# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 20:12:00 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)methyl]phenoxy}methyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(COc2ccccc2C=C3C(=O)c4ccccc4C3=O)cc1
#
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
 BKY  BKY  '4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)methyl]phenoxy}methyl)benzoic acid'  ligand  44  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BKY
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
 BKY  C1   C  CR6    0  -0.104   4.8003   1.3477  -0.1725
 BKY  C2   C  CR16   0  -0.276   4.7192   0.5163   0.9418
 BKY  C3   C  CR16   0  -0.285   3.9498  -0.6376   0.9147
 BKY  C4   C  CR6    0   0.095   3.2479  -0.9928  -0.2323
 BKY  C5   C  CR16   0  -0.279   3.3289  -0.1673  -1.3500
 BKY  C6   C  CR16   0  -0.277   4.0938   0.9886  -1.3183
 BKY  C7   C  CH2    0  -0.278   2.3944  -2.2219  -0.2547
 BKY  C8   C  CR6    0   0.389   0.0942  -2.7422   0.1103
 BKY  C9   C  CR16   0  -0.382   0.2980  -4.1028  -0.1023
 BKY  C10  C  CR16   0  -0.232  -0.7706  -4.9818   0.0022
 BKY  C11  C  CR16   0  -0.276  -2.0437  -4.5263   0.3176
 BKY  C12  C  CR16   0  -0.248  -2.2494  -3.1727   0.5141
 BKY  C13  C  CR6    0  -0.037  -1.1975  -2.2601   0.4111
 BKY  C    C  C      0   0.397   5.6438   2.6175  -0.1405
 BKY  O    O  O      0  -0.592   5.6437   3.3126  -1.1742
 BKY  C14  C  C1     0  -0.221  -1.3662  -0.8484   0.7004
 BKY  C15  C  CR5    0  -0.174  -2.4035  -0.0387   0.4110
 BKY  C16  C  CR5    0   0.352  -2.4340   1.3730   0.8678
 BKY  C17  C  CR56   0  -0.015  -3.6373   1.9889   0.2654
 BKY  C18  C  CR56   0   0.002  -4.2932   1.0485  -0.5216
 BKY  C19  C  CR5    0   0.328  -3.5717  -0.2481  -0.4780
 BKY  C20  C  CR16   0  -0.283  -5.4467   1.3724  -1.2149
 BKY  C21  C  CR16   0  -0.239  -5.9318   2.6682  -1.0922
 BKY  C22  C  CR16   0  -0.239  -5.2739   3.6115  -0.3008
 BKY  C23  C  CR16   0  -0.287  -4.1145   3.2825   0.3895
 BKY  O1   O  OC    -1  -0.592   6.2600   2.8500   0.9171
 BKY  O2   O  O2     0  -0.455   1.0575  -1.8148   0.0312
 BKY  O3   O  O      0  -0.379  -1.6327   1.9229   1.5894
 BKY  O4   O  O      0  -0.370  -3.8856  -1.2391  -1.0968
 BKY  H1   H  HCR6   0   0.244   5.2648   0.7761   1.8394
 BKY  H2   H  HCR6   0   0.248   3.8990  -1.2707   1.7931
 BKY  H3   H  HCR6   0   0.248   2.7923  -0.4329  -2.2535
 BKY  H4   H  HCR6   0   0.245   4.1478   1.6199  -2.1953
 BKY  H5   H  HCH2   0   0.248   2.4302  -2.7061  -1.2355
 BKY  H6   H  HCH2   0   0.249   2.7378  -2.9443   0.4921
 BKY  H7   H  HCR6   0   0.292   1.2762  -4.4919  -0.3475
 BKY  H8   H  HCR6   0   0.270  -0.5971  -6.0378  -0.1588
 BKY  H9   H  HCR6   0   0.262  -2.8656  -5.2215   0.4181
 BKY  H10  H  HCR6   0   0.263  -3.2299  -2.8197   0.7976
 BKY  H11  H  H      0   0.284  -0.5442  -0.3741   1.2316
 BKY  H12  H  HCR6   0   0.274  -5.9570   0.6450  -1.8323
 BKY  H13  H  HCR6   0   0.279  -6.8336   2.9545  -1.6166
