# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:05:30 2021
#   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  69  31  .  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_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  -0.260  12.1852   -4.9138  -17.0493
 L4E  C5   C  C     0   0.112  12.3264   -5.8021  -18.0357
 L4E  C6   C  CH3   0  -0.717  13.6376   -6.3788  -18.4768
 L4E  C7   C  CH3   0  -0.710  11.1351   -6.3264  -18.7835
 L4E  C8   C  CH3   0  -0.727  15.4774   -6.5306  -15.2034
 L4E  C10  C  CH2   0  -0.496  13.5857   -8.9883  -15.2967
 L4E  C13  C  CH3   0  -0.729  16.2703   -9.9517  -13.7256
 L4E  C15  C  CH2   0  -0.496  16.0222   -7.9521  -11.3763
 L4E  C17  C  C     0   0.130  16.7032  -10.1035  -10.2099
 L4E  C20  C  CH2   0  -0.532  16.1603  -12.5831  -10.3247
 L4E  C21  C  CR6   0   0.009  16.2183  -13.3750   -9.0368
 L4E  C22  C  CR16  0  -0.319  16.2795  -12.7625   -7.7935
 L4E  C24  C  CR16  0  -0.407  16.3405  -14.8988   -6.6816
 L4E  C26  C  CR6   0   0.277  16.2259  -14.7693   -9.0896
 L4E  C3   C  CH2   0  -0.495  13.2578   -4.3420  -16.1749
 L4E  C2   C  CH2   0  -0.485  13.4061   -5.1164  -14.8482
 L4E  C1   C  C     0   0.136  13.9882   -6.4904  -15.0376
 L4E  C9   C  C1    0  -0.233  13.1949   -7.5618  -15.0744
 L4E  C11  C  CH2   0  -0.484  13.7570   -9.7734  -13.9815
 L4E  C12  C  C     0   0.134  14.9876   -9.3604  -13.2220
 L4E  C14  C  C1    0  -0.233  14.9040   -8.5052  -12.2017
 L4E  C16  C  CH2   0  -0.485  16.2031   -8.6957  -10.0389
 L4E  C18  C  CH3   0  -0.731  18.1747  -10.2352  -10.4642
 L4E  C19  C  C1    0  -0.265  15.8551  -11.1304  -10.1354
 L4E  C23  C  CR6   0  -0.081  16.3410  -13.5045   -6.6185
 L4E  C29  C  C     0   0.528  16.4052  -12.7806   -5.3334
 L4E  O31  O  O     0  -0.449  16.4140  -11.5748   -5.2327
 L4E  O30  O  OH1   0  -0.599  16.4536  -13.5886   -4.2795
 L4E  C25  C  CR6   0   0.290  16.2829  -15.5257   -7.9102
 L4E  O28  O  OH1   0  -0.647  16.2772  -16.8676   -8.0767
 L4E  O27  O  OH1   0  -0.615  16.1790  -15.3672  -10.2912
 L4E  H1   H  H     0   0.214  11.1741   -4.5972  -16.8017
 L4E  H2   H  HCH3  0   0.235  14.4977   -5.9157  -17.9988
 L4E  H3   H  HCH3  0   0.237  13.6746   -7.4457  -18.2420
 L4E  H4   H  HCH3  0   0.228  13.7589   -6.2879  -19.5594
 L4E  H5   H  HCH3  0   0.233  10.2006   -5.8982  -18.4215
 L4E  H6   H  HCH3  0   0.227  11.2139   -6.1143  -19.8532
 L4E  H7   H  HCH3  0   0.228  11.0656   -7.4137  -18.6900
 L4E  H8   H  HCH3  0   0.225  15.8139   -5.8136  -15.9571
 L4E  H9   H  HCH3  0   0.237  15.9671   -6.2517  -14.2668
 L4E  H10  H  HCH3  0   0.234  15.8563   -7.5105  -15.4863
 L4E  H11  H  HCH2  0   0.231  12.8063   -9.4779  -15.8875
 L4E  H12  H  HCH2  0   0.227  14.4993   -9.0618  -15.8909
 L4E  H13  H  HCH3  0   0.234  17.1557   -9.5072  -13.2768
