# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:25:40 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R)-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c3cc(O)c(O)c(O)c3
#
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
 EGT  EGT  (2R,3R)-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol  ligand  36  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EGT
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
 EGT  O1    O  O2    0  -0.498  -0.6596  -0.5650  -0.4279
 EGT  C2    C  CH1   0  -0.024   0.1349   0.6090  -0.4511
 EGT  C3    C  CH1   0   0.008  -0.3749   1.6200   0.5684
 EGT  C4    C  CH2   0  -0.540  -1.7928   2.0141   0.1741
 EGT  C5    C  CR6   0  -0.157  -2.6189   0.7863  -0.0945
 EGT  C6    C  CR6   0   0.335  -4.0162   0.8025  -0.0659
 EGT  C7    C  CR16  0  -0.502  -4.7674  -0.3505  -0.2646
 EGT  C8    C  CR6   0   0.377  -4.1139  -1.5536  -0.5050
 EGT  C9    C  CR16  0  -0.485  -2.7276  -1.6053  -0.5624
 EGT  C10   C  CR6   0   0.425  -2.0018  -0.4370  -0.3596
 EGT  C11   C  CR6   0   0.089   1.5679   0.2162  -0.2202
 EGT  C12   C  CR16  0  -0.458   2.5606   0.9907  -0.8101
 EGT  C13   C  CR6   0   0.294   3.8990   0.6987  -0.5877
 EGT  C14   C  CR6   0   0.161   4.2563  -0.3755   0.2242
 EGT  C15   C  CR6   0   0.320   3.2563  -1.1490   0.8109
 EGT  C16   C  CR16  0  -0.423   1.9157  -0.8529   0.5923
 EGT  O17   O  OH1   0  -0.656  -0.3201   1.0164   1.8334
 EGT  O18   O  OH1   0  -0.631  -4.7102   1.9356   0.1627
 EGT  O19   O  OH1   0  -0.637  -4.7878  -2.7037  -0.7025
 EGT  O20   O  OH1   0  -0.643   4.9200   1.3999  -1.1290
 EGT  O21   O  OH1   0  -0.645   5.5446  -0.7270   0.4658
 EGT  O22   O  OH1   0  -0.638   3.5650  -2.1972   1.6033
 EGT  HC2   H  HCH1  0   0.262   0.0546   1.0804  -1.4400
 EGT  HC3   H  HCH1  0   0.245   0.2695   2.5064   0.5105
 EGT  HC41  H  HCH2  0   0.260  -2.2206   2.6196   0.9807
 EGT  HC42  H  HCH2  0   0.266  -1.7465   2.6659  -0.7042
 EGT  HC7   H  HCR6  0   0.270  -5.8497  -0.2978  -0.2335
 EGT  HC9   H  HCR6  0   0.263  -2.2159  -2.5378  -0.7644
 EGT  H12   H  HCR6  0   0.265   2.2949   1.8246  -1.4513
 EGT  H16   H  HCR6  0   0.254   1.1630  -1.4685   1.0657
 EGT  H17   H  HOH1  0   0.455  -0.6351   1.6517   2.4840
 EGT  H18   H  HOH1  0   0.482  -4.1278   2.7005   0.2180
 EGT  H19   H  HOH1  0   0.474  -5.7370  -2.5494  -0.6433
 EGT  H20   H  HOH1  0   0.482   4.5876   2.1605  -1.6180
 EGT  H21   H  HOH1  0   0.479   6.1487  -0.0271   0.1931
 EGT  H22   H  HOH1  0   0.472   4.5208  -2.2683   1.7121

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
 EGT  O1   C2    single    1.418  0.020  1.418
 EGT  O1   C10   single    1.350  0.020  1.350
 EGT  C2   C3    single    1.524  0.020  1.524
 EGT  C2   C11   single    1.504  0.020  1.504
 EGT  C2   HC2   single    0.970  0.020  1.090
 EGT  C3   C4    single    1.524  0.020  1.524
 EGT  C3   O17   single    1.403  0.020  1.403
 EGT  C3   HC3   single    0.970  0.020  1.090
 EGT  C4   C5    single    1.504  0.020  1.504
 EGT  C4   HC41  single    0.970  0.020  1.090
