# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 06:32:59 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: 1,3-dihydroxypropan-2-yl (9Z)-octadec-9-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC\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
 YOG  YOG  '1,3-dihydroxypropan-2-yl (9Z)-octadec-9-enoate'  ligand  65  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_YOG
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
 YOG  O01   O  O2    0  -0.469  11.5768  6.7321   -5.1959
 YOG  O02   O  O     0  -0.447  11.9117  4.6654   -5.9869
 YOG  O03   O  OH1   0  -0.666  10.7318  8.4670   -3.1480
 YOG  O04   O  OH1   0  -0.666   8.7001  5.7396   -3.2479
 YOG  C05   C  CH2   0  -0.437  15.8497  6.6037   -6.8443
 YOG  C06   C  CH2   0  -0.415  17.1031  6.2927   -6.0295
 YOG  C07   C  CH2   0  -0.413  20.7036  7.2514  -10.6747
 YOG  C08   C  CH2   0  -0.415  20.7522  6.6268   -9.2847
 YOG  C09   C  CH2   0  -0.435  14.9916  5.3823   -7.1558
 YOG  C10   C  CH2   0  -0.424  19.2893  7.3597  -11.2399
 YOG  C11   C  CH2   0  -0.429  18.0853  5.3583   -6.7282
 YOG  C12   C  CH2   0  -0.414  22.1614  6.3042   -8.8094
 YOG  C13   C  CH2   0  -0.440  13.7364  5.6974   -7.9673
 YOG  C14   C  CH2   0  -0.429  18.3484  8.2127  -10.3948
 YOG  C15   C  CH2   0  -0.484  19.4120  5.2283   -5.9773
 YOG  C16   C  CH2   0  -0.498  22.2014  5.7802   -7.3692
 YOG  C17   C  CH2   0  -0.422  16.9791  8.4412  -11.0283
 YOG  C18   C  CH2   0  -0.588  12.7058  6.5573   -7.2458
 YOG  C19   C  C1    0  -0.205  20.3289  4.2329   -6.6186
 YOG  C20   C  C1    0  -0.215  21.4998  4.4668   -7.2110
 YOG  C21   C  CH3   0  -0.673  16.1671  7.1647  -11.2109
 YOG  C22   C  C     0   0.598  12.0415  5.8595   -6.0879
 YOG  C23   C  CH1   0  -0.040  10.8687  6.2529   -4.0432
 YOG  C24   C  CH2   0  -0.166  11.2084  7.1700   -2.8883
 YOG  C25   C  CH2   0  -0.163   9.3854  6.1952   -4.3892
 YOG  H031  H  HOH1  0   0.457  10.8897  9.0077   -2.3693
 YOG  H041  H  HOH1  0   0.458   7.7581  5.7478   -3.4387
 YOG  H052  H  HCH2  0   0.223  15.2576  7.3440   -6.2984
 YOG  H051  H  HCH2  0   0.215  16.1415  7.0866   -7.7843
 YOG  H062  H  HCH2  0   0.210  16.8153  5.8593   -5.0656
 YOG  H061  H  HCH2  0   0.216  17.6125  7.2334   -5.7976
 YOG  H071  H  HCH2  0   0.213  21.3126  6.6526  -11.3598
 YOG  H072  H  HCH2  0   0.206  21.1661  8.2438  -10.6454
 YOG  H082  H  HCH2  0   0.209  20.2813  7.2999   -8.5612
 YOG  H081  H  HCH2  0   0.212  20.1479  5.7139   -9.2810
 YOG  H092  H  HCH2  0   0.214  14.7195  4.8785   -6.2225
 YOG  H091  H  HCH2  0   0.229  15.5828  4.6577   -7.7216
 YOG  H102  H  HCH2  0   0.212  19.3366  7.7788  -12.2506
 YOG  H101  H  HCH2  0   0.211  18.8791  6.3507  -11.3491
 YOG  H111  H  HCH2  0   0.223  18.2806  5.7264   -7.7408
 YOG  H112  H  HCH2  0   0.218  17.6409  4.3656   -6.8456
 YOG  H122  H  HCH2  0   0.210  22.6173  5.5695   -9.4815
 YOG  H121  H  HCH2  0   0.218  22.7836  7.2023   -8.8723
 YOG  H132  H  HCH2  0   0.233  13.2653  4.7661   -8.2877
 YOG  H131  H  HCH2  0   0.236  14.0282  6.2179   -8.8834
 YOG  H141  H  HCH2  0   0.218  18.2049  7.7496   -9.4124
 YOG  H142  H  HCH2  0   0.213  18.8227  9.1817  -10.2058
 YOG  H152  H  HCH2  0   0.225  19.2012  4.9123   -4.9492