 BKY  H14  H  HCR6   0   0.279  -5.6751   4.6135  -0.2277
 BKY  H15  H  HCR6   0   0.274  -3.6046   4.0146   1.0018

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
 BKY  C10  C9   aromatic  1.388  0.020  1.388
 BKY  C10  C11  aromatic  1.389  0.020  1.389
 BKY  C9   C8   aromatic  1.392  0.020  1.392
 BKY  C11  C12  aromatic  1.383  0.020  1.383
 BKY  C8   O2   single    1.339  0.020  1.339
 BKY  C8   C13  aromatic  1.411  0.020  1.411
 BKY  C12  C13  aromatic  1.396  0.020  1.396
 BKY  C3   C2   aromatic  1.387  0.020  1.387
 BKY  C3   C4   aromatic  1.391  0.020  1.391
 BKY  C7   O2   single    1.426  0.020  1.426
 BKY  C7   C4   single    1.497  0.020  1.497
 BKY  C2   C1   aromatic  1.393  0.020  1.393
 BKY  C4   C5   aromatic  1.392  0.020  1.392
 BKY  C13  C14  single    1.451  0.020  1.451
 BKY  C1   C6   aromatic  1.393  0.020  1.393
 BKY  C1   C    single    1.525  0.020  1.525
 BKY  C5   C6   aromatic  1.386  0.020  1.386
 BKY  O    C    deloc     1.246  0.020  1.246
 BKY  C    O1   deloc     1.246  0.020  1.246
 BKY  C14  C15  double    1.347  0.020  1.347
 BKY  O3   C16  double    1.210  0.020  1.210
 BKY  C15  C16  single    1.484  0.020  1.484
 BKY  C15  C19  single    1.483  0.020  1.483
 BKY  C16  C17  single    1.480  0.020  1.480
 BKY  O4   C19  double    1.210  0.020  1.210
 BKY  C19  C18  single    1.484  0.020  1.484
 BKY  C17  C18  aromatic  1.391  0.020  1.391
 BKY  C17  C23  aromatic  1.384  0.020  1.384
 BKY  C18  C20  aromatic  1.384  0.020  1.384
 BKY  C23  C22  aromatic  1.389  0.020  1.389
 BKY  C20  C21  aromatic  1.389  0.020  1.389
 BKY  C22  C21  aromatic  1.396  0.020  1.396
 BKY  C2   H1   single    0.930  0.020  1.080
 BKY  C3   H2   single    0.930  0.020  1.080
 BKY  C5   H3   single    0.930  0.020  1.080
 BKY  C6   H4   single    0.930  0.020  1.080
 BKY  C7   H5   single    0.970  0.020  1.090
 BKY  C7   H6   single    0.970  0.020  1.090
 BKY  C9   H7   single    0.930  0.020  1.080
 BKY  C10  H8   single    0.930  0.020  1.080
 BKY  C11  H9   single    0.930  0.020  1.080
 BKY  C12  H10  single    0.930  0.020  1.080
 BKY  C14  H11  single    0.930  0.020  1.080
 BKY  C20  H12  single    0.930  0.020  1.080
 BKY  C21  H13  single    0.930  0.020  1.080
 BKY  C22  H14  single    0.930  0.020  1.080
 BKY  C23  H15  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
 BKY  C    C1   C6   120.83  3.000
 BKY  C    C1   C2   120.84  3.000
 BKY  C6   C1   C2   118.34  3.000
 BKY  H1   C2   C3   119.71  3.000
 BKY  H1   C2   C1   119.41  3.000
 BKY  C3   C2   C1   120.88  3.000
 BKY  H2   C3   C4   119.70  3.000
 BKY  H2   C3   C2   119.73  3.000
 BKY  C4   C3   C2   120.56  3.000
 BKY  C7   C4   C5   120.55  3.000
 BKY  C5   C4   C3   118.78  3.000
 BKY  C7   C4   C3   120.66  3.000
 BKY  H3   C5   C6   119.76  3.000
 BKY  H3   C5   C4   119.69  3.000
 BKY  C6   C5   C4   120.54  3.000
 BKY  H4   C6   C5   119.70  3.000
 BKY  H4   C6   C1   119.40  3.000
