# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 20 14:29:21 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (2R,3R,4S,5R,6R)-4-(formylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](NC=O)[C@H]1O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 FNF  FNF  '(2R,3R,4S,5R,6R)-4-(formylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  62  37  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FNF
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.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 FNF  O1F  O  O      0  -0.497   4.8413  -0.7401   3.6499
 FNF  C1F  C  C1     0   0.249   5.7033   0.0829   3.3931
 FNF  N3Q  N  NH1    0  -0.588   5.7174   0.9149   2.3462
 FNF  C3Q  C  CH1    0  -0.136   4.7316   0.9324   1.2932
 FNF  C2Q  C  CH1    0   0.034   5.2689   0.2941   0.0127
 FNF  O2Q  O  OH1    0  -0.659   5.6284  -1.0301   0.2943
 FNF  C4Q  C  CH1    0   0.023   4.2634   2.3597   1.0133
 FNF  O4Q  O  OH1    0  -0.677   5.4092   3.1381   0.7451
 FNF  C5Q  C  CH1    0   0.025   3.2684   2.3562  -0.1454
 FNF  C6Q  C  CH3    0  -0.711   2.8482   3.7473  -0.5723
 FNF  O5Q  O  O2     0  -0.506   3.8240   1.7156  -1.2876
 FNF  C1Q  C  CH1    0   0.250   4.2111   0.3879  -1.0934
 FNF  O3B  O  O2     0  -0.633   3.1399  -0.4348  -0.7461
 FNF  PB   P  P      0   1.349   1.8549  -0.5643  -1.7878
 FNF  O2B  O  O      0  -0.794   2.3742  -0.6140  -3.1893
 FNF  O1B  O  OP    -1  -0.778   0.7895   0.4018  -1.3857
 FNF  O3A  O  O2     0  -0.733   1.4736  -2.0793  -1.2682
 FNF  PA   P  P      0   1.357   0.0515  -2.8390  -1.5518
 FNF  O1A  O  O      0  -0.802  -0.6081  -2.2976  -2.7802
 FNF  O2A  O  OP    -1  -0.793   0.3093  -4.3073  -1.4121
 FNF  O5'  O  O2     0  -0.620  -0.7313  -2.3011  -0.2090
 FNF  C5'  C  CH2    0  -0.161  -2.0718  -2.7032  -0.0346
 FNF  C4'  C  CH1    0   0.013  -2.6504  -2.0196   1.1792
 FNF  O4'  O  O2     0  -0.491  -2.7457  -0.6240   0.9517
 FNF  C3'  C  CH1    0   0.024  -4.0631  -2.5024   1.5113
 FNF  O3'  O  OH1    0  -0.668  -3.9732  -3.5978   2.3875
 FNF  C2'  C  CH2    0  -0.562  -4.7096  -1.2536   2.1110
 FNF  C1'  C  CH1    0   0.219  -3.8686  -0.0855   1.5863
 FNF  N1   N  NR6    0  -0.567  -4.5479   0.8318   0.6717
 FNF  C2   C  CR6    0   0.741  -5.1048   0.3542  -0.4918
 FNF  O2   O  O      0  -0.473  -5.0980  -0.8163  -0.8099
 FNF  C6   C  CR16   0   0.059  -4.5811   2.1696   0.9683
 FNF  C5   C  CR6    0  -0.184  -5.1589   3.1056   0.1956
 FNF  C5M  C  CH3    0  -0.705  -5.1891   4.5555   0.5520
 FNF  C4   C  CR6    0   0.559  -5.7778   2.6740  -1.0408
 FNF  N3   N  NR16   0  -0.733  -5.6877   1.3147  -1.2779
