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Jungfraujoch/image_analysis/structure_refinement/monomers/FAD.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

620 lines
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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
FAD FAD "FLAVIN-ADENINE DINUCLEOTIDE" NON-POLYMER 84 53 .
#
data_comp_FAD
#
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
FAD PA P P 0 20.714 1.770 23.791
FAD O1A O O 0 19.737 0.994 22.985
FAD O2A O OP -1 20.556 3.244 23.868
FAD O5B O O2 0 20.784 1.154 25.265
FAD C5B C CH2 0 21.508 1.920 26.259
FAD C4B C CH1 0 21.685 1.088 27.506
FAD O4B O O2 0 22.496 1.819 28.451
FAD C3B C CH1 0 20.398 0.757 28.265
FAD O3B O OH1 0 20.556 -0.451 28.999
FAD C2B C CH1 0 20.243 1.982 29.172
FAD O2B O OH1 0 19.475 1.727 30.330
FAD C1B C CH1 0 21.699 2.264 29.545
FAD N9A N NR5 0 21.959 3.685 29.781
FAD C8A C CR15 0 22.300 4.646 28.862
FAD N7A N NRD5 0 22.466 5.839 29.380
FAD C5A C CR56 0 22.214 5.654 30.732
FAD C6A C CR6 0 22.225 6.545 31.827
FAD N6A N NH2 0 22.509 7.843 31.720
FAD N1A N NRD6 0 21.925 6.038 33.053
FAD C2A C CR16 0 21.639 4.731 33.155
FAD N3A N NRD6 0 21.600 3.805 32.197
FAD C4A C CR56 0 21.899 4.330 30.993
FAD N1 N NRD6 0 21.477 -2.068 14.310
FAD C2 C CR6 0 21.990 -3.170 13.678
FAD O2 O O 0 23.119 -3.600 13.933
FAD N3 N NR16 0 21.215 -3.824 12.720
FAD C4 C CR6 0 19.939 -3.467 12.324
FAD O4 O O 0 19.331 -4.099 11.476
FAD C4X C CR66 0 19.428 -2.318 12.997
FAD N5 N NRD6 0 18.223 -1.922 12.672
FAD C5X C CR66 0 17.708 -0.822 13.305
FAD C6 C CR16 0 16.407 -0.419 12.939
FAD C7 C CR6 0 15.794 0.671 13.514
FAD C7M C CH3 0 14.398 1.039 13.068
FAD C8 C CR6 0 16.505 1.416 14.514
FAD C8M C CH3 0 15.889 2.619 15.180
FAD C9 C CR16 0 17.784 1.024 14.876
FAD C9A C CR66 0 18.422 -0.094 14.291
FAD N10 N NR6 0 19.717 -0.536 14.620
FAD C10 C CR66 0 20.261 -1.663 13.986
FAD "C1'" C CH2 0 20.546 0.156 15.638
FAD "C2'" C CH1 0 20.455 -0.488 17.014
FAD "O2'" O OH1 0 19.095 -0.421 17.451
FAD "C3'" C CH1 0 21.373 0.159 18.058
FAD "O3'" O OH1 0 22.723 0.097 17.602
FAD "C4'" C CH1 0 21.301 -0.479 19.449
FAD "O4'" O OH1 0 19.957 -0.463 19.936
FAD "C5'" C CH2 0 22.167 0.224 20.481
FAD "O5'" O O2 0 22.110 -0.483 21.743
FAD P P P 0 22.951 0.052 22.986
FAD O1P O O 0 22.742 -0.871 24.130
FAD O2P O OP -1 24.340 0.346 22.551
FAD O3P O O2 0 22.191 1.429 23.280
FAD H51A H H 0 21.005 2.745 26.481
FAD H52A H H 0 22.397 2.180 25.905
FAD H4B H H 0 22.151 0.249 27.259
FAD H3B H H 0 19.629 0.687 27.645
FAD HO3A H H 0 19.777 -0.616 29.334
FAD H2B H H 0 19.868 2.745 28.663
FAD HO2A H H 0 19.501 2.350 30.867
FAD H1B H H 0 21.939 1.734 30.378
