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Jungfraujoch/image_analysis/structure_refinement/monomers/NAP.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
NAP NAP "NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE" NON-POLYMER 73 48 .
#
data_comp_NAP
#
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
NAP PA P P 0 14.707 24.447 12.480
NAP O1A O O 0 13.458 23.637 12.602
NAP O2A O OP -1 16.014 23.726 12.475
NAP O5B O O2 0 14.609 25.379 11.174
NAP C5B C CH2 0 15.409 26.589 11.081
NAP C4B C CH1 0 15.737 26.871 9.636
NAP O4B O O2 0 16.491 28.107 9.568
NAP C3B C CH1 0 16.601 25.819 8.930
NAP O3B O OH1 0 15.781 24.855 8.281
NAP C2B C CH1 0 17.440 26.644 7.958
NAP O2B O O2 0 16.792 26.811 6.691
NAP C1B C CH1 0 17.572 27.988 8.672
NAP N9A N NR5 0 18.813 28.129 9.426
NAP C8A C CR15 0 19.226 27.352 10.480
NAP N7A N NRD5 0 20.388 27.707 10.967
NAP C5A C CR56 0 20.773 28.787 10.187
NAP C6A C CR6 0 21.921 29.609 10.202
NAP N6A N NH2 0 22.922 29.462 11.067
NAP N1A N NRD6 0 21.993 30.607 9.282
NAP C2A C CR16 0 20.979 30.751 8.415
NAP N3A N NRD6 0 19.857 30.039 8.308
NAP C4A C CR56 0 19.809 29.058 9.231
NAP O3 O O2 0 14.727 25.535 13.659
NAP PN P P 0 15.006 25.433 15.236
NAP O1N O O 0 14.417 24.159 15.744
NAP O2N O OP -1 14.583 26.712 15.880
NAP O5D O O2 0 16.607 25.326 15.265
NAP C5D C CH2 0 17.397 26.371 14.640
NAP C4D C CH1 0 18.836 26.241 15.075
NAP O4D O O2 0 19.679 27.018 14.196
NAP C3D C CH1 0 19.161 26.751 16.486
NAP O3D O OH1 0 20.269 26.050 17.038
NAP C2D C CH1 0 19.461 28.232 16.227
NAP O2D O OH1 0 20.299 28.821 17.209
NAP C1D C CH1 0 20.213 28.142 14.894
NAP N1N N NR6 1 20.068 29.345 14.038
NAP C2N C CR16 0 18.841 29.658 13.486
NAP C3N C CR6 0 18.708 30.789 12.681
NAP C7N C C 0 17.375 31.126 12.085
NAP O7N O O 0 16.914 32.269 12.231
NAP N7N N NH2 0 16.721 30.182 11.419
NAP C4N C CR16 0 19.808 31.604 12.444
NAP C5N C CR16 0 21.032 31.285 13.005
NAP C6N C CR16 0 21.155 30.158 13.797
NAP P2B P P 0 17.807 26.912 5.431
NAP O1X O O 0 18.385 25.523 5.232
NAP O2X O OP -1 16.970 27.355 4.247
NAP O3X O OP -1 18.878 27.929 5.783
NAP H51A H H 0 16.247 26.480 11.592
NAP H52A H H 0 14.907 27.351 11.463
NAP H4B H H 0 14.895 26.984 9.146
NAP H3B H H 0 17.191 25.370 9.588
NAP HO3A H H 0 16.276 24.329 7.835
NAP H2B H H 0 18.322 26.219 7.847
NAP H1B H H 0 17.517 28.708 8.003
NAP H8A H H 0 18.721 26.635 10.822
NAP H61A H H 0 23.626 29.985 11.016
NAP H62A H H 0 22.876 28.841 11.686
NAP H2A H H 0 21.074 31.456 7.793
NAP H51N H H 0 17.050 27.259 14.903
NAP H52N H H 0 17.341 26.291 13.658
NAP H4D H H 0 19.094 25.297 15.004
NAP H3D H H 0 18.368 26.662 17.076
NAP HO3N H H 0 20.386 26.311 17.838
NAP H2D H H 0 18.621 28.744 16.127
NAP HO2N H H 0 20.439 29.635 17.009
NAP H1D H H 0 21.174 27.982 15.071
NAP H2N H H 0 18.092 29.108 13.647
NAP H71N H H 0 17.067 29.367 11.311
NAP H72N H H 0 15.919 30.359 11.072
NAP H4N H H 0 19.723 32.370 11.903
NAP H5N H H 0 21.785 31.830 12.847
NAP H6N H H 0 21.988 29.938 14.181
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
NAP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122
