# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:14:41 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: dodecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(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
 DAO  DAO  'dodecanoic acid          '  ligand  38  14  .  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_DAO
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
 DAO  O1    O  O     0  -0.447   1.2675   0.0259  -6.0124
 DAO  O2    O  OH1   0  -0.599  -0.7698   0.0269  -6.9153
 DAO  C1    C  C     0   0.550   0.0685   0.0265  -5.8816
 DAO  C2    C  CH2   0  -0.580  -0.6636   0.0283  -4.5690
 DAO  C3    C  CH2   0  -0.418   0.2463   0.0180  -3.3515
 DAO  C4    C  CH2   0  -0.415  -0.5509   0.0204  -2.0532
 DAO  C5    C  CH2   0  -0.413   0.3329   0.0127  -0.8123
 DAO  C6    C  CH2   0  -0.412  -0.4633   0.0154   0.4866
 DAO  C7    C  CH2   0  -0.412   0.4135   0.0071   1.7329
 DAO  C8    C  CH2   0  -0.411  -0.3883   0.0118   3.0285
 DAO  C9    C  CH2   0  -0.412   0.4825   0.0039   4.2791
 DAO  C10   C  CH2   0  -0.406  -0.3248   0.0104   5.5711
 DAO  C11   C  CH2   0  -0.419   0.5394   0.0026   6.8265
 DAO  C12   C  CH3   0  -0.662  -0.2841   0.0103   8.1070
 DAO  HO2   H  HOH1  0   0.478  -0.2703   0.0271  -7.7453
 DAO  H21   H  HCH2  0   0.275  -1.3346  -0.8368  -4.5532
 DAO  H22   H  HCH2  0   0.275  -1.3206   0.9042  -4.5487
 DAO  H31   H  HCH2  0   0.225   0.9074   0.8887  -3.3739
 DAO  H32   H  HCH2  0   0.225   0.8937  -0.8629  -3.3791
 DAO  H41   H  HCH2  0   0.212  -1.2151  -0.8507  -2.0302
 DAO  H42   H  HCH2  0   0.212  -1.2040   0.8999  -2.0272
 DAO  H51   H  HCH2  0   0.209   0.9967   0.8843  -0.8340
 DAO  H52   H  HCH2  0   0.209   0.9861  -0.8667  -0.8370
 DAO  H61   H  HCH2  0   0.207  -1.1283  -0.8554   0.5061
 DAO  H62   H  HCH2  0   0.207  -1.1166   0.8951   0.5095
 DAO  H71   H  HCH2  0   0.206   1.0792   0.8774   1.7141
 DAO  H72   H  HCH2  0   0.206   1.0658  -0.8733   1.7120
 DAO  H81   H  HCH2  0   0.206  -1.0544  -0.8583   3.0458
 DAO  H82   H  HCH2  0   0.206  -1.0409   0.8921   3.0475
 DAO  H91   H  HCH2  0   0.206   1.1491   0.8736   4.2627
 DAO  H92   H  HCH2  0   0.206   1.1344  -0.8769   4.2621
 DAO  H101  H  HCH2  0   0.205  -0.9920  -0.8591   5.5868
 DAO  H102  H  HCH2  0   0.205  -0.9770   0.8912   5.5874
 DAO  H111  H  HCH2  0   0.210   1.2058   0.8707   6.8120
 DAO  H112  H  HCH2  0   0.210   1.1895  -0.8779   6.8122
 DAO  H121  H  HCH3  0   0.225   0.3484   0.0038   8.9955
 DAO  H122  H  HCH3  0   0.215  -0.9188   0.8971   8.1601
 DAO  H123  H  HCH3  0   0.215  -0.9362  -0.8639   8.1595

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
 DAO  O1   C1    double  1.206  0.020  1.206
 DAO  O2   C1    single  1.331  0.020  1.331
 DAO  O2   HO2   single  0.850  0.020  0.980
 DAO  C1   C2    single  1.503  0.020  1.503
 DAO  C2   C3    single  1.520  0.020  1.520
 DAO  C2   H21   single  0.970  0.020  1.090
 DAO  C2   H22   single  0.970  0.020  1.090
 DAO  C3   C4    single  1.524  0.020  1.524
 DAO  C3   H31   single  0.970  0.020  1.090
 DAO  C3   H32   single  0.970  0.020  1.090
 DAO  C4   C5    single  1.524  0.020  1.524
 DAO  C4   H41   single  0.970  0.020  1.090
 DAO  C4   H42   single  0.970  0.020  1.090
 DAO  C5   C6    single  1.523  0.020  1.523
 DAO  C5   H51   single  0.970  0.020  1.090
 DAO  C5   H52   single  0.970  0.020  1.090
 DAO  C6   C7    single  1.524  0.020  1.524
 DAO  C6   H61   single  0.970  0.020  1.090
 DAO  C6   H62   single  0.970  0.020  1.090
 DAO  C7   C8    single  1.524  0.020  1.524
 DAO  C7   H71   single  0.970  0.020  1.090
 DAO  C7   H72   single  0.970  0.020  1.090
 DAO  C8   C9    single  1.524  0.020  1.524
 DAO  C8   H81   single  0.970  0.020  1.090
 DAO  C8   H82   single  0.970  0.020  1.090
 DAO  C9   C10   single  1.524  0.020  1.524
 DAO  C9   H91   single  0.970  0.020  1.090
 DAO  C9   H92   single  0.970  0.020  1.090
