# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:26:07 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl 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)Oc2cc3OC(=CC(=O)c3c(O)c2O)c4ccccc4
#
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
 0XE  0XE  '5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid'  ligand  49  32  .  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_0XE
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
 0XE  C1   C  CR16   0  -0.237   6.3404   2.7058  -1.0213
 0XE  C2   C  CR16   0  -0.250   5.7098   3.8894  -0.6594
 0XE  C3   C  CR16   0  -0.239   4.4273   3.8532  -0.1291
 0XE  C4   C  CR16   0  -0.276   3.7738   2.6428   0.0403
 0XE  C5   C  CR6    0   0.025   4.4058   1.4486  -0.3142
 0XE  C6   C  CR16   0  -0.301   5.6942   1.4930  -0.8506
 0XE  C7   C  CR6    0   0.411   3.7289   0.1607  -0.1278
 0XE  C8   C  CR16   0  -0.515   4.3458  -1.0354   0.0144
 0XE  C9   C  CR6    0   0.527   3.5898  -2.2454   0.1882
 0XE  O9   O  O      0  -0.502   4.1182  -3.3603   0.3141
 0XE  O12  O  O      0  -0.465   2.3987   0.2783  -0.0982
 0XE  C11  C  CR66   0   0.405   1.6022  -0.8011   0.0752
 0XE  C10  C  CR66   0  -0.325   2.1502  -2.0737   0.2181
 0XE  C17  C  CR6    0   0.301   1.2845  -3.1709   0.3968
 0XE  O17  O  OH1    0  -0.626   1.7494  -4.4119   0.5330
 0XE  C16  C  CR6    0   0.169  -0.0888  -2.9702   0.4178
 0XE  O16  O  OH1    0  -0.620  -0.8840  -4.0483   0.5741
 0XE  C14  C  CR16   0  -0.487   0.2393  -0.5741   0.1059
 0XE  C15  C  CR6    0   0.322  -0.5948  -1.6723   0.2669
 0XE  O18  O  O2     0  -0.516  -1.9437  -1.6023   0.2964
 0XE  C18  C  CH1    0   0.272  -2.5895  -0.4829  -0.2418
 0XE  O22  O  O2     0  -0.484  -2.5883   0.5106   0.7308
 0XE  C22  C  CH1    0  -0.164  -3.1780   1.7088   0.2727
 0XE  C23  C  C      0   0.439  -3.0250   2.8016   1.3481
 0XE  O24  O  O      0  -0.554  -2.2497   2.6083   2.2844
 0XE  O23  O  OC    -1  -0.615  -3.7270   3.8272   1.1431
 0XE  C19  C  CH1    0  -0.038  -4.0160  -0.8846  -0.6007
 0XE  O19  O  OH1    0  -0.665  -4.0386  -1.8536  -1.6187
 0XE  C20  C  CH1    0   0.014  -4.7487   0.3522  -1.1153
 0XE  O20  O  OH1    0  -0.669  -6.1037   0.0805  -1.3617
 0XE  C21  C  CH1    0   0.036  -4.6550   1.4746  -0.0949
 0XE  O21  O  OH1    0  -0.700  -5.2259   2.6351  -0.6290
 0XE  H1   H  HCR6   0   0.268   7.3349   2.7269  -1.4466
 0XE  H2   H  HCR6   0   0.268   6.2143   4.8368  -0.7959
 0XE  H3   H  HCR6   0   0.268   3.9309   4.7718   0.1538
 0XE  H4   H  HCR6   0   0.267   2.7781   2.6372   0.4626
 0XE  H5   H  HCR6   0   0.266   6.1902   0.5819  -1.1580
 0XE  H6   H  HCR6   0   0.285   5.4247  -1.0929   0.0161
 0XE  H8   H  HOH1   0   0.476   2.7332  -4.3562   0.4844
 0XE  H9   H  HOH1   0   0.472  -1.8103  -3.7809   0.5757
 0XE  H10  H  HCR6   0   0.311  -0.1420   0.4342   0.0282
 0XE  H11  H  HCH1   0   0.219  -2.0602  -0.1497  -1.1517
