# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 12:31:42 2022
#   Inital geometry file: a 170 line input string
#   Ligand name: 3,4-bis(oxidanyl)-5-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCCC(/C)=C/CCC(/C)=C/CC\C(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
 L4E  L4E  '3,4-bis(oxidanyl)-5-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]benzoic acid'  ligand  68  31  .  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_L4E
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
 L4E  C4   C  C1     0  -0.236  11.7339   -5.3943  -16.9744
 L4E  C5   C  C      0   0.076  12.0780   -5.1242  -18.2365
 L4E  C6   C  CH3    0  -0.722  13.1388   -4.1466  -18.6497
 L4E  C7   C  CH3    0  -0.702  11.3914   -5.8060  -19.3846
 L4E  C8   C  CH3    0  -0.741  15.0303   -6.2529  -15.7291
 L4E  C10  C  CH2    0  -0.494  14.3437   -9.2980  -15.7998
 L4E  C13  C  CH3    0  -0.733  17.2705   -9.4529  -14.4422
 L4E  C15  C  CH2    0  -0.498  16.5197   -8.4080  -11.5976
 L4E  C17  C  C      0   0.130  16.7527  -10.5220  -10.2040
 L4E  C20  C  CH2    0  -0.534  15.9812  -12.9110   -9.7793
 L4E  C21  C  CR6    0   0.015  15.9404  -13.4898   -8.3809
 L4E  C22  C  CR16   0  -0.357  16.2436  -12.7237   -7.2583
 L4E  C24  C  CR16   0  -0.441  15.8901  -14.5965   -5.8147
 L4E  C26  C  CR6    0   0.242  15.6169  -14.8334   -8.2016
 L4E  C3   C  CH2    0  -0.499  12.2990   -4.8200  -15.7138
 L4E  C2   C  CH2    0  -0.493  12.7278   -5.9077  -14.7175
 L4E  C1   C  C      0   0.132  13.7454   -6.8728  -15.2664
 L4E  C9   C  C1     0  -0.261  13.4780   -8.1807  -15.3102
 L4E  C11  C  CH2    0  -0.487  14.8559  -10.1912  -14.6535
 L4E  C12  C  C      0   0.108  15.9139   -9.5376  -13.8050
 L4E  C14  C  C1     0  -0.241  15.6192   -9.0781  -12.5863
 L4E  C16  C  CH2    0  -0.496  16.4173   -9.0553  -10.2080
 L4E  C18  C  CH3    0  -0.737  18.1432  -10.8576  -10.6545
 L4E  C19  C  C1     0  -0.277  15.8424  -11.4212   -9.8232
 L4E  C23  C  CR6    0  -0.093  16.2291  -13.2549   -5.9737
 L4E  C29  C  C      0   0.393  16.5804  -12.3977   -4.7632
 L4E  O31  O  O      0  -0.592  16.8463  -11.1997   -4.9857
 L4E  O30  O  OC    -1  -0.591  16.5748  -12.9666   -3.6532
 L4E  C25  C  CR6    0   0.282  15.5871  -15.3799   -6.9139
 L4E  O28  O  OH1    0  -0.654  15.2527  -16.6939   -6.8400
 L4E  O27  O  OH1    0  -0.629  15.3408  -15.5933   -9.2868
 L4E  H1   H  H      0   0.214  10.9447   -6.1283  -16.8200
 L4E  H2   H  HCH3   0   0.237  13.6602   -3.6879  -17.8123
 L4E  H3   H  HCH3   0   0.232  13.8850   -4.6355  -19.2811
 L4E  H4   H  HCH3   0   0.236  12.7057   -3.3438  -19.2523
 L4E  H5   H  HCH3   0   0.234  10.6296   -6.5090  -19.0484
 L4E  H6   H  HCH3   0   0.228  10.9113   -5.0779  -20.0438
 L4E  H7   H  HCH3   0   0.228  12.1095   -6.3532  -20.0010
 L4E  H8   H  HCH3   0   0.232  15.4514   -5.6180  -14.9452
 L4E  H9   H  HCH3   0   0.242  15.7871   -6.9852  -16.0018
 L4E  H10  H  HCH3   0   0.242  14.8685   -5.6077  -16.5961