 YOG  H151  H  HCH2  0   0.226  19.8829  6.2111   -5.9060
 YOG  H162  H  HCH2  0   0.234  23.2467  5.6592   -7.0694
 YOG  H161  H  HCH2  0   0.228  21.7774  6.5352   -6.7034
 YOG  H171  H  HCH2  0   0.209  17.1029  8.9376  -11.9960
 YOG  H172  H  HCH2  0   0.218  16.4134  9.1362  -10.4017
 YOG  H182  H  HCH2  0   0.263  13.1327  7.5040   -6.9120
 YOG  H181  H  HCH2  0   0.288  11.9049  6.8278   -7.9430
 YOG  H191  H  H     0   0.224  19.9659  3.2079   -6.6148
 YOG  H201  H  H     0   0.224  22.0111  3.6179   -7.6586
 YOG  H211  H  HCH3  0   0.225  15.1651  7.3830  -11.5824
 YOG  H212  H  HCH3  0   0.221  16.6343  6.4803  -11.9198
 YOG  H213  H  HCH3  0   0.221  16.0583  6.6326  -10.2630
 YOG  H231  H  HCH1  0   0.252  11.2189  5.2514   -3.7792
 YOG  H242  H  HCH2  0   0.212  10.7676  6.7404   -1.9818
 YOG  H241  H  HCH2  0   0.214  12.2972  7.1540   -2.7459
 YOG  H251  H  HCH2  0   0.211   9.2478  5.5156   -5.2398
 YOG  H252  H  HCH2  0   0.207   9.0428  7.1859   -4.7084

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
 YOG  C10  C07   single  1.527  0.020  1.527
 YOG  C10  C14   single  1.525  0.020  1.525
 YOG  C21  C17   single  1.524  0.020  1.524
 YOG  C07  C08   single  1.525  0.020  1.525
 YOG  C17  C14   single  1.526  0.020  1.526
 YOG  C12  C08   single  1.522  0.020  1.522
 YOG  C12  C16   single  1.533  0.020  1.533
 YOG  C16  C20   single  1.497  0.020  1.497
 YOG  C20  C19   double  1.333  0.020  1.333
 YOG  C19  C15   single  1.498  0.020  1.498
 YOG  C15  C11   single  1.530  0.020  1.530
 YOG  C13  C18   single  1.524  0.020  1.524
 YOG  C13  C09   single  1.528  0.020  1.528
 YOG  C11  C06   single  1.525  0.020  1.525
 YOG  C05  C06   single  1.527  0.020  1.527
 YOG  C05  C09   single  1.525  0.020  1.525
 YOG  C18  C22   single  1.506  0.020  1.506
 YOG  C25  O04   single  1.407  0.020  1.407
 YOG  C25  C23   single  1.524  0.020  1.524
 YOG  C22  O02   double  1.205  0.020  1.205
 YOG  C22  O01   single  1.332  0.020  1.332
 YOG  O01  C23   single  1.435  0.020  1.435
 YOG  C23  C24   single  1.513  0.020  1.513
 YOG  O03  C24   single  1.406  0.020  1.406
 YOG  O03  H031  single  0.850  0.020  0.980
 YOG  O04  H041  single  0.850  0.020  0.980
 YOG  C05  H052  single  0.970  0.020  1.090
 YOG  C05  H051  single  0.970  0.020  1.090
 YOG  C06  H062  single  0.970  0.020  1.090
 YOG  C06  H061  single  0.970  0.020  1.090
 YOG  C07  H071  single  0.970  0.020  1.090
 YOG  C07  H072  single  0.970  0.020  1.090
 YOG  C08  H082  single  0.970  0.020  1.090
 YOG  C08  H081  single  0.970  0.020  1.090
 YOG  C09  H092  single  0.970  0.020  1.090
 YOG  C09  H091  single  0.970  0.020  1.090
 YOG  C10  H102  single  0.970  0.020  1.090
 YOG  C10  H101  single  0.970  0.020  1.090
 YOG  C11  H111  single  0.970  0.020  1.090
 YOG  C11  H112  single  0.970  0.020  1.090
 YOG  C12  H122  single  0.970  0.020  1.090
 YOG  C12  H121  single  0.970  0.020  1.090
 YOG  C13  H132  single  0.970  0.020  1.090
 YOG  C13  H131  single  0.970  0.020  1.090
 YOG  C14  H141  single  0.970  0.020  1.090
 YOG  C14  H142  single  0.970  0.020  1.090
 YOG  C15  H152  single  0.970  0.020  1.090
 YOG  C15  H151  single  0.970  0.020  1.090
 YOG  C16  H162  single  0.970  0.020  1.090