 FNF  O4   O  O      0  -0.455  -6.3368   3.4066  -1.8369
 FNF  H1   H  H      0   0.198   6.5822   0.2338   4.0381
 FNF  H2   H  HNH1   0   0.401   6.5050   1.5381   2.2597
 FNF  H3   H  HCH1   0   0.273   3.8701   0.3579   1.6395
 FNF  H4   H  HCH1   0   0.222   6.1370   0.8728  -0.3317
 FNF  H5   H  HOH1   0   0.454   6.1414  -1.3705  -0.4451
 FNF  H6   H  HCH1   0   0.239   3.7389   2.7282   1.9051
 FNF  H7   H  HOH1   0   0.460   5.1821   4.0681   0.8345
 FNF  H8   H  HCH1   0   0.224   2.3748   1.8182   0.1894
 FNF  H9   H  HCH3   0   0.227   3.6832   4.3242  -0.9726
 FNF  H10  H  HCH3   0   0.247   2.0778   3.6917  -1.3409
 FNF  H11  H  HCH3   0   0.235   2.4302   4.2933   0.2743
 FNF  H12  H  HCH1   0   0.232   4.6445   0.0731  -2.0504
 FNF  H15  H  HCH2   0   0.199  -2.6826  -2.4538  -0.9100
 FNF  H16  H  HCH2   0   0.217  -2.1448  -3.7867   0.1224
 FNF  H17  H  HCH1   0   0.231  -2.0058  -2.2084   2.0505
 FNF  H18  H  HCH1   0   0.232  -4.5833  -2.7856   0.5916
 FNF  H19  H  HOH1   0   0.457  -4.8354  -4.0214   2.4305
 FNF  H20  H  HCH2   0   0.276  -5.7691  -1.1560   1.8802
 FNF  H21  H  HCH2   0   0.268  -4.6121  -1.2898   3.1973
 FNF  H22  H  HCH1   0   0.255  -3.5593   0.5492   2.4207
 FNF  H23  H  HCR6   0   0.317  -4.1024   2.4411   1.8998
 FNF  H24  H  HCH3   0   0.247  -4.7142   5.1645  -0.2183
 FNF  H25  H  HCH3   0   0.247  -6.2127   4.9163   0.6628
 FNF  H26  H  HCH3   0   0.246  -4.6686   4.7369   1.4910
 FNF  H27  H  HNR6   0   0.425  -6.1033   0.9734  -2.1360

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.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 FNF  O1A  PA   deloc   1.496  0.020  1.496
 FNF  C6Q  C5Q  single  1.515  0.020  1.515
 FNF  PA   O2A  deloc   1.497  0.020  1.497
 FNF  PA   O5'  single  1.645  0.020  1.645
 FNF  PA   O3A  single  1.637  0.020  1.637
 FNF  C5'  O5'  single  1.410  0.020  1.410
 FNF  C5'  C4'  single  1.508  0.020  1.508
 FNF  C5Q  C4Q  single  1.527  0.020  1.527
 FNF  C5Q  O5Q  single  1.423  0.020  1.423
 FNF  O4'  C4'  single  1.417  0.020  1.417
 FNF  O4'  C1'  single  1.398  0.020  1.398
 FNF  C5M  C5   single  1.493  0.020  1.493
 FNF  C4Q  O4Q  single  1.411  0.020  1.411
 FNF  C4Q  C3Q  single  1.528  0.020  1.528
 FNF  O3A  PB   single  1.646  0.020  1.646
 FNF  C4'  C3'  single  1.529  0.020  1.529
 FNF  C5   C6   double  1.344  0.020  1.344
 FNF  C5   C4   single  1.448  0.020  1.448
 FNF  C6   N1   single  1.371  0.020  1.371
 FNF  O5Q  C1Q  single  1.397  0.020  1.397
 FNF  N1   C1'  single  1.463  0.020  1.463
 FNF  N1   C2   single  1.375  0.020  1.375
