# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:28:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2C(=O)O[C@]3(c4ccc(O)cc4Oc5cc(O)ccc35)c2c1
#
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
 F6Y  F6Y  '3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-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_F6Y
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
 F6Y  O1   O  O      0  -0.418   0.8173   0.0817   4.0539
 F6Y  C1   C  CR5    0   0.541   0.6850   0.0540   2.8597
 F6Y  C2   C  CR56   0  -0.120   1.7028   0.0586   1.8032
 F6Y  C3   C  CR16   0  -0.280   3.0865   0.0980   1.8897
 F6Y  C4   C  CR16   0  -0.291   3.7989   0.0923   0.7026
 F6Y  O2   O  O      0  -0.455  -0.5230   0.0109   2.2764
 F6Y  C5   C  CR5    0   0.037  -0.4308  -0.0167   0.8183
 F6Y  C6   C  CR6    0   0.086  -1.0707  -1.2802   0.3257
 F6Y  C7   C  CR16   0  -0.293  -0.5012  -2.5281   0.5884
 F6Y  C8   C  CR16   0  -0.338  -1.0934  -3.7014   0.1793
 F6Y  C9   C  CR6    0   0.370  -2.3018  -3.6506  -0.5251
 F6Y  O3   O  OH1    0  -0.624  -2.8430  -4.8149  -0.9144
 F6Y  C11  C  CR16   0  -0.489  -2.8892  -2.4262  -0.8013
 F6Y  C12  C  CR6    0   0.351  -2.2693  -1.2577  -0.3703
 F6Y  O4   O  O2     0  -0.491  -2.9120  -0.1086  -0.6823
 F6Y  C13  C  CR6    0   0.350  -2.3336   1.0846  -0.4105
 F6Y  C14  C  CR16   0  -0.442  -3.0185   2.2009  -0.8735
 F6Y  C15  C  CR6    0   0.363  -2.4941   3.4638  -0.6444
 F6Y  O5   O  OH1    0  -0.624  -3.1854   4.5174  -1.1052
 F6Y  C16  C  CR16   0  -0.383  -1.2814   3.6012   0.0387
 F6Y  C17  C  CR16   0  -0.292  -0.6240   2.4750   0.4845
 F6Y  C18  C  CR6    0   0.087  -1.1316   1.1932   0.2760
 F6Y  C19  C  CR56   0   0.180   1.0569   0.0151   0.5873
 F6Y  C20  C  CR16   0  -0.380   1.7630   0.0057  -0.5990
 F6Y  C21  C  CR6    0  -0.087   3.1536   0.0458  -0.5404
 F6Y  C22  C  C      0   0.414   3.9725   0.0379  -1.8320
 F6Y  O6   O  O      0  -0.583   3.3254  -0.0300  -2.8923
 F6Y  O7   O  OC    -1  -0.584   5.2081   0.0992  -1.7028
 F6Y  H3   H  HCR6   0   0.267   3.5912   0.1329   2.8465
 F6Y  H4   H  HCR6   0   0.259   4.8794   0.1226   0.7269
 F6Y  H7   H  HCR6   0   0.267   0.4360  -2.5805   1.1290
 F6Y  H8   H  HCR6   0   0.271  -0.6319  -4.6561   0.3936
 F6Y  HA   H  HOH1   0   0.480  -3.6618  -4.6656  -1.4009
 F6Y  H11  H  HCR6   0   0.289  -3.8213  -2.3633  -1.3512
 F6Y  H14  H  HCR6   0   0.282  -3.9514   2.0804  -1.4101
 F6Y  H5   H  HOH1   0   0.480  -2.7284   5.3402  -0.8972
 F6Y  H16  H  HCR6   0   0.279  -0.8591   4.5823   0.2181
 F6Y  H17  H  HCR6   0   0.269   0.3147   2.5982   1.0108