 DAO  C10  C11   single  1.524  0.020  1.524
 DAO  C10  H101  single  0.970  0.020  1.090
 DAO  C10  H102  single  0.970  0.020  1.090
 DAO  C11  C12   single  1.523  0.020  1.523
 DAO  C11  H111  single  0.970  0.020  1.090
 DAO  C11  H112  single  0.970  0.020  1.090
 DAO  C12  H121  single  0.970  0.020  1.090
 DAO  C12  H122  single  0.970  0.020  1.090
 DAO  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
 DAO  HO2   O2   C1    109.91  3.000
 DAO  C2    C1   O2    111.81  3.000
 DAO  C2    C1   O1    125.38  3.000
 DAO  O2    C1   O1    122.82  3.000
 DAO  H22   C2   H21   105.31  3.000
 DAO  H22   C2   C3    110.47  3.000
 DAO  H21   C2   C3    110.48  3.000
 DAO  H22   C2   C1    108.02  3.000
 DAO  H21   C2   C1    108.07  3.000
 DAO  C3    C2   C1    114.07  3.000
 DAO  H32   C3   H31   106.44  3.000
 DAO  H32   C3   C4    109.42  3.000
 DAO  H31   C3   C4    109.42  3.000
 DAO  H32   C3   C2    109.86  3.000
 DAO  H31   C3   C2    109.89  3.000
 DAO  C4    C3   C2    111.67  3.000
 DAO  H42   C4   H41   106.05  3.000
 DAO  H42   C4   C5    109.30  3.000
 DAO  H41   C4   C5    109.30  3.000
 DAO  H42   C4   C3    109.48  3.000
 DAO  H41   C4   C3    109.50  3.000
 DAO  C5    C4   C3    112.99  3.000
 DAO  H52   C5   H51   106.07  3.000
 DAO  H52   C5   C6    109.40  3.000
 DAO  H51   C5   C6    109.40  3.000
 DAO  H52   C5   C4    109.36  3.000
 DAO  H51   C5   C4    109.34  3.000
 DAO  C6    C5   C4    113.03  3.000
 DAO  H62   C6   H61   106.00  3.000
 DAO  H62   C6   C7    109.28  3.000
 DAO  H61   C6   C7    109.29  3.000
 DAO  H62   C6   C5    109.31  3.000
 DAO  H61   C6   C5    109.33  3.000
 DAO  C7    C6   C5    113.37  3.000
 DAO  H72   C7   H71   106.03  3.000
 DAO  H72   C7   C8    109.38  3.000
 DAO  H71   C7   C8    109.38  3.000
 DAO  H72   C7   C6    109.34  3.000
 DAO  H71   C7   C6    109.34  3.000
 DAO  C8    C7   C6    113.13  3.000
 DAO  H82   C8   H81   105.99  3.000
 DAO  H82   C8   C9    109.28  3.000
 DAO  H81   C8   C9    109.28  3.000
 DAO  H82   C8   C7    109.30  3.000
 DAO  H81   C8   C7    109.32  3.000
 DAO  C9    C8   C7    113.40  3.000
 DAO  H92   C9   H91   106.01  3.000
 DAO  H92   C9   C10   109.38  3.000
 DAO  H91   C9   C10   109.37  3.000
 DAO  H92   C9   C8    109.35  3.000
 DAO  H91   C9   C8    109.34  3.000
 DAO  C10   C9   C8    113.15  3.000
 DAO  H102  C10  H101  105.97  3.000
 DAO  H102  C10  C11   109.22  3.000
 DAO  H101  C10  C11   109.23  3.000
 DAO  H102  C10  C9    109.35  3.000
 DAO  H101  C10  C9    109.35  3.000
 DAO  C11   C10  C9    113.45  3.000
 DAO  H112  C11  H111  106.04  3.000
 DAO  H112  C11  C12   109.65  3.000
 DAO  H111  C11  C12   109.66  3.000
 DAO  H112  C11  C10   109.28  3.000
 DAO  H111  C11  C10   109.29  3.000
 DAO  C12   C11  C10   112.70  3.000
 DAO  H123  C12  H122  107.50  3.000
 DAO  H123  C12  H121  107.60  3.000
 DAO  H122  C12  H121  107.60  3.000
 DAO  H123  C12  C11   111.07  3.000
 DAO  H122  C12  C11   111.07  3.000
 DAO  H121  C12  C11   111.80  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
 DAO  CONST_01  HO2   O2   C1   O1      0.00   0.0  0
 DAO  Var_01    C3    C2   C1   O1     -0.47  30.0  3
 DAO  Var_02    C4    C3   C2   C1    179.99  30.0  3
 DAO  Var_03    C5    C4   C3   C2   -179.90  30.0  3
 DAO  Var_04    C6    C5   C4   C3    179.99  30.0  3
 DAO  Var_05    C7    C6   C5   C4    179.98  30.0  3
 DAO  Var_06    C8    C7   C6   C5    179.92  30.0  3
 DAO  Var_07    C9    C8   C7   C6   -179.99  30.0  3
 DAO  Var_08    C10   C9   C8   C7    179.93  30.0  3
 DAO  Var_09    C11   C10  C9   C8   -180.00  30.0  3
 DAO  Var_10    C12   C11  C10  C9    179.96  30.0  3
 DAO  Var_11    H121  C12  C11  C10   179.95  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
 DAO  plan-1  O1   0.020
 DAO  plan-1  O2   0.020
 DAO  plan-1  C1   0.020
 DAO  plan-1  C2   0.020
 DAO  plan-1  HO2  0.020

