# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:16:27 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2c(c1)C(=O)O[C@@]23c4ccc(O)cc4Oc5cc(O)ccc35
#
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
 F6Z  F6Z  '3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-5-carboxylic acid'  ligand  39  28  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F6Z
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
 F6Z  O1   O  O      0  -0.416   1.3911   0.0249   3.4902
 F6Z  C1   C  CR5    0   0.538   1.0378   0.0193   2.3416
 F6Z  C2   C  CR56   0  -0.082   1.8395   0.0247   1.1128
 F6Z  C3   C  CR16   0  -0.346   3.2157   0.0373   0.9480
 F6Z  C4   C  CR6    0  -0.102   3.7199   0.0395  -0.3464
 F6Z  O2   O  O      0  -0.456  -0.2597   0.0057   1.9962
 F6Z  C5   C  CR5    0   0.036  -0.4448   0.0023   0.5488
 F6Z  C6   C  CR6    0   0.086  -1.2096   1.2335   0.1609
 F6Z  C7   C  CR16   0  -0.295  -0.6626   2.5072   0.3311
 F6Z  C8   C  CR16   0  -0.338  -1.3609   3.6504   0.0138
 F6Z  C9   C  CR6    0   0.370  -2.6589   3.5423  -0.4982
 F6Z  O3   O  OH1    0  -0.624  -3.3075   4.6781  -0.7967
 F6Z  C11  C  CR16   0  -0.489  -3.2251   2.2913  -0.6824
 F6Z  C12  C  CR6    0   0.350  -2.4967   1.1543  -0.3480
 F6Z  O4   O  O2     0  -0.490  -3.1285  -0.0227  -0.5625
 F6Z  C13  C  CR6    0   0.350  -2.4761  -1.1877  -0.3456
 F6Z  C14  C  CR16   0  -0.489  -3.1838  -2.3382  -0.6786
 F6Z  C15  C  CR6    0   0.370  -2.5954  -3.5785  -0.4918
 F6Z  O5   O  OH1    0  -0.624  -3.2228  -4.7265  -0.7894
 F6Z  C16  C  CR16   0  -0.338  -1.2963  -3.6626   0.0220
 F6Z  C17  C  CR16   0  -0.295  -0.6189  -2.5065   0.3376
 F6Z  C18  C  CR6    0   0.087  -1.1879  -1.2431   0.1640
 F6Z  C19  C  CR56   0   0.145   0.9727   0.0143   0.0417
 F6Z  C20  C  CR16   0  -0.317   1.4519   0.0162  -1.2537
 F6Z  C21  C  CR16   0  -0.269   2.8292   0.0288  -1.4276
 F6Z  O6   O  O      0  -0.586   5.9490   0.0621   0.4234
 F6Z  C25  C  C      0   0.412   5.2272   0.0534  -0.5901
 F6Z  O7   O  OC    -1  -0.586   5.5952   0.0553  -1.7788
 F6Z  H3   H  HCR6   0   0.260   3.8833   0.0453   1.7994
 F6Z  H21  H  HCR6   0   0.261   3.2362   0.0303  -2.4296
 F6Z  H7   H  HCR6   0   0.268   0.3434   2.6086   0.7202
 F6Z  H8   H  HCR6   0   0.272  -0.9147   4.6254   0.1577
 F6Z  HA   H  HOH1   0   0.480  -4.1860   4.4876  -1.1452
 F6Z  H11  H  HCR6   0   0.289  -4.2270   2.1833  -1.0821
 F6Z  H14  H  HCR6   0   0.289  -4.1870  -2.2489  -1.0798
 F6Z  H5   H  HOH1   0   0.480  -4.1049  -4.5526  -1.1378
 F6Z  H16  H  HCR6   0   0.272  -0.8330  -4.6292   0.1687
 F6Z  H17  H  HCR6   0   0.266   0.3881  -2.5892   0.7288
