# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:02:41 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 3,4-bis(oxidanyl)-5-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(C)=C\CCC(/C)=C/Cc1cc(cc(O)c1O)C(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
 L4H  L4H  '3,4-bis(oxidanyl)-5-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]benzoic acid'  ligand  56  26  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L4H
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
 L4H  C6   C  CR16  0  -0.321  16.2167  -12.2866   -8.2465
 L4H  C7   C  CR6   0   0.011  16.0989  -12.9199   -9.4749
 L4H  C8   C  CH2   0  -0.534  15.9108  -12.1559  -10.7661
 L4H  C10  C  C     0   0.126  16.5744   -9.7069  -10.7710
 L4H  C13  C  C1    0  -0.235  14.6087   -8.1313  -12.6241
 L4H  C15  C  CH2   0  -0.484  13.1383   -9.4746  -14.0762
 L4H  C17  C  C1    0  -0.260  12.5960   -7.3653  -15.3483
 L4H  C20  C  CH3   0  -0.709  13.0903   -4.9454  -15.3215
 L4H  C21  C  CH3   0  -0.729  15.6441   -9.8447  -14.1366
 L4H  C22  C  CH3   0  -0.732  18.0109   -9.9243  -11.1398
 L4H  C18  C  C     0   0.111  13.4789   -6.3805  -15.5292
 L4H  C19  C  CH3   0  -0.716  14.9130   -6.5832  -15.9133
 L4H  C16  C  CH2   0  -0.496  12.8327   -8.8401  -15.4484
 L4H  C14  C  C     0   0.138  14.4914   -9.0912  -13.5429
 L4H  C12  C  CH2   0  -0.496  15.8604   -7.6074  -11.9952
 L4H  C11  C  CH2   0  -0.486  16.1568   -8.2692  -10.6337
 L4H  C9   C  C1    0  -0.263  15.6860  -10.6860  -10.5921
 L4H  C2   C  CR6   0  -0.081  16.3896  -13.0082   -7.0696
 L4H  C3   C  C     0   0.528  16.5021  -12.2634   -5.7997
 L4H  O4   O  OH1   0  -0.599  16.6452  -13.0528   -4.7403
 L4H  O5   O  O     0  -0.449  16.4684  -11.0569   -5.7150
 L4H  C1   C  CR16  0  -0.406  16.4510  -14.4018   -7.1165
 L4H  C25  C  CR6   0   0.290  16.3413  -15.0489   -8.3311
 L4H  O26  O  OH1   0  -0.647  16.3896  -16.3919   -8.4811
 L4H  C23  C  CR6   0   0.279  16.1655  -14.3133   -9.5116
 L4H  O24  O  OH1   0  -0.614  16.0598  -14.9287  -10.7006
 L4H  H1   H  HCR6  0   0.253  16.1749  -11.2062   -8.2108
 L4H  H2   H  HCH2  0   0.255  15.0481  -12.5742  -11.2939
 L4H  H3   H  HCH2  0   0.255  16.7644  -12.3459  -11.4216
 L4H  H4   H  H     0   0.206  13.6884   -7.6865  -12.2533
 L4H  H5   H  HCH2  0   0.227  12.3570   -9.1807  -13.3699
 L4H  H6   H  HCH2  0   0.225  13.0748  -10.5632  -14.1761
 L4H  H7   H  H     0   0.214  11.5924   -7.0842  -15.0364
 L4H  H8   H  HCH3  0   0.233  12.0420   -4.8377  -15.0429
 L4H  H9   H  HCH3  0   0.228  13.6968   -4.4909  -14.5335
 L4H  H10  H  HCH3  0   0.227  13.2631   -4.3519  -16.2233
 L4H  H11  H  HCH3  0   0.235  16.6153   -9.4890  -13.7994
 L4H  H12  H  HCH3  0   0.237  15.5770  -10.9029  -13.8701
 L4H  H13  H  HCH3  0   0.227  15.6342   -9.7966  -15.2293
 L4H  H14  H  HCH3  0   0.233  18.2977   -9.3174  -12.0022
 L4H  H15  H  HCH3  0   0.240  18.6623   -9.6152  -10.3180
 L4H  H16  H  HCH3  0   0.238  18.2458  -10.9605  -11.3751
 L4H  H17  H  HCH3  0   0.235  15.1596   -7.6175  -16.1412
 L4H  H18  H  HCH3  0   0.228  15.1750   -5.9723  -16.7813
 L4H  H19  H  HCH3  0   0.236  15.5671   -6.2658  -15.0970
