# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 14:56:37 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: 1,3-dihydroxypropan-2-yl (9Z,12Z)-octadeca-9,12-dienoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C\C=C/CCCCCCCC(=O)OC(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
 VL7  VL7  '1,3-dihydroxypropan-2-yl (9Z,12Z)-octadeca-9,12-dienoate'  ligand  63  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VL7
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
 VL7  C10  C  CH2   0  -0.419  15.1895   5.4473   -5.7916
 VL7  C13  C  CH2   0  -0.427  18.9920   5.2569   -6.5971
 VL7  C15  C  CH2   0  -0.496  21.3300   4.5455   -7.3083
 VL7  C17  C  C1    0  -0.211  21.2382   5.4082   -9.7045
 VL7  C20  C  C1    0  -0.192  19.7390   8.5190  -10.2408
 VL7  C21  C  CH2   0  -0.497  18.9867   8.7144   -8.9617
 VL7  C22  C  CH2   0  -0.428  17.4733   8.5860   -9.1463
 VL7  C24  C  CH2   0  -0.429  15.5148   7.0655   -9.6956
 VL7  O01  O  O     0  -0.444  12.3830   5.0351   -5.6045
 VL7  C02  C  C     0   0.605  12.7696   6.1759   -5.5898
 VL7  O03  O  O2    0  -0.472  11.9620   7.2299   -5.4822
 VL7  C04  C  CH1   0  -0.040  10.5454   7.0211   -5.3852
 VL7  C05  C  CH2   0  -0.164   9.9701   7.0300   -6.7973
 VL7  O06  O  OH1   0  -0.666   8.5821   6.8255   -6.6933
 VL7  C07  C  CH2   0  -0.166   9.9865   8.0939   -4.4760
 VL7  O08  O  OH1   0  -0.666  10.1637   9.3585   -5.0634
 VL7  C09  C  CH2   0  -0.594  14.2082   6.6037   -5.6943
 VL7  C11  C  CH2   0  -0.432  16.6150   5.9341   -6.0144
 VL7  C12  C  CH2   0  -0.412  17.6276   4.7987   -6.0994
 VL7  C14  C  CH2   0  -0.421  20.0597   4.1733   -6.5368
 VL7  C16  C  C1    0  -0.210  21.1522   4.4413   -8.7921
 VL7  C18  C  CH2   0  -0.548  21.5089   6.8681   -9.4593
 VL7  C19  C  C1    0  -0.232  20.7954   7.7377  -10.4561
 VL7  C23  C  CH2   0  -0.426  17.0290   7.2261   -9.6690
 VL7  C25  C  CH3   0  -0.659  15.0743   5.6721  -10.1202
 VL7  H2   H  HCH2  0   0.224  14.9080   4.7890   -6.6180
 VL7  H1   H  HCH2  0   0.225  15.1416   4.8405   -4.8831
 VL7  H3   H  HCH2  0   0.208  19.3268   6.1247   -6.0178
 VL7  H4   H  HCH2  0   0.226  18.8878   5.6084   -7.6288
 VL7  H5   H  HCH2  0   0.239  22.1333   3.8621   -7.0151
 VL7  H6   H  HCH2  0   0.229  21.6611   5.5448   -7.0146
 VL7  H7   H  H     0   0.231  21.1068   5.1273  -10.7461
 VL7  H10  H  H     0   0.227  19.3595   9.0881  -11.0869
 VL7  H11  H  HCH2  0   0.233  19.3183   8.0054   -8.1996
 VL7  H12  H  HCH2  0   0.238  19.2023   9.7132   -8.5667
 VL7  H13  H  HCH2  0   0.214  17.1197   9.3704   -9.8238
 VL7  H14  H  HCH2  0   0.220  16.9900   8.7781   -8.1830
 VL7  H16  H  HCH2  0   0.214  15.0815   7.8130  -10.3671
 VL7  H15  H  HCH2  0   0.219  15.1116   7.2854   -8.7021
 VL7  H17  H  HCH1  0   0.252  10.3407   6.0546   -4.9166
 VL7  H18  H  HCH2  0   0.210  10.4513   6.2342   -7.3801
 VL7  H19  H  HCH2  0   0.207  10.2128   7.9806   -7.2851
 VL7  H20  H  HOH1  0   0.458   8.1991   6.9040   -7.5714
 VL7  H22  H  HCH2  0   0.214  10.4903   8.0187   -3.5033
 VL7  H21  H  HCH2  0   0.211   8.9299   7.8631   -4.2999
