# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:28:09 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-[3,4-bis(oxidanyl)phenyl]-3-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5,7-bis(oxidanyl)chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4ccc(O)c(O)c4)[C@H](O)[C@@H](O)[C@H]1O
#
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
 J6O  J6O  "2-[3,4-bis(oxidanyl)phenyl]-3-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5,7-bis(oxidanyl)chromen-4-one"
  ligand  53  33  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J6O
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
 J6O  C4   C  CR6   0   0.267  16.5132  6.3963  -31.8734
 J6O  C5   C  CR16  0  -0.419  15.8284  6.0545  -33.0219
 J6O  C6   C  CR6   0   0.033  16.4817  5.4644  -34.1034
 J6O  C7   C  CR6   0   0.242  15.6943  5.0178  -35.2542
 J6O  C8   C  CR6   0   0.156  14.5589  4.2786  -35.1759
 J6O  C10  C  CR66  0  -0.337  14.4328  4.3411  -37.6086
 J6O  C13  C  CR6   0   0.399  15.6676  5.1368  -39.9774
 J6O  C15  C  CR66  0   0.409  15.6390  5.0427  -37.6027
 J6O  C17  C  CH1   0  -0.033  13.0668  4.1513  -31.8890
 J6O  C20  C  CH1   0   0.026  11.3619  5.9533  -33.5218
 J6O  C21  C  CH2   0  -0.177  11.3244  7.4290  -33.9008
 J6O  C1   C  CR16  0  -0.301  17.8612  5.2911  -34.0510
 J6O  C11  C  CR6   0   0.404  13.8450  4.0341  -38.8618
 J6O  C12  C  CR16  0  -0.455  14.4603  4.4337  -40.0321
 J6O  C14  C  CR16  0  -0.515  16.2733  5.4483  -38.7632
 J6O  C16  C  CH1   0   0.302  12.9375  4.2164  -33.4172
 J6O  C18  C  CH1   0  -0.007  12.2818  5.3027  -31.2452
 J6O  C19  C  CH1   0  -0.033  11.0199  5.6114  -32.0483
 J6O  C2   C  CR16  0  -0.336  18.5600  5.6613  -32.9104
 J6O  C3   C  CR6   0   0.299  17.9016  6.1995  -31.8123
 J6O  C9   C  CR6   0   0.460  13.8324  3.9114  -36.3701
 J6O  O1   O  O     0  -0.494  12.7782  3.2600  -36.3274
 J6O  O10  O  OH1   0  -0.665  12.5661  2.8984  -31.4986
 J6O  O11  O  OH1   0  -0.667  15.9118  6.9223  -30.7862
 J6O  O12  O  OH1   0  -0.621  18.6093  6.5178  -30.7149
 J6O  O2   O  O     0  -0.455  16.2310  5.3639  -36.4364
 J6O  O3   O  OH1   0  -0.613  16.2039  5.4930  -41.1480
 J6O  O4   O  OH1   0  -0.624  12.7001  3.3626  -38.9205
 J6O  O5   O  O2    0  -0.509  14.1648  3.8027  -33.9686
 J6O  O6   O  O2    0  -0.507  12.6744  5.5116  -33.8383
 J6O  O7   O  OH1   0  -0.665   9.9890  7.7981  -34.1393
 J6O  O8   O  OH1   0  -0.654  10.3046  6.6745  -31.4682
 J6O  O9   O  OH1   0  -0.680  13.1176  6.4414  -31.1448
 J6O  H1   H  HCR6  0   0.290  14.7709  6.2656  -33.0783
 J6O  H3   H  HCH1  0   0.241  10.6526  5.4256  -34.1754
 J6O  H4   H  HCH2  0   0.205  11.7956  8.0425  -33.1252
 J6O  H5   H  HCH2  0   0.210  11.9333  7.5401  -34.8076
