# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:41:35 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C(=C/C=C\1C[C@@H](O)C[C@H](O)C\1=C)c2cccc(CCCCCC(C)(C)O)c2
#
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
 E05  E05  (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol  ligand  67  29  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E05
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
 E05  C6   C  CH3   0  -0.657   4.2582   3.4918  -0.9758
 E05  C7   C  CH2   0  -0.553   3.4868   3.4340   0.3440
 E05  C8   C  C     0   0.088   2.2982   2.5032   0.3049
 E05  O9   O  OH1   0  -0.680  -5.8014  -3.3478  -0.3828
 E05  C10  C  CT    0   0.199  -6.8041  -2.3388  -0.4288
 E05  C11  C  CH3   0  -0.681  -7.1184  -1.9762  -1.8798
 E05  C12  C  CH3   0  -0.665  -8.0743  -2.8420   0.2573
 E05  C13  C  CH2   0  -0.407  -6.2481  -1.1401   0.3440
 E05  C14  C  CH2   0  -0.426  -4.9629  -0.5290  -0.2031
 E05  C15  C  CH2   0  -0.415  -4.4484   0.6064   0.6745
 E05  C16  C  CH2   0  -0.409  -3.1850   1.2551   0.1247
 E05  C18  C  CR6   0   0.165  -1.4529   3.0563   0.4308
 E05  C19  C  CR16  0  -0.392  -0.1864   2.5177   0.6298
 E05  C20  C  CR16  0  -0.337  -1.5733   4.2116  -0.3382
 E05  C21  C  CR16  0  -0.219  -0.4456   4.8116  -0.8796
 E05  C22  C  CR16  0  -0.340   0.8112   4.2671  -0.6663
 E05  C23  C  CR6   0   0.122   0.9637   3.0960   0.0831
 E05  C24  C  C1    0  -0.312   2.4277   1.1670   0.4344
 E05  C25  C  C1    0  -0.295   3.6722   0.4642   0.6533
 E05  C26  C  C     0   0.107   3.8134  -0.8655   0.8005
 E05  C27  C  C     0   0.063   2.7032  -1.8362   0.7947
 E05  C28  C  C2    0  -0.584   1.6531  -1.7769   1.6113
 E05  C29  C  CH1   0  -0.028   2.8705  -2.9601  -0.2030
 E05  O30  O  OH1   0  -0.664   2.7899  -2.4565  -1.5233
 E05  C31  C  CH2   0  -0.488   4.2339  -3.6185  -0.0431
 E05  C32  C  CH1   0   0.070   5.3702  -2.6081  -0.1044
 E05  O33  O  OH1   0  -0.673   6.5769  -3.3095   0.1077
 E05  C34  C  CH2   0  -0.535   5.1651  -1.5080   0.9425
 E05  H1   H  HCH3  0   0.233   5.1098   4.1681  -0.8927
 E05  H2   H  HCH3  0   0.228   4.6381   2.5088  -1.2551
 E05  H3   H  HCH3  0   0.227   3.6341   3.8475  -1.7962
 E05  H4   H  HCH2  0   0.253   4.1706   3.1292   1.1389
 E05  H5   H  HCH2  0   0.247   3.1578   4.4391   0.6135
 E05  H6   H  HOH1  0   0.440  -6.1241  -4.1121  -0.8719
 E05  H7   H  HCH3  0   0.235  -6.2245  -1.6682  -2.4231
 E05  H8   H  HCH3  0   0.227  -7.5490  -2.8312  -2.4072
 E05  H9   H  HCH3  0   0.222  -7.8417  -1.1612  -1.9348
 E05  H10  H  HCH3  0   0.222  -8.8578  -2.0831   0.2466
 E05  H11  H  HCH3  0   0.225  -8.4661  -3.7256  -0.2531
 E05  H12  H  HCH3  0   0.228  -7.8798  -3.1103   1.2974
 E05  H13  H  HCH2  0   0.216  -7.0252  -0.3698   0.3798
 E05  H14  H  HCH2  0   0.218  -6.0824  -1.4492   1.3826