 L4E  H14  H  HCH3  0   0.237  16.3009  -11.0233  -13.5112
 L4E  H15  H  HCH3  0   0.227  16.3597   -9.8460  -14.8105
 L4E  H16  H  HCH2  0   0.228  16.9635   -7.9476  -11.9300
 L4E  H17  H  HCH2  0   0.234  15.8059   -6.9045  -11.1493
 L4E  H18  H  HCH2  0   0.254  15.3875  -13.0163  -10.9662
 L4E  H19  H  HCH2  0   0.257  17.0966  -12.7228  -10.8708
 L4E  H20  H  HCR6  0   0.253  16.2807  -11.6818   -7.7447
 L4E  H21  H  HCR6  0   0.282  16.3856  -15.5030   -5.7839
 L4E  H22  H  HCH2  0   0.229  14.2202   -4.3082  -16.6907
 L4E  H23  H  HCH2  0   0.234  13.0078   -3.3047  -15.9367
 L4E  H24  H  HCH2  0   0.225  14.0448   -4.5337  -14.1761
 L4E  H25  H  HCH2  0   0.227  12.4250   -5.1833  -14.3705
 L4E  H26  H  H     0   0.205  12.1332   -7.3974  -14.9062
 L4E  H27  H  HCH2  0   0.227  12.8646   -9.6325  -13.3662
 L4E  H28  H  HCH2  0   0.224  13.8091  -10.8414  -14.2181
 L4E  H29  H  H     0   0.206  13.9109   -8.1710  -11.9103
 L4E  H30  H  HCH2  0   0.228  16.9040   -8.1286   -9.4177
 L4E  H31  H  HCH2  0   0.231  15.2481   -8.6999   -9.5070
 L4E  H32  H  HCH3  0   0.234  18.4988   -9.5833  -11.2787
 L4E  H33  H  HCH3  0   0.240  18.7387   -9.9263   -9.5801
 L4E  H34  H  HCH3  0   0.238  18.4828  -11.2484  -10.7148
 L4E  H35  H  H     0   0.225  14.8165  -10.9075   -9.9053
 L4E  H36  H  HOH1  0   0.485  16.4955  -13.0644   -3.4663
 L4E  H37  H  HOH1  0   0.484  16.3558  -17.3223   -7.2309
 L4E  H38  H  HOH1  0   0.479  16.1898  -16.3278  -10.1956

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    1.499  0.020  1.499
 L4E  C5   C4   double    1.335  0.020  1.335
 L4E  C4   C3   single    1.497  0.020  1.497
 L4E  C3   C2   single    1.543  0.020  1.543
 L4E  C10  C9   single    1.496  0.020  1.496
 L4E  C10  C11  single    1.541  0.020  1.541
 L4E  C9   C1   double    1.334  0.020  1.334
 L4E  C8   C1   single    1.499  0.020  1.499
 L4E  C1   C2   single    1.504  0.020  1.504
 L4E  C11  C12  single    1.504  0.020  1.504
 L4E  C13  C12  single    1.500  0.020  1.500
 L4E  C12  C14  double    1.334  0.020  1.334
 L4E  C14  C15  single    1.496  0.020  1.496
 L4E  C15  C16  single    1.541  0.020  1.541
 L4E  O27  C26  single    1.343  0.020  1.343
 L4E  C18  C17  single    1.499  0.020  1.499
 L4E  C20  C19  single    1.496  0.020  1.496
 L4E  C20  C21  single    1.513  0.020  1.513
 L4E  C17  C19  double    1.334  0.020  1.334
 L4E  C17  C16  single    1.504  0.020  1.504
 L4E  C26  C21  aromatic  1.395  0.020  1.395
 L4E  C26  C25  aromatic  1.402  0.020  1.402
 L4E  C21  C22  aromatic  1.387  0.020  1.387
 L4E  O28  C25  single    1.352  0.020  1.352
 L4E  C25  C24  aromatic  1.380  0.020  1.380
 L4E  C22  C23  aromatic  1.391  0.020  1.391
 L4E  C24  C23  aromatic  1.396  0.020  1.396
 L4E  C23  C29  single    1.476  0.020  1.476
 L4E  C29  O31  double    1.210  0.020  1.210