NAP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122
NAP PA O5B SINGLE n 1.604 0.0133 1.604 0.0133
NAP PA O3 SINGLE n 1.604 0.0133 1.604 0.0133
NAP O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166
NAP C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100
NAP C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100
NAP C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100
NAP O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100
NAP C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100
NAP C3B C2B SINGLE n 1.523 0.0106 1.523 0.0106
NAP C2B O2B SINGLE n 1.425 0.0152 1.425 0.0152
NAP C2B C1B SINGLE n 1.524 0.0100 1.524 0.0100
NAP O2B P2B SINGLE n 1.614 0.0178 1.614 0.0178
NAP C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100
NAP N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100
NAP N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101
NAP C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100
NAP N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100
NAP C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100
NAP C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100
NAP C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100
NAP C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100
NAP N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100
NAP C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100
NAP N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100
NAP O3 PN SINGLE n 1.604 0.0133 1.604 0.0133
NAP PN O1N DOUBLE n 1.493 0.0122 1.493 0.0122
NAP PN O2N SINGLE n 1.493 0.0122 1.493 0.0122
NAP PN O5D SINGLE n 1.604 0.0133 1.604 0.0133
NAP O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166
NAP C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100
NAP C4D O4D SINGLE n 1.443 0.0107 1.443 0.0107
NAP C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100
NAP O4D C1D SINGLE n 1.425 0.0141 1.425 0.0141
NAP C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100
NAP C3D C2D SINGLE n 1.533 0.0100 1.533 0.0100
NAP C2D O2D SINGLE n 1.419 0.0101 1.419 0.0101
NAP C2D C1D SINGLE n 1.533 0.0100 1.533 0.0100
NAP C1D N1N SINGLE n 1.477 0.0138 1.477 0.0138
NAP N1N C2N DOUBLE y 1.377 0.0105 1.377 0.0105
NAP N1N C6N SINGLE y 1.375 0.0105 1.375 0.0105
NAP C2N C3N SINGLE y 1.390 0.0105 1.390 0.0105
NAP C3N C7N SINGLE n 1.497 0.0100 1.497 0.0100
NAP C3N C4N DOUBLE y 1.385 0.0100 1.385 0.0100
NAP C7N O7N DOUBLE n 1.241 0.0105 1.241 0.0105
NAP C7N N7N SINGLE n 1.326 0.0100 1.326 0.0100
NAP C4N C5N SINGLE y 1.380 0.0100 1.380 0.0100
NAP C5N C6N DOUBLE y 1.380 0.0128 1.380 0.0128
NAP P2B O1X DOUBLE n 1.517 0.0192 1.517 0.0192
NAP P2B O2X SINGLE n 1.517 0.0192 1.517 0.0192
NAP P2B O3X SINGLE n 1.517 0.0192 1.517 0.0192
NAP C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200
NAP C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200
NAP C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200
NAP C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200
NAP O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200
NAP C2B H2B SINGLE n 1.089 0.0100 0.985 0.0119