FAD H8A H H 0 22.407 4.462 27.944
FAD H61A H H 0 22.502 8.360 32.433
FAD H62A H H 0 22.705 8.186 30.933
FAD H2A H H 0 21.438 4.425 34.027
FAD HN3 H H 0 21.567 -4.529 12.329
FAD H6 H H 0 15.940 -0.918 12.276
FAD HM71 H H 0 14.059 1.787 13.584
FAD HM72 H H 0 13.809 0.276 13.191
FAD HM73 H H 0 14.414 1.282 12.127
FAD HM81 H H 0 16.515 3.008 15.814
FAD HM82 H H 0 15.082 2.352 15.651
FAD HM83 H H 0 15.664 3.283 14.507
FAD H9 H H 0 18.238 1.530 15.543
FAD "H1'1" H H 0 20.293 1.095 15.702
FAD "H1'2" H H 0 21.480 0.169 15.345
FAD "H2'" H H 0 20.705 -1.452 16.929
FAD "HO2'" H H 0 19.029 -0.034 18.222
FAD "H3'" H H 0 21.118 1.116 18.145
FAD "HO3'" H H 0 23.179 -0.185 18.222
FAD "H4'" H H 0 21.600 -1.422 19.381
FAD "HO4'" H H 0 19.930 -0.056 20.740
FAD "H5'1" H H 0 21.854 1.142 20.606
FAD "H5'2" H H 0 23.095 0.252 20.176
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
FAD PA P(OC)(OP)(O)2
FAD O1A O(PO3)
FAD O2A O(PO3)
FAD O5B O(CC[5]HH)(PO3)
FAD C5B C(C[5]C[5]O[5]H)(OP)(H)2
FAD C4B C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>}
FAD O4B O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>}
FAD C3B C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>}
FAD O3B O(C[5]C[5]2H)(H)
FAD C2B C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>}
FAD O2B O(C[5]C[5]2H)(H)
FAD C1B C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>}
FAD N9A N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>}
FAD C8A C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>}
FAD N7A N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<3>,2|N<2>}
FAD C5A C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]N)(N[5a]C[5a]){1|C<3>,1|C<4>,1|H<1>}
FAD C6A C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a])(NHH){1|C<3>,1|H<1>,1|N<2>,1|N<3>}
FAD N6A N(C[6a]C[5a,6a]N[6a])(H)2
FAD N1A N[6a](C[6a]C[5a,6a]N)(C[6a]N[6a]H){1|C<3>,1|N<2>}
FAD C2A C[6a](N[6a]C[5a,6a])(N[6a]C[6a])(H){1|C<3>,2|N<3>}
FAD N3A N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]H){1|C<4>,1|N<2>,2|C<3>}
FAD C4A C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|N<2>,1|N<3>,1|O<2>,3|H<1>}
FAD N1 N[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,1|N<2>,2|C<3>}
FAD C2 C[6a](N[6a]C[6a,6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<3>,1|O<1>}
FAD O2 O(C[6a]N[6a]2)
FAD N3 N[6a](C[6a]C[6a,6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|N<2>}
FAD C4 C[6a](C[6a,6a]C[6a,6a]N[6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<2>,1|N<3>,1|O<1>}
FAD O4 O(C[6a]C[6a,6a]N[6a])
FAD C4X C[6a,6a](C[6a,6a]N[6a]2)(N[6a]C[6a,6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,3|C<3>}