 L4E  C29  O30  single    1.329  0.020  1.329
 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  O30  H36  single    0.850  0.020  0.980
 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   114.94  3.000
 L4E  H1   C4   C5   117.40  3.000
 L4E  C3   C4   C5   127.57  3.000
 L4E  C7   C5   C6   114.41  3.000
 L4E  C6   C5   C4   124.48  3.000
 L4E  C7   C5   C4   121.10  3.000
 L4E  H4   C6   H3   106.86  3.000
 L4E  H4   C6   H2   108.19  3.000
 L4E  H3   C6   H2   107.13  3.000
 L4E  H4   C6   C5   110.89  3.000
 L4E  H3   C6   C5   109.99  3.000
 L4E  H2   C6   C5   113.50  3.000
 L4E  H7   C7   H6   106.33  3.000
 L4E  H7   C7   H5   107.92  3.000
 L4E  H6   C7   H5   108.09  3.000
 L4E  H7   C7   C5   110.80  3.000
 L4E  H6   C7   C5   111.25  3.000
 L4E  H5   C7   C5   112.20  3.000
 L4E  H10  C8   H9   107.25  3.000
 L4E  H10  C8   H8   107.71  3.000
 L4E  H9   C8   H8   106.58  3.000
 L4E  H10  C8   C1   113.51  3.000
 L4E  H9   C8   C1   110.09  3.000
 L4E  H8   C8   C1   111.37  3.000
 L4E  H12  C10  H11  105.79  3.000
 L4E  H12  C10  C11  109.69  3.000
 L4E  H11  C10  C11  108.18  3.000
 L4E  H12  C10  C9   111.32  3.000
 L4E  H11  C10  C9   108.73  3.000
 L4E  C11  C10  C9   112.83  3.000
 L4E  H15  C13  H14  106.68  3.000
 L4E  H15  C13  H13  107.65  3.000
 L4E  H14  C13  H13  107.27  3.000
 L4E  H15  C13  C12  111.41  3.000
 L4E  H14  C13  C12  110.15  3.000
 L4E  H13  C13  C12  113.36  3.000
 L4E  H17  C15  H16  105.77  3.000
 L4E  H17  C15  C16  107.78  3.000
 L4E  H16  C15  C16  109.93  3.000
 L4E  H17  C15  C14  108.71  3.000
 L4E  H16  C15  C14  111.48  3.000
 L4E  C16  C15  C14  112.84  3.000
 L4E  C19  C17  C18  124.46  3.000
 L4E  C19  C17  C16  120.19  3.000
 L4E  C18  C17  C16  115.34  3.000
 L4E  H19  C20  H18  105.16  3.000
 L4E  H19  C20  C19  111.23  3.000
 L4E  H18  C20  C19  108.33  3.000
 L4E  H19  C20  C21  109.01  3.000
 L4E  H18  C20  C21  108.60  3.000
 L4E  C19  C20  C21  114.10  3.000
 L4E  C26  C21  C22  118.35  3.000
 L4E  C22  C21  C20  122.24  3.000
 L4E  C26  C21  C20  119.41  3.000
 L4E  H20  C22  C23  119.66  3.000
 L4E  H20  C22  C21  118.78  3.000
 L4E  C23  C22  C21  121.56  3.000
 L4E  H21  C24  C25  119.09  3.000
 L4E  H21  C24  C23  121.32  3.000
 L4E  C25  C24  C23  119.60  3.000
 L4E  O27  C26  C25  120.91  3.000
 L4E  C25  C26  C21  120.50  3.000
 L4E  O27  C26  C21  118.59  3.000
 L4E  H23  C3   H22  105.97  3.000
 L4E  H23  C3   C2   108.10  3.000
 L4E  H22  C3   C2   109.68  3.000
 L4E  H23  C3   C4   109.01  3.000
 L4E  H22  C3   C4   111.54  3.000
 L4E  C2   C3   C4   112.28  3.000
 L4E  H25  C2   H24  106.73  3.000
 L4E  H25  C2   C1   110.27  3.000
 L4E  H24  C2   C1   109.73  3.000
 L4E  H25  C2   C3   108.67  3.000
 L4E  H24  C2   C3   108.46  3.000
 L4E  C1   C2   C3   112.79  3.000
