# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:56:40 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (2E,4E,6Z,8E)-3,7-dimethyl-8-[2-(3-methylbutyl)-3-(propan-2-yl)cyclohex-2-en-1-ylidene]octa-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC\1=C(CCCC\1=C\C(C)=C/C=C/C(C)=C/C(O)=O)C(C)C
#
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
 3T2  3T2  '(2E,4E,6Z,8E)-3,7-dimethyl-8-[2-(3-methylbutyl)-3-(propan-2-yl)cyclohex-2-en-1-ylidene]octa-2,4,6-trienoic acid'  ligand  62  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3T2
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
 3T2  C13  C  C1    0  -0.479   5.5801   1.2056  -0.6972
 3T2  C11  C  C1    0  -0.302   3.5775   0.0298  -1.2542
 3T2  C9   C  C1    0  -0.303   1.6465  -1.2691  -2.0036
 3T2  C8   C  C     0   0.132   0.3610  -1.7156  -1.9507
 3T2  C20  C  CH3   0  -0.785   3.5380   1.5417   0.7693
 3T2  O1   O  OH1   0  -0.610   7.7081   2.0695  -0.5980
 3T2  O2   O  O     0  -0.454   6.3021   2.7764   0.9782
 3T2  C1   C  C     0   0.100  -2.5941  -0.8351   0.3795
 3T2  C2   C  C     0   0.082  -3.8400  -1.2294   0.7357
 3T2  C3   C  CH2   0  -0.502  -4.3873  -2.5791   0.3735
 3T2  C4   C  CH2   0  -0.439  -3.2900  -3.5583   0.0201
 3T2  C5   C  CH2   0  -0.531  -2.3696  -2.9452  -1.0186
 3T2  C6   C  C     0   0.120  -1.7765  -1.6429  -0.5460
 3T2  C7   C  C1    0  -0.387  -0.5669  -1.1906  -0.9616
 3T2  C10  C  C1    0  -0.213   2.2937  -0.3595  -1.1006
 3T2  C12  C  C     0   0.211   4.2870   0.9491  -0.3844
 3T2  C14  C  C     0   0.521   6.5124   2.0918  -0.0003
 3T2  C4'  C  CH3   0  -0.668  -0.1804   2.9618   0.5016
 3T2  C3'  C  CH1   0  -0.227  -1.6997   2.9825   0.3607
 3T2  C5'  C  CH3   0  -0.652  -2.1311   4.0956  -0.5889
 3T2  C2'  C  CH2   0  -0.393  -2.2551   1.6384  -0.1131
 3T2  C6'  C  CH1   0  -0.330  -4.7618  -0.3674   1.5719
 3T2  C7'  C  CH3   0  -0.663  -6.2150  -0.4345   1.0983
 3T2  C8'  C  CH3   0  -0.657  -4.6525  -0.7565   3.0495
 3T2  C19  C  CH3   0  -0.769  -0.0675  -2.6989  -3.0055
 3T2  H1   H  H     0   0.263   5.9927   0.7038  -1.5650
 3T2  H2   H  H     0   0.244   4.1401  -0.3668  -2.0947
 3T2  H3   H  H     0   0.236   2.2708  -1.6452  -2.8091
 3T2  H4   H  HCH3  0   0.258   2.6990   2.1361   0.4014
 3T2  H5   H  HCH3  0   0.252   3.1159   0.7520   1.3929
 3T2  H6   H  HCH3  0   0.282   4.1555   2.1764   1.3917
 3T2  H7   H  HOH1  0   0.478   8.3127   2.6655  -0.1330
 3T2  H8   H  HCH2  0   0.247  -4.9830  -2.9616   1.2076
 3T2  H9   H  HCH2  0   0.243  -5.0887  -2.4824  -0.4645
