# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 20:50:49 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-[3,4-bis(oxidanyl)phenyl]-8-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-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)c3C(=O)C=C(Oc23)c4ccc(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
 USE  USE  2-[3,4-bis(oxidanyl)phenyl]-8-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one  ligand  52  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_USE
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
 USE  C4   C  CR6   0   0.330  25.8941  15.7837   5.3693
 USE  C5   C  CR16  0  -0.414  26.9819  15.0411   5.7830
 USE  C6   C  CR6   0   0.017  27.7018  15.3981   6.9286
 USE  C7   C  CR6   0   0.417  28.8338  14.5877   7.3743
 USE  C8   C  CR16  0  -0.518  29.0746  13.3001   7.0371
 USE  C10  C  CR66  0  -0.353  31.0482  13.3712   8.4676
 USE  C13  C  CR6   0   0.361  32.5924  14.8781  10.2191
 USE  C15  C  CR6   0   0.391  32.1915  12.8008   9.0710
 USE  C17  C  CR16  0   0.016  31.2911  17.8784   8.8202
 USE  C20  C  CR16  0  -0.019  29.3834  18.1969  10.9674
 USE  C21  C  CH2   0  -0.167  27.9692  18.0908  11.4968
 USE  C1   C  CR16  0  -0.296  27.3160  16.5263   7.6487
 USE  C2   C  CR16  0  -0.363  26.2220  17.2726   7.2409
 USE  C3   C  CR6   0   0.268  25.5044  16.9122   6.1114
 USE  C9   C  CR6   0   0.537  30.2197  12.6084   7.5586
 USE  O1   O  O     0  -0.507  30.4852  11.4301   7.2682
 USE  C11  C  CR66  0   0.430  30.7223  14.6920   8.7788
 USE  O2   O  O     0  -0.468  29.6425  15.2586   8.2060
 USE  C12  C  CR6   0  -0.176  31.4629  15.4847   9.6509
 USE  C14  C  CR16  0  -0.508  32.9552  13.5599   9.9362
 USE  O3   O  OH1   0  -0.624  32.5377  11.5471   8.8120
 USE  O4   O  OH1   0  -0.609  33.3277  15.6151  11.0571
 USE  C16  C  CR16  0  -0.012  31.0818  16.9012   9.9909
 USE  C18  C  CR16  0   0.024  30.9182  19.2723   9.2911
 USE  C19  C  CR16  0  -0.006  29.5085  19.2684   9.8774
 USE  O5   O  O     0  -0.491  29.7470  16.9360  10.4444
 USE  O7   O  OH1   0  -0.670  29.2766  20.5640  10.3887
 USE  O8   O  OH1   0  -0.664  31.0191  20.1619   8.2099
 USE  O9   O  OH1   0  -0.661  32.6371  17.8866   8.4203
 USE  O10  O  OH1   0  -0.626  25.2351  15.4120   4.2552
 USE  O11  O  OH1   0  -0.629  24.4323  17.5771   5.6476
 USE  H1   H  HCR6  0   0.270  27.2756  14.1878   5.1848
 USE  H2   H  HCR6  0   0.281  28.3918  12.7676   6.3912
 USE  H3   H  HCR6  0   0.223  30.6274  17.6068   7.9881
 USE  H4   H  HCR6  0   0.225  30.0574  18.4681  11.7980
 USE  H5   H  HCH2  0   0.203  27.6575  19.0821  11.8471
 USE  H6   H  HCH2  0   0.201  27.2957  17.8170  10.6717
 USE  H7   H  HCR6  0   0.271  27.8487  16.8231   8.5402
 USE  H8   H  HCR6  0   0.282  25.9213  18.1434   7.8126
 USE  H9   H  HCR6  0   0.284  33.8364  13.1256  10.3949
 USE  H10  H  HOH1  0   0.476  31.8687  11.1865   8.1752
 USE  H11  H  HOH1  0   0.487  34.0609  15.1010  11.4167
 USE  H12  H  HCR6  0   0.245  31.7408  17.2437  10.8000
 USE  H13  H  HCR6  0   0.204  31.6144  19.5541  10.1007
