# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 11:40:45 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C1=NC(=CN([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)F
#
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
 GE6  GE6  '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  47  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GE6
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
 GE6  C01  C  CH1   0   0.014  123.5074  125.2060  128.4498
 GE6  C02  C  CH1   0  -0.066  123.0694  126.6678  128.5342
 GE6  C03  C  CH1   0   0.185  121.5965  126.5573  128.1061
 GE6  C04  C  CH1   0  -0.007  122.7198  124.7106  127.2344
 GE6  C05  C  CH2   0  -0.192  122.4020  123.2285  127.2328
 GE6  C06  C  CR16  0  -0.111  120.1062  125.2538  129.5857
 GE6  C07  C  CR6   0   0.481  119.2984  125.2219  130.6770
 GE6  C08  C  CR6   0  -0.077  119.6175  127.4114  131.1559
 GE6  C09  C  C     0   0.506  119.2642  128.5365  132.1006
 GE6  C10  C  CR6   0   0.630  120.5056  127.5798  130.0179
 GE6  F01  F  F     0  -0.289  118.6891  124.0855  131.0162
 GE6  N01  N  NH2   0  -0.823  119.7931  129.7315  131.8298
 GE6  N02  N  NR6   0  -0.516  120.7035  126.4218  129.2827
 GE6  N03  N  N     0  -0.343  119.0647  126.2675  131.4370
 GE6  O01  O  O2    0  -0.494  121.4898  125.4277  127.3022
 GE6  O02  O  OH1   0  -0.662  123.8053  127.3720  127.5770
 GE6  O03  O  OH1   0  -0.692  124.8996  125.0500  128.3792
 GE6  O04  O  O     0  -0.474  118.5285  128.3123  133.0475
 GE6  O05  O  O     0  -0.496  121.0666  128.6190  129.6793
 GE6  O06  O  O2    0  -0.602  123.6578  122.5648  127.1063
 GE6  O07  O  O2    0  -0.696  125.4663  120.9341  127.3479
 GE6  O08  O  O     0  -0.667  123.2282  120.0882  126.4525
 GE6  O09  O  OH1   0  -0.776  123.4470  120.8095  128.9220
 GE6  O10  O  O2    0  -0.676  127.3815  120.8146  128.9430
 GE6  O11  O  OH1   0  -0.708  127.5068  121.0989  131.3754
 GE6  O12  O  OH1   0  -0.700  127.7027  118.8186  130.4185
 GE6  O13  O  O     0  -0.646  127.5332  122.3893  126.9405
 GE6  O14  O  OH1   0  -0.778  125.9585  122.8289  129.0030
 GE6  O15  O  O     0  -0.713  125.3776  119.9706  130.3580
 GE6  P01  P  P     0   1.485  123.8467  121.0091  127.4167
 GE6  P02  P  P     0   1.494  126.6311  121.8692  127.9711
 GE6  P03  P  P     0   1.514  126.8523  120.1415  130.3102
 GE6  H1   H  HCH1  0   0.292  123.1816  124.6784  129.3511
 GE6  H2   H  HCH1  0   0.297  123.1936  127.0751  129.5399
 GE6  H3   H  HCH1  0   0.311  121.2592  127.4431  127.5650
 GE6  H4   H  HCH1  0   0.278  123.2425  124.9686  126.3053
 GE6  H5   H  HCH2  0   0.279  121.7523  122.9725  126.3935
 GE6  H6   H  HCH2  0   0.244  121.9021  122.9399  128.1622
 GE6  H7   H  HCR6  0   0.346  120.2724  124.3975  128.9521
 GE6  H10  H  HNH2  0   0.405  119.5840  130.5115  132.4315
 GE6  H11  H  HNH2  0   0.422  120.3990  129.8709  131.0356
 GE6  H12  H  HOH1  0   0.477  123.7637  128.3140  127.7708
 GE6  H13  H  HOH1  0   0.484  125.2717  125.6213  127.6929
 GE6  H14  H  HOH1  0   0.500  124.1668  120.4892  129.5478
 GE6  H15  H  HOH1  0   0.518  127.1764  121.0023  132.2803
 GE6  H16  H  HOH1  0   0.516  127.3537  118.0598  129.9284
