# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:12:09 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: N-({(2E)-2-[4-(trifluoromethyl)benzylidene]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)C(F)(F)F)[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
 21N  21N  N-({(2E)-2-[4-(trifluoromethyl)benzylidene]hydrazinyl}carbothioyl)-beta-D-glucopyranosylamine  ligand  45  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_21N
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
 21N  C1   C  CH1   0   0.226  -3.0361  -0.2544   0.4741
 21N  F1   F  F     0  -0.314   6.3520   1.9401  -1.5732
 21N  N1   N  NH1   0  -0.675  -1.7592  -0.8880   0.4972
 21N  S1   S  S1    0  -0.388  -2.7703  -3.3568   0.7740
 21N  C2   C  CH1   0  -0.029  -2.9772   1.0910   1.2014
 21N  F2   F  F     0  -0.301   7.6070   0.6074  -0.4416
 21N  N2   N  NH1   0  -0.479  -0.2819  -2.6209   0.4872
 21N  O2   O  OH1   0  -0.662  -2.6991   0.9263   2.5679
 21N  C3   C  CH1   0  -0.009  -4.3376   1.7642   1.0866
 21N  F3   F  F     0  -0.313   6.5188   2.1742   0.5549
 21N  N3   N  N     0  -0.210   0.7169  -1.7430   0.3328
 21N  O3   O  OH1   0  -0.671  -4.3245   3.0728   1.6035
 21N  C4   C  CH1   0   0.039  -4.7773   1.8530  -0.3702
 21N  O4   O  OH1   0  -0.672  -6.0961   2.3280  -0.4747
 21N  C5   C  CH1   0  -0.013  -4.7123   0.4672  -1.0135
 21N  O5   O  O2    0  -0.485  -3.4099  -0.0617  -0.8677
 21N  C6   C  CH2   0  -0.157  -5.0280   0.5197  -2.4929
 21N  O6   O  OH1   0  -0.668  -5.0263  -0.7908  -3.0063
 21N  C7   C  C     0   0.431  -1.5691  -2.2118   0.5718
 21N  C8   C  C1    0  -0.053   1.9051  -2.1910   0.2578
 21N  C9   C  CR6   0   0.067   3.0413  -1.2916   0.0920
 21N  C10  C  CR16  0  -0.287   4.3150  -1.8417  -0.0207
 21N  C11  C  CR16  0  -0.268   5.4276  -1.0299  -0.1835
 21N  C12  C  CR6   0  -0.199   5.2707   0.3466  -0.2322
 21N  C13  C  CR16  0  -0.248   3.9989   0.9087  -0.1176
 21N  C14  C  CR16  0  -0.270   2.8946   0.0980   0.0428
 21N  C15  C  CT    0   1.053   6.4414   1.2586  -0.4212
 21N  H1   H  HCH1  0   0.235  -3.7506  -0.9132   0.9827
 21N  HN1  H  HNH1  0   0.418  -0.9418  -0.3223   0.3006
 21N  H2   H  HCH1  0   0.231  -2.2245   1.7255   0.7084
 21N  HN2  H  HNH1  0   0.418  -0.1019  -3.6177   0.5489
 21N  HO2  H  HOH1  0   0.458  -1.7627   0.7363   2.6797
 21N  H3   H  HCH1  0   0.221  -5.0702   1.1400   1.6233
 21N  HO3  H  HOH1  0   0.458  -4.2448   3.0237   2.5612
 21N  H4   H  HCH1  0   0.212  -4.0755   2.5138  -0.9049
 21N  HO4  H  HOH1  0   0.454  -6.1468   3.1684  -0.0069
 21N  H5   H  HCH1  0   0.224  -5.4433  -0.1894  -0.5135
 21N  H6   H  HCH2  0   0.214  -6.0025   1.0021  -2.6211
 21N  H6A  H  HCH2  0   0.196  -4.2841   1.1562  -2.9927
 21N  HO6  H  HOH1  0   0.456  -5.3182  -0.7486  -3.9211
 21N  H8   H  H     0   0.263   2.1218  -3.2590   0.3127
 21N  H10  H  HCR6  0   0.271   4.4433  -2.9162   0.0172
 21N  H11  H  HCR6  0   0.277   6.4032  -1.4870  -0.2708
 21N  H13  H  HCR6  0   0.280   3.8626   1.9820  -0.1528
 21N  H14  H  HCR6  0   0.271   1.9133   0.5439   0.1328

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
 21N  C2   C1   single    1.531  0.020  1.531
 21N  N1   C1   single    1.426  0.020  1.426
 21N  O5   C1   single    1.406  0.020  1.406
 21N  C1   H1   single    0.970  0.020  1.090
 21N  F1   C15  single    1.341  0.020  1.341
 21N  N1   C7   single    1.340  0.020  1.340