 YOG  C16  H161  single  0.970  0.020  1.090
 YOG  C17  H171  single  0.970  0.020  1.090
 YOG  C17  H172  single  0.970  0.020  1.090
 YOG  C18  H182  single  0.970  0.020  1.090
 YOG  C18  H181  single  0.970  0.020  1.090
 YOG  C19  H191  single  0.930  0.020  1.080
 YOG  C20  H201  single  0.930  0.020  1.080
 YOG  C21  H211  single  0.970  0.020  1.090
 YOG  C21  H212  single  0.970  0.020  1.090
 YOG  C21  H213  single  0.970  0.020  1.090
 YOG  C23  H231  single  0.970  0.020  1.090
 YOG  C24  H242  single  0.970  0.020  1.090
 YOG  C24  H241  single  0.970  0.020  1.090
 YOG  C25  H251  single  0.970  0.020  1.090
 YOG  C25  H252  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
 YOG  C23   O01  C22   119.43  3.000
 YOG  H031  O03  C24   108.28  3.000
 YOG  H041  O04  C25   108.28  3.000
 YOG  H051  C05  H052  105.89  3.000
 YOG  H051  C05  C09   109.12  3.000
 YOG  H052  C05  C09   109.84  3.000
 YOG  H051  C05  C06   109.19  3.000
 YOG  H052  C05  C06   108.41  3.000
 YOG  C09   C05  C06   114.07  3.000
 YOG  H061  C06  H062  106.01  3.000
 YOG  H061  C06  C11   108.89  3.000
 YOG  H062  C06  C11   109.26  3.000
 YOG  H061  C06  C05   108.66  3.000
 YOG  H062  C06  C05   109.54  3.000
 YOG  C11   C06  C05   114.14  3.000
 YOG  H072  C07  H071  106.10  3.000
 YOG  H072  C07  C10   109.68  3.000
 YOG  H071  C07  C10   108.81  3.000
 YOG  H072  C07  C08   109.47  3.000
 YOG  H071  C07  C08   109.19  3.000
 YOG  C10   C07  C08   113.33  3.000
 YOG  H081  C08  H082  105.85  3.000
 YOG  H081  C08  C12   109.47  3.000
 YOG  H082  C08  C12   108.80  3.000
 YOG  H081  C08  C07   109.09  3.000
 YOG  H082  C08  C07   109.69  3.000
 YOG  C12   C08  C07   113.65  3.000
 YOG  H091  C09  H092  105.70  3.000
 YOG  H091  C09  C13   107.83  3.000
 YOG  H092  C09  C13   110.09  3.000
 YOG  H091  C09  C05   109.41  3.000
 YOG  H092  C09  C05   109.53  3.000
 YOG  C13   C09  C05   113.94  3.000
 YOG  H101  C10  H102  106.07  3.000
 YOG  H101  C10  C14   109.85  3.000
 YOG  H102  C10  C14   108.90  3.000
 YOG  H101  C10  C07   108.58  3.000
 YOG  H102  C10  C07   109.19  3.000
 YOG  C14   C10  C07   113.95  3.000
 YOG  H112  C11  H111  106.15  3.000
 YOG  H112  C11  C15   109.14  3.000
 YOG  H111  C11  C15   109.13  3.000
 YOG  H112  C11  C06   110.09  3.000
 YOG  H111  C11  C06   109.42  3.000
 YOG  C15   C11  C06   112.69  3.000
 YOG  H121  C12  H122  106.18  3.000
 YOG  H121  C12  C16   108.64  3.000
 YOG  H122  C12  C16   109.66  3.000
 YOG  H121  C12  C08   109.55  3.000
 YOG  H122  C12  C08   109.63  3.000
 YOG  C16   C12  C08   112.96  3.000
 YOG  H131  C13  H132  105.98  3.000
 YOG  H131  C13  C18   107.97  3.000
 YOG  H132  C13  C18   109.18  3.000
 YOG  H131  C13  C09   108.91  3.000
 YOG  H132  C13  C09   109.55  3.000
 YOG  C18   C13  C09   114.88  3.000
 YOG  H142  C14  H141  106.02  3.000
 YOG  H142  C14  C17   109.13  3.000
 YOG  H141  C14  C17   108.54  3.000
 YOG  H142  C14  C10   108.85  3.000
 YOG  H141  C14  C10   109.95  3.000
 YOG  C17   C14  C10   114.03  3.000
 YOG  H151  C15  H152  106.33  3.000
 YOG  H151  C15  C19   111.23  3.000
 YOG  H152  C15  C19   109.13  3.000
 YOG  H151  C15  C11   109.24  3.000
 YOG  H152  C15  C11   108.55  3.000
 YOG  C19   C15  C11   112.16  3.000