 USE  H14  H  HCR6  0   0.227  28.7988  19.0334   9.0708
 USE  H15  H  HOH1  0   0.454  27.0394  17.1073  12.8773
 USE  H16  H  HOH1  0   0.460  28.3435  20.7774  10.3004
 USE  H17  H  HOH1  0   0.446  30.7278  21.0273   8.5173
 USE  H18  H  HOH1  0   0.455  32.8134  17.0770   7.9306
 USE  H19  H  HOH1  0   0.474  24.5175  16.0273   4.0621
 USE  H20  H  HOH1  0   0.487  24.2355  18.3502   6.1897
 USE  O6   O  OH1   0  -0.663  27.9368  17.1425  12.5343

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
 USE  O10  C4   single    1.347  0.020  1.347
 USE  C4   C5   aromatic  1.381  0.020  1.381
 USE  C4   C3   aromatic  1.406  0.020  1.406
 USE  O11  C3   single    1.344  0.020  1.344
 USE  C5   C6   aromatic  1.399  0.020  1.399
 USE  C3   C2   aromatic  1.386  0.020  1.386
 USE  C6   C7   single    1.462  0.020  1.462
 USE  C6   C1   aromatic  1.393  0.020  1.393
 USE  C8   C7   double    1.353  0.020  1.353
 USE  C8   C9   single    1.436  0.020  1.436
 USE  C2   C1   aromatic  1.386  0.020  1.386
 USE  O1   C9   double    1.242  0.020  1.242
 USE  C7   O2   single    1.340  0.020  1.340
 USE  C9   C10  single    1.447  0.020  1.447
 USE  O8   C18  single    1.404  0.020  1.404
 USE  O2   C11  single    1.347  0.020  1.347
 USE  C10  C11  aromatic  1.396  0.020  1.396
 USE  C10  C15  aromatic  1.413  0.020  1.413
 USE  O9   C17  single    1.404  0.020  1.404
 USE  C11  C12  aromatic  1.392  0.020  1.392
 USE  O3   C15  single    1.326  0.020  1.326
 USE  C17  C18  single    1.518  0.020  1.518
 USE  C17  C16  single    1.539  0.020  1.539
 USE  C15  C14  aromatic  1.381  0.020  1.381
 USE  C18  C19  single    1.527  0.020  1.527
 USE  C12  C16  single    1.506  0.020  1.506
 USE  C12  C13  aromatic  1.402  0.020  1.402
 USE  C19  O7   single    1.412  0.020  1.412
 USE  C19  C20  single    1.534  0.020  1.534
 USE  C14  C13  aromatic  1.396  0.020  1.396
 USE  C16  O5   single    1.410  0.020  1.410
 USE  C13  O4   single    1.336  0.020  1.336
 USE  O5   C20  single    1.413  0.020  1.413
 USE  C20  C21  single    1.514  0.020  1.514
 USE  C21  O6   single    1.406  0.020  1.406
 USE  C5   H1   single    0.930  0.020  1.080
 USE  C8   H2   single    0.930  0.020  1.080
 USE  C17  H3   single    0.970  0.020  1.090
 USE  C20  H4   single    0.970  0.020  1.090
 USE  C21  H5   single    0.970  0.020  1.090
 USE  C21  H6   single    0.970  0.020  1.090
 USE  C1   H7   single    0.930  0.020  1.080
 USE  C2   H8   single    0.930  0.020  1.080
 USE  C14  H9   single    0.930  0.020  1.080
 USE  O3   H10  single    0.850  0.020  0.980
 USE  O4   H11  single    0.850  0.020  0.980
 USE  C16  H12  single    0.970  0.020  1.090
 USE  C18  H13  single    0.970  0.020  1.090
 USE  C19  H14  single    0.970  0.020  1.090
 USE  O6   H15  single    0.850  0.020  0.980
 USE  O7   H16  single    0.850  0.020  0.980
 USE  O8   H17  single    0.850  0.020  0.980
 USE  O9   H18  single    0.850  0.020  0.980
 USE  O10  H19  single    0.850  0.020  0.980
 USE  O11  H20  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
 USE  O10  C4   C3   121.51  3.000
