# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 14:46:27 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C(=O)Nc3ccccc23
#
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
 NZI  NZI  '[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate'  ligand  47  30  .  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
;

data_comp_NZI
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
 NZI  N    N  NR5   0  -0.639  19.5163  -19.3011   -6.9858
 NZI  C    C  CR15  0  -0.021  18.5634  -20.6983  -10.2425
 NZI  O    O  OH1   0  -0.669  19.0096  -22.0305  -10.2859
 NZI  C1   C  CH2   0  -0.535  18.1679  -20.3848   -8.8090
 NZI  C10  C  CR16  0  -0.277  18.3505  -15.5292   -5.7911
 NZI  C11  C  CR16  0  -0.306  18.9709  -16.4407   -4.9423
 NZI  C2   C  CR15  0   0.228  19.5235  -20.0819   -8.1853
 NZI  C3   C  CR15  0  -0.025  19.7100  -19.6952  -10.4685
 NZI  C4   C  CH2   0  -0.214  19.1869  -18.4377  -11.1321
 NZI  C5   C  CR5   0   0.664  20.0863  -19.7651   -5.8085
 NZI  C6   C  CR56  0   0.316  19.3119  -17.6705   -5.4695
 NZI  C7   C  CR56  0   0.332  19.0466  -18.0060   -6.8019
 NZI  C8   C  CR16  0  -0.290  18.4362  -17.0939   -7.6436
 NZI  C9   C  CR16  0  -0.272  18.0898  -15.8517   -7.1180
 NZI  N1   N  NR15  0  -0.749  19.9333  -18.7588   -4.9000
 NZI  O1   O  O     0  -0.496  20.2482  -19.3982   -9.1909
 NZI  O10  O  OH1   0  -0.759  19.0360  -14.0030  -14.6339
 NZI  O11  O  OH1   0  -0.714  17.6385  -12.0471  -14.2946
 NZI  O12  O  O     0  -0.495  20.6067  -20.8498   -5.6296
 NZI  O2   O  O2    0  -0.556  20.2196  -17.4431  -11.0591
 NZI  O3   O  OH1   0  -0.688  21.3183  -15.3105  -11.0589
 NZI  O4   O  O     0  -0.713  19.8915  -15.9521  -13.1688
 NZI  O5   O  O2    0  -0.685  18.8038  -15.3505  -10.9267
 NZI  O6   O  OH1   0  -0.697  16.6750  -14.3724  -10.3109
 NZI  O7   O  O     0  -0.661  16.7018  -16.2069  -12.1961
 NZI  O8   O  O2    0  -0.696  17.6663  -13.8011  -12.5199
 NZI  O9   O  O     0  -0.683  16.4337  -14.3163  -14.7478
 NZI  P    P  P     0   1.533  20.0676  -16.0154  -11.6962
 NZI  P1   P  P     0   1.489  17.3443  -15.0477  -11.5687
 NZI  P2   P  P     0   1.450  17.5880  -13.6246  -14.1558
 NZI  H    H  HCR5  0   0.258  17.7407  -20.5285  -10.9478
 NZI  H3   H  HOH1  0   0.457  19.2906  -22.2356  -11.1834
 NZI  H4   H  HCH2  0   0.269  17.5039  -19.5208   -8.7741
 NZI  H5   H  HCH2  0   0.285  17.6605  -21.2155   -8.3207
 NZI  H15  H  HCR6  0   0.259  18.0690  -14.5561   -5.4117
 NZI  H16  H  HCR6  0   0.271  19.1814  -16.1972   -3.9095
 NZI  H1   H  HCR5  0   0.259  20.0266  -21.0162   -7.9235
 NZI  H2   H  HCR5  0   0.268  20.4951  -20.1296  -11.0971
 NZI  H7   H  HCH2  0   0.282  18.9347  -18.6522  -12.1723
 NZI  H6   H  HCH2  0   0.247  18.2853  -18.0741  -10.6324
 NZI  H13  H  HCR6  0   0.245  18.2154  -17.3168   -8.6749
 NZI  H14  H  HCR6  0   0.254  17.6110  -15.1252   -7.7601
 NZI  H12  H  HNR5  0   0.422  20.2593  -18.8236   -3.9487
 NZI  H17  H  HOH1  0   0.508  16.7718  -11.6359  -14.4170
 NZI  H8   H  HOH1  0   0.521  21.6567  -14.5419  -11.5412
 NZI  H9   H  HOH1  0   0.521  15.7413  -14.5957  -10.1849
 NZI  H11  H  HOH1  0   0.503  19.4464  -14.7778  -14.1587

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
 NZI  N    C2   single    1.431  0.020  1.431
 NZI  N    C5   single    1.388  0.020  1.388
 NZI  N    C7   single    1.390  0.020  1.390
 NZI  C    O    single    1.406  0.020  1.406
 NZI  C    C1   single    1.520  0.020  1.520