 F6Y  H20  H  HCR6   0   0.252   1.2581  -0.0324  -1.5554

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
 F6Y  O1   C1   double    1.202  0.020  1.202
 F6Y  C1   C2   single    1.467  0.020  1.467
 F6Y  C1   O2   single    1.342  0.020  1.342
 F6Y  C2   C3   aromatic  1.387  0.020  1.387
 F6Y  C2   C19  aromatic  1.377  0.020  1.377
 F6Y  C3   C4   aromatic  1.384  0.020  1.384
 F6Y  C4   C21  aromatic  1.401  0.020  1.401
 F6Y  O2   C5   single    1.461  0.020  1.461
 F6Y  C5   C6   single    1.499  0.020  1.499
 F6Y  C5   C18  single    1.500  0.020  1.500
 F6Y  C5   C19  single    1.506  0.020  1.506
 F6Y  C6   C7   aromatic  1.397  0.020  1.397
 F6Y  C6   C12  aromatic  1.386  0.020  1.386
 F6Y  C7   C8   aromatic  1.376  0.020  1.376
 F6Y  C8   C9   aromatic  1.400  0.020  1.400
 F6Y  C9   O3   single    1.342  0.020  1.342
 F6Y  C9   C11  aromatic  1.386  0.020  1.386
 F6Y  C11  C12  aromatic  1.391  0.020  1.391
 F6Y  C12  O4   single    1.353  0.020  1.353
 F6Y  O4   C13  single    1.354  0.020  1.354
 F6Y  C13  C14  aromatic  1.389  0.020  1.389
 F6Y  C13  C18  aromatic  1.388  0.020  1.388
 F6Y  C14  C15  aromatic  1.387  0.020  1.387
 F6Y  C15  O5   single    1.342  0.020  1.342
 F6Y  C15  C16  aromatic  1.399  0.020  1.399
 F6Y  C16  C17  aromatic  1.378  0.020  1.378
 F6Y  C17  C18  aromatic  1.394  0.020  1.394
 F6Y  C19  C20  aromatic  1.381  0.020  1.381
 F6Y  C20  C21  aromatic  1.392  0.020  1.392
 F6Y  C21  C22  single    1.529  0.020  1.529
 F6Y  C22  O6   deloc     1.244  0.020  1.244
 F6Y  C22  O7   deloc     1.244  0.020  1.244
 F6Y  C3   H3   single    0.930  0.020  1.080
 F6Y  C4   H4   single    0.930  0.020  1.080
 F6Y  C7   H7   single    0.930  0.020  1.080
 F6Y  C8   H8   single    0.930  0.020  1.080
 F6Y  O3   HA   single    0.850  0.020  0.980
 F6Y  C11  H11  single    0.930  0.020  1.080
 F6Y  C14  H14  single    0.930  0.020  1.080
 F6Y  O5   H5   single    0.850  0.020  0.980
 F6Y  C16  H16  single    0.930  0.020  1.080
 F6Y  C17  H17  single    0.930  0.020  1.080
 F6Y  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
 F6Y  O2   C1   C2   108.15  3.000
 F6Y  O2   C1   O1   122.12  3.000
 F6Y  C2   C1   O1   129.73  3.000
 F6Y  C19  C2   C3   121.58  3.000
 F6Y  C19  C2   C1   108.08  3.000
 F6Y  C3   C2   C1   130.34  3.000
 F6Y  H3   C3   C4   121.21  3.000
 F6Y  H3   C3   C2   121.42  3.000
 F6Y  C4   C3   C2   117.37  3.000
 F6Y  H4   C4   C21  118.75  3.000
 F6Y  H4   C4   C3   119.67  3.000
 F6Y  C21  C4   C3   121.59  3.000
 F6Y  C5   O2   C1   112.18  3.000
 F6Y  C19  C5   C18  112.90  3.000
 F6Y  C19  C5   C6   112.89  3.000