 FNF  O4   C4   double  1.218  0.020  1.218
 FNF  C1'  C2'  single  1.532  0.020  1.532
 FNF  C4   N3   single  1.383  0.020  1.383
 FNF  C3Q  N3Q  single  1.442  0.020  1.442
 FNF  C3Q  C2Q  single  1.528  0.020  1.528
 FNF  C2   N3   single  1.371  0.020  1.371
 FNF  C2   O2   double  1.213  0.020  1.213
 FNF  N3Q  C1F  single  1.337  0.020  1.337
 FNF  C3'  C2'  single  1.529  0.020  1.529
 FNF  C3'  O3'  single  1.406  0.020  1.406
 FNF  PB   O3B  single  1.659  0.020  1.659
 FNF  PB   O2B  deloc   1.496  0.020  1.496
 FNF  PB   O1B  deloc   1.493  0.020  1.493
 FNF  O3B  C1Q  single  1.395  0.020  1.395
 FNF  C1Q  C2Q  single  1.533  0.020  1.533
 FNF  O1F  C1F  double  1.219  0.020  1.219
 FNF  C2Q  O2Q  single  1.401  0.020  1.401
 FNF  C1F  H1   single  0.930  0.020  1.080
 FNF  N3Q  H2   single  0.860  0.020  1.020
 FNF  C3Q  H3   single  0.970  0.020  1.090
 FNF  C2Q  H4   single  0.970  0.020  1.090
 FNF  O2Q  H5   single  0.850  0.020  0.980
 FNF  C4Q  H6   single  0.970  0.020  1.090
 FNF  O4Q  H7   single  0.850  0.020  0.980
 FNF  C5Q  H8   single  0.970  0.020  1.090
 FNF  C6Q  H9   single  0.970  0.020  1.090
 FNF  C6Q  H10  single  0.970  0.020  1.090
 FNF  C6Q  H11  single  0.970  0.020  1.090
 FNF  C1Q  H12  single  0.970  0.020  1.090
 FNF  C5'  H15  single  0.970  0.020  1.090
 FNF  C5'  H16  single  0.970  0.020  1.090
 FNF  C4'  H17  single  0.970  0.020  1.090
 FNF  C3'  H18  single  0.970  0.020  1.090
 FNF  O3'  H19  single  0.850  0.020  0.980
 FNF  C2'  H20  single  0.970  0.020  1.090
 FNF  C2'  H21  single  0.970  0.020  1.090
 FNF  C1'  H22  single  0.970  0.020  1.090
 FNF  C6   H23  single  0.930  0.020  1.080
 FNF  C5M  H24  single  0.970  0.020  1.090
 FNF  C5M  H25  single  0.970  0.020  1.090
 FNF  C5M  H26  single  0.970  0.020  1.090
 FNF  N3   H27  single  0.860  0.020  1.020

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
 FNF  H1   C1F  N3Q  111.41  3.000
 FNF  H1   C1F  O1F  122.26  3.000
 FNF  N3Q  C1F  O1F  126.32  3.000
 FNF  H2   N3Q  C3Q  117.63  3.000
 FNF  H2   N3Q  C1F  117.39  3.000
 FNF  C3Q  N3Q  C1F  124.88  3.000
 FNF  H3   C3Q  C4Q  107.93  3.000
 FNF  H3   C3Q  C2Q  108.87  3.000
 FNF  C4Q  C3Q  C2Q  110.14  3.000
 FNF  H3   C3Q  N3Q  107.53  3.000
 FNF  C2Q  C3Q  N3Q  111.49  3.000
 FNF  C4Q  C3Q  N3Q  110.76  3.000
 FNF  H4   C2Q  C1Q  106.67  3.000
 FNF  H4   C2Q  O2Q  110.99  3.000
 FNF  C1Q  C2Q  O2Q  112.33  3.000
 FNF  H4   C2Q  C3Q  108.68  3.000
 FNF  O2Q  C2Q  C3Q  108.46  3.000
 FNF  C1Q  C2Q  C3Q  109.65  3.000
 FNF  H5   O2Q  C2Q  108.47  3.000