 0XE  H12  H  HCH1   0   0.235  -2.6573   2.0610  -0.6353
 0XE  H14  H  HCH1   0   0.238  -4.5173  -1.2420   0.3103
 0XE  H15  H  HOH1   0   0.460  -3.9469  -2.7259  -1.2254
 0XE  H16  H  HCH1   0   0.206  -4.2394   0.6868  -2.0353
 0XE  H17  H  HOH1   0   0.450  -6.1520  -0.6457  -1.9924
 0XE  H18  H  HCH1   0   0.198  -5.1818   1.1479   0.8195
 0XE  H19  H  HOH1   0   0.439  -4.8549   3.3494  -0.0612

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
 0XE  C3   C2   aromatic  1.388  0.020  1.388
 0XE  C3   C4   aromatic  1.386  0.020  1.386
 0XE  C2   C1   aromatic  1.389  0.020  1.389
 0XE  C4   C5   aromatic  1.397  0.020  1.397
 0XE  C1   C6   aromatic  1.385  0.020  1.385
 0XE  C5   C6   aromatic  1.396  0.020  1.396
 0XE  C5   C7   single    1.467  0.020  1.467
 0XE  C8   C7   double    1.353  0.020  1.353
 0XE  C8   C9   single    1.437  0.020  1.437
 0XE  C7   O12  single    1.336  0.020  1.336
 0XE  O9   C9   double    1.240  0.020  1.240
 0XE  C9   C10  single    1.450  0.020  1.450
 0XE  O12  C11  single    1.353  0.020  1.353
 0XE  C10  C11  aromatic  1.393  0.020  1.393
 0XE  C10  C17  aromatic  1.409  0.020  1.409
 0XE  C11  C14  aromatic  1.382  0.020  1.382
 0XE  O17  C17  single    1.332  0.020  1.332
 0XE  C17  C16  aromatic  1.388  0.020  1.388
 0XE  C14  C15  aromatic  1.388  0.020  1.388
 0XE  C16  C15  aromatic  1.401  0.020  1.401
 0XE  C16  O16  single    1.349  0.020  1.349
 0XE  C15  O18  single    1.351  0.020  1.351
 0XE  O24  C23  deloc     1.231  0.020  1.231
 0XE  C23  O23  deloc     1.260  0.020  1.260
 0XE  C23  C22  single    1.541  0.020  1.541
 0XE  O18  C18  single    1.400  0.020  1.400
 0XE  O22  C22  single    1.412  0.020  1.412
 0XE  O22  C18  single    1.390  0.020  1.390
 0XE  C22  C21  single    1.540  0.020  1.540
 0XE  C18  C19  single    1.525  0.020  1.525
 0XE  C21  O21  single    1.399  0.020  1.399
 0XE  C21  C20  single    1.520  0.020  1.520
 0XE  C19  O19  single    1.406  0.020  1.406
 0XE  C19  C20  single    1.527  0.020  1.527
 0XE  C20  O20  single    1.404  0.020  1.404
 0XE  C1   H1   single    0.930  0.020  1.080
 0XE  C2   H2   single    0.930  0.020  1.080
 0XE  C3   H3   single    0.930  0.020  1.080
 0XE  C4   H4   single    0.930  0.020  1.080
 0XE  C6   H5   single    0.930  0.020  1.080
 0XE  C8   H6   single    0.930  0.020  1.080
 0XE  O17  H8   single    0.850  0.020  0.980
 0XE  O16  H9   single    0.850  0.020  0.980
 0XE  C14  H10  single    0.930  0.020  1.080
 0XE  C18  H11  single    0.970  0.020  1.090
 0XE  C22  H12  single    0.970  0.020  1.090
 0XE  C19  H14  single    0.970  0.020  1.090
 0XE  O19  H15  single    0.850  0.020  0.980
 0XE  C20  H16  single    0.970  0.020  1.090
 0XE  O20  H17  single    0.850  0.020  0.980
 0XE  C21  H18  single    0.970  0.020  1.090
 0XE  O21  H19  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
 0XE  H1   C1   C6   119.64  3.000
 0XE  H1   C1   C2   120.21  3.000