 NZI  C    C3   single    1.540  0.020  1.540
 NZI  C1   C2   single    1.523  0.020  1.523
 NZI  C10  C11  aromatic  1.391  0.020  1.391
 NZI  C10  C9   aromatic  1.390  0.020  1.390
 NZI  C11  C6   aromatic  1.381  0.020  1.381
 NZI  C2   O1   single    1.416  0.020  1.416
 NZI  C3   C4   single    1.515  0.020  1.515
 NZI  C3   O1   single    1.418  0.020  1.418
 NZI  C4   O2   single    1.436  0.020  1.436
 NZI  C5   N1   single    1.364  0.020  1.364
 NZI  C5   O12  double    1.216  0.020  1.216
 NZI  C6   C7   aromatic  1.399  0.020  1.399
 NZI  C6   N1   single    1.377  0.020  1.377
 NZI  C7   C8   aromatic  1.383  0.020  1.383
 NZI  C8   C9   aromatic  1.393  0.020  1.393
 NZI  O10  P2   single    1.571  0.020  1.571
 NZI  O11  P2   single    1.584  0.020  1.584
 NZI  O2   P    single    1.571  0.020  1.571
 NZI  O3   P    single    1.571  0.020  1.571
 NZI  O4   P    double    1.484  0.020  1.484
 NZI  O5   P    single    1.622  0.020  1.622
 NZI  O5   P1   single    1.623  0.020  1.623
 NZI  O6   P1   single    1.577  0.020  1.577
 NZI  O7   P1   double    1.466  0.020  1.466
 NZI  O8   P1   single    1.601  0.020  1.601
 NZI  O8   P2   single    1.647  0.020  1.647
 NZI  O9   P2   double    1.470  0.020  1.470
 NZI  C    H    single    0.970  0.020  1.090
 NZI  O    H3   single    0.850  0.020  0.980
 NZI  C1   H4   single    0.970  0.020  1.090
 NZI  C1   H5   single    0.970  0.020  1.090
 NZI  C10  H15  single    0.930  0.020  1.080
 NZI  C11  H16  single    0.930  0.020  1.080
 NZI  C2   H1   single    0.970  0.020  1.090
 NZI  C3   H2   single    0.970  0.020  1.090
 NZI  C4   H7   single    0.970  0.020  1.090
 NZI  C4   H6   single    0.970  0.020  1.090
 NZI  C8   H13  single    0.930  0.020  1.080
 NZI  C9   H14  single    0.930  0.020  1.080
 NZI  N1   H12  single    0.860  0.020  1.020
 NZI  O10  H11  single    0.850  0.020  0.980
 NZI  O11  H17  single    0.850  0.020  0.980
 NZI  O3   H8   single    0.850  0.020  0.980
 NZI  O6   H9   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
 NZI  C7   N    C5   109.76  3.000
 NZI  C7   N    C2   128.39  3.000
 NZI  C5   N    C2   121.77  3.000
 NZI  H    C    C3   111.29  3.000
 NZI  H    C    C1   112.30  3.000
 NZI  C3   C    C1   101.41  3.000
 NZI  H    C    O    111.41  3.000
 NZI  C3   C    O    112.11  3.000
 NZI  C1   C    O    107.89  3.000
 NZI  H3   O    C    108.87  3.000
 NZI  H5   C1   H4   107.85  3.000
 NZI  H5   C1   C2   112.51  3.000
 NZI  H4   C1   C2   111.81  3.000
 NZI  H5   C1   C    112.76  3.000
 NZI  H4   C1   C    110.62  3.000
 NZI  C2   C1   C    101.28  3.000
 NZI  H15  C10  C9   119.65  3.000
 NZI  H15  C10  C11  119.43  3.000
 NZI  C9   C10  C11  120.92  3.000
 NZI  H16  C11  C6   121.13  3.000
 NZI  H16  C11  C10  121.45  3.000
 NZI  C6   C11  C10  117.42  3.000
 NZI  H1   C2   O1   110.33  3.000
 NZI  H1   C2   C1   109.75  3.000
 NZI  O1   C2   C1   105.12  3.000
 NZI  H1   C2   N    105.54  3.000
 NZI  O1   C2   N    109.54  3.000
 NZI  C1   C2   N    116.57  3.000
 NZI  H2   C3   O1   109.15  3.000
 NZI  H2   C3   C4   108.98  3.000
 NZI  O1   C3   C4   110.61  3.000
 NZI  H2   C3   C    111.06  3.000
 NZI  O1   C3   C    106.66  3.000
 NZI  C4   C3   C    110.36  3.000
 NZI  H6   C4   H7   108.08  3.000
 NZI  H6   C4   O2   109.85  3.000
 NZI  H7   C4   O2   110.54  3.000
 NZI  H6   C4   C3   111.14  3.000
 NZI  H7   C4   C3   109.51  3.000
 NZI  O2   C4   C3   107.72  3.000