 F6Y  C18  C5   C6   111.20  3.000
 F6Y  C19  C5   O2   102.41  3.000
 F6Y  C18  C5   O2   108.43  3.000
 F6Y  C6   C5   O2   108.47  3.000
 F6Y  C12  C6   C7   117.48  3.000
 F6Y  C12  C6   C5   121.35  3.000
 F6Y  C7   C6   C5   121.14  3.000
 F6Y  H7   C7   C8   118.64  3.000
 F6Y  H7   C7   C6   119.33  3.000
 F6Y  C8   C7   C6   122.03  3.000
 F6Y  H8   C8   C9   120.00  3.000
 F6Y  H8   C8   C7   120.65  3.000
 F6Y  C9   C8   C7   119.35  3.000
 F6Y  C11  C9   O3   122.54  3.000
 F6Y  C11  C9   C8   119.89  3.000
 F6Y  O3   C9   C8   117.57  3.000
 F6Y  HA   O3   C9   110.77  3.000
 F6Y  H11  C11  C12  119.44  3.000
 F6Y  H11  C11  C9   121.12  3.000
 F6Y  C12  C11  C9   119.44  3.000
 F6Y  O4   C12  C11  115.48  3.000
 F6Y  O4   C12  C6   122.70  3.000
 F6Y  C11  C12  C6   121.82  3.000
 F6Y  C13  O4   C12  119.96  3.000
 F6Y  C18  C13  C14  121.92  3.000
 F6Y  C18  C13  O4   122.56  3.000
 F6Y  C14  C13  O4   115.52  3.000
 F6Y  H14  C14  C15  120.60  3.000
 F6Y  H14  C14  C13  120.03  3.000
 F6Y  C15  C14  C13  119.37  3.000
 F6Y  C16  C15  O5   122.50  3.000
 F6Y  C16  C15  C14  119.87  3.000
 F6Y  O5   C15  C14  117.63  3.000
 F6Y  H5   O5   C15  110.60  3.000
 F6Y  H16  C16  C17  120.04  3.000
 F6Y  H16  C16  C15  120.53  3.000
 F6Y  C17  C16  C15  119.43  3.000
 F6Y  H17  C17  C18  119.52  3.000
 F6Y  H17  C17  C16  118.53  3.000
 F6Y  C18  C17  C16  121.95  3.000
 F6Y  C17  C18  C13  117.45  3.000
 F6Y  C17  C18  C5   121.16  3.000
 F6Y  C13  C18  C5   121.35  3.000
 F6Y  C20  C19  C5   129.56  3.000
 F6Y  C20  C19  C2   121.26  3.000
 F6Y  C5   C19  C2   109.18  3.000
 F6Y  H20  C20  C21  120.27  3.000
 F6Y  H20  C20  C19  121.40  3.000
 F6Y  C21  C20  C19  118.32  3.000
 F6Y  C22  C21  C20  119.94  3.000
 F6Y  C22  C21  C4   120.18  3.000
 F6Y  C20  C21  C4   119.88  3.000
 F6Y  O7   C22  O6   127.44  3.000
 F6Y  O7   C22  C21  116.35  3.000
 F6Y  O6   C22  C21  116.21  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
 F6Y  CONST_01  C21  C4   C3   C2     0.00   0.0  0
 F6Y  CONST_02  C21  C20  C19  C2     0.00   0.0  0
 F6Y  CONST_03  C20  C19  C2   C3     0.00   0.0  0
 F6Y  CONST_04  C20  C21  C4   C3     0.00   0.0  0
 F6Y  CONST_05  C19  C2   C3   C4     0.00   0.0  0
 F6Y  CONST_06  C19  C20  C21  C4     0.00   0.0  0
 F6Y  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 F6Y  CONST_08  C9   C11  C12  C6     0.00   0.0  0
 F6Y  CONST_09  C11  C12  C6   C7     0.00   0.0  0
 F6Y  CONST_10  C11  C9   C8   C7     0.00   0.0  0
 F6Y  CONST_11  C12  C6   C7   C8     0.00   0.0  0
 F6Y  CONST_12  C12  C11  C9   C8     0.00   0.0  0
