# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:21:14 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2E,4E,6E)-3-methyl-7-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/C=C(C)/c1ccc2c(c1)C(C)(C)CCC2(C)C)=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
 R13  R13  '(2E,4E,6E)-3-methyl-7-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid'  ligand  54  25  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R13
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
 R13  C1    C  CT     0  -0.172   1.5870  -0.3787  -4.3092
 R13  C2    C  CH2    0  -0.424   0.9013  -0.9245  -5.5656
 R13  C3    C  CH2    0  -0.423  -0.3397  -0.1390  -5.9341
 R13  C4    C  CT     0  -0.169  -1.4282  -0.2315  -4.8614
 R13  C5    C  CR6    0   0.109  -0.8219  -0.0237  -3.4802
 R13  C6    C  CR16   0  -0.288  -1.6755   0.2171  -2.3979
 R13  C7    C  CR16   0  -0.335  -1.2092   0.4315  -1.1183
 R13  C8    C  CR6    0   0.119   0.1648   0.4206  -0.8550
 R13  C9    C  CR16   0  -0.386   1.0112   0.1808  -1.9332
 R13  C10   C  CR6    0   0.171   0.5543  -0.0746  -3.2286
 R13  C11   C  C      0   0.049   0.7065   0.6507   0.4986
 R13  C12   C  C1     0  -0.289  -0.0231   0.3111   1.5823
 R13  C13   C  C1     0  -0.247   0.3479   0.4656   2.9682
 R13  C14   C  C1     0  -0.290  -0.4406   0.0361   3.9730
 R13  C15   C  C      0   0.170  -0.1540   0.1494   5.3976
 R13  C16   C  C1     0  -0.482  -1.0661  -0.3546   6.2542
 R13  C17   C  C      0   0.393  -1.0606  -0.4136   7.7624
 R13  C18   C  CH3    0  -0.636  -2.1070  -1.6082  -4.9098
 R13  C19   C  CH3    0  -0.646  -2.4745   0.8454  -5.1726
 R13  C20   C  CH3    0  -0.636   2.3588   0.9046  -4.6462
 R13  C21   C  CH3    0  -0.643   2.5835  -1.4425  -3.8314
 R13  C22   C  CH3    0  -0.760   2.0924   1.2218   0.5900
 R13  C23   C  CH3    0  -0.771   1.1381   0.8008   5.7923
 R13  O1    O  O      0  -0.593  -0.2418   0.2722   8.4091
 R13  O2    O  OC    -1  -0.618  -1.9246  -1.1759   8.2485
 R13  H21   H  HCH2   0   0.232   1.6186  -0.9170  -6.3914
 R13  H22   H  HCH2   0   0.226   0.6382  -1.9752  -5.4068
 R13  H31   H  HCH2   0   0.226  -0.0769   0.9124  -6.0891
 R13  H32   H  HCH2   0   0.231  -0.7474  -0.4921  -6.8856
 R13  H6    H  HCR6   0   0.241  -2.7455   0.2497  -2.5600
 R13  H7    H  HCR6   0   0.243  -1.9201   0.6384  -0.3278
 R13  H9    H  HCR6   0   0.237   2.0796   0.1742  -1.7598
 R13  H12   H  H      0   0.238  -0.9903  -0.1543   1.4176
 R13  H13   H  H      0   0.250   1.2941   0.9390   3.2031
 R13  H14   H  H      0   0.235  -1.3824  -0.4413   3.7126
 R13  H16   H  H      0   0.216  -1.9412  -0.8177   5.8044
 R13  H181  H  HCH3   0   0.230  -2.8927  -1.6887  -4.1563
 R13  H182  H  HCH3   0   0.224  -2.5655  -1.7724  -5.8880
 R13  H183  H  HCH3   0   0.229  -1.3999  -2.4200  -4.7320
 R13  H191  H  HCH3   0   0.229  -3.3417   0.8038  -4.5126
 R13  H192  H  HCH3   0   0.228  -2.0431   1.8455  -5.0991
 R13  H193  H  HCH3   0   0.229  -2.8419   0.7173  -6.1933
 R13  H201  H  HCH3   0   0.229   2.8503   1.3166  -3.7635
 R13  H202  H  HCH3   0   0.225   3.1313   0.6981  -5.3902
 R13  H203  H  HCH3   0   0.230   1.7080   1.6814  -5.0510