 USE  C3   C4   C5   119.48  3.000
 USE  O10  C4   C5   119.01  3.000
 USE  H1   C5   C6   120.92  3.000
 USE  H1   C5   C4   118.17  3.000
 USE  C6   C5   C4   120.89  3.000
 USE  C1   C6   C7   120.39  3.000
 USE  C1   C6   C5   119.17  3.000
 USE  C7   C6   C5   120.43  3.000
 USE  O2   C7   C8   121.59  3.000
 USE  O2   C7   C6   112.27  3.000
 USE  C8   C7   C6   126.13  3.000
 USE  H2   C8   C9   118.93  3.000
 USE  H2   C8   C7   120.38  3.000
 USE  C9   C8   C7   120.67  3.000
 USE  C11  C10  C9   120.35  3.000
 USE  C11  C10  C15  118.41  3.000
 USE  C9   C10  C15  121.24  3.000
 USE  O4   C13  C14  120.32  3.000
 USE  O4   C13  C12  117.30  3.000
 USE  C14  C13  C12  122.38  3.000
 USE  O3   C15  C14  119.83  3.000
 USE  C14  C15  C10  119.54  3.000
 USE  O3   C15  C10  120.63  3.000
 USE  H3   C17  O9   111.40  3.000
 USE  H3   C17  C18  108.29  3.000
 USE  O9   C17  C18  108.57  3.000
 USE  H3   C17  C16  109.69  3.000
 USE  C18  C17  C16  108.28  3.000
 USE  O9   C17  C16  110.53  3.000
 USE  H4   C20  O5   109.92  3.000
 USE  H4   C20  C19  108.26  3.000
 USE  O5   C20  C19  109.85  3.000
 USE  H4   C20  C21  108.94  3.000
 USE  O5   C20  C21  107.91  3.000
 USE  C19  C20  C21  111.95  3.000
 USE  H6   C21  H5   106.89  3.000
 USE  H6   C21  O6   111.81  3.000
 USE  H5   C21  O6   111.56  3.000
 USE  H6   C21  C20  109.10  3.000
 USE  H5   C21  C20  108.30  3.000
 USE  O6   C21  C20  109.08  3.000
 USE  H7   C1   C2   118.96  3.000
 USE  H7   C1   C6   120.85  3.000
 USE  C2   C1   C6   120.19  3.000
 USE  H8   C2   C3   119.67  3.000
 USE  H8   C2   C1   119.76  3.000
 USE  C3   C2   C1   120.57  3.000
 USE  O11  C3   C2   124.45  3.000
 USE  C2   C3   C4   119.70  3.000
 USE  O11  C3   C4   115.85  3.000
 USE  O1   C9   C10  121.63  3.000
 USE  C10  C9   C8   115.51  3.000
 USE  O1   C9   C8   122.85  3.000
 USE  C12  C11  O2   116.95  3.000
 USE  C12  C11  C10  123.68  3.000
 USE  O2   C11  C10  119.37  3.000
 USE  C11  O2   C7   122.48  3.000
 USE  C16  C12  C11  122.86  3.000
 USE  C16  C12  C13  121.29  3.000
 USE  C11  C12  C13  115.85  3.000
 USE  H9   C14  C15  119.62  3.000
 USE  H9   C14  C13  120.24  3.000
 USE  C15  C14  C13  120.14  3.000
 USE  H10  O3   C15  107.04  3.000
 USE  H11  O4   C13  110.97  3.000
 USE  H12  C16  O5   108.87  3.000
 USE  H12  C16  C12  107.93  3.000
 USE  O5   C16  C12  109.60  3.000
 USE  H12  C16  C17  106.30  3.000
 USE  O5   C16  C17  110.95  3.000
 USE  C12  C16  C17  113.02  3.000
 USE  H13  C18  O8   110.95  3.000
 USE  H13  C18  C19  107.53  3.000
 USE  O8   C18  C19  111.33  3.000
 USE  H13  C18  C17  107.88  3.000
 USE  C19  C18  C17  110.10  3.000
 USE  O8   C18  C17  108.99  3.000
 USE  H14  C19  O7   110.83  3.000
 USE  H14  C19  C18  108.34  3.000
 USE  O7   C19  C18  106.76  3.000
 USE  H14  C19  C20  108.62  3.000
 USE  O7   C19  C20  111.74  3.000
 USE  C18  C19  C20  110.49  3.000
 USE  C16  O5   C20  112.63  3.000
 USE  H16  O7   C19  109.26  3.000
 USE  H17  O8   C18  107.56  3.000
 USE  H18  O9   C17  108.39  3.000
 USE  H19  O10  C4   110.70  3.000
