# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:09:40 2022
#   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  55  26  .  2022-03-22  2022-03-22
;
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  -0.358  16.4453  -12.5688   -7.8398
 L4H  C7   C  CR6    0   0.015  16.0271  -13.2609   -8.9732
 L4H  C8   C  CH2    0  -0.532  15.8298  -12.5689  -10.3044
 L4H  C10  C  C      0   0.128  16.4333  -10.1192  -10.6611
 L4H  C13  C  C1     0  -0.251  14.8882   -8.4887  -12.6632
 L4H  C15  C  CH2    0  -0.492  13.8636   -9.4448  -14.6928
 L4H  C17  C  C1     0  -0.236  12.8383   -7.2808  -15.4624
 L4H  C20  C  CH3    0  -0.703  12.5993   -4.8284  -15.3137
 L4H  C21  C  CH3    0  -0.742  16.2421   -8.5715  -14.7770
 L4H  C22  C  CH3    0  -0.738  17.7114  -10.3519  -11.4102
 L4H  C18  C  C      0   0.078  13.2315   -6.0716  -15.8707
 L4H  C19  C  CH3    0  -0.723  14.3016   -5.8094  -16.8890
 L4H  C16  C  CH2    0  -0.500  13.3490   -8.6216  -15.8846
 L4H  C14  C  C      0   0.122  15.0099   -8.8068  -13.9549
 L4H  C12  C  CH2    0  -0.499  15.9082   -7.8786  -11.7549
 L4H  C11  C  CH2    0  -0.495  16.0662   -8.6747  -10.4507
 L4H  C9   C  C1     0  -0.277  15.6441  -11.0881  -10.1909
 L4H  C2   C  CR6    0  -0.092  16.6468  -13.2014   -6.6189
 L4H  C3   C  C      0   0.391  17.1085  -12.4219   -5.3935
 L4H  O4   O  OC    -1  -0.592  17.3191  -13.0844   -4.3579
 L4H  O5   O  O      0  -0.591  17.2377  -11.1891   -5.5292
 L4H  C1   C  CR16   0  -0.441  16.4162  -14.5725   -6.5366
 L4H  C25  C  CR6    0   0.282  15.9995  -15.2838   -7.6478
 L4H  O26  O  OH1    0  -0.654  15.7533  -16.6195   -7.6461
 L4H  C23  C  CR6    0   0.242  15.8083  -14.6332   -8.8717
 L4H  O24  O  OH1    0  -0.629  15.4189  -15.3183   -9.9717
 L4H  H1   H  HCR6   0   0.229  16.6194  -11.5037   -7.9156
 L4H  H2   H  HCH2   0   0.248  14.9445  -12.9849  -10.7950
 L4H  H3   H  HCH2   0   0.253  16.6649  -12.8134  -10.9662
 L4H  H4   H  H      0   0.213  13.9336   -8.7053  -12.1865
 L4H  H5   H  HCH2   0   0.229  13.0364   -9.6257  -14.0008
 L4H  H6   H  HCH2   0   0.232  14.1775  -10.4254  -15.0679
 L4H  H7   H  H      0   0.213  12.0511   -7.3184  -14.7114
 L4H  H8   H  HCH3   0   0.234  11.8204   -5.0527  -14.5851
 L4H  H9   H  HCH3   0   0.228  13.3455   -4.1952  -14.8262
 L4H  H10  H  HCH3   0   0.228  12.1548   -4.2241  -16.1088
 L4H  H11  H  HCH3   0   0.240  17.0989   -8.2482  -14.1894
 L4H  H12  H  HCH3   0   0.232  16.5279   -9.4797  -15.3136
 L4H  H13  H  HCH3   0   0.246  16.0641   -7.8059  -15.5361
 L4H  H14  H  HCH3   0   0.234  18.5173   -9.7447  -10.9909
 L4H  H15  H  HCH3   0   0.242  18.0359  -11.3904  -11.3946
 L4H  H16  H  HCH3   0   0.244  17.6116  -10.0561  -12.4575
 L4H  H17  H  HCH3   0   0.238  14.7551   -6.7119  -17.2937
 L4H  H18  H  HCH3   0   0.236  13.8988   -5.2354  -17.7277
 L4H  H19  H  HCH3   0   0.232  15.0995   -5.1999  -16.4568
 L4H  H20  H  HCH2   0   0.239  12.5350   -9.1876  -16.3492
 L4H  H21  H  HCH2   0   0.234  14.1254   -8.5368  -16.6457
 L4H  H22  H  HCH2   0   0.234  16.8753   -7.7764  -12.2487
