# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:32:48 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1-hydroxydodecan-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC(=O)CCCO
#
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
 HDO  HDO  '1-hydroxydodecan-4-one   '  ligand  38  14  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HDO
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
 HDO  C02   C  CH2   0  -0.137   6.0894  -0.7272  -0.0097
 HDO  C03   C  CH2   0  -0.457   4.8984   0.2116  -0.0068
 HDO  C04   C  CH2   0  -0.564   3.5960  -0.5706   0.0066
 HDO  C05   C  C     0   0.409   2.3447   0.2732   0.0065
 HDO  C07   C  CH2   0  -0.554   1.0457  -0.4939   0.0142
 HDO  C08   C  CH2   0  -0.416  -0.2130   0.3580   0.0109
 HDO  C09   C  CH2   0  -0.415  -1.4770  -0.4939   0.0140
 HDO  C10   C  CH2   0  -0.413  -2.7540   0.3367   0.0122
 HDO  C11   C  CH2   0  -0.412  -4.0212  -0.5094   0.0134
 HDO  C12   C  CH2   0  -0.407  -5.2977   0.3224   0.0123
 HDO  C13   C  CH2   0  -0.419  -6.5684  -0.5191   0.0116
 HDO  C14   C  CH3   0  -0.662  -7.8341   0.3273   0.0093
 HDO  O01   O  OH1   0  -0.675   7.2754   0.0373  -0.0259
 HDO  O02   O  O     0  -0.410   2.3828   1.4831   0.0002
 HDO  H021  H  HCH2  0   0.190   6.0420  -1.3747   0.8764
 HDO  H022  H  HCH2  0   0.190   6.0267  -1.3878  -0.8849
 HDO  H031  H  HCH2  0   0.231   4.9527   0.8652   0.8674
 HDO  H032  H  HCH2  0   0.231   4.9405   0.8540  -0.8900
 HDO  H042  H  HCH2  0   0.266   3.5398  -1.2449  -0.8559
 HDO  H041  H  HCH2  0   0.266   3.5486  -1.2313   0.8801
 HDO  H071  H  HCH2  0   0.263   1.0542  -1.1698  -0.8490
 HDO  H072  H  HCH2  0   0.263   1.0577  -1.1576   0.8867
 HDO  H082  H  HCH2  0   0.221  -0.2181   1.0171   0.8836
 HDO  H081  H  HCH2  0   0.221  -0.2182   1.0100  -0.8672
 HDO  H092  H  HCH2  0   0.210  -1.4733  -1.1559  -0.8592
 HDO  H091  H  HCH2  0   0.210  -1.4727  -1.1504   0.8915
 HDO  H102  H  HCH2  0   0.208  -2.7581   0.9973   0.8867
 HDO  H101  H  HCH2  0   0.208  -2.7578   0.9947  -0.8641
 HDO  H111  H  HCH2  0   0.207  -4.0174  -1.1701  -0.8609
 HDO  H112  H  HCH2  0   0.207  -4.0172  -1.1672   0.8899
 HDO  H121  H  HCH2  0   0.206  -5.3018   0.9824   0.8872
 HDO  H122  H  HCH2  0   0.206  -5.3007   0.9818  -0.8633
 HDO  H131  H  HCH2  0   0.210  -6.5652  -1.1778  -0.8626
 HDO  H132  H  HCH2  0   0.210  -6.5671  -1.1770   0.8864
 HDO  H142  H  HCH3  0   0.216  -7.8772   0.9717   0.8896
 HDO  H14   H  HCH3  0   0.215  -7.8737   0.9714  -0.8714
 HDO  H141  H  HCH3  0   0.226  -8.7335  -0.2898   0.0073
 HDO  H011  H  HOH1  0   0.453   8.0220  -0.5680  -0.0334

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
 HDO  C02  C03   single  1.517  0.020  1.517
 HDO  C02  O01   single  1.411  0.020  1.411
 HDO  C03  C04   single  1.519  0.020  1.519
 HDO  C04  C05   single  1.509  0.020  1.509
 HDO  C14  C13   single  1.523  0.020  1.523
 HDO  O02  C05   double  1.210  0.020  1.210
 HDO  C05  C07   single  1.509  0.020  1.509
 HDO  C13  C12   single  1.524  0.020  1.524
 HDO  C07  C08   single  1.520  0.020  1.520
 HDO  C12  C11   single  1.524  0.020  1.524
 HDO  C11  C10   single  1.524  0.020  1.524
 HDO  C08  C09   single  1.524  0.020  1.524
 HDO  C09  C10   single  1.523  0.020  1.523
 HDO  C02  H021  single  0.970  0.020  1.090
 HDO  C02  H022  single  0.970  0.020  1.090
 HDO  C03  H031  single  0.970  0.020  1.090
 HDO  C03  H032  single  0.970  0.020  1.090
 HDO  C04  H042  single  0.970  0.020  1.090
 HDO  C04  H041  single  0.970  0.020  1.090
 HDO  C07  H071  single  0.970  0.020  1.090
 HDO  C07  H072  single  0.970  0.020  1.090
 HDO  C08  H082  single  0.970  0.020  1.090
 HDO  C08  H081  single  0.970  0.020  1.090
 HDO  C09  H092  single  0.970  0.020  1.090
 HDO  C09  H091  single  0.970  0.020  1.090
 HDO  C10  H102  single  0.970  0.020  1.090
