# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 24 00:26:39 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2E,4E,6Z,8E)-8-(3,4-dihydronaphthalen-1(2H)-ylidene)-3,7-dimethylocta-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/C=C(C)\C=C1/CCCc2ccccc12)=C\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
 1O8  1O8  '(2E,4E,6Z,8E)-8-(3,4-dihydronaphthalen-1(2H)-ylidene)-3,7-dimethylocta-2,4,6-trienoic acid'  ligand  43  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1O8
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
 1O8  C2'  C  CH2    0  -0.521  -1.7611  -1.1143  -1.1171
 1O8  C1'  C  CH2    0  -0.459  -1.3811   0.1611  -1.8605
 1O8  C18  C  CH2    0  -0.497  -2.5911   1.0727  -1.9685
 1O8  C5   C  CR6    0   0.055  -3.3471   1.2132  -0.6720
 1O8  C4   C  CR16   0  -0.295  -4.2687   2.2523  -0.5436
 1O8  C3   C  CR16   0  -0.258  -5.0274   2.4113   0.6024
 1O8  C2   C  CR16   0  -0.256  -4.8764   1.5095   1.6498
 1O8  C1   C  CR16   0  -0.321  -3.9626   0.4782   1.5389
 1O8  C6   C  CR6    0   0.106  -3.1717   0.3162   0.3939
 1O8  C7   C  C      0   0.103  -2.1748  -0.7760   0.2869
 1O8  C8   C  C1     0  -0.395  -1.6801  -1.3894   1.3726
 1O8  C9   C  C      0   0.060  -0.7246  -2.5092   1.4068
 1O8  C19  C  CH3    0  -0.715  -1.2630  -3.7705   2.0165
 1O8  C10  C  C1     0  -0.273   0.5503  -2.4268   0.9848
 1O8  C11  C  C1     0  -0.242   1.1990  -1.2446   0.4633
 1O8  C12  C  C1     0  -0.291   2.4522  -1.2610  -0.0264
 1O8  C13  C  C      0   0.169   3.1893  -0.1173  -0.5522
 1O8  C20  C  CH3    0  -0.775   2.5095   1.2187  -0.5187
 1O8  C14  C  C1     0  -0.483   4.4357  -0.3445  -1.0149
 1O8  C15  C  C      0   0.392   5.4505   0.6095  -1.5954
 1O8  O1   O  O      0  -0.594   5.0957   1.7509  -1.9571
 1O8  O2   O  OC    -1  -0.618   6.6083   0.1431  -1.6720
 1O8  H1   H  HCH2   0   0.245  -2.6053  -1.5859  -1.6350
 1O8  H2   H  HCH2   0   0.256  -0.9432  -1.8309  -1.1269
 1O8  H3   H  HCH2   0   0.234  -0.5723   0.6689  -1.3264
 1O8  H4   H  HCH2   0   0.243  -1.0011  -0.0746  -2.8559
 1O8  H5   H  HCH2   0   0.251  -2.3011   2.0601  -2.3344
 1O8  H6   H  HCH2   0   0.247  -3.2749   0.6619  -2.7193
 1O8  H7   H  HCR6   0   0.247  -4.3910   2.9488  -1.3655
 1O8  H8   H  HCR6   0   0.253  -5.7366   3.2255   0.6768
 1O8  H9   H  HCR6   0   0.253  -5.4751   1.6049   2.5465
 1O8  H10  H  HCR6   0   0.247  -3.8776  -0.2272   2.3551
 1O8  H11  H  H      0   0.248  -2.0518  -1.0985   2.3526
 1O8  H12  H  HCH3   0   0.242  -2.1128  -4.1475   1.4430
 1O8  H13  H  HCH3   0   0.241  -0.5073  -4.5540   2.0650
 1O8  H14  H  HCH3   0   0.241  -1.6281  -3.5897   3.0310
 1O8  H15  H  H      0   0.233   1.1679  -3.3189   1.0550
 1O8  H16  H  H      0   0.249   0.6349  -0.3177   0.4905
 1O8  H17  H  H      0   0.232   2.9804  -2.2118  -0.0452
 1O8  H18  H  HCH3   0   0.230   2.1633   1.4499   0.4907
 1O8  H19  H  HCH3   0   0.271   3.1696   2.0074  -0.8589
 1O8  H20  H  HCH3   0   0.234   1.6236   1.2152  -1.1588
 1O8  H21  H  H      0   0.214   4.7916  -1.3698  -0.9443

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
 1O8  C19  C9   single    1.501  0.020  1.501
 1O8  C10  C9   double    1.345  0.020  1.345
 1O8  C10  C11  single    1.446  0.020  1.446
 1O8  C12  C11  double    1.346  0.020  1.346
 1O8  C12  C13  single    1.459  0.020  1.459
 1O8  C9   C8   single    1.472  0.020  1.472
