# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:53:27 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: decanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(O)=O
#
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
 DKA  DKA  'decanoic acid            '  ligand  32  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DKA
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
 DKA  C1    C  C     0   0.549  -4.6507  -0.0611   0.0143
 DKA  O1    O  O     0  -0.446  -4.7901  -1.2589   0.0296
 DKA  C2    C  CH2   0  -0.580  -3.3329   0.6621   0.0044
 DKA  C3    C  CH2   0  -0.418  -2.1213  -0.2557   0.0074
 DKA  C4    C  CH2   0  -0.415  -0.8182   0.5339   0.0014
 DKA  C5    C  CH2   0  -0.413   0.4179  -0.3567   0.0041
 DKA  C6    C  CH2   0  -0.412   1.7207   0.4328  -0.0001
 DKA  C7    C  CH2   0  -0.412   2.9631  -0.4497   0.0059
 DKA  C8    C  CH2   0  -0.406   4.2618   0.3467   0.0017
 DKA  C9    C  CH2   0  -0.419   5.5100  -0.5280   0.0096
 DKA  C10   C  CH3   0  -0.662   6.7972   0.2856   0.0078
 DKA  O2    O  OH1   0  -0.599  -5.6780   0.7850   0.0046
 DKA  H21   H  HCH2  0   0.275  -3.3130   1.3200  -0.8706
 DKA  H22   H  HCH2  0   0.275  -3.3080   1.3318   0.8704
 DKA  H31   H  HCH2  0   0.225  -2.1486  -0.9048   0.8870
 DKA  H32   H  HCH2  0   0.225  -2.1513  -0.9145  -0.8648
 DKA  H41   H  HCH2  0   0.212  -0.7914   1.1882  -0.8771
 DKA  H42   H  HCH2  0   0.212  -0.7886   1.1967   0.8735
 DKA  H51   H  HCH2  0   0.209   0.3914  -1.0116   0.8822
 DKA  H52   H  HCH2  0   0.209   0.3905  -1.0185  -0.8688
 DKA  H61   H  HCH2  0   0.207   1.7457   1.0864  -0.8795
 DKA  H62   H  HCH2  0   0.207   1.7450   1.0977   0.8707
 DKA  H71   H  HCH2  0   0.206   2.9401  -1.1034   0.8852
 DKA  H72   H  HCH2  0   0.206   2.9406  -1.1138  -0.8656
 DKA  H81   H  HCH2  0   0.206   4.2845   1.0000  -0.8781
 DKA  H82   H  HCH2  0   0.206   4.2823   1.0126   0.8720
 DKA  H91   H  HCH2  0   0.210   5.4885  -1.1805   0.8881
 DKA  H92   H  HCH2  0   0.210   5.4927  -1.1913  -0.8609
 DKA  H101  H  HCH3  0   0.215   6.8554   0.9267  -0.8741
 DKA  H102  H  HCH3  0   0.215   6.8549   0.9309   0.8868
 DKA  H103  H  HCH3  0   0.225   7.6805  -0.3541   0.0097
 DKA  HO2   H  HOH1  0   0.478  -6.5119   0.2921   0.0145

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
 DKA  C1   O1    double  1.206  0.020  1.206
 DKA  C1   C2    single  1.503  0.020  1.503
 DKA  C1   O2    single  1.331  0.020  1.331
 DKA  C2   C3    single  1.520  0.020  1.520
 DKA  C2   H21   single  0.970  0.020  1.090
 DKA  C2   H22   single  0.970  0.020  1.090
 DKA  C3   C4    single  1.524  0.020  1.524
 DKA  C3   H31   single  0.970  0.020  1.090
 DKA  C3   H32   single  0.970  0.020  1.090
 DKA  C4   C5    single  1.524  0.020  1.524
 DKA  C4   H41   single  0.970  0.020  1.090
 DKA  C4   H42   single  0.970  0.020  1.090
 DKA  C5   C6    single  1.523  0.020  1.523
 DKA  C5   H51   single  0.970  0.020  1.090
 DKA  C5   H52   single  0.970  0.020  1.090
 DKA  C6   C7    single  1.524  0.020  1.524
 DKA  C6   H61   single  0.970  0.020  1.090
 DKA  C6   H62   single  0.970  0.020  1.090
 DKA  C7   C8    single  1.524  0.020  1.524
 DKA  C7   H71   single  0.970  0.020  1.090
 DKA  C7   H72   single  0.970  0.020  1.090
 DKA  C8   C9    single  1.524  0.020  1.524
