# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 10:02:32 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: 1,3-dihydroxypropan-2-yl dodecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=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
 VLZ  VLZ  '1,3-dihydroxypropan-2-yl dodecanoate'  ligand  49  19  .  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_VLZ
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
 VLZ  O01   O  O2    0  -0.471   3.6427  10.9643  16.9279
 VLZ  O02   O  O     0  -0.445   1.6320  10.0941  16.4635
 VLZ  O03   O  OH1   0  -0.666   4.0119   9.1508  20.0283
 VLZ  O04   O  OH1   0  -0.666   6.2393  10.7107  17.9680
 VLZ  C05   C  CH2   0  -0.420   0.0366  15.9941  14.1670
 VLZ  C06   C  CH2   0  -0.429  -0.4188  17.1074  15.1066
 VLZ  C07   C  CH2   0  -0.419   0.3338  14.6926  14.8998
 VLZ  C08   C  CH2   0  -0.427  -0.7859  18.4230  14.4086
 VLZ  C09   C  CH2   0  -0.425   0.7842  13.5717  13.9692
 VLZ  C10   C  CH2   0  -0.419  -2.2685  18.5810  14.0741
 VLZ  C11   C  CH2   0  -0.428   1.0216  12.2376  14.6717
 VLZ  C12   C  CH2   0  -0.410  -2.8413  17.5329  13.1281
 VLZ  C13   C  CH2   0  -0.588   2.2085  12.2763  15.6243
 VLZ  C14   C  CH2   0  -0.412  -4.2941  17.8010  12.7544
 VLZ  C15   C  CH3   0  -0.658  -4.8591  16.7565  11.8017
 VLZ  C16   C  C     0   0.607   2.4352  10.9867  16.3650
 VLZ  C17   C  CH1   0  -0.041   4.0117   9.8605  17.7674
 VLZ  C18   C  CH2   0  -0.162   3.6322  10.2217  19.1991
 VLZ  C19   C  CH2   0  -0.167   5.4864   9.5970  17.5557
 VLZ  H031  H  HOH1  0   0.458   3.8117   9.3886  20.9379
 VLZ  H041  H  HOH1  0   0.457   7.1710  10.4831  17.9061
 VLZ  H051  H  HCH2  0   0.209   0.9342  16.3235  13.6323
 VLZ  H052  H  HCH2  0   0.218  -0.7205  15.8122  13.3995
 VLZ  H062  H  HCH2  0   0.209  -1.2746  16.7583  15.6955
 VLZ  H061  H  HCH2  0   0.218   0.3828  17.2879  15.8290
 VLZ  H072  H  HCH2  0   0.207  -0.5636  14.3692  15.4391
 VLZ  H071  H  HCH2  0   0.213   1.0947  14.8821  15.6638
 VLZ  H081  H  HCH2  0   0.209  -0.1918  18.5292  13.4945
 VLZ  H082  H  HCH2  0   0.222  -0.4981  19.2622  15.0470
 VLZ  H091  H  HCH2  0   0.211   1.6943  13.8758  13.4409
 VLZ  H092  H  HCH2  0   0.223   0.0208  13.4276  13.1989
 VLZ  H102  H  HCH2  0   0.211  -2.4233  19.5725  13.6356
 VLZ  H101  H  HCH2  0   0.205  -2.8452  18.5727  15.0058
 VLZ  H112  H  HCH2  0   0.223   0.1172  11.9507  15.2140
 VLZ  H111  H  HCH2  0   0.233   1.1906  11.4612  13.9215
 VLZ  H121  H  HCH2  0   0.211  -2.7743  16.5398  13.5832
 VLZ  H122  H  HCH2  0   0.202  -2.2338  17.4923  12.2167
 VLZ  H131  H  HCH2  0   0.265   3.1218  12.5516  15.0903
 VLZ  H132  H  HCH2  0   0.279   2.0699  13.0519  16.3848
 VLZ  H141  H  HCH2  0   0.208  -4.3748  18.7937  12.3008
 VLZ  H142  H  HCH2  0   0.208  -4.9010  17.8339  13.6647
 VLZ  H153  H  HCH3  0   0.224  -5.9011  16.9605  11.5529
 VLZ  H151  H  HCH3  0   0.214  -4.2955  16.7308  10.8671
 VLZ  H152  H  HCH3  0   0.214  -4.8132  15.7576  12.2392
 VLZ  H171  H  HCH1  0   0.253   3.4724   8.9592  17.4639
 VLZ  H181  H  HCH2  0   0.206   4.1249  11.1582  19.4837
 VLZ  H182  H  HCH2  0   0.210   2.5499  10.3996  19.2418
 VLZ  H192  H  HCH2  0   0.212   5.7459   8.6913  18.1154
