# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 21:56:50 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: dodecan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCO
#
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
 1DO  1DO  'dodecan-1-ol             '  ligand  39  13  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1DO
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
 1DO  O2S   O  OH1   0  -0.676  -7.4227   0.3603   0.0037
 1DO  C1    C  CH2   0  -0.138  -6.2807  -0.4708   0.0135
 1DO  C2    C  CH2   0  -0.454  -5.0338   0.3915   0.0091
 1DO  C3    C  CH2   0  -0.424  -3.7615  -0.4471   0.0127
 1DO  C4    C  CH2   0  -0.410  -2.4909   0.3939   0.0108
 1DO  C5    C  CH2   0  -0.412  -1.2198  -0.4462   0.0114
 1DO  C6    C  CH2   0  -0.412   0.0543   0.3893   0.0102
 1DO  C7    C  CH2   0  -0.412   1.3248  -0.4523   0.0096
 1DO  C8    C  CH2   0  -0.412   2.5994   0.3825   0.0081
 1DO  C9    C  CH2   0  -0.412   3.8706  -0.4579   0.0084
 1DO  C10   C  CH2   0  -0.406   5.1437   0.3790   0.0048
 1DO  C11   C  CH2   0  -0.419   6.4182  -0.4568   0.0088
 1DO  C12   C  CH3   0  -0.662   7.6800   0.3953   0.0066
 1DO  H2S   H  HOH1  0   0.451  -8.2024  -0.2016   0.0110
 1DO  H1C1  H  HCH2  0   0.186  -6.2622  -1.1347  -0.8616
 1DO  H1C2  H  HCH2  0   0.186  -6.2663  -1.1194   0.9000
 1DO  H2C1  H  HCH2  0   0.217  -5.0421   1.0487   0.8849
 1DO  H2C2  H  HCH2  0   0.217  -5.0426   1.0401  -0.8730
 1DO  H3C1  H  HCH2  0   0.211  -3.7572  -1.1087  -0.8606
 1DO  H3C2  H  HCH2  0   0.211  -3.7584  -1.1032   0.8902
 1DO  H4C1  H  HCH2  0   0.208  -2.4908   1.0545   0.8850
 1DO  H4C2  H  HCH2  0   0.208  -2.4917   1.0512  -0.8660
 1DO  H5C1  H  HCH2  0   0.207  -1.2212  -1.1065  -0.8633
 1DO  H5C2  H  HCH2  0   0.207  -1.2208  -1.1048   0.8873
 1DO  H6C1  H  HCH2  0   0.206   0.0568   1.0488   0.8855
 1DO  H6C2  H  HCH2  0   0.206   0.0554   1.0486  -0.8652
 1DO  H7C1  H  HCH2  0   0.206   1.3224  -1.1124  -0.8652
 1DO  H7C2  H  HCH2  0   0.206   1.3235  -1.1112   0.8854
 1DO  H8C1  H  HCH2  0   0.206   2.6014   1.0429   0.8828
 1DO  H8C2  H  HCH2  0   0.206   2.6005   1.0413  -0.8677
 1DO  H9C1  H  HCH2  0   0.206   3.8684  -1.1192  -0.8655
 1DO  H9C2  H  HCH2  0   0.206   3.8707  -1.1155   0.8851
 1DO  H101  H  HCH2  0   0.205   5.1442   1.0428   0.8770
 1DO  H102  H  HCH2  0   0.206   5.1446   1.0349  -0.8733
 1DO  H111  H  HCH2  0   0.210   6.4195  -1.1186  -0.8630
 1DO  H112  H  HCH2  0   0.210   6.4182  -1.1117   0.8859
 1DO  H121  H  HCH3  0   0.215   7.7207   1.0383   0.8880
 1DO  H122  H  HCH3  0   0.225   8.5822  -0.2175   0.0034
 1DO  H123  H  HCH3  0   0.215   7.7162   1.0408  -0.8732

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
 1DO  O2S  C1    single  1.412  0.020  1.412
 1DO  O2S  H2S   single  0.850  0.020  0.980
 1DO  C1   C2    single  1.516  0.020  1.516
 1DO  C1   H1C1  single  0.970  0.020  1.090
 1DO  C1   H1C2  single  0.970  0.020  1.090
 1DO  C2   C3    single  1.524  0.020  1.524
 1DO  C2   H2C1  single  0.970  0.020  1.090
 1DO  C2   H2C2  single  0.970  0.020  1.090
 1DO  C3   C4    single  1.524  0.020  1.524
 1DO  C3   H3C1  single  0.970  0.020  1.090
 1DO  C3   H3C2  single  0.970  0.020  1.090
 1DO  C4   C5    single  1.524  0.020  1.524
 1DO  C4   H4C1  single  0.970  0.020  1.090
 1DO  C4   H4C2  single  0.970  0.020  1.090
 1DO  C5   C6    single  1.524  0.020  1.524
 1DO  C5   H5C1  single  0.970  0.020  1.090
 1DO  C5   H5C2  single  0.970  0.020  1.090
 1DO  C6   C7    single  1.524  0.020  1.524
 1DO  C6   H6C1  single  0.970  0.020  1.090
 1DO  C6   H6C2  single  0.970  0.020  1.090
 1DO  C7   C8    single  1.524  0.020  1.524
 1DO  C7   H7C1  single  0.970  0.020  1.090
 1DO  C7   H7C2  single  0.970  0.020  1.090
 1DO  C8   C9    single  1.524  0.020  1.524
 1DO  C8   H8C1  single  0.970  0.020  1.090
 1DO  C8   H8C2  single  0.970  0.020  1.090
