# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 22 13:15:54 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@H](CO)[C@@H](F)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
#
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
 G4F  G4F  '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate'  ligand  61  39  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G4F
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
 G4F  O13  O  O      0  -0.797  -0.3200   2.5440   2.4479
 G4F  P    P  P      0   1.368   0.5549   3.1977   1.4237
 G4F  O4   O  OP    -1  -0.786   1.0271   4.6060   1.6058
 G4F  O5   O  O2     0  -0.737   1.8961   2.3021   1.1431
 G4F  P1   P  P      0   1.347   2.0418   0.6827   1.4096
 G4F  O11  O  OP    -1  -0.747   0.9438  -0.0608   0.7280
 G4F  O12  O  O      0  -0.795   2.3962   0.4335   2.8411
 G4F  O6   O  O2     0  -0.636   3.4238   0.5709   0.4915
 G4F  C8   C  CH1    0   0.241   4.4362  -0.3143   0.8499
 G4F  O8   O  O2     0  -0.497   4.0350  -1.6509   0.7793
 G4F  C10  C  CH1    0  -0.051   3.6253  -2.0990  -0.4991
 G4F  C11  C  CH2    0  -0.162   3.2854  -3.5703  -0.3845
 G4F  O9   O  OH1    0  -0.664   2.1672  -3.7274   0.4524
 G4F  C12  C  CH1    0   0.171   4.7512  -1.8810  -1.5090
 G4F  F    F  F      0  -0.380   4.2587  -2.1735  -2.7858
 G4F  C13  C  CH1    0  -0.022   5.2427  -0.4432  -1.5022
 G4F  O10  O  OH1    0  -0.668   6.3577  -0.2581  -2.3377
 G4F  C9   C  CH1    0  -0.027   5.6217  -0.0464  -0.0830
 G4F  O7   O  OH1    0  -0.669   6.7352  -0.8141   0.2999
 G4F  O3   O  O2     0  -0.623  -0.1235   3.0592  -0.0700
 G4F  C7   C  CH2    0  -0.152  -1.5199   3.1485  -0.2150
 G4F  C6   C  CR15   0  -0.002  -1.9668   2.3595  -1.4259
 G4F  C5   C  CR15   0  -0.049  -3.4927   2.3451  -1.5478
 G4F  O2   O  OH1    0  -0.659  -3.9235   3.3555  -2.4196
 G4F  C4   C  CR15   0  -0.034  -3.7793   0.9304  -2.0636
 G4F  O1   O  OH1    0  -0.669  -3.5770   0.8511  -3.4485
 G4F  O14  O  O      0  -0.474  -1.5669   0.9945  -1.3297
 G4F  C3   C  CR15   0   0.171  -2.6570   0.1394  -1.3961
 G4F  N1   N  NR5    0  -0.547  -3.0221  -0.2940  -0.0444
 G4F  C2   C  CR15   0   0.063  -2.3439  -0.0452   1.1271
 G4F  N    N  N      0  -0.456  -2.8834  -0.6384   2.1503
 G4F  C14  C  CR56   0   0.500  -4.0435  -1.1350   0.2711
 G4F  C1   C  CR56   0  -0.089  -3.9517  -1.3264   1.6373
 G4F  N2   N  N      0  -0.515  -4.9319  -1.6651  -0.5845
 G4F  C15  C  CR6    0   0.680  -5.8098  -2.4418  -0.0024
 G4F  N3   N  NH2    0  -0.832  -6.7348  -3.0787  -0.7381
 G4F  N4   N  NR16   0  -0.726  -5.8181  -2.6782   1.3421
 G4F  C    C  CR6    0   0.497  -4.9098  -2.1640   2.2765
 G4F  O    O  O      0  -0.477  -5.0082  -2.4528   3.4582
 G4F  H3   H  HCH1   0   0.240   4.7391  -0.1638   1.8928
 G4F  H4   H  HCH1   0   0.238   2.7348  -1.5487  -0.8300
 G4F  H5   H  HCH2   0   0.208   3.0919  -3.9562  -1.3922
 G4F  H6   H  HCH2   0   0.195   4.1643  -4.1074   0.0001
 G4F  H7   H  HOH1   0   0.455   1.9320  -4.6593   0.4560
 G4F  H8   H  HCH1   0   0.218   5.5789  -2.5716  -1.3201
 G4F  H9   H  HCH1   0   0.238   4.4091   0.1998  -1.8146
 G4F  H10  H  HOH1   0   0.455   6.0595  -0.2914  -3.2516
 G4F  H11  H  HCH1   0   0.238   5.8485   1.0276  -0.0586
 G4F  H12  H  HOH1   0   0.456   7.0530  -0.4921   1.1492