 L4H  H20  H  HCH2  0   0.234  11.9365   -9.3186  -15.8524
 L4H  H21  H  HCH2  0   0.229  13.6379   -9.0760  -16.1478
 L4H  H22  H  HCH2  0   0.229  16.7210   -7.7188  -12.6581
 L4H  H23  H  HCH2  0   0.234  15.7491   -6.5323  -11.8296
 L4H  H24  H  HCH2  0   0.229  16.9446   -7.6985  -10.1320
 L4H  H25  H  HCH2  0   0.232  15.2654   -8.1942  -10.0059
 L4H  H26  H  H     0   0.225  14.6805  -10.4026  -10.2936
 L4H  H27  H  HOH1  0   0.485  16.7111  -12.5149   -3.9377
 L4H  H28  H  HCR6  0   0.281  16.5862  -14.9892   -6.2168
 L4H  H29  H  HOH1  0   0.484  16.5612  -16.8288   -7.6397
 L4H  H30  H  HOH1  0   0.479  16.1266  -15.8862  -10.5980

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
 L4H  C19  C18  single    1.498  0.020  1.498
 L4H  C18  C20  single    1.501  0.020  1.501
 L4H  C18  C17  double    1.335  0.020  1.335
 L4H  C16  C17  single    1.497  0.020  1.497
 L4H  C16  C15  single    1.542  0.020  1.542
 L4H  C15  C14  single    1.504  0.020  1.504
 L4H  C21  C14  single    1.500  0.020  1.500
 L4H  C14  C13  double    1.334  0.020  1.334
 L4H  C13  C12  single    1.496  0.020  1.496
 L4H  C12  C11  single    1.543  0.020  1.543
 L4H  C22  C10  single    1.499  0.020  1.499
 L4H  C10  C9   double    1.334  0.020  1.334
 L4H  C10  C11  single    1.503  0.020  1.503
 L4H  O24  C23  single    1.343  0.020  1.343
 L4H  C8   C9   single    1.497  0.020  1.497
 L4H  C8   C7   single    1.512  0.020  1.512
 L4H  C23  C7   aromatic  1.395  0.020  1.395
 L4H  C23  C25  aromatic  1.402  0.020  1.402
 L4H  C7   C6   aromatic  1.387  0.020  1.387
 L4H  O26  C25  single    1.352  0.020  1.352
 L4H  C25  C1   aromatic  1.381  0.020  1.381
 L4H  C6   C2   aromatic  1.391  0.020  1.391
 L4H  C1   C2   aromatic  1.396  0.020  1.396
 L4H  C2   C3   single    1.476  0.020  1.476
 L4H  C3   O5   double    1.210  0.020  1.210
 L4H  C3   O4   single    1.329  0.020  1.329
 L4H  C6   H1   single    0.930  0.020  1.080
 L4H  C8   H2   single    0.970  0.020  1.090
 L4H  C8   H3   single    0.970  0.020  1.090
 L4H  C13  H4   single    0.930  0.020  1.080
 L4H  C15  H5   single    0.970  0.020  1.090
 L4H  C15  H6   single    0.970  0.020  1.090
 L4H  C17  H7   single    0.930  0.020  1.080
 L4H  C20  H8   single    0.970  0.020  1.090
 L4H  C20  H9   single    0.970  0.020  1.090
 L4H  C20  H10  single    0.970  0.020  1.090
 L4H  C21  H11  single    0.970  0.020  1.090
 L4H  C21  H12  single    0.970  0.020  1.090
 L4H  C21  H13  single    0.970  0.020  1.090
 L4H  C22  H14  single    0.970  0.020  1.090
 L4H  C22  H15  single    0.970  0.020  1.090
 L4H  C22  H16  single    0.970  0.020  1.090
 L4H  C19  H17  single    0.970  0.020  1.090
 L4H  C19  H18  single    0.970  0.020  1.090
 L4H  C19  H19  single    0.970  0.020  1.090
 L4H  C16  H20  single    0.970  0.020  1.090
 L4H  C16  H21  single    0.970  0.020  1.090
 L4H  C12  H22  single    0.970  0.020  1.090
 L4H  C12  H23  single    0.970  0.020  1.090
 L4H  C11  H24  single    0.970  0.020  1.090
 L4H  C11  H25  single    0.970  0.020  1.090
 L4H  C9   H26  single    0.930  0.020  1.080
