# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:04:00 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{[(2E)-2-(4-chlorobenzylidene)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(Cl)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
 17T  17T  N-{[(2E)-2-(4-chlorobenzylidene)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_17T
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
 17T  C1   C   CH1   0   0.224  -2.3910   0.2875  -0.4890
 17T  N1   N   NH1   0  -0.675  -1.0734   0.8308  -0.4889
 17T  S1   S   S1    0  -0.394  -1.8799   3.3474  -0.9587
 17T  CL1  CL  CL    0  -0.118   7.0813  -2.0217   0.8441
 17T  C2   C   CH1   0  -0.029  -2.4122  -1.0544  -1.2248
 17T  N2   N   NH1   0  -0.479   0.5354   2.4374  -0.5589
 17T  O2   O   OH1   0  -0.662  -2.1011  -0.8991  -2.5854
 17T  C3   C   CH1   0  -0.008  -3.8146  -1.6388  -1.1358
 17T  N3   N   N     0  -0.215   1.4545   1.4939  -0.3061
 17T  O3   O   OH1   0  -0.671  -3.8775  -2.9408  -1.6651
 17T  C4   C   CH1   0   0.036  -4.2761  -1.7115   0.3149
 17T  O4   O   OH1   0  -0.671  -5.6244  -2.0989   0.4002
 17T  C5   C   CH1   0  -0.013  -4.1296  -0.3392   0.9748
 17T  O5   O   O2    0  -0.486  -2.7968   0.1134   0.8463
 17T  C6   C   CH2   0  -0.157  -4.4575  -0.3914   2.4516
 17T  O6   O   OH1   0  -0.669  -4.3911   0.9109   2.9810
 17T  C7   C   C     0   0.429  -0.7774   2.1278  -0.6481
 17T  C8   C   C1    0  -0.054   2.6784   1.8389  -0.2716
 17T  C9   C   CR6   0   0.069   3.7309   0.8696   0.0063
 17T  C10  C   CR16  0  -0.306   5.0582   1.2935  -0.0277
 17T  C11  C   CR16  0  -0.196   6.0959   0.4109   0.2266
 17T  C12  C   CR6   0  -0.047   5.7966  -0.9091   0.5204
 17T  C13  C   CR16  0  -0.192   4.4815  -1.3568   0.5626
 17T  C14  C   CR16  0  -0.287   3.4560  -0.4673   0.3055
 17T  H1   H   HCH1  0   0.235  -3.0484   0.9979  -1.0047
 17T  HN1  H   HNH1  0   0.419  -0.3036   0.2166  -0.2494
 17T  H2   H   HCH1  0   0.230  -1.7110  -1.7414  -0.7260
 17T  HN2  H   HNH1  0   0.417   0.8009   3.4054  -0.7035
 17T  HO2  H   HOH1  0   0.458  -1.1531  -0.7642  -2.6783
 17T  H3   H   HCH1  0   0.220  -4.4994  -0.9641  -1.6750
 17T  HO3  H   HOH1  0   0.458  -3.7682  -2.8891  -2.6196
 17T  H4   H   HCH1  0   0.213  -3.6255  -2.4220   0.8502
 17T  HO4  H   HOH1  0   0.455  -5.7164  -2.9540  -0.0328
 17T  H5   H   HCH1  0   0.225  -4.8166   0.3663   0.4790
 17T  H6   H   HCH2  0   0.214  -5.4563  -0.8240   2.5689
 17T  H6A  H   HCH2  0   0.197  -3.7506  -1.0719   2.9473
 17T  HO6  H   HOH1  0   0.457  -4.6800   0.8704   3.8968
 17T  H8   H   H     0   0.261   2.9914   2.8692  -0.4503
 17T  H10  H   HCR6  0   0.272   5.2913   2.3256  -0.2579
 17T  H11  H   HCR6  0   0.286   7.1216   0.7509   0.1946
 17T  H13  H   HCR6  0   0.286   4.2613  -2.3894   0.7960
 17T  H14  H   HCR6  0   0.271   2.4324  -0.8155   0.3423

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
 17T  C2   C1   single    1.531  0.020  1.531
 17T  C1   O5   single    1.406  0.020  1.406
 17T  C1   N1   single    1.425  0.020  1.425
 17T  C1   H1   single    0.970  0.020  1.090
 17T  N1   C7   single    1.340  0.020  1.340
 17T  N1   HN1  single    0.860  0.020  1.020
