# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:02:13 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: N-{[(2E)-2-(4-methylbenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)\C=N\NC(=S)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
#
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
 18S  18S  N-{[(2E)-2-(4-methylbenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  ligand  45  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_18S
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
 18S  C1    C  CH1   0   0.221  -1.9357  -0.2979   0.5027
 18S  N1    N  NH1   0  -0.673  -0.5766  -0.7259   0.5508
 18S  S1    S  S1    0  -0.402  -1.1632  -3.2449   1.2768
 18S  C2    C  CH1   0  -0.026  -2.1009   1.0479   1.2115
 18S  N2    N  NH1   0  -0.480   1.1651  -2.1682   0.7888
 18S  O2    O  OH1   0  -0.663  -1.8125   0.9423   2.5821
 18S  C3    C  CH1   0  -0.005  -3.5492   1.4959   1.0746
 18S  N3    N  N     0  -0.221   2.0025  -1.1854   0.4163
 18S  O3    O  OH1   0  -0.671  -3.7522   2.7931   1.5800
 18S  C4    C  CH1   0   0.034  -3.9726   1.5035  -0.3897
 18S  O4    O  OH1   0  -0.671  -5.3499   1.7511  -0.5223
 18S  C5    C  CH1   0  -0.013  -3.6744   0.1433  -1.0254
 18S  O5    O  O2    0  -0.486  -2.3108  -0.1823  -0.8474
 18S  C6    C  CH2   0  -0.157  -3.9552   0.1495  -2.5129
 18S  O6    O  OH1   0  -0.669  -3.7554  -1.1479  -3.0196
 18S  C7    C  C     0   0.427  -0.1686  -1.9679   0.8437
 18S  C8    C  C1    0  -0.058   3.2506  -1.4348   0.4127
 18S  C9    C  CR6   0   0.045   4.2297  -0.4378   0.0022
 18S  C10   C  CR16  0  -0.286   5.5834  -0.7605   0.0674
 18S  C11   C  CR16  0  -0.288   6.5498   0.1561  -0.3196
 18S  C12   C  CR6   0   0.094   6.1935   1.4174  -0.7865
 18S  C13   C  CR16  0  -0.276   4.8336   1.7369  -0.8458
 18S  C14   C  CR16  0  -0.271   3.8654   0.8305  -0.4603
 18S  C15   C  CH3   0  -0.723   7.2300   2.4010  -1.2399
 18S  H1    H  HCH1  0   0.235  -2.5426  -1.0554   1.0135
 18S  HN1   H  HNH1  0   0.418   0.1406  -0.0679   0.2672
 18S  H2    H  HCH1  0   0.230  -1.4531   1.7899   0.7199
 18S  HN2   H  HNH1  0   0.415   1.5127  -3.0882   1.0367
 18S  HO2   H  HOH1  0   0.458  -0.8582   0.9098   2.7001
 18S  H3    H  HCH1  0   0.218  -4.1834   0.7666   1.6044
 18S  HO3   H  HOH1  0   0.457  -3.6568   2.7678   2.5373
 18S  H4    H  HCH1  0   0.214  -3.3802   2.2679  -0.9179
 18S  HO4   H  HOH1  0   0.455  -5.5395   2.6151  -0.1421
 18S  H5    H  HCH1  0   0.225  -4.3085  -0.6180  -0.5416
 18S  H6    H  HCH2  0   0.213  -4.9833   0.4918  -2.6679
 18S  H6A   H  HCH2  0   0.197  -3.2937   0.8843  -2.9931
 18S  HO6   H  HOH1  0   0.457  -3.9745  -1.1372  -3.9553
 18S  H8    H  H     0   0.257   3.6396  -2.4092   0.7162
 18S  H10   H  HCR6  0   0.258   5.8871  -1.7361   0.4281
 18S  H11   H  HCR6  0   0.254   7.5962  -0.1167  -0.2562
 18S  H13   H  HCR6  0   0.254   4.5316   2.7141  -1.2037
 18S  H14   H  HCR6  0   0.258   2.8200   1.1047  -0.5206
 18S  H15   H  HCH3  0   0.252   7.2781   2.4364  -2.3303
 18S  H15A  H  HCH3  0   0.248   7.0010   3.4101  -0.8973
 18S  H15B  H  HCH3  0   0.247   8.2215   2.1345  -0.8771

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
 18S  C2   C1    single    1.530  0.020  1.530
 18S  N1   C1    single    1.426  0.020  1.426
 18S  O5   C1    single    1.406  0.020  1.406
 18S  C1   H1    single    0.970  0.020  1.090
 18S  N1   C7    single    1.340  0.020  1.340
 18S  N1   HN1   single    0.860  0.020  1.020
