# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 10:23:25 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-oxotetradecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=O)CC(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
 Z6X  Z6X  '3-oxotetradecanoic acid  '  ligand  43  17  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Z6X
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
 Z6X  C1    C  CH3   0  -0.662   9.6399  -0.2542  -0.0124
 Z6X  C2    C  CH2   0  -0.419   8.3501   0.5515   0.0605
 Z6X  C3    C  CH2   0  -0.406   7.1043  -0.3250   0.0083
 Z6X  C4    C  CH2   0  -0.412   5.8037   0.4665   0.0635
 Z6X  C5    C  CH2   0  -0.412   4.5624  -0.4160   0.0120
 Z6X  C6    C  CH2   0  -0.412   3.2587   0.3720   0.0412
 Z6X  C7    C  CH2   0  -0.412   2.0211  -0.5159  -0.0065
 Z6X  C8    C  CH2   0  -0.414   0.7150   0.2684  -0.0068
 Z6X  C9    C  CH2   0  -0.416  -0.5177  -0.6261  -0.0471
 Z6X  C10   C  CH2   0  -0.418  -1.8231   0.1600  -0.0726
 Z6X  C11   C  CH2   0  -0.558  -3.0332  -0.7596  -0.1029
 Z6X  C12   C  C     0   0.406  -4.3630  -0.0621  -0.1506
 Z6X  O1    O  O     0  -0.392  -4.4878   1.1389  -0.1255
 Z6X  C13   C  CH2   0  -0.664  -5.5710  -0.9767  -0.2517
 Z6X  C14   C  C     0   0.531  -6.8542  -0.1954  -0.1936
 Z6X  O2    O  O     0  -0.436  -7.5139   0.1068  -1.1548
 Z6X  O3    O  OH1   0  -0.585  -7.1703   0.1382   1.0499
 Z6X  H11   H  HCH3  0   0.215   9.7097  -0.9620   0.8161
 Z6X  H12   H  HCH3  0   0.215   9.6914  -0.8287  -0.9395
 Z6X  H13   H  HCH3  0   0.225  10.5207   0.3878   0.0271
 Z6X  H21   H  HCH2  0   0.210   8.3372   1.1441   0.9808
 Z6X  H22   H  HCH2  0   0.210   8.3201   1.2712  -0.7634
 Z6X  H31   H  HCH2  0   0.205   7.1239  -0.9261  -0.9081
 Z6X  H32   H  HCH2  0   0.206   7.1310  -1.0402   0.8383
 Z6X  H41   H  HCH2  0   0.206   5.7830   1.0701   0.9780
 Z6X  H42   H  HCH2  0   0.206   5.7769   1.1783  -0.7692
 Z6X  H51   H  HCH2  0   0.206   4.5927  -1.0306  -0.8949
 Z6X  H52   H  HCH2  0   0.206   4.5819  -1.1181   0.8532
 Z6X  H61   H  HCH2  0   0.207   3.2271   0.9915   0.9447
 Z6X  H62   H  HCH2  0   0.206   3.2375   1.0689  -0.8042
 Z6X  H71   H  HCH2  0   0.207   2.0633  -1.1478  -0.9009
 Z6X  H72   H  HCH2  0   0.207   2.0337  -1.2014   0.8483
 Z6X  H81   H  HCH2  0   0.209   0.6719   0.9066   0.8829
 Z6X  H82   H  HCH2  0   0.209   0.6994   0.9466  -0.8673
 Z6X  H91   H  HCH2  0   0.212  -0.4658  -1.2747  -0.9287
 Z6X  H92   H  HCH2  0   0.212  -0.5093  -1.2943   0.8212
 Z6X  H101  H  HCH2  0   0.225  -1.8737   0.8111   0.8045
 Z6X  H102  H  HCH2  0   0.225  -1.8341   0.8169  -0.9468
 Z6X  H111  H  HCH2  0   0.272  -2.9823  -1.4397  -0.9611
 Z6X  H112  H  HCH2  0   0.274  -3.0396  -1.4181   0.7738
 Z6X  H131  H  HCH2  0   0.312  -5.5133  -1.5196  -1.1975
 Z6X  H132  H  HCH2  0   0.308  -5.5242  -1.7223   0.5458
 Z6X  H3O   H  HOH1  0   0.484  -7.9830   0.6663   1.0578

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
