# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:04:00 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-[[3,5-bis(bromanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-ylidene]-[3,5-bis(bromanyl)-4-oxidanyl-phenyl]methyl]benzenesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(Br)cc(cc1Br)C(=C2C=C(Br)C(=O)C(=C2)Br)c3ccccc3[S](O)(=O)=O
#
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
 LYE  LYE  '2-[[3,5-bis(bromanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-ylidene]-[3,5-bis(bromanyl)-4-oxidanyl-phenyl]methyl]benzenesulfonic acid'  ligand  38  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LYE
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
 LYE  C02   C   CR16   0  -0.237  -12.6395  -11.4004   3.3269
 LYE  C04   C   CR6    0  -0.264  -14.1807  -12.7634   4.5866
 LYE  C07   C   C      0   0.144  -16.4594  -11.8166   5.1722
 LYE  C08   C   CR6    0   0.049  -17.6126  -11.6380   4.4415
 LYE  C01   C   CR16   0  -0.239  -13.5844  -10.3911   3.2448
 LYE  C03   C   CR16   0  -0.250  -12.9445  -12.5851   3.9852
 LYE  C05   C   CR6    0  -0.004  -15.1412  -11.7470   4.5102
 LYE  C06   C   CR16   0  -0.252  -14.8290  -10.5692   3.8286
 LYE  C09   C   CR16   0  -0.238  -18.8586  -11.2749   5.0617
 LYE  C10   C   CR6    0  -0.272  -19.9698  -11.0757   4.3281
 LYE  C11   C   CR6    0   0.469  -20.0117  -11.2243   2.8711
 LYE  C13   C   CR6    0  -0.275  -18.7214  -11.5942   2.2835
 LYE  C14   C   CR16   0  -0.211  -17.6025  -11.7794   3.0097
 LYE  C17   C   CR6    0   0.024  -16.4590  -11.9469   6.6259
 LYE  C18   C   CR16   0  -0.243  -17.3822  -12.7624   7.2828
 LYE  C19   C   CR6    0  -0.220  -17.3524  -12.8795   8.6549
 LYE  C20   C   CR6    0   0.462  -16.4068  -12.1983   9.4335
 LYE  C21   C   CR6    0  -0.227  -15.4813  -11.3961   8.7544
 LYE  C22   C   CR16   0  -0.231  -15.4931  -11.2850   7.3792
 LYE  O12   O   O      0  -0.391  -21.0196  -11.0464   2.2121
 LYE  O24   O   OH1    0  -0.576  -16.4516  -12.3690  10.7478
 LYE  O27   O   OS     0  -0.727  -13.6232  -15.3065   4.7615
 LYE  O28   O   OS     0  -0.727  -15.9545  -14.5888   5.0940
 LYE  O29   O   OS    -1  -0.728  -14.2476  -14.1225   6.8173
 LYE  S26   S   S      0   1.427  -14.5342  -14.3392   5.3929
 LYE  BR3   BR  BR     0  -0.019  -18.7080  -11.8178   0.4177
 LYE  BR4   BR  BR     0  -0.019  -21.5756  -10.5348   5.1399
 LYE  BR2   BR  BR     0  -0.004  -14.1705  -10.4593   9.7357
 LYE  BR1   BR  BR     0  -0.002  -18.5914  -13.9972   9.5223
 LYE  H021  H   HCR6   0   0.268  -11.6672  -11.2765   2.8688
 LYE  H011  H   HCR6   0   0.269  -13.3599   -9.4675   2.7282
 LYE  H031  H   HCR6   0   0.273  -12.2131  -13.3810   4.0159
 LYE  H061  H   HCR6   0   0.275  -15.5648   -9.7766   3.7753
 LYE  H091  H   HCR6   0   0.308  -18.8790  -11.0997   6.1286
 LYE  H141  H   HCR6   0   0.303  -16.6833  -12.0796   2.5250
 LYE  H181  H   HCR6   0   0.304  -18.0992  -13.3343   6.7100
 LYE  H221  H   HCR6   0   0.294  -14.7586  -10.6615   6.8865
 LYE  H241  H   HOH1   0   0.486  -15.7678  -11.8709  11.2157

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
 LYE  BR3  C13   single    1.879  0.020  1.879
 LYE  O12  C11   double    1.217  0.020  1.217
 LYE  C13  C11   single    1.465  0.020  1.465
 LYE  C13  C14   double    1.347  0.020  1.347
 LYE  C11  C10   single    1.465  0.020  1.465
 LYE  C14  C08   single    1.439  0.020  1.439
 LYE  C02  C01   aromatic  1.385  0.020  1.385
