# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:58:54 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: phenyl 1-thio-beta-D-glucopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)Sc2ccccc2
#
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
 FYJ  FYJ  'phenyl 1-thio-beta-D-glucopyranosiduronic acid'  D-saccharide  33  19  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_FYJ
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
 FYJ  C10  C  C     0   0.498  -2.0038   2.4028   0.1035
 FYJ  C02  C  CH1   0   0.018  -2.3486  -1.4000  -0.3529
 FYJ  C03  C  CH1   0   0.012  -1.0967  -1.7262   0.4601
 FYJ  C05  C  CH1   0  -0.143  -0.0429  -0.6418   0.2311
 FYJ  C07  C  CH1   0  -0.065  -1.6329   0.9848  -0.2763
 FYJ  C08  C  CH1   0   0.006  -2.8258   0.0197  -0.0752
 FYJ  C14  C  CR6   0  -0.139   2.6783  -0.1732   0.3909
 FYJ  C15  C  CR16  0  -0.218   2.7483   1.2163   0.3267
 FYJ  C16  C  CR16  0  -0.245   3.7787   1.8211  -0.3791
 FYJ  C17  C  CR16  0  -0.253   4.7497   1.0459  -1.0009
 FYJ  C18  C  CR16  0  -0.246   4.6861  -0.3389  -0.9232
 FYJ  C19  C  CR16  0  -0.239   3.6488  -0.9511  -0.2323
 FYJ  O01  O  OH1   0  -0.661  -3.3985  -2.2763  -0.0448
 FYJ  O04  O  OH1   0  -0.660  -0.6501  -2.9843   0.0308
 FYJ  O06  O  O2    0  -0.461  -0.5626   0.6205   0.5550
 FYJ  O09  O  OH1   0  -0.656  -3.8778   0.2997  -0.9538
 FYJ  O11  O  O     0  -0.420  -1.7174   2.9160   1.1515
 FYJ  O12  O  OH1   0  -0.585  -2.7037   2.9933  -0.8524
 FYJ  S13  S  S2    0   0.028   1.3795  -0.9653   1.3020
 FYJ  H1   H  HCH1  0   0.220  -2.0795  -1.4630  -1.4209
 FYJ  H2   H  HCH1  0   0.236  -1.3666  -1.7302   1.5271
 FYJ  H3   H  HCH1  0   0.272   0.3036  -0.6735  -0.8113
 FYJ  H4   H  HCH1  0   0.268  -1.3406   0.9615  -1.3368
 FYJ  H5   H  HCH1  0   0.244  -3.1427   0.0858   0.9752
 FYJ  H6   H  HCR6  0   0.269   2.0013   1.8208   0.8235
 FYJ  H7   H  HCR6  0   0.264   3.8280   2.9008  -0.4349
 FYJ  H8   H  HCR6  0   0.264   5.5569   1.5216  -1.5422
 FYJ  H9   H  HCR6  0   0.264   5.4410  -0.9459  -1.4055
 FYJ  H10  H  HCR6  0   0.269   3.5913  -2.0307  -0.1809
 FYJ  H11  H  HOH1  0   0.454  -3.1189  -3.1706  -0.2663
 FYJ  H12  H  HOH1  0   0.456   0.0472  -3.2893   0.6211
 FYJ  H13  H  HOH1  0   0.461  -4.4454   0.9727  -0.5684
 FYJ  H14  H  HOH1  0   0.489  -2.9732   3.8813  -0.5708

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
 FYJ  O11  C10  double    1.201  0.020  1.201
 FYJ  O12  C10  single    1.324  0.020  1.324
 FYJ  O09  C08  single    1.399  0.020  1.399
 FYJ  C10  C07  single    1.514  0.020  1.514
 FYJ  C08  C07  single    1.547  0.020  1.547
 FYJ  C08  C02  single    1.523  0.020  1.523
 FYJ  C07  O06  single    1.403  0.020  1.403
 FYJ  O01  C02  single    1.402  0.020  1.402
 FYJ  O06  C05  single    1.403  0.020  1.403
 FYJ  C02  C03  single    1.528  0.020  1.528
 FYJ  C03  C05  single    1.529  0.020  1.529
 FYJ  C03  O04  single    1.402  0.020  1.402
 FYJ  C05  S13  single    1.810  0.020  1.810
 FYJ  C15  C16  aromatic  1.388  0.020  1.388
 FYJ  C15  C14  aromatic  1.393  0.020  1.393
 FYJ  S13  C14  single    1.773  0.020  1.773
 FYJ  C16  C17  aromatic  1.389  0.020  1.389
 FYJ  C14  C19  aromatic  1.391  0.020  1.391
 FYJ  C17  C18  aromatic  1.388  0.020  1.388
 FYJ  C19  C18  aromatic  1.389  0.020  1.389
 FYJ  C02  H1   single    0.970  0.020  1.090
 FYJ  C03  H2   single    0.970  0.020  1.090
 FYJ  C05  H3   single    0.970  0.020  1.090
 FYJ  C07  H4   single    0.970  0.020  1.090
 FYJ  C08  H5   single    0.970  0.020  1.090
 FYJ  C15  H6   single    0.930  0.020  1.080
 FYJ  C16  H7   single    0.930  0.020  1.080
 FYJ  C17  H8   single    0.930  0.020  1.080
 FYJ  C18  H9   single    0.930  0.020  1.080
 FYJ  C19  H10  single    0.930  0.020  1.080
 FYJ  O01  H11  single    0.850  0.020  0.980
 FYJ  O04  H12  single    0.850  0.020  0.980
 FYJ  O09  H13  single    0.850  0.020  0.980
 FYJ  O12  H14  single    0.850  0.020  0.980