 E05  H15  H  HCH2  0   0.216  -4.1901  -1.2977  -0.2880
 E05  H16  H  HCH2  0   0.214  -5.1280  -0.1452  -1.2145
 E05  H17  H  HCH2  0   0.210  -5.2281   1.3690   0.7791
 E05  H18  H  HCH2  0   0.211  -4.2547   0.2281   1.6843
 E05  H19  H  HCH2  0   0.218  -2.4008   0.4990   0.0130
 E05  H20  H  HCH2  0   0.220  -3.3805   1.6453  -0.8793
 E05  H21  H  HCH2  0   0.236  -3.4603   3.1295   1.1498
 E05  H22  H  HCH2  0   0.237  -2.4345   1.9913   2.0038
 E05  H23  H  HCR6  0   0.235  -0.0902   1.6403   1.2604
 E05  H24  H  HCR6  0   0.244  -2.5511   4.6499  -0.5003
 E05  H25  H  HCR6  0   0.252  -0.5445   5.7139  -1.4698
 E05  H26  H  HCR6  0   0.250   1.6737   4.7556  -1.1006
 E05  H27  H  H     0   0.240   1.5419   0.5495   0.3393
 E05  H28  H  H     0   0.239   4.5813   1.0568   0.6738
 E05  H29  H  H     0   0.249   1.5400  -0.9894   2.3459
 E05  H30  H  H     0   0.247   0.8748  -2.5300   1.5811
 E05  H31  H  HCH1  0   0.228   2.0907  -3.7121  -0.0249
 E05  H32  H  HOH1  0   0.451   1.9571  -1.9821  -1.6124
 E05  H33  H  HCH2  0   0.239   4.2560  -4.1341   0.9223
 E05  H34  H  HCH2  0   0.252   4.3633  -4.3817  -0.8156
 E05  H35  H  HCH1  0   0.208   5.3715  -2.1363  -1.0960
 E05  H36  H  HOH1  0   0.450   7.3077  -2.6977  -0.0266
 E05  H37  H  HCH2  0   0.249   5.9557  -0.7575   0.8609
 E05  H38  H  HCH2  0   0.241   5.2474  -1.9641   1.9368
 E05  C17  C  CH2   0  -0.507  -2.6676   2.3888   1.0120

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
 E05  C12  C10  single    1.529  0.020  1.529
 E05  C11  C10  single    1.528  0.020  1.528
 E05  C10  C13  single    1.531  0.020  1.531
 E05  C10  O9   single    1.423  0.020  1.423
 E05  C13  C14  single    1.525  0.020  1.525
 E05  C14  C15  single    1.525  0.020  1.525
 E05  C15  C16  single    1.523  0.020  1.523
 E05  C16  C17  single    1.530  0.020  1.530
 E05  C6   C7   single    1.530  0.020  1.530
 E05  C28  C27  double    1.332  0.020  1.332
 E05  C17  C18  single    1.503  0.020  1.503
 E05  C34  C26  single    1.503  0.020  1.503
 E05  C34  C32  single    1.533  0.020  1.533
 E05  C27  C26  single    1.475  0.020  1.475
 E05  C27  C29  single    1.512  0.020  1.512
 E05  C31  C32  single    1.522  0.020  1.522
 E05  C31  C29  single    1.523  0.020  1.523
 E05  O30  C29  single    1.415  0.020  1.415
 E05  C26  C25  double    1.345  0.020  1.345
 E05  C7   C8   single    1.510  0.020  1.510
 E05  C19  C18  aromatic  1.391  0.020  1.391
 E05  C19  C23  aromatic  1.399  0.020  1.399
 E05  C25  C24  single    1.446  0.020  1.446
 E05  C32  O33  single    1.412  0.020  1.412
 E05  C18  C20  aromatic  1.393  0.020  1.393
 E05  C8   C24  double    1.349  0.020  1.349
 E05  C8   C23  single    1.477  0.020  1.477
 E05  C23  C22  aromatic  1.399  0.020  1.399
 E05  C20  C21  aromatic  1.387  0.020  1.387