 L4H  H23  H  HCH2   0   0.241  15.6015   -6.8618  -11.4879
 L4H  H24  H  HCH2   0   0.234  16.8406   -8.1893   -9.8463
 L4H  H25  H  HCH2   0   0.230  15.1388   -8.6125   -9.8752
 L4H  H26  H  H      0   0.227  14.7456  -10.7855   -9.6573
 L4H  H28  H  HCR6   0   0.253  16.5653  -15.0874   -5.5942
 L4H  H29  H  HOH1   0   0.477  15.9008  -16.9916   -6.7697
 L4H  H30  H  HOH1   0   0.469  15.2678  -16.2448   -9.7499

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    1.500  0.020  1.500
 L4H  C18  C20  single    1.502  0.020  1.502
 L4H  C18  C17  double    1.335  0.020  1.335
 L4H  C16  C17  single    1.496  0.020  1.496
 L4H  C16  C15  single    1.537  0.020  1.537
 L4H  C15  C14  single    1.505  0.020  1.505
 L4H  C21  C14  single    1.500  0.020  1.500
 L4H  C14  C13  double    1.336  0.020  1.336
 L4H  C13  C12  single    1.496  0.020  1.496
 L4H  C12  C11  single    1.536  0.020  1.536
 L4H  C22  C10  single    1.500  0.020  1.500
 L4H  C10  C9   double    1.335  0.020  1.335
 L4H  C10  C11  single    1.505  0.020  1.505
 L4H  O24  C23  single    1.353  0.020  1.353
 L4H  C8   C9   single    1.497  0.020  1.497
 L4H  C8   C7   single    1.513  0.020  1.513
 L4H  C23  C7   aromatic  1.393  0.020  1.393
 L4H  C23  C25  aromatic  1.399  0.020  1.399
 L4H  C7   C6   aromatic  1.392  0.020  1.392
 L4H  O26  C25  single    1.358  0.020  1.358
 L4H  C25  C1   aromatic  1.384  0.020  1.384
 L4H  C6   C2   aromatic  1.390  0.020  1.390
 L4H  C1   C2   aromatic  1.393  0.020  1.393
 L4H  C2   C3   single    1.524  0.020  1.524
 L4H  C3   O5   deloc     1.247  0.020  1.247
 L4H  C3   O4   deloc     1.247  0.020  1.247
 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  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   119.10  3.000
 L4H  H1   C6   C7   118.73  3.000
 L4H  C2   C6   C7   122.17  3.000
 L4H  C23  C7   C8   119.60  3.000
 L4H  C23  C7   C6   118.52  3.000
 L4H  C8   C7   C6   121.87  3.000
 L4H  H3   C8   H2   105.16  3.000
 L4H  H3   C8   C9   111.22  3.000
 L4H  H2   C8   C9   108.04  3.000
 L4H  H3   C8   C7   109.31  3.000
 L4H  H2   C8   C7   109.03  3.000
 L4H  C9   C8   C7   113.70  3.000
 L4H  C9   C10  C11  120.20  3.000
 L4H  C11  C10  C22  115.25  3.000
 L4H  C9   C10  C22  124.54  3.000
 L4H  H4   C13  C12  114.40  3.000
 L4H  H4   C13  C14  117.12  3.000
 L4H  C12  C13  C14  128.47  3.000
 L4H  H6   C15  H5   106.58  3.000
 L4H  H6   C15  C14  109.20  3.000
 L4H  H5   C15  C14  109.64  3.000
 L4H  H6   C15  C16  108.04  3.000
 L4H  H5   C15  C16  109.03  3.000
 L4H  C14  C15  C16  114.08  3.000
 L4H  H7   C17  C16  114.25  3.000
 L4H  H7   C17  C18  117.07  3.000
 L4H  C16  C17  C18  128.67  3.000
 L4H  H10  C20  H9   106.36  3.000
 L4H  H10  C20  H8   108.02  3.000
 L4H  H9   C20  H8   108.00  3.000
 L4H  H10  C20  C18  111.04  3.000
 L4H  H9   C20  C18  110.94  3.000
 L4H  H8   C20  C18  112.23  3.000
 L4H  H13  C21  H12  106.48  3.000
 L4H  H13  C21  H11  107.17  3.000
 L4H  H12  C21  H11  107.83  3.000