 EGT  C4   HC42  single    0.970  0.020  1.090
 EGT  C5   C6    aromatic  1.398  0.020  1.398
 EGT  C5   C10   aromatic  1.396  0.020  1.396
 EGT  C6   C7    aromatic  1.390  0.020  1.390
 EGT  C6   O18   single    1.348  0.020  1.348
 EGT  C7   C8    aromatic  1.390  0.020  1.390
 EGT  C7   HC7   single    0.930  0.020  1.080
 EGT  C8   C9    aromatic  1.388  0.020  1.388
 EGT  C8   O19   single    1.348  0.020  1.348
 EGT  C9   C10   aromatic  1.390  0.020  1.390
 EGT  C9   HC9   single    0.930  0.020  1.080
 EGT  C11  C12   aromatic  1.390  0.020  1.390
 EGT  C11  C16   aromatic  1.387  0.020  1.387
 EGT  C12  C13   aromatic  1.388  0.020  1.388
 EGT  C12  H12   single    0.930  0.020  1.080
 EGT  C13  C14   aromatic  1.393  0.020  1.393
 EGT  C13  O20   single    1.352  0.020  1.352
 EGT  C14  C15   aromatic  1.394  0.020  1.394
 EGT  C14  O21   single    1.357  0.020  1.357
 EGT  C15  C16   aromatic  1.390  0.020  1.390
 EGT  C15  O22   single    1.350  0.020  1.350
 EGT  C16  H16   single    0.930  0.020  1.080
 EGT  O17  H17   single    0.850  0.020  0.980
 EGT  O18  H18   single    0.850  0.020  0.980
 EGT  O19  H19   single    0.850  0.020  0.980
 EGT  O20  H20   single    0.850  0.020  0.980
 EGT  O21  H21   single    0.850  0.020  0.980
 EGT  O22  H22   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
 EGT  C10   O1   C2    118.65  3.000
 EGT  HC2   C2   C11   108.66  3.000
 EGT  HC2   C2   C3    107.05  3.000
 EGT  C11   C2   C3    112.92  3.000
 EGT  HC2   C2   O1    109.22  3.000
 EGT  C11   C2   O1    108.37  3.000
 EGT  C3    C2   O1    110.55  3.000
 EGT  HC3   C3   O17   111.85  3.000
 EGT  HC3   C3   C4    108.90  3.000
 EGT  O17   C3   C4    112.40  3.000
 EGT  HC3   C3   C2    107.71  3.000
 EGT  O17   C3   C2    107.75  3.000
 EGT  C4    C3   C2    108.06  3.000
 EGT  HC42  C4   HC41  106.15  3.000
 EGT  HC42  C4   C5    111.47  3.000
 EGT  HC41  C4   C5    111.60  3.000
 EGT  HC42  C4   C3    108.80  3.000
 EGT  HC41  C4   C3    108.42  3.000
 EGT  C5    C4   C3    110.25  3.000
 EGT  C10   C5   C6    117.14  3.000
 EGT  C10   C5   C4    120.44  3.000
 EGT  C6    C5   C4    122.41  3.000
 EGT  O18   C6   C7    116.30  3.000
 EGT  O18   C6   C5    121.86  3.000
 EGT  C7    C6   C5    121.85  3.000
 EGT  HC7   C7   C8    121.09  3.000
 EGT  HC7   C7   C6    119.68  3.000
 EGT  C8    C7   C6    119.24  3.000
 EGT  O19   C8   C9    117.48  3.000
 EGT  O19   C8   C7    121.93  3.000
 EGT  C9    C8   C7    120.58  3.000
 EGT  HC9   C9   C10   120.28  3.000
 EGT  HC9   C9   C8    120.78  3.000
 EGT  C10   C9   C8    118.95  3.000
 EGT  C9    C10  C5    122.24  3.000
 EGT  C9    C10  O1    115.60  3.000
 EGT  C5    C10  O1    122.16  3.000
 EGT  C16   C11  C12   119.92  3.000
 EGT  C16   C11  C2    122.02  3.000
 EGT  C12   C11  C2    118.02  3.000
 EGT  H12   C12  C13   119.51  3.000
 EGT  H12   C12  C11   120.27  3.000
 EGT  C13   C12  C11   120.22  3.000
 EGT  O20   C13  C14   116.08  3.000
 EGT  O20   C13  C12   123.72  3.000
 EGT  C14   C13  C12   120.20  3.000
