# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:01:50 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: N-{[(2E)-2-(4-methoxybenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(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
 17S  17S  N-{[(2E)-2-(4-methoxybenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  ligand  46  25  .  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_17S
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
 17S  C1    C  CH1   0   0.224  -2.3235   0.2821  -0.4997
 17S  N1    N  NH1   0  -0.675  -0.9931   0.7918  -0.5252
 17S  S1    S  S1    0  -0.405  -1.7356   3.3063  -1.1064
 17S  C2    C  CH1   0  -0.028  -2.3864  -1.0720  -1.2100
 17S  N2    N  NH1   0  -0.480   0.6584   2.3443  -0.6912
 17S  O2    O  OH1   0  -0.663  -2.0882  -0.9471  -2.5767
 17S  C3    C  CH1   0  -0.008  -3.8005  -1.6222  -1.0933
 17S  N3    N  N     0  -0.229   1.5545   1.3849  -0.3958
 17S  O3    O  OH1   0  -0.671  -3.9001  -2.9321  -1.5977
 17S  C4    C  CH1   0   0.036  -4.2440  -1.6580   0.3643
 17S  O4    O  OH1   0  -0.672  -5.5996  -2.0120   0.4757
 17S  C5    C  CH1   0  -0.013  -4.0579  -0.2771   0.9969
 17S  O5    O  O2    0  -0.486  -2.7175   0.1435   0.8436
 17S  C6    C  CH2   0  -0.157  -4.3674  -0.2950   2.4785
 17S  O6    O  OH1   0  -0.669  -4.2698   1.0159   2.9817
 17S  C7    C  C     0   0.427  -0.6609   2.0708  -0.7505
 17S  O7    O  O2    0  -0.463   6.8040  -1.9870   0.8622
 17S  C8    C  C1    0  -0.054   2.7883   1.6995  -0.3973
 17S  C9    C  CR6   0   0.035   3.8249   0.7330  -0.0737
 17S  C10   C  CR16  0  -0.267   3.5380  -0.5849   0.3059
 17S  C11   C  CR16  0  -0.323   4.5497  -1.4666   0.6094
 17S  C12   C  CR6   0   0.385   5.8896  -1.0602   0.5431
 17S  C13   C  CR16  0  -0.371   6.1895   0.2464   0.1648
 17S  C14   C  CR16  0  -0.285   5.1585   1.1249  -0.1367
 17S  C15   C  CH3   0  -0.440   8.1741  -1.6342   0.8181
 17S  H1    H  HCH1  0   0.234  -2.9686   0.9991  -1.0218
 17S  HN1   H  HNH1  0   0.418  -0.2366   0.1659  -0.2733
 17S  H2    H  HCH1  0   0.230  -1.6951  -1.7665  -0.7080
 17S  HN2   H  HNH1  0   0.414   0.9521   3.2946  -0.8890
 17S  HO2   H  HOH1  0   0.457  -1.1389  -0.8324  -2.6821
 17S  H3    H  HCH1  0   0.219  -4.4775  -0.9422  -1.6357
 17S  HO3   H  HOH1  0   0.458  -3.8054  -2.9007  -2.5548
 17S  H4    H  HCH1  0   0.213  -3.6025  -2.3731   0.9044
 17S  HO4   H  HOH1  0   0.455  -5.7191  -2.8721   0.0593
 17S  H5    H  HCH1  0   0.224  -4.7356   0.4344   0.4966
 17S  H6    H  HCH2  0   0.214  -5.3724  -0.7064   2.6171
 17S  H6A   H  HCH2  0   0.197  -3.6666  -0.9790   2.9778
 17S  HO6   H  HOH1  0   0.457  -4.5365   0.9974   3.9049
 17S  H8    H  H     0   0.255   3.1199   2.7109  -0.6420
 17S  H10   H  HCR6  0   0.262   2.5100  -0.9173   0.3679
 17S  H11   H  HCR6  0   0.270   4.3175  -2.4818   0.9057
 17S  H13   H  HCR6  0   0.285   7.2103   0.5966   0.0992
 17S  H14   H  HCR6  0   0.264   5.4079   2.1380  -0.4288
 17S  H15   H  HCH3  0   0.263   8.7294  -2.5185   1.1194
 17S  H15A  H  HCH3  0   0.233   8.4877  -1.3468  -0.1884
 17S  H15B  H  HCH3  0   0.232   8.4065  -0.8196   1.5082

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
 17S  C2   C1    single    1.530  0.020  1.530
 17S  C1   O5    single    1.407  0.020  1.407
 17S  C1   N1    single    1.425  0.020  1.425
 17S  C1   H1    single    0.970  0.020  1.090
 17S  N1   C7    single    1.341  0.020  1.341
 17S  N1   HN1   single    0.860  0.020  1.020
 17S  C7   S1    double    1.676  0.020  1.676