 1O8  C14  C13  double    1.349  0.020  1.349
 1O8  C14  C15  single    1.509  0.020  1.509
 1O8  C13  C20  single    1.499  0.020  1.499
 1O8  O1   C15  deloc     1.249  0.020  1.249
 1O8  C15  O2   deloc     1.251  0.020  1.251
 1O8  C2'  C1'  single    1.524  0.020  1.524
 1O8  C2'  C7   single    1.502  0.020  1.502
 1O8  C8   C7   double    1.342  0.020  1.342
 1O8  C1'  C18  single    1.519  0.020  1.519
 1O8  C7   C6   single    1.483  0.020  1.483
 1O8  C18  C5   single    1.507  0.020  1.507
 1O8  C6   C5   aromatic  1.404  0.020  1.404
 1O8  C6   C1   aromatic  1.401  0.020  1.401
 1O8  C5   C4   aromatic  1.395  0.020  1.395
 1O8  C1   C2   aromatic  1.382  0.020  1.382
 1O8  C4   C3   aromatic  1.384  0.020  1.384
 1O8  C2   C3   aromatic  1.390  0.020  1.390
 1O8  C2'  H1   single    0.970  0.020  1.090
 1O8  C2'  H2   single    0.970  0.020  1.090
 1O8  C1'  H3   single    0.970  0.020  1.090
 1O8  C1'  H4   single    0.970  0.020  1.090
 1O8  C18  H5   single    0.970  0.020  1.090
 1O8  C18  H6   single    0.970  0.020  1.090
 1O8  C4   H7   single    0.930  0.020  1.080
 1O8  C3   H8   single    0.930  0.020  1.080
 1O8  C2   H9   single    0.930  0.020  1.080
 1O8  C1   H10  single    0.930  0.020  1.080
 1O8  C8   H11  single    0.930  0.020  1.080
 1O8  C19  H12  single    0.970  0.020  1.090
 1O8  C19  H13  single    0.970  0.020  1.090
 1O8  C19  H14  single    0.970  0.020  1.090
 1O8  C10  H15  single    0.930  0.020  1.080
 1O8  C11  H16  single    0.930  0.020  1.080
 1O8  C12  H17  single    0.930  0.020  1.080
 1O8  C20  H18  single    0.970  0.020  1.090
 1O8  C20  H19  single    0.970  0.020  1.090
 1O8  C20  H20  single    0.970  0.020  1.090
 1O8  C14  H21  single    0.930  0.020  1.080

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
 1O8  H2   C2'  H1   106.94  3.000
 1O8  H2   C2'  C7   111.34  3.000
 1O8  H1   C2'  C7   109.03  3.000
 1O8  H2   C2'  C1'  111.06  3.000
 1O8  H1   C2'  C1'  108.74  3.000
 1O8  C7   C2'  C1'  109.64  3.000
 1O8  H4   C1'  H3   106.74  3.000
 1O8  H4   C1'  C18  110.01  3.000
 1O8  H3   C1'  C18  110.18  3.000
 1O8  H4   C1'  C2'  110.55  3.000
 1O8  H3   C1'  C2'  109.54  3.000
 1O8  C18  C1'  C2'  109.77  3.000
 1O8  H6   C18  H5   105.97  3.000
 1O8  H6   C18  C5   108.14  3.000
 1O8  H5   C18  C5   109.70  3.000
 1O8  H6   C18  C1'  108.72  3.000
 1O8  H5   C18  C1'  110.79  3.000
 1O8  C5   C18  C1'  113.22  3.000
 1O8  C6   C5   C4   119.24  3.000
 1O8  C4   C5   C18  118.68  3.000
 1O8  C6   C5   C18  122.06  3.000
 1O8  H7   C4   C3   119.48  3.000
 1O8  H7   C4   C5   118.90  3.000
 1O8  C3   C4   C5   121.62  3.000
 1O8  H8   C3   C2   120.49  3.000
 1O8  H8   C3   C4   120.18  3.000
 1O8  C2   C3   C4   119.33  3.000
 1O8  H9   C2   C1   119.86  3.000
 1O8  H9   C2   C3   120.45  3.000
 1O8  C1   C2   C3   119.68  3.000
 1O8  H10  C1   C6   119.78  3.000
 1O8  H10  C1   C2   118.53  3.000
 1O8  C6   C1   C2   121.67  3.000
 1O8  C7   C6   C1   121.59  3.000
 1O8  C1   C6   C5   118.43  3.000
 1O8  C7   C6   C5   119.98  3.000
 1O8  C8   C7   C6   121.76  3.000
 1O8  C6   C7   C2'  114.74  3.000
 1O8  C8   C7   C2'  123.49  3.000
 1O8  H11  C8   C9   113.84  3.000
 1O8  H11  C8   C7   118.74  3.000
 1O8  C9   C8   C7   127.29  3.000
 1O8  C10  C9   C19  121.25  3.000
 1O8  C10  C9   C8   124.13  3.000
 1O8  C19  C9   C8   114.57  3.000