 VLZ  H191  H  HCH2  0   0.214   5.6452   9.3653  16.4940

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
 VLZ  C15  C14   single  1.522  0.020  1.522
 VLZ  C14  C12   single  1.524  0.020  1.524
 VLZ  C12  C10   single  1.524  0.020  1.524
 VLZ  C09  C11   single  1.526  0.020  1.526
 VLZ  C09  C07   single  1.525  0.020  1.525
 VLZ  C10  C08   single  1.528  0.020  1.528
 VLZ  C05  C07   single  1.523  0.020  1.523
 VLZ  C05  C06   single  1.526  0.020  1.526
 VLZ  C08  C06   single  1.534  0.020  1.534
 VLZ  C11  C13   single  1.522  0.020  1.522
 VLZ  C13  C16   single  1.504  0.020  1.504
 VLZ  C16  O02   double  1.205  0.020  1.205
 VLZ  C16  O01   single  1.332  0.020  1.332
 VLZ  O01  C17   single  1.435  0.020  1.435
 VLZ  C17  C19   single  1.513  0.020  1.513
 VLZ  C17  C18   single  1.525  0.020  1.525
 VLZ  C19  O04   single  1.406  0.020  1.406
 VLZ  C18  O03   single  1.407  0.020  1.407
 VLZ  O03  H031  single  0.850  0.020  0.980
 VLZ  O04  H041  single  0.850  0.020  0.980
 VLZ  C05  H051  single  0.970  0.020  1.090
 VLZ  C05  H052  single  0.970  0.020  1.090
 VLZ  C06  H062  single  0.970  0.020  1.090
 VLZ  C06  H061  single  0.970  0.020  1.090
 VLZ  C07  H072  single  0.970  0.020  1.090
 VLZ  C07  H071  single  0.970  0.020  1.090
 VLZ  C08  H081  single  0.970  0.020  1.090
 VLZ  C08  H082  single  0.970  0.020  1.090
 VLZ  C09  H091  single  0.970  0.020  1.090
 VLZ  C09  H092  single  0.970  0.020  1.090
 VLZ  C10  H102  single  0.970  0.020  1.090
 VLZ  C10  H101  single  0.970  0.020  1.090
 VLZ  C11  H112  single  0.970  0.020  1.090
 VLZ  C11  H111  single  0.970  0.020  1.090
 VLZ  C12  H121  single  0.970  0.020  1.090
 VLZ  C12  H122  single  0.970  0.020  1.090
 VLZ  C13  H131  single  0.970  0.020  1.090
 VLZ  C13  H132  single  0.970  0.020  1.090
 VLZ  C14  H141  single  0.970  0.020  1.090
 VLZ  C14  H142  single  0.970  0.020  1.090
 VLZ  C15  H153  single  0.970  0.020  1.090
 VLZ  C15  H151  single  0.970  0.020  1.090
 VLZ  C15  H152  single  0.970  0.020  1.090
 VLZ  C17  H171  single  0.970  0.020  1.090
 VLZ  C18  H181  single  0.970  0.020  1.090
 VLZ  C18  H182  single  0.970  0.020  1.090
 VLZ  C19  H192  single  0.970  0.020  1.090
 VLZ  C19  H191  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
 VLZ  C17   O01  C16   119.55  3.000
 VLZ  H031  O03  C18   108.26  3.000
 VLZ  H041  O04  C19   108.22  3.000
 VLZ  H052  C05  H051  105.95  3.000
 VLZ  H052  C05  C07   109.31  3.000
 VLZ  H051  C05  C07   109.39  3.000
 VLZ  H052  C05  C06   110.29  3.000
 VLZ  H051  C05  C06   109.00  3.000
 VLZ  C07   C05  C06   112.67  3.000
 VLZ  H061  C06  H062  105.65  3.000
 VLZ  H061  C06  C08   109.53  3.000
 VLZ  H062  C06  C08   109.32  3.000
 VLZ  H061  C06  C05   107.95  3.000
 VLZ  H062  C06  C05   109.36  3.000
 VLZ  C08   C06  C05   114.64  3.000
 VLZ  H071  C07  H072  106.07  3.000
 VLZ  H071  C07  C09   110.36  3.000
 VLZ  H072  C07  C09   108.99  3.000
 VLZ  H071  C07  C05   108.87  3.000
 VLZ  H072  C07  C05   109.22  3.000
 VLZ  C09   C07  C05   113.09  3.000
 VLZ  H082  C08  H081  105.67  3.000
 VLZ  H082  C08  C10   107.69  3.000
 VLZ  H081  C08  C10   109.48  3.000
 VLZ  H082  C08  C06   109.25  3.000
 VLZ  H081  C08  C06   109.46  3.000
