# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:56:22 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: 2-{[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraen-1-yl]oxy}propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C/C=C\C\C=C/C\C=C/CCCCOC(CO)CO
#
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
 VKV  VKV  2-{[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraen-1-yl]oxy}propane-1,3-diol  ligand  66  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VKV
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
 VKV  C10  C  CH1   0   0.003  10.4943  5.7710   -4.6178
 VKV  C15  C  CH2   0  -0.186   9.8651  6.9871   -3.9555
 VKV  C17  C  CH3   0  -0.665  15.2093  8.1005  -11.3823
 VKV  C21  C  CH2   0  -0.551  21.4612  5.6161   -8.8070
 VKV  C22  C  C1    0  -0.179  17.5852  4.8299   -6.3422
 VKV  O01  O  O2    0  -0.492  11.6354  6.0846   -5.3826
 VKV  O03  O  OH1   0  -0.668  10.0528  3.8021   -5.8809
 VKV  C04  C  CH2   0  -0.454  13.9870  6.4698   -5.5743
 VKV  C05  C  CH2   0  -0.418  13.8860  7.6920   -6.4791
 VKV  C06  C  CH2   0  -0.142  12.8106  6.2957   -4.6355
 VKV  C07  C  CH2   0  -0.431  18.8310  9.0321  -10.2821
 VKV  C08  C  CH2   0  -0.424  17.6000  8.1698  -10.5265
 VKV  C11  C  CH2   0  -0.492  20.0179  8.2758   -9.6881
 VKV  C12  C  CH2   0  -0.415  16.4228  8.9658  -11.0759
 VKV  C14  C  CH2   0  -0.156   9.5082  5.0505   -5.5200
 VKV  C16  C  C1    0  -0.209  20.5094  7.1693  -10.5739
 VKV  C19  C  CH2   0  -0.597  17.6203  5.9520   -7.3410
 VKV  C23  C  C1    0  -0.214  21.0665  4.1934   -8.5337
 VKV  C09  C  CH2   0  -0.508  15.0857  7.8379   -7.4206
 VKV  C13  C  C1    0  -0.203  16.3699  8.0674   -6.6888
 VKV  C18  C  C1    0  -0.201  17.4419  7.2770   -6.6554
 VKV  C20  C  C1    0  -0.222  21.1107  6.0403  -10.2031
 VKV  C24  C  CH2   0  -0.575  20.0772  4.4677   -6.2100
 VKV  C25  C  C1    0  -0.227  18.6415  4.1919   -5.8446
 VKV  C26  C  C1    0  -0.196  20.4897  3.7062   -7.4368
 VKV  O02  O  OH1   0  -0.667   9.4038  7.8819   -4.9401
 VKV  H1   H  HCH1  0   0.207  10.7648  5.0849   -3.7982
 VKV  H2   H  HCH2  0   0.201   9.0509  6.6287   -3.3114
 VKV  H3   H  HCH2  0   0.212  10.5972  7.4620   -3.2892
 VKV  H4   H  HCH3  0   0.224  14.3778  8.6952  -11.7626
 VKV  H5   H  HCH3  0   0.215  15.4432  7.3436  -12.1335
 VKV  H6   H  HCH3  0   0.220  14.8602  7.5790  -10.4892
 VKV  H7   H  HCH2  0   0.256  22.5504  5.6971   -8.6937
 VKV  H8   H  HCH2  0   0.246  21.0384  6.2989   -8.0688
 VKV  H9   H  H     0   0.240  16.5969  4.5471   -5.9920
 VKV  H10  H  HOH1  0   0.451   9.4687  3.3968   -6.5275
 VKV  H11  H  HCH2  0   0.217  14.1081  5.5666   -6.1820