 18S  C7   S1    double    1.676  0.020  1.676
 18S  C2   C3    single    1.522  0.020  1.522
 18S  C2   O2    single    1.405  0.020  1.405
 18S  C2   H2    single    0.970  0.020  1.090
 18S  N3   N2    single    1.344  0.020  1.344
 18S  N2   C7    single    1.350  0.020  1.350
 18S  N2   HN2   single    0.860  0.020  1.020
 18S  O2   HO2   single    0.850  0.020  0.980
 18S  O3   C3    single    1.407  0.020  1.407
 18S  C4   C3    single    1.524  0.020  1.524
 18S  C3   H3    single    0.970  0.020  1.090
 18S  C8   N3    double    1.273  0.020  1.273
 18S  O3   HO3   single    0.850  0.020  0.980
 18S  C4   O4    single    1.406  0.020  1.406
 18S  C4   C5    single    1.531  0.020  1.531
 18S  C4   H4    single    0.970  0.020  1.090
 18S  O4   HO4   single    0.850  0.020  0.980
 18S  C6   C5    single    1.514  0.020  1.514
 18S  O5   C5    single    1.413  0.020  1.413
 18S  C5   H5    single    0.970  0.020  1.090
 18S  C6   O6    single    1.407  0.020  1.407
 18S  C6   H6    single    0.970  0.020  1.090
 18S  C6   H6A   single    0.970  0.020  1.090
 18S  O6   HO6   single    0.850  0.020  0.980
 18S  C9   C8    single    1.456  0.020  1.456
 18S  C8   H8    single    0.930  0.020  1.080
 18S  C10  C9    aromatic  1.393  0.020  1.393
 18S  C14  C9    aromatic  1.398  0.020  1.398
 18S  C11  C10   aromatic  1.387  0.020  1.387
 18S  C10  H10   single    0.930  0.020  1.080
 18S  C12  C11   aromatic  1.391  0.020  1.391
 18S  C11  H11   single    0.930  0.020  1.080
 18S  C15  C12   single    1.499  0.020  1.499
 18S  C12  C13   aromatic  1.398  0.020  1.398
 18S  C13  C14   aromatic  1.381  0.020  1.381
 18S  C13  H13   single    0.930  0.020  1.080
 18S  C14  H14   single    0.930  0.020  1.080
 18S  C15  H15   single    0.970  0.020  1.090
 18S  C15  H15A  single    0.970  0.020  1.090
 18S  C15  H15B  single    0.970  0.020  1.090

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
 18S  H1    C1   O5    110.88  3.000
 18S  H1    C1   C2    109.39  3.000
 18S  O5    C1   C2    110.10  3.000
 18S  H1    C1   N1    107.72  3.000
 18S  O5    C1   N1    108.14  3.000
 18S  C2    C1   N1    110.57  3.000
 18S  HN1   N1   C7    116.58  3.000
 18S  HN1   N1   C1    118.04  3.000
 18S  C7    N1   C1    125.17  3.000
 18S  H2    C2   C3    108.75  3.000
 18S  H2    C2   O2    111.44  3.000
 18S  C3    C2   O2    107.77  3.000
 18S  H2    C2   C1    108.81  3.000
 18S  O2    C2   C1    111.33  3.000
 18S  C3    C2   C1    108.66  3.000
 18S  HN2   N2   C7    117.61  3.000
 18S  HN2   N2   N3    121.16  3.000
 18S  C7    N2   N3    121.23  3.000
 18S  HO2   O2   C2    109.02  3.000
 18S  H3    C3   C4    107.77  3.000
 18S  H3    C3   O3    110.76  3.000
 18S  C4    C3   O3    107.49  3.000
 18S  H3    C3   C2    108.03  3.000
 18S  C4    C3   C2    110.62  3.000
 18S  O3    C3   C2    112.11  3.000
 18S  C8    N3   N2    117.94  3.000
 18S  HO3   O3   C3    108.59  3.000
 18S  H4    C4   C5    108.22  3.000
 18S  H4    C4   O4    111.06  3.000
 18S  C5    C4   O4    107.95  3.000
 18S  H4    C4   C3    108.34  3.000
 18S  C5    C4   C3    109.90  3.000
 18S  O4    C4   C3    111.32  3.000
 18S  HO4   O4   C4    108.28  3.000
 18S  H5    C5   C6    109.10  3.000
 18S  H5    C5   O5    109.91  3.000
 18S  C6    C5   O5    107.68  3.000
 18S  H5    C5   C4    108.62  3.000
 18S  O5    C5   C4    109.90  3.000
 18S  C6    C5   C4    111.61  3.000
 18S  C5    O5   C1    113.41  3.000
 18S  H6A   C6   H6    107.12  3.000
 18S  H6A   C6   O6    111.94  3.000