 J6O  H6   H  HCR6  0   0.259  18.3968  4.8397  -34.8759
 J6O  H7   H  HCR6  0   0.278  14.0108  4.2032  -40.9896
 J6O  H8   H  HCR6  0   0.293  17.2090  5.9922  -38.7187
 J6O  H9   H  HCH1  0   0.233  12.1303  3.5418  -33.7446
 J6O  H10  H  HCH1  0   0.250  11.9759  4.9785  -30.2394
 J6O  H11  H  HCH1  0   0.244  10.4175  4.6932  -32.0453
 J6O  H12  H  HCR6  0   0.268  19.6309  5.5102  -32.8580
 J6O  H13  H  HOH1  0   0.458  12.7847  2.7513  -30.5728
 J6O  H14  H  HOH1  0   0.478  14.9487  6.7655  -30.8285
 J6O  H15  H  HOH1  0   0.473  18.0214  6.8339  -30.0173
 J6O  H16  H  HOH1  0   0.482  17.0311  5.9731  -41.0190
 J6O  H17  H  HOH1  0   0.476  12.4282  3.1533  -37.9950
 J6O  H18  H  HOH1  0   0.454   9.9675  8.7450  -34.3024
 J6O  H19  H  HOH1  0   0.459   9.8975  6.3562  -30.6552
 J6O  H20  H  HOH1  0   0.466  12.5823  7.1830  -30.8367
 J6O  H2   H  HCH1  0   0.252  14.1233  4.2654  -31.6111

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
 J6O  O3   C13  single    1.336  0.020  1.336
 J6O  C13  C12  aromatic  1.398  0.020  1.398
 J6O  C13  C14  aromatic  1.392  0.020  1.392
 J6O  C12  C11  aromatic  1.381  0.020  1.381
 J6O  C14  C15  aromatic  1.383  0.020  1.383
 J6O  O4   C11  single    1.329  0.020  1.329
 J6O  C11  C10  aromatic  1.418  0.020  1.418
 J6O  C15  C10  aromatic  1.395  0.020  1.395
 J6O  C15  O2   single    1.347  0.020  1.347
 J6O  C10  C9   single    1.442  0.020  1.442
 J6O  O2   C7   single    1.344  0.020  1.344
 J6O  C9   O1   double    1.240  0.020  1.240
 J6O  C9   C8   single    1.445  0.020  1.445
 J6O  C7   C8   double    1.357  0.020  1.357
 J6O  C7   C6   single    1.464  0.020  1.464
 J6O  C8   O5   single    1.356  0.020  1.356
 J6O  C1   C6   aromatic  1.391  0.020  1.391
 J6O  C1   C2   aromatic  1.388  0.020  1.388
 J6O  C6   C5   aromatic  1.395  0.020  1.395
 J6O  O5   C16  single    1.408  0.020  1.408
 J6O  C16  O6   single    1.387  0.020  1.387
 J6O  C16  C17  single    1.535  0.020  1.535
 J6O  O6   C20  single    1.421  0.020  1.421
 J6O  C2   C3   aromatic  1.389  0.020  1.389
 J6O  C20  C21  single    1.524  0.020  1.524
 J6O  C20  C19  single    1.551  0.020  1.551
 J6O  C5   C4   aromatic  1.380  0.020  1.380
 J6O  C21  O7   single    1.406  0.020  1.406
 J6O  O10  C17  single    1.405  0.020  1.405
 J6O  C17  C18  single    1.535  0.020  1.535
 J6O  C3   C4   aromatic  1.404  0.020  1.404
 J6O  C3   O12  single    1.344  0.020  1.344
 J6O  C4   O11  single    1.349  0.020  1.349
 J6O  C19  C18  single    1.527  0.020  1.527
 J6O  C19  O8   single    1.407  0.020  1.407
 J6O  C18  O9   single    1.416  0.020  1.416
 J6O  C5   H1   single    0.930  0.020  1.080
 J6O  C17  H2   single    0.970  0.020  1.090
 J6O  C20  H3   single    0.970  0.020  1.090