 VKV  H12  H  HCH2  0   0.227  14.8866  6.5427   -4.9573
 VKV  H13  H  HCH2  0   0.212  13.7921  8.5935   -5.8641
 VKV  H14  H  HCH2  0   0.229  12.9776  7.6348   -7.0826
 VKV  H15  H  HCH2  0   0.206  12.9932  5.4421   -3.9670
 VKV  H16  H  HCH2  0   0.193  12.7250  7.1842   -3.9943
 VKV  H17  H  HCH2  0   0.211  19.1386  9.4976  -11.2249
 VKV  H18  H  HCH2  0   0.219  18.5662  9.8543   -9.6105
 VKV  H19  H  HCH2  0   0.232  17.3030  7.6842   -9.5906
 VKV  H20  H  HCH2  0   0.209  17.8452  7.3614  -11.2235
 VKV  H21  H  HCH2  0   0.234  19.7509  7.8915   -8.6995
 VKV  H22  H  HCH2  0   0.242  20.8313  8.9903   -9.5193
 VKV  H23  H  HCH2  0   0.210  16.7346  9.4921  -11.9836
 VKV  H24  H  HCH2  0   0.209  16.1473  9.7438  -10.3567
 VKV  H25  H  HCH2  0   0.202   9.2909  5.6669   -6.4004
 VKV  H26  H  HCH2  0   0.192   8.5649  4.9345   -4.9701
 VKV  H27  H  H     0   0.229  20.3742  7.3315  -11.6408
 VKV  H28  H  HCH2  0   0.258  18.5680  5.9506   -7.8858
 VKV  H29  H  HCH2  0   0.252  16.8397  5.7890   -8.0866
 VKV  H30  H  H     0   0.234  21.3013  3.4905   -9.3287
 VKV  H31  H  HCH2  0   0.231  15.1479  6.9553   -8.0609
 VKV  H32  H  HCH2  0   0.242  14.9039  8.6870   -8.0878
 VKV  H33  H  H     0   0.230  16.4087  8.9866   -6.1090
 VKV  H34  H  H     0   0.234  18.2870  7.5905   -6.0486
 VKV  H35  H  H     0   0.231  21.4191  5.3512  -10.9849
 VKV  H36  H  HCH2  0   0.256  20.7142  4.1635   -5.3741
 VKV  H37  H  HCH2  0   0.252  20.2437  5.5381   -6.3393
 VKV  H38  H  H     0   0.235  18.4689  3.3925   -5.1311
 VKV  H39  H  H     0   0.236  20.2867  2.6395   -7.4067
 VKV  H40  H  HOH1  0   0.454   9.0109  8.6390   -4.4976

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
 VKV  C17  C12  single  1.522  0.020  1.522
 VKV  C16  C20  double  1.332  0.020  1.332
 VKV  C16  C11  single  1.500  0.020  1.500
 VKV  C12  C08  single  1.524  0.020  1.524
 VKV  C07  C08  single  1.523  0.020  1.523
 VKV  C07  C11  single  1.528  0.020  1.528
 VKV  C20  C21  single  1.501  0.020  1.501
 VKV  C21  C23  single  1.501  0.020  1.501
 VKV  C23  C26  double  1.332  0.020  1.332
 VKV  C26  C24  single  1.502  0.020  1.502
 VKV  C09  C05  single  1.532  0.020  1.532
 VKV  C09  C13  single  1.496  0.020  1.496
 VKV  C24  C25  single  1.507  0.020  1.507
 VKV  C19  C22  single  1.503  0.020  1.503
 VKV  C19  C18  single  1.502  0.020  1.502
 VKV  C05  C04  single  1.524  0.020  1.524
 VKV  O03  C14  single  1.409  0.020  1.409
 VKV  C25  C22  double  1.331  0.020  1.331
 VKV  C13  C18  double  1.332  0.020  1.332
 VKV  C14  C10  single  1.518  0.020  1.518
 VKV  C04  C06  single  1.515  0.020  1.515