 L4E  H11  H  HCH2   0   0.236  13.7526   -9.9260  -16.4733
 L4E  H12  H  HCH2   0   0.232  15.1838   -8.9354  -16.3946
 L4E  H13  H  HCH3   0   0.238  18.0198   -8.9844  -13.8077
 L4E  H14  H  HCH3   0   0.233  17.6321  -10.4497  -14.7068
 L4E  H15  H  HCH3   0   0.239  17.2344   -8.8831  -15.3741
 L4E  H16  H  HCH2   0   0.234  17.5578   -8.4045  -11.9329
 L4E  H17  H  HCH2   0   0.240  16.2340   -7.3555  -11.4960
 L4E  H18  H  HCH2   0   0.248  15.1663  -13.3432  -10.3674
 L4E  H19  H  HCH2   0   0.253  16.8977  -13.2383  -10.2774
 L4E  H20  H  HCR6   0   0.228  16.4988  -11.6808   -7.3924
 L4E  H21  H  HCR6   0   0.253  15.8668  -15.0309   -4.8217
 L4E  H22  H  HCH2   0   0.233  13.1344   -4.1479  -15.9160
 L4E  H23  H  HCH2   0   0.240  11.5364   -4.2054  -15.2232
 L4E  H24  H  HCH2   0   0.232  13.1364   -5.4114  -13.8301
 L4E  H25  H  HCH2   0   0.228  11.8434   -6.4587  -14.3864
 L4E  H26  H  H      0   0.215  12.5124   -8.5011  -14.9234
 L4E  H27  H  HCH2   0   0.231  14.0062  -10.4905  -14.0341
 L4E  H28  H  HCH2   0   0.228  15.2610  -11.1106  -15.0891
 L4E  H29  H  H      0   0.211  14.5947   -9.2086  -12.2412
 L4E  H30  H  HCH2   0   0.234  17.0940   -8.5242   -9.5298
 L4E  H31  H  HCH2   0   0.230  15.4055   -8.9075   -9.8213
 L4E  H32  H  HCH3   0   0.235  18.8729  -10.2297  -10.1375
 L4E  H33  H  HCH3   0   0.242  18.4171  -11.8960  -10.4788
 L4E  H34  H  HCH3   0   0.242  18.2683  -10.6620  -11.7227
 L4E  H35  H  H      0   0.226  14.8709  -11.0472   -9.5077
 L4E  H37  H  HOH1   0   0.476  15.2458  -16.9909   -5.9237
 L4E  H38  H  HOH1   0   0.469  15.1029  -16.4872   -9.0136

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
 L4E  C7   C5   single    1.501  0.020  1.501
 L4E  C6   C5   single    1.501  0.020  1.501
 L4E  C5   C4   double    1.336  0.020  1.336
 L4E  C4   C3   single    1.496  0.020  1.496
 L4E  C3   C2   single    1.536  0.020  1.536
 L4E  C10  C9   single    1.496  0.020  1.496
 L4E  C10  C11  single    1.541  0.020  1.541
 L4E  C9   C1   double    1.336  0.020  1.336
 L4E  C8   C1   single    1.500  0.020  1.500
 L4E  C1   C2   single    1.506  0.020  1.506
 L4E  C11  C12  single    1.505  0.020  1.505
 L4E  C13  C12  single    1.501  0.020  1.501
 L4E  C12  C14  double    1.335  0.020  1.335
 L4E  C14  C15  single    1.496  0.020  1.496
 L4E  C15  C16  single    1.536  0.020  1.536
 L4E  O27  C26  single    1.353  0.020  1.353
 L4E  C18  C17  single    1.500  0.020  1.500
 L4E  C20  C19  single    1.497  0.020  1.497
 L4E  C20  C21  single    1.514  0.020  1.514
 L4E  C17  C19  double    1.335  0.020  1.335
 L4E  C17  C16  single    1.505  0.020  1.505
 L4E  C26  C21  aromatic  1.394  0.020  1.394
 L4E  C26  C25  aromatic  1.399  0.020  1.399
 L4E  C21  C22  aromatic  1.392  0.020  1.392
 L4E  O28  C25  single    1.358  0.020  1.358
 L4E  C25  C24  aromatic  1.383  0.020  1.383
 L4E  C22  C23  aromatic  1.390  0.020  1.390
 L4E  C24  C23  aromatic  1.393  0.020  1.393
 L4E  C23  C29  single    1.524  0.020  1.524