 F6Y  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 F6Y  CONST_14  C16  C17  C18  C13    0.00   0.0  0
 F6Y  CONST_15  C17  C18  C13  C14    0.00   0.0  0
 F6Y  CONST_16  C17  C16  C15  C14    0.00   0.0  0
 F6Y  CONST_17  C18  C13  C14  C15    0.00   0.0  0
 F6Y  CONST_18  C18  C17  C16  C15    0.00   0.0  0
 F6Y  CONST_19  C5   C19  C2   C1     0.00   0.0  0
 F6Y  CONST_20  C5   C19  C2   C3   180.00   0.0  0
 F6Y  CONST_21  C21  C20  C19  C5   180.00   0.0  0
 F6Y  CONST_22  C22  C21  C4   C3   180.00   0.0  0
 F6Y  CONST_23  O3   C9   C8   C7   180.00   0.0  0
 F6Y  CONST_24  C12  C11  C9   O3   180.00   0.0  0
 F6Y  CONST_25  O5   C15  C14  C13  180.00   0.0  0
 F6Y  CONST_26  C17  C16  C15  O5   180.00   0.0  0
 F6Y  CONST_27  C22  C21  C20  C19  180.00   0.0  0
 F6Y  CONST_28  H3   C3   C2   C1     0.00   0.0  0
 F6Y  CONST_29  H4   C4   C3   C2   180.00   0.0  0
 F6Y  CONST_30  H20  C20  C19  C2   180.00   0.0  0
 F6Y  CONST_31  H7   C7   C6   C5     0.00   0.0  0
 F6Y  CONST_32  H17  C17  C18  C5     0.00   0.0  0
 F6Y  CONST_33  H8   C8   C7   C6   180.00   0.0  0
 F6Y  CONST_34  H11  C11  C12  C6   180.00   0.0  0
 F6Y  CONST_35  H14  C14  C13  O4     0.00   0.0  0
 F6Y  CONST_36  H16  C16  C15  C14  180.00   0.0  0
 F6Y  Var_01    O2   C1   C2   C3   179.90  30.0  1
 F6Y  Var_02    C14  C13  O4   C12  174.60  30.0  1
 F6Y  Var_03    O6   C22  C21  C4   178.69  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
 F6Y  chir_01  C5  C6  C18  C19  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
 F6Y  plan-1  C1   0.020
 F6Y  plan-1  C2   0.020
 F6Y  plan-1  C3   0.020
 F6Y  plan-1  C4   0.020
 F6Y  plan-1  C5   0.020
 F6Y  plan-1  C19  0.020
 F6Y  plan-1  C20  0.020
 F6Y  plan-1  C21  0.020
 F6Y  plan-1  C22  0.020
 F6Y  plan-1  H3   0.020
 F6Y  plan-1  H4   0.020
 F6Y  plan-1  H20  0.020
 F6Y  plan-2  C5   0.020
 F6Y  plan-2  C6   0.020
 F6Y  plan-2  C7   0.020
 F6Y  plan-2  C8   0.020
 F6Y  plan-2  C9   0.020
 F6Y  plan-2  O3   0.020
 F6Y  plan-2  C11  0.020
 F6Y  plan-2  C12  0.020
 F6Y  plan-2  O4   0.020
 F6Y  plan-2  H7   0.020
 F6Y  plan-2  H8   0.020
 F6Y  plan-2  H11  0.020
 F6Y  plan-3  C5   0.020
 F6Y  plan-3  O4   0.020
 F6Y  plan-3  C13  0.020
 F6Y  plan-3  C14  0.020
 F6Y  plan-3  C15  0.020
 F6Y  plan-3  O5   0.020
 F6Y  plan-3  C16  0.020
 F6Y  plan-3  C17  0.020
 F6Y  plan-3  C18  0.020
 F6Y  plan-3  H14  0.020
 F6Y  plan-3  H16  0.020
 F6Y  plan-3  H17  0.020
 F6Y  plan-4  C21  0.020
 F6Y  plan-4  C22  0.020
 F6Y  plan-4  O6   0.020
 F6Y  plan-4  O7   0.020
 F6Y  plan-5  O1   0.020
 F6Y  plan-5  C1   0.020
 F6Y  plan-5  C2   0.020
 F6Y  plan-5  O2   0.020