FAD N5 N[6a](C[6a,6a]C[6a,6a]C[6a])2{1|H<1>,1|N<2>,1|O<1>,2|C<3>,2|N<3>}
FAD C5X C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a])(C[6a]C[6a]H){1|H<1>,2|C<4>,3|C<3>}
FAD C6 C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|C<4>,1|N<3>,2|C<3>}
FAD C7 C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<2>}
FAD C7M C(C[6a]C[6a]2)(H)3
FAD C8 C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<3>}
FAD C8M C(C[6a]C[6a]2)(H)3
FAD C9 C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|N<2>,2|C<3>,2|C<4>}
FAD C9A C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(C[6a]C[6a]H){1|C<4>,1|H<1>,1|N<2>,2|C<3>}
FAD N10 N[6a](C[6a,6a]C[6a,6a]C[6a])(C[6a,6a]C[6a,6a]N[6a])(CCHH){1|H<1>,1|N<2>,4|C<3>}
FAD C10 C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(N[6a]C[6a]){1|N<3>,2|C<3>,2|O<1>}
FAD "C1'" C(N[6a]C[6a,6a]2)(CCHO)(H)2
FAD "C2'" C(CN[6a]HH)(CCHO)(OH)(H)
FAD "O2'" O(CCCH)(H)
FAD "C3'" C(CCHO)2(OH)(H)
FAD "O3'" O(CCCH)(H)
FAD "C4'" C(CCHO)(CHHO)(OH)(H)
FAD "O4'" O(CCCH)(H)
FAD "C5'" C(CCHO)(OP)(H)2
FAD "O5'" O(CCHH)(PO3)
FAD P P(OC)(OP)(O)2
FAD O1P O(PO3)
FAD O2P O(PO3)
FAD O3P O(PO3)2
FAD H51A H(CC[5]HO)
FAD H52A H(CC[5]HO)
FAD H4B H(C[5]C[5]O[5]C)
FAD H3B H(C[5]C[5]2O)
FAD HO3A H(OC[5])
FAD H2B H(C[5]C[5]2O)
FAD HO2A H(OC[5])
FAD H1B H(C[5]N[5a]C[5]O[5])
FAD H8A H(C[5a]N[5a]2)
FAD H61A H(NC[6a]H)
FAD H62A H(NC[6a]H)
FAD H2A H(C[6a]N[6a]2)
FAD HN3 H(N[6a]C[6a]2)
FAD H6 H(C[6a]C[6a,6a]C[6a])
FAD HM71 H(CC[6a]HH)
FAD HM72 H(CC[6a]HH)
FAD HM73 H(CC[6a]HH)
FAD HM81 H(CC[6a]HH)
FAD HM82 H(CC[6a]HH)
FAD HM83 H(CC[6a]HH)
FAD H9 H(C[6a]C[6a,6a]C[6a])
FAD "H1'1" H(CN[6a]CH)
FAD "H1'2" H(CN[6a]CH)
FAD "H2'" H(CCCO)
FAD "HO2'" H(OC)
FAD "H3'" H(CCCO)
FAD "HO3'" H(OC)
FAD "H4'" H(CCCO)
FAD "HO4'" H(OC)
FAD "H5'1" H(CCHO)
FAD "H5'2" H(CCHO)
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
FAD PA O1A DOUBLE n 1.485 0.0100 1.485 0.0100
FAD PA O2A SINGLE n 1.485 0.0100 1.485 0.0100
FAD PA O5B SINGLE n 1.598 0.0100 1.598 0.0100
FAD PA O3P SINGLE n 1.600 0.0185 1.600 0.0185
FAD O5B C5B SINGLE n 1.445 0.0200 1.445 0.0200
FAD C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100
FAD C4B O4B SINGLE n 1.444 0.0100 1.444 0.0100
FAD C4B C3B SINGLE n 1.532 0.0100 1.532 0.0100
FAD O4B C1B SINGLE n 1.423 0.0100 1.423 0.0100
FAD C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100
FAD C3B C2B SINGLE n 1.532 0.0103 1.532 0.0103
FAD C2B O2B SINGLE n 1.412 0.0100 1.412 0.0100
FAD C2B C1B SINGLE n 1.528 0.0100 1.528 0.0100
FAD C1B N9A SINGLE n 1.462 0.0102 1.462 0.0102
FAD N9A C8A SINGLE y 1.371 0.0100 1.371 0.0100
FAD N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101
