# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:00:19 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{[(2E)-2-(4-fluorobenzylidene)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(F)cc2)[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
 20X  20X  N-{[(2E)-2-(4-fluorobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  42  24  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_20X
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
 20X  C1   C  CH1   0   0.223  -2.0183   0.2836  -0.5092
 20X  F1   F  F     0  -0.309   6.9794  -2.2292   1.1540
 20X  N1   N  NH1   0  -0.673  -0.6678   0.7400  -0.5235
 20X  S1   S  S1    0  -0.399  -1.2938   3.2537  -1.2302
 20X  C2   C  CH1   0  -0.029  -2.1232  -1.0868  -1.1820
 20X  N2   N  NH1   0  -0.480   1.0482   2.2209  -0.7097
 20X  O2   O  OH1   0  -0.663  -1.7944  -1.0131  -2.5454
 20X  C3   C  CH1   0  -0.006  -3.5612  -1.5745  -1.0777
 20X  N3   N  N     0  -0.219   1.8974   1.2441  -0.3526
 20X  O3   O  OH1   0  -0.670  -3.9965   1.1865   2.9212
 20X  C4   C  CH1   0   0.034  -4.0318  -1.5516   0.3718
 20X  O4   O  OH1   0  -0.671  -5.4039  -1.8402   0.4676
 20X  C5   C  CH1   0  -0.012  -3.7972  -0.1638   0.9735
 20X  O5   O  O2    0  -0.486  -2.4393   0.2003   0.8299
 20X  C6   C  CH2   0  -0.157  -4.1266  -0.1336   2.4507
 20X  O6   O  OH1   0  -0.671  -3.7070  -2.8923  -1.5482
 20X  C7   C  C     0   0.428  -0.2809   1.9936  -0.7937
 20X  C8   C  C1    0  -0.052   3.1417   1.5076  -0.3294
 20X  C9   C  CR6   0   0.048   4.1233   0.5044   0.0630
 20X  C10  C  CR16  0  -0.283   5.4766   0.8383   0.0215
 20X  C11  C  CR16  0  -0.398   6.4508  -0.0782   0.3860
 20X  C12  C  CR6   0   0.528   6.0495  -1.3343   0.7947
 20X  C13  C  CR16  0  -0.393   4.7150  -1.7017   0.8495
 20X  C14  C  CR16  0  -0.264   3.7555  -0.7775   0.4822
 20X  H1   H  HCH1  0   0.235  -2.6235   1.0104  -1.0645
 20X  HN1  H  HNH1  0   0.419   0.0568   0.0951  -0.2295
 20X  H2   H  HCH1  0   0.230  -1.4705  -1.7941  -0.6472
 20X  HN2  H  HNH1  0   0.416   1.3833   3.1482  -0.9472
 20X  HO2  H  HOH1  0   0.458  -0.8383  -0.9607  -2.6365
 20X  H3   H  HCH1  0   0.219  -4.1996  -0.8824  -1.6505
 20X  HO3  H  HOH1  0   0.457  -4.2699   1.1996   3.8426
 20X  H4   H  HCH1  0   0.214  -3.4331  -2.2801   0.9421
 20X  HO4  H  HOH1  0   0.455  -5.5535  -2.7186   0.1026
 20X  H5   H  HCH1  0   0.225  -4.4398   0.5614   0.4474
 20X  H6   H  HCH2  0   0.197  -3.4528  -0.8245   2.9768
 20X  H6A  H  HCH2  0   0.214  -5.1449  -0.5118   2.5857
 20X  HO6  H  HOH1  0   0.457  -3.5897  -2.8923  -2.5034
 20X  H8   H  H     0   0.260   3.5252   2.4929  -0.6014
 20X  H10  H  HCR6  0   0.273   5.7785   1.8265  -0.3025
 20X  H11  H  HCR6  0   0.287   7.5003   0.1822   0.3537
 20X  H13  H  HCR6  0   0.287   4.4330  -2.6935   1.1771
 20X  H14  H  HCR6  0   0.272   2.7107  -1.0543   0.5255

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
 20X  C2   C1   single    1.530  0.020  1.530
 20X  C1   O5   single    1.406  0.020  1.406
 20X  C1   N1   single    1.426  0.020  1.426
 20X  C1   H1   single    0.970  0.020  1.090
 20X  C12  F1   single    1.340  0.020  1.340
 20X  N1   C7   single    1.339  0.020  1.339