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
 FYJ  O12  C10  O11  124.43  3.000
 FYJ  O12  C10  C07  111.48  3.000
 FYJ  O11  C10  C07  124.08  3.000
 FYJ  H1   C02  O01  111.09  3.000
 FYJ  H1   C02  C08  107.82  3.000
 FYJ  O01  C02  C08  107.93  3.000
 FYJ  H1   C02  C03  107.64  3.000
 FYJ  O01  C02  C03  111.30  3.000
 FYJ  C08  C02  C03  111.02  3.000
 FYJ  H2   C03  O04  111.82  3.000
 FYJ  H2   C03  C05  108.46  3.000
 FYJ  O04  C03  C05  111.77  3.000
 FYJ  H2   C03  C02  108.40  3.000
 FYJ  O04  C03  C02  106.83  3.000
 FYJ  C05  C03  C02  109.48  3.000
 FYJ  H3   C05  S13  107.96  3.000
 FYJ  H3   C05  O06  111.21  3.000
 FYJ  S13  C05  O06  108.38  3.000
 FYJ  H3   C05  C03  109.81  3.000
 FYJ  S13  C05  C03  109.04  3.000
 FYJ  O06  C05  C03  110.38  3.000
 FYJ  H4   C07  O06  111.28  3.000
 FYJ  H4   C07  C08  108.47  3.000
 FYJ  O06  C07  C08  110.43  3.000
 FYJ  H4   C07  C10  109.06  3.000
 FYJ  O06  C07  C10  106.34  3.000
 FYJ  C08  C07  C10  111.26  3.000
 FYJ  H5   C08  O09  111.80  3.000
 FYJ  H5   C08  C07  107.99  3.000
 FYJ  O09  C08  C07  111.91  3.000
 FYJ  H5   C08  C02  108.70  3.000
 FYJ  C07  C08  C02  108.43  3.000
 FYJ  O09  C08  C02  107.92  3.000
 FYJ  S13  C14  C19  119.43  3.000
 FYJ  C19  C14  C15  120.14  3.000
 FYJ  S13  C14  C15  120.41  3.000
 FYJ  H6   C15  C16  120.18  3.000
 FYJ  H6   C15  C14  120.11  3.000
 FYJ  C16  C15  C14  119.71  3.000
 FYJ  H7   C16  C17  120.12  3.000
 FYJ  H7   C16  C15  119.66  3.000
 FYJ  C17  C16  C15  120.22  3.000
 FYJ  H8   C17  C18  120.04  3.000
 FYJ  H8   C17  C16  119.99  3.000
 FYJ  C18  C17  C16  119.97  3.000
 FYJ  H9   C18  C19  119.71  3.000
 FYJ  H9   C18  C17  120.17  3.000
 FYJ  C19  C18  C17  120.12  3.000
 FYJ  H10  C19  C18  120.21  3.000
 FYJ  H10  C19  C14  119.96  3.000
 FYJ  C18  C19  C14  119.83  3.000
 FYJ  H11  O01  C02  108.21  3.000
 FYJ  H12  O04  C03  109.09  3.000
 FYJ  C07  O06  C05  112.29  3.000
 FYJ  H13  O09  C08  109.42  3.000
 FYJ  H14  O12  C10  110.22  3.000
 FYJ  C14  S13  C05  101.06  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
 FYJ  CONST_01  C17  C16  C15  C14    0.00   0.0  0
 FYJ  CONST_02  C17  C18  C19  C14    0.00   0.0  0
 FYJ  CONST_03  C18  C17  C16  C15    0.00   0.0  0
 FYJ  CONST_04  C18  C19  C14  C15    0.00   0.0  0
 FYJ  CONST_05  C19  C14  C15  C16    0.00   0.0  0
 FYJ  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 FYJ  CONST_07  S13  C14  C15  C16  180.00   0.0  0
 FYJ  CONST_08  S13  C14  C19  C18  180.00   0.0  0
 FYJ  CONST_09  H7   C16  C15  C14  180.00   0.0  0
 FYJ  CONST_10  H9   C18  C19  C14  180.00   0.0  0
 FYJ  CONST_11  H8   C17  C16  C15  180.00   0.0  0
 FYJ  CONST_12  H10  C19  C14  C15  180.00   0.0  0
 FYJ  CONST_13  H6   C15  C16  C17  180.00   0.0  0
 FYJ  CONST_14  H14  O12  C10  C07  180.00   0.0  0
 FYJ  Var_01    C15  C14  S13  C05   71.88  30.0  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
 FYJ  chir_01  C02  C08  O01  C03  positiv
 FYJ  chir_02  C03  O04  C02  C05  positiv
 FYJ  chir_03  C05  S13  O06  C03  positiv
 FYJ  chir_04  C07  O06  C08  C10  negativ
 FYJ  chir_05  C08  O09  C07  C02  positiv

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
 FYJ  plan-1  C14  0.020
 FYJ  plan-1  C15  0.020
 FYJ  plan-1  C16  0.020
 FYJ  plan-1  C17  0.020
 FYJ  plan-1  C18  0.020
 FYJ  plan-1  C19  0.020
 FYJ  plan-1  S13  0.020
 FYJ  plan-1  H6   0.020
 FYJ  plan-1  H7   0.020
 FYJ  plan-1  H8   0.020
 FYJ  plan-1  H9   0.020
 FYJ  plan-1  H10  0.020
 FYJ  plan-2  C10  0.020
 FYJ  plan-2  C07  0.020
 FYJ  plan-2  O11  0.020
 FYJ  plan-2  O12  0.020
 FYJ  plan-2  H14  0.020