 NZI  O12  C5   N1   127.43  3.000
 NZI  O12  C5   N    126.77  3.000
 NZI  N1   C5   N    105.80  3.000
 NZI  N1   C6   C7   106.85  3.000
 NZI  N1   C6   C11  131.12  3.000
 NZI  C7   C6   C11  122.03  3.000
 NZI  C8   C7   C6   120.33  3.000
 NZI  C8   C7   N    133.09  3.000
 NZI  C6   C7   N    106.58  3.000
 NZI  H13  C8   C9   119.64  3.000
 NZI  H13  C8   C7   122.43  3.000
 NZI  C9   C8   C7   117.93  3.000
 NZI  H14  C9   C8   119.04  3.000
 NZI  H14  C9   C10  119.59  3.000
 NZI  C8   C9   C10  121.37  3.000
 NZI  H12  N1   C6   125.98  3.000
 NZI  H12  N1   C5   123.02  3.000
 NZI  C6   N1   C5   110.99  3.000
 NZI  C3   O1   C2   110.16  3.000
 NZI  H11  O10  P2   114.92  3.000
 NZI  H17  O11  P2   113.94  3.000
 NZI  P    O2   C4   122.65  3.000
 NZI  H8   O3   P    115.61  3.000
 NZI  P1   O5   P    126.12  3.000
 NZI  H9   O6   P1   114.48  3.000
 NZI  P2   O8   P1   131.61  3.000
 NZI  O5   P    O4   111.14  3.000
 NZI  O5   P    O3   104.12  3.000
 NZI  O4   P    O3   118.55  3.000
 NZI  O5   P    O2   104.80  3.000
 NZI  O4   P    O2   116.91  3.000
 NZI  O3   P    O2    99.57  3.000
 NZI  O8   P1   O7   116.71  3.000
 NZI  O8   P1   O6   103.05  3.000
 NZI  O7   P1   O6   119.60  3.000
 NZI  O8   P1   O5   101.51  3.000
 NZI  O7   P1   O5   114.57  3.000
 NZI  O6   P1   O5    98.40  3.000
 NZI  O9   P2   O8   112.76  3.000
 NZI  O9   P2   O11  117.27  3.000
 NZI  O8   P2   O11  101.08  3.000
 NZI  O9   P2   O10  119.20  3.000
 NZI  O8   P2   O10  103.45  3.000
 NZI  O11  P2   O10  100.59  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
 NZI  CONST_01  C7   C6   C11  C10    0.00   0.0  0
 NZI  CONST_02  C7   C8   C9   C10    0.00   0.0  0
 NZI  CONST_03  C8   C9   C10  C11    0.00   0.0  0
 NZI  CONST_04  C8   C7   C6   C11    0.00   0.0  0
 NZI  CONST_05  C9   C10  C11  C6     0.00   0.0  0
 NZI  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 NZI  CONST_07  C6   N1   C5   N      0.00   0.0  0
 NZI  CONST_08  N1   C6   C7   N      0.00   0.0  0
 NZI  CONST_09  N1   C5   N    C2   180.00   0.0  0
 NZI  CONST_10  C6   C7   N    C2   180.00   0.0  0
 NZI  CONST_11  C6   C7   N    C5     0.00   0.0  0
 NZI  CONST_12  C7   C6   N1   C5     0.00   0.0  0
 NZI  CONST_13  N1   C5   N    C7     0.00   0.0  0
 NZI  CONST_14  O12  C5   N    C2     0.00   0.0  0
 NZI  CONST_15  O12  C5   N1   C6   180.00   0.0  0
 NZI  CONST_16  O12  C5   N    C7   180.00   0.0  0
 NZI  CONST_17  H13  C8   C7   N      0.00   0.0  0
 NZI  CONST_18  H14  C9   C10  C11  180.00   0.0  0
 NZI  CONST_19  H15  C10  C11  C6   180.00   0.0  0
 NZI  CONST_20  H16  C11  C6   C7   180.00   0.0  0
 NZI  CONST_21  H12  N1   C5   N    180.00   0.0  0
 NZI  Var_01    O3   P    O2   C4   168.84  30.0  3
 NZI  Var_02    H7   C4   O2   P     57.86  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
 NZI  chir_01  C   O   C1  C3  negativ
 NZI  chir_02  C2  O1  N   C1  negativ
 NZI  chir_03  C3  O1  C   C4  negativ
 NZI  chir_04  P   O3  O4  O5  both
 NZI  chir_05  P1  O6  O7  O8  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
 NZI  plan-1  N    0.020
 NZI  plan-1  C10  0.020
 NZI  plan-1  C11  0.020
 NZI  plan-1  C2   0.020
 NZI  plan-1  C5   0.020
 NZI  plan-1  C6   0.020
 NZI  plan-1  C7   0.020
 NZI  plan-1  C8   0.020
 NZI  plan-1  C9   0.020
 NZI  plan-1  N1   0.020
 NZI  plan-1  O12  0.020
 NZI  plan-1  H15  0.020
 NZI  plan-1  H16  0.020
 NZI  plan-1  H13  0.020
 NZI  plan-1  H14  0.020
 NZI  plan-1  H12  0.020