 0XE  C6   C1   C2   120.15  3.000
 0XE  H2   C2   C3   120.12  3.000
 0XE  H2   C2   C1   120.10  3.000
 0XE  C3   C2   C1   119.78  3.000
 0XE  H3   C3   C4   119.56  3.000
 0XE  H3   C3   C2   120.11  3.000
 0XE  C4   C3   C2   120.33  3.000
 0XE  H4   C4   C5   120.74  3.000
 0XE  H4   C4   C3   119.10  3.000
 0XE  C5   C4   C3   120.15  3.000
 0XE  C7   C5   C6   120.17  3.000
 0XE  C7   C5   C4   120.64  3.000
 0XE  C6   C5   C4   119.19  3.000
 0XE  H5   C6   C5   120.35  3.000
 0XE  H5   C6   C1   119.25  3.000
 0XE  C5   C6   C1   120.39  3.000
 0XE  O12  C7   C8   121.97  3.000
 0XE  O12  C7   C5   112.65  3.000
 0XE  C8   C7   C5   125.38  3.000
 0XE  H6   C8   C9   118.70  3.000
 0XE  H6   C8   C7   120.16  3.000
 0XE  C9   C8   C7   121.13  3.000
 0XE  C10  C9   O9   121.82  3.000
 0XE  C10  C9   C8   115.15  3.000
 0XE  O9   C9   C8   123.02  3.000
 0XE  C11  O12  C7   121.27  3.000
 0XE  C14  C11  C10  122.40  3.000
 0XE  C14  C11  O12  116.91  3.000
 0XE  C10  C11  O12  120.70  3.000
 0XE  C17  C10  C11  118.86  3.000
 0XE  C17  C10  C9   121.36  3.000
 0XE  C11  C10  C9   119.78  3.000
 0XE  C16  C17  O17  118.58  3.000
 0XE  C16  C17  C10  119.82  3.000
 0XE  O17  C17  C10  121.60  3.000
 0XE  H8   O17  C17  106.88  3.000
 0XE  C15  C16  O16  122.68  3.000
 0XE  O16  C16  C17  118.01  3.000
 0XE  C15  C16  C17  119.31  3.000
 0XE  H9   O16  C16  110.18  3.000
 0XE  H10  C14  C15  122.30  3.000
 0XE  H10  C14  C11  119.97  3.000
 0XE  C15  C14  C11  117.72  3.000
 0XE  O18  C15  C14  124.15  3.000
 0XE  O18  C15  C16  113.97  3.000
 0XE  C14  C15  C16  121.89  3.000
 0XE  C18  O18  C15  119.58  3.000
 0XE  H11  C18  C19  109.51  3.000
 0XE  H11  C18  O22  111.13  3.000
 0XE  C19  C18  O22  110.71  3.000
 0XE  H11  C18  O18  109.70  3.000
 0XE  C19  C18  O18  108.14  3.000
 0XE  O22  C18  O18  107.58  3.000
 0XE  C22  O22  C18  112.28  3.000
 0XE  H12  C22  C21  107.73  3.000
 0XE  H12  C22  C23  107.50  3.000
 0XE  C21  C22  C23  111.70  3.000
 0XE  H12  C22  O22  109.91  3.000
 0XE  C21  C22  O22  110.43  3.000
 0XE  C23  C22  O22  109.51  3.000
 0XE  O23  C23  O24  127.07  3.000
 0XE  O23  C23  C22  114.11  3.000
 0XE  O24  C23  C22  118.82  3.000
 0XE  H14  C19  C20  108.89  3.000
 0XE  H14  C19  O19  111.63  3.000
 0XE  C20  C19  O19  107.85  3.000
 0XE  H14  C19  C18  108.49  3.000
 0XE  C20  C19  C18  108.35  3.000
 0XE  O19  C19  C18  111.54  3.000
 0XE  H15  O19  C19  109.13  3.000
 0XE  H16  C20  C21  107.90  3.000
 0XE  H16  C20  O20  110.97  3.000
 0XE  C21  C20  O20  108.69  3.000
 0XE  H16  C20  C19  107.77  3.000
 0XE  O20  C20  C19  111.44  3.000
 0XE  C21  C20  C19  110.02  3.000
 0XE  H17  O20  C20  108.02  3.000
 0XE  H18  C21  O21  111.50  3.000
 0XE  H18  C21  C20  107.94  3.000
 0XE  O21  C21  C20  109.33  3.000
 0XE  H18  C21  C22  107.74  3.000
 0XE  C20  C21  C22  109.38  3.000
 0XE  O21  C21  C22  110.87  3.000
