# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 17:29:33 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 1,3,5,8-tetrakis(oxidanyl)xanthen-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)c3c(O)ccc(O)c3Oc2c1
#
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
 EKU  EKU  "1,3,5,8-tetrakis(oxidanyl)xanthen-9-one"
  ligand  27  19  .  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_EKU
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
 EKU  C1   C  CR16  0  -0.457  20.8655  -0.3183  23.9804
 EKU  C2   C  CR6   0   0.406  22.0277  -0.3569  23.2344
 EKU  C3   C  CR66  0  -0.318  23.1079  -1.1857  23.6377
 EKU  C4   C  CR6   0   0.558  24.3344  -1.2445  22.8944
 EKU  C5   C  CR66  0  -0.252  25.3677  -2.1204  23.4069
 EKU  C6   C  CR66  0   0.283  25.1146  -2.8518  24.5718
 EKU  C    C  CR6   0   0.406  20.7562  -1.0976  25.1341
 EKU  O    O  OH1   0  -0.608  19.6105  -1.0080  25.8094
 EKU  C10  C  CR16  0  -0.334  27.2807  -3.8179  24.4668
 EKU  C11  C  CR16  0  -0.355  27.5608  -3.1073  23.3088
 EKU  C12  C  CR6   0   0.352  26.6155  -2.2515  22.7623
 EKU  C7   C  CR66  0   0.422  22.9499  -1.9538  24.7991
 EKU  C8   C  CR16  0  -0.519  21.7960  -1.9267  25.5546
 EKU  C9   C  CR6   0   0.254  26.0621  -3.7092  25.1214
 EKU  O1   O  OH1   0  -0.618  22.1134   0.3911  22.1415
 EKU  O2   O  O     0  -0.492  23.9356  -2.7623  25.2266
 EKU  O3   O  OH1   0  -0.625  25.8509  -4.4281  26.2434
 EKU  O4   O  OH1   0  -0.628  26.9114  -1.5787  21.6480
 EKU  O5   O  O     0  -0.536  24.5087  -0.5732  21.8569
 EKU  H1   H  HCR6  0   0.282  20.0438   0.3158  23.6733
 EKU  H    H  HOH1  0   0.485  19.6197  -1.5690  26.5950
 EKU  H5   H  HCR6  0   0.284  28.0332  -4.4786  24.8790
 EKU  H6   H  HCR6  0   0.274  28.5236  -3.2186  22.8280
 EKU  H3   H  HCR6  0   0.295  21.7104  -2.5334  26.4478
 EKU  H2   H  HOH1  0   0.484  22.9989   0.2491  21.7388
 EKU  H4   H  HOH1  0   0.475  24.9877  -4.2365  26.6274
 EKU  H7   H  HOH1  0   0.481  26.1380  -1.0280  21.4064

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
 EKU  O4   C12  single    1.335  0.020  1.335
 EKU  O5   C4   double    1.248  0.020  1.248
 EKU  O1   C2   single    1.327  0.020  1.327
 EKU  C12  C11  aromatic  1.387  0.020  1.387
 EKU  C12  C5   aromatic  1.411  0.020  1.411
 EKU  C4   C5   single    1.448  0.020  1.448
 EKU  C4   C3   single    1.435  0.020  1.435
 EKU  C2   C3   aromatic  1.420  0.020  1.420
 EKU  C2   C1   aromatic  1.382  0.020  1.382
 EKU  C11  C10  aromatic  1.387  0.020  1.387
 EKU  C5   C6   aromatic  1.399  0.020  1.399
 EKU  C3   C7   aromatic  1.401  0.020  1.401
 EKU  C1   C    aromatic  1.397  0.020  1.397