 EGT  O21   C14  C15   117.55  3.000
 EGT  O21   C14  C13   123.16  3.000
 EGT  C15   C14  C13   119.29  3.000
 EGT  O22   C15  C16   118.57  3.000
 EGT  O22   C15  C14   120.93  3.000
 EGT  C16   C15  C14   120.50  3.000
 EGT  H16   C16  C15   118.75  3.000
 EGT  H16   C16  C11   121.37  3.000
 EGT  C15   C16  C11   119.88  3.000
 EGT  H17   O17  C3    108.23  3.000
 EGT  H18   O18  C6    111.47  3.000
 EGT  H19   O19  C8    110.30  3.000
 EGT  H20   O20  C13   110.62  3.000
 EGT  H21   O21  C14   110.89  3.000
 EGT  H22   O22  C15   110.49  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
 EGT  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 EGT  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 EGT  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 EGT  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 EGT  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 EGT  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 EGT  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 EGT  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 EGT  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 EGT  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 EGT  CONST_11  C16  C11  C12  C13    0.00   0.0  0
 EGT  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 EGT  CONST_13  C13  C12  C11  C2   180.00   0.0  0
 EGT  CONST_14  C15  C16  C11  C2   180.00   0.0  0
 EGT  CONST_15  O18  C6   C5   C4     0.00   0.0  0
 EGT  CONST_16  O19  C8   C7   C6   180.00   0.0  0
 EGT  CONST_17  O18  C6   C7   C8   180.00   0.0  0
 EGT  CONST_18  O18  C6   C5   C10  180.00   0.0  0
 EGT  CONST_19  O19  C8   C9   C10  180.00   0.0  0
 EGT  CONST_20  O20  C13  C12  C11  180.00   0.0  0
 EGT  CONST_21  O22  C15  C16  C11  180.00   0.0  0
 EGT  CONST_22  O21  C14  C13  C12  180.00   0.0  0
 EGT  CONST_23  O22  C15  C14  C13  180.00   0.0  0
 EGT  CONST_24  O20  C13  C14  C15  180.00   0.0  0
 EGT  CONST_25  O21  C14  C15  C16  180.00   0.0  0
 EGT  CONST_26  HC9  C9   C10  O1     0.00   0.0  0
 EGT  CONST_27  H12  C12  C11  C2     0.00   0.0  0
 EGT  CONST_28  H16  C16  C11  C2     0.00   0.0  0
 EGT  CONST_29  HC7  C7   C6   C5   180.00   0.0  0
 EGT  Var_01    C5   C10  O1   C2   -10.61  30.0  1
 EGT  Var_02    C6   C5   C4   C3   159.64  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
 EGT  chir_01  C2  O1   C3  C11  negativ
 EGT  chir_02  C3  O17  C2  C4   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
 EGT  plan-1  C2   0.020
 EGT  plan-1  C11  0.020
 EGT  plan-1  C12  0.020
 EGT  plan-1  C13  0.020
 EGT  plan-1  C14  0.020
 EGT  plan-1  C15  0.020
 EGT  plan-1  C16  0.020
 EGT  plan-1  O20  0.020
 EGT  plan-1  O21  0.020
 EGT  plan-1  O22  0.020
 EGT  plan-1  H12  0.020
 EGT  plan-1  H16  0.020
 EGT  plan-2  O1   0.020
 EGT  plan-2  C4   0.020
 EGT  plan-2  C5   0.020
 EGT  plan-2  C6   0.020
 EGT  plan-2  C7   0.020
 EGT  plan-2  C8   0.020
 EGT  plan-2  C9   0.020
 EGT  plan-2  C10  0.020
 EGT  plan-2  O18  0.020
 EGT  plan-2  O19  0.020
 EGT  plan-2  HC7  0.020
 EGT  plan-2  HC9  0.020