FAD C8A N7A DOUBLE y 1.311 0.0100 1.311 0.0100
FAD N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100
FAD C5A C6A SINGLE y 1.407 0.0100 1.407 0.0100
FAD C5A C4A DOUBLE y 1.382 0.0100 1.382 0.0100
FAD C6A N6A SINGLE n 1.332 0.0107 1.332 0.0107
FAD C6A N1A DOUBLE y 1.355 0.0106 1.355 0.0106
FAD N1A C2A SINGLE y 1.338 0.0100 1.338 0.0100
FAD C2A N3A DOUBLE y 1.329 0.0100 1.329 0.0100
FAD N3A C4A SINGLE y 1.344 0.0100 1.344 0.0100
FAD N1 C2 SINGLE y 1.369 0.0100 1.369 0.0100
FAD N1 C10 DOUBLE y 1.317 0.0100 1.317 0.0100
FAD C2 O2 DOUBLE n 1.235 0.0100 1.235 0.0100
FAD C2 N3 SINGLE y 1.393 0.0104 1.393 0.0104
FAD N3 C4 SINGLE y 1.377 0.0130 1.377 0.0130
FAD C4 O4 DOUBLE n 1.218 0.0100 1.218 0.0100
FAD C4 C4X SINGLE y 1.398 0.0190 1.398 0.0190
FAD C4X N5 DOUBLE y 1.308 0.0122 1.308 0.0122
FAD C4X C10 SINGLE y 1.443 0.0100 1.443 0.0100
FAD N5 C5X SINGLE y 1.368 0.0100 1.368 0.0100
FAD C5X C6 SINGLE y 1.409 0.0100 1.409 0.0100
FAD C5X C9A DOUBLE y 1.410 0.0100 1.410 0.0100
FAD C6 C7 DOUBLE y 1.376 0.0100 1.376 0.0100
FAD C7 C7M SINGLE n 1.507 0.0100 1.507 0.0100
FAD C7 C8 SINGLE y 1.417 0.0165 1.417 0.0165
FAD C8 C8M SINGLE n 1.504 0.0100 1.504 0.0100
FAD C8 C9 DOUBLE y 1.379 0.0100 1.379 0.0100
FAD C9 C9A SINGLE y 1.403 0.0100 1.403 0.0100
FAD C9A N10 SINGLE y 1.392 0.0100 1.392 0.0100
FAD N10 C10 SINGLE y 1.385 0.0119 1.385 0.0119
FAD N10 "C1'" SINGLE n 1.475 0.0100 1.475 0.0100
FAD "C1'" "C2'" SINGLE n 1.518 0.0148 1.518 0.0148
FAD "C2'" "O2'" SINGLE n 1.429 0.0132 1.429 0.0132
FAD "C2'" "C3'" SINGLE n 1.529 0.0130 1.529 0.0130
FAD "C3'" "O3'" SINGLE n 1.426 0.0100 1.426 0.0100
FAD "C3'" "C4'" SINGLE n 1.528 0.0126 1.528 0.0126
FAD "C4'" "O4'" SINGLE n 1.429 0.0111 1.429 0.0111
FAD "C4'" "C5'" SINGLE n 1.518 0.0135 1.518 0.0135
FAD "C5'" "O5'" SINGLE n 1.445 0.0200 1.445 0.0200
FAD "O5'" P SINGLE n 1.592 0.0137 1.592 0.0137
FAD P O1P DOUBLE n 1.485 0.0100 1.485 0.0100
FAD P O2P SINGLE n 1.485 0.0100 1.485 0.0100
FAD P O3P SINGLE n 1.600 0.0185 1.600 0.0185
FAD C5B H51A SINGLE n 1.089 0.0100 0.991 0.0200
FAD C5B H52A SINGLE n 1.089 0.0100 0.991 0.0200
FAD C4B H4B SINGLE n 1.089 0.0100 0.990 0.0200
FAD C3B H3B SINGLE n 1.089 0.0100 0.991 0.0200
FAD O3B HO3A SINGLE n 0.970 0.0120 0.839 0.0200
FAD C2B H2B SINGLE n 1.089 0.0100 0.991 0.0200
FAD O2B HO2A SINGLE n 0.970 0.0120 0.839 0.0200
FAD C1B H1B SINGLE n 1.089 0.0100 1.016 0.0200
FAD C8A H8A SINGLE n 1.082 0.0130 0.942 0.0168
FAD N6A H61A SINGLE n 1.016 0.0100 0.880 0.0200
FAD N6A H62A SINGLE n 1.016 0.0100 0.880 0.0200
FAD C2A H2A SINGLE n 1.082 0.0130 0.946 0.0200
FAD N3 HN3 SINGLE n 1.016 0.0100 0.880 0.0100
FAD C6 H6 SINGLE n 1.082 0.0130 0.952 0.0100
