# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:10:24 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hex-2-enylidene]cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC\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
 E0E  E0E  (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hex-2-enylidene]cyclohexane-1,3-diol  ligand  70  30  .  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_E0E
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
 E0E  C5   C  CH3   0  -0.665  -5.5338   3.9932   0.5349
 E0E  C6   C  CH2   0  -0.424  -4.2778   3.1547   0.7221
 E0E  C7   C  CH2   0  -0.551  -3.4283   3.0960  -0.5517
 E0E  C8   C  C     0   0.098  -2.1848   2.2506  -0.4198
 E0E  O9   O  OH1   0  -0.679   7.2554  -1.8549   1.7158
 E0E  C10  C  CT    0   0.202   7.0073  -2.2201   0.3625
 E0E  C11  C  CH3   0  -0.664   8.3146  -2.6466  -0.3058
 E0E  C12  C  CH3   0  -0.667   6.0475  -3.4027   0.4175
 E0E  C13  C  CH2   0  -0.431   6.4034  -1.0405  -0.4137
 E0E  C14  C  CH2   0  -0.419   5.1056  -0.4707   0.1450
 E0E  C15  C  CH2   0  -0.415   4.6058   0.7209  -0.6639
 E0E  C16  C  CH2   0  -0.409   3.3088   1.3090  -0.1245
 E0E  C18  C  CR6   0   0.166   1.5203   3.0584  -0.4357
 E0E  C19  C  CR16  0  -0.389   0.2992   2.4345  -0.6700
 E0E  C20  C  CR16  0  -0.339   1.5377   4.2234   0.3269
 E0E  C21  C  CR16  0  -0.220   0.3545   4.7516   0.8249
 E0E  C22  C  CR16  0  -0.341  -0.8552   4.1233   0.5753
 E0E  C23  C  CR6   0   0.118  -0.9030   2.9382  -0.1656
 E0E  C24  C  C1    0  -0.314  -2.2193   0.9045  -0.5004
 E0E  C25  C  C1    0  -0.295  -3.4049   0.1119  -0.7398
 E0E  C26  C  C     0   0.107  -3.4601  -1.2292  -0.8338
 E0E  C27  C  C     0   0.064  -2.2955  -2.1298  -0.7538
 E0E  C28  C  C2    0  -0.584  -1.2191  -2.0300  -1.5318
 E0E  C29  C  CH1   0  -0.028  -2.4302  -3.2334   0.2712
 E0E  O30  O  OH1   0  -0.664  -2.4100  -2.6906   1.5782
 E0E  C31  C  CH2   0  -0.489  -3.7516  -3.9694   0.0982
 E0E  C32  C  CH1   0   0.070  -4.9410  -3.0204   0.0974
 E0E  O33  O  OH1   0  -0.673  -6.1041  -3.7926  -0.1123
 E0E  C34  C  CH2   0  -0.535  -4.7687  -1.9531  -0.9885
 E0E  H1   H  HCH3  0   0.220  -5.2880   5.0225   0.2670
 E0E  H2   H  HCH3  0   0.219  -6.1651   3.5873  -0.2577
 E0E  H3   H  HCH3  0   0.231  -6.1287   4.0228   1.4482
 E0E  H4   H  HCH2  0   0.226  -3.6855   3.5615   1.5461
 E0E  H5   H  HCH2  0   0.226  -4.5524   2.1399   1.0205
 E0E  H6   H  HCH2  0   0.248  -4.0461   2.7112  -1.3671
 E0E  H7   H  HCH2  0   0.245  -3.1551   4.1120  -0.8465
 E0E  H8   H  HOH1  0   0.440   7.8480  -1.0955   1.7178
 E0E  H9   H  HCH3  0   0.224   9.0347  -1.8247  -0.3204
 E0E  H10  H  HCH3  0   0.229   8.7685  -3.4847   0.2264
 E0E  H11  H  HCH3  0   0.221   8.1504  -2.9551  -1.3393
 E0E  H12  H  HCH3  0   0.223   5.7738  -3.7198  -0.5890
 E0E  H13  H  HCH3  0   0.231   6.5066  -4.2542   0.9228
 E0E  H14  H  HCH3  0   0.234   5.1283  -3.1537   0.9491