 FNF  H6   C4Q  C5Q  107.80  3.000
 FNF  H6   C4Q  O4Q  110.92  3.000
 FNF  C5Q  C4Q  O4Q  112.71  3.000
 FNF  H6   C4Q  C3Q  108.12  3.000
 FNF  O4Q  C4Q  C3Q  107.54  3.000
 FNF  C5Q  C4Q  C3Q  109.66  3.000
 FNF  H7   O4Q  C4Q  108.92  3.000
 FNF  H8   C5Q  O5Q  110.05  3.000
 FNF  H8   C5Q  C6Q  108.11  3.000
 FNF  O5Q  C5Q  C6Q  107.20  3.000
 FNF  H8   C5Q  C4Q  107.50  3.000
 FNF  O5Q  C5Q  C4Q  110.84  3.000
 FNF  C6Q  C5Q  C4Q  113.11  3.000
 FNF  H11  C6Q  H10  107.59  3.000
 FNF  H11  C6Q  H9   108.26  3.000
 FNF  H10  C6Q  H9   108.02  3.000
 FNF  H11  C6Q  C5Q  110.33  3.000
 FNF  H10  C6Q  C5Q  110.37  3.000
 FNF  H9   C6Q  C5Q  112.13  3.000
 FNF  C1Q  O5Q  C5Q  115.13  3.000
 FNF  H12  C1Q  O3B  110.57  3.000
 FNF  H12  C1Q  O5Q  105.14  3.000
 FNF  O3B  C1Q  O5Q  112.49  3.000
 FNF  H12  C1Q  C2Q  109.84  3.000
 FNF  O3B  C1Q  C2Q  108.31  3.000
 FNF  O5Q  C1Q  C2Q  110.47  3.000
 FNF  PB   O3B  C1Q  118.99  3.000
 FNF  O3A  PB   O1B  110.19  3.000
 FNF  O1B  PB   O2B  121.44  3.000
 FNF  O3A  PB   O2B  110.22  3.000
 FNF  O1B  PB   O3B  109.45  3.000
 FNF  O2B  PB   O3B  108.78  3.000
 FNF  O3A  PB   O3B   93.04  3.000
 FNF  PA   O3A  PB   125.00  3.000
 FNF  O5'  PA   O2A  109.06  3.000
 FNF  O5'  PA   O1A  110.01  3.000
 FNF  O2A  PA   O1A  120.50  3.000
 FNF  O5'  PA   O3A   96.91  3.000
 FNF  O2A  PA   O3A  106.81  3.000
 FNF  O1A  PA   O3A  110.94  3.000
 FNF  C5'  O5'  PA   117.39  3.000
 FNF  H16  C5'  H15  107.57  3.000
 FNF  H16  C5'  C4'  107.87  3.000
 FNF  H15  C5'  C4'  109.01  3.000
 FNF  H16  C5'  O5'  111.25  3.000
 FNF  H15  C5'  O5'  111.47  3.000
 FNF  C4'  C5'  O5'  109.57  3.000
 FNF  H17  C4'  C3'  108.36  3.000
 FNF  H17  C4'  O4'  109.60  3.000
 FNF  C3'  C4'  O4'  106.48  3.000
 FNF  H17  C4'  C5'  109.56  3.000
 FNF  C3'  C4'  C5'  112.70  3.000
 FNF  O4'  C4'  C5'  110.05  3.000
 FNF  C1'  O4'  C4'  111.13  3.000
 FNF  H18  C3'  C2'  109.89  3.000
 FNF  H18  C3'  O3'  110.66  3.000
 FNF  C2'  C3'  O3'  114.78  3.000
 FNF  H18  C3'  C4'  109.78  3.000
 FNF  O3'  C3'  C4'  108.80  3.000
 FNF  C2'  C3'  C4'  102.58  3.000
 FNF  H19  O3'  C3'  108.28  3.000
 FNF  H21  C2'  H20  107.51  3.000
 FNF  H21  C2'  C1'  108.49  3.000
 FNF  H20  C2'  C1'  113.16  3.000
 FNF  H21  C2'  C3'  109.01  3.000
 FNF  H20  C2'  C3'  113.68  3.000
 FNF  C1'  C2'  C3'  104.86  3.000
 FNF  H22  C1'  N1   104.16  3.000
 FNF  H22  C1'  C2'  109.67  3.000
 FNF  N1   C1'  C2'  115.94  3.000
 FNF  H22  C1'  O4'  110.06  3.000
 FNF  C2'  C1'  O4'  107.62  3.000
 FNF  N1   C1'  O4'  109.32  3.000
 FNF  C6   N1   C2   120.80  3.000