 3T2  H10  H  HCH2  0   0.224  -2.7194  -3.8113   0.9185
 3T2  H11  H  HCH2  0   0.235  -3.7119  -4.4899  -0.3616
 3T2  H12  H  HCH2  0   0.252  -1.5844  -3.6541  -1.2686
 3T2  H13  H  HCH2  0   0.240  -2.9420  -2.7720  -1.9377
 3T2  H14  H  H     0   0.218  -0.2348  -0.2617  -0.5218
 3T2  H15  H  H     0   0.246   1.7322   0.0159  -0.2534
 3T2  H16  H  HCH3  0   0.231   0.1999   3.9400   0.8009
 3T2  H17  H  HCH3  0   0.227   0.1553   2.2429   1.2505
 3T2  H18  H  HCH3  0   0.210   0.2953   2.7019  -0.4488
 3T2  H19  H  HCH1  0   0.211  -2.1291   3.1941   1.3480
 3T2  H20  H  HCH3  0   0.212  -1.7561   3.9151  -1.5995
 3T2  H21  H  HCH3  0   0.223  -3.2186   4.1693  -0.6485
 3T2  H22  H  HCH3  0   0.224  -1.7492   5.0652  -0.2646
 3T2  H23  H  HCH2  0   0.223  -3.3312   1.7438  -0.2872
 3T2  H24  H  HCH2  0   0.217  -1.8159   1.3920  -1.0853
 3T2  H25  H  HCH2  0   0.251  -2.4946   0.7503   1.8247
 3T2  H26  H  HCH2  0   0.239  -0.9803   0.3749   1.1029
 3T2  H27  H  HCH1  0   0.235  -4.4595   0.6773   1.4782
 3T2  H28  H  HCH3  0   0.230  -6.8146   0.2885   1.6536
 3T2  H29  H  HCH3  0   0.238  -6.3028  -0.1942   0.0376
 3T2  H30  H  HCH3  0   0.228  -6.6584  -1.4178   1.2601
 3T2  H31  H  HCH3  0   0.236  -3.6352  -0.6219   3.4198
 3T2  H32  H  HCH3  0   0.235  -5.3183  -0.1437   3.6601
 3T2  H33  H  HCH3  0   0.229  -4.9283  -1.8012   3.2044
 3T2  H34  H  HCH3  0   0.257  -0.0758  -3.7232  -2.6298
 3T2  H35  H  HCH3  0   0.252  -1.0671  -2.4857  -3.3822
 3T2  H36  H  HCH3  0   0.262   0.6222  -2.6779  -3.8486
 3T2  C1'  C  CH2   0  -0.588  -2.0407   0.4852   0.8690

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
 3T2  C19  C8   single  1.504  0.020  1.504
 3T2  C9   C8   double  1.362  0.020  1.362
 3T2  C9   C10  single  1.436  0.020  1.436
 3T2  C8   C7   single  1.454  0.020  1.454
 3T2  C11  C10  double  1.350  0.020  1.350
 3T2  C11  C12  single  1.451  0.020  1.451
 3T2  C5   C4   single  1.517  0.020  1.517
 3T2  C5   C6   single  1.507  0.020  1.507
 3T2  C13  C12  double  1.355  0.020  1.355
 3T2  C13  C14  single  1.463  0.020  1.463
 3T2  C4   C3   single  1.513  0.020  1.513
 3T2  C12  C20  single  1.498  0.020  1.498
 3T2  C7   C6   double  1.357  0.020  1.357
 3T2  O2   C14  double  1.213  0.020  1.213
 3T2  C14  O1   single  1.337  0.020  1.337
 3T2  C6   C1   single  1.476  0.020  1.476
 3T2  C3   C2   single  1.501  0.020  1.501
 3T2  C1   C2   double  1.355  0.020  1.355
 3T2  C1   C1'  single  1.513  0.020  1.513
 3T2  C2   C6'  single  1.514  0.020  1.514
 3T2  C1'  C2'  single  1.530  0.020  1.530