 J6O  C21  H4   single    0.970  0.020  1.090
 J6O  C21  H5   single    0.970  0.020  1.090
 J6O  C1   H6   single    0.930  0.020  1.080
 J6O  C12  H7   single    0.930  0.020  1.080
 J6O  C14  H8   single    0.930  0.020  1.080
 J6O  C16  H9   single    0.970  0.020  1.090
 J6O  C18  H10  single    0.970  0.020  1.090
 J6O  C19  H11  single    0.970  0.020  1.090
 J6O  C2   H12  single    0.930  0.020  1.080
 J6O  O10  H13  single    0.850  0.020  0.980
 J6O  O11  H14  single    0.850  0.020  0.980
 J6O  O12  H15  single    0.850  0.020  0.980
 J6O  O3   H16  single    0.850  0.020  0.980
 J6O  O4   H17  single    0.850  0.020  0.980
 J6O  O7   H18  single    0.850  0.020  0.980
 J6O  O8   H19  single    0.850  0.020  0.980
 J6O  O9   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
 J6O  O11  C4   C3   117.42  3.000
 J6O  O11  C4   C5   123.09  3.000
 J6O  C3   C4   C5   119.49  3.000
 J6O  H1   C5   C6   120.07  3.000
 J6O  H1   C5   C4   118.75  3.000
 J6O  C6   C5   C4   121.18  3.000
 J6O  C1   C6   C7   121.65  3.000
 J6O  C1   C6   C5   119.22  3.000
 J6O  C7   C6   C5   119.12  3.000
 J6O  O2   C7   C8   121.68  3.000
 J6O  C8   C7   C6   124.80  3.000
 J6O  O2   C7   C6   113.46  3.000
 J6O  O5   C8   C9   120.02  3.000
 J6O  O5   C8   C7   119.05  3.000
 J6O  C9   C8   C7   120.75  3.000
 J6O  C9   C10  C11  121.47  3.000
 J6O  C9   C10  C15  120.41  3.000
 J6O  C11  C10  C15  118.09  3.000
 J6O  O3   C13  C14  122.00  3.000
 J6O  C14  C13  C12  121.48  3.000
 J6O  O3   C13  C12  116.52  3.000
 J6O  O2   C15  C14  117.07  3.000
 J6O  O2   C15  C10  120.23  3.000
 J6O  C14  C15  C10  122.70  3.000
 J6O  H2   C17  O10  111.42  3.000
 J6O  H2   C17  C18  107.93  3.000
 J6O  O10  C17  C18  111.73  3.000
 J6O  H2   C17  C16  109.18  3.000
 J6O  C18  C17  C16  110.04  3.000
 J6O  O10  C17  C16  106.53  3.000
 J6O  H3   C20  O6   108.32  3.000
 J6O  H3   C20  C19  108.47  3.000
 J6O  O6   C20  C19  110.30  3.000
 J6O  H3   C20  C21  107.52  3.000
 J6O  C19  C20  C21  116.38  3.000
 J6O  O6   C20  C21  105.57  3.000
 J6O  H5   C21  H4   106.83  3.000
 J6O  H5   C21  O7   111.10  3.000
 J6O  H4   C21  O7   112.44  3.000
 J6O  H5   C21  C20  106.85  3.000
 J6O  H4   C21  C20  110.83  3.000
 J6O  O7   C21  C20  108.65  3.000
 J6O  H6   C1   C2   119.24  3.000
 J6O  H6   C1   C6   120.93  3.000
 J6O  C2   C1   C6   119.79  3.000
 J6O  O4   C11  C12  119.52  3.000
 J6O  O4   C11  C10  120.38  3.000
 J6O  C12  C11  C10  120.10  3.000
 J6O  H7   C12  C11  120.19  3.000
 J6O  H7   C12  C13  120.01  3.000
 J6O  C11  C12  C13  119.80  3.000
 J6O  H8   C14  C15  120.59  3.000
 J6O  H8   C14  C13  121.60  3.000
 J6O  C15  C14  C13  117.81  3.000
 J6O  H9   C16  O6   110.03  3.000