 VL7  H23  H  HOH1  0   0.457   9.7548  10.0150   -4.4931
 VL7  H25  H  HCH2  0   0.274  14.4431   7.2398   -4.8351
 VL7  H24  H  HCH2  0   0.277  14.3013   7.2556   -6.5695
 VL7  H27  H  HCH2  0   0.229  16.6468   6.5211   -6.9382
 VL7  H26  H  HCH2  0   0.214  16.9049   6.6220   -5.2133
 VL7  H29  H  HCH2  0   0.207  17.2503   4.0212   -6.7729
 VL7  H28  H  HCH2  0   0.211  17.7251   4.3253   -5.1165
 VL7  H31  H  HCH2  0   0.212  19.6588   3.2353   -6.9367
 VL7  H30  H  HCH2  0   0.222  20.3136   3.9720   -5.4923
 VL7  H32  H  H     0   0.227  20.9389   3.4379   -9.1534
 VL7  H35  H  HCH2  0   0.249  22.5849   7.0531   -9.5592
 VL7  H34  H  HCH2  0   0.245  21.2520   7.1420   -8.4357
 VL7  H36  H  H     0   0.231  21.2000   7.7053  -11.4640
 VL7  H38  H  HCH2  0   0.215  17.4656   6.4377   -9.0461
 VL7  H39  H  HCH2  0   0.220  17.4283   7.0623  -10.6751
 VL7  H40  H  HCH3  0   0.224  13.9875   5.5829  -10.1395
 VL7  H41  H  HCH3  0   0.216  15.4457   5.4261  -11.1167
 VL7  H42  H  HCH3  0   0.215  15.4547   4.9150   -9.4313

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
 VL7  C20  C19  double  1.331  0.020  1.331
 VL7  C20  C21  single  1.497  0.020  1.497
 VL7  C25  C24  single  1.522  0.020  1.522
 VL7  C19  C18  single  1.503  0.020  1.503
 VL7  C24  C23  single  1.523  0.020  1.523
 VL7  C22  C23  single  1.523  0.020  1.523
 VL7  C22  C21  single  1.530  0.020  1.530
 VL7  C18  C17  single  1.505  0.020  1.505
 VL7  C17  C16  double  1.332  0.020  1.332
 VL7  C16  C15  single  1.498  0.020  1.498
 VL7  C15  C14  single  1.532  0.020  1.532
 VL7  C13  C14  single  1.523  0.020  1.523
 VL7  C13  C12  single  1.523  0.020  1.523
 VL7  C11  C10  single  1.523  0.020  1.523
 VL7  C11  C12  single  1.524  0.020  1.524
 VL7  C09  C10  single  1.520  0.020  1.520
 VL7  C09  C02  single  1.505  0.020  1.505
 VL7  C05  O06  single  1.407  0.020  1.407
 VL7  C05  C04  single  1.525  0.020  1.525
 VL7  C02  O01  double  1.205  0.020  1.205
 VL7  C02  O03  single  1.332  0.020  1.332
 VL7  O03  C04  single  1.435  0.020  1.435
 VL7  O08  C07  single  1.406  0.020  1.406
 VL7  C04  C07  single  1.513  0.020  1.513
 VL7  C10  H2   single  0.970  0.020  1.090
 VL7  C10  H1   single  0.970  0.020  1.090
 VL7  C13  H3   single  0.970  0.020  1.090
 VL7  C13  H4   single  0.970  0.020  1.090
 VL7  C15  H5   single  0.970  0.020  1.090
 VL7  C15  H6   single  0.970  0.020  1.090
 VL7  C17  H7   single  0.930  0.020  1.080
 VL7  C20  H10  single  0.930  0.020  1.080
 VL7  C21  H11  single  0.970  0.020  1.090
 VL7  C21  H12  single  0.970  0.020  1.090
 VL7  C22  H13  single  0.970  0.020  1.090
 VL7  C22  H14  single  0.970  0.020  1.090
 VL7  C24  H16  single  0.970  0.020  1.090
 VL7  C24  H15  single  0.970  0.020  1.090
 VL7  C04  H17  single  0.970  0.020  1.090
 VL7  C05  H18  single  0.970  0.020  1.090
 VL7  C05  H19  single  0.970  0.020  1.090
 VL7  O06  H20  single  0.850  0.020  0.980
 VL7  C07  H22  single  0.970  0.020  1.090
 VL7  C07  H21  single  0.970  0.020  1.090
 VL7  O08  H23  single  0.850  0.020  0.980
 VL7  C09  H25  single  0.970  0.020  1.090
 VL7  C09  H24  single  0.970  0.020  1.090