 FNF  C2   N1   C1'  119.95  3.000
 FNF  C6   N1   C1'  119.21  3.000
 FNF  N3   C2   O2   121.87  3.000
 FNF  O2   C2   N1   123.68  3.000
 FNF  N3   C2   N1   114.45  3.000
 FNF  H23  C6   C5   120.69  3.000
 FNF  H23  C6   N1   114.87  3.000
 FNF  C5   C6   N1   124.44  3.000
 FNF  C4   C5   C5M  118.97  3.000
 FNF  C4   C5   C6   117.83  3.000
 FNF  C5M  C5   C6   123.20  3.000
 FNF  H26  C5M  H25  107.81  3.000
 FNF  H26  C5M  H24  107.93  3.000
 FNF  H25  C5M  H24  107.19  3.000
 FNF  H26  C5M  C5   110.97  3.000
 FNF  H25  C5M  C5   111.36  3.000
 FNF  H24  C5M  C5   111.39  3.000
 FNF  O4   C4   N3   120.61  3.000
 FNF  N3   C4   C5   114.30  3.000
 FNF  O4   C4   C5   125.10  3.000
 FNF  H27  N3   C4   116.73  3.000
 FNF  H27  N3   C2   115.10  3.000
 FNF  C4   N3   C2   128.17  3.000

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
 FNF  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 FNF  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 FNF  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 FNF  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 FNF  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 FNF  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 FNF  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 FNF  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 FNF  CONST_09  H27  N3   C2   N1    180.00   0.0  0
 FNF  CONST_10  C3Q  N3Q  C1F  O1F     0.00   0.0  0
 FNF  CONST_11  H2   N3Q  C1F  O1F   180.00   0.0  0
 FNF  Var_01    H24  C5M  C5   C6    121.57  30.0  3
 FNF  Var_02    O3A  PB   O3B  C1Q   152.33  30.0  1
 FNF  Var_03    C4'  C5'  O5'  PA   -175.17  30.0  2
 FNF  Var_04    O1A  PA   O3A  PB     24.69  30.0  1

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
 FNF  chir_01  C3Q  C4Q  N3Q  C2Q  positiv
 FNF  chir_02  C2Q  O2Q  C3Q  C1Q  positiv
 FNF  chir_03  C4Q  O4Q  C3Q  C5Q  positiv
 FNF  chir_04  C5Q  O5Q  C4Q  C6Q  negativ
 FNF  chir_05  C1Q  O5Q  O3B  C2Q  positiv
 FNF  chir_08  C4'  C5'  O4'  C3'  negativ
 FNF  chir_09  C3'  O3'  C4'  C2'  positiv
 FNF  chir_10  C1'  O4'  N1   C2'  negativ

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
 FNF  plan-1  O1F  0.020
 FNF  plan-1  C1F  0.020
 FNF  plan-1  N3Q  0.020
 FNF  plan-1  C3Q  0.020
 FNF  plan-1  H1   0.020
 FNF  plan-1  H2   0.020
 FNF  plan-2  C1'  0.020
 FNF  plan-2  N1   0.020
 FNF  plan-2  C2   0.020
 FNF  plan-2  O2   0.020
 FNF  plan-2  C6   0.020
 FNF  plan-2  C5   0.020
 FNF  plan-2  C5M  0.020
 FNF  plan-2  C4   0.020
 FNF  plan-2  N3   0.020
 FNF  plan-2  O4   0.020
 FNF  plan-2  H23  0.020
 FNF  plan-2  H27  0.020