 EKU  C10  C9   aromatic  1.388  0.020  1.388
 EKU  C6   C9   aromatic  1.391  0.020  1.391
 EKU  C6   O2   single    1.352  0.020  1.352
 EKU  C7   O2   single    1.345  0.020  1.345
 EKU  C7   C8   aromatic  1.379  0.020  1.379
 EKU  C9   O3   single    1.349  0.020  1.349
 EKU  C    C8   aromatic  1.395  0.020  1.395
 EKU  C    O    single    1.333  0.020  1.333
 EKU  C1   H1   single    0.930  0.020  1.080
 EKU  O    H    single    0.850  0.020  0.980
 EKU  C10  H5   single    0.930  0.020  1.080
 EKU  C11  H6   single    0.930  0.020  1.080
 EKU  C8   H3   single    0.930  0.020  1.080
 EKU  O1   H2   single    0.850  0.020  0.980
 EKU  O3   H4   single    0.850  0.020  0.980
 EKU  O4   H7   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
 EKU  H1   C1   C    120.12  3.000
 EKU  H1   C1   C2   120.12  3.000
 EKU  C    C1   C2   119.76  3.000
 EKU  O1   C2   C3   120.91  3.000
 EKU  C3   C2   C1   120.19  3.000
 EKU  O1   C2   C1   118.90  3.000
 EKU  C7   C3   C4   120.20  3.000
 EKU  C7   C3   C2   118.00  3.000
 EKU  C4   C3   C2   121.79  3.000
 EKU  O5   C4   C5   121.32  3.000
 EKU  C5   C4   C3   116.82  3.000
 EKU  O5   C4   C3   121.86  3.000
 EKU  C12  C5   C6   119.48  3.000
 EKU  C6   C5   C4   118.80  3.000
 EKU  C12  C5   C4   121.72  3.000
 EKU  O2   C6   C9   116.33  3.000
 EKU  O2   C6   C5   121.79  3.000
 EKU  C9   C6   C5   121.88  3.000
 EKU  C8   C    O    121.87  3.000
 EKU  O    C    C1   116.63  3.000
 EKU  C8   C    C1   121.49  3.000
 EKU  H    O    C    111.40  3.000
 EKU  H5   C10  C9   118.59  3.000
 EKU  H5   C10  C11  119.33  3.000
 EKU  C9   C10  C11  122.08  3.000
 EKU  H6   C11  C12  119.66  3.000
 EKU  H6   C11  C10  119.87  3.000
 EKU  C12  C11  C10  120.48  3.000
 EKU  O4   C12  C11  119.25  3.000
 EKU  C11  C12  C5   118.69  3.000
 EKU  O4   C12  C5   122.05  3.000
 EKU  O2   C7   C8   116.80  3.000
 EKU  C8   C7   C3   122.51  3.000
 EKU  O2   C7   C3   120.69  3.000
 EKU  H3   C8   C7   120.44  3.000
 EKU  H3   C8   C    121.51  3.000
 EKU  C7   C8   C    118.05  3.000
 EKU  O3   C9   C10  119.21  3.000
 EKU  O3   C9   C6   123.40  3.000
 EKU  C10  C9   C6   117.39  3.000
 EKU  H2   O1   C2   108.31  3.000
 EKU  C7   O2   C6   121.68  3.000
 EKU  H4   O3   C9   111.44  3.000
 EKU  H7   O4   C12  108.31  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
 EKU  CONST_01  C7   C3   C2   C1     0.00  0.0  0
 EKU  CONST_02  C7   C8   C    C1     0.00  0.0  0
 EKU  CONST_03  C5   C4   C3   C2   180.00  0.0  0
 EKU  CONST_04  C8   C7   C3   C2     0.00  0.0  0
 EKU  CONST_05  C8   C    C1   C2     0.00  0.0  0
 EKU  CONST_06  C12  C5   C4   C3   180.00  0.0  0