 G4F  H13  H  HCH2   0   0.212  -2.0382   2.7747   0.6735
 G4F  H14  H  HCH2   0   0.222  -1.8375   4.1894  -0.3589
 G4F  H15  H  HCR5   0   0.245  -1.5203   2.7815  -2.3333
 G4F  H16  H  HCR5   0   0.247  -3.9461   2.4624  -0.5555
 G4F  H17  H  HOH1   0   0.468  -4.8502   3.5452  -2.2402
 G4F  H18  H  HCR5   0   0.259  -4.7747   0.5758  -1.7781
 G4F  H19  H  HOH1   0   0.450  -3.8744   1.6855  -3.8327
 G4F  H20  H  HCR5   0   0.282  -2.3903  -0.7518  -1.9710
 G4F  H21  H  HCR5   0   0.330  -1.4473   0.5552   1.1577
 G4F  H22  H  HNH2   0   0.411  -6.8474  -2.7852  -1.6937
 G4F  H23  H  HNH2   0   0.413  -7.5419  -3.4922  -0.3036
 G4F  H24  H  HNR6   0   0.424  -6.5339  -3.2874   1.7174

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
 G4F  C2   N    aromatic  1.300  0.020  1.300
 G4F  C2   N1   aromatic  1.376  0.020  1.376
 G4F  O14  C6   single    1.426  0.020  1.426
 G4F  O14  C3   single    1.387  0.020  1.387
 G4F  N    C1   aromatic  1.370  0.020  1.370
 G4F  N1   C3   single    1.466  0.020  1.466
 G4F  N1   C14  aromatic  1.360  0.020  1.360
 G4F  C6   C7   single    1.513  0.020  1.513
 G4F  C6   C5   single    1.531  0.020  1.531
 G4F  C3   C4   single    1.527  0.020  1.527
 G4F  C7   O3   single    1.407  0.020  1.407
 G4F  C1   C14  aromatic  1.383  0.020  1.383
 G4F  C1   C    single    1.424  0.020  1.424
 G4F  C14  N2   single    1.343  0.020  1.343
 G4F  O2   C5   single    1.402  0.020  1.402
 G4F  O13  P    deloc     1.497  0.020  1.497
 G4F  O    C    double    1.220  0.020  1.220
 G4F  C    N4   single    1.401  0.020  1.401
 G4F  C5   C4   single    1.533  0.020  1.533
 G4F  C4   O1   single    1.402  0.020  1.402
 G4F  N2   C15  double    1.309  0.020  1.309
 G4F  O3   P    single    1.646  0.020  1.646
 G4F  N4   C15  single    1.365  0.020  1.365
 G4F  P    O5   single    1.637  0.020  1.637
 G4F  P    O4   deloc     1.496  0.020  1.496
 G4F  C15  N3   single    1.343  0.020  1.343
 G4F  O12  P1   deloc     1.496  0.020  1.496
 G4F  O5   P1   single    1.648  0.020  1.648
 G4F  O8   C8   single    1.397  0.020  1.397
 G4F  O8   C10  single    1.415  0.020  1.415
 G4F  O9   C11  single    1.406  0.020  1.406
 G4F  P1   O11  deloc     1.491  0.020  1.491
 G4F  P1   O6   single    1.663  0.020  1.663
 G4F  C11  C10  single    1.514  0.020  1.514
 G4F  C8   O6   single    1.392  0.020  1.392
 G4F  C8   C9   single    1.532  0.020  1.532
 G4F  C10  C12  single    1.528  0.020  1.528
 G4F  O7   C9   single    1.406  0.020  1.406
 G4F  C9   C13  single    1.522  0.020  1.522
 G4F  C12  C13  single    1.520  0.020  1.520
 G4F  C12  F    single    1.399  0.020  1.399
 G4F  C13  O10  single    1.406  0.020  1.406
 G4F  C8   H3   single    0.970  0.020  1.090
 G4F  C10  H4   single    0.970  0.020  1.090
 G4F  C11  H5   single    0.970  0.020  1.090
 G4F  C11  H6   single    0.970  0.020  1.090
 G4F  O9   H7   single    0.850  0.020  0.980
 G4F  C12  H8   single    0.970  0.020  1.090
 G4F  C13  H9   single    0.970  0.020  1.090
 G4F  O10  H10  single    0.850  0.020  0.980
 G4F  C9   H11  single    0.970  0.020  1.090
 G4F  O7   H12  single    0.850  0.020  0.980
 G4F  C7   H13  single    0.970  0.020  1.090
 G4F  C7   H14  single    0.970  0.020  1.090
