# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:33:14 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C[C@@H](OC(=O)c3cc(O)c(O)c(O)c3)[C@H](Oc2c1)c4cc(O)c(O)c(O)c4
#
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
 EGG  EGG  '(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate'  ligand  51  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EGG
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
 EGG  O1    O  O2    0  -0.497  -2.2558  -0.3623   0.5992
 EGG  C2    C  CH1   0  -0.027  -1.9565  -1.1098  -0.5649
 EGG  C3    C  CH1   0  -0.034  -1.2943  -0.2241  -1.6134
 EGG  C4    C  CH2   0  -0.474  -2.2439   0.8911  -2.0064
 EGG  C5    C  CR6   0  -0.134  -2.8677   1.5023  -0.7841
 EGG  C6    C  CR6   0   0.338  -3.4983   2.7480  -0.8308
 EGG  C7    C  CR16  0  -0.541  -4.0501   3.3337   0.3022
 EGG  C8    C  CR6   0   0.379  -3.9741   2.6607   1.5192
 EGG  C9    C  CR16  0  -0.485  -3.3665   1.4164   1.6008
 EGG  C10   C  CR6   0   0.424  -2.8284   0.8539   0.4475
 EGG  C11   C  CR6   0   0.086  -1.1008  -2.2835  -0.1780
 EGG  C12   C  CR16  0  -0.423  -1.2120  -3.4494  -0.9224
 EGG  C13   C  CR6   0   0.320  -0.3923  -4.5375  -0.6489
 EGG  C14   C  CR6   0   0.166   0.5363  -4.4664   0.3871
 EGG  C15   C  CR6   0   0.296   0.6346  -3.2960   1.1375
 EGG  C16   C  CR16  0  -0.455  -0.1730  -2.2033   0.8535
 EGG  O17   O  O2    0  -0.465  -0.1191   0.3027  -1.0005
 EGG  C18   C  C     0   0.621   0.9237   0.6176  -1.7567
 EGG  O18   O  OH1   0  -0.624  -3.5444   3.3517  -2.0331
 EGG  C19   C  CR6   0  -0.101   2.0666   1.1115  -0.9573
 EGG  O19   O  OH1   0  -0.636  -4.4911   3.1770   2.6509
 EGG  C20   C  CR16  0  -0.387   3.2320   1.4568  -1.6328
 EGG  O20   O  OH1   0  -0.636  -0.5259  -5.6535  -1.3938
 EGG  C21   C  CR6   0   0.326   4.3316   1.9193  -0.9278
 EGG  O21   O  OH1   0  -0.644   1.2923  -5.5662   0.6272
 EGG  C22   C  CR6   0   0.195   4.2672   2.0409   0.4613
 EGG  O22   O  OH1   0  -0.641   1.5568  -3.3091   2.1260
 EGG  C23   C  CR6   0   0.302   3.0939   1.6916   1.1328
 EGG  O23   O  O     0  -0.450   0.9365   0.5077  -2.9597
 EGG  C24   C  CR16  0  -0.432   1.9952   1.2274   0.4300
 EGG  O24   O  OH1   0  -0.633   5.4494   2.2444  -1.6056
 EGG  O25   O  OH1   0  -0.631   5.3644   2.5015   1.0934
 EGG  O26   O  OH1   0  -0.642   3.1246   1.8395   2.4744
 EGG  H2    H  HCH1  0   0.272  -2.8889  -1.4801  -1.0124
 EGG  H3    H  HCH1  0   0.287  -1.0373  -0.8303  -2.4840
 EGG  H4    H  HCH2  0   0.271  -1.7166   1.6382  -2.6021
 EGG  H4A   H  HCH2  0   0.267  -3.0065   0.4641  -2.6647
 EGG  H7    H  HCR6  0   0.278  -4.5378   4.3011   0.2358
 EGG  H9    H  HCR6  0   0.264  -3.3139   0.8856   2.5429
 EGG  H12   H  HCR6  0   0.259  -1.9350  -3.5255  -1.7261
 EGG  H16   H  HCR6  0   0.263  -0.0827  -1.3038   1.4490
 EGG  HO18  H  HOH1  0   0.478  -3.9773   4.2100  -1.9650
 EGG  HO19  H  HOH1  0   0.475  -4.9024   4.0297   2.4730
 EGG  H20   H  HCR6  0   0.269   3.2950   1.3660  -2.7091
 EGG  HO20  H  HOH1  0   0.473   0.1044  -6.3273  -1.1123
 EGG  HO21  H  HOH1  0   0.479   2.0278  -5.3568   1.2141
 EGG  HO22  H  HOH1  0   0.479   1.5776  -2.4642   2.5880
 EGG  H24   H  HCR6  0   0.279   1.0923   0.9664   0.9668
 EGG  HO24  H  HOH1  0   0.475   6.1475   2.5234  -1.0013