 USE  H20  O11  C3   111.42  3.000
 USE  H15  O6   C21  108.03  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
 USE  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 USE  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 USE  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 USE  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 USE  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 USE  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 USE  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 USE  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 USE  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 USE  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 USE  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 USE  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 USE  CONST_13  C7   C6   C5   C4    180.00   0.0  0
 USE  CONST_14  C2   C1   C6   C7    180.00   0.0  0
 USE  CONST_15  C16  C12  C11  C10   180.00   0.0  0
 USE  CONST_16  C16  C12  C11  O2      0.00   0.0  0
 USE  CONST_17  C16  C12  C13  C14   180.00   0.0  0
 USE  CONST_18  O11  C3   C4   C5    180.00   0.0  0
 USE  CONST_19  O10  C4   C5   C6    180.00   0.0  0
 USE  CONST_20  O3   C15  C14  C13   180.00   0.0  0
 USE  CONST_21  O4   C13  C14  C15   180.00   0.0  0
 USE  CONST_22  O11  C3   C2   C1    180.00   0.0  0
 USE  CONST_23  O10  C4   C3   C2    180.00   0.0  0
 USE  CONST_24  O3   C15  C10  C9      0.00   0.0  0
 USE  CONST_25  O3   C15  C10  C11   180.00   0.0  0
 USE  CONST_26  O4   C13  C12  C11   180.00   0.0  0
 USE  CONST_27  C16  C12  C13  O4      0.00   0.0  0
 USE  CONST_28  H8   C2   C3   C4    180.00   0.0  0
 USE  CONST_29  H7   C1   C6   C5    180.00   0.0  0
 USE  CONST_30  H1   C5   C6   C7      0.00   0.0  0
 USE  CONST_31  H9   C14  C15  C10   180.00   0.0  0
 USE  Var_01    C8   C7   C6   C5    -20.08  30.0  2
 USE  Var_02    C9   C8   C7   C6   -179.23  30.0  1
 USE  Var_03    C10  C9   C8   C7      1.29  30.0  1
 USE  Var_04    C10  C11  O2   C7      2.24  30.0  1
 USE  Var_05    C11  C10  C9   C8     -0.50  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
 USE  chir_01  C17  O9  C18  C16  positiv
 USE  chir_02  C20  O5  C19  C21  negativ
 USE  chir_03  C16  O5  C17  C12  positiv
 USE  chir_04  C18  O8  C17  C19  positiv
 USE  chir_05  C19  O7  C20  C18  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
 USE  plan-1  C4   0.020
 USE  plan-1  C5   0.020
 USE  plan-1  C6   0.020
 USE  plan-1  C7   0.020
 USE  plan-1  C1   0.020
 USE  plan-1  C2   0.020
 USE  plan-1  C3   0.020
 USE  plan-1  O10  0.020
 USE  plan-1  O11  0.020
 USE  plan-1  H1   0.020
 USE  plan-1  H7   0.020
 USE  plan-1  H8   0.020
 USE  plan-2  C10  0.020
 USE  plan-2  C13  0.020
 USE  plan-2  C15  0.020
 USE  plan-2  C9   0.020
 USE  plan-2  C11  0.020
 USE  plan-2  O2   0.020
 USE  plan-2  C12  0.020
 USE  plan-2  C14  0.020
 USE  plan-2  O3   0.020
 USE  plan-2  O4   0.020
 USE  plan-2  C16  0.020
 USE  plan-2  H9   0.020
 USE  plan-3  C8   0.020
 USE  plan-3  C10  0.020
 USE  plan-3  C9   0.020
 USE  plan-3  O1   0.020