 GE6  H17  H  HOH1  0   0.524  125.5701  123.7126  128.6959

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
 GE6  O08  P01  double  1.470  0.020  1.470
 GE6  O06  P01  single  1.598  0.020  1.598
 GE6  O06  C05  single  1.426  0.020  1.426
 GE6  C04  O01  single  1.425  0.020  1.425
 GE6  C04  C05  single  1.516  0.020  1.516
 GE6  C04  C01  single  1.531  0.020  1.531
 GE6  O01  C03  single  1.391  0.020  1.391
 GE6  O02  C02  single  1.398  0.020  1.398
 GE6  O03  C01  single  1.403  0.020  1.403
 GE6  P01  O07  single  1.623  0.020  1.623
 GE6  P01  O09  single  1.570  0.020  1.570
 GE6  O07  P02  single  1.619  0.020  1.619
 GE6  C01  C02  single  1.528  0.020  1.528
 GE6  C03  C02  single  1.538  0.020  1.538
 GE6  C03  N02  single  1.483  0.020  1.483
 GE6  O13  P02  double  1.465  0.020  1.465
 GE6  O15  P03  double  1.485  0.020  1.485
 GE6  P02  O10  single  1.619  0.020  1.619
 GE6  P02  O14  single  1.561  0.020  1.561
 GE6  N02  C06  single  1.346  0.020  1.346
 GE6  N02  C10  single  1.386  0.020  1.386
 GE6  O05  C10  double  1.228  0.020  1.228
 GE6  C06  C07  double  1.358  0.020  1.358
 GE6  O10  P03  single  1.613  0.020  1.613
 GE6  C10  C08  single  1.453  0.020  1.453
 GE6  P03  O12  single  1.576  0.020  1.576
 GE6  P03  O11  single  1.575  0.020  1.575
 GE6  C07  F01  single  1.333  0.020  1.333
 GE6  C07  N03  single  1.314  0.020  1.314
 GE6  C08  N03  double  1.301  0.020  1.301
 GE6  C08  C09  single  1.511  0.020  1.511
 GE6  N01  C09  single  1.335  0.020  1.335
 GE6  C09  O04  double  1.220  0.020  1.220
 GE6  C01  H1   single  0.970  0.020  1.090
 GE6  C02  H2   single  0.970  0.020  1.090
 GE6  C03  H3   single  0.970  0.020  1.090
 GE6  C04  H4   single  0.970  0.020  1.090
 GE6  C05  H5   single  0.970  0.020  1.090
 GE6  C05  H6   single  0.970  0.020  1.090
 GE6  C06  H7   single  0.930  0.020  1.080
 GE6  N01  H10  single  0.860  0.020  1.020
 GE6  N01  H11  single  0.860  0.020  1.020
 GE6  O02  H12  single  0.850  0.020  0.980
 GE6  O03  H13  single  0.850  0.020  0.980
 GE6  O09  H14  single  0.850  0.020  0.980
 GE6  O11  H15  single  0.850  0.020  0.980
 GE6  O12  H16  single  0.850  0.020  0.980
 GE6  O14  H17  single  0.850  0.020  0.980

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
 GE6  H1   C01  O03  106.46  3.000
 GE6  H1   C01  C04  110.17  3.000
 GE6  O03  C01  C04  115.77  3.000
 GE6  H1   C01  C02  109.29  3.000
 GE6  O03  C01  C02  113.19  3.000
 GE6  C04  C01  C02  101.88  3.000
 GE6  H2   C02  O02  112.51  3.000
 GE6  H2   C02  C03  113.08  3.000
 GE6  O02  C02  C03  110.48  3.000
 GE6  H2   C02  C01  112.02  3.000
 GE6  C03  C02  C01  100.98  3.000
 GE6  O02  C02  C01  107.04  3.000
 GE6  H3   C03  O01  110.42  3.000
 GE6  H3   C03  N02  106.34  3.000
 GE6  O01  C03  N02  109.76  3.000
 GE6  H3   C03  C02  112.07  3.000
 GE6  N02  C03  C02  111.24  3.000
 GE6  O01  C03  C02  107.03  3.000
 GE6  H4   C04  O01  109.47  3.000
 GE6  H4   C04  C05  109.21  3.000
 GE6  O01  C04  C05  108.12  3.000
 GE6  H4   C04  C01  110.56  3.000
 GE6  C05  C04  C01  115.16  3.000
 GE6  O01  C04  C01  104.09  3.000
 GE6  H6   C05  H5   108.61  3.000
 GE6  H6   C05  O06  110.79  3.000