 EGG  HO25  H  HOH1  0   0.485   5.2421   2.5052   2.0504
 EGG  HO26  H  HOH1  0   0.484   2.2891   1.5694   2.8712

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
 EGG  O1   C2    single    1.415  0.020  1.415
 EGG  O1   C10   single    1.353  0.020  1.353
 EGG  C2   C3    single    1.524  0.020  1.524
 EGG  C2   C11   single    1.503  0.020  1.503
 EGG  C3   C4    single    1.516  0.020  1.516
 EGG  C3   O17   single    1.426  0.020  1.426
 EGG  C4   C5    single    1.502  0.020  1.502
 EGG  C5   C6    aromatic  1.397  0.020  1.397
 EGG  C5   C10   aromatic  1.392  0.020  1.392
 EGG  C6   C7    aromatic  1.390  0.020  1.390
 EGG  C6   O18   single    1.346  0.020  1.346
 EGG  C7   C8    aromatic  1.393  0.020  1.393
 EGG  C8   C9    aromatic  1.387  0.020  1.387
 EGG  C8   O19   single    1.347  0.020  1.347
 EGG  C9   C10   aromatic  1.391  0.020  1.391
 EGG  C11  C12   aromatic  1.388  0.020  1.388
 EGG  C11  C16   aromatic  1.390  0.020  1.390
 EGG  C12  C13   aromatic  1.389  0.020  1.389
 EGG  C13  C14   aromatic  1.393  0.020  1.393
 EGG  C13  O20   single    1.348  0.020  1.348
 EGG  C14  C15   aromatic  1.394  0.020  1.394
 EGG  C14  O21   single    1.356  0.020  1.356
 EGG  C15  C16   aromatic  1.388  0.020  1.388
 EGG  C15  O22   single    1.352  0.020  1.352
 EGG  O17  C18   single    1.326  0.020  1.326
 EGG  C18  C19   single    1.480  0.020  1.480
 EGG  C18  O23   double    1.208  0.020  1.208
 EGG  C19  C20   aromatic  1.391  0.020  1.391
 EGG  C19  C24   aromatic  1.394  0.020  1.394
 EGG  C20  C21   aromatic  1.386  0.020  1.386
 EGG  C21  C22   aromatic  1.396  0.020  1.396
 EGG  C21  O24   single    1.347  0.020  1.347
 EGG  C22  C23   aromatic  1.396  0.020  1.396
 EGG  C22  O25   single    1.347  0.020  1.347
 EGG  C23  C24   aromatic  1.384  0.020  1.384
 EGG  C23  O26   single    1.350  0.020  1.350
 EGG  C2   H2    single    0.970  0.020  1.090
 EGG  C3   H3    single    0.970  0.020  1.090
 EGG  C4   H4    single    0.970  0.020  1.090
 EGG  C4   H4A   single    0.970  0.020  1.090
 EGG  C7   H7    single    0.930  0.020  1.080
 EGG  C9   H9    single    0.930  0.020  1.080
 EGG  C12  H12   single    0.930  0.020  1.080
 EGG  C16  H16   single    0.930  0.020  1.080
 EGG  O18  HO18  single    0.850  0.020  0.980
 EGG  O19  HO19  single    0.850  0.020  0.980
 EGG  C20  H20   single    0.930  0.020  1.080
 EGG  O20  HO20  single    0.850  0.020  0.980
 EGG  O21  HO21  single    0.850  0.020  0.980
 EGG  O22  HO22  single    0.850  0.020  0.980
 EGG  C24  H24   single    0.930  0.020  1.080
 EGG  O24  HO24  single    0.850  0.020  0.980
 EGG  O25  HO25  single    0.850  0.020  0.980
 EGG  O26  HO26  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
 EGG  C10   O1   C2   118.17  3.000
 EGG  H2    C2   C11  108.95  3.000
 EGG  H2    C2   C3   106.53  3.000
 EGG  C11   C2   C3   112.55  3.000
 EGG  H2    C2   O1   109.48  3.000
 EGG  C11   C2   O1   108.73  3.000
 EGG  C3    C2   O1   110.54  3.000
 EGG  H3    C3   O17  110.72  3.000
 EGG  H3    C3   C4   110.43  3.000
 EGG  O17   C3   C4   110.84  3.000
 EGG  H3    C3   C2   109.17  3.000
 EGG  O17   C3   C2   106.09  3.000
 EGG  C4    C3   C2   109.49  3.000
