# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 10:50:55 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E,4E,6E,8E)-9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C/C=C/C(C)=C/C(O)=O)\C=C\c1c(C)cc(O)c(C)c1C
#
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
 R12  R12  '(2E,4E,6E,8E)-9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid'  ligand  47  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R12
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
 R12  C1   C  CR6   0   0.330  -5.9166  -0.9631   0.3248
 R12  C2   C  CR6   0  -0.065  -5.6997   0.4152   0.4170
 R12  C3   C  CR6   0   0.043  -4.4151   0.9039   0.1614
 R12  C4   C  CR6   0   0.036  -3.3752   0.0414  -0.2414
 R12  C5   C  CR6   0   0.068  -3.6317  -1.3350  -0.3769
 R12  C6   C  CR16  0  -0.396  -4.8984  -1.8142  -0.0791
 R12  C7   C  C1    0  -0.344  -2.0630   0.6197  -0.5607
 R12  C8   C  C1    0  -0.259  -0.8737   0.1211  -0.1870
 R12  C9   C  C     0   0.132   0.4193   0.6888  -0.5286
 R12  C10  C  C1    0  -0.309   1.5274   0.0500  -0.0779
 R12  C11  C  C1    0  -0.230   2.8941   0.4309  -0.3040
 R12  C12  C  C1    0  -0.296   3.9344  -0.2901   0.1638
 R12  C13  C  C     0   0.205   5.3361   0.0337  -0.0349
 R12  C14  C  C1    0  -0.474   6.2396  -0.8372   0.4734
 R12  C15  C  C     0   0.523   7.6997  -0.7554   0.3950
 R12  C18  C  CH3   0  -0.773   5.6645   1.2854  -0.7883
 R12  C19  C  CH3   0  -0.764   0.4506   1.9323  -1.3627
 R12  C20  C  CH3   0  -0.752  -2.6056  -2.3239  -0.8584
 R12  C23  C  CH3   0  -0.765  -4.1419   2.3752   0.3425
 R12  O1   O  OH1   0  -0.631  -7.1083  -1.5358   0.6017
 R12  O2   O  O     0  -0.453   8.3696   0.1027  -0.1385
 R12  O3   O  OH1   0  -0.608   8.2575  -1.8011   1.0120
 R12  H2   H  HCR6  0   0.250  -5.1088  -2.8736  -0.1735
 R12  H3   H  H     0   0.263  -2.0788   1.5360  -1.1428
 R12  H4   H  H     0   0.241  -0.8469  -0.7708   0.4306
 R12  H5   H  H     0   0.245   1.3809  -0.8490   0.5150
 R12  H6   H  H     0   0.263   3.0876   1.3296  -0.8776
 R12  H7   H  H     0   0.249   3.7238  -1.1926   0.7304
 R12  H8   H  H     0   0.266   5.8598  -1.7087   0.9943
 R12  H9   H  HCH3  0   0.251   5.1318   2.1363  -0.3624
 R12  H10  H  HCH3  0   0.279   6.7234   1.5088  -0.7899
 R12  H11  H  HCH3  0   0.257   5.3351   1.1932  -1.8252
 R12  H12  H  HCH3  0   0.250  -0.1186   2.7337  -0.8879
 R12  H13  H  HCH3  0   0.259   1.4560   2.3055  -1.5368
 R12  H14  H  HCH3  0   0.253  -0.0085   1.7540  -2.3371
 R12  H15  H  HCH3  0   0.246  -1.9725  -2.6820  -0.0444
 R12  H16  H  HCH3  0   0.250  -3.0942  -3.1971  -1.2893
 R12  H17  H  HCH3  0   0.247  -1.9450  -1.8967  -1.6113
 R12  H18  H  HCH3  0   0.254  -4.6896   2.7814   1.1911
 R12  H19  H  HCH3  0   0.253  -3.0889   2.5758   0.5247
 R12  H20  H  HCH3  0   0.252  -4.4378   2.9522  -0.5374
 R12  H21  H  HOH1  0   0.478  -7.7374  -0.8873   0.9343
 R12  H22  H  HOH1  0   0.478   9.2215  -1.7380   0.9474
 R12  C16  C  CH3   0  -0.773  -6.8428   1.3207   0.7916
 R12  H1   H  HCH3  0   0.258  -7.0083   1.3536   1.8715
 R12  H23  H  HCH3  0   0.268  -6.6807   2.3423   0.4597
 R12  H24  H  HCH3  0   0.245  -7.7808   1.0078   0.3274

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
 R12  O2   C15  double    1.212  0.020  1.212
 R12  C15  O3   single    1.336  0.020  1.336
 R12  C15  C14  single    1.464  0.020  1.464
 R12  C14  C13  double    1.354  0.020  1.354
 R12  C13  C18  single    1.497  0.020  1.497
 R12  C13  C12  single    1.452  0.020  1.452
 R12  C12  C11  double    1.349  0.020  1.349
 R12  C11  C10  single    1.437  0.020  1.437
 R12  C10  C9   double    1.356  0.020  1.356
 R12  C9   C19  single    1.498  0.020  1.498