 17T  C7   S1   double    1.673  0.020  1.673
 17T  C12  CL1  single    1.730  0.020  1.730
 17T  C3   C2   single    1.522  0.020  1.522
 17T  O2   C2   single    1.404  0.020  1.404
 17T  C2   H2   single    0.970  0.020  1.090
 17T  C7   N2   single    1.352  0.020  1.352
 17T  N2   N3   single    1.341  0.020  1.341
 17T  N2   HN2  single    0.860  0.020  1.020
 17T  O2   HO2  single    0.850  0.020  0.980
 17T  O3   C3   single    1.407  0.020  1.407
 17T  C3   C4   single    1.524  0.020  1.524
 17T  C3   H3   single    0.970  0.020  1.090
 17T  N3   C8   double    1.272  0.020  1.272
 17T  O3   HO3  single    0.850  0.020  0.980
 17T  O4   C4   single    1.405  0.020  1.405
 17T  C4   C5   single    1.530  0.020  1.530
 17T  C4   H4   single    0.970  0.020  1.090
 17T  O4   HO4  single    0.850  0.020  0.980
 17T  C5   C6   single    1.514  0.020  1.514
 17T  C5   O5   single    1.413  0.020  1.413
 17T  C5   H5   single    0.970  0.020  1.090
 17T  O6   C6   single    1.407  0.020  1.407
 17T  C6   H6   single    0.970  0.020  1.090
 17T  C6   H6A  single    0.970  0.020  1.090
 17T  O6   HO6  single    0.850  0.020  0.980
 17T  C8   C9   single    1.458  0.020  1.458
 17T  C8   H8   single    0.930  0.020  1.080
 17T  C9   C10  aromatic  1.394  0.020  1.394
 17T  C9   C14  aromatic  1.397  0.020  1.397
 17T  C10  C11  aromatic  1.386  0.020  1.386
 17T  C10  H10  single    0.930  0.020  1.080
 17T  C11  C12  aromatic  1.385  0.020  1.385
 17T  C11  H11  single    0.930  0.020  1.080
 17T  C13  C12  aromatic  1.390  0.020  1.390
 17T  C14  C13  aromatic  1.382  0.020  1.382
 17T  C13  H13  single    0.930  0.020  1.080
 17T  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
 17T  H1   C1   O5   110.71  3.000
 17T  H1   C1   C2   109.48  3.000
 17T  O5   C1   C2   110.12  3.000
 17T  H1   C1   N1   107.90  3.000
 17T  O5   C1   N1   108.29  3.000
 17T  C2   C1   N1   110.31  3.000
 17T  HN1  N1   C7   116.54  3.000
 17T  HN1  N1   C1   118.11  3.000
 17T  C7   N1   C1   124.98  3.000
 17T  H2   C2   C3   108.71  3.000
 17T  H2   C2   O2   111.52  3.000
 17T  C3   C2   O2   107.66  3.000
 17T  H2   C2   C1   108.69  3.000
 17T  O2   C2   C1   111.45  3.000
 17T  C3   C2   C1   108.74  3.000
 17T  HN2  N2   C7   117.61  3.000
 17T  HN2  N2   N3   121.26  3.000
 17T  C7   N2   N3   121.12  3.000
 17T  HO2  O2   C2   109.11  3.000
 17T  H3   C3   C4   107.86  3.000
 17T  H3   C3   O3   110.77  3.000
 17T  C4   C3   O3   107.48  3.000
 17T  H3   C3   C2   107.99  3.000
 17T  C4   C3   C2   110.67  3.000
 17T  O3   C3   C2   112.00  3.000
 17T  C8   N3   N2   118.27  3.000
 17T  HO3  O3   C3   108.57  3.000
 17T  H4   C4   C5   108.20  3.000
 17T  H4   C4   O4   111.05  3.000
 17T  C5   C4   O4   108.24  3.000
 17T  H4   C4   C3   108.32  3.000
 17T  C5   C4   C3   109.80  3.000
 17T  O4   C4   C3   111.19  3.000
 17T  HO4  O4   C4   108.01  3.000
 17T  H5   C5   C6   109.02  3.000
 17T  H5   C5   O5   109.99  3.000
 17T  C6   C5   O5   107.70  3.000
 17T  H5   C5   C4   108.69  3.000
 17T  O5   C5   C4   109.77  3.000
 17T  C6   C5   C4   111.66  3.000
 17T  C5   O5   C1   113.46  3.000
 17T  H6A  C6   H6   107.08  3.000