 EGG  H4A   C4   H4   105.99  3.000
 EGG  H4A   C4   C5   111.04  3.000
 EGG  H4    C4   C5   111.48  3.000
 EGG  H4A   C4   C3   107.78  3.000
 EGG  H4    C4   C3   110.02  3.000
 EGG  C5    C4   C3   110.38  3.000
 EGG  C10   C5   C6   117.22  3.000
 EGG  C10   C5   C4   121.24  3.000
 EGG  C6    C5   C4   121.54  3.000
 EGG  O18   C6   C7   121.71  3.000
 EGG  O18   C6   C5   116.43  3.000
 EGG  C7    C6   C5   121.86  3.000
 EGG  H7    C7   C8   120.57  3.000
 EGG  H7    C7   C6   120.28  3.000
 EGG  C8    C7   C6   119.15  3.000
 EGG  O19   C8   C9   117.54  3.000
 EGG  O19   C8   C7   121.87  3.000
 EGG  C9    C8   C7   120.58  3.000
 EGG  H9    C9   C10  120.29  3.000
 EGG  H9    C9   C8   120.82  3.000
 EGG  C10   C9   C8   118.89  3.000
 EGG  C9    C10  C5   122.28  3.000
 EGG  C9    C10  O1   115.73  3.000
 EGG  C5    C10  O1   121.99  3.000
 EGG  C16   C11  C12  120.01  3.000
 EGG  C16   C11  C2   121.74  3.000
 EGG  C12   C11  C2   118.19  3.000
 EGG  H12   C12  C13  118.98  3.000
 EGG  H12   C12  C11  120.68  3.000
 EGG  C13   C12  C11  120.33  3.000
 EGG  O20   C13  C14  121.27  3.000
 EGG  O20   C13  C12  118.75  3.000
 EGG  C14   C13  C12  119.98  3.000
 EGG  O21   C14  C15  123.12  3.000
 EGG  O21   C14  C13  117.51  3.000
 EGG  C15   C14  C13  119.35  3.000
 EGG  O22   C15  C16  123.65  3.000
 EGG  O22   C15  C14  115.70  3.000
 EGG  C16   C15  C14  120.65  3.000
 EGG  H16   C16  C15  119.54  3.000
 EGG  H16   C16  C11  120.79  3.000
 EGG  C15   C16  C11  119.66  3.000
 EGG  C18   O17  C3   119.39  3.000
 EGG  O23   C18  C19  124.07  3.000
 EGG  O23   C18  O17  123.68  3.000
 EGG  C19   C18  O17  112.25  3.000
 EGG  HO18  O18  C6   110.59  3.000
 EGG  C24   C19  C20  120.38  3.000
 EGG  C24   C19  C18  121.73  3.000
 EGG  C20   C19  C18  117.89  3.000
 EGG  HO19  O19  C8   110.37  3.000
 EGG  H20   C20  C21  119.20  3.000
 EGG  H20   C20  C19  120.75  3.000
 EGG  C21   C20  C19  120.05  3.000
 EGG  HO20  O20  C13  110.62  3.000
 EGG  O24   C21  C22  121.20  3.000
 EGG  O24   C21  C20  118.88  3.000
 EGG  C22   C21  C20  119.92  3.000
 EGG  HO21  O21  C14  110.92  3.000
 EGG  O25   C22  C23  122.97  3.000
 EGG  O25   C22  C21  117.33  3.000
 EGG  C23   C22  C21  119.70  3.000
 EGG  HO22  O22  C15  110.91  3.000
 EGG  O26   C23  C24  124.01  3.000
 EGG  O26   C23  C22  115.55  3.000
 EGG  C24   C23  C22  120.44  3.000
 EGG  H24   C24  C23  119.41  3.000
 EGG  H24   C24  C19  121.09  3.000
 EGG  C23   C24  C19  119.50  3.000
 EGG  HO24  O24  C21  110.80  3.000
 EGG  HO25  O25  C22  111.32  3.000
 EGG  HO26  O26  C23  111.03  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
 EGG  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 EGG  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 EGG  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 EGG  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 EGG  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 EGG  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 EGG  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 EGG  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 EGG  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 EGG  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 EGG  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 EGG  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 EGG  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 EGG  CONST_14  C22  C23  C24  C19     0.00   0.0  0