 E0E  H15  H  HCH2  0   0.216   7.1532  -0.2402  -0.4612
 E0E  H16  H  HCH2  0   0.215   6.2423  -1.3554  -1.4499
 E0E  H17  H  HCH2  0   0.215   4.3283  -1.2405   0.1519
 E0E  H18  H  HCH2  0   0.212   5.2494  -0.1688   1.1863
 E0E  H19  H  HCH2  0   0.212   5.3755   1.5000  -0.6834
 E0E  H20  H  HCH2  0   0.210   4.4583   0.4150  -1.7056
 E0E  H21  H  HCH2  0   0.217   2.5427   0.5282  -0.0749
 E0E  H22  H  HCH2  0   0.220   3.4597   1.6561   0.9027
 E0E  H23  H  HCH2  0   0.236   3.5603   3.2435  -1.0387
 E0E  H24  H  HCH2  0   0.236   2.6286   2.1131  -2.0001
 E0E  H25  H  HCR6  0   0.235   0.2799   1.5469  -1.2935
 E0E  H26  H  HCR6  0   0.244   2.4785   4.7267   0.5170
 E0E  H27  H  HCR6  0   0.252   0.3741   5.6623   1.4102
 E0E  H28  H  HCR6  0   0.250  -1.7638   4.5552   0.9741
 E0E  H29  H  H     0   0.240  -1.2994   0.3531  -0.3427
 E0E  H30  H  H     0   0.237  -4.3483   0.6429  -0.8189
 E0E  H31  H  H     0   0.249  -1.1245  -1.2592  -2.2865
 E0E  H32  H  H     0   0.247  -0.3993  -2.7334  -1.4481
 E0E  H33  H  HCH1  0   0.228  -1.6074  -3.9469   0.1339
 E0E  H34  H  HOH1  0   0.450  -1.6056  -2.1708   1.6744
 E0E  H35  H  HCH2  0   0.239  -3.7217  -4.5151  -0.8502
 E0E  H36  H  HCH2  0   0.252  -3.8606  -4.7142   0.8916
 E0E  H37  H  HCH1  0   0.208  -4.9895  -2.5117   1.0693
 E0E  H38  H  HOH1  0   0.450  -6.8687  -3.2159  -0.0175
 E0E  H39  H  HCH2  0   0.249  -5.6013  -1.2453  -0.9574
 E0E  H40  H  HCH2  0   0.241  -4.7976  -2.4529  -1.9646
 E0E  C17  C  CH2   0  -0.508   2.7915   2.4683  -0.9783

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
 E0E  C11  C10  single    1.529  0.020  1.529
 E0E  C12  C10  single    1.524  0.020  1.524
 E0E  C10  C13  single    1.536  0.020  1.536
 E0E  C10  O9   single    1.424  0.020  1.424
 E0E  C13  C14  single    1.524  0.020  1.524
 E0E  C14  C15  single    1.525  0.020  1.525
 E0E  C15  C16  single    1.523  0.020  1.523
 E0E  C5   C6   single    1.522  0.020  1.522
 E0E  C16  C17  single    1.530  0.020  1.530
 E0E  C28  C27  double    1.332  0.020  1.332
 E0E  C6   C7   single    1.532  0.020  1.532
 E0E  C34  C26  single    1.503  0.020  1.503
 E0E  C34  C32  single    1.532  0.020  1.532
 E0E  C27  C26  single    1.474  0.020  1.474
 E0E  C27  C29  single    1.512  0.020  1.512
 E0E  C31  C32  single    1.522  0.020  1.522
 E0E  C31  C29  single    1.522  0.020  1.522
 E0E  C26  C25  double    1.346  0.020  1.346
 E0E  C17  C18  single    1.503  0.020  1.503
 E0E  O30  C29  single    1.415  0.020  1.415
 E0E  C25  C24  single    1.446  0.020  1.446
 E0E  C32  O33  single    1.412  0.020  1.412
 E0E  C19  C18  aromatic  1.391  0.020  1.391
 E0E  C19  C23  aromatic  1.398  0.020  1.398
 E0E  C18  C20  aromatic  1.393  0.020  1.393
 E0E  C24  C8   double    1.349  0.020  1.349
 E0E  C8   C7   single    1.509  0.020  1.509
 E0E  C8   C23  single    1.477  0.020  1.477
 E0E  C23  C22  aromatic  1.398  0.020  1.398