 R12  C9   C8   single    1.453  0.020  1.453
 R12  C8   C7   double    1.343  0.020  1.343
 R12  C7   C4   single    1.469  0.020  1.469
 R12  C20  C5   single    1.504  0.020  1.504
 R12  C4   C5   aromatic  1.407  0.020  1.407
 R12  C4   C3   aromatic  1.410  0.020  1.410
 R12  C5   C6   aromatic  1.387  0.020  1.387
 R12  C23  C3   single    1.507  0.020  1.507
 R12  C3   C2   aromatic  1.398  0.020  1.398
 R12  C6   C1   aromatic  1.387  0.020  1.387
 R12  C2   C1   aromatic  1.398  0.020  1.398
 R12  C1   O1   single    1.351  0.020  1.351
 R12  C6   H2   single    0.930  0.020  1.080
 R12  C7   H3   single    0.930  0.020  1.080
 R12  C8   H4   single    0.930  0.020  1.080
 R12  C10  H5   single    0.930  0.020  1.080
 R12  C11  H6   single    0.930  0.020  1.080
 R12  C12  H7   single    0.930  0.020  1.080
 R12  C14  H8   single    0.930  0.020  1.080
 R12  C18  H9   single    0.970  0.020  1.090
 R12  C18  H10  single    0.970  0.020  1.090
 R12  C18  H11  single    0.970  0.020  1.090
 R12  C19  H12  single    0.970  0.020  1.090
 R12  C19  H13  single    0.970  0.020  1.090
 R12  C19  H14  single    0.970  0.020  1.090
 R12  C20  H15  single    0.970  0.020  1.090
 R12  C20  H16  single    0.970  0.020  1.090
 R12  C20  H17  single    0.970  0.020  1.090
 R12  C23  H18  single    0.970  0.020  1.090
 R12  C23  H19  single    0.970  0.020  1.090
 R12  C23  H20  single    0.970  0.020  1.090
 R12  O1   H21  single    0.850  0.020  0.980
 R12  O3   H22  single    0.850  0.020  0.980
 R12  C2   C16  single    1.506  0.020  1.506
 R12  C16  H1   single    0.970  0.020  1.090
 R12  C16  H23  single    0.970  0.020  1.090
 R12  C16  H24  single    0.970  0.020  1.090

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
 R12  O1   C1   C6   116.56  3.000
 R12  O1   C1   C2   122.76  3.000
 R12  C6   C1   C2   120.68  3.000
 R12  C16  C2   C3   122.20  3.000
 R12  C16  C2   C1   119.44  3.000
 R12  C3   C2   C1   118.36  3.000
 R12  C23  C3   C4   119.85  3.000
 R12  C23  C3   C2   119.06  3.000
 R12  C4   C3   C2   121.08  3.000
 R12  C7   C4   C5   121.81  3.000
 R12  C5   C4   C3   119.45  3.000
 R12  C7   C4   C3   118.69  3.000
 R12  C20  C5   C6   117.69  3.000
 R12  C6   C5   C4   118.95  3.000
 R12  C20  C5   C4   123.35  3.000
 R12  H2   C6   C5   119.75  3.000
 R12  H2   C6   C1   118.84  3.000
 R12  C5   C6   C1   121.40  3.000
 R12  H3   C7   C8   118.39  3.000
 R12  H3   C7   C4   115.84  3.000
 R12  C8   C7   C4   125.77  3.000
 R12  H4   C8   C9   115.66  3.000
 R12  H4   C8   C7   119.05  3.000
 R12  C9   C8   C7   125.29  3.000
 R12  C19  C9   C10  124.00  3.000
 R12  C19  C9   C8   118.29  3.000
 R12  C10  C9   C8   117.71  3.000
 R12  H5   C10  C11  115.69  3.000
 R12  H5   C10  C9   117.44  3.000
 R12  C11  C10  C9   126.88  3.000
 R12  H6   C11  C12  119.28  3.000
 R12  H6   C11  C10  118.23  3.000
 R12  C12  C11  C10  122.49  3.000
 R12  H7   C12  C13  116.34  3.000
 R12  H7   C12  C11  118.38  3.000
 R12  C13  C12  C11  125.28  3.000
 R12  C18  C13  C14  125.47  3.000
 R12  C18  C13  C12  117.83  3.000
 R12  C14  C13  C12  116.70  3.000
 R12  H8   C14  C15  114.83  3.000
 R12  H8   C14  C13  117.63  3.000
 R12  C15  C14  C13  127.54  3.000
 R12  O3   C15  O2   121.76  3.000
 R12  O3   C15  C14  110.36  3.000
 R12  O2   C15  C14  127.88  3.000
 R12  H11  C18  H10  108.13  3.000
 R12  H11  C18  H9   106.83  3.000
 R12  H10  C18  H9   108.51  3.000
 R12  H11  C18  C13  109.94  3.000
 R12  H10  C18  C13  112.82  3.000
 R12  H9   C18  C13  110.40  3.000
 R12  H14  C19  H13  107.59  3.000
 R12  H14  C19  H12  106.78  3.000
 R12  H13  C19  H12  107.46  3.000