 1DO  C9   C10   single  1.524  0.020  1.524
 1DO  C9   H9C1  single  0.970  0.020  1.090
 1DO  C9   H9C2  single  0.970  0.020  1.090
 1DO  C10  C11   single  1.524  0.020  1.524
 1DO  C10  H101  single  0.970  0.020  1.090
 1DO  C10  H102  single  0.970  0.020  1.090
 1DO  C11  C12   single  1.523  0.020  1.523
 1DO  C11  H111  single  0.970  0.020  1.090
 1DO  C11  H112  single  0.970  0.020  1.090
 1DO  C12  H121  single  0.970  0.020  1.090
 1DO  C12  H122  single  0.970  0.020  1.090
 1DO  C12  H123  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
 1DO  H2S   O2S  C1    108.17  3.000
 1DO  H1C2  C1   H1C1  106.61  3.000
 1DO  H1C2  C1   C2    109.10  3.000
 1DO  H1C1  C1   C2    109.12  3.000
 1DO  H1C2  C1   O2S   111.32  3.000
 1DO  H1C1  C1   O2S   111.33  3.000
 1DO  C2    C1   O2S   109.29  3.000
 1DO  H2C2  C2   H2C1  106.78  3.000
 1DO  H2C2  C2   C3    109.55  3.000
 1DO  H2C1  C2   C3    109.56  3.000
 1DO  H2C2  C2   C1    109.43  3.000
 1DO  H2C1  C2   C1    109.44  3.000
 1DO  C3    C2   C1    111.95  3.000
 1DO  H3C2  C3   H3C1  106.06  3.000
 1DO  H3C2  C3   C4    109.22  3.000
 1DO  H3C1  C3   C4    109.21  3.000
 1DO  H3C2  C3   C2    109.50  3.000
 1DO  H3C1  C3   C2    109.49  3.000
 1DO  C4    C3   C2    113.11  3.000
 1DO  H4C2  C4   H4C1  106.07  3.000
 1DO  H4C2  C4   C5    109.37  3.000
 1DO  H4C1  C4   C5    109.39  3.000
 1DO  H4C2  C4   C3    109.36  3.000
 1DO  H4C1  C4   C3    109.38  3.000
 1DO  C5    C4   C3    113.04  3.000
 1DO  H5C2  C5   H5C1  106.01  3.000
 1DO  H5C2  C5   C6    109.32  3.000
 1DO  H5C1  C5   C6    109.32  3.000
 1DO  H5C2  C5   C4    109.33  3.000
 1DO  H5C1  C5   C4    109.32  3.000
 1DO  C6    C5   C4    113.28  3.000
 1DO  H6C2  C6   H6C1  106.02  3.000
 1DO  H6C2  C6   C7    109.34  3.000
 1DO  H6C1  C6   C7    109.32  3.000
 1DO  H6C2  C6   C5    109.35  3.000
 1DO  H6C1  C6   C5    109.34  3.000
 1DO  C7    C6   C5    113.23  3.000
 1DO  H7C2  C7   H7C1  106.01  3.000
 1DO  H7C2  C7   C8    109.34  3.000
 1DO  H7C1  C7   C8    109.33  3.000
 1DO  H7C2  C7   C6    109.31  3.000
 1DO  H7C1  C7   C6    109.34  3.000
 1DO  C8    C7   C6    113.26  3.000
 1DO  H8C2  C8   H8C1  106.00  3.000
 1DO  H8C2  C8   C9    109.32  3.000
 1DO  H8C1  C8   C9    109.31  3.000
 1DO  H8C2  C8   C7    109.33  3.000
 1DO  H8C1  C8   C7    109.32  3.000
 1DO  C9    C8   C7    113.31  3.000
 1DO  H9C2  C9   H9C1  106.01  3.000
 1DO  H9C2  C9   C10   109.35  3.000
 1DO  H9C1  C9   C10   109.34  3.000
 1DO  H9C2  C9   C8    109.34  3.000
 1DO  H9C1  C9   C8    109.33  3.000
 1DO  C10   C9   C8    113.21  3.000
 1DO  H102  C10  H101  105.97  3.000
 1DO  H102  C10  C11   109.24  3.000
 1DO  H101  C10  C11   109.25  3.000
 1DO  H102  C10  C9    109.35  3.000
 1DO  H101  C10  C9    109.34  3.000
 1DO  C11   C10  C9    113.42  3.000
 1DO  H112  C11  H111  106.05  3.000
 1DO  H112  C11  C12   109.63  3.000
 1DO  H111  C11  C12   109.65  3.000
 1DO  H112  C11  C10   109.28  3.000
 1DO  H111  C11  C10   109.30  3.000
 1DO  C12   C11  C10   112.71  3.000
 1DO  H123  C12  H122  107.61  3.000
 1DO  H123  C12  H121  107.52  3.000
 1DO  H122  C12  H121  107.61  3.000
 1DO  H123  C12  C11   111.07  3.000
 1DO  H122  C12  C11   111.78  3.000
 1DO  H121  C12  C11   111.05  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
 1DO  Var_01  C3    C2   C1   O2S  -179.74  30.0  3
 1DO  Var_02  C4    C3   C2   C1   -179.91  30.0  3
 1DO  Var_03  C5    C4   C3   C2   -179.88  30.0  3
 1DO  Var_04  C6    C5   C4   C3   -179.97  30.0  3
 1DO  Var_05  C7    C6   C5   C4   -179.95  30.0  3
 1DO  Var_06  C8    C7   C6   C5    179.99  30.0  3
 1DO  Var_07  C9    C8   C7   C6    179.96  30.0  3
 1DO  Var_08  C10   C9   C8   C7    179.91  30.0  3
 1DO  Var_09  C11   C10  C9   C8    179.85  30.0  3
 1DO  Var_10  C12   C11  C10  C9   -179.94  30.0  3
 1DO  Var_11  H121  C12  C11  C10    60.15  30.0  3