FAD C7M HM71 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C7M HM72 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C7M HM73 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C8M HM81 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C8M HM82 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C8M HM83 SINGLE n 1.089 0.0100 0.972 0.0144
FAD C9 H9 SINGLE n 1.082 0.0130 0.954 0.0100
FAD "C1'" "H1'1" SINGLE n 1.089 0.0100 0.980 0.0162
FAD "C1'" "H1'2" SINGLE n 1.089 0.0100 0.980 0.0162
FAD "C2'" "H2'" SINGLE n 1.089 0.0100 1.000 0.0200
FAD "O2'" "HO2'" SINGLE n 0.970 0.0120 0.864 0.0200
FAD "C3'" "H3'" SINGLE n 1.089 0.0100 0.994 0.0118
FAD "O3'" "HO3'" SINGLE n 0.970 0.0120 0.864 0.0200
FAD "C4'" "H4'" SINGLE n 1.089 0.0100 0.991 0.0117
FAD "O4'" "HO4'" SINGLE n 0.970 0.0120 0.864 0.0200
FAD "C5'" "H5'1" SINGLE n 1.089 0.0100 0.978 0.0200
FAD "C5'" "H5'2" SINGLE n 1.089 0.0100 0.978 0.0200
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
FAD O1A PA O2A 118.805 3.00
FAD O1A PA O5B 109.340 2.31
FAD O1A PA O3P 109.053 3.00
FAD O2A PA O5B 109.340 2.31
FAD O2A PA O3P 109.053 3.00
FAD O5B PA O3P 100.137 3.00
FAD PA O5B C5B 116.362 1.50
FAD O5B C5B C4B 109.454 1.61
FAD O5B C5B H51A 109.882 1.50
FAD O5B C5B H52A 109.882 1.50
FAD C4B C5B H51A 109.589 1.50
FAD C4B C5B H52A 109.589 1.50
FAD H51A C5B H52A 108.471 1.50
FAD C5B C4B O4B 109.154 1.50
FAD C5B C4B C3B 115.288 1.50
FAD C5B C4B H4B 108.351 1.59
FAD O4B C4B C3B 105.318 1.50
FAD O4B C4B H4B 109.120 1.50
FAD C3B C4B H4B 109.322 2.54
FAD C4B O4B C1B 109.502 2.85
FAD C4B C3B O3B 110.713 3.00
FAD C4B C3B C2B 102.593 1.50
FAD C4B C3B H3B 110.577 3.00
FAD O3B C3B C2B 111.671 3.00
FAD O3B C3B H3B 110.541 2.08
FAD C2B C3B H3B 110.454 1.85
FAD C3B O3B HO3A 109.389 3.00
FAD C3B C2B O2B 112.677 3.00
FAD C3B C2B C1B 101.406 1.50
FAD C3B C2B H2B 110.788 1.91
FAD O2B C2B C1B 110.814 3.00
FAD O2B C2B H2B 110.904 1.50
FAD C1B C2B H2B 110.342 1.91
FAD C2B O2B HO2A 109.217 3.00
FAD O4B C1B C2B 106.114 1.65
FAD O4B C1B N9A 108.577 1.50
FAD O4B C1B H1B 109.833 2.53
FAD C2B C1B N9A 113.380 2.77
FAD C2B C1B H1B 109.222 1.50
FAD N9A C1B H1B 109.411 1.50
FAD C1B N9A C8A 127.072 3.00
FAD C1B N9A C4A 126.969 2.94
FAD C8A N9A C4A 105.958 1.50
FAD N9A C8A N7A 113.692 1.50
FAD N9A C8A H8A 122.949 1.50
FAD N7A C8A H8A 123.359 1.50
FAD C8A N7A C5A 103.906 1.50
FAD N7A C5A C6A 131.998 1.50
FAD N7A C5A C4A 110.646 1.50
FAD C6A C5A C4A 117.356 1.50
FAD C5A C6A N6A 123.773 1.50
FAD C5A C6A N1A 117.375 1.50
FAD N6A C6A N1A 118.852 1.50
FAD C6A N6A H61A 119.818 3.00
FAD C6A N6A H62A 119.818 3.00
FAD H61A N6A H62A 120.363 3.00