NAP C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200
NAP C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170
NAP N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200
NAP N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200
NAP C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200
NAP C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200
NAP C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200
NAP C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200
NAP C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200
NAP O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200
NAP C2D H2D SINGLE n 1.089 0.0100 0.989 0.0200
NAP O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200
NAP C1D H1D SINGLE n 1.089 0.0100 0.990 0.0173
NAP C2N H2N SINGLE n 1.082 0.0130 0.943 0.0170
NAP N7N H71N SINGLE n 1.016 0.0100 0.891 0.0200
NAP N7N H72N SINGLE n 1.016 0.0100 0.891 0.0200
NAP C4N H4N SINGLE n 1.082 0.0130 0.941 0.0168
NAP C5N H5N SINGLE n 1.082 0.0130 0.943 0.0190
NAP C6N H6N SINGLE n 1.082 0.0130 0.943 0.0169
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
NAP O1A PA O2A 118.411 2.35
NAP O1A PA O5B 109.410 1.50
NAP O1A PA O3 108.816 2.14
NAP O2A PA O5B 109.410 1.50
NAP O2A PA O3 108.816 2.14
NAP O5B PA O3 101.065 1.97
NAP PA O5B C5B 118.553 2.41
NAP O5B C5B C4B 109.342 1.50
NAP O5B C5B H51A 109.845 1.50
NAP O5B C5B H52A 109.845 1.50
NAP C4B C5B H51A 109.624 1.50
NAP C4B C5B H52A 109.624 1.50
NAP H51A C5B H52A 108.472 1.50
NAP C5B C4B O4B 109.123 1.50
NAP C5B C4B C3B 116.008 1.52
NAP C5B C4B H4B 108.268 1.50
NAP O4B C4B C3B 105.388 1.50
NAP O4B C4B H4B 108.947 1.50
NAP C3B C4B H4B 109.363 1.86
NAP C4B O4B C1B 109.903 1.50
NAP C4B C3B O3B 111.281 2.46
NAP C4B C3B C2B 102.352 1.50
NAP C4B C3B H3B 110.452 2.54
NAP O3B C3B C2B 112.463 2.73
NAP O3B C3B H3B 110.380 1.67
NAP C2B C3B H3B 110.255 2.04
NAP C3B O3B HO3A 108.744 3.00
NAP C3B C2B O2B 110.766 3.00
NAP C3B C2B C1B 101.388 1.50
NAP C3B C2B H2B 110.255 2.04
NAP O2B C2B C1B 110.738 2.44
NAP O2B C2B H2B 110.343 1.64
NAP C1B C2B H2B 111.050 1.62
NAP C2B O2B P2B 109.471 3.00
NAP O4B C1B C2B 106.416 1.50
NAP O4B C1B N9A 108.477 1.50
NAP O4B C1B H1B 109.807 1.50
NAP C2B C1B N9A 113.659 1.50
NAP C2B C1B H1B 109.319 1.50
NAP N9A C1B H1B 109.561 1.50
NAP C1B N9A C8A 126.848 1.91
NAP C1B N9A C4A 127.459 1.80
NAP C8A N9A C4A 105.693 1.50
NAP N9A C8A N7A 113.469 1.50
NAP N9A C8A H8A 123.206 1.50
NAP N7A C8A H8A 123.326 1.50
NAP C8A N7A C5A 104.739 1.50
NAP N7A C5A C6A 132.250 1.50
NAP N7A C5A C4A 110.483 1.50
NAP C6A C5A C4A 117.267 1.50
NAP C5A C6A N6A 123.792 1.50
NAP C5A C6A N1A 117.409 1.50
NAP N6A C6A N1A 118.799 1.50
NAP C6A N6A H61A 119.723 1.50
NAP C6A N6A H62A 119.723 1.50
NAP H61A N6A H62A 120.554 1.88
NAP C6A N1A C2A 118.521 1.50
NAP N1A C2A N3A 129.332 1.50
NAP N1A C2A H2A 115.313 1.50
NAP N3A C2A H2A 115.355 1.50
NAP C2A N3A C4A 110.982 1.50
NAP N9A C4A C5A 105.616 1.50
NAP N9A C4A N3A 127.895 1.50
NAP C5A C4A N3A 126.489 1.50
NAP PA O3 PN 132.542 3.00
NAP O3 PN O1N 108.816 2.14
NAP O3 PN O2N 108.816 2.14
NAP O3 PN O5D 101.065 1.97
NAP O1N PN O2N 118.411 2.35