 E0E  C20  C21  aromatic  1.388  0.020  1.388
 E0E  C22  C21  aromatic  1.386  0.020  1.386
 E0E  C5   H1   single    0.970  0.020  1.090
 E0E  C5   H2   single    0.970  0.020  1.090
 E0E  C5   H3   single    0.970  0.020  1.090
 E0E  C6   H4   single    0.970  0.020  1.090
 E0E  C6   H5   single    0.970  0.020  1.090
 E0E  C7   H6   single    0.970  0.020  1.090
 E0E  C7   H7   single    0.970  0.020  1.090
 E0E  O9   H8   single    0.850  0.020  0.980
 E0E  C11  H9   single    0.970  0.020  1.090
 E0E  C11  H10  single    0.970  0.020  1.090
 E0E  C11  H11  single    0.970  0.020  1.090
 E0E  C12  H12  single    0.970  0.020  1.090
 E0E  C12  H13  single    0.970  0.020  1.090
 E0E  C12  H14  single    0.970  0.020  1.090
 E0E  C13  H15  single    0.970  0.020  1.090
 E0E  C13  H16  single    0.970  0.020  1.090
 E0E  C14  H17  single    0.970  0.020  1.090
 E0E  C14  H18  single    0.970  0.020  1.090
 E0E  C15  H19  single    0.970  0.020  1.090
 E0E  C15  H20  single    0.970  0.020  1.090
 E0E  C16  H21  single    0.970  0.020  1.090
 E0E  C16  H22  single    0.970  0.020  1.090
 E0E  C17  H23  single    0.970  0.020  1.090
 E0E  C17  H24  single    0.970  0.020  1.090
 E0E  C19  H25  single    0.930  0.020  1.080
 E0E  C20  H26  single    0.930  0.020  1.080
 E0E  C21  H27  single    0.930  0.020  1.080
 E0E  C22  H28  single    0.930  0.020  1.080
 E0E  C24  H29  single    0.930  0.020  1.080
 E0E  C25  H30  single    0.930  0.020  1.080
 E0E  C28  H31  single    0.930  0.020  1.080
 E0E  C28  H32  single    0.930  0.020  1.080
 E0E  C29  H33  single    0.970  0.020  1.090
 E0E  O30  H34  single    0.850  0.020  0.980
 E0E  C31  H35  single    0.970  0.020  1.090
 E0E  C31  H36  single    0.970  0.020  1.090
 E0E  C32  H37  single    0.970  0.020  1.090
 E0E  O33  H38  single    0.850  0.020  0.980
 E0E  C34  H39  single    0.970  0.020  1.090
 E0E  C34  H40  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
 E0E  H3   C5   H2   107.62  3.000
 E0E  H3   C5   H1   107.62  3.000
 E0E  H2   C5   H1   107.61  3.000
 E0E  H3   C5   C6   111.25  3.000
 E0E  H2   C5   C6   111.21  3.000
 E0E  H1   C5   C6   111.34  3.000
 E0E  H5   C6   H4   106.01  3.000
 E0E  H5   C6   C7   109.31  3.000
 E0E  H4   C6   C7   109.91  3.000
 E0E  H5   C6   C5   109.75  3.000
 E0E  H4   C6   C5   109.56  3.000
 E0E  C7   C6   C5   112.12  3.000
 E0E  H7   C7   H6   105.51  3.000
 E0E  H7   C7   C8   109.78  3.000
 E0E  H6   C7   C8   109.49  3.000
 E0E  H7   C7   C6   109.11  3.000
 E0E  H6   C7   C6   108.68  3.000
 E0E  C8   C7   C6   113.92  3.000
 E0E  C24  C8   C23  119.81  3.000
 E0E  C23  C8   C7   117.99  3.000
 E0E  C24  C8   C7   122.18  3.000
 E0E  H8   O9   C10  108.15  3.000
 E0E  C13  C10  C12  111.51  3.000
 E0E  C13  C10  C11  109.24  3.000
 E0E  C12  C10  C11  109.74  3.000
 E0E  C13  C10  O9   110.61  3.000
 E0E  C12  C10  O9   105.93  3.000
 E0E  C11  C10  O9   109.76  3.000
