# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:51:51 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{[(2E)-2-(3-bromobenzylidene)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/c2cccc(Br)c2)[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
 22O  22O  N-{[(2E)-2-(3-bromobenzylidene)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_22O
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
 22O  C1   C   CH1   0   0.226  -2.6455  -0.4127   0.5197
 22O  N1   N   NH1   0  -0.675  -1.3945  -1.0958   0.4980
 22O  S1   S   S1    0  -0.391  -2.5012  -3.5299   0.7135
 22O  BR1  BR  BR    0  -0.038   4.3019   2.3415  -0.1785
 22O  C2   C   CH1   0  -0.029  -2.5242   0.9063   1.2863
 22O  N2   N   NH1   0  -0.479   0.0075  -2.8870   0.3864
 22O  O2   O   OH1   0  -0.662  -2.2253   0.6915   2.6414
 22O  C3   C   CH1   0  -0.008  -3.8640   1.6273   1.2203
 22O  N3   N   N     0  -0.213   1.0398  -2.0464   0.2337
 22O  O3   O   OH1   0  -0.671  -3.7970   2.9189   1.7740
 22O  C4   C   CH1   0   0.038  -4.3347   1.7732  -0.2226
 22O  O4   O   OH1   0  -0.672  -5.6424   2.2856  -0.2809
 22O  C5   C   CH1   0  -0.013  -4.3236   0.4071  -0.9098
 22O  O5   O   O2    0  -0.484  -3.0353  -0.1621  -0.8075
 22O  C6   C   CH2   0  -0.157  -4.6696   0.5135  -2.3797
 22O  O6   O   OH1   0  -0.668  -4.7126  -0.7804  -2.9316
 22O  C7   C   C     0   0.430  -1.2578  -2.4283   0.5200
 22O  C8   C   C1    0  -0.052   2.2037  -2.5427   0.1040
 22O  C9   C   CR6   0   0.064   3.3774  -1.6917  -0.0609
 22O  C10  C   CR16  0  -0.296   4.6203  -2.2948  -0.2403
 22O  C11  C   CR16  0  -0.235   5.7576  -1.5188  -0.4034
 22O  C12  C   CR16  0  -0.232   5.6736  -0.1350  -0.3882
 22O  C13  C   CR6   0  -0.090   4.4287   0.4572  -0.2046
 22O  C14  C   CR16  0  -0.262   3.2830  -0.2976  -0.0416
 22O  H1   H   HCH1  0   0.234  -3.3763  -1.0600   1.0199
 22O  HN1  H   HNH1  0   0.418  -0.5602  -0.5567   0.2981
 22O  H2   H   HCH1  0   0.231  -1.7605   1.5297   0.7964
 22O  HN2  H   HNH1  0   0.417   0.1467  -3.8917   0.4065
 22O  HO2  H   HOH1  0   0.458  -1.2924   0.4741   2.7289
 22O  H3   H   HCH1  0   0.219  -4.6039   1.0109   1.7562
 22O  HO3  H   HOH1  0   0.458  -3.6862   2.8391   2.7266
 22O  H4   H   HCH1  0   0.213  -3.6275   2.4315  -0.7532
 22O  HO4  H   HOH1  0   0.455  -5.6545   3.1269   0.1878
 22O  H5   H   HCH1  0   0.224  -5.0630  -0.2432  -0.4134
 22O  H6   H   HCH2  0   0.213  -5.6335   1.0249  -2.4700
 22O  H6A  H   HCH2  0   0.196  -3.9204   1.1458  -2.8769
 22O  HO6  H   HOH1  0   0.456  -5.0142  -0.7026  -3.8409
 22O  H8   H   H     0   0.264   2.3735  -3.6207   0.1100
 22O  H10  H   HCR6  0   0.269   4.6981  -3.3747  -0.2529
 22O  H11  H   HCR6  0   0.276   6.7202  -1.9913  -0.5453
 22O  H12  H   HCR6  0   0.286   6.5640   0.4650  -0.5176
 22O  H14  H   HCR6  0   0.283   2.3207   0.1749   0.1043

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
 22O  O5   C1   single    1.406  0.020  1.406
 22O  N1   C1   single    1.425  0.020  1.425
 22O  C2   C1   single    1.530  0.020  1.530
 22O  C1   H1   single    0.970  0.020  1.090
 22O  N1   C7   single    1.340  0.020  1.340
 22O  N1   HN1  single    0.860  0.020  1.020