 Z6X  C1   C2    single  1.523  0.020  1.523
 Z6X  C1   H11   single  0.970  0.020  1.090
 Z6X  C1   H12   single  0.970  0.020  1.090
 Z6X  C1   H13   single  0.970  0.020  1.090
 Z6X  C2   C3    single  1.524  0.020  1.524
 Z6X  C2   H21   single  0.970  0.020  1.090
 Z6X  C2   H22   single  0.970  0.020  1.090
 Z6X  C3   C4    single  1.523  0.020  1.523
 Z6X  C3   H31   single  0.970  0.020  1.090
 Z6X  C3   H32   single  0.970  0.020  1.090
 Z6X  C4   C5    single  1.524  0.020  1.524
 Z6X  C4   H41   single  0.970  0.020  1.090
 Z6X  C4   H42   single  0.970  0.020  1.090
 Z6X  C5   C6    single  1.524  0.020  1.524
 Z6X  C5   H51   single  0.970  0.020  1.090
 Z6X  C5   H52   single  0.970  0.020  1.090
 Z6X  C6   C7    single  1.524  0.020  1.524
 Z6X  C6   H61   single  0.970  0.020  1.090
 Z6X  C6   H62   single  0.970  0.020  1.090
 Z6X  C7   C8    single  1.523  0.020  1.523
 Z6X  C7   H71   single  0.970  0.020  1.090
 Z6X  C7   H72   single  0.970  0.020  1.090
 Z6X  C8   C9    single  1.524  0.020  1.524
 Z6X  C8   H81   single  0.970  0.020  1.090
 Z6X  C8   H82   single  0.970  0.020  1.090
 Z6X  C9   C10   single  1.524  0.020  1.524
 Z6X  C9   H91   single  0.970  0.020  1.090
 Z6X  C9   H92   single  0.970  0.020  1.090
 Z6X  C10  C11   single  1.520  0.020  1.520
 Z6X  C10  H101  single  0.970  0.020  1.090
 Z6X  C10  H102  single  0.970  0.020  1.090
 Z6X  C11  C12   single  1.502  0.020  1.502
 Z6X  C11  H111  single  0.970  0.020  1.090
 Z6X  C11  H112  single  0.970  0.020  1.090
 Z6X  C12  C13   single  1.518  0.020  1.518
 Z6X  C12  O1    double  1.208  0.020  1.208
 Z6X  C13  C14   single  1.504  0.020  1.504
 Z6X  C13  H131  single  0.970  0.020  1.090
 Z6X  C13  H132  single  0.970  0.020  1.090
 Z6X  C14  O3    single  1.326  0.020  1.326
 Z6X  C14  O2    double  1.204  0.020  1.204
 Z6X  O3   H3O   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
 Z6X  H13   C1   H12   107.60  3.000
 Z6X  H13   C1   H11   107.61  3.000
 Z6X  H12   C1   H11   107.47  3.000
 Z6X  H13   C1   C2    111.77  3.000
 Z6X  H12   C1   C2    111.04  3.000
 Z6X  H11   C1   C2    111.16  3.000
 Z6X  H22   C2   H21   106.06  3.000
 Z6X  H22   C2   C3    109.27  3.000
 Z6X  H21   C2   C3    109.30  3.000
 Z6X  H22   C2   C1    109.59  3.000
 Z6X  H21   C2   C1    109.68  3.000
 Z6X  C3    C2   C1    112.73  3.000
 Z6X  H32   C3   H31   105.95  3.000
 Z6X  H32   C3   C4    109.42  3.000
 Z6X  H31   C3   C4    109.29  3.000
 Z6X  H32   C3   C2    109.23  3.000
 Z6X  H31   C3   C2    109.23  3.000
 Z6X  C4    C3   C2    113.44  3.000
 Z6X  H42   C4   H41   106.01  3.000
 Z6X  H42   C4   C5    109.30  3.000
 Z6X  H41   C4   C5    109.37  3.000
 Z6X  H42   C4   C3    109.32  3.000
 Z6X  H41   C4   C3    109.42  3.000
 Z6X  C5    C4   C3    113.16  3.000
 Z6X  H52   C5   H51   105.98  3.000
 Z6X  H52   C5   C6    109.38  3.000
 Z6X  H51   C5   C6    109.24  3.000
 Z6X  H52   C5   C4    109.31  3.000