 E0E  H11  C11  H10  107.89  3.000
 E0E  H11  C11  H9   107.41  3.000
 E0E  H10  C11  H9   108.06  3.000
 E0E  H11  C11  C10  111.36  3.000
 E0E  H10  C11  C10  110.89  3.000
 E0E  H9   C11  C10  111.07  3.000
 E0E  H14  C12  H13  107.88  3.000
 E0E  H14  C12  H12  107.74  3.000
 E0E  H13  C12  H12  107.82  3.000
 E0E  H14  C12  C10  111.79  3.000
 E0E  H13  C12  C10  110.93  3.000
 E0E  H12  C12  C10  110.52  3.000
 E0E  H16  C13  H15  105.62  3.000
 E0E  H16  C13  C14  109.23  3.000
 E0E  H15  C13  C14  108.97  3.000
 E0E  H16  C13  C10  108.37  3.000
 E0E  H15  C13  C10  108.26  3.000
 E0E  C14  C13  C10  115.90  3.000
 E0E  H18  C14  H17  106.36  3.000
 E0E  H18  C14  C15  109.42  3.000
 E0E  H17  C14  C15  108.69  3.000
 E0E  H18  C14  C13  109.90  3.000
 E0E  H17  C14  C13  110.15  3.000
 E0E  C15  C14  C13  112.15  3.000
 E0E  H20  C15  H19  106.04  3.000
 E0E  H20  C15  C16  109.27  3.000
 E0E  H19  C15  C16  109.28  3.000
 E0E  H20  C15  C14  109.29  3.000
 E0E  H19  C15  C14  109.57  3.000
 E0E  C16  C15  C14  113.15  3.000
 E0E  H22  C16  H21  106.26  3.000
 E0E  H22  C16  C17  109.27  3.000
 E0E  H21  C16  C17  109.21  3.000
 E0E  H22  C16  C15  109.72  3.000
 E0E  H21  C16  C15  109.67  3.000
 E0E  C17  C16  C15  112.52  3.000
 E0E  C20  C18  C19  118.59  3.000
 E0E  C20  C18  C17  121.04  3.000
 E0E  C19  C18  C17  120.37  3.000
 E0E  H25  C19  C23  119.14  3.000
 E0E  H25  C19  C18  118.65  3.000
 E0E  C23  C19  C18  122.18  3.000
 E0E  H26  C20  C21  120.01  3.000
 E0E  H26  C20  C18  119.70  3.000
 E0E  C21  C20  C18  120.28  3.000
 E0E  H27  C21  C22  119.64  3.000
 E0E  H27  C21  C20  119.91  3.000
 E0E  C22  C21  C20  120.45  3.000
 E0E  H28  C22  C23  120.31  3.000
 E0E  H28  C22  C21  119.05  3.000
 E0E  C23  C22  C21  120.63  3.000
 E0E  C22  C23  C19  117.85  3.000
 E0E  C22  C23  C8   121.03  3.000
 E0E  C19  C23  C8   121.11  3.000
 E0E  H29  C24  C25  116.17  3.000
 E0E  H29  C24  C8   118.50  3.000
 E0E  C25  C24  C8   125.30  3.000
 E0E  H30  C25  C26  116.54  3.000
 E0E  H30  C25  C24  117.16  3.000
 E0E  C26  C25  C24  126.26  3.000
 E0E  C34  C26  C27  113.52  3.000
 E0E  C27  C26  C25  124.94  3.000
 E0E  C34  C26  C25  121.52  3.000
 E0E  C29  C27  C28  121.51  3.000
 E0E  C29  C27  C26  114.34  3.000
 E0E  C28  C27  C26  124.12  3.000
 E0E  H32  C28  H31  116.73  3.000
 E0E  H32  C28  C27  121.18  3.000
 E0E  H31  C28  C27  122.08  3.000
 E0E  H33  C29  C31  108.80  3.000
 E0E  H33  C29  O30  110.74  3.000
 E0E  C31  C29  O30  107.62  3.000
 E0E  H33  C29  C27  108.83  3.000
 E0E  O30  C29  C27  110.16  3.000
 E0E  C31  C29  C27  110.68  3.000
 E0E  H34  O30  C29  108.14  3.000
 E0E  H36  C31  H35  106.96  3.000
 E0E  H36  C31  C32  110.32  3.000
 E0E  H35  C31  C32  109.38  3.000
 E0E  H36  C31  C29  109.47  3.000
 E0E  H35  C31  C29  108.41  3.000
 E0E  C32  C31  C29  112.15  3.000
 E0E  H37  C32  C34  108.03  3.000