 EGG  CONST_15  C23  C24  C19  C20     0.00   0.0  0
 EGG  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 EGG  CONST_17  C24  C19  C20  C21     0.00   0.0  0
 EGG  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 EGG  CONST_19  C13  C12  C11  C2    180.00   0.0  0
 EGG  CONST_20  C15  C16  C11  C2    180.00   0.0  0
 EGG  CONST_21  O18  C6   C5   C4      0.00   0.0  0
 EGG  CONST_22  O19  C8   C7   C6    180.00   0.0  0
 EGG  CONST_23  O18  C6   C7   C8    180.00   0.0  0
 EGG  CONST_24  O18  C6   C5   C10   180.00   0.0  0
 EGG  CONST_25  O19  C8   C9   C10   180.00   0.0  0
 EGG  CONST_26  O20  C13  C12  C11   180.00   0.0  0
 EGG  CONST_27  O22  C15  C16  C11   180.00   0.0  0
 EGG  CONST_28  O21  C14  C13  C12   180.00   0.0  0
 EGG  CONST_29  O22  C15  C14  C13   180.00   0.0  0
 EGG  CONST_30  O20  C13  C14  C15   180.00   0.0  0
 EGG  CONST_31  O21  C14  C15  C16   180.00   0.0  0
 EGG  CONST_32  C21  C20  C19  C18   180.00   0.0  0
 EGG  CONST_33  C23  C24  C19  C18   180.00   0.0  0
 EGG  CONST_34  O24  C21  C20  C19   180.00   0.0  0
 EGG  CONST_35  O26  C23  C24  C19   180.00   0.0  0
 EGG  CONST_36  O25  C22  C21  C20   180.00   0.0  0
 EGG  CONST_37  O26  C23  C22  C21   180.00   0.0  0
 EGG  CONST_38  O24  C21  C22  C23   180.00   0.0  0
 EGG  CONST_39  O25  C22  C23  C24   180.00   0.0  0
 EGG  CONST_40  H9   C9   C10  O1      0.00   0.0  0
 EGG  CONST_41  H12  C12  C11  C2      0.00   0.0  0
 EGG  CONST_42  H16  C16  C11  C2      0.00   0.0  0
 EGG  CONST_43  H7   C7   C6   C5    180.00   0.0  0
 EGG  CONST_44  H24  C24  C19  C20   180.00   0.0  0
 EGG  CONST_45  H20  C20  C21  C22   180.00   0.0  0
 EGG  Var_01    C5   C10  O1   C2    -13.94  30.0  1
 EGG  Var_02    C6   C5   C4   C3    163.20  30.0  1
 EGG  Var_03    C19  C18  O17  C3   -178.36  30.0  3
 EGG  Var_04    C20  C19  C18  O17   179.04  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
 EGG  chir_01  C2  O1   C3  C11  negativ
 EGG  chir_02  C3  O17  C4  C2   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
 EGG  plan-1  C2   0.020
 EGG  plan-1  C11  0.020
 EGG  plan-1  C12  0.020
 EGG  plan-1  C13  0.020
 EGG  plan-1  C14  0.020
 EGG  plan-1  C15  0.020
 EGG  plan-1  C16  0.020
 EGG  plan-1  O20  0.020
 EGG  plan-1  O21  0.020
 EGG  plan-1  O22  0.020
 EGG  plan-1  H12  0.020
 EGG  plan-1  H16  0.020
 EGG  plan-2  C18  0.020
 EGG  plan-2  C19  0.020
 EGG  plan-2  C20  0.020
 EGG  plan-2  C21  0.020
 EGG  plan-2  C22  0.020
 EGG  plan-2  C23  0.020
 EGG  plan-2  C24  0.020
 EGG  plan-2  O24  0.020
 EGG  plan-2  O25  0.020
 EGG  plan-2  O26  0.020
 EGG  plan-2  H20  0.020
 EGG  plan-2  H24  0.020
 EGG  plan-3  O1   0.020
 EGG  plan-3  C4   0.020
 EGG  plan-3  C5   0.020
 EGG  plan-3  C6   0.020
 EGG  plan-3  C7   0.020
 EGG  plan-3  C8   0.020
 EGG  plan-3  C9   0.020
 EGG  plan-3  C10  0.020
 EGG  plan-3  O18  0.020
 EGG  plan-3  O19  0.020
 EGG  plan-3  H7   0.020
 EGG  plan-3  H9   0.020
 EGG  plan-4  O17  0.020
 EGG  plan-4  C18  0.020
 EGG  plan-4  C19  0.020
 EGG  plan-4  O23  0.020