 L4H  O4   H27  single    0.850  0.020  0.980
 L4H  C1   H28  single    0.930  0.020  1.080
 L4H  O26  H29  single    0.850  0.020  0.980
 L4H  O24  H30  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
 L4H  H1   C6   C2   119.67  3.000
 L4H  H1   C6   C7   118.81  3.000
 L4H  C2   C6   C7   121.53  3.000
 L4H  C23  C7   C8   119.21  3.000
 L4H  C23  C7   C6   118.37  3.000
 L4H  C8   C7   C6   122.42  3.000
 L4H  H3   C8   H2   105.07  3.000
 L4H  H3   C8   C9   110.96  3.000
 L4H  H2   C8   C9   108.23  3.000
 L4H  H3   C8   C7   109.10  3.000
 L4H  H2   C8   C7   108.46  3.000
 L4H  C9   C8   C7   114.55  3.000
 L4H  C9   C10  C11  120.31  3.000
 L4H  C11  C10  C22  115.30  3.000
 L4H  C9   C10  C22  124.38  3.000
 L4H  H4   C13  C12  114.94  3.000
 L4H  H4   C13  C14  117.05  3.000
 L4H  C12  C13  C14  127.98  3.000
 L4H  H6   C15  H5   106.54  3.000
 L4H  H6   C15  C14  109.75  3.000
 L4H  H5   C15  C14  110.20  3.000
 L4H  H6   C15  C16  108.45  3.000
 L4H  H5   C15  C16  108.82  3.000
 L4H  C14  C15  C16  112.88  3.000
 L4H  H7   C17  C16  114.81  3.000
 L4H  H7   C17  C18  117.28  3.000
 L4H  C16  C17  C18  127.81  3.000
 L4H  H10  C20  H9   106.33  3.000
 L4H  H10  C20  H8   108.01  3.000
 L4H  H9   C20  H8   107.95  3.000
 L4H  H10  C20  C18  111.34  3.000
 L4H  H9   C20  C18  110.70  3.000
 L4H  H8   C20  C18  112.26  3.000
 L4H  H13  C21  H12  106.59  3.000
 L4H  H13  C21  H11  107.65  3.000
 L4H  H12  C21  H11  107.20  3.000
 L4H  H13  C21  C14  111.50  3.000
 L4H  H12  C21  C14  110.04  3.000
 L4H  H11  C21  C14  113.53  3.000
 L4H  H16  C22  H15  107.65  3.000
 L4H  H16  C22  H14  107.55  3.000
 L4H  H15  C22  H14  106.25  3.000
 L4H  H16  C22  C10  113.47  3.000
 L4H  H15  C22  C10  110.18  3.000
 L4H  H14  C22  C10  111.41  3.000
 L4H  C19  C18  C20  114.36  3.000
 L4H  C20  C18  C17  121.01  3.000
 L4H  C19  C18  C17  124.61  3.000
 L4H  H19  C19  H18  106.69  3.000
 L4H  H19  C19  H17  107.27  3.000
 L4H  H18  C19  H17  108.10  3.000
 L4H  H19  C19  C18  110.00  3.000
 L4H  H18  C19  C18  110.94  3.000
 L4H  H17  C19  C18  113.54  3.000
 L4H  H21  C16  H20  105.85  3.000
 L4H  H21  C16  C17  111.85  3.000
 L4H  H20  C16  C17  109.04  3.000
 L4H  H21  C16  C15  109.55  3.000
 L4H  H20  C16  C15  108.12  3.000
 L4H  C17  C16  C15  112.15  3.000
 L4H  C21  C14  C15  115.03  3.000
 L4H  C21  C14  C13  124.52  3.000
 L4H  C15  C14  C13  120.45  3.000
 L4H  H23  C12  H22  105.81  3.000
 L4H  H23  C12  C11  107.92  3.000
 L4H  H22  C12  C11  109.91  3.000
 L4H  H23  C12  C13  108.84  3.000
 L4H  H22  C12  C13  111.63  3.000
 L4H  C11  C12  C13  112.44  3.000
 L4H  H25  C11  H24  106.74  3.000
 L4H  H25  C11  C12  108.72  3.000
 L4H  H24  C11  C12  108.61  3.000
 L4H  H25  C11  C10  110.16  3.000
 L4H  H24  C11  C10  109.91  3.000
 L4H  C12  C11  C10  112.53  3.000
 L4H  H26  C9   C10  117.50  3.000
 L4H  H26  C9   C8   115.28  3.000
 L4H  C10  C9   C8   127.22  3.000
 L4H  C1   C2   C3   121.95  3.000
 L4H  C3   C2   C6   118.38  3.000
 L4H  C1   C2   C6   119.66  3.000
 L4H  O5   C3   O4   122.65  3.000
 L4H  O4   C3   C2   113.22  3.000
 L4H  O5   C3   C2   124.13  3.000