FAD C6A N1A C2A 118.603 1.50
FAD N1A C2A N3A 129.210 1.50
FAD N1A C2A H2A 115.363 1.50
FAD N3A C2A H2A 115.427 1.50
FAD C2A N3A C4A 111.101 1.50
FAD N9A C4A C5A 105.797 1.50
FAD N9A C4A N3A 127.848 1.50
FAD C5A C4A N3A 126.355 1.50
FAD C2 N1 C10 118.461 1.50
FAD N1 C2 O2 121.468 1.50
FAD N1 C2 N3 119.897 1.50
FAD O2 C2 N3 118.636 1.50
FAD C2 N3 C4 126.347 1.50
FAD C2 N3 HN3 117.238 1.50
FAD C4 N3 HN3 116.415 2.90
FAD N3 C4 O4 122.539 1.50
FAD N3 C4 C4X 112.794 1.50
FAD O4 C4 C4X 124.668 1.50
FAD C4 C4X N5 117.421 1.50
FAD C4 C4X C10 117.741 1.50
FAD N5 C4X C10 124.838 1.50
FAD C4X N5 C5X 117.454 1.50
FAD N5 C5X C6 118.145 1.50
FAD N5 C5X C9A 122.298 1.50
FAD C6 C5X C9A 119.556 1.50
FAD C5X C6 C7 121.774 1.50
FAD C5X C6 H6 118.910 1.63
FAD C7 C6 H6 119.325 1.50
FAD C6 C7 C7M 119.966 1.50
FAD C6 C7 C8 119.488 1.50
FAD C7M C7 C8 120.546 1.50
FAD C7 C7M HM71 109.566 1.50
FAD C7 C7M HM72 109.566 1.50
FAD C7 C7M HM73 109.566 1.50
FAD HM71 C7M HM72 109.334 1.91
FAD HM71 C7M HM73 109.334 1.91
FAD HM72 C7M HM73 109.334 1.91
FAD C7 C8 C8M 120.546 1.50
FAD C7 C8 C9 119.488 1.50
FAD C8M C8 C9 119.966 1.50
FAD C8 C8M HM81 109.566 1.50
FAD C8 C8M HM82 109.566 1.50
FAD C8 C8M HM83 109.566 1.50
FAD HM81 C8M HM82 109.334 1.91
FAD HM81 C8M HM83 109.334 1.91
FAD HM82 C8M HM83 109.334 1.91
FAD C8 C9 C9A 120.779 1.50
FAD C8 C9 H9 119.551 1.50
FAD C9A C9 H9 119.670 1.50
FAD C5X C9A C9 118.907 1.50
FAD C5X C9A N10 118.199 1.50
FAD C9 C9A N10 122.894 1.50
FAD C9A N10 C10 120.671 1.50
FAD C9A N10 "C1'" 120.592 1.50
FAD C10 N10 "C1'" 118.737 1.50
FAD N1 C10 C4X 124.761 1.50
FAD N1 C10 N10 118.699 1.50
FAD C4X C10 N10 116.541 1.50
FAD N10 "C1'" "C2'" 112.123 2.65
FAD N10 "C1'" "H1'1" 108.981 1.50
FAD N10 "C1'" "H1'2" 108.981 1.50
FAD "C2'" "C1'" "H1'1" 109.180 1.50
FAD "C2'" "C1'" "H1'2" 109.180 1.50
FAD "H1'1" "C1'" "H1'2" 107.924 2.79
FAD "C1'" "C2'" "O2'" 109.718 2.99
FAD "C1'" "C2'" "C3'" 111.239 3.00
FAD "C1'" "C2'" "H2'" 108.435 1.50
FAD "O2'" "C2'" "C3'" 109.426 3.00
FAD "O2'" "C2'" "H2'" 108.176 3.00
FAD "C3'" "C2'" "H2'" 108.439 2.58
FAD "C2'" "O2'" "HO2'" 109.126 3.00
FAD "C2'" "C3'" "O3'" 109.426 3.00
FAD "C2'" "C3'" "C4'" 113.599 3.00
FAD "C2'" "C3'" "H3'" 108.439 2.58
FAD "O3'" "C3'" "C4'" 109.190 2.87
FAD "O3'" "C3'" "H3'" 108.315 1.83
FAD "C4'" "C3'" "H3'" 108.171 1.50
FAD "C3'" "O3'" "HO3'" 108.910 3.00
FAD "C3'" "C4'" "O4'" 109.920 2.94
FAD "C3'" "C4'" "C5'" 112.050 2.78
FAD "C3'" "C4'" "H4'" 108.859 1.50
FAD "O4'" "C4'" "C5'" 109.162 3.00
FAD "O4'" "C4'" "H4'" 108.709 1.50
FAD "C5'" "C4'" "H4'" 108.615 1.79
FAD "C4'" "O4'" "HO4'" 109.757 3.00
FAD "C4'" "C5'" "O5'" 109.303 3.00
FAD "C4'" "C5'" "H5'1" 109.594 1.50