 F6Z  H20  H  HCR6   0   0.260   0.7823   0.0084  -2.1044

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
 F6Z  O1   C1   double    1.202  0.020  1.202
 F6Z  C1   C2   single    1.467  0.020  1.467
 F6Z  C1   O2   single    1.343  0.020  1.343
 F6Z  C2   C3   aromatic  1.386  0.020  1.386
 F6Z  C2   C19  aromatic  1.378  0.020  1.378
 F6Z  C3   C4   aromatic  1.389  0.020  1.389
 F6Z  C4   C21  aromatic  1.401  0.020  1.401
 F6Z  C4   C25  single    1.527  0.020  1.527
 F6Z  O2   C5   single    1.459  0.020  1.459
 F6Z  C5   C6   single    1.500  0.020  1.500
 F6Z  C5   C18  single    1.500  0.020  1.500
 F6Z  C5   C19  single    1.506  0.020  1.506
 F6Z  C6   C7   aromatic  1.397  0.020  1.397
 F6Z  C6   C12  aromatic  1.386  0.020  1.386
 F6Z  C7   C8   aromatic  1.377  0.020  1.377
 F6Z  C8   C9   aromatic  1.400  0.020  1.400
 F6Z  C9   O3   single    1.342  0.020  1.342
 F6Z  C9   C11  aromatic  1.385  0.020  1.385
 F6Z  C11  C12  aromatic  1.391  0.020  1.391
 F6Z  C12  O4   single    1.353  0.020  1.353
 F6Z  O4   C13  single    1.353  0.020  1.353
 F6Z  C13  C14  aromatic  1.391  0.020  1.391
 F6Z  C13  C18  aromatic  1.386  0.020  1.386
 F6Z  C14  C15  aromatic  1.385  0.020  1.385
 F6Z  C15  O5   single    1.342  0.020  1.342
 F6Z  C15  C16  aromatic  1.400  0.020  1.400
 F6Z  C16  C17  aromatic  1.377  0.020  1.377
 F6Z  C17  C18  aromatic  1.397  0.020  1.397
 F6Z  C19  C20  aromatic  1.381  0.020  1.381
 F6Z  C20  C21  aromatic  1.388  0.020  1.388
 F6Z  O6   C25  deloc     1.244  0.020  1.244
 F6Z  C25  O7   deloc     1.244  0.020  1.244
 F6Z  C3   H3   single    0.930  0.020  1.080
 F6Z  C21  H21  single    0.930  0.020  1.080
 F6Z  C7   H7   single    0.930  0.020  1.080
 F6Z  C8   H8   single    0.930  0.020  1.080
 F6Z  O3   HA   single    0.850  0.020  0.980
 F6Z  C11  H11  single    0.930  0.020  1.080
 F6Z  C14  H14  single    0.930  0.020  1.080
 F6Z  O5   H5   single    0.850  0.020  0.980
 F6Z  C16  H16  single    0.930  0.020  1.080
 F6Z  C17  H17  single    0.930  0.020  1.080
 F6Z  C20  H20  single    0.930  0.020  1.080

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
 F6Z  O2   C1   C2   108.22  3.000
 F6Z  O2   C1   O1   122.01  3.000
 F6Z  C2   C1   O1   129.77  3.000
 F6Z  C19  C2   C3   122.16  3.000
 F6Z  C19  C2   C1   107.89  3.000
 F6Z  C3   C2   C1   129.95  3.000
 F6Z  H3   C3   C4   120.61  3.000
 F6Z  H3   C3   C2   121.28  3.000
 F6Z  C4   C3   C2   118.11  3.000
 F6Z  C25  C4   C21  120.30  3.000
 F6Z  C25  C4   C3   120.47  3.000
 F6Z  C21  C4   C3   119.23  3.000
 F6Z  C5   O2   C1   112.19  3.000
 F6Z  C19  C5   C18  112.74  3.000
 F6Z  C19  C5   C6   112.73  3.000