NAP O1N PN O5D 109.410 1.50
NAP O2N PN O5D 109.410 1.50
NAP PN O5D C5D 118.553 2.41
NAP O5D C5D C4D 109.342 1.50
NAP O5D C5D H51N 109.845 1.50
NAP O5D C5D H52N 109.845 1.50
NAP C4D C5D H51N 109.624 1.50
NAP C4D C5D H52N 109.624 1.50
NAP H51N C5D H52N 108.472 1.50
NAP C5D C4D O4D 109.615 1.50
NAP C5D C4D C3D 116.008 1.52
NAP C5D C4D H4D 108.268 1.50
NAP O4D C4D C3D 104.439 1.50
NAP O4D C4D H4D 108.698 1.50
NAP C3D C4D H4D 109.363 1.86
NAP C4D O4D C1D 109.578 1.50
NAP C4D C3D O3D 111.281 2.46
NAP C4D C3D C2D 102.071 1.50
NAP C4D C3D H3D 110.452 2.54
NAP O3D C3D C2D 111.993 3.00
NAP O3D C3D H3D 110.380 1.67
NAP C2D C3D H3D 110.108 1.66
NAP C3D O3D HO3N 108.744 3.00
NAP C3D C2D O2D 112.861 2.52
NAP C3D C2D C1D 101.269 1.50
NAP C3D C2D H2D 110.799 1.82
NAP O2D C2D C1D 109.476 3.00
NAP O2D C2D H2D 111.022 1.77
NAP C1D C2D H2D 110.760 1.63
NAP C2D O2D HO2N 109.449 1.85
NAP O4D C1D C2D 106.825 1.50
NAP O4D C1D N1N 108.092 1.50
NAP O4D C1D H1D 109.327 1.50
NAP C2D C1D N1N 113.620 1.99
NAP C2D C1D H1D 109.776 1.83
NAP N1N C1D H1D 108.901 1.50
NAP C1D N1N C2N 119.705 1.50
NAP C1D N1N C6N 119.705 1.50
NAP C2N N1N C6N 120.590 1.50
NAP N1N C2N C3N 119.549 3.00
NAP N1N C2N H2N 120.430 1.53
NAP C3N C2N H2N 120.021 1.50
NAP C2N C3N C7N 119.660 2.75
NAP C2N C3N C4N 119.402 1.64
NAP C7N C3N C4N 120.938 2.50
NAP C3N C7N O7N 119.730 1.50
NAP C3N C7N N7N 118.032 1.50
NAP O7N C7N N7N 122.238 1.50
NAP C7N N7N H71N 120.236 2.75
NAP C7N N7N H72N 120.236 2.75
NAP H71N N7N H72N 119.529 2.83
NAP C3N C4N C5N 119.166 1.50
NAP C3N C4N H4N 120.513 1.50
NAP C5N C4N H4N 120.320 1.50
NAP C4N C5N C6N 120.016 1.50
NAP C4N C5N H5N 120.300 1.50
NAP C6N C5N H5N 119.683 1.50
NAP N1N C6N C5N 121.277 1.50
NAP N1N C6N H6N 118.693 1.53
NAP C5N C6N H6N 120.031 1.59
NAP O2B P2B O1X 106.518 3.00
NAP O2B P2B O2X 106.518 3.00
NAP O2B P2B O3X 106.518 3.00
NAP O1X P2B O2X 112.139 1.52
NAP O1X P2B O3X 112.139 1.52
NAP 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
NAP sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3
NAP sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3
NAP sp3_sp3_82 C2B O2B P2B O1X 180.000 10.0 3
NAP sp2_sp3_1 C8A N9A C1B O4B 150.000 10.0 6
NAP const_34 N7A C8A N9A C1B 180.000 10.0 2
NAP const_46 C5A C4A N9A C1B 180.000 10.0 2
NAP const_37 N9A C8A N7A C5A 0.000 10.0 2
NAP const_40 C6A C5A N7A C8A 180.000 10.0 2
NAP const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2
NAP const_41 N9A C4A C5A N7A 0.000 10.0 2
NAP sp2_sp2_1 C5A C6A N6A H61A 180.000 5.0 2
NAP const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2
NAP const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2
NAP const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2
NAP const_12 N9A C4A N3A C2A 180.000 10.0 2
NAP sp3_sp3_87 PA O3 PN O1N 60.000 10.0 3
NAP sp3_sp3_88 C5D O5D PN O3 180.000 10.0 3
NAP sp3_sp3_91 C4D C5D O5D PN 180.000 10.0 3
NAP sp3_sp3_94 O4D C4D C5D O5D 180.000 10.0 3
NAP sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3
NAP sp3_sp3_107 O3D C3D C4D C5D 180.000 10.0 3
NAP sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3
NAP sp3_sp3_112 C4D C3D O3D HO3N 180.000 10.0 3
