# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:08:13 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-[3-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2,4,6-tris(oxidanyl)phenyl]-3-(4-hydroxyphenyl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2c(O)cc(O)c(C(=O)CCc3ccc(O)cc3)c2O
#
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
 E7F  E7F  1-[3-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2,4,6-tris(oxidanyl)phenyl]-3-(4-hydroxyphenyl)propan-1-one  ligand  55  31  .  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_E7F
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
 E7F  C01  C  CR6   0   0.403  -1.6117  -0.7565  -1.6727
 E7F  C02  C  CR6   0  -0.182  -1.7899  -0.0163  -0.4994
 E7F  C03  C  CR6   0   0.373  -0.6474   0.4892   0.1237
 E7F  C04  C  CR6   0  -0.314   0.6779   0.2548  -0.3730
 E7F  C05  C  CR6   0   0.347   0.7797  -0.4745  -1.5848
 E7F  C06  C  CR16  0  -0.520  -0.3472  -0.9720  -2.2101
 E7F  C07  C  C     0   0.492   1.8035   0.7299   0.4297
 E7F  C08  C  CH2   0  -0.654   3.2387   0.3798   0.1088
 E7F  C09  C  CH2   0  -0.492   4.2318   0.7743   1.2032
 E7F  C10  C  CR6   0   0.096   5.6240   0.3380   0.8361
 E7F  C11  C  CR16  0  -0.294   6.4557   1.1461   0.0638
 E7F  C12  C  CR16  0  -0.323   7.7262   0.7356  -0.3079
 E7F  C13  C  CR6   0   0.338   8.1978  -0.5124   0.0929
 E7F  C14  C  CR16  0  -0.368   7.3810  -1.3334   0.8650
 E7F  C15  C  CR16  0  -0.295   6.1115  -0.9051   1.2260
 E7F  C16  C  CH2   0  -0.160  -5.6162  -2.2429   1.1650
 E7F  C17  C  CH1   0   0.037  -6.0038   0.0449   0.1827
 E7F  C18  C  CH1   0  -0.005  -5.3434   1.3918  -0.0900
 E7F  C19  C  CH1   0   0.003  -4.0012   1.1891  -0.7744
 E7F  C20  C  CH1   0   0.002  -3.1539   0.2368   0.0825
 E7F  C21  C  CH1   0  -0.008  -5.0424  -0.8564   0.9611
 E7F  O01  O  OH1   0  -0.612   1.9239  -0.7478  -2.2237
 E7F  O02  O  OH1   0  -0.600  -2.6939  -1.2396  -2.2824
 E7F  O03  O  OH1   0  -0.622  -0.8257   1.1975   1.2272
 E7F  O04  O  O     0  -0.486   1.6041   1.4168   1.4367
 E7F  O05  O  OH1   0  -0.635   9.4422  -0.8706  -0.2876
 E7F  O06  O  O2    0  -0.488  -3.8270  -0.9908   0.2615
 E7F  O07  O  OH1   0  -0.675  -6.2380   2.1487  -0.8721
 E7F  O08  O  OH1   0  -0.669  -3.3839   2.4490  -0.8900
 E7F  O10  O  OH1   0  -0.671  -4.7291  -2.9899   1.9637
 E7F  H1   H  HCR6  0   0.283  -0.2322  -1.5229  -3.1363
 E7F  H2   H  HCH2  0   0.296   3.3232  -0.6959  -0.0718
 E7F  H3   H  HCH2  0   0.289   3.5372   0.8968  -0.8134
 E7F  H4   H  HCH2  0   0.256   4.2053   1.8538   1.3555
 E7F  H5   H  HCH2  0   0.256   3.9379   0.3125   2.1470
 E7F  H6   H  HCR6  0   0.249   6.1089   2.1223  -0.2557
 E7F  H7   H  HCR6  0   0.261   8.3560   1.3815  -0.9073
 E7F  H8   H  HCR6  0   0.268   7.7331  -2.3056   1.1916
 E7F  H9   H  HCR6  0   0.252   5.4927  -1.5575   1.8312
 E7F  H10  H  HCH2  0   0.212  -6.6000  -2.1459   1.6355
 E7F  H11  H  HCH2  0   0.194  -5.7734  -2.7108   0.1828
 E7F  H12  H  HCH1  0   0.209  -6.2206  -0.4361  -0.7848
 E7F  H13  H  HCH1  0   0.209  -5.1643   1.8827   0.8810
 E7F  H14  H  HCH1  0   0.224  -4.1793   0.7423  -1.7612
 E7F  H15  H  HCH1  0   0.238  -3.0285   0.7227   1.0599
 E7F  H16  H  HCH1  0   0.212  -4.8608  -0.3955   1.9473
