# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:25:24 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-oxopentadecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC(=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
 LIM  LIM  '3-oxopentadecanoic acid  '  ligand  45  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIM
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
 LIM  C1J   C  C      0   0.435   0.6883  -1.1356  -6.6868
 LIM  C2J   C  CH2    0  -0.715   0.7880   0.3471  -6.2346
 LIM  C3J   C  C      0   0.425  -0.0270   0.5783  -4.9953
 LIM  C4J   C  CH2    0  -0.561   0.6719   0.3185  -3.6874
 LIM  C5J   C  CH2    0  -0.416  -0.2119   0.3609  -2.4527
 LIM  C6J   C  CH2    0  -0.413   0.5849   0.1562  -1.1702
 LIM  C7J   C  CH2    0  -0.412  -0.2757   0.2121   0.0857
 LIM  C8J   C  CH2    0  -0.411   0.5254   0.0298   1.3685
 LIM  C9J   C  CH2    0  -0.412  -0.3276   0.1027   2.6289
 LIM  C0X   C  CH2    0  -0.411   0.4780  -0.0691   3.9104
 LIM  C1X   C  CH2    0  -0.411  -0.3708   0.0168   5.1727
 LIM  C2X   C  CH2    0  -0.411   0.4370  -0.1459   6.4541
 LIM  C3X   C  CH2    0  -0.406  -0.4113  -0.0527   7.7161
 LIM  C4X   C  CH2    0  -0.418   0.3951  -0.2026   9.0002
 LIM  C5X   C  CH3    0  -0.662  -0.4664  -0.1073  10.2520
 LIM  O1J   O  O      0  -0.596   0.0070  -1.8892  -5.9670
 LIM  O2J   O  O      0  -0.428  -1.1769   0.9632  -5.0473
 LIM  O3J   O  OC    -1  -0.606   1.2998  -1.4279  -7.7273
 LIM  H2J1  H  HCH2   0   0.258   0.4346   0.9925  -7.0430
 LIM  H2J2  H  HCH2   0   0.252   1.8402   0.5896  -6.0599
 LIM  H4J1  H  HCH2   0   0.255   1.4709   1.0669  -3.6083
 LIM  H4J2  H  HCH2   0   0.257   1.1931  -0.6409  -3.7627
 LIM  H5J1  H  HCH2   0   0.217  -0.9876  -0.4071  -2.5278
 LIM  H5J2  H  HCH2   0   0.216  -0.7346   1.3203  -2.4048
 LIM  H6J1  H  HCH2   0   0.208   1.3681   0.9199  -1.1046
 LIM  H6J2  H  HCH2   0   0.209   1.1056  -0.8072  -1.2105
 LIM  H7J1  H  HCH2   0   0.207  -1.0533  -0.5576   0.0285
 LIM  H7J2  H  HCH2   0   0.206  -0.8025   1.1725   0.1200
 LIM  H8J1  H  HCH2   0   0.206   1.3082   0.7952   1.4177
 LIM  H8J2  H  HCH2   0   0.206   1.0468  -0.9337   1.3386
 LIM  H9J1  H  HCH2   0   0.206  -1.1085  -0.6647   2.5842
 LIM  H9J2  H  HCH2   0   0.206  -0.8512   1.0652   2.6558
 LIM  H0X1  H  HCH2   0   0.206   1.2629   0.6947   3.9497
 LIM  H0X2  H  HCH2   0   0.206   0.9971  -1.0342   3.8873
 LIM  H1X1  H  HCH2   0   0.206  -1.1535  -0.7493   5.1368
 LIM  H1X2  H  HCH2   0   0.205  -0.8924   0.9805   5.1928
 LIM  H2X1  H  HCH2   0   0.206   1.2214   0.6187   6.4875
 LIM  H2X2  H  HCH2   0   0.206   0.9566  -1.1108   6.4366
 LIM  H3X1  H  HCH2   0   0.205  -1.1918  -0.8216   7.6869
 LIM  H3X2  H  HCH2   0   0.205  -0.9365   0.9093   7.7296
 LIM  H4X1  H  HCH2   0   0.210   1.1725   0.5673   9.0311
 LIM  H4X2  H  HCH2   0   0.209   0.9209  -1.1627   8.9880
 LIM  H5X1  H  HCH3   0   0.225   0.1296  -0.2035  11.1605
 LIM  H5X2  H  HCH3   0   0.215  -0.9858   0.8519  10.2986
 LIM  H5X3  H  HCH3   0   0.215  -1.2249  -0.8921  10.2692

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