FAD "C4'" "C5'" "H5'2" 109.594 1.50
FAD "O5'" "C5'" "H5'1" 108.621 3.00
FAD "O5'" "C5'" "H5'2" 108.621 3.00
FAD "H5'1" "C5'" "H5'2" 108.315 1.66
FAD "C5'" "O5'" P 119.008 2.40
FAD "O5'" P O1P 108.662 3.00
FAD "O5'" P O2P 108.662 3.00
FAD "O5'" P O3P 100.260 3.00
FAD O1P P O2P 118.805 3.00
FAD O1P P O3P 109.053 3.00
FAD O2P P O3P 109.053 3.00
FAD PA O3P P 133.108 3.00
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
FAD sp3_sp3_27 C5B O5B PA O1A 60.000 10.0 3
FAD sp3_sp3_30 P O3P PA O1A 60.000 10.0 3
FAD sp2_sp3_1 C8A N9A C1B O4B 150.000 10.0 6
FAD const_48 N7A C8A N9A C1B 180.000 0.0 2
FAD const_80 C5A C4A N9A C1B 180.000 0.0 2
FAD const_51 N9A C8A N7A C5A 0.000 0.0 2
FAD const_54 C6A C5A N7A C8A 180.000 0.0 2
FAD const_38 N7A C5A C6A N6A 0.000 0.0 2
FAD const_55 N9A C4A C5A N7A 0.000 0.0 2
FAD sp2_sp2_83 C5A C6A N6A H61A 180.000 20 2
FAD const_40 N6A C6A N1A C2A 180.000 0.0 2
FAD const_41 N3A C2A N1A C6A 0.000 0.0 2
FAD const_43 N1A C2A N3A C4A 0.000 0.0 2
FAD const_46 N9A C4A N3A C2A 180.000 0.0 2
FAD const_sp2_sp2_2 O2 C2 N1 C10 180.000 0.0 2
FAD const_87 C4X C10 N1 C2 0.000 0.0 2
FAD const_sp2_sp2_5 O2 C2 N3 C4 180.000 0.0 2
FAD const_sp2_sp2_9 O4 C4 N3 C2 180.000 0.0 2
FAD const_14 O4 C4 C4X N5 0.000 0.0 2
FAD const_20 C4 C4X N5 C5X 180.000 0.0 2
FAD const_15 N1 C10 C4X C4 0.000 0.0 2
FAD const_22 C6 C5X N5 C4X 180.000 0.0 2
FAD const_61 N5 C5X C6 C7 180.000 0.0 2
FAD const_24 N5 C5X C9A C9 180.000 0.0 2
FAD const_64 C5X C6 C7 C7M 180.000 0.0 2
FAD sp2_sp3_7 C6 C7 C7M HM71 150.000 10.0 6
FAD const_70 C7M C7 C8 C8M 0.000 0.0 2
FAD sp2_sp3_13 C7 C8 C8M HM81 150.000 10.0 6
FAD const_73 C8M C8 C9 C9A 180.000 0.0 2
FAD const_75 C8 C9 C9A C5X 0.000 0.0 2
FAD const_28 C5X C9A N10 "C1'" 180.000 0.0 2
FAD const_34 N1 C10 N10 "C1'" 0.000 0.0 2
FAD sp2_sp3_20 C9A N10 "C1'" "C2'" -90.000 10.0 6
FAD sp3_sp3_31 C4B C5B O5B PA 180.000 10.0 3
FAD sp3_sp3_58 N10 "C1'" "C2'" "O2'" 180.000 10.0 3
FAD sp3_sp3_67 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3
FAD sp3_sp3_70 "C1'" "C2'" "C3'" "O3'" 180.000 10.0 3
FAD sp3_sp3_79 "C2'" "C3'" "O3'" "HO3'" 180.000 10.0 3
FAD sp3_sp3_82 "C2'" "C3'" "C4'" "O4'" 180.000 10.0 3
FAD sp3_sp3_91 "C3'" "C4'" "O4'" "HO4'" 180.000 10.0 3
FAD sp3_sp3_94 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3
FAD sp3_sp3_103 "C4'" "C5'" "O5'" P 180.000 10.0 3
FAD sp3_sp3_108 "C5'" "O5'" P O1P 60.000 10.0 3
FAD sp3_sp3_110 PA O3P P "O5'" -60.000 10.0 3
FAD sp3_sp3_34 O4B C4B C5B O5B 180.000 10.0 3
FAD sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3
FAD sp3_sp3_47 O3B C3B C4B C5B 180.000 10.0 3
FAD sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3