 L4E  C29  O31  deloc     1.247  0.020  1.247
 L4E  C29  O30  deloc     1.247  0.020  1.247
 L4E  C4   H1   single    0.930  0.020  1.080
 L4E  C6   H2   single    0.970  0.020  1.090
 L4E  C6   H3   single    0.970  0.020  1.090
 L4E  C6   H4   single    0.970  0.020  1.090
 L4E  C7   H5   single    0.970  0.020  1.090
 L4E  C7   H6   single    0.970  0.020  1.090
 L4E  C7   H7   single    0.970  0.020  1.090
 L4E  C8   H8   single    0.970  0.020  1.090
 L4E  C8   H9   single    0.970  0.020  1.090
 L4E  C8   H10  single    0.970  0.020  1.090
 L4E  C10  H11  single    0.970  0.020  1.090
 L4E  C10  H12  single    0.970  0.020  1.090
 L4E  C13  H13  single    0.970  0.020  1.090
 L4E  C13  H14  single    0.970  0.020  1.090
 L4E  C13  H15  single    0.970  0.020  1.090
 L4E  C15  H16  single    0.970  0.020  1.090
 L4E  C15  H17  single    0.970  0.020  1.090
 L4E  C20  H18  single    0.970  0.020  1.090
 L4E  C20  H19  single    0.970  0.020  1.090
 L4E  C22  H20  single    0.930  0.020  1.080
 L4E  C24  H21  single    0.930  0.020  1.080
 L4E  C3   H22  single    0.970  0.020  1.090
 L4E  C3   H23  single    0.970  0.020  1.090
 L4E  C2   H24  single    0.970  0.020  1.090
 L4E  C2   H25  single    0.970  0.020  1.090
 L4E  C9   H26  single    0.930  0.020  1.080
 L4E  C11  H27  single    0.970  0.020  1.090
 L4E  C11  H28  single    0.970  0.020  1.090
 L4E  C14  H29  single    0.930  0.020  1.080
 L4E  C16  H30  single    0.970  0.020  1.090
 L4E  C16  H31  single    0.970  0.020  1.090
 L4E  C18  H32  single    0.970  0.020  1.090
 L4E  C18  H33  single    0.970  0.020  1.090
 L4E  C18  H34  single    0.970  0.020  1.090
 L4E  C19  H35  single    0.930  0.020  1.080
 L4E  O28  H37  single    0.850  0.020  0.980
 L4E  O27  H38  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
 L4E  H1   C4   C3   114.40  3.000
 L4E  H1   C4   C5   117.20  3.000
 L4E  C3   C4   C5   128.40  3.000
 L4E  C7   C5   C6   114.12  3.000
 L4E  C6   C5   C4   125.03  3.000
 L4E  C7   C5   C4   120.86  3.000
 L4E  H4   C6   H3   106.29  3.000
 L4E  H4   C6   H2   107.74  3.000
 L4E  H3   C6   H2   107.82  3.000
 L4E  H4   C6   C5   110.49  3.000
 L4E  H3   C6   C5   110.50  3.000
 L4E  H2   C6   C5   113.68  3.000
 L4E  H7   C7   H6   106.37  3.000
 L4E  H7   C7   H5   108.07  3.000
 L4E  H6   C7   H5   107.98  3.000
 L4E  H7   C7   C5   110.98  3.000
 L4E  H6   C7   C5   111.06  3.000
 L4E  H5   C7   C5   112.13  3.000
 L4E  H10  C8   H9   107.55  3.000
 L4E  H10  C8   H8   106.45  3.000
 L4E  H9   C8   H8   107.62  3.000
 L4E  H10  C8   C1   111.22  3.000
 L4E  H9   C8   C1   113.27  3.000
 L4E  H8   C8   C1   110.42  3.000
 L4E  H12  C10  H11  105.73  3.000
 L4E  H12  C10  C11  110.00  3.000
 L4E  H11  C10  C11  107.74  3.000
 L4E  H12  C10  C9   112.07  3.000
 L4E  H11  C10  C9   108.52  3.000
 L4E  C11  C10  C9   112.45  3.000
 L4E  H15  C13  H14  106.27  3.000
 L4E  H15  C13  H13  107.19  3.000
 L4E  H14  C13  H13  107.82  3.000
 L4E  H15  C13  C12  111.20  3.000
