# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:32:29 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  46  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   0.325  -5.9387  -0.9700   0.2940
 R12  C2   C  CR6    0  -0.072  -5.6865   0.3908   0.4823
 R12  C3   C  CR6    0   0.040  -4.4051   0.8767   0.1889
 R12  C4   C  CR6    0   0.033  -3.3940   0.0318  -0.3015
 R12  C5   C  CR6    0   0.067  -3.6788  -1.3311  -0.5049
 R12  C6   C  CR16   0  -0.398  -4.9443  -1.8057  -0.1997
 R12  C7   C  C1     0  -0.358  -2.0761   0.5982  -0.6327
 R12  C8   C  C1     0  -0.250  -0.8966   0.0896  -0.2451
 R12  C9   C  C      0   0.117   0.4090   0.6350  -0.5792
 R12  C10  C  C1     0  -0.303   1.5053   0.0005  -0.0993
 R12  C11  C  C1     0  -0.254   2.8833   0.3674  -0.3004
 R12  C12  C  C1     0  -0.285   3.9051  -0.3479   0.2116
 R12  C13  C  C      0   0.172   5.3219  -0.0431   0.0590
 R12  C14  C  C1     0  -0.486   6.2025  -0.8886   0.6346
 R12  C15  C  C      0   0.395   7.7122  -0.8662   0.6574
 R12  C18  C  CH3    0  -0.775   5.6815   1.1805  -0.7302
 R12  C19  C  CH3    0  -0.763   0.4620   1.8627  -1.4369
 R12  C20  C  CH3    0  -0.747  -2.6805  -2.3051  -1.0682
 R12  C23  C  CH3    0  -0.749  -4.1356   2.3347   0.4455
 R12  O1   O  OH1    0  -0.636  -7.1275  -1.5571   0.5573
 R12  O2   O  O      0  -0.591   8.3315   0.0639   0.0997
 R12  O3   O  OC    -1  -0.617   8.2308  -1.8303   1.2619
 R12  H2   H  HCR6   0   0.248  -5.1770  -2.8528  -0.3579
 R12  H3   H  H      0   0.257  -2.0814   1.5027  -1.2334
 R12  H4   H  H      0   0.236  -0.8903  -0.7951   0.3849
 R12  H5   H  H      0   0.238   1.3415  -0.8862   0.5086
 R12  H6   H  H      0   0.252   3.0985   1.2544  -0.8849
 R12  H7   H  H      0   0.236   3.6672  -1.2362   0.7920
 R12  H8   H  H      0   0.214   5.7741  -1.7346   1.1668
 R12  H9   H  HCH3   0   0.230   5.1826   2.0627  -0.3236
 R12  H10  H  HCH3   0   0.274   6.7514   1.3479  -0.7275
 R12  H11  H  HCH3   0   0.233   5.3461   1.0815  -1.7654
 R12  H12  H  HCH3   0   0.245  -0.0992   2.6824  -0.9833
 R12  H13  H  HCH3   0   0.256   1.4744   2.2180  -1.6091
 R12  H14  H  HCH3   0   0.247   0.0085   1.6736  -2.4123
 R12  H15  H  HCH3   0   0.244  -2.0409  -2.7270  -0.2906
 R12  H16  H  HCH3   0   0.247  -3.1928  -3.1400  -1.5450
 R12  H17  H  HCH3   0   0.246  -2.0232  -1.8427  -1.8030
 R12  H18  H  HCH3   0   0.248  -4.3956   2.6060   1.4705
 R12  H19  H  HCH3   0   0.253  -3.0929   2.6046   0.3030
 R12  H20  H  HCH3   0   0.248  -4.7356   2.9746  -0.2056
 R12  H21  H  HOH1   0   0.468  -7.7536  -0.9260   0.9246
 R12  C16  C  CH3    0  -0.734  -6.7373   1.3398   0.9926
 R12  H1   H  HCH3   0   0.256  -6.4711   1.7419   1.9720
 R12  H23  H  HCH3   0   0.256  -6.8569   2.1907   0.3210
 R12  H24  H  HCH3   0   0.236  -7.7280   0.8986   1.0980

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  deloc     1.249  0.020  1.249
 R12  C15  O3   deloc     1.251  0.020  1.251
 R12  C15  C14  single    1.510  0.020  1.510
 R12  C14  C13  double    1.350  0.020  1.350
 R12  C13  C18  single    1.500  0.020  1.500
 R12  C13  C12  single    1.457  0.020  1.457
 R12  C12  C11  double    1.348  0.020  1.348
 R12  C11  C10  single    1.440  0.020  1.440
 R12  C10  C9   double    1.355  0.020  1.355
 R12  C9   C19  single    1.499  0.020  1.499
 R12  C9   C8   single    1.454  0.020  1.454
 R12  C8   C7   double    1.342  0.020  1.342
 R12  C7   C4   single    1.472  0.020  1.472
 R12  C20  C5   single    1.504  0.020  1.504
 R12  C4   C5   aromatic  1.407  0.020  1.407
 R12  C4   C3   aromatic  1.406  0.020  1.406
 R12  C5   C6   aromatic  1.386  0.020  1.386
 R12  C23  C3   single    1.505  0.020  1.505
 R12  C3   C2   aromatic  1.401  0.020  1.401
 R12  C6   C1   aromatic  1.390  0.020  1.390