 VKV  O01  C10  single  1.409  0.020  1.409
 VKV  O01  C06  single  1.408  0.020  1.408
 VKV  C10  C15  single  1.521  0.020  1.521
 VKV  O02  C15  single  1.408  0.020  1.408
 VKV  C10  H1   single  0.970  0.020  1.090
 VKV  C15  H2   single  0.970  0.020  1.090
 VKV  C15  H3   single  0.970  0.020  1.090
 VKV  C17  H4   single  0.970  0.020  1.090
 VKV  C17  H5   single  0.970  0.020  1.090
 VKV  C17  H6   single  0.970  0.020  1.090
 VKV  C21  H7   single  0.970  0.020  1.090
 VKV  C21  H8   single  0.970  0.020  1.090
 VKV  C22  H9   single  0.930  0.020  1.080
 VKV  O03  H10  single  0.850  0.020  0.980
 VKV  C04  H11  single  0.970  0.020  1.090
 VKV  C04  H12  single  0.970  0.020  1.090
 VKV  C05  H13  single  0.970  0.020  1.090
 VKV  C05  H14  single  0.970  0.020  1.090
 VKV  C06  H15  single  0.970  0.020  1.090
 VKV  C06  H16  single  0.970  0.020  1.090
 VKV  C07  H17  single  0.970  0.020  1.090
 VKV  C07  H18  single  0.970  0.020  1.090
 VKV  C08  H19  single  0.970  0.020  1.090
 VKV  C08  H20  single  0.970  0.020  1.090
 VKV  C11  H21  single  0.970  0.020  1.090
 VKV  C11  H22  single  0.970  0.020  1.090
 VKV  C12  H23  single  0.970  0.020  1.090
 VKV  C12  H24  single  0.970  0.020  1.090
 VKV  C14  H25  single  0.970  0.020  1.090
 VKV  C14  H26  single  0.970  0.020  1.090
 VKV  C16  H27  single  0.930  0.020  1.080
 VKV  C19  H28  single  0.970  0.020  1.090
 VKV  C19  H29  single  0.970  0.020  1.090
 VKV  C23  H30  single  0.930  0.020  1.080
 VKV  C09  H31  single  0.970  0.020  1.090
 VKV  C09  H32  single  0.970  0.020  1.090
 VKV  C13  H33  single  0.930  0.020  1.080
 VKV  C18  H34  single  0.930  0.020  1.080
 VKV  C20  H35  single  0.930  0.020  1.080
 VKV  C24  H36  single  0.970  0.020  1.090
 VKV  C24  H37  single  0.970  0.020  1.090
 VKV  C25  H38  single  0.930  0.020  1.080
 VKV  C26  H39  single  0.930  0.020  1.080
 VKV  O02  H40  single  0.850  0.020  0.980

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
 VKV  H1   C10  C14  107.81  3.000
 VKV  H1   C10  O01  110.08  3.000
 VKV  C14  C10  O01  108.00  3.000
 VKV  H1   C10  C15  105.98  3.000
 VKV  O01  C10  C15  113.16  3.000
 VKV  C14  C10  C15  111.68  3.000
 VKV  H3   C15  H2   106.24  3.000
 VKV  H3   C15  O02  111.59  3.000
 VKV  H2   C15  O02  112.00  3.000
 VKV  H3   C15  C10  109.52  3.000
 VKV  H2   C15  C10  107.53  3.000
 VKV  O02  C15  C10  109.82  3.000
 VKV  H6   C17  H5   107.48  3.000
 VKV  H6   C17  H4   107.58  3.000
 VKV  H5   C17  H4   107.55  3.000
 VKV  H6   C17  C12  111.22  3.000
 VKV  H5   C17  C12  111.22  3.000
 VKV  H4   C17  C12  111.59  3.000
 VKV  H8   C21  H7   105.58  3.000