 E0E  H37  C32  O33  110.40  3.000
 E0E  C34  C32  O33  111.62  3.000
 E0E  H37  C32  C31  108.85  3.000
 E0E  O33  C32  C31  107.63  3.000
 E0E  C34  C32  C31  110.30  3.000
 E0E  H38  O33  C32  108.19  3.000
 E0E  H40  C34  H39  107.47  3.000
 E0E  H40  C34  C32  108.07  3.000
 E0E  H39  C34  C32  110.19  3.000
 E0E  H40  C34  C26  109.50  3.000
 E0E  H39  C34  C26  110.38  3.000
 E0E  C32  C34  C26  111.12  3.000
 E0E  H24  C17  H23  106.45  3.000
 E0E  H24  C17  C18  109.80  3.000
 E0E  H23  C17  C18  109.65  3.000
 E0E  H24  C17  C16  109.00  3.000
 E0E  H23  C17  C16  109.28  3.000
 E0E  C18  C17  C16  112.47  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
 E0E  CONST_01  C22  C23  C19  C18     0.00   0.0  0
 E0E  CONST_02  C22  C21  C20  C18     0.00   0.0  0
 E0E  CONST_03  C21  C20  C18  C19     0.00   0.0  0
 E0E  CONST_04  C21  C22  C23  C19     0.00   0.0  0
 E0E  CONST_05  C23  C19  C18  C20     0.00   0.0  0
 E0E  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 E0E  CONST_07  C18  C19  C23  C8    180.00   0.0  0
 E0E  CONST_08  C21  C22  C23  C8    180.00   0.0  0
 E0E  CONST_09  C23  C19  C18  C17   180.00   0.0  0
 E0E  CONST_10  C21  C20  C18  C17   180.00   0.0  0
 E0E  CONST_11  H27  C21  C20  C18   180.00   0.0  0
 E0E  CONST_12  H26  C20  C18  C19   180.00   0.0  0
 E0E  CONST_13  H28  C22  C23  C19   180.00   0.0  0
 E0E  CONST_14  H25  C19  C18  C20   180.00   0.0  0
 E0E  Var_01    C32  C34  C26  C27    52.66  30.0  1
 E0E  Var_02    C34  C26  C27  C29   -51.18  30.0  1
 E0E  Var_03    C19  C23  C8   C7   -147.33  30.0  2
 E0E  Var_04    C19  C18  C17  C16   -79.72  30.0  2
 E0E  Var_05    H31  C28  C27  C26     0.42  30.0  2
 E0E  Var_06    C25  C24  C8   C23   179.79   0.0  2
 E0E  Var_07    C23  C8   C7   C6    -99.26  30.0  2
 E0E  Var_08    C26  C25  C24  C8    179.46  30.0  1
 E0E  Var_09    C18  C17  C16  C15  -179.32  30.0  3
 E0E  Var_10    C8   C7   C6   C5   -178.83  30.0  3
 E0E  Var_11    C14  C13  C10  O9    -57.71  30.0  3
 E0E  Var_12    C15  C14  C13  C10   178.23  30.0  3
 E0E  Var_13    C16  C15  C14  C13  -179.98  30.0  3
 E0E  Var_14    C17  C16  C15  C14  -177.75  30.0  3
 E0E  Var_15    H1   C5   C6   C7    -60.13  30.0  3
 E0E  Var_16    H9   C11  C10  O9    -61.68  30.0  3
 E0E  Var_17    H12  C12  C10  O9    177.72  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
 E0E  chir_01  C29  C27  C31  O30  positiv
 E0E  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
 E0E  plan-1  C8   0.020
 E0E  plan-1  C18  0.020
 E0E  plan-1  C19  0.020
 E0E  plan-1  C20  0.020
 E0E  plan-1  C21  0.020
 E0E  plan-1  C22  0.020
 E0E  plan-1  C23  0.020
 E0E  plan-1  H25  0.020
 E0E  plan-1  H26  0.020
 E0E  plan-1  H27  0.020
 E0E  plan-1  H28  0.020
 E0E  plan-1  C17  0.020
 E0E  plan-2  C7   0.020
 E0E  plan-2  C8   0.020
 E0E  plan-2  C23  0.020
 E0E  plan-2  C24  0.020
 E0E  plan-2  C25  0.020
 E0E  plan-2  H29  0.020