 GE6  H5   C05  O06  110.29  3.000
 GE6  H6   C05  C04  110.66  3.000
 GE6  H5   C05  C04  110.78  3.000
 GE6  O06  C05  C04  105.70  3.000
 GE6  H7   C06  N02  119.23  3.000
 GE6  H7   C06  C07  123.04  3.000
 GE6  N02  C06  C07  117.72  3.000
 GE6  N03  C07  F01  116.74  3.000
 GE6  N03  C07  C06  123.51  3.000
 GE6  F01  C07  C06  119.76  3.000
 GE6  N03  C08  C10  122.05  3.000
 GE6  N03  C08  C09  114.85  3.000
 GE6  C10  C08  C09  123.11  3.000
 GE6  O04  C09  N01  124.14  3.000
 GE6  O04  C09  C08  119.30  3.000
 GE6  N01  C09  C08  116.56  3.000
 GE6  O05  C10  N02  119.70  3.000
 GE6  O05  C10  C08  126.36  3.000
 GE6  N02  C10  C08  113.95  3.000
 GE6  H11  N01  H10  119.22  3.000
 GE6  H11  N01  C09  121.44  3.000
 GE6  H10  N01  C09  119.34  3.000
 GE6  C10  N02  C06  122.83  3.000
 GE6  C10  N02  C03  115.50  3.000
 GE6  C06  N02  C03  121.66  3.000
 GE6  C08  N03  C07  119.95  3.000
 GE6  C04  O01  C03  111.71  3.000
 GE6  H12  O02  C02  109.41  3.000
 GE6  H13  O03  C01  110.59  3.000
 GE6  P01  O06  C05  122.69  3.000
 GE6  P02  O07  P01  132.47  3.000
 GE6  H14  O09  P01  117.04  3.000
 GE6  P03  O10  P02  128.95  3.000
 GE6  H15  O11  P03  115.45  3.000
 GE6  H16  O12  P03  115.37  3.000
 GE6  H17  O14  P02  120.07  3.000
 GE6  O09  P01  O08  116.24  3.000
 GE6  O09  P01  O07  106.79  3.000
 GE6  O08  P01  O07  111.30  3.000
 GE6  O09  P01  O06  106.26  3.000
 GE6  O07  P01  O06   98.90  3.000
 GE6  O08  P01  O06  115.66  3.000
 GE6  O14  P02  O13  120.79  3.000
 GE6  O14  P02  O10  101.73  3.000
 GE6  O13  P02  O10  111.60  3.000
 GE6  O14  P02  O07  107.43  3.000
 GE6  O10  P02  O07  100.86  3.000
 GE6  O13  P02  O07  112.17  3.000
 GE6  O15  P03  O12  115.90  3.000
 GE6  O12  P03  O11  103.86  3.000
 GE6  O15  P03  O11  117.44  3.000
 GE6  O11  P03  O10  100.56  3.000
 GE6  O12  P03  O10  103.38  3.000
 GE6  O15  P03  O10  113.64  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
 GE6  CONST_01  C08  C10  N02  C03  180.00   0.0  0
 GE6  CONST_02  C08  C10  N02  C06    0.00   0.0  0
 GE6  CONST_03  O05  C10  N02  C03    0.00   0.0  0
 GE6  CONST_04  O05  C10  N02  C06  180.00   0.0  0
 GE6  CONST_05  H10  N01  C09  C08  180.00   0.0  0
 GE6  CONST_06  H11  N01  C09  C08    0.00   0.0  0
 GE6  Var_01    N01  C09  C08  C10    1.24  30.0  2
 GE6  Var_02    O08  P01  O06  C05   70.39  30.0  3
 GE6  Var_03    H5   C05  O06  P01  -75.63  30.0  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
 GE6  chir_01  C01  C04  O03  C02  negativ
 GE6  chir_02  C02  O02  C01  C03  positiv
 GE6  chir_03  C03  O01  N02  C02  negativ
 GE6  chir_04  C04  O01  C05  C01  positiv
 GE6  chir_05  P01  O06  O07  O09  both
 GE6  chir_06  P02  O13  O10  O14  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
 GE6  plan-1  C03  0.020
 GE6  plan-1  C06  0.020
 GE6  plan-1  C07  0.020
 GE6  plan-1  C08  0.020
 GE6  plan-1  C09  0.020
 GE6  plan-1  C10  0.020
 GE6  plan-1  F01  0.020
 GE6  plan-1  N02  0.020
 GE6  plan-1  N03  0.020
 GE6  plan-1  O05  0.020
 GE6  plan-1  H7   0.020
 GE6  plan-2  C08  0.020
 GE6  plan-2  C09  0.020
 GE6  plan-2  N01  0.020
 GE6  plan-2  O04  0.020
 GE6  plan-2  H10  0.020
 GE6  plan-2  H11  0.020