 21N  N1   HN1  single    0.860  0.020  1.020
 21N  C7   S1   double    1.672  0.020  1.672
 21N  C2   C3   single    1.522  0.020  1.522
 21N  C2   O2   single    1.404  0.020  1.404
 21N  C2   H2   single    0.970  0.020  1.090
 21N  F2   C15  single    1.335  0.020  1.335
 21N  N3   N2   single    1.339  0.020  1.339
 21N  N2   C7   single    1.353  0.020  1.353
 21N  N2   HN2  single    0.860  0.020  1.020
 21N  O2   HO2  single    0.850  0.020  0.980
 21N  O3   C3   single    1.407  0.020  1.407
 21N  C4   C3   single    1.524  0.020  1.524
 21N  C3   H3   single    0.970  0.020  1.090
 21N  F3   C15  single    1.341  0.020  1.341
 21N  C8   N3   double    1.272  0.020  1.272
 21N  O3   HO3  single    0.850  0.020  0.980
 21N  C4   O4   single    1.406  0.020  1.406
 21N  C4   C5   single    1.529  0.020  1.529
 21N  C4   H4   single    0.970  0.020  1.090
 21N  O4   HO4  single    0.850  0.020  0.980
 21N  C6   C5   single    1.514  0.020  1.514
 21N  O5   C5   single    1.413  0.020  1.413
 21N  C5   H5   single    0.970  0.020  1.090
 21N  O6   C6   single    1.407  0.020  1.407
 21N  C6   H6   single    0.970  0.020  1.090
 21N  C6   H6A  single    0.970  0.020  1.090
 21N  O6   HO6  single    0.850  0.020  0.980
 21N  C9   C8   single    1.459  0.020  1.459
 21N  C8   H8   single    0.930  0.020  1.080
 21N  C10  C9   aromatic  1.392  0.020  1.392
 21N  C14  C9   aromatic  1.398  0.020  1.398
 21N  C11  C10  aromatic  1.387  0.020  1.387
 21N  C10  H10  single    0.930  0.020  1.080
 21N  C12  C11  aromatic  1.386  0.020  1.386
 21N  C11  H11  single    0.930  0.020  1.080
 21N  C15  C12  single    1.496  0.020  1.496
 21N  C12  C13  aromatic  1.395  0.020  1.395
 21N  C13  C14  aromatic  1.379  0.020  1.379
 21N  C13  H13  single    0.930  0.020  1.080
 21N  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
 21N  H1   C1   O5   110.59  3.000
 21N  H1   C1   C2   109.43  3.000
 21N  O5   C1   C2   110.07  3.000
 21N  H1   C1   N1   108.00  3.000
 21N  O5   C1   N1   108.33  3.000
 21N  C2   C1   N1   110.39  3.000
 21N  HN1  N1   C7   116.62  3.000
 21N  HN1  N1   C1   118.12  3.000
 21N  C7   N1   C1   124.56  3.000
 21N  H2   C2   C3   108.81  3.000
 21N  H2   C2   O2   111.59  3.000
 21N  C3   C2   O2   107.59  3.000
 21N  H2   C2   C1   108.67  3.000
 21N  O2   C2   C1   111.53  3.000
 21N  C3   C2   C1   108.57  3.000
 21N  HN2  N2   C7   117.51  3.000
 21N  HN2  N2   N3   121.26  3.000
 21N  C7   N2   N3   121.24  3.000
 21N  HO2  O2   C2   109.21  3.000
 21N  H3   C3   C4   107.86  3.000
 21N  H3   C3   O3   110.74  3.000
 21N  C4   C3   O3   107.44  3.000
 21N  H3   C3   C2   107.87  3.000
 21N  C4   C3   C2   110.83  3.000
 21N  O3   C3   C2   112.04  3.000
 21N  C8   N3   N2   118.21  3.000
 21N  HO3  O3   C3   108.60  3.000
 21N  H4   C4   C5   108.19  3.000
 21N  H4   C4   O4   111.02  3.000
 21N  C5   C4   O4   108.35  3.000
 21N  H4   C4   C3   108.35  3.000
 21N  C5   C4   C3   109.70  3.000
 21N  O4   C4   C3   111.18  3.000
 21N  HO4  O4   C4   107.94  3.000
 21N  H5   C5   C6   109.01  3.000
 21N  H5   C5   O5   109.96  3.000
 21N  C6   C5   O5   107.82  3.000
 21N  H5   C5   C4   108.70  3.000
 21N  O5   C5   C4   109.57  3.000
 21N  C6   C5   C4   111.77  3.000
 21N  C5   O5   C1   113.25  3.000
 21N  H6A  C6   H6   107.09  3.000
 21N  H6A  C6   O6   111.87  3.000
 21N  H6   C6   O6   111.63  3.000