 J6O  H9   C16  O5   110.02  3.000
 J6O  O6   C16  O5   108.72  3.000
 J6O  H9   C16  C17  109.37  3.000
 J6O  O6   C16  C17  110.96  3.000
 J6O  O5   C16  C17  107.70  3.000
 J6O  H10  C18  O9   109.65  3.000
 J6O  H10  C18  C19  108.09  3.000
 J6O  O9   C18  C19  111.25  3.000
 J6O  H10  C18  C17  107.74  3.000
 J6O  O9   C18  C17  109.33  3.000
 J6O  C19  C18  C17  110.71  3.000
 J6O  H11  C19  O8   110.61  3.000
 J6O  H11  C19  C18  106.43  3.000
 J6O  O8   C19  C18  110.86  3.000
 J6O  H11  C19  C20  107.93  3.000
 J6O  O8   C19  C20  109.71  3.000
 J6O  C18  C19  C20  111.22  3.000
 J6O  H12  C2   C3   118.99  3.000
 J6O  H12  C2   C1   120.03  3.000
 J6O  C3   C2   C1   120.96  3.000
 J6O  O12  C3   C2   119.19  3.000
 J6O  O12  C3   C4   121.54  3.000
 J6O  C2   C3   C4   119.26  3.000
 J6O  O1   C9   C10  122.69  3.000
 J6O  O1   C9   C8   122.17  3.000
 J6O  C10  C9   C8   115.13  3.000
 J6O  H13  O10  C17  108.83  3.000
 J6O  H14  O11  C4   110.00  3.000
 J6O  H15  O12  C3   110.29  3.000
 J6O  C15  O2   C7   121.66  3.000
 J6O  H16  O3   C13  111.07  3.000
 J6O  H17  O4   C11  107.64  3.000
 J6O  C16  O5   C8   119.93  3.000
 J6O  C16  O6   C20  113.45  3.000
 J6O  H18  O7   C21  107.98  3.000
 J6O  H19  O8   C19  108.25  3.000
 J6O  H20  O9   C18  108.25  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
 J6O  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 J6O  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 J6O  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 J6O  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 J6O  CONST_05  C15  O2   C7   C6    180.00   0.0  0
 J6O  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 J6O  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 J6O  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 J6O  CONST_09  C13  C14  C15  C10     0.00   0.0  0
 J6O  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 J6O  CONST_11  C12  C11  C10  C15     0.00   0.0  0
 J6O  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 J6O  CONST_13  C14  C15  C10  C11     0.00   0.0  0
 J6O  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 J6O  CONST_15  C2   C1   C6   C7    180.00   0.0  0
 J6O  CONST_16  O12  C3   C4   C5    180.00   0.0  0
 J6O  CONST_17  O11  C4   C5   C6    180.00   0.0  0
 J6O  CONST_18  O4   C11  C12  C13   180.00   0.0  0
 J6O  CONST_19  O3   C13  C14  C15   180.00   0.0  0
 J6O  CONST_20  O4   C11  C10  C15   180.00   0.0  0
 J6O  CONST_21  O12  C3   C2   C1    180.00   0.0  0
 J6O  CONST_22  O3   C13  C12  C11   180.00   0.0  0
 J6O  CONST_23  O11  C4   C3   C2    180.00   0.0  0
 J6O  CONST_24  O4   C11  C10  C9      0.00   0.0  0
 J6O  CONST_25  H12  C2   C3   C4    180.00   0.0  0
