# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 19 05:47:30 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-{[(2E)-2-(4-nitrobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=S)N\N=C\c2ccc(cc2)[N+]([O-])=O)[C@H](O)[C@@H](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
 18O  18O  N-{[(2E)-2-(4-nitrobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  44  26  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_18O
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
 18O  C1   C  CH1    0   0.225  -2.5999   0.2896  -0.4705
 18O  N1   N  NH1    0  -0.674  -1.2993   0.8743  -0.4767
 18O  S1   S  S1     0  -0.380  -2.1960   3.3781  -0.8244
 18O  C2   C  CH1    0  -0.030  -2.5865  -1.0459  -1.2182
 18O  N2   N  NH1    0  -0.477   0.2550   2.5388  -0.5061
 18O  O2   O  OH1    0  -0.662  -2.2932  -0.8702  -2.5801
 18O  C3   C  CH1    0  -0.009  -3.9702  -1.6725  -1.1210
 18O  N3   N  N      0  -0.204   1.2074   1.6239  -0.3135
 18O  O3   O  OH1    0  -0.671  -3.9984  -2.9725  -1.6581
 18O  C4   C  CH1    0   0.037  -4.4192  -1.7684   0.3322
 18O  N4   N  N      1   0.330   6.6987  -1.6284   0.5565
 18O  O4   O  OH1    0  -0.672  -5.7548  -2.1971   0.4239
 18O  C5   C  CH1    0  -0.013  -4.3078  -0.3965   0.9992
 18O  O5   O  O2     0  -0.485  -2.9877   0.0911   0.8661
 18O  C6   C  CH2    0  -0.157  -4.6276  -0.4642   2.4772
 18O  O6   O  OH1    0  -0.669  -4.5855   0.8364   3.0136
 18O  C7   C  C      0   0.432  -1.0517   2.1848  -0.5860
 18O  O7   O  O      0  -0.377   6.4369  -2.7949   0.7341
 18O  C8   C  C1     0  -0.049   2.4197   2.0076  -0.2640
 18O  O8   O  O     -1  -0.378   7.8225  -1.1839   0.5434
 18O  C9   C  CR6    0   0.074   3.4956   1.0472  -0.0503
 18O  C10  C  CR16   0  -0.276   3.2498  -0.3156   0.1411
 18O  C11  C  CR16   0  -0.250   4.2940  -1.1942   0.3404
 18O  C12  C  CR6    0   0.248   5.5957  -0.7052   0.3466
 18O  C13  C  CR16   0  -0.251   5.8679   0.6410   0.1587
 18O  C14  C  CR16   0  -0.295   4.8108   1.5109  -0.0377
 18O  H1   H  HCH1   0   0.236  -3.2847   0.9836  -0.9730
 18O  HN1  H  HNH1   0   0.420  -0.5071   0.2763  -0.2722
 18O  H2   H  HCH1   0   0.231  -1.8603  -1.7145  -0.7308
 18O  HN2  H  HNH1   0   0.420   0.4806   3.5233  -0.6027
 18O  HO2  H  HOH1   0   0.458  -1.3477  -0.7265  -2.6838
 18O  H3   H  HCH1   0   0.221  -4.6789  -1.0153  -1.6510
 18O  HO3  H  HOH1   0   0.458  -3.8948  -2.9122  -2.6129
 18O  H4   H  HCH1   0   0.213  -3.7442  -2.4627   0.8585
 18O  HO4  H  HOH1   0   0.455  -5.8295  -3.0369  -0.0416
 18O  H5   H  HCH1   0   0.225  -5.0148   0.2931   0.5094
 18O  H6   H  HCH2   0   0.214  -5.6170  -0.9177   2.5960
 18O  H6A  H  HCH2   0   0.196  -3.9049  -1.1327   2.9663
 18O  HO6  H  HOH1   0   0.457  -4.8738   0.7857   3.9291
 18O  H8   H  H      0   0.268   2.7012   3.0552  -0.3782
 18O  H10  H  HCR6   0   0.279   2.2357  -0.6906   0.1366
 18O  H11  H  HCR6   0   0.301   4.0910  -2.2446   0.4881
 18O  H13  H  HCR6   0   0.302   6.8804   1.0169   0.1631
 18O  H14  H  HCR6   0   0.280   5.0134   2.5639  -0.1847

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
 18O  C1   O5   single    1.406  0.020  1.406
 18O  C1   N1   single    1.426  0.020  1.426
 18O  N1   C7   single    1.338  0.020  1.338
 18O  C2   C1   single    1.531  0.020  1.531
 18O  N2   N3   single    1.335  0.020  1.335
 18O  O2   C2   single    1.404  0.020  1.404
 18O  C3   C2   single    1.522  0.020  1.522