 20X  N1   HN1  single    0.860  0.020  1.020
 20X  C7   S1   double    1.675  0.020  1.675
 20X  C3   C2   single    1.522  0.020  1.522
 20X  O2   C2   single    1.404  0.020  1.404
 20X  C2   H2   single    0.970  0.020  1.090
 20X  C7   N2   single    1.351  0.020  1.351
 20X  N2   N3   single    1.343  0.020  1.343
 20X  N2   HN2  single    0.860  0.020  1.020
 20X  O2   HO2  single    0.850  0.020  0.980
 20X  O6   C3   single    1.407  0.020  1.407
 20X  C3   C4   single    1.524  0.020  1.524
 20X  C3   H3   single    0.970  0.020  1.090
 20X  N3   C8   double    1.272  0.020  1.272
 20X  O3   C6   single    1.407  0.020  1.407
 20X  O3   HO3  single    0.850  0.020  0.980
 20X  O4   C4   single    1.405  0.020  1.405
 20X  C4   C5   single    1.531  0.020  1.531
 20X  C4   H4   single    0.970  0.020  1.090
 20X  O4   HO4  single    0.850  0.020  0.980
 20X  C5   C6   single    1.514  0.020  1.514
 20X  C5   O5   single    1.413  0.020  1.413
 20X  C5   H5   single    0.970  0.020  1.090
 20X  C6   H6   single    0.970  0.020  1.090
 20X  C6   H6A  single    0.970  0.020  1.090
 20X  O6   HO6  single    0.850  0.020  0.980
 20X  C8   C9   single    1.457  0.020  1.457
 20X  C8   H8   single    0.930  0.020  1.080
 20X  C9   C10  aromatic  1.394  0.020  1.394
 20X  C9   C14  aromatic  1.398  0.020  1.398
 20X  C10  C11  aromatic  1.386  0.020  1.386
 20X  C10  H10  single    0.930  0.020  1.080
 20X  C11  C12  aromatic  1.381  0.020  1.381
 20X  C11  H11  single    0.930  0.020  1.080
 20X  C13  C12  aromatic  1.385  0.020  1.385
 20X  C14  C13  aromatic  1.382  0.020  1.382
 20X  C13  H13  single    0.930  0.020  1.080
 20X  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
 20X  H1   C1   O5   110.86  3.000
 20X  H1   C1   C2   109.45  3.000
 20X  O5   C1   C2   110.19  3.000
 20X  H1   C1   N1   107.79  3.000
 20X  O5   C1   N1   108.19  3.000
 20X  C2   C1   N1   110.32  3.000
 20X  HN1  N1   C7   116.59  3.000
 20X  HN1  N1   C1   118.07  3.000
 20X  C7   N1   C1   125.12  3.000
 20X  H2   C2   C3   108.72  3.000
 20X  H2   C2   O2   111.50  3.000
 20X  C3   C2   O2   107.73  3.000
 20X  H2   C2   C1   108.73  3.000
 20X  O2   C2   C1   111.33  3.000
 20X  C3   C2   C1   108.76  3.000
 20X  HN2  N2   C7   117.67  3.000
 20X  HN2  N2   N3   121.23  3.000
 20X  C7   N2   N3   121.09  3.000
 20X  HO2  O2   C2   109.12  3.000
 20X  H3   C3   O6   110.75  3.000
 20X  H3   C3   C4   107.82  3.000
 20X  O6   C3   C4   107.47  3.000
 20X  H3   C3   C2   108.09  3.000
 20X  C4   C3   C2   110.61  3.000
 20X  O6   C3   C2   112.03  3.000
 20X  C8   N3   N2   118.22  3.000
 20X  HO3  O3   C6   107.88  3.000
 20X  H4   C4   C5   108.22  3.000
 20X  H4   C4   O4   111.06  3.000
 20X  C5   C4   O4   108.00  3.000
 20X  H4   C4   C3   108.33  3.000
 20X  C5   C4   C3   109.88  3.000
 20X  O4   C4   C3   111.29  3.000
 20X  HO4  O4   C4   108.25  3.000
 20X  H5   C5   C6   109.01  3.000
 20X  H5   C5   O5   110.00  3.000
 20X  C6   C5   O5   107.65  3.000
 20X  H5   C5   C4   108.63  3.000
 20X  O5   C5   C4   109.93  3.000
 20X  C6   C5   C4   111.61  3.000
 20X  C5   O5   C1   113.56  3.000
 20X  H6A  C6   H6   107.10  3.000