 DKA  C8   H81   single  0.970  0.020  1.090
 DKA  C8   H82   single  0.970  0.020  1.090
 DKA  C9   C10   single  1.523  0.020  1.523
 DKA  C9   H91   single  0.970  0.020  1.090
 DKA  C9   H92   single  0.970  0.020  1.090
 DKA  C10  H101  single  0.970  0.020  1.090
 DKA  C10  H102  single  0.970  0.020  1.090
 DKA  C10  H103  single  0.970  0.020  1.090
 DKA  O2   HO2   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
 DKA  O2    C1   C2    111.76  3.000
 DKA  O2    C1   O1    122.84  3.000
 DKA  C2    C1   O1    125.40  3.000
 DKA  H22   C2   H21   105.32  3.000
 DKA  H22   C2   C3    110.47  3.000
 DKA  H21   C2   C3    110.48  3.000
 DKA  H22   C2   C1    107.99  3.000
 DKA  H21   C2   C1    108.07  3.000
 DKA  C3    C2   C1    114.10  3.000
 DKA  H32   C3   H31   106.46  3.000
 DKA  H32   C3   C4    109.42  3.000
 DKA  H31   C3   C4    109.40  3.000
 DKA  H32   C3   C2    109.89  3.000
 DKA  H31   C3   C2    109.88  3.000
 DKA  C4    C3   C2    111.64  3.000
 DKA  H42   C4   H41   106.04  3.000
 DKA  H42   C4   C5    109.29  3.000
 DKA  H41   C4   C5    109.31  3.000
 DKA  H42   C4   C3    109.47  3.000
 DKA  H41   C4   C3    109.48  3.000
 DKA  C5    C4   C3    113.01  3.000
 DKA  H52   C5   H51   106.07  3.000
 DKA  H52   C5   C6    109.40  3.000
 DKA  H51   C5   C6    109.43  3.000
 DKA  H52   C5   C4    109.35  3.000
 DKA  H51   C5   C4    109.34  3.000
 DKA  C6    C5   C4    113.01  3.000
 DKA  H62   C6   H61   105.97  3.000
 DKA  H62   C6   C7    109.27  3.000
 DKA  H61   C6   C7    109.27  3.000
 DKA  H62   C6   C5    109.34  3.000
 DKA  H61   C6   C5    109.32  3.000
 DKA  C7    C6   C5    113.40  3.000
 DKA  H72   C7   H71   106.03  3.000
 DKA  H72   C7   C8    109.39  3.000
 DKA  H71   C7   C8    109.39  3.000
 DKA  H72   C7   C6    109.33  3.000
 DKA  H71   C7   C6    109.36  3.000
 DKA  C8    C7   C6    113.10  3.000
 DKA  H82   C8   H81   105.95  3.000
 DKA  H82   C8   C9    109.23  3.000
 DKA  H81   C8   C9    109.23  3.000
 DKA  H82   C8   C7    109.35  3.000
 DKA  H81   C8   C7    109.36  3.000
 DKA  C9    C8   C7    113.46  3.000
 DKA  H92   C9   H91   106.07  3.000
 DKA  H92   C9   C10   109.65  3.000
 DKA  H91   C9   C10   109.64  3.000
 DKA  H92   C9   C8    109.31  3.000
 DKA  H91   C9   C8    109.28  3.000
 DKA  C10   C9   C8    112.68  3.000
 DKA  H103  C10  H102  107.60  3.000
 DKA  H103  C10  H101  107.61  3.000
 DKA  H102  C10  H101  107.49  3.000
 DKA  H103  C10  C9    111.79  3.000
 DKA  H102  C10  C9    111.07  3.000
 DKA  H101  C10  C9    111.08  3.000
 DKA  HO2   O2   C1    109.94  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
 DKA  CONST_01  HO2   O2   C1  O1     0.00   0.0  0
 DKA  Var_01    C4    C3   C2  C1  -179.83  30.0  3
 DKA  Var_02    C3    C2   C1  O1     0.34  30.0  3
 DKA  Var_03    C5    C4   C3  C2  -179.99  30.0  3
 DKA  Var_04    C6    C5   C4  C3  -179.93  30.0  3
 DKA  Var_05    C7    C6   C5  C4   179.86  30.0  3
 DKA  Var_06    C8    C7   C6  C5  -180.00  30.0  3
 DKA  Var_07    C9    C8   C7  C6   179.92  30.0  3
 DKA  Var_08    C10   C9   C8  C7  -179.89  30.0  3
 DKA  Var_09    H101  C10  C9  C8   -59.56  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
 DKA  plan-1  C1   0.020
 DKA  plan-1  O1   0.020
 DKA  plan-1  C2   0.020
 DKA  plan-1  O2   0.020
 DKA  plan-1  HO2  0.020