 E05  C22  C21  aromatic  1.386  0.020  1.386
 E05  C6   H1   single    0.970  0.020  1.090
 E05  C6   H2   single    0.970  0.020  1.090
 E05  C6   H3   single    0.970  0.020  1.090
 E05  C7   H4   single    0.970  0.020  1.090
 E05  C7   H5   single    0.970  0.020  1.090
 E05  O9   H6   single    0.850  0.020  0.980
 E05  C11  H7   single    0.970  0.020  1.090
 E05  C11  H8   single    0.970  0.020  1.090
 E05  C11  H9   single    0.970  0.020  1.090
 E05  C12  H10  single    0.970  0.020  1.090
 E05  C12  H11  single    0.970  0.020  1.090
 E05  C12  H12  single    0.970  0.020  1.090
 E05  C13  H13  single    0.970  0.020  1.090
 E05  C13  H14  single    0.970  0.020  1.090
 E05  C14  H15  single    0.970  0.020  1.090
 E05  C14  H16  single    0.970  0.020  1.090
 E05  C15  H17  single    0.970  0.020  1.090
 E05  C15  H18  single    0.970  0.020  1.090
 E05  C16  H19  single    0.970  0.020  1.090
 E05  C16  H20  single    0.970  0.020  1.090
 E05  C17  H21  single    0.970  0.020  1.090
 E05  C17  H22  single    0.970  0.020  1.090
 E05  C19  H23  single    0.930  0.020  1.080
 E05  C20  H24  single    0.930  0.020  1.080
 E05  C21  H25  single    0.930  0.020  1.080
 E05  C22  H26  single    0.930  0.020  1.080
 E05  C24  H27  single    0.930  0.020  1.080
 E05  C25  H28  single    0.930  0.020  1.080
 E05  C28  H29  single    0.930  0.020  1.080
 E05  C28  H30  single    0.930  0.020  1.080
 E05  C29  H31  single    0.970  0.020  1.090
 E05  O30  H32  single    0.850  0.020  0.980
 E05  C31  H33  single    0.970  0.020  1.090
 E05  C31  H34  single    0.970  0.020  1.090
 E05  C32  H35  single    0.970  0.020  1.090
 E05  O33  H36  single    0.850  0.020  0.980
 E05  C34  H37  single    0.970  0.020  1.090
 E05  C34  H38  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
 E05  H3   C6   H2   107.50  3.000
 E05  H3   C6   H1   107.58  3.000
 E05  H2   C6   H1   107.85  3.000
 E05  H3   C6   C7   111.89  3.000
 E05  H2   C6   C7   111.26  3.000
 E05  H1   C6   C7   110.58  3.000
 E05  H5   C7   H4   105.43  3.000
 E05  H5   C7   C8   109.68  3.000
 E05  H4   C7   C8   109.85  3.000
 E05  H5   C7   C6   109.29  3.000
 E05  H4   C7   C6   108.83  3.000
 E05  C8   C7   C6   113.44  3.000
 E05  C24  C8   C23  119.92  3.000
 E05  C23  C8   C7   117.88  3.000
 E05  C24  C8   C7   122.18  3.000
 E05  H6   O9   C10  108.06  3.000
 E05  C13  C10  C12  109.45  3.000
 E05  C13  C10  C11  111.61  3.000
 E05  C12  C10  C11  109.47  3.000
 E05  C13  C10  O9   106.44  3.000
 E05  C11  C10  O9   110.10  3.000
 E05  C12  C10  O9   109.72  3.000
 E05  H9   C11  H8   107.39  3.000
 E05  H9   C11  H7   107.90  3.000
 E05  H8   C11  H7   107.67  3.000
 E05  H9   C11  C10  111.18  3.000
 E05  H8   C11  C10  110.71  3.000
 E05  H7   C11  C10  111.80  3.000