 J6O  CONST_26  H6   C1   C6   C5    180.00   0.0  0
 J6O  CONST_27  H12  C2   C1   C6    180.00   0.0  0
 J6O  CONST_28  H6   C1   C6   C7      0.00   0.0  0
 J6O  CONST_29  H1   C5   C6   C7      0.00   0.0  0
 J6O  CONST_30  H7   C12  C11  C10   180.00   0.0  0
 J6O  CONST_31  H8   C14  C15  C10   180.00   0.0  0
 J6O  CONST_32  H1   C5   C6   C1    180.00   0.0  0
 J6O  CONST_33  H8   C14  C13  C12   180.00   0.0  0
 J6O  CONST_34  H7   C12  C13  C14   180.00   0.0  0
 J6O  CONST_35  H6   C1   C2   C3    180.00   0.0  0
 J6O  CONST_36  H1   C5   C4   C3    180.00   0.0  0
 J6O  CONST_37  H8   C14  C15  O2      0.00   0.0  0
 J6O  Var_01    O2   C7   C6   C5    135.01  30.0  2
 J6O  Var_02    C8   C7   C6   C5    -47.57  30.0  2
 J6O  Var_03    C9   C8   C7   C6    178.54  30.0  1
 J6O  Var_04    C14  C15  O2   C7    179.91  30.0  1
 J6O  Var_05    C10  C15  O2   C7      0.44  30.0  1
 J6O  Var_06    C10  C9   C8   C7      2.31  30.0  1
 J6O  Var_07    C11  C10  C9   C8    178.94  30.0  1
 J6O  Var_08    C15  C10  C9   C8      0.83  30.0  1
 J6O  Var_09    C15  O2   C7   C8      2.84  30.0  1
 J6O  Var_10    C1   C6   C7   C8    131.15  30.0  2
 J6O  Var_11    O2   C7   C6   C1    -46.27  30.0  2
 J6O  Var_12    O2   C7   C8   C9     -4.23  30.0  1
 J6O  Var_13    O5   C8   C7   C6     -6.28  30.0  1
 J6O  Var_14    O1   C9   C8   C7   -178.52  30.0  1
 J6O  Var_15    C16  O5   C8   C7    117.49  30.0  3
 J6O  Var_16    O5   C8   C9   C10  -172.81  30.0  1
 J6O  Var_17    O1   C9   C10  C15  -178.34  30.0  1
 J6O  Var_18    O1   C9   C10  C11    -0.23  30.0  1
 J6O  Var_19    C9   C8   O5   C16   -67.30  30.0  2
 J6O  Var_20    O5   C8   C7   O2    170.94  30.0  1
 J6O  Var_21    O5   C8   C9   O1      6.35  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
 J6O  chir_01  C17  C16  O10  C18  positiv
 J6O  chir_02  C20  O6   C19  C21  negativ
 J6O  chir_03  C16  O5   O6   C17  positiv
 J6O  chir_04  C18  O9   C17  C19  positiv
 J6O  chir_05  C19  O8   C18  C20  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
 J6O  plan-1  C4   0.020
 J6O  plan-1  C5   0.020
 J6O  plan-1  C6   0.020
 J6O  plan-1  C7   0.020
 J6O  plan-1  C1   0.020
 J6O  plan-1  C2   0.020
 J6O  plan-1  C3   0.020
 J6O  plan-1  O11  0.020
 J6O  plan-1  O12  0.020
 J6O  plan-1  H1   0.020
 J6O  plan-1  H6   0.020
 J6O  plan-1  H12  0.020
 J6O  plan-2  C10  0.020
 J6O  plan-2  C13  0.020
 J6O  plan-2  C15  0.020
 J6O  plan-2  C11  0.020
 J6O  plan-2  C12  0.020
 J6O  plan-2  C14  0.020
 J6O  plan-2  C9   0.020
 J6O  plan-2  O2   0.020
 J6O  plan-2  O3   0.020
 J6O  plan-2  O4   0.020
 J6O  plan-2  H7   0.020
 J6O  plan-2  H8   0.020
 J6O  plan-3  C8   0.020
 J6O  plan-3  C10  0.020
 J6O  plan-3  C9   0.020
 J6O  plan-3  O1   0.020