 G4F  C6   H15  single    0.970  0.020  1.090
 G4F  C5   H16  single    0.970  0.020  1.090
 G4F  O2   H17  single    0.850  0.020  0.980
 G4F  C4   H18  single    0.970  0.020  1.090
 G4F  O1   H19  single    0.850  0.020  0.980
 G4F  C3   H20  single    0.970  0.020  1.090
 G4F  C2   H21  single    0.930  0.020  1.080
 G4F  N3   H22  single    0.890  0.020  1.040
 G4F  N3   H23  single    0.890  0.020  1.040
 G4F  N4   H24  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
 G4F  O3   P    O5    97.82  3.000
 G4F  O5   P    O4   106.10  3.000
 G4F  O3   P    O4   108.64  3.000
 G4F  O4   P    O13  120.80  3.000
 G4F  O5   P    O13  110.92  3.000
 G4F  O3   P    O13  110.06  3.000
 G4F  P1   O5   P    125.63  3.000
 G4F  O6   P1   O12  108.68  3.000
 G4F  O6   P1   O11  109.03  3.000
 G4F  O12  P1   O11  121.94  3.000
 G4F  O6   P1   O5    92.88  3.000
 G4F  O11  P1   O5   110.55  3.000
 G4F  O12  P1   O5   109.85  3.000
 G4F  C8   O6   P1   120.34  3.000
 G4F  H3   C8   C9   109.97  3.000
 G4F  H3   C8   O8   104.99  3.000
 G4F  C9   C8   O8   111.02  3.000
 G4F  H3   C8   O6   111.01  3.000
 G4F  C9   C8   O6   107.15  3.000
 G4F  O8   C8   O6   112.74  3.000
 G4F  C10  O8   C8   115.57  3.000
 G4F  H4   C10  C12  109.09  3.000
 G4F  H4   C10  C11  109.13  3.000
 G4F  C12  C10  C11  110.74  3.000
 G4F  H4   C10  O8   110.38  3.000
 G4F  C12  C10  O8   109.79  3.000
 G4F  C11  C10  O8   107.71  3.000
 G4F  H6   C11  H5   106.90  3.000
 G4F  H6   C11  O9   111.91  3.000
 G4F  H5   C11  O9   111.56  3.000
 G4F  H6   C11  C10  108.77  3.000
 G4F  H5   C11  C10  108.18  3.000
 G4F  O9   C11  C10  109.41  3.000
 G4F  H7   O9   C11  107.77  3.000
 G4F  H8   C12  C13  110.59  3.000
 G4F  H8   C12  F    106.97  3.000
 G4F  C13  C12  F    108.41  3.000
 G4F  H8   C12  C10  110.68  3.000
 G4F  F    C12  C10  108.29  3.000
 G4F  C13  C12  C10  111.74  3.000
 G4F  H9   C13  C9   107.56  3.000
 G4F  H9   C13  O10  110.85  3.000
 G4F  C9   C13  O10  108.81  3.000
 G4F  H9   C13  C12  107.89  3.000
 G4F  O10  C13  C12  112.24  3.000
 G4F  C9   C13  C12  109.36  3.000
 G4F  H10  O10  C13  108.32  3.000
 G4F  H11  C9   O7   111.38  3.000
 G4F  H11  C9   C13  109.10  3.000
 G4F  O7   C9   C13  108.00  3.000
 G4F  H11  C9   C8   108.50  3.000
 G4F  C13  C9   C8   109.24  3.000
 G4F  O7   C9   C8   110.58  3.000
 G4F  H12  O7   C9   108.63  3.000
 G4F  C7   O3   P    119.81  3.000
 G4F  H14  C7   H13  107.05  3.000
 G4F  H14  C7   C6   107.70  3.000
 G4F  H13  C7   C6   109.38  3.000
 G4F  H14  C7   O3   111.16  3.000
 G4F  H13  C7   O3   111.40  3.000
 G4F  C6   C7   O3   110.04  3.000
 G4F  H15  C6   O14  108.08  3.000
 G4F  H15  C6   C5   110.11  3.000
 G4F  O14  C6   C5   106.02  3.000
 G4F  H15  C6   C7   109.98  3.000
 G4F  C5   C6   C7   111.29  3.000
 G4F  O14  C6   C7   111.25  3.000
 G4F  H16  C5   C4   109.01  3.000
 G4F  H16  C5   O2   110.99  3.000
 G4F  C4   C5   O2   113.47  3.000
 G4F  H16  C5   C6   109.80  3.000
 G4F  C4   C5   C6   102.82  3.000
 G4F  O2   C5   C6   110.42  3.000
 G4F  H17  O2   C5   108.78  3.000
 G4F  H18  C4   C3   112.74  3.000
 G4F  H18  C4   O1   111.75  3.000
 G4F  C3   C4   O1   107.25  3.000
 G4F  H18  C4   C5   112.41  3.000
 G4F  O1   C4   C5   110.96  3.000