 R12  C2   C1   aromatic  1.397  0.020  1.397
 R12  C1   O1   single    1.352  0.020  1.352
 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  C2   C16  single    1.505  0.020  1.505
 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   115.94  3.000
 R12  O1   C1   C2   123.76  3.000
 R12  C6   C1   C2   120.30  3.000
 R12  C16  C2   C3   119.39  3.000
 R12  C16  C2   C1   122.27  3.000
 R12  C3   C2   C1   118.34  3.000
 R12  C23  C3   C4   120.86  3.000
 R12  C23  C3   C2   117.65  3.000
 R12  C4   C3   C2   121.48  3.000
 R12  C7   C4   C5   121.42  3.000
 R12  C5   C4   C3   119.14  3.000
 R12  C7   C4   C3   119.41  3.000
 R12  C20  C5   C6   117.83  3.000
 R12  C6   C5   C4   119.00  3.000
 R12  C20  C5   C4   123.16  3.000
 R12  H2   C6   C5   119.65  3.000
 R12  H2   C6   C1   118.62  3.000
 R12  C5   C6   C1   121.73  3.000
 R12  H3   C7   C8   118.67  3.000
 R12  H3   C7   C4   116.15  3.000
 R12  C8   C7   C4   125.18  3.000
 R12  H4   C8   C9   115.70  3.000
 R12  H4   C8   C7   118.78  3.000
 R12  C9   C8   C7   125.52  3.000
 R12  C19  C9   C10  123.91  3.000
 R12  C19  C9   C8   118.07  3.000
 R12  C10  C9   C8   118.02  3.000
 R12  H5   C10  C11  115.46  3.000
 R12  H5   C10  C9   117.26  3.000
 R12  C11  C10  C9   127.27  3.000
 R12  H6   C11  C12  119.25  3.000
 R12  H6   C11  C10  118.28  3.000
 R12  C12  C11  C10  122.47  3.000
 R12  H7   C12  C13  116.07  3.000
 R12  H7   C12  C11  118.05  3.000
 R12  C13  C12  C11  125.87  3.000
 R12  C18  C13  C14  125.39  3.000
 R12  C18  C13  C12  117.32  3.000
 R12  C14  C13  C12  117.30  3.000
 R12  H8   C14  C15  113.45  3.000
 R12  H8   C14  C13  116.05  3.000
 R12  C15  C14  C13  130.50  3.000
 R12  O3   C15  O2   125.76  3.000
 R12  O3   C15  C14  114.23  3.000
 R12  O2   C15  C14  120.01  3.000
 R12  H11  C18  H10  108.64  3.000
 R12  H11  C18  H9   106.60  3.000
 R12  H10  C18  H9   109.00  3.000
 R12  H11  C18  C13  110.55  3.000
 R12  H10  C18  C13  111.20  3.000
 R12  H9   C18  C13  110.71  3.000
 R12  H14  C19  H13  107.57  3.000
 R12  H14  C19  H12  106.71  3.000
 R12  H13  C19  H12  107.41  3.000
 R12  H14  C19  C9   110.77  3.000
 R12  H13  C19  C9   113.05  3.000
 R12  H12  C19  C9   111.04  3.000
 R12  H17  C20  H16  108.29  3.000
 R12  H17  C20  H15  106.93  3.000
 R12  H16  C20  H15  106.92  3.000
 R12  H17  C20  C5   112.23  3.000
 R12  H16  C20  C5   110.36  3.000
 R12  H15  C20  C5   111.86  3.000
 R12  H20  C23  H19  107.67  3.000
 R12  H20  C23  H18  106.45  3.000
 R12  H19  C23  H18  106.86  3.000
 R12  H20  C23  C3   111.57  3.000
 R12  H19  C23  C3   112.97  3.000
 R12  H18  C23  C3   110.99  3.000
 R12  H21  O1   C1   111.21  3.000
 R12  H24  C16  H23  106.01  3.000
 R12  H24  C16  H1   106.50  3.000
 R12  H23  C16  H1   106.97  3.000
 R12  H24  C16  C2   114.35  3.000
 R12  H23  C16  C2   111.08  3.000
 R12  H1   C16  C2   111.48  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  Var_01    C8   C7   C4   C3    131.99  30.0  2
 R12  Var_02    H1   C16  C2   C1    114.66  30.0  2
 R12  Var_03    H18  C23  C3   C2     53.29  30.0  2
 R12  Var_04    H15  C20  C5   C4     86.25  30.0  2
 R12  Var_05    C9   C8   C7   C4    179.33   0.0  2
 R12  Var_06    C11  C10  C9   C8   -179.74   0.0  2
 R12  Var_07    C13  C12  C11  C10  -179.77   0.0  2
 R12  Var_08    C15  C14  C13  C12   179.56   0.0  2
 R12  Var_09    C10  C9   C8   C7    179.68  30.0  2
 R12  Var_10    C12  C11  C10  C9   -179.13  30.0  1
 R12  Var_11    C14  C13  C12  C11  -179.29  30.0  2
 R12  Var_12    O2   C15  C14  C13     1.59  30.0  2
 R12  Var_13    H12  C19  C9   C8     57.34  30.0  3
 R12  Var_14    H9   C18  C13  C12    55.02  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-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