 21N  H6A  C6   C5   108.86  3.000
 21N  H6   C6   C5   108.39  3.000
 21N  O6   C6   C5   108.90  3.000
 21N  HO6  O6   C6   107.82  3.000
 21N  N2   C7   S1   118.94  3.000
 21N  N2   C7   N1   115.49  3.000
 21N  S1   C7   N1   125.57  3.000
 21N  H8   C8   C9   117.04  3.000
 21N  H8   C8   N3   121.81  3.000
 21N  C9   C8   N3   121.14  3.000
 21N  C14  C9   C10  119.08  3.000
 21N  C14  C9   C8   122.35  3.000
 21N  C10  C9   C8   118.57  3.000
 21N  H10  C10  C11  119.33  3.000
 21N  H10  C10  C9   119.86  3.000
 21N  C11  C10  C9   120.81  3.000
 21N  H11  C11  C12  121.28  3.000
 21N  H11  C11  C10  119.08  3.000
 21N  C12  C11  C10  119.64  3.000
 21N  C15  C12  C13  118.57  3.000
 21N  C13  C12  C11  120.02  3.000
 21N  C15  C12  C11  121.41  3.000
 21N  H13  C13  C14  119.06  3.000
 21N  H13  C13  C12  120.77  3.000
 21N  C14  C13  C12  120.17  3.000
 21N  H14  C14  C13  119.59  3.000
 21N  H14  C14  C9   120.13  3.000
 21N  C13  C14  C9   120.28  3.000
 21N  C12  C15  F3   111.68  3.000
 21N  C12  C15  F2   112.81  3.000
 21N  F3   C15  F2   107.08  3.000
 21N  C12  C15  F1   111.47  3.000
 21N  F3   C15  F1   106.39  3.000
 21N  F2   C15  F1   107.03  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
 21N  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 21N  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 21N  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 21N  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 21N  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 21N  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 21N  CONST_07  C11  C10  C9   C8    180.00   0.0  0
 21N  CONST_08  C13  C14  C9   C8    180.00   0.0  0
 21N  CONST_09  C15  C12  C11  C10   180.00   0.0  0
 21N  CONST_10  C15  C12  C13  C14   180.00   0.0  0
 21N  CONST_11  H11  C11  C10  C9    180.00   0.0  0
 21N  CONST_12  H13  C13  C14  C9    180.00   0.0  0
 21N  CONST_13  H14  C14  C9   C10   180.00   0.0  0
 21N  CONST_14  H10  C10  C11  C12   180.00   0.0  0
 21N  CONST_15  S1   C7   N1   C1      0.00   0.0  0
 21N  CONST_16  N2   C7   N1   C1    180.00   0.0  0
 21N  CONST_17  N3   N2   C7   N1      0.00   0.0  0
 21N  CONST_18  N3   N2   C7   S1    180.00   0.0  0
 21N  CONST_19  HN2  N2   C7   N1    180.00   0.0  0
 21N  CONST_20  HN1  N1   C7   S1    180.00   0.0  0
 21N  Var_01    C11  C12  C15  F1    116.26  30.0  2
 21N  Var_02    C10  C9   C8   N3   -178.26  30.0  3
 21N  Var_03    C9   C8   N3   N2   -179.88   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
 21N  chir_01  C1  C2  N1  O5  positiv
 21N  chir_02  C2  O2  C1  C3  negativ
 21N  chir_03  C3  O3  C2  C4  positiv
 21N  chir_04  C4  O4  C5  C3  positiv
 21N  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
 21N  plan-1  C8   0.020
 21N  plan-1  C9   0.020
 21N  plan-1  C10  0.020
 21N  plan-1  C11  0.020
 21N  plan-1  C12  0.020
 21N  plan-1  C13  0.020
 21N  plan-1  C14  0.020
 21N  plan-1  C15  0.020
 21N  plan-1  H10  0.020
 21N  plan-1  H11  0.020
 21N  plan-1  H13  0.020
 21N  plan-1  H14  0.020
 21N  plan-2  C1   0.020
 21N  plan-2  N1   0.020
 21N  plan-2  S1   0.020
 21N  plan-2  N2   0.020
 21N  plan-2  N3   0.020
 21N  plan-2  C7   0.020
 21N  plan-2  HN1  0.020
 21N  plan-2  HN2  0.020
 21N  plan-3  N2   0.020
 21N  plan-3  N3   0.020
 21N  plan-3  C8   0.020
 21N  plan-3  C9   0.020
 21N  plan-3  H8   0.020