 E05  H12  C12  H11  108.06  3.000
 E05  H12  C12  H10  107.95  3.000
 E05  H11  C12  H10  107.48  3.000
 E05  H12  C12  C10  111.13  3.000
 E05  H11  C12  C10  110.76  3.000
 E05  H10  C12  C10  111.31  3.000
 E05  H14  C13  H13  105.95  3.000
 E05  H14  C13  C14  109.00  3.000
 E05  H13  C13  C14  109.15  3.000
 E05  H14  C13  C10  108.20  3.000
 E05  H13  C13  C10  108.04  3.000
 E05  C14  C13  C10  116.03  3.000
 E05  H16  C14  H15  106.35  3.000
 E05  H16  C14  C15  108.77  3.000
 E05  H15  C14  C15  109.26  3.000
 E05  H16  C14  C13  110.18  3.000
 E05  H15  C14  C13  109.99  3.000
 E05  C15  C14  C13  112.11  3.000
 E05  H18  C15  H17  106.15  3.000
 E05  H18  C15  C16  109.46  3.000
 E05  H17  C15  C16  109.17  3.000
 E05  H18  C15  C14  109.46  3.000
 E05  H17  C15  C14  109.46  3.000
 E05  C16  C15  C14  112.92  3.000
 E05  H20  C16  H19  106.28  3.000
 E05  H20  C16  C17  109.16  3.000
 E05  H19  C16  C17  109.20  3.000
 E05  H20  C16  C15  109.56  3.000
 E05  H19  C16  C15  109.68  3.000
 E05  C17  C16  C15  112.76  3.000
 E05  C20  C18  C19  118.61  3.000
 E05  C20  C18  C17  120.79  3.000
 E05  C19  C18  C17  120.58  3.000
 E05  H23  C19  C23  119.26  3.000
 E05  H23  C19  C18  118.51  3.000
 E05  C23  C19  C18  122.20  3.000
 E05  H24  C20  C21  120.01  3.000
 E05  H24  C20  C18  119.73  3.000
 E05  C21  C20  C18  120.26  3.000
 E05  H25  C21  C22  119.61  3.000
 E05  H25  C21  C20  119.93  3.000
 E05  C22  C21  C20  120.46  3.000
 E05  H26  C22  C23  120.40  3.000
 E05  H26  C22  C21  118.91  3.000
 E05  C23  C22  C21  120.68  3.000
 E05  C22  C23  C19  117.78  3.000
 E05  C22  C23  C8   121.00  3.000
 E05  C19  C23  C8   121.22  3.000
 E05  H27  C24  C25  116.09  3.000
 E05  H27  C24  C8   118.52  3.000
 E05  C25  C24  C8   125.36  3.000
 E05  H28  C25  C26  116.73  3.000
 E05  H28  C25  C24  117.28  3.000
 E05  C26  C25  C24  125.96  3.000
 E05  C34  C26  C27  113.33  3.000
 E05  C27  C26  C25  124.83  3.000
 E05  C34  C26  C25  121.81  3.000
 E05  C29  C27  C28  121.66  3.000
 E05  C29  C27  C26  114.11  3.000
 E05  C28  C27  C26  124.19  3.000
 E05  H30  C28  H29  116.70  3.000
 E05  H30  C28  C27  121.23  3.000
 E05  H29  C28  C27  122.06  3.000
 E05  H31  C29  C31  108.83  3.000
 E05  H31  C29  O30  110.77  3.000
 E05  C31  C29  O30  107.63  3.000
 E05  H31  C29  C27  108.88  3.000
 E05  O30  C29  C27  110.16  3.000
 E05  C31  C29  C27  110.56  3.000
 E05  H32  O30  C29  108.12  3.000
 E05  H34  C31  H33  106.97  3.000
 E05  H34  C31  C32  110.28  3.000
 E05  H33  C31  C32  109.47  3.000
 E05  H34  C31  C29  109.48  3.000
 E05  H33  C31  C29  108.32  3.000
 E05  C32  C31  C29  112.17  3.000
 E05  H35  C32  C34  107.97  3.000
 E05  H35  C32  O33  110.37  3.000
 E05  C34  C32  O33  111.62  3.000
 E05  H35  C32  C31  108.82  3.000