 18O  C3   C4   single    1.524  0.020  1.524
 18O  N3   C8   double    1.273  0.020  1.273
 18O  O3   C3   single    1.407  0.020  1.407
 18O  C4   C5   single    1.530  0.020  1.530
 18O  O8   N4   single    1.209  0.020  1.209
 18O  N4   O7   double    1.209  0.020  1.209
 18O  O4   C4   single    1.406  0.020  1.406
 18O  C5   C6   single    1.514  0.020  1.514
 18O  C5   O5   single    1.414  0.020  1.414
 18O  O6   C6   single    1.407  0.020  1.407
 18O  C7   S1   double    1.670  0.020  1.670
 18O  C7   N2   single    1.356  0.020  1.356
 18O  C8   C9   single    1.458  0.020  1.458
 18O  C9   C14  aromatic  1.395  0.020  1.395
 18O  C9   C10  aromatic  1.398  0.020  1.398
 18O  C10  C11  aromatic  1.379  0.020  1.379
 18O  C11  C12  aromatic  1.391  0.020  1.391
 18O  C12  N4   single    1.454  0.020  1.454
 18O  C13  C12  aromatic  1.386  0.020  1.386
 18O  C14  C13  aromatic  1.383  0.020  1.383
 18O  C1   H1   single    0.970  0.020  1.090
 18O  N1   HN1  single    0.860  0.020  1.020
 18O  C2   H2   single    0.970  0.020  1.090
 18O  N2   HN2  single    0.860  0.020  1.020
 18O  O2   HO2  single    0.850  0.020  0.980
 18O  C3   H3   single    0.970  0.020  1.090
 18O  O3   HO3  single    0.850  0.020  0.980
 18O  C4   H4   single    0.970  0.020  1.090
 18O  O4   HO4  single    0.850  0.020  0.980
 18O  C5   H5   single    0.970  0.020  1.090
 18O  C6   H6   single    0.970  0.020  1.090
 18O  C6   H6A  single    0.970  0.020  1.090
 18O  O6   HO6  single    0.850  0.020  0.980
 18O  C8   H8   single    0.930  0.020  1.080
 18O  C10  H10  single    0.930  0.020  1.080
 18O  C11  H11  single    0.930  0.020  1.080
 18O  C13  H13  single    0.930  0.020  1.080
 18O  C14  H14  single    0.930  0.020  1.080

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
 18O  H1   C1   O5   110.65  3.000
 18O  H1   C1   C2   109.50  3.000
 18O  O5   C1   C2   110.10  3.000
 18O  H1   C1   N1   107.94  3.000
 18O  C2   C1   N1   110.34  3.000
 18O  O5   C1   N1   108.28  3.000
 18O  HN1  N1   C7   116.73  3.000
 18O  HN1  N1   C1   118.05  3.000
 18O  C7   N1   C1   124.80  3.000
 18O  H2   C2   C3   108.75  3.000
 18O  H2   C2   O2   111.57  3.000
 18O  C3   C2   O2   107.66  3.000
 18O  H2   C2   C1   108.63  3.000
 18O  C3   C2   C1   108.66  3.000
 18O  O2   C2   C1   111.50  3.000
 18O  HN2  N2   C7   117.51  3.000
 18O  HN2  N2   N3   121.35  3.000
 18O  C7   N2   N3   121.14  3.000
 18O  HO2  O2   C2   109.18  3.000
 18O  H3   C3   C4   107.85  3.000
 18O  H3   C3   O3   110.76  3.000
 18O  C4   C3   O3   107.45  3.000
 18O  H3   C3   C2   107.96  3.000
 18O  O3   C3   C2   111.98  3.000
 18O  C4   C3   C2   110.77  3.000
 18O  C8   N3   N2   118.60  3.000
 18O  HO3  O3   C3   108.58  3.000
 18O  H4   C4   C5   108.19  3.000
 18O  H4   C4   O4   111.02  3.000
 18O  C5   C4   O4   108.32  3.000
 18O  H4   C4   C3   108.33  3.000
 18O  O4   C4   C3   111.18  3.000
 18O  C5   C4   C3   109.75  3.000
 18O  C12  N4   O8   118.07  3.000
 18O  C12  N4   O7   118.02  3.000
 18O  O8   N4   O7   123.92  3.000
 18O  HO4  O4   C4   107.94  3.000
 18O  H5   C5   C6   109.04  3.000
 18O  H5   C5   O5   109.96  3.000
 18O  C6   C5   O5   107.74  3.000
 18O  H5   C5   C4   108.70  3.000
 18O  O5   C5   C4   109.66  3.000
 18O  C6   C5   C4   111.73  3.000
 18O  C5   O5   C1   113.32  3.000
 18O  H6A  C6   H6   107.09  3.000
 18O  H6A  C6   O6   111.89  3.000
 18O  H6   C6   O6   111.62  3.000