 1O8  H14  C19  H13  108.01  3.000
 1O8  H14  C19  H12  106.52  3.000
 1O8  H13  C19  H12  108.35  3.000
 1O8  H14  C19  C9   110.97  3.000
 1O8  H13  C19  C9   111.94  3.000
 1O8  H12  C19  C9   110.85  3.000
 1O8  H15  C10  C11  116.06  3.000
 1O8  H15  C10  C9   117.89  3.000
 1O8  C11  C10  C9   126.04  3.000
 1O8  H16  C11  C12  120.24  3.000
 1O8  H16  C11  C10  117.13  3.000
 1O8  C12  C11  C10  122.62  3.000
 1O8  H17  C12  C13  115.70  3.000
 1O8  H17  C12  C11  117.98  3.000
 1O8  C13  C12  C11  126.31  3.000
 1O8  C14  C13  C20  125.22  3.000
 1O8  C20  C13  C12  117.48  3.000
 1O8  C14  C13  C12  117.29  3.000
 1O8  H20  C20  H19  108.20  3.000
 1O8  H20  C20  H18  106.57  3.000
 1O8  H19  C20  H18  109.23  3.000
 1O8  H20  C20  C13  110.58  3.000
 1O8  H19  C20  C13  111.44  3.000
 1O8  H18  C20  C13  110.67  3.000
 1O8  H21  C14  C15  113.64  3.000
 1O8  H21  C14  C13  116.03  3.000
 1O8  C15  C14  C13  130.31  3.000
 1O8  O2   C15  O1   125.89  3.000
 1O8  O2   C15  C14  114.23  3.000
 1O8  O1   C15  C14  119.88  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
 1O8  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 1O8  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 1O8  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 1O8  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 1O8  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 1O8  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 1O8  CONST_07  H7   C4   C5   C18     0.00   0.0  0
 1O8  CONST_08  H10  C1   C6   C5    180.00   0.0  0
 1O8  CONST_09  H8   C3   C4   C5    180.00   0.0  0
 1O8  CONST_10  H9   C2   C3   C4    180.00   0.0  0
 1O8  Var_01    C5   C18  C1'  C2'    46.08  30.0  1
 1O8  Var_02    C5   C6   C7   C2'   -19.75  30.0  1
 1O8  Var_03    C6   C7   C2'  C1'    49.62  30.0  1
 1O8  Var_04    C6   C5   C18  C1'   -16.64  30.0  1
 1O8  Var_05    C7   C2'  C1'  C18   -63.04  30.0  1
 1O8  Var_06    C9   C8   C7   C2'    -3.03  30.0  2
 1O8  Var_07    C19  C9   C8   C7   -117.03  30.0  3
 1O8  Var_08    C11  C10  C9   C8      1.42   0.0  2
 1O8  Var_09    C13  C12  C11  C10  -179.03   0.0  2
 1O8  Var_10    C15  C14  C13  C12  -179.05   0.0  2
 1O8  Var_11    C12  C11  C10  C9   -175.27  30.0  2
 1O8  Var_12    C14  C13  C12  C11  -179.16  30.0  2
 1O8  Var_13    O1   C15  C14  C13   -14.72  30.0  2
 1O8  Var_14    H12  C19  C9   C8     61.73  30.0  3
 1O8  Var_15    H18  C20  C13  C12    53.79  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
 1O8  plan-1  C14  0.020
 1O8  plan-1  C15  0.020
 1O8  plan-1  O1   0.020
 1O8  plan-1  O2   0.020
 1O8  plan-2  C18  0.020
 1O8  plan-2  C5   0.020
 1O8  plan-2  C4   0.020
 1O8  plan-2  C3   0.020
 1O8  plan-2  C2   0.020
 1O8  plan-2  C1   0.020
 1O8  plan-2  C6   0.020
 1O8  plan-2  C7   0.020
 1O8  plan-2  H7   0.020
 1O8  plan-2  H8   0.020
 1O8  plan-2  H9   0.020
 1O8  plan-2  H10  0.020
 1O8  plan-3  C8   0.020
 1O8  plan-3  C9   0.020
 1O8  plan-3  C19  0.020
 1O8  plan-3  C10  0.020
 1O8  plan-3  C11  0.020
 1O8  plan-3  H15  0.020
 1O8  plan-4  C10  0.020
 1O8  plan-4  C11  0.020
 1O8  plan-4  C12  0.020
 1O8  plan-4  C13  0.020
 1O8  plan-4  H16  0.020
 1O8  plan-4  H17  0.020
 1O8  plan-5  C12  0.020
 1O8  plan-5  C13  0.020
 1O8  plan-5  C20  0.020
 1O8  plan-5  C14  0.020
 1O8  plan-5  C15  0.020
 1O8  plan-5  H21  0.020