 LYE  C02  C03   aromatic  1.389  0.020  1.389
 LYE  C01  C06   aromatic  1.386  0.020  1.386
 LYE  C03  C04   aromatic  1.386  0.020  1.386
 LYE  C06  C05   aromatic  1.396  0.020  1.396
 LYE  O27  S26   deloc     1.471  0.020  1.471
 LYE  C10  BR4   single    1.879  0.020  1.879
 LYE  C10  C09   double    1.346  0.020  1.346
 LYE  C04  C05   aromatic  1.400  0.020  1.400
 LYE  C04  S26   single    1.805  0.020  1.805
 LYE  C08  C09   single    1.438  0.020  1.438
 LYE  C08  C07   double    1.377  0.020  1.377
 LYE  C05  C07   single    1.477  0.020  1.477
 LYE  O28  S26   deloc     1.473  0.020  1.473
 LYE  S26  O29   deloc     1.469  0.020  1.469
 LYE  C07  C17   single    1.460  0.020  1.460
 LYE  C17  C18   aromatic  1.396  0.020  1.396
 LYE  C17  C22   aromatic  1.392  0.020  1.392
 LYE  C18  C19   aromatic  1.377  0.020  1.377
 LYE  C22  C21   aromatic  1.380  0.020  1.380
 LYE  C19  C20   aromatic  1.402  0.020  1.402
 LYE  C19  BR1   single    1.881  0.020  1.881
 LYE  C21  C20   aromatic  1.400  0.020  1.400
 LYE  C21  BR2   single    1.886  0.020  1.886
 LYE  C20  O24   single    1.326  0.020  1.326
 LYE  C02  H021  single    0.930  0.020  1.080
 LYE  C01  H011  single    0.930  0.020  1.080
 LYE  C03  H031  single    0.930  0.020  1.080
 LYE  C06  H061  single    0.930  0.020  1.080
 LYE  C09  H091  single    0.930  0.020  1.080
 LYE  C14  H141  single    0.930  0.020  1.080
 LYE  C18  H181  single    0.930  0.020  1.080
 LYE  C22  H221  single    0.930  0.020  1.080
 LYE  O24  H241  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
 LYE  H021  C02  C03  119.71  3.000
 LYE  H021  C02  C01  120.30  3.000
 LYE  C03   C02  C01  119.99  3.000
 LYE  S26   C04  C05  121.57  3.000
 LYE  S26   C04  C03  118.73  3.000
 LYE  C05   C04  C03  119.65  3.000
 LYE  C17   C07  C05  116.78  3.000
 LYE  C17   C07  C08  122.70  3.000
 LYE  C05   C07  C08  120.24  3.000
 LYE  C14   C08  C09  117.38  3.000
 LYE  C09   C08  C07  121.97  3.000
 LYE  C14   C08  C07  120.63  3.000
 LYE  H011  C01  C06  119.81  3.000
 LYE  H011  C01  C02  120.59  3.000
 LYE  C06   C01  C02  119.60  3.000
 LYE  H031  C03  C04  119.75  3.000
 LYE  H031  C03  C02  119.51  3.000
 LYE  C04   C03  C02  120.73  3.000
 LYE  C06   C05  C07  117.27  3.000
 LYE  C07   C05  C04  123.61  3.000
 LYE  C06   C05  C04  119.04  3.000
 LYE  H061  C06  C05  119.31  3.000
 LYE  H061  C06  C01  119.69  3.000
 LYE  C05   C06  C01  120.98  3.000
 LYE  H091  C09  C10  119.87  3.000
 LYE  H091  C09  C08  118.86  3.000
 LYE  C10   C09  C08  121.15  3.000
 LYE  BR4   C10  C11  115.75  3.000
 LYE  BR4   C10  C09  120.83  3.000
 LYE  C11   C10  C09  123.40  3.000
 LYE  O12   C11  C13  123.29  3.000
 LYE  C13   C11  C10  113.53  3.000
 LYE  O12   C11  C10  123.18  3.000
 LYE  BR3   C13  C14  120.87  3.000
 LYE  C14   C13  C11  123.37  3.000
 LYE  BR3   C13  C11  115.75  3.000
 LYE  H141  C14  C13  120.17  3.000
 LYE  H141  C14  C08  118.63  3.000
 LYE  C13   C14  C08  121.15  3.000
 LYE  C22   C17  C18  118.81  3.000
 LYE  C22   C17  C07  119.77  3.000
 LYE  C18   C17  C07  121.38  3.000
 LYE  H181  C18  C19  119.81  3.000
 LYE  H181  C18  C17  119.88  3.000
 LYE  C19   C18  C17  120.27  3.000
 LYE  BR1   C19  C20  118.50  3.000
 LYE  BR1   C19  C18  119.72  3.000
 LYE  C20   C19  C18  121.78  3.000
 LYE  O24   C20  C21  125.21  3.000
 LYE  O24   C20  C19  117.72  3.000
 LYE  C21   C20  C19  117.06  3.000