 R13  H211  H  HCH3   0   0.228   3.1902  -1.1098  -2.9891
 R13  H212  H  HCH3   0   0.228   2.0678  -2.3580  -3.5358
 R13  H213  H  HCH3   0   0.228   3.2691  -1.6928  -4.6442
 R13  H221  H  HCH3   0   0.258   2.3166   1.6156   1.5784
 R13  H222  H  HCH3   0   0.248   2.8484   0.4628   0.3724
 R13  H223  H  HCH3   0   0.246   2.2353   2.0281  -0.1301
 R13  H231  H  HCH3   0   0.271   1.2818   0.7747   6.8657
 R13  H232  H  HCH3   0   0.230   1.9825   0.3074   5.3066
 R13  H233  H  HCH3   0   0.233   1.1591   1.8439   5.4674

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
 R13  C1   C2    single    1.532  0.020  1.532
 R13  C1   C10   single    1.525  0.020  1.525
 R13  C1   C20   single    1.535  0.020  1.535
 R13  C1   C21   single    1.534  0.020  1.534
 R13  C2   C3    single    1.514  0.020  1.514
 R13  C2   H21   single    0.970  0.020  1.090
 R13  C2   H22   single    0.970  0.020  1.090
 R13  C3   C4    single    1.531  0.020  1.531
 R13  C3   H31   single    0.970  0.020  1.090
 R13  C3   H32   single    0.970  0.020  1.090
 R13  C4   C5    single    1.523  0.020  1.523
 R13  C4   C18   single    1.536  0.020  1.536
 R13  C4   C19   single    1.533  0.020  1.533
 R13  C5   C6    aromatic  1.399  0.020  1.399
 R13  C5   C10   aromatic  1.400  0.020  1.400
 R13  C6   C7    aromatic  1.379  0.020  1.379
 R13  C6   H6    single    0.930  0.020  1.080
 R13  C7   C8    aromatic  1.399  0.020  1.399
 R13  C7   H7    single    0.930  0.020  1.080
 R13  C8   C9    aromatic  1.392  0.020  1.392
 R13  C8   C11   single    1.476  0.020  1.476
 R13  C9   C10   aromatic  1.397  0.020  1.397
 R13  C9   H9    single    0.930  0.020  1.080
 R13  C11  C12   double    1.350  0.020  1.350
 R13  C11  C22   single    1.502  0.020  1.502
 R13  C12  C13   single    1.443  0.020  1.443
 R13  C12  H12   single    0.930  0.020  1.080
 R13  C13  C14   double    1.348  0.020  1.348
 R13  C13  H13   single    0.930  0.020  1.080
 R13  C14  C15   single    1.458  0.020  1.458
 R13  C14  H14   single    0.930  0.020  1.080
 R13  C15  C16   double    1.349  0.020  1.349
 R13  C15  C23   single    1.500  0.020  1.500
 R13  C16  C17   single    1.509  0.020  1.509
 R13  C16  H16   single    0.930  0.020  1.080
 R13  C17  O1    deloc     1.249  0.020  1.249
 R13  C17  O2    deloc     1.251  0.020  1.251
 R13  C18  H181  single    0.970  0.020  1.090
 R13  C18  H182  single    0.970  0.020  1.090
 R13  C18  H183  single    0.970  0.020  1.090
 R13  C19  H191  single    0.970  0.020  1.090
 R13  C19  H192  single    0.970  0.020  1.090
 R13  C19  H193  single    0.970  0.020  1.090
 R13  C20  H201  single    0.970  0.020  1.090
 R13  C20  H202  single    0.970  0.020  1.090
 R13  C20  H203  single    0.970  0.020  1.090
 R13  C21  H211  single    0.970  0.020  1.090
 R13  C21  H212  single    0.970  0.020  1.090
 R13  C21  H213  single    0.970  0.020  1.090
 R13  C22  H221  single    0.970  0.020  1.090
 R13  C22  H222  single    0.970  0.020  1.090
 R13  C22  H223  single    0.970  0.020  1.090
 R13  C23  H231  single    0.970  0.020  1.090
 R13  C23  H232  single    0.970  0.020  1.090