 VL7  C11  H27  single  0.970  0.020  1.090
 VL7  C11  H26  single  0.970  0.020  1.090
 VL7  C12  H29  single  0.970  0.020  1.090
 VL7  C12  H28  single  0.970  0.020  1.090
 VL7  C14  H31  single  0.970  0.020  1.090
 VL7  C14  H30  single  0.970  0.020  1.090
 VL7  C16  H32  single  0.930  0.020  1.080
 VL7  C18  H35  single  0.970  0.020  1.090
 VL7  C18  H34  single  0.970  0.020  1.090
 VL7  C19  H36  single  0.930  0.020  1.080
 VL7  C23  H38  single  0.970  0.020  1.090
 VL7  C23  H39  single  0.970  0.020  1.090
 VL7  C25  H40  single  0.970  0.020  1.090
 VL7  C25  H41  single  0.970  0.020  1.090
 VL7  C25  H42  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
 VL7  H1   C10  H2   106.41  3.000
 VL7  H1   C10  C11  109.88  3.000
 VL7  H2   C10  C11  108.84  3.000
 VL7  H1   C10  C09  109.92  3.000
 VL7  H2   C10  C09  109.89  3.000
 VL7  C11  C10  C09  111.75  3.000
 VL7  H4   C13  H3   105.84  3.000
 VL7  H4   C13  C14  109.42  3.000
 VL7  H3   C13  C14  109.17  3.000
 VL7  H4   C13  C12  108.62  3.000
 VL7  H3   C13  C12  109.83  3.000
 VL7  C14  C13  C12  113.65  3.000
 VL7  H6   C15  H5   106.05  3.000
 VL7  H6   C15  C16  111.45  3.000
 VL7  H5   C15  C16  107.99  3.000
 VL7  H6   C15  C14  109.76  3.000
 VL7  H5   C15  C14  108.78  3.000
 VL7  C16  C15  C14  112.55  3.000
 VL7  H7   C17  C18  115.38  3.000
 VL7  H7   C17  C16  117.45  3.000
 VL7  C18  C17  C16  127.17  3.000
 VL7  H10  C20  C19  117.26  3.000
 VL7  H10  C20  C21  114.90  3.000
 VL7  C19  C20  C21  127.85  3.000
 VL7  H12  C21  H11  106.29  3.000
 VL7  H12  C21  C22  108.34  3.000
 VL7  H11  C21  C22  109.27  3.000
 VL7  H12  C21  C20  109.16  3.000
 VL7  H11  C21  C20  111.03  3.000
 VL7  C22  C21  C20  112.52  3.000
 VL7  H14  C22  H13  106.03  3.000
 VL7  H14  C22  C23  109.26  3.000
 VL7  H13  C22  C23  109.45  3.000
 VL7  H14  C22  C21  108.40  3.000
 VL7  H13  C22  C21  109.51  3.000
 VL7  C23  C22  C21  113.88  3.000
 VL7  H15  C24  H16  105.89  3.000
 VL7  H15  C24  C25  109.31  3.000
 VL7  H16  C24  C25  109.86  3.000
 VL7  H15  C24  C23  109.22  3.000
 VL7  H16  C24  C23  109.41  3.000
 VL7  C25  C24  C23  112.91  3.000
 VL7  C09  C02  O03  111.12  3.000
 VL7  O03  C02  O01  123.76  3.000
 VL7  C09  C02  O01  125.12  3.000
 VL7  C04  O03  C02  119.26  3.000
 VL7  H17  C04  C07  107.46  3.000
 VL7  H17  C04  C05  109.36  3.000
 VL7  C07  C04  C05  114.39  3.000
 VL7  H17  C04  O03  110.02  3.000
 VL7  C07  C04  O03  107.58  3.000
 VL7  C05  C04  O03  108.00  3.000
 VL7  H19  C05  H18  107.19  3.000
 VL7  H19  C05  O06  112.18  3.000
 VL7  H18  C05  O06  111.49  3.000
 VL7  H19  C05  C04  109.50  3.000
 VL7  H18  C05  C04  108.79  3.000
 VL7  O06  C05  C04  107.63  3.000
 VL7  H20  O06  C05  108.29  3.000
 VL7  H21  C07  H22  106.60  3.000
 VL7  H21  C07  O08  112.23  3.000
 VL7  H22  C07  O08  111.96  3.000
 VL7  H21  C07  C04  107.66  3.000
 VL7  H22  C07  C04  108.31  3.000
 VL7  O08  C07  C04  109.89  3.000
 VL7  H23  O08  C07  108.23  3.000
 VL7  H24  C09  H25  105.26  3.000
 VL7  H24  C09  C02  107.82  3.000
 VL7  H25  C09  C02  108.42  3.000