 VKV  H8   C21  C20  111.23  3.000
 VKV  H7   C21  C20  107.87  3.000
 VKV  H8   C21  C23  111.59  3.000
 VKV  H7   C21  C23  108.18  3.000
 VKV  C20  C21  C23  112.07  3.000
 VKV  H9   C22  C25  118.49  3.000
 VKV  H9   C22  C19  115.47  3.000
 VKV  C25  C22  C19  126.02  3.000
 VKV  C06  O01  C10  114.91  3.000
 VKV  H10  O03  C14  108.13  3.000
 VKV  H12  C04  H11  106.09  3.000
 VKV  H12  C04  C06  107.27  3.000
 VKV  H11  C04  C06  109.57  3.000
 VKV  H12  C04  C05  109.64  3.000
 VKV  H11  C04  C05  109.83  3.000
 VKV  C06  C04  C05  114.11  3.000
 VKV  H14  C05  H13  106.38  3.000
 VKV  H14  C05  C09  108.47  3.000
 VKV  H13  C05  C09  109.50  3.000
 VKV  H14  C05  C04  109.95  3.000
 VKV  H13  C05  C04  109.41  3.000
 VKV  C09  C05  C04  112.91  3.000
 VKV  H16  C06  H15  106.61  3.000
 VKV  H16  C06  C04  109.22  3.000
 VKV  H15  C06  C04  109.69  3.000
 VKV  H16  C06  O01  111.45  3.000
 VKV  H15  C06  O01  110.16  3.000
 VKV  C04  C06  O01  109.66  3.000
 VKV  H18  C07  H17  106.07  3.000
 VKV  H18  C07  C11  108.75  3.000
 VKV  H17  C07  C11  109.08  3.000
 VKV  H18  C07  C08  109.17  3.000
 VKV  H17  C07  C08  109.24  3.000
 VKV  C11  C07  C08  114.21  3.000
 VKV  H20  C08  H19  106.10  3.000
 VKV  H20  C08  C12  109.21  3.000
 VKV  H19  C08  C12  109.28  3.000
 VKV  H20  C08  C07  109.82  3.000
 VKV  H19  C08  C07  109.46  3.000
 VKV  C12  C08  C07  112.74  3.000
 VKV  H22  C11  H21  105.73  3.000
 VKV  H22  C11  C16  109.20  3.000
 VKV  H21  C11  C16  110.77  3.000
 VKV  H22  C11  C07  108.29  3.000
 VKV  H21  C11  C07  109.62  3.000
 VKV  C16  C11  C07  112.96  3.000
 VKV  H24  C12  H23  105.95  3.000
 VKV  H24  C12  C08  109.20  3.000
 VKV  H23  C12  C08  109.28  3.000
 VKV  H24  C12  C17  109.62  3.000
 VKV  H23  C12  C17  109.49  3.000
 VKV  C08  C12  C17  113.06  3.000
 VKV  H26  C14  H25  106.94  3.000
 VKV  H26  C14  O03  111.51  3.000
 VKV  H25  C14  O03  111.66  3.000
 VKV  H26  C14  C10  108.09  3.000
 VKV  H25  C14  C10  109.82  3.000
 VKV  O03  C14  C10  108.76  3.000
 VKV  H27  C16  C20  117.11  3.000
 VKV  H27  C16  C11  115.37  3.000
 VKV  C20  C16  C11  127.50  3.000
 VKV  H29  C19  H28  106.22  3.000
 VKV  H29  C19  C18  111.01  3.000
 VKV  H28  C19  C18  109.36  3.000
 VKV  H29  C19  C22  109.01  3.000
 VKV  H28  C19  C22  110.52  3.000
 VKV  C18  C19  C22  110.64  3.000
 VKV  H30  C23  C26  117.35  3.000
 VKV  H30  C23  C21  115.02  3.000
 VKV  C26  C23  C21  127.62  3.000
 VKV  H32  C09  H31  106.19  3.000
 VKV  H32  C09  C13  108.76  3.000
 VKV  H31  C09  C13  111.22  3.000
 VKV  H32  C09  C05  108.56  3.000
 VKV  H31  C09  C05  109.14  3.000
 VKV  C13  C09  C05  112.73  3.000