 LYE  BR2   C21  C22  118.98  3.000
 LYE  BR2   C21  C20  119.43  3.000
 LYE  C22   C21  C20  121.59  3.000
 LYE  H221  C22  C21  119.63  3.000
 LYE  H221  C22  C17  119.90  3.000
 LYE  C21   C22  C17  120.46  3.000
 LYE  H241  O24  C20  112.92  3.000
 LYE  O29   S26  O28  114.20  3.000
 LYE  O29   S26  O27  113.10  3.000
 LYE  O28   S26  O27  113.50  3.000
 LYE  O29   S26  C04  105.43  3.000
 LYE  O28   S26  C04  104.25  3.000
 LYE  O27   S26  C04  105.13  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
 LYE  CONST_01  C05   C06  C01  C02     0.00   0.0  0
 LYE  CONST_02  C05   C04  C03  C02     0.00   0.0  0
 LYE  CONST_03  C01   C02  C03  C04     0.00   0.0  0
 LYE  CONST_04  C01   C06  C05  C04     0.00   0.0  0
 LYE  CONST_05  C06   C01  C02  C03     0.00   0.0  0
 LYE  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 LYE  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 LYE  CONST_08  C20   C21  C22  C17     0.00   0.0  0
 LYE  CONST_09  C21   C22  C17  C18     0.00   0.0  0
 LYE  CONST_10  C21   C20  C19  C18     0.00   0.0  0
 LYE  CONST_11  C22   C17  C18  C19     0.00   0.0  0
 LYE  CONST_12  C22   C21  C20  C19     0.00   0.0  0
 LYE  CONST_13  S26   C04  C03  C02   180.00   0.0  0
 LYE  CONST_14  C01   C06  C05  C07   180.00   0.0  0
 LYE  CONST_15  C03   C04  C05  C07   180.00   0.0  0
 LYE  CONST_16  C19   C18  C17  C07   180.00   0.0  0
 LYE  CONST_17  C21   C22  C17  C07   180.00   0.0  0
 LYE  CONST_18  S26   C04  C05  C06   180.00   0.0  0
 LYE  CONST_19  BR1   C19  C18  C17   180.00   0.0  0
 LYE  CONST_20  BR2   C21  C22  C17   180.00   0.0  0
 LYE  CONST_21  O24   C20  C19  C18   180.00   0.0  0
 LYE  CONST_22  BR2   C21  C20  C19   180.00   0.0  0
 LYE  CONST_23  BR1   C19  C20  C21   180.00   0.0  0
 LYE  CONST_24  O24   C20  C21  C22   180.00   0.0  0
 LYE  CONST_25  H061  C06  C01  C02   180.00   0.0  0
 LYE  CONST_26  H021  C02  C03  C04   180.00   0.0  0
 LYE  CONST_27  H031  C03  C02  C01   180.00   0.0  0
 LYE  CONST_28  H011  C01  C02  C03   180.00   0.0  0
 LYE  CONST_29  H221  C22  C17  C18   180.00   0.0  0
 LYE  CONST_30  H181  C18  C19  C20   180.00   0.0  0
 LYE  Var_01    C14   C08  C07  C05    18.66   0.0  2
 LYE  Var_02    C08   C07  C05  C04  -125.60  30.0  2
 LYE  Var_03    C18   C17  C07  C08    44.81  30.0  2
 LYE  Var_04    O27   S26  C04  C03   -22.98  30.0  2

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
 LYE  plan-1  C02   0.020
 LYE  plan-1  C04   0.020
 LYE  plan-1  C07   0.020
 LYE  plan-1  C01   0.020
 LYE  plan-1  C03   0.020
 LYE  plan-1  C05   0.020
 LYE  plan-1  C06   0.020
 LYE  plan-1  S26   0.020
 LYE  plan-1  H021  0.020
 LYE  plan-1  H011  0.020
 LYE  plan-1  H031  0.020
 LYE  plan-1  H061  0.020
 LYE  plan-2  C07   0.020
 LYE  plan-2  C08   0.020
 LYE  plan-2  C05   0.020
 LYE  plan-2  C09   0.020
 LYE  plan-2  C10   0.020
 LYE  plan-2  C11   0.020
 LYE  plan-2  C13   0.020
 LYE  plan-2  C14   0.020
 LYE  plan-2  C17   0.020
 LYE  plan-2  O12   0.020
 LYE  plan-2  BR3   0.020
 LYE  plan-2  BR4   0.020
 LYE  plan-2  H091  0.020
 LYE  plan-2  H141  0.020
 LYE  plan-3  C07   0.020
 LYE  plan-3  C17   0.020
 LYE  plan-3  C18   0.020
 LYE  plan-3  C19   0.020
 LYE  plan-3  C20   0.020
 LYE  plan-3  C21   0.020
 LYE  plan-3  C22   0.020
 LYE  plan-3  O24   0.020
 LYE  plan-3  BR2   0.020
 LYE  plan-3  BR1   0.020
 LYE  plan-3  H181  0.020
 LYE  plan-3  H221  0.020