 18S  H6    C6   O6    111.76  3.000
 18S  H6A   C6   C5    108.69  3.000
 18S  H6    C6   C5    108.34  3.000
 18S  O6    C6   C5    108.89  3.000
 18S  HO6   O6   C6    107.94  3.000
 18S  N2    C7   S1    118.94  3.000
 18S  N2    C7   N1    115.45  3.000
 18S  S1    C7   N1    125.61  3.000
 18S  H8    C8   C9    116.72  3.000
 18S  H8    C8   N3    121.55  3.000
 18S  C9    C8   N3    121.72  3.000
 18S  C14   C9   C10   118.60  3.000
 18S  C14   C9   C8    122.62  3.000
 18S  C10   C9   C8    118.78  3.000
 18S  H10   C10  C11   119.51  3.000
 18S  H10   C10  C9    119.76  3.000
 18S  C11   C10  C9    120.73  3.000
 18S  H11   C11  C12   119.69  3.000
 18S  H11   C11  C10   119.36  3.000
 18S  C12   C11  C10   120.95  3.000
 18S  C15   C12  C13   120.64  3.000
 18S  C13   C12  C11   118.07  3.000
 18S  C15   C12  C11   121.28  3.000
 18S  H13   C13  C14   119.25  3.000
 18S  H13   C13  C12   119.42  3.000
 18S  C14   C13  C12   121.33  3.000
 18S  H14   C14  C13   119.69  3.000
 18S  H14   C14  C9    119.98  3.000
 18S  C13   C14  C9    120.33  3.000
 18S  H15B  C15  H15A  108.25  3.000
 18S  H15B  C15  H15   107.49  3.000
 18S  H15A  C15  H15   107.04  3.000
 18S  H15B  C15  C12   111.61  3.000
 18S  H15A  C15  C12   111.54  3.000
 18S  H15   C15  C12   110.71  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
 18S  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 18S  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 18S  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 18S  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 18S  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 18S  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 18S  CONST_07  C11  C10  C9   C8   180.00   0.0  0
 18S  CONST_08  C13  C14  C9   C8   180.00   0.0  0
 18S  CONST_09  C15  C12  C11  C10  180.00   0.0  0
 18S  CONST_10  C15  C12  C13  C14  180.00   0.0  0
 18S  CONST_11  H11  C11  C10  C9   180.00   0.0  0
 18S  CONST_12  H13  C13  C14  C9   180.00   0.0  0
 18S  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 18S  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 18S  CONST_15  S1   C7   N1   C1     0.00   0.0  0
 18S  CONST_16  N2   C7   N1   C1   180.00   0.0  0
 18S  CONST_17  N3   N2   C7   N1     0.00   0.0  0
 18S  CONST_18  N3   N2   C7   S1   180.00   0.0  0
 18S  CONST_19  HN2  N2   C7   N1   180.00   0.0  0
 18S  CONST_20  HN1  N1   C7   S1   180.00   0.0  0
 18S  Var_01    C10  C9   C8   N3   177.73  30.0  2
 18S  Var_02    H15  C15  C12  C11  102.25  30.0  2
 18S  Var_03    C9   C8   N3   N2   178.95   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
 18S  chir_01  C1  C2  N1  O5  positiv
 18S  chir_02  C2  O2  C1  C3  negativ
 18S  chir_03  C3  O3  C2  C4  positiv
 18S  chir_04  C4  O4  C5  C3  positiv
 18S  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
 18S  plan-1  C8   0.020
 18S  plan-1  C9   0.020
 18S  plan-1  C10  0.020
 18S  plan-1  C11  0.020
 18S  plan-1  C12  0.020
 18S  plan-1  C13  0.020
 18S  plan-1  C14  0.020
 18S  plan-1  C15  0.020
 18S  plan-1  H10  0.020
 18S  plan-1  H11  0.020
 18S  plan-1  H13  0.020
 18S  plan-1  H14  0.020
 18S  plan-2  C1   0.020
 18S  plan-2  N1   0.020
 18S  plan-2  S1   0.020
 18S  plan-2  N2   0.020
 18S  plan-2  N3   0.020
 18S  plan-2  C7   0.020
 18S  plan-2  HN1  0.020
 18S  plan-2  HN2  0.020
 18S  plan-3  N2   0.020
 18S  plan-3  N3   0.020
 18S  plan-3  C8   0.020
 18S  plan-3  C9   0.020
 18S  plan-3  H8   0.020