 L4E  H14  C13  C12  110.51  3.000
 L4E  H13  C13  C12  113.52  3.000
 L4E  H17  C15  H16  105.87  3.000
 L4E  H17  C15  C16  107.67  3.000
 L4E  H16  C15  C16  110.05  3.000
 L4E  H17  C15  C14  109.55  3.000
 L4E  H16  C15  C14  111.78  3.000
 L4E  C16  C15  C14  111.66  3.000
 L4E  C19  C17  C18  124.55  3.000
 L4E  C19  C17  C16  120.36  3.000
 L4E  C18  C17  C16  115.09  3.000
 L4E  H19  C20  H18  105.15  3.000
 L4E  H19  C20  C19  111.24  3.000
 L4E  H18  C20  C19  107.97  3.000
 L4E  H19  C20  C21  109.20  3.000
 L4E  H18  C20  C21  108.99  3.000
 L4E  C19  C20  C21  113.90  3.000
 L4E  C26  C21  C22  118.51  3.000
 L4E  C22  C21  C20  121.90  3.000
 L4E  C26  C21  C20  119.58  3.000
 L4E  H20  C22  C23  119.03  3.000
 L4E  H20  C22  C21  118.79  3.000
 L4E  C23  C22  C21  122.17  3.000
 L4E  H21  C24  C25  119.75  3.000
 L4E  H21  C24  C23  119.72  3.000
 L4E  C25  C24  C23  120.53  3.000
 L4E  O27  C26  C25  120.95  3.000
 L4E  C25  C26  C21  119.99  3.000
 L4E  O27  C26  C21  119.06  3.000
 L4E  H23  C3   H22  105.69  3.000
 L4E  H23  C3   C2   107.52  3.000
 L4E  H22  C3   C2   110.04  3.000
 L4E  H23  C3   C4   109.26  3.000
 L4E  H22  C3   C4   111.69  3.000
 L4E  C2   C3   C4   112.34  3.000
 L4E  H25  C2   H24  106.54  3.000
 L4E  H25  C2   C1   109.51  3.000
 L4E  H24  C2   C1   109.48  3.000
 L4E  H25  C2   C3   109.11  3.000
 L4E  H24  C2   C3   107.98  3.000
 L4E  C1   C2   C3   113.95  3.000
 L4E  C9   C1   C2   120.28  3.000
 L4E  C2   C1   C8   115.24  3.000
 L4E  C9   C1   C8   124.48  3.000
 L4E  H26  C9   C1   117.01  3.000
 L4E  H26  C9   C10  114.20  3.000
 L4E  C1   C9   C10  128.78  3.000
 L4E  H28  C11  H27  106.44  3.000
 L4E  H28  C11  C12  109.19  3.000
 L4E  H27  C11  C12  110.22  3.000
 L4E  H28  C11  C10  108.29  3.000
 L4E  H27  C11  C10  108.78  3.000
 L4E  C12  C11  C10  113.66  3.000
 L4E  C14  C12  C11  120.58  3.000
 L4E  C14  C12  C13  124.57  3.000
 L4E  C11  C12  C13  114.85  3.000
 L4E  H29  C14  C12  117.10  3.000
 L4E  H29  C14  C15  114.24  3.000
 L4E  C12  C14  C15  128.65  3.000
 L4E  H31  C16  H30  106.69  3.000
 L4E  H31  C16  C17  109.71  3.000
 L4E  H30  C16  C17  109.47  3.000
 L4E  H31  C16  C15  108.95  3.000
 L4E  H30  C16  C15  108.33  3.000
 L4E  C17  C16  C15  113.47  3.000
 L4E  H34  C18  H33  107.44  3.000
 L4E  H34  C18  H32  106.45  3.000
 L4E  H33  C18  H32  107.69  3.000
 L4E  H34  C18  C17  111.07  3.000
 L4E  H33  C18  C17  113.47  3.000
 L4E  H32  C18  C17  110.39  3.000
 L4E  H35  C19  C20  114.62  3.000
 L4E  H35  C19  C17  117.39  3.000
 L4E  C20  C19  C17  127.99  3.000
 L4E  C29  C23  C24  120.47  3.000
 L4E  C29  C23  C22  121.10  3.000
 L4E  C24  C23  C22  118.43  3.000
 L4E  O30  C29  O31  126.72  3.000
 L4E  O30  C29  C23  116.69  3.000
 L4E  O31  C29  C23  116.59  3.000
 L4E  O28  C25  C26  115.67  3.000
 L4E  O28  C25  C24  123.96  3.000
 L4E  C26  C25  C24  120.36  3.000
 L4E  H37  O28  C25  110.60  3.000
 L4E  H38  O27  C26  110.10  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
