# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:44:47 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  32  19  .  2023-02-15  2023-02-15
;
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   0.441  -1.9987   2.4066   0.0368
 FYJ  C02  C  CH1    0   0.020  -2.3760  -1.4305  -0.4192
 FYJ  C03  C  CH1    0   0.011  -1.1219  -1.7961   0.3757
 FYJ  C05  C  CH1    0  -0.136  -0.0615  -0.7107   0.1678
 FYJ  C07  C  CH1    0  -0.154  -1.6340   0.9449  -0.2874
 FYJ  C08  C  CH1    0   0.034  -2.8219  -0.0126  -0.1003
 FYJ  C14  C  C      0  -0.138   2.6657  -0.2208   0.3492
 FYJ  C15  C  C1     0  -0.230   2.5678   1.1416   0.0680
 FYJ  C16  C  C1     0  -0.244   3.6097   1.7828  -0.5870
 FYJ  C17  C  C1     0  -0.256   4.7592   1.0846  -0.9355
 FYJ  C18  C  C1     0  -0.246   4.8613  -0.2672  -0.6372
 FYJ  C19  C  C1     0  -0.250   3.8142  -0.9233  -0.0037
 FYJ  O01  O  OH1    0  -0.668  -3.4369  -2.3071  -0.1336
 FYJ  O04  O  OH1    0  -0.663  -0.6900  -3.0491  -0.0884
 FYJ  O06  O  O2     0  -0.460  -0.5599   0.5419   0.5306
 FYJ  O09  O  OH1    0  -0.701  -3.8868   0.3378  -0.9394
 FYJ  O11  O  O      0  -0.555  -1.1771   3.0984   0.6403
 FYJ  O12  O  OC    -1  -0.615  -3.1302   2.7688  -0.3832
 FYJ  S13  S  S2     0   0.028   1.3753  -1.0778   1.2102
 FYJ  H1   H  HCH1   0   0.205  -2.1128  -1.4684  -1.4898
 FYJ  H2   H  HCH1   0   0.228  -1.3823  -1.8270   1.4446
 FYJ  H3   H  HCH1   0   0.258   0.2757  -0.7215  -0.8792
 FYJ  H4   H  HCH1   0   0.228  -1.3355   0.9088  -1.3506
 FYJ  H5   H  HCH1   0   0.194  -3.1179   0.0247   0.9629
 FYJ  H6   H  H      0   0.276   1.6827   1.6969   0.3505
 FYJ  H7   H  H      0   0.262   3.5260   2.8376  -0.8147
 FYJ  H8   H  H      0   0.261   5.5723   1.5925  -1.4372
 FYJ  H9   H  H      0   0.262   5.7517  -0.8190  -0.9094
 FYJ  H10  H  H      0   0.267   3.8878  -1.9822   0.2090
 FYJ  H11  H  HOH1   0   0.450  -3.1688  -3.1963  -0.3869
 FYJ  H12  H  HOH1   0   0.454   0.0046  -3.3774   0.4923
 FYJ  H13  H  HOH1   0   0.439  -3.8978   1.3214  -0.8796

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  deloc     1.232  0.020  1.232
 FYJ  O12  C10  deloc     1.260  0.020  1.260
 FYJ  O09  C08  single    1.400  0.020  1.400
 FYJ  C10  C07  single    1.541  0.020  1.541
 FYJ  C08  C07  single    1.537  0.020  1.537
 FYJ  C08  C02  single    1.520  0.020  1.520
 FYJ  C07  O06  single    1.409  0.020  1.409
 FYJ  O01  C02  single    1.405  0.020  1.405
 FYJ  O06  C05  single    1.396  0.020  1.396
 FYJ  C02  C03  single    1.529  0.020  1.529
 FYJ  C03  C05  single    1.532  0.020  1.532
 FYJ  C03  O04  single    1.404  0.020  1.404
 FYJ  C05  S13  single    1.813  0.020  1.813
 FYJ  C15  C16  aromatic  1.388  0.020  1.388
 FYJ  C15  C14  aromatic  1.394  0.020  1.394
 FYJ  S13  C14  single    1.772  0.020  1.772
 FYJ  C16  C17  aromatic  1.389  0.020  1.389
 FYJ  C14  C19  aromatic  1.392  0.020  1.392
 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

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  126.92  3.000
 FYJ  O12  C10  C07  114.52  3.000
 FYJ  O11  C10  C07  118.54  3.000
 FYJ  H1   C02  O01  110.85  3.000
 FYJ  H1   C02  C08  107.80  3.000
 FYJ  O01  C02  C08  108.52  3.000
 FYJ  H1   C02  C03  107.49  3.000
 FYJ  O01  C02  C03  111.36  3.000
 FYJ  C08  C02  C03  110.76  3.000
 FYJ  H2   C03  O04  111.63  3.000
 FYJ  H2   C03  C05  108.39  3.000
 FYJ  O04  C03  C05  111.99  3.000
 FYJ  H2   C03  C02  108.52  3.000
 FYJ  O04  C03  C02  107.09  3.000
 FYJ  C05  C03  C02  109.14  3.000
 FYJ  H3   C05  S13  107.60  3.000
 FYJ  H3   C05  O06  111.44  3.000
 FYJ  S13  C05  O06  108.37  3.000
 FYJ  H3   C05  C03  109.54  3.000
 FYJ  S13  C05  C03  109.10  3.000
 FYJ  O06  C05  C03  110.69  3.000
 FYJ  H4   C07  O06  110.08  3.000
 FYJ  H4   C07  C08  107.79  3.000
 FYJ  O06  C07  C08  109.90  3.000
 FYJ  H4   C07  C10  107.30  3.000
 FYJ  O06  C07  C10  109.25  3.000
 FYJ  C08  C07  C10  112.48  3.000
 FYJ  H5   C08  O09  111.39  3.000
 FYJ  H5   C08  C07  107.65  3.000
 FYJ  O09  C08  C07  111.03  3.000
 FYJ  H5   C08  C02  108.19  3.000
 FYJ  C07  C08  C02  109.19  3.000
 FYJ  O09  C08  C02  109.31  3.000
 FYJ  S13  C14  C19  118.68  3.000
 FYJ  C19  C14  C15  120.00  3.000
 FYJ  S13  C14  C15  121.28  3.000
 FYJ  H6   C15  C16  120.00  3.000
 FYJ  H6   C15  C14  120.40  3.000
 FYJ  C16  C15  C14  119.60  3.000
 FYJ  H7   C16  C17  120.07  3.000
 FYJ  H7   C16  C15  119.44  3.000
 FYJ  C17  C16  C15  120.49  3.000
 FYJ  H8   C17  C18  120.10  3.000
 FYJ  H8   C17  C16  120.14  3.000
 FYJ  C18  C17  C16  119.76  3.000
 FYJ  H9   C18  C19  119.62  3.000
 FYJ  H9   C18  C17  120.20  3.000
 FYJ  C19  C18  C17  120.18  3.000
 FYJ  H10  C19  C18  120.03  3.000
 FYJ  H10  C19  C14  120.01  3.000
 FYJ  C18  C19  C14  119.96  3.000
 FYJ  H11  O01  C02  108.21  3.000
 FYJ  H12  O04  C03  109.07  3.000
 FYJ  C07  O06  C05  112.20  3.000
 FYJ  H13  O09  C08  102.82  3.000
 FYJ  C14  S13  C05  101.53  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  Var_01    C15  C14  S13  C05   55.59  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