 E7F  H17  H  HOH1  0   0.490   2.6686  -0.2257  -1.9134
 E7F  H18  H  HOH1  0   0.483  -2.4480  -1.6927  -3.0980
 E7F  H19  H  HOH1  0   0.484   0.0778   1.4663   1.5543
 E7F  H20  H  HOH1  0   0.473   9.6524  -1.7510   0.0427
 E7F  H21  H  HOH1  0   0.455  -5.9070   3.0506  -0.9268
 E7F  H22  H  HOH1  0   0.456  -2.6383   2.3699  -1.4931
 E7F  H24  H  HOH1  0   0.456  -5.1451  -3.8340   2.1584
 E7F  O09  O  OH1   0  -0.674  -7.1770   0.1951   0.9447
 E7F  H23  H  HOH1  0   0.453  -7.7651   0.7953   0.4743

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
 E7F  O07  C18  single    1.409  0.020  1.409
 E7F  C18  C19  single    1.520  0.020  1.520
 E7F  C18  C17  single    1.525  0.020  1.525
 E7F  O08  C19  single    1.408  0.020  1.408
 E7F  O09  C17  single    1.407  0.020  1.407
 E7F  C19  C20  single    1.536  0.020  1.536
 E7F  C17  C21  single    1.531  0.020  1.531
 E7F  O02  C01  single    1.333  0.020  1.333
 E7F  C20  O06  single    1.411  0.020  1.411
 E7F  C20  C02  single    1.504  0.020  1.504
 E7F  C21  O06  single    1.409  0.020  1.409
 E7F  C21  C16  single    1.514  0.020  1.514
 E7F  O10  C16  single    1.408  0.020  1.408
 E7F  C01  C02  aromatic  1.399  0.020  1.399
 E7F  C01  C06  aromatic  1.391  0.020  1.391
 E7F  C02  C03  aromatic  1.396  0.020  1.396
 E7F  C06  C05  aromatic  1.381  0.020  1.381
 E7F  C03  O03  single    1.323  0.020  1.323
 E7F  C03  C04  aromatic  1.435  0.020  1.435
 E7F  C05  C04  aromatic  1.418  0.020  1.418
 E7F  C05  O01  single    1.339  0.020  1.339
 E7F  C04  C07  single    1.462  0.020  1.462
 E7F  C07  O04  double    1.235  0.020  1.235
 E7F  C07  C08  single    1.512  0.020  1.512
 E7F  C08  C09  single    1.530  0.020  1.530
 E7F  C09  C10  single    1.504  0.020  1.504
 E7F  C15  C10  aromatic  1.391  0.020  1.391
 E7F  C15  C14  aromatic  1.388  0.020  1.388
 E7F  C10  C11  aromatic  1.393  0.020  1.393
 E7F  C14  C13  aromatic  1.392  0.020  1.392
 E7F  C11  C12  aromatic  1.386  0.020  1.386
 E7F  C13  C12  aromatic  1.393  0.020  1.393
 E7F  C13  O05  single    1.350  0.020  1.350
 E7F  C06  H1   single    0.930  0.020  1.080
 E7F  C08  H2   single    0.970  0.020  1.090
 E7F  C08  H3   single    0.970  0.020  1.090
 E7F  C09  H4   single    0.970  0.020  1.090
 E7F  C09  H5   single    0.970  0.020  1.090
 E7F  C11  H6   single    0.930  0.020  1.080
 E7F  C12  H7   single    0.930  0.020  1.080
 E7F  C14  H8   single    0.930  0.020  1.080
 E7F  C15  H9   single    0.930  0.020  1.080
 E7F  C16  H10  single    0.970  0.020  1.090
 E7F  C16  H11  single    0.970  0.020  1.090
 E7F  C17  H12  single    0.970  0.020  1.090
 E7F  C18  H13  single    0.970  0.020  1.090
 E7F  C19  H14  single    0.970  0.020  1.090
 E7F  C20  H15  single    0.970  0.020  1.090
 E7F  C21  H16  single    0.970  0.020  1.090
 E7F  O01  H17  single    0.850  0.020  0.980
 E7F  O02  H18  single    0.850  0.020  0.980
 E7F  O03  H19  single    0.850  0.020  0.980
 E7F  O05  H20  single    0.850  0.020  0.980
 E7F  O07  H21  single    0.850  0.020  0.980
 E7F  O08  H22  single    0.850  0.020  0.980
 E7F  O09  H23  single    0.850  0.020  0.980
 E7F  O10  H24  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