 BKY  C5   C6   C1   120.90  3.000
 BKY  H6   C7   H5   108.01  3.000
 BKY  H6   C7   O2   110.23  3.000
 BKY  H5   C7   O2   109.66  3.000
 BKY  H6   C7   C4   110.67  3.000
 BKY  H5   C7   C4   110.99  3.000
 BKY  O2   C7   C4   107.29  3.000
 BKY  O2   C8   C13  115.74  3.000
 BKY  C13  C8   C9   120.03  3.000
 BKY  O2   C8   C9   124.22  3.000
 BKY  H7   C9   C10  119.07  3.000
 BKY  H7   C9   C8   121.26  3.000
 BKY  C10  C9   C8   119.67  3.000
 BKY  H8   C10  C11  120.06  3.000
 BKY  H8   C10  C9   118.91  3.000
 BKY  C11  C10  C9   121.02  3.000
 BKY  H9   C11  C12  120.20  3.000
 BKY  H9   C11  C10  120.48  3.000
 BKY  C12  C11  C10  119.32  3.000
 BKY  H10  C12  C13  119.32  3.000
 BKY  H10  C12  C11  119.48  3.000
 BKY  C13  C12  C11  121.14  3.000
 BKY  C14  C13  C12  122.25  3.000
 BKY  C14  C13  C8   118.78  3.000
 BKY  C12  C13  C8   118.81  3.000
 BKY  O1   C    O    126.89  3.000
 BKY  O1   C    C1   116.54  3.000
 BKY  O    C    C1   116.57  3.000
 BKY  H11  C14  C15  115.13  3.000
 BKY  H11  C14  C13  115.71  3.000
 BKY  C15  C14  C13  129.15  3.000
 BKY  C19  C15  C16  107.62  3.000
 BKY  C19  C15  C14  130.58  3.000
 BKY  C16  C15  C14  121.42  3.000
 BKY  O3   C16  C17  126.29  3.000
 BKY  C17  C16  C15  106.70  3.000
 BKY  O3   C16  C15  127.02  3.000
 BKY  C23  C17  C18  121.34  3.000
 BKY  C23  C17  C16  129.25  3.000
 BKY  C18  C17  C16  109.41  3.000
 BKY  C20  C18  C19  128.62  3.000
 BKY  C20  C18  C17  121.21  3.000
 BKY  C19  C18  C17  110.17  3.000
 BKY  O4   C19  C18  125.05  3.000
 BKY  C18  C19  C15  106.09  3.000
 BKY  O4   C19  C15  128.81  3.000
 BKY  H12  C20  C21  120.86  3.000
 BKY  H12  C20  C18  121.43  3.000
 BKY  C21  C20  C18  117.71  3.000
 BKY  H13  C21  C22  119.26  3.000
 BKY  H13  C21  C20  119.68  3.000
 BKY  C22  C21  C20  121.05  3.000
 BKY  H14  C22  C23  119.69  3.000
 BKY  H14  C22  C21  119.30  3.000
 BKY  C23  C22  C21  121.00  3.000
 BKY  H15  C23  C22  120.95  3.000
 BKY  H15  C23  C17  121.37  3.000
 BKY  C22  C23  C17  117.68  3.000
 BKY  C8   O2   C7   119.23  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
 BKY  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 BKY  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 BKY  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 BKY  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 BKY  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 BKY  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 BKY  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 BKY  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 BKY  CONST_09  C12  C11  C10  C9      0.00   0.0  0
 BKY  CONST_10  C12  C13  C8   C9      0.00   0.0  0
 BKY  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 BKY  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 BKY  CONST_13  C21  C20  C18  C17     0.00   0.0  0
 BKY  CONST_14  C21  C22  C23  C17     0.00   0.0  0
 BKY  CONST_15  C22  C23  C17  C18     0.00   0.0  0