 F6Z  C18  C5   C6   111.24  3.000
 F6Z  C19  C5   O2   102.40  3.000
 F6Z  C18  C5   O2   108.61  3.000
 F6Z  C6   C5   O2   108.61  3.000
 F6Z  C12  C6   C7   117.42  3.000
 F6Z  C12  C6   C5   121.42  3.000
 F6Z  C7   C6   C5   121.15  3.000
 F6Z  H7   C7   C8   118.43  3.000
 F6Z  H7   C7   C6   119.52  3.000
 F6Z  C8   C7   C6   122.05  3.000
 F6Z  H8   C8   C9   120.05  3.000
 F6Z  H8   C8   C7   120.57  3.000
 F6Z  C9   C8   C7   119.38  3.000
 F6Z  C11  C9   O3   122.50  3.000
 F6Z  C11  C9   C8   119.83  3.000
 F6Z  O3   C9   C8   117.67  3.000
 F6Z  HA   O3   C9   110.71  3.000
 F6Z  H11  C11  C12  119.41  3.000
 F6Z  H11  C11  C9   121.11  3.000
 F6Z  C12  C11  C9   119.48  3.000
 F6Z  O4   C12  C11  115.37  3.000
 F6Z  O4   C12  C6   122.78  3.000
 F6Z  C11  C12  C6   121.84  3.000
 F6Z  C13  O4   C12  119.91  3.000
 F6Z  C18  C13  C14  121.84  3.000
 F6Z  C18  C13  O4   122.78  3.000
 F6Z  C14  C13  O4   115.37  3.000
 F6Z  H14  C14  C15  121.11  3.000
 F6Z  H14  C14  C13  119.41  3.000
 F6Z  C15  C14  C13  119.48  3.000
 F6Z  C16  C15  O5   117.65  3.000
 F6Z  C16  C15  C14  119.83  3.000
 F6Z  O5   C15  C14  122.51  3.000
 F6Z  H5   O5   C15  110.72  3.000
 F6Z  H16  C16  C17  120.57  3.000
 F6Z  H16  C16  C15  120.06  3.000
 F6Z  C17  C16  C15  119.37  3.000
 F6Z  H17  C17  C18  119.51  3.000
 F6Z  H17  C17  C16  118.43  3.000
 F6Z  C18  C17  C16  122.06  3.000
 F6Z  C17  C18  C13  117.41  3.000
 F6Z  C17  C18  C5   121.15  3.000
 F6Z  C13  C18  C5   121.42  3.000
 F6Z  C20  C19  C5   129.98  3.000
 F6Z  C20  C19  C2   120.71  3.000
 F6Z  C5   C19  C2   109.30  3.000
 F6Z  H20  C20  C21  121.02  3.000
 F6Z  H20  C20  C19  121.49  3.000
 F6Z  C21  C20  C19  117.49  3.000
 F6Z  H21  C21  C20  119.30  3.000
 F6Z  H21  C21  C4   118.41  3.000
 F6Z  C20  C21  C4   122.29  3.000
 F6Z  O7   C25  O6   127.34  3.000
 F6Z  O7   C25  C4   116.38  3.000
 F6Z  O6   C25  C4   116.27  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
 F6Z  CONST_01  C21  C4   C3   C2      0.00   0.0  0
 F6Z  CONST_02  C21  C20  C19  C2      0.00   0.0  0
 F6Z  CONST_03  C20  C19  C2   C3      0.00   0.0  0
 F6Z  CONST_04  C20  C21  C4   C3      0.00   0.0  0
 F6Z  CONST_05  C19  C2   C3   C4      0.00   0.0  0
 F6Z  CONST_06  C19  C20  C21  C4      0.00   0.0  0
 F6Z  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 F6Z  CONST_08  C9   C11  C12  C6      0.00   0.0  0
 F6Z  CONST_09  C11  C12  C6   C7      0.00   0.0  0
 F6Z  CONST_10  C11  C9   C8   C7      0.00   0.0  0
 F6Z  CONST_11  C12  C6   C7   C8      0.00   0.0  0
 F6Z  CONST_12  C12  C11  C9   C8      0.00   0.0  0
