# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:25:02 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-{[(2E)-2-(pyridin-4-ylmethylidene)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/c2ccncc2)[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
 12E  12E  N-{[(2E)-2-(pyridin-4-ylmethylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  41  23  .  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_12E
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
 12E  C1   C  CH1   0   0.223  -1.6201  -0.2044   0.5548
 12E  N1   N  NH1   0  -0.673  -0.2384  -0.5568   0.5885
 12E  S1   S  S1    0  -0.382  -0.6913  -3.0598   1.4414
 12E  C2   C  CH1   0  -0.027  -1.8210   1.2340   1.0362
 12E  N2   N  NH1   0  -0.478   1.5675  -1.9319   0.7798
 12E  O2   O  OH1   0  -0.662  -1.4638   1.3791   2.3863
 12E  C3   C  CH1   0  -0.007  -3.2970   1.5877   0.9081
 12E  N3   N  N     0  -0.201   2.3443  -0.9399   0.3361
 12E  O3   O  OH1   0  -0.671  -3.5400   2.9435   1.1937
 12E  C4   C  CH1   0   0.036  -3.7973   1.3195  -0.5069
 12E  N4   N  N     0  -0.404   6.2644   1.8581  -1.1556
 12E  O4   O  OH1   0  -0.672  -5.1903   1.4873  -0.5941
 12E  C5   C  CH1   0  -0.013  -3.4627  -0.1179  -0.9079
 12E  O5   O  O2    0  -0.484  -2.0737  -0.3374  -0.7686
 12E  C6   C  CH2   0  -0.157  -3.8359  -0.4024  -2.3472
 12E  O6   O  OH1   0  -0.668  -3.5943  -1.7613  -2.6200
 12E  C7   C  C     0   0.432   0.2274  -1.7717   0.9042
 12E  C8   C  C1    0  -0.052   3.5967  -1.1423   0.2477
 12E  C9   C  CR6   0   0.148   4.4871  -0.0930  -0.2378
 12E  C10  C  CR16  0  -0.375   5.8552  -0.3378  -0.3057
 12E  C11  C  CR16  0  -0.054   6.6946   0.6645  -0.7687
 12E  C12  C  CR16  0  -0.057   4.9552   2.0892  -1.0889
 12E  C13  C  CR16  0  -0.353   4.0318   1.1612  -0.6437
 12E  H1   H  HCH1  0   0.235  -2.1556  -0.8912   1.2220
 12E  HN1  H  HNH1  0   0.419   0.4327   0.1045   0.2150
 12E  H2   H  HCH1  0   0.230  -1.2393   1.9077   0.3884
 12E  HN2  H  HNH1  0   0.419   1.9586  -2.8321   1.0364
 12E  HO2  H  HOH1  0   0.458  -0.5045   1.3908   2.4594
 12E  H3   H  HCH1  0   0.220  -3.8632   0.9369   1.5936
 12E  HO3  H  HOH1  0   0.458  -3.4242   3.0839   2.1387
 12E  H4   H  HCH1  0   0.213  -3.2730   2.0013  -1.1960
 12E  HO4  H  HOH1  0   0.455  -5.4010   2.3872  -0.3231
 12E  H5   H  HCH1  0   0.224  -4.0188  -0.8052  -0.2495
 12E  H6   H  HCH2  0   0.213  -4.8901  -0.1417  -2.4862
 12E  H6A  H  HCH2  0   0.197  -3.2506   0.2571  -3.0031
 12E  HO6  H  HOH1  0   0.456  -3.8754  -1.9360  -3.5225
 12E  H8   H  H     0   0.266   4.0527  -2.0926   0.5287
 12E  H10  H  HCR6  0   0.276   6.2673  -1.2914  -0.0014
 12E  H11  H  HCR6  0   0.270   7.7628   0.4891  -0.8272
 12E  H12  H  HCR6  0   0.269   4.6209   3.0694  -1.4090
 12E  H13  H  HCR6  0   0.274   2.9807   1.4136  -0.6165

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
 12E  N1   C1   single    1.426  0.020  1.426
 12E  O5   C1   single    1.405  0.020  1.405
 12E  C2   C1   single    1.530  0.020  1.530
 12E  C1   H1   single    0.970  0.020  1.090