 22O  C7   S1   double    1.672  0.020  1.672
 22O  BR1  C13  single    1.889  0.020  1.889
 22O  C2   C3   single    1.523  0.020  1.523
 22O  C2   O2   single    1.404  0.020  1.404
 22O  C2   H2   single    0.970  0.020  1.090
 22O  N3   N2   single    1.340  0.020  1.340
 22O  N2   C7   single    1.352  0.020  1.352
 22O  N2   HN2  single    0.860  0.020  1.020
 22O  O2   HO2  single    0.850  0.020  0.980
 22O  O3   C3   single    1.407  0.020  1.407
 22O  C4   C3   single    1.525  0.020  1.525
 22O  C3   H3   single    0.970  0.020  1.090
 22O  C8   N3   double    1.272  0.020  1.272
 22O  O3   HO3  single    0.850  0.020  0.980
 22O  C4   O4   single    1.406  0.020  1.406
 22O  C4   C5   single    1.529  0.020  1.529
 22O  C4   H4   single    0.970  0.020  1.090
 22O  O4   HO4  single    0.850  0.020  0.980
 22O  O5   C5   single    1.412  0.020  1.412
 22O  C6   C5   single    1.514  0.020  1.514
 22O  C5   H5   single    0.970  0.020  1.090
 22O  O6   C6   single    1.407  0.020  1.407
 22O  C6   H6   single    0.970  0.020  1.090
 22O  C6   H6A  single    0.970  0.020  1.090
 22O  O6   HO6  single    0.850  0.020  0.980
 22O  C9   C8   single    1.459  0.020  1.459
 22O  C8   H8   single    0.930  0.020  1.080
 22O  C14  C9   aromatic  1.397  0.020  1.397
 22O  C10  C9   aromatic  1.393  0.020  1.393
 22O  C11  C10  aromatic  1.386  0.020  1.386
 22O  C10  H10  single    0.930  0.020  1.080
 22O  C12  C11  aromatic  1.386  0.020  1.386
 22O  C11  H11  single    0.930  0.020  1.080
 22O  C12  C13  aromatic  1.391  0.020  1.391
 22O  C12  H12  single    0.930  0.020  1.080
 22O  C13  C14  aromatic  1.382  0.020  1.382
 22O  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
 22O  H1   C1   O5   110.55  3.000
 22O  H1   C1   C2   109.45  3.000
 22O  O5   C1   C2   109.96  3.000
 22O  H1   C1   N1   107.99  3.000
 22O  C2   C1   N1   110.55  3.000
 22O  O5   C1   N1   108.32  3.000
 22O  HN1  N1   C7   116.64  3.000
 22O  HN1  N1   C1   118.08  3.000
 22O  C7   N1   C1   124.47  3.000
 22O  H2   C2   C3   108.84  3.000
 22O  H2   C2   O2   111.62  3.000
 22O  C3   C2   O2   107.55  3.000
 22O  H2   C2   C1   108.67  3.000
 22O  O2   C2   C1   111.62  3.000
 22O  C3   C2   C1   108.46  3.000
 22O  HN2  N2   C7   117.53  3.000
 22O  HN2  N2   N3   121.18  3.000
 22O  C7   N2   N3   121.28  3.000
 22O  HO2  O2   C2   109.20  3.000
 22O  H3   C3   C4   107.85  3.000
 22O  H3   C3   O3   110.74  3.000
 22O  C4   C3   O3   107.42  3.000
 22O  H3   C3   C2   107.74  3.000
 22O  C4   C3   C2   110.97  3.000
 22O  O3   C3   C2   112.07  3.000
 22O  C8   N3   N2   118.15  3.000
 22O  HO3  O3   C3   108.59  3.000
 22O  H4   C4   C5   108.22  3.000
 22O  H4   C4   O4   111.05  3.000
 22O  C5   C4   O4   108.28  3.000
 22O  H4   C4   C3   108.34  3.000
 22O  C5   C4   C3   109.73  3.000
 22O  O4   C4   C3   111.18  3.000
 22O  HO4  O4   C4   108.06  3.000
 22O  H5   C5   C6   108.98  3.000
 22O  H5   C5   O5   109.96  3.000
 22O  C6   C5   O5   107.89  3.000
 22O  H5   C5   C4   108.64  3.000
 22O  C6   C5   C4   111.83  3.000
 22O  O5   C5   C4   109.52  3.000
 22O  C5   O5   C1   113.16  3.000
 22O  H6A  C6   H6   107.10  3.000