 F6Z  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 F6Z  CONST_14  C16  C17  C18  C13     0.00   0.0  0
 F6Z  CONST_15  C17  C18  C13  C14     0.00   0.0  0
 F6Z  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 F6Z  CONST_17  C18  C13  C14  C15     0.00   0.0  0
 F6Z  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 F6Z  CONST_19  C5   C19  C2   C1      0.00   0.0  0
 F6Z  CONST_20  C5   C19  C2   C3    180.00   0.0  0
 F6Z  CONST_21  C21  C20  C19  C5    180.00   0.0  0
 F6Z  CONST_22  C25  C4   C3   C2    180.00   0.0  0
 F6Z  CONST_23  O3   C9   C8   C7    180.00   0.0  0
 F6Z  CONST_24  C12  C11  C9   O3    180.00   0.0  0
 F6Z  CONST_25  O5   C15  C14  C13   180.00   0.0  0
 F6Z  CONST_26  C17  C16  C15  O5    180.00   0.0  0
 F6Z  CONST_27  C25  C4   C21  C20   180.00   0.0  0
 F6Z  CONST_28  H3   C3   C2   C1      0.00   0.0  0
 F6Z  CONST_29  H20  C20  C19  C2    180.00   0.0  0
 F6Z  CONST_30  H21  C21  C4   C3    180.00   0.0  0
 F6Z  CONST_31  H7   C7   C6   C5      0.00   0.0  0
 F6Z  CONST_32  H17  C17  C18  C5      0.00   0.0  0
 F6Z  CONST_33  H8   C8   C7   C6    180.00   0.0  0
 F6Z  CONST_34  H11  C11  C12  C6    180.00   0.0  0
 F6Z  CONST_35  H14  C14  C13  O4      0.00   0.0  0
 F6Z  CONST_36  H16  C16  C15  C14   180.00   0.0  0
 F6Z  Var_01    O2   C1   C2   C3   -179.96  30.0  1
 F6Z  Var_02    C14  C13  O4   C12  -175.97  30.0  1
 F6Z  Var_03    O6   C25  C4   C3      0.01  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
 F6Z  chir_01  C5  C6  C18  C19  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
 F6Z  plan-1  C1   0.020
 F6Z  plan-1  C2   0.020
 F6Z  plan-1  C3   0.020
 F6Z  plan-1  C4   0.020
 F6Z  plan-1  C5   0.020
 F6Z  plan-1  C19  0.020
 F6Z  plan-1  C20  0.020
 F6Z  plan-1  C21  0.020
 F6Z  plan-1  C25  0.020
 F6Z  plan-1  H3   0.020
 F6Z  plan-1  H21  0.020
 F6Z  plan-1  H20  0.020
 F6Z  plan-2  C5   0.020
 F6Z  plan-2  C6   0.020
 F6Z  plan-2  C7   0.020
 F6Z  plan-2  C8   0.020
 F6Z  plan-2  C9   0.020
 F6Z  plan-2  O3   0.020
 F6Z  plan-2  C11  0.020
 F6Z  plan-2  C12  0.020
 F6Z  plan-2  O4   0.020
 F6Z  plan-2  H7   0.020
 F6Z  plan-2  H8   0.020
 F6Z  plan-2  H11  0.020
 F6Z  plan-3  C5   0.020
 F6Z  plan-3  O4   0.020
 F6Z  plan-3  C13  0.020
 F6Z  plan-3  C14  0.020
 F6Z  plan-3  C15  0.020
 F6Z  plan-3  O5   0.020
 F6Z  plan-3  C16  0.020
 F6Z  plan-3  C17  0.020
 F6Z  plan-3  C18  0.020
 F6Z  plan-3  H14  0.020
 F6Z  plan-3  H16  0.020
 F6Z  plan-3  H17  0.020
 F6Z  plan-4  C4   0.020
 F6Z  plan-4  O6   0.020
 F6Z  plan-4  C25  0.020
 F6Z  plan-4  O7   0.020
 F6Z  plan-5  O1   0.020
 F6Z  plan-5  C1   0.020
 F6Z  plan-5  C2   0.020
 F6Z  plan-5  O2   0.020