 17S  C3   C2    single    1.522  0.020  1.522
 17S  O2   C2    single    1.404  0.020  1.404
 17S  C2   H2    single    0.970  0.020  1.090
 17S  C7   N2    single    1.349  0.020  1.349
 17S  N2   N3    single    1.346  0.020  1.346
 17S  N2   HN2   single    0.860  0.020  1.020
 17S  O2   HO2   single    0.850  0.020  0.980
 17S  O3   C3    single    1.407  0.020  1.407
 17S  C3   C4    single    1.524  0.020  1.524
 17S  C3   H3    single    0.970  0.020  1.090
 17S  N3   C8    double    1.273  0.020  1.273
 17S  O3   HO3   single    0.850  0.020  0.980
 17S  O4   C4    single    1.406  0.020  1.406
 17S  C4   C5    single    1.530  0.020  1.530
 17S  C4   H4    single    0.970  0.020  1.090
 17S  O4   HO4   single    0.850  0.020  0.980
 17S  C5   C6    single    1.514  0.020  1.514
 17S  C5   O5    single    1.413  0.020  1.413
 17S  C5   H5    single    0.970  0.020  1.090
 17S  O6   C6    single    1.408  0.020  1.408
 17S  C6   H6    single    0.970  0.020  1.090
 17S  C6   H6A   single    0.970  0.020  1.090
 17S  O6   HO6   single    0.850  0.020  0.980
 17S  C12  O7    single    1.341  0.020  1.341
 17S  O7   C15   single    1.415  0.020  1.415
 17S  C8   C9    single    1.454  0.020  1.454
 17S  C8   H8    single    0.930  0.020  1.080
 17S  C9   C14   aromatic  1.391  0.020  1.391
 17S  C9   C10   aromatic  1.401  0.020  1.401
 17S  C10  C11   aromatic  1.376  0.020  1.376
 17S  C10  H10   single    0.930  0.020  1.080
 17S  C11  C12   aromatic  1.402  0.020  1.402
 17S  C11  H11   single    0.930  0.020  1.080
 17S  C13  C12   aromatic  1.393  0.020  1.393
 17S  C14  C13   aromatic  1.388  0.020  1.388
 17S  C13  H13   single    0.930  0.020  1.080
 17S  C14  H14   single    0.930  0.020  1.080
 17S  C15  H15   single    0.970  0.020  1.090
 17S  C15  H15A  single    0.970  0.020  1.090
 17S  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
 17S  H1    C1   O5    110.75  3.000
 17S  H1    C1   C2    109.47  3.000
 17S  O5    C1   C2    110.15  3.000
 17S  H1    C1   N1    107.87  3.000
 17S  O5    C1   N1    108.29  3.000
 17S  C2    C1   N1    110.28  3.000
 17S  HN1   N1   C7    116.48  3.000
 17S  HN1   N1   C1    118.13  3.000
 17S  C7    N1   C1    125.15  3.000
 17S  H2    C2   C3    108.69  3.000
 17S  H2    C2   O2    111.50  3.000
 17S  C3    C2   O2    107.70  3.000
 17S  H2    C2   C1    108.70  3.000
 17S  O2    C2   C1    111.36  3.000
 17S  C3    C2   C1    108.82  3.000
 17S  HN2   N2   C7    117.70  3.000
 17S  HN2   N2   N3    121.20  3.000
 17S  C7    N2   N3    121.09  3.000
 17S  HO2   O2   C2    109.07  3.000
 17S  H3    C3   C4    107.84  3.000
 17S  H3    C3   O3    110.76  3.000
 17S  C4    C3   O3    107.48  3.000
 17S  H3    C3   C2    108.06  3.000
 17S  C4    C3   C2    110.62  3.000
 17S  O3    C3   C2    112.02  3.000
 17S  C8    N3   N2    117.96  3.000
 17S  HO3   O3   C3    108.61  3.000
 17S  H4    C4   C5    108.19  3.000
 17S  H4    C4   O4    111.05  3.000
 17S  C5    C4   O4    108.17  3.000
 17S  H4    C4   C3    108.34  3.000
 17S  C5    C4   C3    109.80  3.000
 17S  O4    C4   C3    111.25  3.000
 17S  HO4   O4   C4    108.08  3.000
 17S  H5    C5   C6    109.03  3.000
 17S  H5    C5   O5    109.98  3.000
 17S  C6    C5   O5    107.67  3.000
 17S  H5    C5   C4    108.66  3.000
 17S  O5    C5   C4    109.82  3.000
 17S  C6    C5   C4    111.66  3.000
 17S  C5    O5   C1    113.49  3.000
 17S  H6A   C6   H6    107.09  3.000
 17S  H6A   C6   O6    111.90  3.000