 HDO  C10  H101  single  0.970  0.020  1.090
 HDO  C11  H111  single  0.970  0.020  1.090
 HDO  C11  H112  single  0.970  0.020  1.090
 HDO  C12  H121  single  0.970  0.020  1.090
 HDO  C12  H122  single  0.970  0.020  1.090
 HDO  C13  H131  single  0.970  0.020  1.090
 HDO  C13  H132  single  0.970  0.020  1.090
 HDO  C14  H142  single  0.970  0.020  1.090
 HDO  C14  H14   single  0.970  0.020  1.090
 HDO  C14  H141  single  0.970  0.020  1.090
 HDO  O01  H011  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
 HDO  H022  C02  H021  106.61  3.000
 HDO  H022  C02  O01   111.39  3.000
 HDO  H021  C02  O01   111.40  3.000
 HDO  H022  C02  C03   109.20  3.000
 HDO  H021  C02  C03   109.24  3.000
 HDO  O01   C02  C03   108.94  3.000
 HDO  H032  C03  H031  107.03  3.000
 HDO  H032  C03  C04   110.05  3.000
 HDO  H031  C03  C04   110.09  3.000
 HDO  H032  C03  C02   109.40  3.000
 HDO  H031  C03  C02   109.43  3.000
 HDO  C04   C03  C02   110.76  3.000
 HDO  H041  C04  H042  104.72  3.000
 HDO  H041  C04  C05   107.53  3.000
 HDO  H042  C04  C05   107.54  3.000
 HDO  H041  C04  C03   110.76  3.000
 HDO  H042  C04  C03   110.71  3.000
 HDO  C05   C04  C03   115.01  3.000
 HDO  O02   C05  C07   122.37  3.000
 HDO  C07   C05  C04   115.44  3.000
 HDO  O02   C05  C04   122.19  3.000
 HDO  H072  C07  H071  104.67  3.000
 HDO  H072  C07  C08   110.49  3.000
 HDO  H071  C07  C08   110.50  3.000
 HDO  H072  C07  C05   107.61  3.000
 HDO  H071  C07  C05   107.63  3.000
 HDO  C08   C07  C05   115.35  3.000
 HDO  H081  C08  H082  106.34  3.000
 HDO  H081  C08  C09   109.32  3.000
 HDO  H082  C08  C09   109.35  3.000
 HDO  H081  C08  C07   109.87  3.000
 HDO  H082  C08  C07   109.87  3.000
 HDO  C09   C08  C07   111.93  3.000
 HDO  H091  C09  H092  106.03  3.000
 HDO  H091  C09  C10   109.32  3.000
 HDO  H092  C09  C10   109.34  3.000
 HDO  H091  C09  C08   109.47  3.000
 HDO  H092  C09  C08   109.46  3.000
 HDO  C10   C09  C08   112.98  3.000
 HDO  H101  C10  H102  106.03  3.000
 HDO  H101  C10  C11   109.34  3.000
 HDO  H102  C10  C11   109.33  3.000
 HDO  H101  C10  C09   109.34  3.000
 HDO  H102  C10  C09   109.32  3.000
 HDO  C11   C10  C09   113.23  3.000
 HDO  H112  C11  H111  106.03  3.000
 HDO  H112  C11  C12   109.35  3.000
 HDO  H111  C11  C12   109.36  3.000
 HDO  H112  C11  C10   109.32  3.000
 HDO  H111  C11  C10   109.35  3.000
 HDO  C12   C11  C10   113.18  3.000
 HDO  H122  C12  H121  105.98  3.000
 HDO  H122  C12  C13   109.24  3.000
 HDO  H121  C12  C13   109.25  3.000
 HDO  H122  C12  C11   109.35  3.000
 HDO  H121  C12  C11   109.35  3.000
 HDO  C13   C12  C11   113.40  3.000
 HDO  H132  C13  H131  106.06  3.000
 HDO  H132  C13  C14   109.65  3.000
 HDO  H131  C13  C14   109.62  3.000
 HDO  H132  C13  C12   109.30  3.000
 HDO  H131  C13  C12   109.28  3.000
 HDO  C14   C13  C12   112.72  3.000
 HDO  H141  C14  H14   107.60  3.000
 HDO  H141  C14  H142  107.62  3.000
 HDO  H14   C14  H142  107.50  3.000
 HDO  H141  C14  C13   111.78  3.000
 HDO  H14   C14  C13   111.06  3.000
 HDO  H142  C14  C13   111.08  3.000
 HDO  H011  O01  C02   108.16  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
 HDO  Var_01  C05   C04  C03  C02  -179.84  30.0  3
 HDO  Var_02  O02   C05  C04  C03    -0.21  30.0  3
 HDO  Var_03  O01   C02  C03  C04   179.84  30.0  1
 HDO  Var_04  C08   C07  C05  C04  -179.87  30.0  3
 HDO  Var_05  C09   C08  C07  C05   179.80  30.0  3
 HDO  Var_06  C10   C09  C08  C07   179.94  30.0  3
 HDO  Var_07  C11   C10  C09  C08   179.92  30.0  3
 HDO  Var_08  C12   C11  C10  C09   179.97  30.0  1
 HDO  Var_09  C13   C12  C11  C10   179.92  30.0  1
 HDO  Var_10  C14   C13  C12  C11  -179.95  30.0  1
 HDO  Var_11  H142  C14  C13  C12   -59.86  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
 HDO  plan-1  C04  0.020
 HDO  plan-1  C05  0.020
 HDO  plan-1  C07  0.020
 HDO  plan-1  O02  0.020