 VLZ  C10   C08  C06   114.87  3.000
 VLZ  H092  C09  H091  106.07  3.000
 VLZ  H092  C09  C11   108.51  3.000
 VLZ  H091  C09  C11   109.60  3.000
 VLZ  H092  C09  C07   108.69  3.000
 VLZ  H091  C09  C07   109.61  3.000
 VLZ  C11   C09  C07   114.05  3.000
 VLZ  H101  C10  H102  105.84  3.000
 VLZ  H101  C10  C12   108.95  3.000
 VLZ  H102  C10  C12   108.73  3.000
 VLZ  H101  C10  C08   108.89  3.000
 VLZ  H102  C10  C08   108.57  3.000
 VLZ  C12   C10  C08   115.44  3.000
 VLZ  H111  C11  H112  106.39  3.000
 VLZ  H111  C11  C13   109.09  3.000
 VLZ  H112  C11  C13   109.96  3.000
 VLZ  H111  C11  C09   109.21  3.000
 VLZ  H112  C11  C09   109.21  3.000
 VLZ  C13   C11  C09   112.77  3.000
 VLZ  H122  C12  H121  106.15  3.000
 VLZ  H122  C12  C14   109.33  3.000
 VLZ  H121  C12  C14   108.66  3.000
 VLZ  H122  C12  C10   109.48  3.000
 VLZ  H121  C12  C10   110.06  3.000
 VLZ  C14   C12  C10   112.93  3.000
 VLZ  H132  C13  H131  105.46  3.000
 VLZ  H132  C13  C16   106.52  3.000
 VLZ  H131  C13  C16   109.30  3.000
 VLZ  H132  C13  C11   110.72  3.000
 VLZ  H131  C13  C11   110.62  3.000
 VLZ  C16   C13  C11   113.82  3.000
 VLZ  H142  C14  H141  106.05  3.000
 VLZ  H142  C14  C15   109.59  3.000
 VLZ  H141  C14  C15   109.60  3.000
 VLZ  H142  C14  C12   109.27  3.000
 VLZ  H141  C14  C12   109.36  3.000
 VLZ  C15   C14  C12   112.74  3.000
 VLZ  H152  C15  H151  107.45  3.000
 VLZ  H152  C15  H153  107.62  3.000
 VLZ  H151  C15  H153  107.60  3.000
 VLZ  H152  C15  C14   111.19  3.000
 VLZ  H151  C15  C14   111.12  3.000
 VLZ  H153  C15  C14   111.66  3.000
 VLZ  C13   C16  O02   125.09  3.000
 VLZ  O02   C16  O01   123.86  3.000
 VLZ  C13   C16  O01   111.04  3.000
 VLZ  H171  C17  C19   107.36  3.000
 VLZ  H171  C17  C18   109.46  3.000
 VLZ  C19   C17  C18   114.54  3.000
 VLZ  H171  C17  O01   110.17  3.000
 VLZ  C18   C17  O01   107.65  3.000
 VLZ  C19   C17  O01   107.62  3.000
 VLZ  H182  C18  H181  107.14  3.000
 VLZ  H182  C18  C17   108.69  3.000
 VLZ  H181  C18  C17   109.54  3.000
 VLZ  H182  C18  O03   111.51  3.000
 VLZ  H181  C18  O03   112.09  3.000
 VLZ  C17   C18  O03   107.82  3.000
 VLZ  H191  C19  H192  106.56  3.000
 VLZ  H191  C19  C17   108.24  3.000
 VLZ  H192  C19  C17   107.66  3.000
 VLZ  H191  C19  O04   111.91  3.000
 VLZ  H192  C19  O04   112.21  3.000
 VLZ  C17   C19  O04   110.06  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
 VLZ  Var_01  C11   C13  C16  O01   165.19  30.0  2
 VLZ  Var_02  O04   C19  C17  O01    63.19  30.0  3
 VLZ  Var_03  O03   C18  C17  O01  -179.07  30.0  3
 VLZ  Var_04  C11   C09  C07  C05  -177.14  30.0  1
 VLZ  Var_05  C10   C08  C06  C05    93.81  30.0  1
 VLZ  Var_06  C09   C07  C05  C06   179.76  30.0  3
 VLZ  Var_07  C12   C10  C08  C06   -60.92  30.0  1
 VLZ  Var_08  C13   C11  C09  C07   -67.08  30.0  3
 VLZ  Var_09  C08   C06  C05  C07  -177.61  30.0  3
 VLZ  Var_10  C14   C12  C10  C08  -175.87  30.0  1
 VLZ  Var_11  C16   C13  C11  C09   178.02  30.0  3
 VLZ  Var_12  C15   C14  C12  C10   179.61  30.0  1
 VLZ  Var_13  H153  C15  C14  C12   179.51  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
 VLZ  plan-1  O01  0.020
 VLZ  plan-1  O02  0.020
 VLZ  plan-1  C13  0.020
 VLZ  plan-1  C16  0.020