 LIM  C1J  C2J   single  1.553  0.020  1.553
 LIM  C1J  O1J   deloc   1.245  0.020  1.245
 LIM  C1J  O3J   deloc   1.242  0.020  1.242
 LIM  C2J  C3J   single  1.501  0.020  1.501
 LIM  C2J  H2J1  single  0.970  0.020  1.090
 LIM  C2J  H2J2  single  0.970  0.020  1.090
 LIM  C3J  C4J   single  1.505  0.020  1.505
 LIM  C3J  O2J   double  1.214  0.020  1.214
 LIM  C4J  C5J   single  1.519  0.020  1.519
 LIM  C4J  H4J1  single  0.970  0.020  1.090
 LIM  C4J  H4J2  single  0.970  0.020  1.090
 LIM  C5J  C6J   single  1.524  0.020  1.524
 LIM  C5J  H5J1  single  0.970  0.020  1.090
 LIM  C5J  H5J2  single  0.970  0.020  1.090
 LIM  C6J  C7J   single  1.523  0.020  1.523
 LIM  C6J  H6J1  single  0.970  0.020  1.090
 LIM  C6J  H6J2  single  0.970  0.020  1.090
 LIM  C7J  C8J   single  1.523  0.020  1.523
 LIM  C7J  H7J1  single  0.970  0.020  1.090
 LIM  C7J  H7J2  single  0.970  0.020  1.090
 LIM  C8J  C9J   single  1.524  0.020  1.524
 LIM  C8J  H8J1  single  0.970  0.020  1.090
 LIM  C8J  H8J2  single  0.970  0.020  1.090
 LIM  C9J  C0X   single  1.523  0.020  1.523
 LIM  C9J  H9J1  single  0.970  0.020  1.090
 LIM  C9J  H9J2  single  0.970  0.020  1.090
 LIM  C0X  C1X   single  1.524  0.020  1.524
 LIM  C0X  H0X1  single  0.970  0.020  1.090
 LIM  C0X  H0X2  single  0.970  0.020  1.090
 LIM  C1X  C2X   single  1.523  0.020  1.523
 LIM  C1X  H1X1  single  0.970  0.020  1.090
 LIM  C1X  H1X2  single  0.970  0.020  1.090
 LIM  C2X  C3X   single  1.523  0.020  1.523
 LIM  C2X  H2X1  single  0.970  0.020  1.090
 LIM  C2X  H2X2  single  0.970  0.020  1.090
 LIM  C3X  C4X   single  1.524  0.020  1.524
 LIM  C3X  H3X1  single  0.970  0.020  1.090
 LIM  C3X  H3X2  single  0.970  0.020  1.090
 LIM  C4X  C5X   single  1.523  0.020  1.523
 LIM  C4X  H4X1  single  0.970  0.020  1.090
 LIM  C4X  H4X2  single  0.970  0.020  1.090
 LIM  C5X  H5X1  single  0.970  0.020  1.090
 LIM  C5X  H5X2  single  0.970  0.020  1.090
 LIM  C5X  H5X3  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
 LIM  O3J   C1J  O1J   127.69  3.000
 LIM  O3J   C1J  C2J   115.91  3.000
 LIM  O1J   C1J  C2J   116.39  3.000
 LIM  H2J2  C2J  H2J1  107.35  3.000
 LIM  H2J2  C2J  C3J   110.87  3.000
 LIM  H2J1  C2J  C3J   110.13  3.000
 LIM  H2J2  C2J  C1J   108.65  3.000
 LIM  H2J1  C2J  C1J   109.11  3.000
 LIM  C3J   C2J  C1J   110.64  3.000
 LIM  O2J   C3J  C4J   122.13  3.000
 LIM  O2J   C3J  C2J   121.86  3.000
 LIM  C4J   C3J  C2J   116.01  3.000
 LIM  H4J2  C4J  H4J1  104.84  3.000
 LIM  H4J2  C4J  C5J   110.94  3.000
 LIM  H4J1  C4J  C5J   110.23  3.000
 LIM  H4J2  C4J  C3J   108.22  3.000
 LIM  H4J1  C4J  C3J   106.43  3.000
 LIM  C5J   C4J  C3J   115.54  3.000
 LIM  H5J2  C5J  H5J1  106.26  3.000
 LIM  H5J2  C5J  C6J   109.33  3.000
 LIM  H5J1  C5J  C6J   109.52  3.000
 LIM  H5J2  C5J  C4J   109.77  3.000
 LIM  H5J1  C5J  C4J   109.70  3.000
 LIM  C6J   C5J  C4J   112.09  3.000
 LIM  H6J2  C6J  H6J1  105.98  3.000
 LIM  H6J2  C6J  C7J   109.33  3.000
 LIM  H6J1  C6J  C7J   109.19  3.000
 LIM  H6J2  C6J  C5J   109.61  3.000