 L4E  CONST_01  C24  C25  C26  C21     0.00   0.0  0
 L4E  CONST_02  C24  C23  C22  C21     0.00   0.0  0
 L4E  CONST_03  C25  C26  C21  C22     0.00   0.0  0
 L4E  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 L4E  CONST_05  C23  C22  C21  C26     0.00   0.0  0
 L4E  CONST_06  C23  C24  C25  C26     0.00   0.0  0
 L4E  CONST_07  C25  C26  C21  C20   180.00   0.0  0
 L4E  CONST_08  C23  C22  C21  C20   180.00   0.0  0
 L4E  CONST_09  O28  C25  C26  C21   180.00   0.0  0
 L4E  CONST_10  C29  C23  C22  C21   180.00   0.0  0
 L4E  CONST_11  O27  C26  C21  C22   180.00   0.0  0
 L4E  CONST_12  O27  C26  C25  C24   180.00   0.0  0
 L4E  CONST_13  O28  C25  C24  C23   180.00   0.0  0
 L4E  CONST_14  C25  C24  C23  C29   180.00   0.0  0
 L4E  CONST_15  H21  C24  C23  C22   180.00   0.0  0
 L4E  CONST_16  H20  C22  C23  C24   180.00   0.0  0
 L4E  Var_01    C19  C20  C21  C22   -22.37  30.0  2
 L4E  Var_02    O31  C29  C23  C22     1.67  30.0  2
 L4E  Var_03    C21  C20  C19  C17   113.74  30.0  1
 L4E  Var_04    C3   C4   C5   C6     -0.29   0.0  2
 L4E  Var_05    C10  C9   C1   C8      0.20   0.0  2
 L4E  Var_06    C15  C14  C12  C13    -0.47   0.0  2
 L4E  Var_07    C18  C17  C19  C20    -1.06   0.0  2
 L4E  Var_08    C1   C2   C3   C4     57.66  30.0  3
 L4E  Var_09    C2   C3   C4   C5   -128.17  30.0  3
 L4E  Var_10    C3   C2   C1   C8     58.92  30.0  3
 L4E  Var_11    C13  C12  C11  C10   -74.88  30.0  3
 L4E  Var_12    C14  C15  C16  C17    58.33  30.0  1
 L4E  Var_13    C11  C10  C9   C1    109.25  30.0  1
 L4E  Var_14    C12  C11  C10  C9    -72.45  30.0  3
 L4E  Var_15    C16  C15  C14  C12  -129.81  30.0  3
 L4E  Var_16    H5   C7   C5   C4     -0.38  30.0  3
 L4E  Var_17    H2   C6   C5   C4      2.73  30.0  3
 L4E  Var_18    H8   C8   C1   C2     51.99  30.0  3
 L4E  Var_19    H13  C13  C12  C11  -179.53  30.0  3
 L4E  Var_20    H32  C18  C17  C16    48.92  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
 L4E  plan-1  C20  0.020
 L4E  plan-1  C21  0.020
 L4E  plan-1  C22  0.020
 L4E  plan-1  C24  0.020
 L4E  plan-1  C26  0.020
 L4E  plan-1  C23  0.020
 L4E  plan-1  C29  0.020
 L4E  plan-1  C25  0.020
 L4E  plan-1  O28  0.020
 L4E  plan-1  O27  0.020
 L4E  plan-1  H20  0.020
 L4E  plan-1  H21  0.020
 L4E  plan-2  C23  0.020
 L4E  plan-2  C29  0.020
 L4E  plan-2  O31  0.020
 L4E  plan-2  O30  0.020
 L4E  plan-3  C4   0.020
 L4E  plan-3  C5   0.020
 L4E  plan-3  C6   0.020
 L4E  plan-3  C7   0.020
 L4E  plan-3  C3   0.020
 L4E  plan-3  H1   0.020
 L4E  plan-4  C8   0.020
 L4E  plan-4  C10  0.020
 L4E  plan-4  C2   0.020
 L4E  plan-4  C1   0.020
 L4E  plan-4  C9   0.020
 L4E  plan-4  H26  0.020
 L4E  plan-5  C13  0.020
 L4E  plan-5  C15  0.020
 L4E  plan-5  C11  0.020
 L4E  plan-5  C12  0.020
 L4E  plan-5  C14  0.020
 L4E  plan-5  H29  0.020
 L4E  plan-6  C17  0.020
 L4E  plan-6  C20  0.020
 L4E  plan-6  C16  0.020
 L4E  plan-6  C18  0.020
 L4E  plan-6  C19  0.020
 L4E  plan-6  H35  0.020