 BKY  CONST_16  C22  C21  C20  C18     0.00   0.0  0
 BKY  CONST_17  C23  C17  C18  C20     0.00   0.0  0
 BKY  CONST_18  C23  C22  C21  C20     0.00   0.0  0
 BKY  CONST_19  C7   C4   C3   C2    180.00   0.0  0
 BKY  CONST_20  C    C1   C2   C3    180.00   0.0  0
 BKY  CONST_21  C    C1   C6   C5    180.00   0.0  0
 BKY  CONST_22  C7   C4   C5   C6    180.00   0.0  0
 BKY  CONST_23  C14  C13  C8   C9    180.00   0.0  0
 BKY  CONST_24  O2   C8   C9   C10   180.00   0.0  0
 BKY  CONST_25  C14  C13  C12  C11   180.00   0.0  0
 BKY  CONST_26  O2   C8   C13  C12   180.00   0.0  0
 BKY  CONST_27  H2   C3   C2   C1    180.00   0.0  0
 BKY  CONST_28  H3   C5   C6   C1    180.00   0.0  0
 BKY  CONST_29  H4   C6   C1   C2    180.00   0.0  0
 BKY  CONST_30  H1   C2   C3   C4    180.00   0.0  0
 BKY  CONST_31  H8   C10  C9   C8    180.00   0.0  0
 BKY  CONST_32  H10  C12  C13  C8    180.00   0.0  0
 BKY  CONST_33  H9   C11  C10  C9    180.00   0.0  0
 BKY  CONST_34  H7   C9   C10  C11   180.00   0.0  0
 BKY  CONST_35  H15  C23  C17  C16     0.00   0.0  0
 BKY  CONST_36  H12  C20  C18  C17   180.00   0.0  0
 BKY  CONST_37  H14  C22  C23  C17   180.00   0.0  0
 BKY  CONST_38  H13  C21  C20  C18   180.00   0.0  0
 BKY  Var_01    C18  C17  C16  C15    -0.95  30.0  1
 BKY  Var_02    C17  C18  C19  C15     0.13  30.0  1
 BKY  Var_03    C18  C19  C15  C16    -0.71  30.0  1
 BKY  Var_04    C19  C15  C16  C17     1.01  30.0  1
 BKY  Var_05    C15  C14  C13  C8    145.52  30.0  2
 BKY  Var_06    C16  C15  C14  C13   176.01  30.0  2
 BKY  Var_07    O    C    C1   C2   -178.96  30.0  2
 BKY  Var_08    O2   C7   C4   C3     95.82  30.0  2
 BKY  Var_09    C9   C8   O2   C7     -1.66  30.0  1

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
 BKY  plan-1  C1   0.020
 BKY  plan-1  C2   0.020
 BKY  plan-1  C3   0.020
 BKY  plan-1  C4   0.020
 BKY  plan-1  C5   0.020
 BKY  plan-1  C6   0.020
 BKY  plan-1  C7   0.020
 BKY  plan-1  C    0.020
 BKY  plan-1  H1   0.020
 BKY  plan-1  H2   0.020
 BKY  plan-1  H3   0.020
 BKY  plan-1  H4   0.020
 BKY  plan-2  C8   0.020
 BKY  plan-2  C9   0.020
 BKY  plan-2  C10  0.020
 BKY  plan-2  C11  0.020
 BKY  plan-2  C12  0.020
 BKY  plan-2  C13  0.020
 BKY  plan-2  C14  0.020
 BKY  plan-2  O2   0.020
 BKY  plan-2  H7   0.020
 BKY  plan-2  H8   0.020
 BKY  plan-2  H9   0.020
 BKY  plan-2  H10  0.020
 BKY  plan-3  C16  0.020
 BKY  plan-3  C17  0.020
 BKY  plan-3  C18  0.020
 BKY  plan-3  C19  0.020
 BKY  plan-3  C20  0.020
 BKY  plan-3  C21  0.020
 BKY  plan-3  C22  0.020
 BKY  plan-3  C23  0.020
 BKY  plan-3  H12  0.020
 BKY  plan-3  H13  0.020
 BKY  plan-3  H14  0.020
 BKY  plan-3  H15  0.020
 BKY  plan-4  C15  0.020
 BKY  plan-4  C16  0.020
 BKY  plan-4  C17  0.020
 BKY  plan-4  O3   0.020
 BKY  plan-5  C15  0.020
 BKY  plan-5  C18  0.020
 BKY  plan-5  C19  0.020
 BKY  plan-5  O4   0.020
 BKY  plan-6  C1   0.020
 BKY  plan-6  C    0.020
 BKY  plan-6  O    0.020
 BKY  plan-6  O1   0.020