 E7F  O02  C01  C06  120.35  3.000
 E7F  C06  C01  C02  121.47  3.000
 E7F  O02  C01  C02  118.17  3.000
 E7F  C20  C02  C03  120.56  3.000
 E7F  C03  C02  C01  117.50  3.000
 E7F  C20  C02  C01  121.94  3.000
 E7F  O03  C03  C04  120.04  3.000
 E7F  C04  C03  C02  122.84  3.000
 E7F  O03  C03  C02  117.11  3.000
 E7F  C07  C04  C05  125.53  3.000
 E7F  C07  C04  C03  117.91  3.000
 E7F  C05  C04  C03  116.51  3.000
 E7F  O01  C05  C06  114.06  3.000
 E7F  O01  C05  C04  125.05  3.000
 E7F  C06  C05  C04  120.89  3.000
 E7F  H1   C06  C05  118.90  3.000
 E7F  H1   C06  C01  120.36  3.000
 E7F  C05  C06  C01  120.73  3.000
 E7F  O04  C07  C08  117.07  3.000
 E7F  C08  C07  C04  122.63  3.000
 E7F  O04  C07  C04  120.27  3.000
 E7F  H3   C08  H2   107.65  3.000
 E7F  H3   C08  C09  107.63  3.000
 E7F  H2   C08  C09  108.76  3.000
 E7F  H3   C08  C07  109.10  3.000
 E7F  H2   C08  C07  109.64  3.000
 E7F  C09  C08  C07  113.88  3.000
 E7F  H5   C09  H4   106.96  3.000
 E7F  H5   C09  C10  109.73  3.000
 E7F  H4   C09  C10  110.10  3.000
 E7F  H5   C09  C08  109.56  3.000
 E7F  H4   C09  C08  109.85  3.000
 E7F  C10  C09  C08  110.57  3.000
 E7F  C15  C10  C11  117.68  3.000
 E7F  C11  C10  C09  121.30  3.000
 E7F  C15  C10  C09  121.00  3.000
 E7F  H6   C11  C12  118.75  3.000
 E7F  H6   C11  C10  119.64  3.000
 E7F  C12  C11  C10  121.61  3.000
 E7F  H7   C12  C13  119.77  3.000
 E7F  H7   C12  C11  120.32  3.000
 E7F  C13  C12  C11  119.90  3.000
 E7F  O05  C13  C14  122.74  3.000
 E7F  O05  C13  C12  117.96  3.000
 E7F  C14  C13  C12  119.30  3.000
 E7F  H8   C14  C15  119.70  3.000
 E7F  H8   C14  C13  120.36  3.000
 E7F  C15  C14  C13  119.94  3.000
 E7F  H9   C15  C14  118.80  3.000
 E7F  H9   C15  C10  119.63  3.000
 E7F  C14  C15  C10  121.57  3.000
 E7F  H11  C16  H10  107.05  3.000
 E7F  H11  C16  O10  111.78  3.000
 E7F  H10  C16  O10  111.67  3.000
 E7F  H11  C16  C21  108.88  3.000
 E7F  H10  C16  C21  108.49  3.000
 E7F  O10  C16  C21  108.87  3.000
 E7F  H12  C17  O09  110.98  3.000
 E7F  H12  C17  C21  108.24  3.000
 E7F  O09  C17  C21  108.13  3.000
 E7F  H12  C17  C18  108.29  3.000
 E7F  C21  C17  C18  109.82  3.000
 E7F  O09  C17  C18  111.33  3.000
 E7F  H13  C18  O07  110.66  3.000
 E7F  H13  C18  C19  108.21  3.000
 E7F  O07  C18  C19  112.48  3.000
 E7F  H13  C18  C17  107.83  3.000
 E7F  C19  C18  C17  110.19  3.000
 E7F  O07  C18  C17  107.39  3.000
 E7F  H14  C19  O08  111.20  3.000
 E7F  H14  C19  C20  109.80  3.000
 E7F  O08  C19  C20  111.03  3.000
 E7F  H14  C19  C18  108.40  3.000
 E7F  C20  C19  C18  108.57  3.000
 E7F  O08  C19  C18  107.74  3.000
 E7F  H15  C20  O06  109.04  3.000
 E7F  H15  C20  C19  106.57  3.000
 E7F  O06  C20  C19  110.30  3.000
 E7F  H15  C20  C02  108.36  3.000
 E7F  O06  C20  C02  109.58  3.000
 E7F  C19  C20  C02  112.88  3.000
 E7F  H16  C21  O06  109.97  3.000
 E7F  H16  C21  C17  108.17  3.000
 E7F  O06  C21  C17  110.21  3.000
 E7F  H16  C21  C16  108.94  3.000
 E7F  O06  C21  C16  107.84  3.000
 E7F  C17  C21  C16  111.69  3.000
 E7F  H17  O01  C05  113.41  3.000
 E7F  H18  O02  C01  110.49  3.000
 E7F  H19  O03  C03  107.19  3.000
 E7F  H20  O05  C13  110.31  3.000
 E7F  C21  O06  C20  113.04  3.000