 EKU  CONST_07  C6   C5   C4   C3     0.00  0.0  0
 EKU  CONST_08  C    C1   C2   C3     0.00  0.0  0
 EKU  CONST_09  C6   O2   C7   C3     0.00  0.0  0
 EKU  CONST_10  C    C8   C7   C3     0.00  0.0  0
 EKU  CONST_11  C10  C11  C12  C5     0.00  0.0  0
 EKU  CONST_12  C7   C3   C4   C5     0.00  0.0  0
 EKU  CONST_13  C10  C9   C6   C5     0.00  0.0  0
 EKU  CONST_14  C7   O2   C6   C5     0.00  0.0  0
 EKU  CONST_15  C11  C12  C5   C6     0.00  0.0  0
 EKU  CONST_16  C11  C10  C9   C6     0.00  0.0  0
 EKU  CONST_17  C8   C7   O2   C6   180.00  0.0  0
 EKU  CONST_18  C9   C10  C11  C12    0.00  0.0  0
 EKU  CONST_19  C9   C6   C5   C12    0.00  0.0  0
 EKU  CONST_20  C9   C6   O2   C7   180.00  0.0  0
 EKU  CONST_21  O5   C4   C3   C2     0.00  0.0  0
 EKU  CONST_22  O    C    C1   C2   180.00  0.0  0
 EKU  CONST_23  O4   C12  C5   C4     0.00  0.0  0
 EKU  CONST_24  O1   C2   C3   C4     0.00  0.0  0
 EKU  CONST_25  O3   C9   C6   C5   180.00  0.0  0
 EKU  CONST_26  O4   C12  C5   C6   180.00  0.0  0
 EKU  CONST_27  O5   C4   C5   C6   180.00  0.0  0
 EKU  CONST_28  O1   C2   C1   C    180.00  0.0  0
 EKU  CONST_29  C7   C8   C    O    180.00  0.0  0
 EKU  CONST_30  O4   C12  C11  C10  180.00  0.0  0
 EKU  CONST_31  O3   C9   C10  C11  180.00  0.0  0
 EKU  CONST_32  O5   C4   C5   C12    0.00  0.0  0
 EKU  CONST_33  O5   C4   C3   C7   180.00  0.0  0
 EKU  CONST_34  O1   C2   C3   C7   180.00  0.0  0
 EKU  CONST_35  O3   C9   C6   O2     0.00  0.0  0
 EKU  CONST_36  H3   C8   C    C1   180.00  0.0  0
 EKU  CONST_37  H1   C1   C2   C3   180.00  0.0  0
 EKU  CONST_38  H3   C8   C7   C3   180.00  0.0  0
 EKU  CONST_39  H6   C11  C12  C5   180.00  0.0  0
 EKU  CONST_40  H5   C10  C9   C6   180.00  0.0  0
 EKU  CONST_41  H5   C10  C11  C12  180.00  0.0  0
 EKU  CONST_42  H1   C1   C    C8   180.00  0.0  0
 EKU  CONST_43  H6   C11  C10  C9   180.00  0.0  0
 EKU  CONST_44  H3   C8   C7   O2     0.00  0.0  0

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
 EKU  plan-1  C3   0.020
 EKU  plan-1  C4   0.020
 EKU  plan-1  C5   0.020
 EKU  plan-1  O5   0.020
 EKU  plan-2  C1   0.020
 EKU  plan-2  C2   0.020
 EKU  plan-2  C3   0.020
 EKU  plan-2  C4   0.020
 EKU  plan-2  C    0.020
 EKU  plan-2  O    0.020
 EKU  plan-2  C7   0.020
 EKU  plan-2  C8   0.020
 EKU  plan-2  O1   0.020
 EKU  plan-2  O2   0.020
 EKU  plan-2  H1   0.020
 EKU  plan-2  H3   0.020
 EKU  plan-3  C4   0.020
 EKU  plan-3  C5   0.020
 EKU  plan-3  C6   0.020
 EKU  plan-3  C10  0.020
 EKU  plan-3  C11  0.020
 EKU  plan-3  C12  0.020
 EKU  plan-3  C9   0.020
 EKU  plan-3  O2   0.020
 EKU  plan-3  O3   0.020
 EKU  plan-3  O4   0.020
 EKU  plan-3  H5   0.020
 EKU  plan-3  H6   0.020