FAD sp3_sp3_52 C4B C3B O3B HO3A 180.000 10.0 3
FAD sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3
FAD sp3_sp3_55 C3B C2B O2B HO2A 180.000 10.0 3
FAD 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
FAD chir_1 PA O3P O5B O2A both
FAD chir_2 C4B O4B C3B C5B negative
FAD chir_3 C3B O3B C4B C2B positive
FAD chir_4 C2B O2B C1B C3B negative
FAD chir_5 C1B O4B N9A C2B negative
FAD chir_6 "C2'" "O2'" "C3'" "C1'" positive
FAD chir_7 "C3'" "O3'" "C4'" "C2'" positive
FAD chir_8 "C4'" "O4'" "C3'" "C5'" negative
FAD chir_9 P O3P "O5'" O2P both
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
FAD plan-1 C1B 0.020
FAD plan-1 C4A 0.020
FAD plan-1 C5A 0.020
FAD plan-1 C6A 0.020
FAD plan-1 C8A 0.020
FAD plan-1 H8A 0.020
FAD plan-1 N3A 0.020
FAD plan-1 N7A 0.020
FAD plan-1 N9A 0.020
FAD plan-2 C2A 0.020
FAD plan-2 C4A 0.020
FAD plan-2 C5A 0.020
FAD plan-2 C6A 0.020
FAD plan-2 H2A 0.020
FAD plan-2 N1A 0.020
FAD plan-2 N3A 0.020
FAD plan-2 N6A 0.020
FAD plan-2 N7A 0.020
FAD plan-2 N9A 0.020
FAD plan-3 C10 0.020
FAD plan-3 C2 0.020
FAD plan-3 C4 0.020
FAD plan-3 C4X 0.020
FAD plan-3 HN3 0.020
FAD plan-3 N1 0.020
FAD plan-3 N10 0.020
FAD plan-3 N3 0.020
FAD plan-3 N5 0.020
FAD plan-3 O2 0.020
FAD plan-3 O4 0.020
FAD plan-4 "C1'" 0.020
FAD plan-4 C10 0.020
FAD plan-4 C4 0.020
FAD plan-4 C4X 0.020
FAD plan-4 C5X 0.020
FAD plan-4 C6 0.020
FAD plan-4 C9 0.020
FAD plan-4 C9A 0.020
FAD plan-4 N1 0.020
FAD plan-4 N10 0.020
FAD plan-4 N5 0.020
FAD plan-5 C5X 0.020
FAD plan-5 C6 0.020
FAD plan-5 C7 0.020
FAD plan-5 C7M 0.020
FAD plan-5 C8 0.020
FAD plan-5 C8M 0.020
FAD plan-5 C9 0.020
FAD plan-5 C9A 0.020
FAD plan-5 H6 0.020
FAD plan-5 H9 0.020
FAD plan-5 N10 0.020
FAD plan-5 N5 0.020
FAD plan-6 C6A 0.020
FAD plan-6 H61A 0.020
FAD plan-6 H62A 0.020
FAD plan-6 N6A 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
FAD SMILES ACDLabs 10.04 "O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C"
FAD SMILES_CANONICAL CACTVS 3.341 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C"
FAD SMILES CACTVS 3.341 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C"
FAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O"
FAD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O"
FAD InChI InChI 1.03 "InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1"
FAD InChIKey InChI 1.03 VWWQXMAJTJZDQX-UYBVJOGSSA-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
FAD acedrg 275 "dictionary generator"
FAD acedrg_database 12 "data source"
FAD rdkit 2019.09.1 "Chemoinformatics tool"
FAD refmac5 5.8.0405 "optimization tool"
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