 22O  H6A  C6   O6   111.86  3.000
 22O  H6   C6   O6   111.73  3.000
 22O  H6A  C6   C5   108.90  3.000
 22O  H6   C6   C5   108.31  3.000
 22O  O6   C6   C5   108.85  3.000
 22O  HO6  O6   C6   107.83  3.000
 22O  N2   C7   S1   118.92  3.000
 22O  N2   C7   N1   115.54  3.000
 22O  S1   C7   N1   125.53  3.000
 22O  H8   C8   C9   116.85  3.000
 22O  H8   C8   N3   121.82  3.000
 22O  C9   C8   N3   121.34  3.000
 22O  C14  C9   C10  119.59  3.000
 22O  C10  C9   C8   118.67  3.000
 22O  C14  C9   C8   121.73  3.000
 22O  H10  C10  C11  119.86  3.000
 22O  H10  C10  C9   119.82  3.000
 22O  C11  C10  C9   120.32  3.000
 22O  H11  C11  C12  119.43  3.000
 22O  H11  C11  C10  120.07  3.000
 22O  C12  C11  C10  120.50  3.000
 22O  H12  C12  C13  121.10  3.000
 22O  H12  C12  C11  120.17  3.000
 22O  C13  C12  C11  118.73  3.000
 22O  C14  C13  C12  121.68  3.000
 22O  C14  C13  BR1  119.19  3.000
 22O  C12  C13  BR1  119.13  3.000
 22O  H14  C14  C13  120.99  3.000
 22O  H14  C14  C9   119.84  3.000
 22O  C13  C14  C9   119.17  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
 22O  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 22O  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 22O  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 22O  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 22O  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 22O  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 22O  CONST_07  C11  C12  C13  BR1   180.00   0.0  0
 22O  CONST_08  C9   C14  C13  BR1   180.00   0.0  0
 22O  CONST_09  C13  C14  C9   C8    180.00   0.0  0
 22O  CONST_10  C11  C10  C9   C8    180.00   0.0  0
 22O  CONST_11  H11  C11  C10  C9    180.00   0.0  0
 22O  CONST_12  H14  C14  C9   C10   180.00   0.0  0
 22O  CONST_13  H12  C12  C11  C10   180.00   0.0  0
 22O  CONST_14  H10  C10  C11  C12   180.00   0.0  0
 22O  CONST_15  S1   C7   N1   C1      0.00   0.0  0
 22O  CONST_16  N2   C7   N1   C1    180.00   0.0  0
 22O  CONST_17  N3   N2   C7   N1      0.00   0.0  0
 22O  CONST_18  N3   N2   C7   S1    180.00   0.0  0
 22O  CONST_19  HN2  N2   C7   N1    180.00   0.0  0
 22O  CONST_20  HN1  N1   C7   S1    180.00   0.0  0
 22O  Var_01    C14  C9   C8   N3      2.05  30.0  2
 22O  Var_02    C9   C8   N3   N2   -179.75   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
 22O  chir_01  C1  O5  N1  C2  negativ
 22O  chir_02  C2  O2  C1  C3  negativ
 22O  chir_03  C3  O3  C2  C4  positiv
 22O  chir_04  C4  O4  C5  C3  positiv
 22O  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
 22O  plan-1  BR1  0.020
 22O  plan-1  C8   0.020
 22O  plan-1  C9   0.020
 22O  plan-1  C10  0.020
 22O  plan-1  C11  0.020
 22O  plan-1  C12  0.020
 22O  plan-1  C13  0.020
 22O  plan-1  C14  0.020
 22O  plan-1  H10  0.020
 22O  plan-1  H11  0.020
 22O  plan-1  H12  0.020
 22O  plan-1  H14  0.020
 22O  plan-2  C1   0.020
 22O  plan-2  N1   0.020
 22O  plan-2  S1   0.020
 22O  plan-2  N2   0.020
 22O  plan-2  N3   0.020
 22O  plan-2  C7   0.020
 22O  plan-2  HN1  0.020
 22O  plan-2  HN2  0.020
 22O  plan-3  N2   0.020
 22O  plan-3  N3   0.020
 22O  plan-3  C8   0.020
 22O  plan-3  C9   0.020
 22O  plan-3  H8   0.020