 12E  N1   C7   single    1.339  0.020  1.339
 12E  N1   HN1  single    0.860  0.020  1.020
 12E  C7   S1   double    1.671  0.020  1.671
 12E  C2   C3   single    1.523  0.020  1.523
 12E  C2   O2   single    1.404  0.020  1.404
 12E  C2   H2   single    0.970  0.020  1.090
 12E  N3   N2   single    1.336  0.020  1.336
 12E  N2   C7   single    1.355  0.020  1.355
 12E  N2   HN2  single    0.860  0.020  1.020
 12E  O2   HO2  single    0.850  0.020  0.980
 12E  O3   C3   single    1.407  0.020  1.407
 12E  C4   C3   single    1.525  0.020  1.525
 12E  C3   H3   single    0.970  0.020  1.090
 12E  C8   N3   double    1.272  0.020  1.272
 12E  O3   HO3  single    0.850  0.020  0.980
 12E  C4   O4   single    1.406  0.020  1.406
 12E  C4   C5   single    1.529  0.020  1.529
 12E  C4   H4   single    0.970  0.020  1.090
 12E  N4   C11  aromatic  1.326  0.020  1.326
 12E  N4   C12  aromatic  1.331  0.020  1.331
 12E  O4   HO4  single    0.850  0.020  0.980
 12E  C6   C5   single    1.514  0.020  1.514
 12E  O5   C5   single    1.413  0.020  1.413
 12E  C5   H5   single    0.970  0.020  1.090
 12E  C6   O6   single    1.407  0.020  1.407
 12E  C6   H6   single    0.970  0.020  1.090
 12E  C6   H6A  single    0.970  0.020  1.090
 12E  O6   HO6  single    0.850  0.020  0.980
 12E  C9   C8   single    1.459  0.020  1.459
 12E  C8   H8   single    0.930  0.020  1.080
 12E  C10  C9   aromatic  1.391  0.020  1.391
 12E  C13  C9   aromatic  1.395  0.020  1.395
 12E  C11  C10  aromatic  1.387  0.020  1.387
 12E  C10  H10  single    0.930  0.020  1.080
 12E  C11  H11  single    0.930  0.020  1.080
 12E  C12  C13  aromatic  1.383  0.020  1.383
 12E  C12  H12  single    0.930  0.020  1.080
 12E  C13  H13  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
 12E  H1   C1   O5   110.85  3.000
 12E  H1   C1   C2   109.46  3.000
 12E  O5   C1   C2   110.06  3.000
 12E  H1   C1   N1   107.68  3.000
 12E  C2   C1   N1   110.61  3.000
 12E  O5   C1   N1   108.15  3.000
 12E  HN1  N1   C7   116.65  3.000
 12E  HN1  N1   C1   118.13  3.000
 12E  C7   N1   C1   124.53  3.000
 12E  H2   C2   C3   108.69  3.000
 12E  H2   C2   O2   111.60  3.000
 12E  C3   C2   O2   107.66  3.000
 12E  H2   C2   C1   108.71  3.000
 12E  O2   C2   C1   111.48  3.000
 12E  C3   C2   C1   108.61  3.000
 12E  HN2  N2   C7   117.57  3.000
 12E  HN2  N2   N3   121.26  3.000
 12E  C7   N2   N3   121.17  3.000
 12E  HO2  O2   C2   109.15  3.000
 12E  H3   C3   C4   107.75  3.000
 12E  H3   C3   O3   110.74  3.000
 12E  C4   C3   O3   107.54  3.000
 12E  H3   C3   C2   107.97  3.000
 12E  C4   C3   C2   110.81  3.000
 12E  O3   C3   C2   111.97  3.000
 12E  C8   N3   N2   118.52  3.000
 12E  HO3  O3   C3   108.62  3.000
 12E  H4   C4   C5   108.27  3.000
 12E  H4   C4   O4   111.02  3.000
 12E  C5   C4   O4   108.22  3.000
 12E  H4   C4   C3   108.38  3.000
 12E  C5   C4   C3   109.69  3.000
 12E  O4   C4   C3   111.21  3.000
 12E  C12  N4   C11  117.42  3.000
 12E  HO4  O4   C4   108.11  3.000
 12E  H5   C5   C6   109.04  3.000
 12E  H5   C5   O5   109.89  3.000
 12E  C6   C5   O5   107.87  3.000