 G4F  C3   C4   C5   101.17  3.000
 G4F  H19  O1   C4   107.44  3.000
 G4F  C3   O14  C6   111.51  3.000
 G4F  H20  C3   N1   107.73  3.000
 G4F  H20  C3   O14  109.63  3.000
 G4F  N1   C3   O14  109.51  3.000
 G4F  H20  C3   C4   111.82  3.000
 G4F  N1   C3   C4   111.92  3.000
 G4F  O14  C3   C4   106.21  3.000
 G4F  C14  N1   C2   106.52  3.000
 G4F  C14  N1   C3   125.72  3.000
 G4F  C2   N1   C3   127.50  3.000
 G4F  H21  C2   N    125.19  3.000
 G4F  H21  C2   N1   122.27  3.000
 G4F  N    C2   N1   112.52  3.000
 G4F  C1   N    C2   104.95  3.000
 G4F  N2   C14  C1   128.25  3.000
 G4F  N2   C14  N1   126.38  3.000
 G4F  C1   C14  N1   105.37  3.000
 G4F  C    C1   C14  118.70  3.000
 G4F  C    C1   N    130.67  3.000
 G4F  C14  C1   N    110.62  3.000
 G4F  C15  N2   C14  113.25  3.000
 G4F  N4   C15  N3   116.96  3.000
 G4F  N3   C15  N2   120.00  3.000
 G4F  N4   C15  N2   123.02  3.000
 G4F  H23  N3   H22  116.14  3.000
 G4F  H23  N3   C15  120.75  3.000
 G4F  H22  N3   C15  117.34  3.000
 G4F  H24  N4   C    115.60  3.000
 G4F  H24  N4   C15  118.28  3.000
 G4F  C    N4   C15  126.12  3.000
 G4F  O    C    N4   120.45  3.000
 G4F  N4   C    C1   110.65  3.000
 G4F  O    C    C1   128.90  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
 G4F  CONST_01  C1   N    C2   N1      0.00   0.0  0
 G4F  CONST_02  N    C1   C14  N1      0.00   0.0  0
 G4F  CONST_03  C14  C1   N    C2      0.00   0.0  0
 G4F  CONST_04  C1   C14  N1   C2      0.00   0.0  0
 G4F  CONST_05  C14  N1   C2   N       0.00   0.0  0
 G4F  CONST_06  N    C2   N1   C3    180.00   0.0  0
 G4F  CONST_07  C1   C14  N1   C3    180.00   0.0  0
 G4F  CONST_08  N2   C14  N1   C3      0.00   0.0  0
 G4F  CONST_09  N4   C15  N2   C14     0.00   0.0  0
 G4F  CONST_10  C15  N4   C    C1      0.00   0.0  0
 G4F  CONST_11  C    N4   C15  N2      0.00   0.0  0
 G4F  CONST_12  N3   C15  N2   C14   180.00   0.0  0
 G4F  CONST_13  O    C    N4   C15   180.00   0.0  0
 G4F  CONST_14  C    N4   C15  N3    180.00   0.0  0
 G4F  CONST_15  H21  C2   N1   C3      0.00   0.0  0
 G4F  CONST_16  H24  N4   C    C1    180.00   0.0  0
 G4F  CONST_17  H22  N3   C15  N2      0.00   0.0  0
 G4F  CONST_18  H23  N3   C15  N2    180.00   0.0  0
 G4F  Var_01    C6   C7   O3   P    -152.27  30.0  2
 G4F  Var_02    O12  P1   O5   P     -84.25  30.0  3
 G4F  Var_03    O3   P    O5   P1    -91.51  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
 G4F  chir_03  C8   O8   O6   C9   positiv
 G4F  chir_04  C10  O8   C11  C12  positiv
 G4F  chir_05  C12  F    C13  C10  negativ
 G4F  chir_06  C13  O10  C9   C12  positiv
 G4F  chir_07  C9   O7   C13  C8   negativ
 G4F  chir_08  C6   O14  C7   C5   positiv
 G4F  chir_09  C5   O2   C6   C4   positiv
 G4F  chir_10  C4   O1   C5   C3   positiv
 G4F  chir_11  C3   O14  N1   C4   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
 G4F  plan-1  C3   0.020
 G4F  plan-1  N1   0.020
 G4F  plan-1  C2   0.020
 G4F  plan-1  N    0.020
 G4F  plan-1  C14  0.020
 G4F  plan-1  C1   0.020
 G4F  plan-1  N2   0.020
 G4F  plan-1  C15  0.020
 G4F  plan-1  N3   0.020
 G4F  plan-1  N4   0.020
 G4F  plan-1  C    0.020
 G4F  plan-1  O    0.020
 G4F  plan-1  H21  0.020
 G4F  plan-1  H22  0.020
 G4F  plan-1  H23  0.020
 G4F  plan-1  H24  0.020