 20X  H6A  C6   C5   108.42  3.000
 20X  H6   C6   C5   108.74  3.000
 20X  H6A  C6   O3   111.64  3.000
 20X  H6   C6   O3   111.89  3.000
 20X  C5   C6   O3   108.95  3.000
 20X  HO6  O6   C3   108.62  3.000
 20X  N2   C7   S1   118.99  3.000
 20X  N2   C7   N1   115.40  3.000
 20X  S1   C7   N1   125.60  3.000
 20X  H8   C8   C9   116.86  3.000
 20X  H8   C8   N3   121.73  3.000
 20X  C9   C8   N3   121.41  3.000
 20X  C14  C9   C10  118.94  3.000
 20X  C14  C9   C8   122.33  3.000
 20X  C10  C9   C8   118.74  3.000
 20X  H10  C10  C11  119.08  3.000
 20X  H10  C10  C9   119.87  3.000
 20X  C11  C10  C9   121.06  3.000
 20X  H11  C11  C12  120.66  3.000
 20X  H11  C11  C10  120.98  3.000
 20X  C12  C11  C10  118.36  3.000
 20X  C13  C12  C11  122.22  3.000
 20X  C13  C12  F1   118.75  3.000
 20X  C11  C12  F1   119.04  3.000
 20X  H13  C13  C14  120.83  3.000
 20X  H13  C13  C12  120.42  3.000
 20X  C14  C13  C12  118.75  3.000
 20X  H14  C14  C13  119.27  3.000
 20X  H14  C14  C9   120.05  3.000
 20X  C13  C14  C9   120.68  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
 20X  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 20X  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 20X  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 20X  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 20X  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 20X  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 20X  CONST_07  C10  C11  C12  F1   180.00   0.0  0
 20X  CONST_08  C14  C13  C12  F1   180.00   0.0  0
 20X  CONST_09  C11  C10  C9   C8   180.00   0.0  0
 20X  CONST_10  C13  C14  C9   C8   180.00   0.0  0
 20X  CONST_11  H11  C11  C10  C9   180.00   0.0  0
 20X  CONST_12  H13  C13  C14  C9   180.00   0.0  0
 20X  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 20X  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 20X  CONST_15  S1   C7   N1   C1     0.00   0.0  0
 20X  CONST_16  N2   C7   N1   C1   180.00   0.0  0
 20X  CONST_17  N3   N2   C7   N1     0.00   0.0  0
 20X  CONST_18  N3   N2   C7   S1   180.00   0.0  0
 20X  CONST_19  HN2  N2   C7   N1   180.00   0.0  0
 20X  CONST_20  HN1  N1   C7   S1   180.00   0.0  0
 20X  Var_01    C10  C9   C8   N3   177.67  30.0  2
 20X  Var_02    C9   C8   N3   N2   179.26   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
 20X  chir_01  C1  C2  O5  N1  negativ
 20X  chir_02  C2  O2  C1  C3  negativ
 20X  chir_03  C3  O6  C2  C4  positiv
 20X  chir_04  C4  O4  C5  C3  positiv
 20X  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
 20X  plan-1  F1   0.020
 20X  plan-1  C8   0.020
 20X  plan-1  C9   0.020
 20X  plan-1  C10  0.020
 20X  plan-1  C11  0.020
 20X  plan-1  C12  0.020
 20X  plan-1  C13  0.020
 20X  plan-1  C14  0.020
 20X  plan-1  H10  0.020
 20X  plan-1  H11  0.020
 20X  plan-1  H13  0.020
 20X  plan-1  H14  0.020
 20X  plan-2  C1   0.020
 20X  plan-2  N1   0.020
 20X  plan-2  S1   0.020
 20X  plan-2  N2   0.020
 20X  plan-2  N3   0.020
 20X  plan-2  C7   0.020
 20X  plan-2  HN1  0.020
 20X  plan-2  HN2  0.020
 20X  plan-3  N2   0.020
 20X  plan-3  N3   0.020
 20X  plan-3  C8   0.020
 20X  plan-3  C9   0.020
 20X  plan-3  H8   0.020