 R12  H14  C19  C9   110.65  3.000
 R12  H13  C19  C9   113.19  3.000
 R12  H12  C19  C9   110.88  3.000
 R12  H17  C20  H16  108.24  3.000
 R12  H17  C20  H15  107.00  3.000
 R12  H16  C20  H15  106.99  3.000
 R12  H17  C20  C5   112.16  3.000
 R12  H16  C20  C5   110.34  3.000
 R12  H15  C20  C5   111.88  3.000
 R12  H20  C23  H19  107.44  3.000
 R12  H20  C23  H18  107.11  3.000
 R12  H19  C23  H18  106.72  3.000
 R12  H20  C23  C3   111.69  3.000
 R12  H19  C23  C3   112.07  3.000
 R12  H18  C23  C3   111.51  3.000
 R12  H21  O1   C1   111.20  3.000
 R12  H22  O3   C15  109.50  3.000
 R12  H24  C16  H23  105.52  3.000
 R12  H24  C16  H1   107.36  3.000
 R12  H23  C16  H1   107.22  3.000
 R12  H24  C16  C2   111.96  3.000
 R12  H23  C16  C2   112.11  3.000
 R12  H1   C16  C2   112.27  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
 R12  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 R12  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 R12  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 R12  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 R12  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 R12  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 R12  CONST_07  C20  C5   C6   C1    180.00   0.0  0
 R12  CONST_08  C23  C3   C2   C1    180.00   0.0  0
 R12  CONST_09  C7   C4   C3   C2    180.00   0.0  0
 R12  CONST_10  C20  C5   C4   C3    180.00   0.0  0
 R12  CONST_11  O1   C1   C2   C3    180.00   0.0  0
 R12  CONST_12  C16  C2   C3   C4    180.00   0.0  0
 R12  CONST_13  C23  C3   C4   C5    180.00   0.0  0
 R12  CONST_14  O1   C1   C6   C5    180.00   0.0  0
 R12  CONST_15  C7   C4   C5   C6    180.00   0.0  0
 R12  CONST_16  C16  C2   C1   C6    180.00   0.0  0
 R12  CONST_17  H2   C6   C1   C2    180.00   0.0  0
 R12  CONST_18  H22  O3   C15  C14   180.00   0.0  0
 R12  Var_01    C8   C7   C4   C3    136.98  30.0  3
 R12  Var_02    H1   C16  C2   C1     81.81  30.0  2
 R12  Var_03    H18  C23  C3   C2     36.64  30.0  2
 R12  Var_04    H15  C20  C5   C4     85.45  30.0  2
 R12  Var_05    C9   C8   C7   C4    178.85   0.0  2
 R12  Var_06    C11  C10  C9   C8    179.59   0.0  2
 R12  Var_07    C13  C12  C11  C10   179.63   0.0  2
 R12  Var_08    C15  C14  C13  C12   179.06   0.0  2
 R12  Var_09    C10  C9   C8   C7   -179.41  30.0  3
 R12  Var_10    C12  C11  C10  C9   -178.47  30.0  1
 R12  Var_11    C14  C13  C12  C11  -177.82  30.0  2
 R12  Var_12    O2   C15  C14  C13    -0.09  30.0  3
 R12  Var_13    H12  C19  C9   C8     56.97  30.0  3
 R12  Var_14    H9   C18  C13  C12    51.71  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
 R12  plan-1  C1   0.020
 R12  plan-1  C2   0.020
 R12  plan-1  C3   0.020
 R12  plan-1  C4   0.020
 R12  plan-1  C5   0.020
 R12  plan-1  C6   0.020
 R12  plan-1  C7   0.020
 R12  plan-1  C20  0.020
 R12  plan-1  C23  0.020
 R12  plan-1  O1   0.020
 R12  plan-1  H2   0.020
 R12  plan-1  C16  0.020
 R12  plan-2  C14  0.020
 R12  plan-2  C15  0.020
 R12  plan-2  O2   0.020
 R12  plan-2  O3   0.020
 R12  plan-2  H22  0.020
 R12  plan-3  C12  0.020
 R12  plan-3  C13  0.020
 R12  plan-3  C14  0.020
 R12  plan-3  C15  0.020
 R12  plan-3  C18  0.020
 R12  plan-3  H8   0.020
 R12  plan-4  C10  0.020
 R12  plan-4  C11  0.020
 R12  plan-4  C12  0.020
 R12  plan-4  C13  0.020
 R12  plan-4  H6   0.020
 R12  plan-4  H7   0.020
 R12  plan-5  C8   0.020
 R12  plan-5  C9   0.020
 R12  plan-5  C10  0.020
 R12  plan-5  C11  0.020
 R12  plan-5  C19  0.020
 R12  plan-5  H5   0.020
 R12  plan-6  C4   0.020
 R12  plan-6  C7   0.020
 R12  plan-6  C8   0.020
 R12  plan-6  C9   0.020
 R12  plan-6  H3   0.020
 R12  plan-6  H4   0.020