 VKV  H33  C13  C18  117.35  3.000
 VKV  H33  C13  C09  114.91  3.000
 VKV  C18  C13  C09  127.74  3.000
 VKV  H34  C18  C13  117.94  3.000
 VKV  H34  C18  C19  114.64  3.000
 VKV  C13  C18  C19  127.39  3.000
 VKV  H35  C20  C16  117.74  3.000
 VKV  H35  C20  C21  115.07  3.000
 VKV  C16  C20  C21  127.16  3.000
 VKV  H37  C24  H36  105.93  3.000
 VKV  H37  C24  C26  111.03  3.000
 VKV  H36  C24  C26  108.86  3.000
 VKV  H37  C24  C25  110.71  3.000
 VKV  H36  C24  C25  108.58  3.000
 VKV  C26  C24  C25  111.53  3.000
 VKV  H38  C25  C24  116.47  3.000
 VKV  H38  C25  C22  118.21  3.000
 VKV  C24  C25  C22  125.31  3.000
 VKV  H39  C26  C24  115.09  3.000
 VKV  H39  C26  C23  117.58  3.000
 VKV  C24  C26  C23  127.33  3.000
 VKV  H40  O02  C15  108.22  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
 VKV  Var_01  C11  C16  C20  C21    -1.11   0.0  2
 VKV  Var_02  C24  C26  C23  C21     0.84   0.0  2
 VKV  Var_03  C24  C25  C22  C19    -0.93   0.0  2
 VKV  Var_04  C09  C13  C18  C19    -0.41   0.0  2
 VKV  Var_05  C04  C06  O01  C10   173.72  30.0  3
 VKV  Var_06  O03  C14  C10  C15  -168.11  30.0  2
 VKV  Var_07  C07  C08  C12  C17   177.38  30.0  3
 VKV  Var_08  C13  C18  C19  C22  -107.76  30.0  3
 VKV  Var_09  C26  C24  C25  C22   -85.74  30.0  2
 VKV  Var_10  O02  C15  C10  O01    63.27  30.0  3
 VKV  Var_11  C05  C04  C06  O01    63.21  30.0  1
 VKV  Var_12  C13  C09  C05  C04   -63.83  30.0  2
 VKV  Var_13  C18  C13  C09  C05   116.18  30.0  3
 VKV  Var_14  C09  C05  C04  C06  -179.74  30.0  1
 VKV  Var_15  C14  C10  O01  C06  -157.69  30.0  3
 VKV  Var_16  C20  C16  C11  C07  -151.39  30.0  2
 VKV  Var_17  C16  C11  C07  C08    60.96  30.0  3
 VKV  Var_18  C12  C08  C07  C11   178.12  30.0  3
 VKV  Var_19  C23  C21  C20  C16   133.48  30.0  3
 VKV  Var_20  C25  C24  C26  C23   128.14  30.0  3
 VKV  Var_21  C25  C22  C19  C18  -100.60  30.0  3
 VKV  Var_22  C26  C23  C21  C20  -137.27  30.0  3
 VKV  Var_23  H4   C17  C12  C08   179.33  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
 VKV  plan-1  C21  0.020
 VKV  plan-1  C11  0.020
 VKV  plan-1  C16  0.020
 VKV  plan-1  C20  0.020
 VKV  plan-1  H27  0.020
 VKV  plan-1  H35  0.020
 VKV  plan-2  C21  0.020
 VKV  plan-2  C23  0.020
 VKV  plan-2  C24  0.020
 VKV  plan-2  C26  0.020
 VKV  plan-2  H30  0.020
 VKV  plan-2  H39  0.020
 VKV  plan-3  C22  0.020
 VKV  plan-3  C19  0.020
 VKV  plan-3  C24  0.020
 VKV  plan-3  C25  0.020
 VKV  plan-3  H9   0.020
 VKV  plan-3  H38  0.020
 VKV  plan-4  C19  0.020
 VKV  plan-4  C09  0.020
 VKV  plan-4  C13  0.020
 VKV  plan-4  C18  0.020
 VKV  plan-4  H33  0.020
 VKV  plan-4  H34  0.020