 3T2  C8'  C6'  single  1.532  0.020  1.532
 3T2  C6'  C7'  single  1.530  0.020  1.530
 3T2  C2'  C3'  single  1.530  0.020  1.530
 3T2  C3'  C5'  single  1.525  0.020  1.525
 3T2  C3'  C4'  single  1.526  0.020  1.526
 3T2  C13  H1   single  0.930  0.020  1.080
 3T2  C11  H2   single  0.930  0.020  1.080
 3T2  C9   H3   single  0.930  0.020  1.080
 3T2  C20  H4   single  0.970  0.020  1.090
 3T2  C20  H5   single  0.970  0.020  1.090
 3T2  C20  H6   single  0.970  0.020  1.090
 3T2  O1   H7   single  0.850  0.020  0.980
 3T2  C3   H8   single  0.970  0.020  1.090
 3T2  C3   H9   single  0.970  0.020  1.090
 3T2  C4   H10  single  0.970  0.020  1.090
 3T2  C4   H11  single  0.970  0.020  1.090
 3T2  C5   H12  single  0.970  0.020  1.090
 3T2  C5   H13  single  0.970  0.020  1.090
 3T2  C7   H14  single  0.930  0.020  1.080
 3T2  C10  H15  single  0.930  0.020  1.080
 3T2  C4'  H16  single  0.970  0.020  1.090
 3T2  C4'  H17  single  0.970  0.020  1.090
 3T2  C4'  H18  single  0.970  0.020  1.090
 3T2  C3'  H19  single  0.970  0.020  1.090
 3T2  C5'  H20  single  0.970  0.020  1.090
 3T2  C5'  H21  single  0.970  0.020  1.090
 3T2  C5'  H22  single  0.970  0.020  1.090
 3T2  C2'  H23  single  0.970  0.020  1.090
 3T2  C2'  H24  single  0.970  0.020  1.090
 3T2  C1'  H25  single  0.970  0.020  1.090
 3T2  C1'  H26  single  0.970  0.020  1.090
 3T2  C6'  H27  single  0.970  0.020  1.090
 3T2  C7'  H28  single  0.970  0.020  1.090
 3T2  C7'  H29  single  0.970  0.020  1.090
 3T2  C7'  H30  single  0.970  0.020  1.090
 3T2  C8'  H31  single  0.970  0.020  1.090
 3T2  C8'  H32  single  0.970  0.020  1.090
 3T2  C8'  H33  single  0.970  0.020  1.090
 3T2  C19  H34  single  0.970  0.020  1.090
 3T2  C19  H35  single  0.970  0.020  1.090
 3T2  C19  H36  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
 3T2  H1   C13  C14  114.78  3.000
 3T2  H1   C13  C12  117.42  3.000
 3T2  C14  C13  C12  127.80  3.000
 3T2  H2   C11  C12  116.22  3.000
 3T2  H2   C11  C10  118.37  3.000
 3T2  C12  C11  C10  125.41  3.000
 3T2  H3   C9   C10  115.25  3.000
 3T2  H3   C9   C8   117.24  3.000
 3T2  C10  C9   C8   127.50  3.000
 3T2  C19  C8   C7   122.08  3.000
 3T2  C7   C8   C9   120.69  3.000
 3T2  C19  C8   C9   117.13  3.000
 3T2  H6   C20  H5   108.44  3.000
 3T2  H6   C20  H4   108.23  3.000
 3T2  H5   C20  H4   106.81  3.000
 3T2  H6   C20  C12  112.94  3.000
 3T2  H5   C20  C12  110.33  3.000
 3T2  H4   C20  C12  109.88  3.000
 3T2  H7   O1   C14  109.49  3.000
 3T2  C1'  C1   C6   118.56  3.000
 3T2  C1'  C1   C2   120.36  3.000