 E7F  H21  O07  C18  108.46  3.000
 E7F  H22  O08  C19  108.52  3.000
 E7F  H24  O10  C16  107.95  3.000
 E7F  H23  O09  C17  108.13  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
 E7F  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 E7F  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 E7F  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 E7F  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 E7F  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 E7F  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 E7F  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 E7F  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 E7F  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 E7F  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 E7F  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 E7F  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 E7F  CONST_13  C20  C02  C03  C04   180.00   0.0  0
 E7F  CONST_14  C20  C02  C01  C06   180.00   0.0  0
 E7F  CONST_15  O03  C03  C02  C01   180.00   0.0  0
 E7F  CONST_16  O01  C05  C06  C01   180.00   0.0  0
 E7F  CONST_17  C07  C04  C03  C02   180.00   0.0  0
 E7F  CONST_18  O02  C01  C02  C03   180.00   0.0  0
 E7F  CONST_19  O01  C05  C04  C03   180.00   0.0  0
 E7F  CONST_20  O02  C01  C06  C05   180.00   0.0  0
 E7F  CONST_21  O03  C03  C04  C05   180.00   0.0  0
 E7F  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 E7F  CONST_23  C14  C15  C10  C09   180.00   0.0  0
 E7F  CONST_24  C12  C11  C10  C09   180.00   0.0  0
 E7F  CONST_25  O05  C13  C12  C11   180.00   0.0  0
 E7F  CONST_26  O05  C13  C14  C15   180.00   0.0  0
 E7F  CONST_27  O02  C01  C02  C20     0.00   0.0  0
 E7F  CONST_28  O03  C03  C02  C20     0.00   0.0  0
 E7F  CONST_29  H1   C06  C01  C02   180.00   0.0  0
 E7F  CONST_30  H8   C14  C15  C10   180.00   0.0  0
 E7F  CONST_31  H7   C12  C11  C10   180.00   0.0  0
 E7F  CONST_32  H9   C15  C10  C11   180.00   0.0  0
 E7F  CONST_33  H6   C11  C12  C13   180.00   0.0  0
 E7F  Var_01    O04  C07  C04  C03    -6.53  30.0  2
 E7F  Var_02    C15  C10  C09  C08   -91.18  30.0  2
 E7F  Var_03    C09  C08  C07  C04  -169.99  30.0  3
 E7F  Var_04    C10  C09  C08  C07   177.46  30.0  3

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
 E7F  chir_01  C17  C18  O09  C21  positiv
 E7F  chir_02  C18  O07  C17  C19  negativ
 E7F  chir_03  C19  O08  C18  C20  positiv
 E7F  chir_04  C20  O06  C19  C02  positiv
 E7F  chir_05  C21  O06  C16  C17  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
 E7F  plan-1  C01  0.020
 E7F  plan-1  C02  0.020
 E7F  plan-1  C03  0.020
 E7F  plan-1  C04  0.020
 E7F  plan-1  C05  0.020
 E7F  plan-1  C06  0.020
 E7F  plan-1  C07  0.020
 E7F  plan-1  C20  0.020
 E7F  plan-1  O01  0.020
 E7F  plan-1  O02  0.020
 E7F  plan-1  O03  0.020
 E7F  plan-1  H1   0.020
 E7F  plan-2  C09  0.020
 E7F  plan-2  C10  0.020
 E7F  plan-2  C11  0.020
 E7F  plan-2  C12  0.020
 E7F  plan-2  C13  0.020
 E7F  plan-2  C14  0.020
 E7F  plan-2  C15  0.020
 E7F  plan-2  O05  0.020
 E7F  plan-2  H6   0.020
 E7F  plan-2  H7   0.020
 E7F  plan-2  H8   0.020
 E7F  plan-2  H9   0.020
 E7F  plan-3  C04  0.020
 E7F  plan-3  C07  0.020
 E7F  plan-3  C08  0.020
 E7F  plan-3  O04  0.020