 LIM  H6J1  C6J  C5J   109.30  3.000
 LIM  C7J   C6J  C5J   113.17  3.000
 LIM  H7J2  C7J  H7J1  106.03  3.000
 LIM  H7J2  C7J  C8J   109.35  3.000
 LIM  H7J1  C7J  C8J   109.45  3.000
 LIM  H7J2  C7J  C6J   109.24  3.000
 LIM  H7J1  C7J  C6J   109.40  3.000
 LIM  C8J   C7J  C6J   113.13  3.000
 LIM  H8J2  C8J  H8J1  105.99  3.000
 LIM  H8J2  C8J  C9J   109.33  3.000
 LIM  H8J1  C8J  C9J   109.23  3.000
 LIM  H8J2  C8J  C7J   109.41  3.000
 LIM  H8J1  C8J  C7J   109.26  3.000
 LIM  C9J   C8J  C7J   113.36  3.000
 LIM  H9J2  C9J  H9J1  106.00  3.000
 LIM  H9J2  C9J  C0X   109.33  3.000
 LIM  H9J1  C9J  C0X   109.40  3.000
 LIM  H9J2  C9J  C8J   109.25  3.000
 LIM  H9J1  C9J  C8J   109.37  3.000
 LIM  C0X   C9J  C8J   113.23  3.000
 LIM  H0X2  C0X  H0X1  105.98  3.000
 LIM  H0X2  C0X  C1X   109.33  3.000
 LIM  H0X1  C0X  C1X   109.27  3.000
 LIM  H0X2  C0X  C9J   109.39  3.000
 LIM  H0X1  C0X  C9J   109.29  3.000
 LIM  C1X   C0X  C9J   113.33  3.000
 LIM  H1X2  C1X  H1X1  105.98  3.000
 LIM  H1X2  C1X  C2X   109.32  3.000
 LIM  H1X1  C1X  C2X   109.37  3.000
 LIM  H1X2  C1X  C0X   109.26  3.000
 LIM  H1X1  C1X  C0X   109.35  3.000
 LIM  C2X   C1X  C0X   113.29  3.000
 LIM  H2X2  C2X  H2X1  105.99  3.000
 LIM  H2X2  C2X  C3X   109.33  3.000
 LIM  H2X1  C2X  C3X   109.30  3.000
 LIM  H2X2  C2X  C1X   109.39  3.000
 LIM  H2X1  C2X  C1X   109.31  3.000
 LIM  C3X   C2X  C1X   113.26  3.000
 LIM  H3X2  C3X  H3X1  105.95  3.000
 LIM  H3X2  C3X  C4X   109.24  3.000
 LIM  H3X1  C3X  C4X   109.29  3.000
 LIM  H3X2  C3X  C2X   109.31  3.000
 LIM  H3X1  C3X  C2X   109.36  3.000
 LIM  C4X   C3X  C2X   113.41  3.000
 LIM  H4X2  C4X  H4X1  106.02  3.000
 LIM  H4X2  C4X  C5X   109.62  3.000
 LIM  H4X1  C4X  C5X   109.55  3.000
 LIM  H4X2  C4X  C3X   109.34  3.000
 LIM  H4X1  C4X  C3X   109.30  3.000
 LIM  C5X   C4X  C3X   112.79  3.000
 LIM  H5X3  C5X  H5X2  107.48  3.000
 LIM  H5X3  C5X  H5X1  107.64  3.000
 LIM  H5X2  C5X  H5X1  107.58  3.000
 LIM  H5X3  C5X  C4X   111.17  3.000
 LIM  H5X2  C5X  C4X   111.05  3.000
 LIM  H5X1  C5X  C4X   111.72  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
 LIM  Var_01  C4J   C3J  C2J  C1J    87.51  30.0  3
 LIM  Var_02  C5J   C4J  C3J  C2J  -171.57  30.0  3
 LIM  Var_03  O1J   C1J  C2J  C3J    -1.81  30.0  2
 LIM  Var_04  C6J   C5J  C4J  C3J  -177.19  30.0  3
 LIM  Var_05  C7J   C6J  C5J  C4J   179.26  30.0  3
 LIM  Var_06  C8J   C7J  C6J  C5J  -179.07  30.0  3
 LIM  Var_07  C9J   C8J  C7J  C6J   179.26  30.0  3
 LIM  Var_08  C0X   C9J  C8J  C7J  -179.55  30.0  3
 LIM  Var_09  C1X   C0X  C9J  C8J   179.44  30.0  3
 LIM  Var_10  C2X   C1X  C0X  C9J  -179.62  30.0  3
 LIM  Var_11  C3X   C2X  C1X  C0X   179.70  30.0  3
 LIM  Var_12  C4X   C3X  C2X  C1X  -179.49  30.0  3
 LIM  Var_13  C5X   C4X  C3X  C2X  -180.00  30.0  3
 LIM  Var_14  H5X1  C5X  C4X  C3X  -179.24  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
 LIM  plan-1  C2J  0.020
 LIM  plan-1  C3J  0.020
 LIM  plan-1  C4J  0.020
 LIM  plan-1  O2J  0.020
 LIM  plan-2  C1J  0.020
 LIM  plan-2  C2J  0.020
 LIM  plan-2  O1J  0.020
 LIM  plan-2  O3J  0.020