 0XE  H19  O21  C21  103.16  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
 0XE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 0XE  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 0XE  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 0XE  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 0XE  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 0XE  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 0XE  CONST_07  C16  C17  C10  C11     0.00   0.0  0
 0XE  CONST_08  C16  C15  C14  C11     0.00   0.0  0
 0XE  CONST_09  C15  C14  C11  C10     0.00   0.0  0
 0XE  CONST_10  C15  C16  C17  C10     0.00   0.0  0
 0XE  CONST_11  C14  C11  C10  C17     0.00   0.0  0
 0XE  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 0XE  CONST_13  C7   C5   C6   C1    180.00   0.0  0
 0XE  CONST_14  C7   C5   C4   C3    180.00   0.0  0
 0XE  CONST_15  O17  C17  C10  C9      0.00   0.0  0
 0XE  CONST_16  O17  C17  C10  C11   180.00   0.0  0
 0XE  CONST_17  O18  C15  C14  C11   180.00   0.0  0
 0XE  CONST_18  O16  C16  C17  C10   180.00   0.0  0
 0XE  CONST_19  O18  C15  C16  C17   180.00   0.0  0
 0XE  CONST_20  C15  C16  C17  O17   180.00   0.0  0
 0XE  CONST_21  C14  C15  C16  O16   180.00   0.0  0
 0XE  CONST_22  H3   C3   C2   C1    180.00   0.0  0
 0XE  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 0XE  CONST_24  H5   C6   C1   C2    180.00   0.0  0
 0XE  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 0XE  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 0XE  CONST_27  H10  C14  C11  O12     0.00   0.0  0
 0XE  Var_01    C8   C7   C5   C4   -155.85  30.0  2
 0XE  Var_02    C9   C8   C7   C5   -179.80  30.0  1
 0XE  Var_03    C10  C9   C8   C7     -0.91  30.0  1
 0XE  Var_04    C10  C11  O12  C7     -0.50  30.0  1
 0XE  Var_05    C11  C10  C9   C8      0.35  30.0  1

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
 0XE  chir_01  C18  O18  O22  C19  positiv
 0XE  chir_02  C22  O22  C21  C23  negativ
 0XE  chir_03  C19  O19  C18  C20  negativ
 0XE  chir_04  C20  O20  C19  C21  positiv
 0XE  chir_05  C21  O21  C20  C22  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
 0XE  plan-1  C1   0.020
 0XE  plan-1  C2   0.020
 0XE  plan-1  C3   0.020
 0XE  plan-1  C4   0.020
 0XE  plan-1  C5   0.020
 0XE  plan-1  C6   0.020
 0XE  plan-1  C7   0.020
 0XE  plan-1  H1   0.020
 0XE  plan-1  H2   0.020
 0XE  plan-1  H3   0.020
 0XE  plan-1  H4   0.020
 0XE  plan-1  H5   0.020
 0XE  plan-2  C9   0.020
 0XE  plan-2  O12  0.020
 0XE  plan-2  C11  0.020
 0XE  plan-2  C10  0.020
 0XE  plan-2  C17  0.020
 0XE  plan-2  O17  0.020
 0XE  plan-2  C16  0.020
 0XE  plan-2  O16  0.020
 0XE  plan-2  C14  0.020
 0XE  plan-2  C15  0.020
 0XE  plan-2  O18  0.020
 0XE  plan-2  H10  0.020
 0XE  plan-3  C8   0.020
 0XE  plan-3  C9   0.020
 0XE  plan-3  O9   0.020
 0XE  plan-3  C10  0.020
 0XE  plan-4  C22  0.020
 0XE  plan-4  C23  0.020
 0XE  plan-4  O24  0.020
 0XE  plan-4  O23  0.020