NAP sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3
NAP sp3_sp3_115 C3D C2D O2D HO2N 180.000 10.0 3
NAP sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3
NAP sp2_sp3_7 C2N N1N C1D O4D 150.000 10.0 6
NAP const_14 C3N C2N N1N C1D 180.000 10.0 2
NAP const_50 C5N C6N N1N C1D 180.000 10.0 2
NAP const_18 N1N C2N C3N C7N 180.000 10.0 2
NAP sp2_sp2_6 C2N C3N C7N O7N 0.000 5.0 2
NAP const_23 C7N C3N C4N C5N 180.000 10.0 2
NAP sp2_sp2_11 O7N C7N N7N H71N 0.000 5.0 2
NAP sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3
NAP const_25 C3N C4N C5N C6N 0.000 10.0 2
NAP const_29 C4N C5N C6N N1N 0.000 10.0 2
NAP sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3
NAP sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3
NAP sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3
NAP sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3
NAP sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3
NAP sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3
NAP sp3_sp3_79 C3B C2B O2B P2B 180.000 10.0 3
NAP 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
NAP chir_1 PA O3 O5B O2A both
NAP chir_2 C4B O4B C3B C5B negative
NAP chir_3 C3B O3B C2B C4B negative
NAP chir_4 C2B O2B C1B C3B negative
NAP chir_5 C1B O4B N9A C2B negative
NAP chir_6 PN O3 O5D O2N both
NAP chir_7 C4D O4D C3D C5D negative
NAP chir_8 C3D O3D C4D C2D positive
NAP chir_9 C2D O2D C1D C3D negative
NAP 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
NAP plan-1 C1B 0.020
NAP plan-1 C2A 0.020
NAP plan-1 C4A 0.020
NAP plan-1 C5A 0.020
NAP plan-1 C6A 0.020
NAP plan-1 C8A 0.020
NAP plan-1 H2A 0.020
NAP plan-1 H8A 0.020
NAP plan-1 N1A 0.020
NAP plan-1 N3A 0.020
NAP plan-1 N6A 0.020
NAP plan-1 N7A 0.020
NAP plan-1 N9A 0.020
NAP plan-2 C1D 0.020
NAP plan-2 C2N 0.020
NAP plan-2 C3N 0.020
NAP plan-2 C4N 0.020
NAP plan-2 C5N 0.020
NAP plan-2 C6N 0.020
NAP plan-2 C7N 0.020
NAP plan-2 H2N 0.020
NAP plan-2 H4N 0.020
NAP plan-2 H5N 0.020
NAP plan-2 H6N 0.020
NAP plan-2 N1N 0.020
NAP plan-3 C6A 0.020
NAP plan-3 H61A 0.020
NAP plan-3 H62A 0.020
NAP plan-3 N6A 0.020
NAP plan-4 C3N 0.020
NAP plan-4 C7N 0.020
NAP plan-4 N7N 0.020
NAP plan-4 O7N 0.020
NAP plan-5 C7N 0.020
NAP plan-5 H71N 0.020
NAP plan-5 H72N 0.020
NAP plan-5 N7N 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
NAP SMILES_CANONICAL CACTVS 3.341 NC(=O)c1ccc[n+](c1)[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
NAP SMILES CACTVS 3.341 NC(=O)c1ccc[n+](c1)[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
NAP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
NAP SMILES "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
NAP InChI InChI 1.03 InChI=1S/C21H28N7O17P3/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/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
NAP InChIKey InChI 1.03 XJLXINKUBYWONI-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
NAP acedrg 243 "dictionary generator"
NAP acedrg_database 11 "data source"
NAP rdkit 2017.03.2 "Chemoinformatics tool"
NAP refmac5 5.8.0238 "optimization tool"
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