 E05  O33  C32  C31  107.60  3.000
 E05  C34  C32  C31  110.44  3.000
 E05  H36  O33  C32  108.19  3.000
 E05  H38  C34  H37  107.39  3.000
 E05  H38  C34  C32  108.10  3.000
 E05  H37  C34  C32  110.18  3.000
 E05  H38  C34  C26  109.32  3.000
 E05  H37  C34  C26  110.48  3.000
 E05  C32  C34  C26  111.26  3.000
 E05  H22  C17  H21  106.64  3.000
 E05  H22  C17  C18  109.86  3.000
 E05  H21  C17  C18  109.50  3.000
 E05  H22  C17  C16  109.19  3.000
 E05  H21  C17  C16  109.26  3.000
 E05  C18  C17  C16  112.22  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
 E05  CONST_01  C22  C23  C19  C18     0.00   0.0  0
 E05  CONST_02  C22  C21  C20  C18     0.00   0.0  0
 E05  CONST_03  C21  C20  C18  C19     0.00   0.0  0
 E05  CONST_04  C21  C22  C23  C19     0.00   0.0  0
 E05  CONST_05  C23  C19  C18  C20     0.00   0.0  0
 E05  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 E05  CONST_07  C18  C19  C23  C8    180.00   0.0  0
 E05  CONST_08  C21  C22  C23  C8    180.00   0.0  0
 E05  CONST_09  C23  C19  C18  C17   180.00   0.0  0
 E05  CONST_10  C21  C20  C18  C17   180.00   0.0  0
 E05  CONST_11  H25  C21  C20  C18   180.00   0.0  0
 E05  CONST_12  H24  C20  C18  C19   180.00   0.0  0
 E05  CONST_13  H26  C22  C23  C19   180.00   0.0  0
 E05  CONST_14  H23  C19  C18  C20   180.00   0.0  0
 E05  Var_01    C32  C34  C26  C27    52.75  30.0  1
 E05  Var_02    C34  C26  C27  C29   -51.95  30.0  1
 E05  Var_03    C19  C23  C8   C7   -149.24  30.0  2
 E05  Var_04    C19  C18  C17  C16   -83.63  30.0  2
 E05  Var_05    H29  C28  C27  C26     0.43  30.0  2
 E05  Var_06    C25  C24  C8   C23   179.97   0.0  2
 E05  Var_07    C23  C8   C7   C6    -98.85  30.0  3
 E05  Var_08    C26  C25  C24  C8    179.13  30.0  2
 E05  Var_09    C18  C17  C16  C15  -177.71  30.0  3
 E05  Var_10    C14  C13  C10  O9     60.66  30.0  3
 E05  Var_11    C15  C14  C13  C10  -176.88  30.0  3
 E05  Var_12    C16  C15  C14  C13  -178.46  30.0  3
 E05  Var_13    C17  C16  C15  C14  -179.69  30.0  3
 E05  Var_14    H1   C6   C7   C8   -179.45  30.0  3
 E05  Var_15    H10  C12  C10  O9    179.36  30.0  3
 E05  Var_16    H7   C11  C10  O9    -55.90  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E05  chir_01  C29  C27  C31  O30  positiv
 E05  chir_02  C32  O33  C34  C31  positiv

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
 E05  plan-1  C8   0.020
 E05  plan-1  C18  0.020
 E05  plan-1  C19  0.020
 E05  plan-1  C20  0.020
 E05  plan-1  C21  0.020
 E05  plan-1  C22  0.020
 E05  plan-1  C23  0.020
 E05  plan-1  H23  0.020
 E05  plan-1  H24  0.020
 E05  plan-1  H25  0.020
 E05  plan-1  H26  0.020
 E05  plan-1  C17  0.020
 E05  plan-2  C7   0.020
 E05  plan-2  C8   0.020
 E05  plan-2  C23  0.020
 E05  plan-2  C24  0.020
 E05  plan-2  C25  0.020
 E05  plan-2  H27  0.020