 L4E  C9   C1   C2   120.47  3.000
 L4E  C2   C1   C8   115.02  3.000
 L4E  C9   C1   C8   124.50  3.000
 L4E  H26  C9   C1   117.07  3.000
 L4E  H26  C9   C10  114.98  3.000
 L4E  C1   C9   C10  127.94  3.000
 L4E  H28  C11  H27  106.62  3.000
 L4E  H28  C11  C12  109.76  3.000
 L4E  H27  C11  C12  110.39  3.000
 L4E  H28  C11  C10  108.52  3.000
 L4E  H27  C11  C10  108.90  3.000
 L4E  C12  C11  C10  112.46  3.000
 L4E  C14  C12  C11  120.73  3.000
 L4E  C14  C12  C13  124.29  3.000
 L4E  C11  C12  C13  114.96  3.000
 L4E  H29  C14  C12  117.34  3.000
 L4E  H29  C14  C15  114.91  3.000
 L4E  C12  C14  C15  127.75  3.000
 L4E  H31  C16  H30  106.57  3.000
 L4E  H31  C16  C17  110.02  3.000
 L4E  H30  C16  C17  109.66  3.000
 L4E  H31  C16  C15  108.76  3.000
 L4E  H30  C16  C15  108.52  3.000
 L4E  C17  C16  C15  113.09  3.000
 L4E  H34  C18  H33  107.65  3.000
 L4E  H34  C18  H32  107.46  3.000
 L4E  H33  C18  H32  106.34  3.000
 L4E  H34  C18  C17  113.50  3.000
 L4E  H33  C18  C17  110.14  3.000
 L4E  H32  C18  C17  111.42  3.000
 L4E  H35  C19  C20  114.88  3.000
 L4E  H35  C19  C17  117.48  3.000
 L4E  C20  C19  C17  127.63  3.000
 L4E  C29  C23  C24  121.95  3.000
 L4E  C29  C23  C22  118.40  3.000
 L4E  C24  C23  C22  119.65  3.000
 L4E  O30  C29  O31  122.66  3.000
 L4E  O30  C29  C23  113.19  3.000
 L4E  O31  C29  C23  124.15  3.000
 L4E  H36  O30  C29  109.78  3.000
 L4E  O28  C25  C26  115.57  3.000
 L4E  O28  C25  C24  124.08  3.000
 L4E  C26  C25  C24  120.35  3.000
 L4E  H37  O28  C25  111.10  3.000
 L4E  H38  O27  C26  110.74  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  CONST_17  H36  O30  C29  C23  180.00   0.0  0
 L4E  Var_01    C19  C20  C21  C22  -13.52  30.0  2
 L4E  Var_02    O31  C29  C23  C22   -0.35  30.0  2
 L4E  Var_03    C21  C20  C19  C17  104.16  30.0  2
 L4E  Var_04    C3   C4   C5   C6    -1.57   0.0  2
 L4E  Var_05    C10  C9   C1   C8    -0.80   0.0  2
 L4E  Var_06    C15  C14  C12  C13    0.84   0.0  2
 L4E  Var_07    C18  C17  C19  C20   -2.06   0.0  2
 L4E  Var_08    C1   C2   C3   C4    69.99  30.0  3
 L4E  Var_09    C2   C3   C4   C5   -94.68  30.0  3
 L4E  Var_10    C3   C2   C1   C8    79.66  30.0  3
 L4E  Var_11    C13  C12  C11  C10  -79.56  30.0  3
 L4E  Var_12    C14  C15  C16  C17   68.37  30.0  2
 L4E  Var_13    C11  C10  C9   C1    96.40  30.0  2
 L4E  Var_14    C12  C11  C10  C9   -71.42  30.0  3
 L4E  Var_15    C16  C15  C14  C12  -98.64  30.0  3
 L4E  Var_16    H5   C7   C5   C4     0.03  30.0  3
 L4E  Var_17    H2   C6   C5   C4    -7.14  30.0  3
 L4E  Var_18    H8   C8   C1   C2   -49.57  30.0  3
 L4E  Var_19    H13  C13  C12  C11  169.91  30.0  3
 L4E  Var_20    H32  C18  C17  C16  -50.81  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-2  H36  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

