 0.020
NDP plan-1 N7A 0.020
NDP plan-1 N9A 0.020
NDP plan-2 C6A 0.020
NDP plan-2 H61A 0.020
NDP plan-2 H62A 0.020
NDP plan-2 N6A 0.020
NDP plan-3 C1D 0.020
NDP plan-3 C2N 0.020
NDP plan-3 C6N 0.020
NDP plan-3 N1N 0.020
NDP plan-4 C2N 0.020
NDP plan-4 C3N 0.020
NDP plan-4 H2N 0.020
NDP plan-4 N1N 0.020
NDP plan-5 C2N 0.020
NDP plan-5 C3N 0.020
NDP plan-5 C4N 0.020
NDP plan-5 C7N 0.020
NDP plan-6 C3N 0.020
NDP plan-6 C7N 0.020
NDP plan-6 N7N 0.020
NDP plan-6 O7N 0.020
NDP plan-7 C7N 0.020
NDP plan-7 H71N 0.020
NDP plan-7 H72N 0.020
NDP plan-7 N7N 0.020
NDP plan-8 C4N 0.020
NDP plan-8 C5N 0.020
NDP plan-8 C6N 0.020
NDP plan-8 H5N 0.020
NDP plan-9 C5N 0.020
NDP plan-9 C6N 0.020
NDP plan-9 H6N 0.020
NDP plan-9 N1N 0.020
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
NDP SMILES_CANONICAL CACTVS 3.341 NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
NDP SMILES CACTVS 3.341 NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
NDP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
NDP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
NDP InChI InChI 1.03 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
NDP InChIKey InChI 1.03 ACFIXJIJDZMPPO-NNYOXOHSSA-N
loop_
_pdbx_chem_comp_description_generator.comp_id
_pdbx_chem_comp_description_generator.program_name
_pdbx_chem_comp_description_generator.program_version
_pdbx_chem_comp_description_generator.descriptor
NDP acedrg 243 "dictionary generator"
NDP acedrg_database 11 "data source"
NDP rdkit 2017.03.2 "Chemoinformatics tool"
NDP refmac5 5.8.0238 "optimization tool"
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