 L4H  H13  C21  C14  110.91  3.000
 L4H  H12  C21  C14  110.71  3.000
 L4H  H11  C21  C14  113.43  3.000
 L4H  H16  C22  H15  107.42  3.000
 L4H  H16  C22  H14  106.54  3.000
 L4H  H15  C22  H14  107.76  3.000
 L4H  H16  C22  C10  111.03  3.000
 L4H  H15  C22  C10  113.27  3.000
 L4H  H14  C22  C10  110.52  3.000
 L4H  C19  C18  C20  114.03  3.000
 L4H  C20  C18  C17  120.81  3.000
 L4H  C19  C18  C17  125.16  3.000
 L4H  H19  C19  H18  106.24  3.000
 L4H  H19  C19  H17  107.77  3.000
 L4H  H18  C19  H17  107.68  3.000
 L4H  H19  C19  C18  110.47  3.000
 L4H  H18  C19  C18  110.47  3.000
 L4H  H17  C19  C18  113.87  3.000
 L4H  H21  C16  H20  105.86  3.000
 L4H  H21  C16  C17  111.74  3.000
 L4H  H20  C16  C17  109.23  3.000
 L4H  H21  C16  C15  110.15  3.000
 L4H  H20  C16  C15  107.52  3.000
 L4H  C17  C16  C15  112.06  3.000
 L4H  C21  C14  C15  115.05  3.000
 L4H  C21  C14  C13  124.58  3.000
 L4H  C15  C14  C13  120.37  3.000
 L4H  H23  C12  H22  105.77  3.000
 L4H  H23  C12  C11  107.64  3.000
 L4H  H22  C12  C11  109.98  3.000
 L4H  H23  C12  C13  109.62  3.000
 L4H  H22  C12  C13  111.59  3.000
 L4H  C11  C12  C13  111.98  3.000
 L4H  H25  C11  H24  106.49  3.000
 L4H  H25  C11  C12  109.28  3.000
 L4H  H24  C11  C12  108.14  3.000
 L4H  H25  C11  C10  109.57  3.000
 L4H  H24  C11  C10  109.26  3.000
 L4H  C12  C11  C10  113.82  3.000
 L4H  H26  C9   C10  117.32  3.000
 L4H  H26  C9   C8   114.51  3.000
 L4H  C10  C9   C8   128.16  3.000
 L4H  C1   C2   C3   120.41  3.000
 L4H  C3   C2   C6   121.16  3.000
 L4H  C1   C2   C6   118.42  3.000
 L4H  O5   C3   O4   126.72  3.000
 L4H  O4   C3   C2   116.56  3.000
 L4H  O5   C3   C2   116.72  3.000
 L4H  H28  C1   C25  119.69  3.000
 L4H  H28  C1   C2   119.74  3.000
 L4H  C25  C1   C2   120.57  3.000
 L4H  C23  C25  O26  115.70  3.000
 L4H  O26  C25  C1   124.00  3.000
 L4H  C23  C25  C1   120.31  3.000
 L4H  H29  O26  C25  110.69  3.000
 L4H  O24  C23  C25  121.00  3.000
 L4H  C25  C23  C7   120.01  3.000
 L4H  O24  C23  C7   118.99  3.000
 L4H  H30  O24  C23  110.15  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  Var_01    C9   C8   C7   C6    -20.49  30.0  3
 L4H  Var_02    O5   C3   C2   C6      3.02  30.0  2
 L4H  Var_03    C10  C9   C8   C7    116.06  30.0  3
 L4H  Var_04    C22  C10  C9   C8     -0.61   0.0  2
 L4H  Var_05    C12  C13  C14  C15   178.74   0.0  2
 L4H  Var_06    C16  C17  C18  C20  -179.38   0.0  2
 L4H  Var_07    C13  C12  C11  C10    57.08  30.0  3
 L4H  Var_08    C16  C15  C14  C13   119.30  30.0  2
 L4H  Var_09    C18  C17  C16  C15   122.49  30.0  3
 L4H  Var_10    C14  C15  C16  C17   -60.90  30.0  3
 L4H  Var_11    C12  C11  C10  C22    58.83  30.0  3
 L4H  Var_12    C11  C12  C13  C14  -128.84  30.0  3
 L4H  Var_13    H11  C21  C14  C13     8.70  30.0  3
 L4H  Var_14    H17  C19  C18  C17     0.17  30.0  3
 L4H  Var_15    H8   C20  C18  C17    -0.52  30.0  3
 L4H  Var_16    H14  C22  C10  C11    48.91  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-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