 12E  H5   C5   C4   108.61  3.000
 12E  O5   C5   C4   109.59  3.000
 12E  C6   C5   C4   111.84  3.000
 12E  C5   O5   C1   113.28  3.000
 12E  H6A  C6   H6   107.11  3.000
 12E  H6A  C6   O6   111.86  3.000
 12E  H6   C6   O6   111.76  3.000
 12E  H6A  C6   C5   108.87  3.000
 12E  H6   C6   C5   108.26  3.000
 12E  O6   C6   C5   108.88  3.000
 12E  HO6  O6   C6   107.90  3.000
 12E  N2   C7   S1   118.82  3.000
 12E  N2   C7   N1   115.44  3.000
 12E  S1   C7   N1   125.74  3.000
 12E  H8   C8   C9   117.20  3.000
 12E  H8   C8   N3   122.17  3.000
 12E  C9   C8   N3   120.63  3.000
 12E  C13  C9   C10  117.71  3.000
 12E  C13  C9   C8   122.97  3.000
 12E  C10  C9   C8   119.32  3.000
 12E  H10  C10  C11  120.00  3.000
 12E  H10  C10  C9   121.04  3.000
 12E  C11  C10  C9   118.96  3.000
 12E  H11  C11  C10  119.83  3.000
 12E  H11  C11  N4   116.71  3.000
 12E  C10  C11  N4   123.47  3.000
 12E  H12  C12  C13  119.73  3.000
 12E  H12  C12  N4   116.46  3.000
 12E  C13  C12  N4   123.81  3.000
 12E  H13  C13  C12  120.04  3.000
 12E  H13  C13  C9   121.33  3.000
 12E  C12  C13  C9   118.63  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
 12E  CONST_01  C9   C10  C11  N4     0.00   0.0  0
 12E  CONST_02  C9   C13  C12  N4     0.00   0.0  0
 12E  CONST_03  C12  C13  C9   C10    0.00   0.0  0
 12E  CONST_04  C12  N4   C11  C10    0.00   0.0  0
 12E  CONST_05  C13  C12  N4   C11    0.00   0.0  0
 12E  CONST_06  C13  C9   C10  C11    0.00   0.0  0
 12E  CONST_07  C11  C10  C9   C8   180.00   0.0  0
 12E  CONST_08  C12  C13  C9   C8   180.00   0.0  0
 12E  CONST_09  H10  C10  C11  N4   180.00   0.0  0
 12E  CONST_10  H13  C13  C12  N4   180.00   0.0  0
 12E  CONST_11  H11  C11  C10  C9   180.00   0.0  0
 12E  CONST_12  H12  C12  C13  C9   180.00   0.0  0
 12E  CONST_13  S1   C7   N1   C1     0.00   0.0  0
 12E  CONST_14  N2   C7   N1   C1   180.00   0.0  0
 12E  CONST_15  N3   N2   C7   N1     0.00   0.0  0
 12E  CONST_16  N3   N2   C7   S1   180.00   0.0  0
 12E  CONST_17  HN2  N2   C7   N1   180.00   0.0  0
 12E  CONST_18  HN1  N1   C7   S1   180.00   0.0  0
 12E  Var_01    C10  C9   C8   N3   179.11  30.0  3
 12E  Var_02    C9   C8   N3   N2   179.68   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
 12E  chir_01  C1  N1  O5  C2  positiv
 12E  chir_02  C2  O2  C1  C3  negativ
 12E  chir_03  C3  O3  C2  C4  positiv
 12E  chir_04  C4  O4  C5  C3  positiv
 12E  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
 12E  plan-1  N4   0.020
 12E  plan-1  C8   0.020
 12E  plan-1  C9   0.020
 12E  plan-1  C10  0.020
 12E  plan-1  C11  0.020
 12E  plan-1  C12  0.020
 12E  plan-1  C13  0.020
 12E  plan-1  H10  0.020
 12E  plan-1  H11  0.020
 12E  plan-1  H12  0.020
 12E  plan-1  H13  0.020
 12E  plan-2  C1   0.020
 12E  plan-2  N1   0.020
 12E  plan-2  S1   0.020
 12E  plan-2  N2   0.020
 12E  plan-2  N3   0.020
 12E  plan-2  C7   0.020
 12E  plan-2  HN1  0.020
 12E  plan-2  HN2  0.020
 12E  plan-3  N2   0.020
 12E  plan-3  N3   0.020
 12E  plan-3  C8   0.020
 12E  plan-3  C9   0.020
 12E  plan-3  H8   0.020