 17S  H6    C6   O6    111.62  3.000
 17S  H6A   C6   C5    108.76  3.000
 17S  H6    C6   C5    108.42  3.000
 17S  O6    C6   C5    108.95  3.000
 17S  HO6   O6   C6    107.83  3.000
 17S  N2    C7   S1    119.15  3.000
 17S  N2    C7   N1    115.38  3.000
 17S  S1    C7   N1    125.47  3.000
 17S  C15   O7   C12   118.72  3.000
 17S  H8    C8   C9    116.68  3.000
 17S  H8    C8   N3    121.55  3.000
 17S  C9    C8   N3    121.77  3.000
 17S  C14   C9   C10   118.26  3.000
 17S  C10   C9   C8    122.66  3.000
 17S  C14   C9   C8    119.09  3.000
 17S  H10   C10  C11   119.27  3.000
 17S  H10   C10  C9    119.93  3.000
 17S  C11   C10  C9    120.79  3.000
 17S  H11   C11  C12   119.33  3.000
 17S  H11   C11  C10   120.23  3.000
 17S  C12   C11  C10   120.44  3.000
 17S  C13   C12  C11   119.38  3.000
 17S  C13   C12  O7    124.49  3.000
 17S  C11   C12  O7    116.12  3.000
 17S  H13   C13  C14   118.90  3.000
 17S  H13   C13  C12   121.57  3.000
 17S  C14   C13  C12   119.53  3.000
 17S  H14   C14  C13   118.66  3.000
 17S  H14   C14  C9    119.74  3.000
 17S  C13   C14  C9    121.60  3.000
 17S  H15B  C15  H15A  108.94  3.000
 17S  H15B  C15  H15   108.83  3.000
 17S  H15A  C15  H15   108.83  3.000
 17S  H15B  C15  O7    111.84  3.000
 17S  H15A  C15  O7    111.85  3.000
 17S  H15   C15  O7    106.45  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
 17S  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 17S  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 17S  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 17S  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 17S  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 17S  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 17S  CONST_07  C10  C11  C12  O7   180.00   0.0  0
 17S  CONST_08  C14  C13  C12  O7   180.00   0.0  0
 17S  CONST_09  C13  C14  C9   C8   180.00   0.0  0
 17S  CONST_10  C11  C10  C9   C8   180.00   0.0  0
 17S  CONST_11  H13  C13  C14  C9   180.00   0.0  0
 17S  CONST_12  H11  C11  C10  C9   180.00   0.0  0
 17S  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 17S  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 17S  CONST_15  S1   C7   N1   C1     0.00   0.0  0
 17S  CONST_16  N2   C7   N1   C1   180.00   0.0  0
 17S  CONST_17  N3   N2   C7   N1     0.00   0.0  0
 17S  CONST_18  N3   N2   C7   S1   180.00   0.0  0
 17S  CONST_19  HN2  N2   C7   N1   180.00   0.0  0
 17S  CONST_20  HN1  N1   C7   S1   180.00   0.0  0
 17S  Var_01    C14  C9   C8   N3   177.83  30.0  2
 17S  Var_02    C9   C8   N3   N2   179.21   0.0  2
 17S  Var_03    H15  C15  O7   C12  179.41  30.0  3

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
 17S  chir_01  C1  C2  O5  N1  negativ
 17S  chir_02  C2  O2  C1  C3  negativ
 17S  chir_03  C3  O3  C2  C4  positiv
 17S  chir_04  C4  O4  C5  C3  positiv
 17S  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
 17S  plan-1  O7   0.020
 17S  plan-1  C8   0.020
 17S  plan-1  C9   0.020
 17S  plan-1  C10  0.020
 17S  plan-1  C11  0.020
 17S  plan-1  C12  0.020
 17S  plan-1  C13  0.020
 17S  plan-1  C14  0.020
 17S  plan-1  H10  0.020
 17S  plan-1  H11  0.020
 17S  plan-1  H13  0.020
 17S  plan-1  H14  0.020
 17S  plan-2  C1   0.020
 17S  plan-2  N1   0.020
 17S  plan-2  S1   0.020
 17S  plan-2  N2   0.020
 17S  plan-2  N3   0.020
 17S  plan-2  C7   0.020
 17S  plan-2  HN1  0.020
 17S  plan-2  HN2  0.020
 17S  plan-3  N2   0.020
 17S  plan-3  N3   0.020
 17S  plan-3  C8   0.020
 17S  plan-3  C9   0.020
 17S  plan-3  H8   0.020