 R13  C23  H233  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
 R13  C21   C1   C20   108.76  3.000
 R13  C21   C1   C10   110.94  3.000
 R13  C20   C1   C10   109.22  3.000
 R13  C21   C1   C2    107.41  3.000
 R13  C20   C1   C2    110.05  3.000
 R13  C10   C1   C2    110.43  3.000
 R13  H22   C2   H21   105.89  3.000
 R13  H22   C2   C3    109.64  3.000
 R13  H21   C2   C3    110.50  3.000
 R13  H22   C2   C1    109.30  3.000
 R13  H21   C2   C1    108.86  3.000
 R13  C3    C2   C1    112.43  3.000
 R13  H32   C3   H31   106.04  3.000
 R13  H32   C3   C4    108.97  3.000
 R13  H31   C3   C4    109.14  3.000
 R13  H32   C3   C2    110.47  3.000
 R13  H31   C3   C2    109.63  3.000
 R13  C4    C3   C2    112.38  3.000
 R13  C19   C4   C18   108.76  3.000
 R13  C19   C4   C5    111.10  3.000
 R13  C18   C4   C5    109.08  3.000
 R13  C19   C4   C3    107.48  3.000
 R13  C18   C4   C3    110.26  3.000
 R13  C5    C4   C3    110.13  3.000
 R13  C10   C5   C6    117.84  3.000
 R13  C10   C5   C4    123.33  3.000
 R13  C6    C5   C4    118.83  3.000
 R13  H6    C6   C7    117.94  3.000
 R13  H6    C6   C5    119.49  3.000
 R13  C7    C6   C5    122.57  3.000
 R13  H7    C7   C8    120.58  3.000
 R13  H7    C7   C6    119.02  3.000
 R13  C8    C7   C6    120.38  3.000
 R13  C11   C8   C9    120.94  3.000
 R13  C11   C8   C7    122.13  3.000
 R13  C9    C8   C7    116.93  3.000
 R13  H9    C9   C10   118.05  3.000
 R13  H9    C9   C8    118.51  3.000
 R13  C10   C9   C8    123.43  3.000
 R13  C9    C10  C5    118.78  3.000
 R13  C9    C10  C1    118.15  3.000
 R13  C5    C10  C1    123.06  3.000
 R13  C22   C11  C12   123.06  3.000
 R13  C22   C11  C8    116.99  3.000
 R13  C12   C11  C8    119.91  3.000
 R13  H12   C12  C13   114.87  3.000
 R13  H12   C12  C11   117.87  3.000
 R13  C13   C12  C11   127.24  3.000
 R13  H13   C13  C14   119.24  3.000
 R13  H13   C13  C12   118.64  3.000
 R13  C14   C13  C12   122.11  3.000
 R13  H14   C14  C15   116.01  3.000
 R13  H14   C14  C13   117.91  3.000
 R13  C15   C14  C13   126.08  3.000
 R13  C23   C15  C16   125.28  3.000
 R13  C23   C15  C14   117.41  3.000
 R13  C16   C15  C14   117.30  3.000
 R13  H16   C16  C17   113.55  3.000
 R13  H16   C16  C15   116.14  3.000
 R13  C17   C16  C15   130.29  3.000
 R13  O2    C17  O1    125.91  3.000
 R13  O2    C17  C16   114.19  3.000
 R13  O1    C17  C16   119.90  3.000
 R13  H183  C18  H182  107.82  3.000
 R13  H183  C18  H181  107.40  3.000
 R13  H182  C18  H181  107.74  3.000
 R13  H183  C18  C4    112.05  3.000
 R13  H182  C18  C4    110.39  3.000
 R13  H181  C18  C4    111.25  3.000
 R13  H193  C19  H192  107.65  3.000
 R13  H193  C19  H191  107.08  3.000
 R13  H192  C19  H191  107.96  3.000
 R13  H193  C19  C4    109.68  3.000
 R13  H192  C19  C4    111.11  3.000
 R13  H191  C19  C4    113.13  3.000
 R13  H203  C20  H202  107.67  3.000
 R13  H203  C20  H201  107.46  3.000
 R13  H202  C20  H201  107.69  3.000
 R13  H203  C20  C1    112.13  3.000
 R13  H202  C20  C1    110.31  3.000
 R13  H201  C20  C1    111.38  3.000
 R13  H213  C21  H212  107.81  3.000