 YOG  H161  C16  H162  106.28  3.000
 YOG  H161  C16  C20   111.10  3.000
 YOG  H162  C16  C20   108.76  3.000
 YOG  H161  C16  C12   109.04  3.000
 YOG  H162  C16  C12   108.67  3.000
 YOG  C20   C16  C12   112.75  3.000
 YOG  H172  C17  H171  106.07  3.000
 YOG  H172  C17  C21   108.99  3.000
 YOG  H171  C17  C21   109.52  3.000
 YOG  H172  C17  C14   108.75  3.000
 YOG  H171  C17  C14   109.48  3.000
 YOG  C21   C17  C14   113.73  3.000
 YOG  H181  C18  H182  105.46  3.000
 YOG  H181  C18  C22   106.33  3.000
 YOG  H182  C18  C22   109.84  3.000
 YOG  H181  C18  C13   109.42  3.000
 YOG  H182  C18  C13   111.71  3.000
 YOG  C22   C18  C13   113.63  3.000
 YOG  H191  C19  C20   117.40  3.000
 YOG  H191  C19  C15   114.88  3.000
 YOG  C20   C19  C15   127.70  3.000
 YOG  H201  C20  C19   117.33  3.000
 YOG  H201  C20  C16   114.89  3.000
 YOG  C19   C20  C16   127.77  3.000
 YOG  H213  C21  H212  107.52  3.000
 YOG  H213  C21  H211  107.55  3.000
 YOG  H212  C21  H211  107.33  3.000
 YOG  H213  C21  C17   110.92  3.000
 YOG  H212  C21  C17   112.05  3.000
 YOG  H211  C21  C17   111.27  3.000
 YOG  C18   C22  O02   124.81  3.000
 YOG  O02   C22  O01   123.75  3.000
 YOG  C18   C22  O01   111.42  3.000
 YOG  H231  C23  C25   109.38  3.000
 YOG  H231  C23  C24   107.39  3.000
 YOG  C25   C23  C24   114.49  3.000
 YOG  H231  C23  O01   109.98  3.000
 YOG  C24   C23  O01   107.45  3.000
 YOG  C25   C23  O01   108.09  3.000
 YOG  H241  C24  H242  106.61  3.000
 YOG  H241  C24  C23   108.22  3.000
 YOG  H242  C24  C23   107.67  3.000
 YOG  H241  C24  O03   111.93  3.000
 YOG  H242  C24  O03   112.22  3.000
 YOG  C23   C24  O03   109.99  3.000
 YOG  H252  C25  H251  107.15  3.000
 YOG  H252  C25  C23   109.64  3.000
 YOG  H251  C25  C23   108.75  3.000
 YOG  H252  C25  O04   112.14  3.000
 YOG  H251  C25  O04   111.53  3.000
 YOG  C23   C25  O04   107.59  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
 YOG  Var_01  C16   C20  C19  C15     0.86   0.0  2
 YOG  Var_02  C13   C18  C22  O01   155.58  30.0  2
 YOG  Var_03  O04   C25  C23  O01  -179.32  30.0  2
 YOG  Var_04  O03   C24  C23  O01    64.09  30.0  3
 YOG  Var_05  C15   C11  C06  C05   171.75  30.0  1
 YOG  Var_06  C18   C13  C09  C05   -65.88  30.0  1
 YOG  Var_07  C19   C15  C11  C06   175.83  30.0  1
 YOG  Var_08  C13   C09  C05  C06   179.82  30.0  3
 YOG  Var_09  C17   C14  C10  C07   174.03  30.0  3
 YOG  Var_10  C16   C12  C08  C07   175.47  30.0  2
 YOG  Var_11  C14   C10  C07  C08    60.19  30.0  2
 YOG  Var_12  C20   C16  C12  C08    64.48  30.0  3
 YOG  Var_13  C22   C18  C13  C09   -68.09  30.0  3
 YOG  Var_14  C11   C06  C05  C09    62.20  30.0  3
 YOG  Var_15  C12   C08  C07  C10   170.47  30.0  3
 YOG  Var_16  C21   C17  C14  C10    63.73  30.0  2
 YOG  Var_17  C20   C19  C15  C11   114.00  30.0  2
 YOG  Var_18  C19   C20  C16  C12  -107.38  30.0  3
 YOG  Var_19  H211  C21  C17  C14   174.92  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
 YOG  plan-1  C15   0.020
 YOG  plan-1  C16   0.020
 YOG  plan-1  C19   0.020
 YOG  plan-1  C20   0.020
 YOG  plan-1  H191  0.020
 YOG  plan-1  H201  0.020
 YOG  plan-2  O01   0.020
 YOG  plan-2  O02   0.020
 YOG  plan-2  C18   0.020
 YOG  plan-2  C22   0.020