 VL7  H24  C09  C10  110.29  3.000
 VL7  H25  C09  C10  110.72  3.000
 VL7  C02  C09  C10  113.92  3.000
 VL7  H26  C11  H27  105.83  3.000
 VL7  H26  C11  C12  109.45  3.000
 VL7  H27  C11  C12  109.45  3.000
 VL7  H26  C11  C10  109.98  3.000
 VL7  H27  C11  C10  108.78  3.000
 VL7  C12  C11  C10  113.09  3.000
 VL7  H28  C12  H29  105.99  3.000
 VL7  H28  C12  C11  109.34  3.000
 VL7  H29  C12  C11  109.52  3.000
 VL7  H28  C12  C13  110.09  3.000
 VL7  H29  C12  C13  108.73  3.000
 VL7  C11  C12  C13  112.92  3.000
 VL7  H30  C14  H31  106.03  3.000
 VL7  H30  C14  C15  109.46  3.000
 VL7  H31  C14  C15  109.12  3.000
 VL7  H30  C14  C13  109.37  3.000
 VL7  H31  C14  C13  109.77  3.000
 VL7  C15  C14  C13  112.87  3.000
 VL7  H32  C16  C17  117.05  3.000
 VL7  H32  C16  C15  114.61  3.000
 VL7  C17  C16  C15  128.33  3.000
 VL7  H34  C18  H35  105.92  3.000
 VL7  H34  C18  C19  111.43  3.000
 VL7  H35  C18  C19  107.93  3.000
 VL7  H34  C18  C17  110.75  3.000
 VL7  H35  C18  C17  108.99  3.000
 VL7  C19  C18  C17  111.58  3.000
 VL7  H36  C19  C18  114.90  3.000
 VL7  H36  C19  C20  117.58  3.000
 VL7  C18  C19  C20  127.52  3.000
 VL7  H39  C23  H38  105.63  3.000
 VL7  H39  C23  C24  109.32  3.000
 VL7  H38  C23  C24  109.28  3.000
 VL7  H39  C23  C22  110.03  3.000
 VL7  H38  C23  C22  109.34  3.000
 VL7  C24  C23  C22  112.97  3.000
 VL7  H42  C25  H41  107.53  3.000
 VL7  H42  C25  H40  107.55  3.000
 VL7  H41  C25  H40  107.73  3.000
 VL7  H42  C25  C24  110.97  3.000
 VL7  H41  C25  C24  111.26  3.000
 VL7  H40  C25  C24  111.61  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
 VL7  Var_01  C18  C17  C16  C15    -1.48   0.0  2
 VL7  Var_02  C18  C19  C20  C21    -0.89   0.0  2
 VL7  Var_03  C13  C12  C11  C10   168.41  30.0  3
 VL7  Var_04  O01  C02  C09  C10    -1.41  30.0  3
 VL7  Var_05  C16  C15  C14  C13   -74.88  30.0  1
 VL7  Var_06  C12  C13  C14  C15   167.68  30.0  2
 VL7  Var_07  C20  C19  C18  C17   108.08  30.0  1
 VL7  Var_08  C14  C15  C16  C17   117.71  30.0  3
 VL7  Var_09  C23  C22  C21  C20    60.32  30.0  2
 VL7  Var_10  C24  C23  C22  C21   173.48  30.0  3
 VL7  Var_11  C25  C24  C23  C22  -175.76  30.0  2
 VL7  Var_12  C19  C20  C21  C22  -131.26  30.0  2
 VL7  Var_13  C11  C10  C09  C02   175.13  30.0  3
 VL7  Var_14  C05  C04  O03  C02   -90.52  30.0  3
 VL7  Var_15  O06  C05  C04  O03  -179.97  30.0  2
 VL7  Var_16  O08  C07  C04  O03    64.47  30.0  3
 VL7  Var_17  C09  C02  O03  C04   179.36  30.0  1
 VL7  Var_18  C12  C11  C10  C09   179.29  30.0  2
 VL7  Var_19  C14  C13  C12  C11   173.34  30.0  2
 VL7  Var_20  C19  C18  C17  C16  -146.98  30.0  2
 VL7  Var_21  H40  C25  C24  C23  -179.55  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
 VL7  plan-1  C20  0.020
 VL7  plan-1  C21  0.020
 VL7  plan-1  C18  0.020
 VL7  plan-1  C19  0.020
 VL7  plan-1  H10  0.020
 VL7  plan-1  H36  0.020
 VL7  plan-2  C15  0.020
 VL7  plan-2  C17  0.020
 VL7  plan-2  C16  0.020
 VL7  plan-2  C18  0.020
 VL7  plan-2  H7   0.020
 VL7  plan-2  H32  0.020
 VL7  plan-3  O01  0.020
 VL7  plan-3  C02  0.020
 VL7  plan-3  O03  0.020
 VL7  plan-3  C09  0.020