 17T  H6A  C6   O6   111.90  3.000
 17T  H6   C6   O6   111.61  3.000
 17T  H6A  C6   C5   108.78  3.000
 17T  H6   C6   C5   108.41  3.000
 17T  O6   C6   C5   108.96  3.000
 17T  HO6  O6   C6   107.78  3.000
 17T  N2   C7   S1   119.03  3.000
 17T  N2   C7   N1   115.37  3.000
 17T  S1   C7   N1   125.60  3.000
 17T  H8   C8   C9   116.87  3.000
 17T  H8   C8   N3   121.83  3.000
 17T  C9   C8   N3   121.30  3.000
 17T  C14  C9   C10  118.92  3.000
 17T  C14  C9   C8   122.35  3.000
 17T  C10  C9   C8   118.73  3.000
 17T  H10  C10  C11  119.00  3.000
 17T  H10  C10  C9   120.01  3.000
 17T  C11  C10  C9   120.99  3.000
 17T  H11  C11  C12  120.74  3.000
 17T  H11  C11  C10  120.31  3.000
 17T  C12  C11  C10  118.95  3.000
 17T  C13  C12  C11  121.20  3.000
 17T  C13  C12  CL1  119.33  3.000
 17T  C11  C12  CL1  119.48  3.000
 17T  H13  C13  C14  120.25  3.000
 17T  H13  C13  C12  120.46  3.000
 17T  C14  C13  C12  119.29  3.000
 17T  H14  C14  C13  119.25  3.000
 17T  H14  C14  C9   120.09  3.000
 17T  C13  C14  C9   120.65  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
 17T  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 17T  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 17T  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 17T  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 17T  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 17T  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 17T  CONST_07  C10  C11  C12  CL1  180.00   0.0  0
 17T  CONST_08  C14  C13  C12  CL1  180.00   0.0  0
 17T  CONST_09  C11  C10  C9   C8   180.00   0.0  0
 17T  CONST_10  C13  C14  C9   C8   180.00   0.0  0
 17T  CONST_11  H11  C11  C10  C9   180.00   0.0  0
 17T  CONST_12  H13  C13  C14  C9   180.00   0.0  0
 17T  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 17T  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 17T  CONST_15  S1   C7   N1   C1     0.00   0.0  0
 17T  CONST_16  N2   C7   N1   C1   180.00   0.0  0
 17T  CONST_17  N3   N2   C7   N1     0.00   0.0  0
 17T  CONST_18  N3   N2   C7   S1   180.00   0.0  0
 17T  CONST_19  HN2  N2   C7   N1   180.00   0.0  0
 17T  CONST_20  HN1  N1   C7   S1   180.00   0.0  0
 17T  Var_01    C10  C9   C8   N3   177.17  30.0  2
 17T  Var_02    C9   C8   N3   N2   179.58   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
 17T  chir_01  C1  C2  O5  N1  negativ
 17T  chir_02  C2  O2  C1  C3  negativ
 17T  chir_03  C3  O3  C2  C4  positiv
 17T  chir_04  C4  O4  C5  C3  positiv
 17T  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
 17T  plan-1  CL1  0.020
 17T  plan-1  C8   0.020
 17T  plan-1  C9   0.020
 17T  plan-1  C10  0.020
 17T  plan-1  C11  0.020
 17T  plan-1  C12  0.020
 17T  plan-1  C13  0.020
 17T  plan-1  C14  0.020
 17T  plan-1  H10  0.020
 17T  plan-1  H11  0.020
 17T  plan-1  H13  0.020
 17T  plan-1  H14  0.020
 17T  plan-2  C1   0.020
 17T  plan-2  N1   0.020
 17T  plan-2  S1   0.020
 17T  plan-2  N2   0.020
 17T  plan-2  N3   0.020
 17T  plan-2  C7   0.020
 17T  plan-2  HN1  0.020
 17T  plan-2  HN2  0.020
 17T  plan-3  N2   0.020
 17T  plan-3  N3   0.020
 17T  plan-3  C8   0.020
 17T  plan-3  C9   0.020
 17T  plan-3  H8   0.020