 3T2  C6   C1   C2   121.01  3.000
 3T2  C6'  C2   C3   115.04  3.000
 3T2  C6'  C2   C1   122.66  3.000
 3T2  C3   C2   C1   122.26  3.000
 3T2  H9   C3   H8   105.37  3.000
 3T2  H9   C3   C4   110.03  3.000
 3T2  H8   C3   C4   110.29  3.000
 3T2  H9   C3   C2   109.77  3.000
 3T2  H8   C3   C2   109.20  3.000
 3T2  C4   C3   C2   111.96  3.000
 3T2  H11  C4   H10  106.94  3.000
 3T2  H11  C4   C5   109.87  3.000
 3T2  H10  C4   C5   109.84  3.000
 3T2  H11  C4   C3   110.72  3.000
 3T2  H10  C4   C3   109.65  3.000
 3T2  C5   C4   C3   109.78  3.000
 3T2  H13  C5   H12  106.70  3.000
 3T2  H13  C5   C6   109.38  3.000
 3T2  H12  C5   C6   110.57  3.000
 3T2  H13  C5   C4   108.72  3.000
 3T2  H12  C5   C4   109.40  3.000
 3T2  C6   C5   C4   111.92  3.000
 3T2  C7   C6   C5   122.89  3.000
 3T2  C7   C6   C1   120.24  3.000
 3T2  C5   C6   C1   116.85  3.000
 3T2  H14  C7   C6   115.86  3.000
 3T2  H14  C7   C8   113.03  3.000
 3T2  C6   C7   C8   131.06  3.000
 3T2  H15  C10  C9   118.53  3.000
 3T2  H15  C10  C11  118.80  3.000
 3T2  C9   C10  C11  122.66  3.000
 3T2  C20  C12  C11  117.90  3.000
 3T2  C20  C12  C13  125.47  3.000
 3T2  C11  C12  C13  116.63  3.000
 3T2  O2   C14  O1   121.69  3.000
 3T2  O1   C14  C13  110.30  3.000
 3T2  O2   C14  C13  128.02  3.000
 3T2  H18  C4'  H17  107.82  3.000
 3T2  H18  C4'  H16  107.44  3.000
 3T2  H17  C4'  H16  107.17  3.000
 3T2  H18  C4'  C3'  110.85  3.000
 3T2  H17  C4'  C3'  112.25  3.000
 3T2  H16  C4'  C3'  111.10  3.000
 3T2  H19  C3'  C2'  107.82  3.000
 3T2  H19  C3'  C5'  107.98  3.000
 3T2  C2'  C3'  C5'  110.22  3.000
 3T2  H19  C3'  C4'  108.01  3.000
 3T2  C5'  C3'  C4'  110.42  3.000
 3T2  C2'  C3'  C4'  112.22  3.000
 3T2  H22  C5'  H21  107.75  3.000
 3T2  H22  C5'  H20  107.54  3.000
 3T2  H21  C5'  H20  107.61  3.000
 3T2  H22  C5'  C3'  111.37  3.000
 3T2  H21  C5'  C3'  111.41  3.000
 3T2  H20  C5'  C3'  110.98  3.000
 3T2  H24  C2'  H23  105.94  3.000
 3T2  H24  C2'  C1'  110.13  3.000
 3T2  H23  C2'  C1'  108.20  3.000
 3T2  H24  C2'  C3'  109.09  3.000
 3T2  H23  C2'  C3'  108.75  3.000
 3T2  C1'  C2'  C3'  114.37  3.000
 3T2  H27  C6'  C8'  107.83  3.000
 3T2  H27  C6'  C7'  106.17  3.000
 3T2  C8'  C6'  C7'  110.81  3.000
 3T2  H27  C6'  C2   109.20  3.000
 3T2  C7'  C6'  C2   112.48  3.000
 3T2  C8'  C6'  C2   110.16  3.000
 3T2  H30  C7'  H29  108.06  3.000
 3T2  H30  C7'  H28  107.36  3.000
 3T2  H29  C7'  H28  107.73  3.000
 3T2  H30  C7'  C6'  112.32  3.000
 3T2  H29  C7'  C6'  111.58  3.000
 3T2  H28  C7'  C6'  109.59  3.000