 18O  H6A  C6   C5   108.83  3.000
 18O  H6   C6   C5   108.39  3.000
 18O  O6   C6   C5   108.93  3.000
 18O  HO6  O6   C6   107.78  3.000
 18O  N2   C7   S1   118.81  3.000
 18O  N2   C7   N1   115.41  3.000
 18O  S1   C7   N1   125.77  3.000
 18O  H8   C8   C9   117.23  3.000
 18O  H8   C8   N3   122.10  3.000
 18O  C9   C8   N3   120.67  3.000
 18O  C14  C9   C10  119.26  3.000
 18O  C10  C9   C8   122.17  3.000
 18O  C14  C9   C8   118.57  3.000
 18O  H10  C10  C11  119.33  3.000
 18O  H10  C10  C9   120.16  3.000
 18O  C11  C10  C9   120.51  3.000
 18O  H11  C11  C12  121.16  3.000
 18O  H11  C11  C10  119.81  3.000
 18O  C12  C11  C10  119.03  3.000
 18O  C13  C12  C11  121.65  3.000
 18O  C13  C12  N4   119.16  3.000
 18O  C11  C12  N4   119.18  3.000
 18O  H13  C13  C14  119.88  3.000
 18O  H13  C13  C12  121.44  3.000
 18O  C14  C13  C12  118.68  3.000
 18O  H14  C14  C13  119.22  3.000
 18O  H14  C14  C9   119.92  3.000
 18O  C13  C14  C9   120.86  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
 18O  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 18O  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 18O  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 18O  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 18O  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 18O  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 18O  CONST_07  C10  C11  C12  N4   180.00   0.0  0
 18O  CONST_08  C14  C13  C12  N4   180.00   0.0  0
 18O  CONST_09  C13  C14  C9   C8   180.00   0.0  0
 18O  CONST_10  C11  C10  C9   C8   180.00   0.0  0
 18O  CONST_11  H13  C13  C14  C9   180.00   0.0  0
 18O  CONST_12  H11  C11  C10  C9   180.00   0.0  0
 18O  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 18O  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 18O  CONST_15  C11  C12  N4   O7     0.00   0.0  0
 18O  CONST_16  C13  C12  N4   O7   180.00   0.0  0
 18O  CONST_17  C11  C12  N4   O8   180.00   0.0  0
 18O  CONST_18  C13  C12  N4   O8     0.00   0.0  0
 18O  CONST_19  S1   C7   N1   C1     0.00   0.0  0
 18O  CONST_20  N2   C7   N1   C1   180.00   0.0  0
 18O  CONST_21  N3   N2   C7   N1     0.00   0.0  0
 18O  CONST_22  N3   N2   C7   S1   180.00   0.0  0
 18O  CONST_23  HN2  N2   C7   N1   180.00   0.0  0
 18O  CONST_24  HN1  N1   C7   S1   180.00   0.0  0
 18O  Var_01    C14  C9   C8   N3   178.39  30.0  2
 18O  Var_02    C9   C8   N3   N2   179.76   0.0  2

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
 18O  chir_01  C1  O5  N1  C2  negativ
 18O  chir_02  C2  O2  C1  C3  negativ
 18O  chir_03  C3  O3  C2  C4  positiv
 18O  chir_04  C4  O4  C5  C3  positiv
 18O  chir_05  C5  O5  C4  C6  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
 18O  plan-1  N4   0.020
 18O  plan-1  C8   0.020
 18O  plan-1  C9   0.020
 18O  plan-1  C10  0.020
 18O  plan-1  C11  0.020
 18O  plan-1  C12  0.020
 18O  plan-1  C13  0.020
 18O  plan-1  C14  0.020
 18O  plan-1  H10  0.020
 18O  plan-1  H11  0.020
 18O  plan-1  H13  0.020
 18O  plan-1  H14  0.020
 18O  plan-2  N4   0.020
 18O  plan-2  O7   0.020
 18O  plan-2  O8   0.020
 18O  plan-2  C12  0.020
 18O  plan-3  C1   0.020
 18O  plan-3  N1   0.020
 18O  plan-3  S1   0.020
 18O  plan-3  N2   0.020
 18O  plan-3  N3   0.020
 18O  plan-3  C7   0.020
 18O  plan-3  HN1  0.020
 18O  plan-3  HN2  0.020
 18O  plan-4  N2   0.020
 18O  plan-4  N3   0.020
 18O  plan-4  C8   0.020
 18O  plan-4  C9   0.020
 18O  plan-4  H8   0.020