 L4H  H27  O4   C3   109.76  3.000
 L4H  H28  C1   C25  119.11  3.000
 L4H  H28  C1   C2   121.28  3.000
 L4H  C25  C1   C2   119.61  3.000
 L4H  C23  C25  O26  115.61  3.000
 L4H  O26  C25  C1   124.07  3.000
 L4H  C23  C25  C1   120.32  3.000
 L4H  H29  O26  C25  111.09  3.000
 L4H  O24  C23  C25  120.99  3.000
 L4H  C25  C23  C7   120.51  3.000
 L4H  O24  C23  C7   118.50  3.000
 L4H  H30  O24  C23  110.79  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
 L4H  CONST_01  C25  C23  C7   C6      0.00   0.0  0
 L4H  CONST_02  C25  C1   C2   C6      0.00   0.0  0
 L4H  CONST_03  C1   C25  C23  C7      0.00   0.0  0
 L4H  CONST_04  C1   C2   C6   C7      0.00   0.0  0
 L4H  CONST_05  C23  C7   C6   C2      0.00   0.0  0
 L4H  CONST_06  C23  C25  C1   C2      0.00   0.0  0
 L4H  CONST_07  O24  C23  C7   C6    180.00   0.0  0
 L4H  CONST_08  O26  C25  C23  C7    180.00   0.0  0
 L4H  CONST_09  C3   C2   C6   C7    180.00   0.0  0
 L4H  CONST_10  C25  C23  C7   C8    180.00   0.0  0
 L4H  CONST_11  C2   C6   C7   C8    180.00   0.0  0
 L4H  CONST_12  O26  C25  C1   C2    180.00   0.0  0
 L4H  CONST_13  C25  C1   C2   C3    180.00   0.0  0
 L4H  CONST_14  O24  C23  C25  C1    180.00   0.0  0
 L4H  CONST_15  H28  C1   C2   C6    180.00   0.0  0
 L4H  CONST_16  H1   C6   C2   C1    180.00   0.0  0
 L4H  CONST_17  H27  O4   C3   C2    180.00   0.0  0
 L4H  Var_01    C9   C8   C7   C6     -7.51  30.0  2
 L4H  Var_02    O5   C3   C2   C6     -0.85  30.0  2
 L4H  Var_03    C10  C9   C8   C7    102.04  30.0  3
 L4H  Var_04    C22  C10  C9   C8     -2.46   0.0  2
 L4H  Var_05    C12  C13  C14  C15  -179.16   0.0  2
 L4H  Var_06    C16  C17  C18  C20  -176.86   0.0  2
 L4H  Var_07    C13  C12  C11  C10    70.34  30.0  2
 L4H  Var_08    C16  C15  C14  C13    99.95  30.0  2
 L4H  Var_09    C18  C17  C16  C15    94.85  30.0  3
 L4H  Var_10    C14  C15  C16  C17   -70.90  30.0  3
 L4H  Var_11    C12  C11  C10  C22    80.73  30.0  3
 L4H  Var_12    C11  C12  C13  C14   -96.40  30.0  3
 L4H  Var_13    H11  C21  C14  C13    -4.11  30.0  3
 L4H  Var_14    H17  C19  C18  C17     6.22  30.0  3
 L4H  Var_15    H8   C20  C18  C17    -1.29  30.0  3
 L4H  Var_16    H14  C22  C10  C11   -49.89  30.0  3

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
 L4H  plan-1  C6   0.020
 L4H  plan-1  C7   0.020
 L4H  plan-1  C8   0.020
 L4H  plan-1  C2   0.020
 L4H  plan-1  C3   0.020
 L4H  plan-1  C1   0.020
 L4H  plan-1  C25  0.020
 L4H  plan-1  O26  0.020
 L4H  plan-1  C23  0.020
 L4H  plan-1  O24  0.020
 L4H  plan-1  H1   0.020
 L4H  plan-1  H28  0.020
 L4H  plan-2  C2   0.020
 L4H  plan-2  C3   0.020
 L4H  plan-2  O4   0.020
 L4H  plan-2  O5   0.020
 L4H  plan-2  H27  0.020
 L4H  plan-3  C17  0.020
 L4H  plan-3  C20  0.020
 L4H  plan-3  C18  0.020
 L4H  plan-3  C19  0.020
 L4H  plan-3  C16  0.020
 L4H  plan-3  H7   0.020
 L4H  plan-4  C13  0.020
 L4H  plan-4  C15  0.020
 L4H  plan-4  C21  0.020
 L4H  plan-4  C14  0.020
 L4H  plan-4  C12  0.020
 L4H  plan-4  H4   0.020
 L4H  plan-5  C8   0.020
 L4H  plan-5  C10  0.020
 L4H  plan-5  C22  0.020
 L4H  plan-5  C11  0.020
 L4H  plan-5  C9   0.020
 L4H  plan-5  H26  0.020