 Z6X  H51   C5   C4    109.28  3.000
 Z6X  C6    C5   C4    113.39  3.000
 Z6X  H62   C6   H61   106.02  3.000
 Z6X  H62   C6   C7    109.32  3.000
 Z6X  H61   C6   C7    109.37  3.000
 Z6X  H62   C6   C5    109.31  3.000
 Z6X  H61   C6   C5    109.44  3.000
 Z6X  C7    C6   C5    113.14  3.000
 Z6X  H72   C7   H71   105.99  3.000
 Z6X  H72   C7   C8    109.39  3.000
 Z6X  H71   C7   C8    109.25  3.000
 Z6X  H72   C7   C6    109.32  3.000
 Z6X  H71   C7   C6    109.28  3.000
 Z6X  C8    C7   C6    113.35  3.000
 Z6X  H82   C8   H81   106.06  3.000
 Z6X  H82   C8   C9    109.34  3.000
 Z6X  H81   C8   C9    109.36  3.000
 Z6X  H82   C8   C7    109.33  3.000
 Z6X  H81   C8   C7    109.47  3.000
 Z6X  C9    C8   C7    113.04  3.000
 Z6X  H92   C9   H91   106.04  3.000
 Z6X  H92   C9   C10   109.54  3.000
 Z6X  H91   C9   C10   109.41  3.000
 Z6X  H92   C9   C8    109.32  3.000
 Z6X  H91   C9   C8    109.29  3.000
 Z6X  C10   C9   C8    112.99  3.000
 Z6X  H102  C10  H101  106.44  3.000
 Z6X  H102  C10  C11   109.84  3.000
 Z6X  H101  C10  C11   109.84  3.000
 Z6X  H102  C10  C9    109.38  3.000
 Z6X  H101  C10  C9    109.47  3.000
 Z6X  C11   C10  C9    111.72  3.000
 Z6X  H112  C11  H111  104.70  3.000
 Z6X  H112  C11  C12   107.40  3.000
 Z6X  H111  C11  C12   107.71  3.000
 Z6X  H112  C11  C10   110.61  3.000
 Z6X  H111  C11  C10   110.73  3.000
 Z6X  C12   C11  C10   115.11  3.000
 Z6X  C13   C12  O1    121.20  3.000
 Z6X  O1    C12  C11   123.54  3.000
 Z6X  C13   C12  C11   115.25  3.000
 Z6X  H132  C13  H131  106.89  3.000
 Z6X  H132  C13  C14   111.28  3.000
 Z6X  H131  C13  C14   109.68  3.000
 Z6X  H132  C13  C12   109.17  3.000
 Z6X  H131  C13  C12   108.37  3.000
 Z6X  C14   C13  C12   111.31  3.000
 Z6X  O3    C14  O2    123.71  3.000
 Z6X  O2    C14  C13   124.55  3.000
 Z6X  O3    C14  C13   111.75  3.000
 Z6X  H3O   O3   C14   110.16  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
 Z6X  CONST_01  H3O  O3   C14  C13   180.00   0.0  0
 Z6X  Var_01    C4   C3   C2   C1   -179.31  30.0  3
 Z6X  Var_02    C5   C4   C3   C2   -179.95  30.0  3
 Z6X  Var_03    C6   C5   C4   C3   -178.94  30.0  3
 Z6X  Var_04    C7   C6   C5   C4   -179.84  30.0  3
 Z6X  Var_05    C8   C7   C6   C5   -178.80  30.0  3
 Z6X  Var_06    C9   C8   C7   C6   -179.69  30.0  3
 Z6X  Var_07    C10  C9   C8   C7   -178.97  30.0  3
 Z6X  Var_08    C11  C10  C9   C8   -179.61  30.0  3
 Z6X  Var_09    C12  C11  C10  C9   -179.11  30.0  3
 Z6X  Var_10    C13  C12  C11  C10   177.05  30.0  3
 Z6X  Var_11    C14  C13  C12  C11   175.91  30.0  3
 Z6X  Var_12    O3   C14  C13  C12   -79.41  30.0  3
 Z6X  Var_13    H11  C1   C2   C3    -59.70  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
 Z6X  plan-1  C11  0.020
 Z6X  plan-1  C12  0.020
 Z6X  plan-1  O1   0.020
 Z6X  plan-1  C13  0.020
 Z6X  plan-2  C13  0.020
 Z6X  plan-2  C14  0.020
 Z6X  plan-2  O2   0.020
 Z6X  plan-2  O3   0.020
 Z6X  plan-2  H3O  0.020