 R13  H213  C21  H211  107.19  3.000
 R13  H212  C21  H211  108.04  3.000
 R13  H213  C21  C1    109.56  3.000
 R13  H212  C21  C1    111.05  3.000
 R13  H211  C21  C1    112.99  3.000
 R13  H223  C22  H222  106.94  3.000
 R13  H223  C22  H221  107.78  3.000
 R13  H222  C22  H221  106.85  3.000
 R13  H223  C22  C11   111.22  3.000
 R13  H222  C22  C11   111.23  3.000
 R13  H221  C22  C11   112.54  3.000
 R13  H233  C23  H232  106.51  3.000
 R13  H233  C23  H231  108.37  3.000
 R13  H232  C23  H231  109.10  3.000
 R13  H233  C23  C15   110.66  3.000
 R13  H232  C23  C15   110.66  3.000
 R13  H231  C23  C15   111.39  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
 R13  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 R13  CONST_02  C8    C9   C10  C5      0.00   0.0  0
 R13  CONST_03  C9    C10  C5   C6      0.00   0.0  0
 R13  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 R13  CONST_05  C10   C5   C6   C7      0.00   0.0  0
 R13  CONST_06  C10   C9   C8   C7      0.00   0.0  0
 R13  CONST_07  C11   C8   C7   C6    180.00   0.0  0
 R13  CONST_08  C11   C8   C9   C10   180.00   0.0  0
 R13  CONST_09  H9    C9   C10  C1      0.00   0.0  0
 R13  CONST_10  H6    C6   C5   C4      0.00   0.0  0
 R13  CONST_11  H7    C7   C6   C5    180.00   0.0  0
 R13  Var_01    C4    C3   C2   C1    -63.58  30.0  1
 R13  Var_02    C5    C10  C1   C2    -13.13  30.0  1
 R13  Var_03    C5    C4   C3   C2     45.60  30.0  1
 R13  Var_04    C10   C1   C2   C3     44.38  30.0  1
 R13  Var_05    C6    C5   C4   C3    166.33  30.0  1
 R13  Var_06    C12   C11  C8   C7     28.85  30.0  2
 R13  Var_07    H201  C20  C1   C2    179.58  30.0  3
 R13  Var_08    H211  C21  C1   C2    174.80  30.0  3
 R13  Var_09    H181  C18  C4   C3   -179.51  30.0  3
 R13  Var_10    H191  C19  C4   C3    174.89  30.0  3
 R13  Var_11    C13   C12  C11  C8   -179.92   0.0  2
 R13  Var_12    H221  C22  C11  C8    164.16  30.0  3
 R13  Var_13    C15   C14  C13  C12  -179.87   0.0  2
 R13  Var_14    C17   C16  C15  C14   179.04   0.0  2
 R13  Var_15    C14   C13  C12  C11  -177.07  30.0  2
 R13  Var_16    C16   C15  C14  C13  -179.38  30.0  2
 R13  Var_17    O1    C17  C16  C15    13.84  30.0  2
 R13  Var_18    H231  C23  C15  C14  -176.23  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
 R13  plan-1  C16  0.020
 R13  plan-1  C17  0.020
 R13  plan-1  O1   0.020
 R13  plan-1  O2   0.020
 R13  plan-2  C1   0.020
 R13  plan-2  C4   0.020
 R13  plan-2  C5   0.020
 R13  plan-2  C6   0.020
 R13  plan-2  C7   0.020
 R13  plan-2  C8   0.020
 R13  plan-2  C9   0.020
 R13  plan-2  C10  0.020
 R13  plan-2  C11  0.020
 R13  plan-2  H6   0.020
 R13  plan-2  H7   0.020
 R13  plan-2  H9   0.020
 R13  plan-3  C8   0.020
 R13  plan-3  C11  0.020
 R13  plan-3  C12  0.020
 R13  plan-3  C13  0.020
 R13  plan-3  C22  0.020
 R13  plan-3  H12  0.020
 R13  plan-4  C12  0.020
 R13  plan-4  C13  0.020
 R13  plan-4  C14  0.020
 R13  plan-4  C15  0.020
 R13  plan-4  H13  0.020
 R13  plan-4  H14  0.020
 R13  plan-5  C14  0.020
 R13  plan-5  C15  0.020
 R13  plan-5  C16  0.020
 R13  plan-5  C17  0.020
 R13  plan-5  C23  0.020
 R13  plan-5  H16  0.020