 3T2  H33  C8'  H32  107.68  3.000
 3T2  H33  C8'  H31  107.78  3.000
 3T2  H32  C8'  H31  108.04  3.000
 3T2  H33  C8'  C6'  111.22  3.000
 3T2  H32  C8'  C6'  110.70  3.000
 3T2  H31  C8'  C6'  111.26  3.000
 3T2  H36  C19  H35  108.03  3.000
 3T2  H36  C19  H34  106.82  3.000
 3T2  H35  C19  H34  107.21  3.000
 3T2  H36  C19  C8   110.47  3.000
 3T2  H35  C19  C8   112.08  3.000
 3T2  H34  C19  C8   111.98  3.000
 3T2  H26  C1'  H25  103.95  3.000
 3T2  H26  C1'  C2'  110.48  3.000
 3T2  H25  C1'  C2'  108.72  3.000
 3T2  H26  C1'  C1   109.66  3.000
 3T2  H25  C1'  C1   110.09  3.000
 3T2  C2'  C1'  C1   113.50  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
 3T2  CONST_01  H7   O1   C14  C13   180.00   0.0  0
 3T2  Var_01    C4   C5   C6   C1    -30.54  30.0  1
 3T2  Var_02    C4   C3   C2   C1     19.36  30.0  1
 3T2  Var_03    C5   C4   C3   C2    -51.28  30.0  1
 3T2  Var_04    C5   C6   C1   C2     -2.67  30.0  1
 3T2  Var_05    C6   C5   C4   C3     57.16  30.0  1
 3T2  Var_06    C6   C1   C2   C3      8.59  30.0  1
 3T2  Var_07    C8'  C6'  C2   C1    -95.52  30.0  3
 3T2  Var_08    C2'  C1'  C1   C2    -94.19  30.0  3
 3T2  Var_09    C6   C7   C8   C9   -165.45  30.0  2
 3T2  Var_10    C3'  C2'  C1'  C1   -179.85  30.0  3
 3T2  Var_11    H31  C8'  C6'  C2     60.18  30.0  3
 3T2  Var_12    H28  C7'  C6'  C2   -173.40  30.0  3
 3T2  Var_13    C14  C13  C12  C11   179.56   0.0  2
 3T2  Var_14    C12  C11  C10  C9    179.64   0.0  2
 3T2  Var_15    C10  C9   C8   C7      5.20   0.0  2
 3T2  Var_16    C10  C11  C12  C13   179.31  30.0  3
 3T2  Var_17    C8   C9   C10  C11  -179.32  30.0  1
 3T2  Var_18    C12  C13  C14  O1    179.13  30.0  2
 3T2  Var_19    C1'  C2'  C3'  C4'    64.34  30.0  1
 3T2  Var_20    H4   C20  C12  C13   117.62  30.0  3
 3T2  Var_21    H34  C19  C8   C9    101.01  30.0  3
 3T2  Var_22    H20  C5'  C3'  C4'    64.01  30.0  3
 3T2  Var_23    H16  C4'  C3'  C5'    54.28  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
 3T2  plan-1  C13  0.020
 3T2  plan-1  O1   0.020
 3T2  plan-1  O2   0.020
 3T2  plan-1  C14  0.020
 3T2  plan-1  H7   0.020
 3T2  plan-2  C9   0.020
 3T2  plan-2  C8   0.020
 3T2  plan-2  C7   0.020
 3T2  plan-2  C10  0.020
 3T2  plan-2  C19  0.020
 3T2  plan-2  H3   0.020
 3T2  plan-3  C11  0.020
 3T2  plan-3  C9   0.020
 3T2  plan-3  C10  0.020
 3T2  plan-3  C12  0.020
 3T2  plan-3  H2   0.020
 3T2  plan-3  H15  0.020
 3T2  plan-4  C13  0.020
 3T2  plan-4  C11  0.020
 3T2  plan-4  C20  0.020
 3T2  plan-4  C12  0.020
 3T2  plan-4  C14  0.020
 3T2  plan-4  H1   0.020

