# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 18:59:00 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  46  18  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.557   0.1944   0.3656  -7.4325
 LIM  C2J   C  CH2   0  -0.697   0.8191  -0.2117  -6.1911
 LIM  C3J   C  C     0   0.418  -0.0634  -0.1060  -4.9632
 LIM  C4J   C  CH2   0  -0.569   0.6698  -0.0054  -3.6569
 LIM  C5J   C  CH2   0  -0.416  -0.2017  -0.0920  -2.4160
 LIM  C6J   C  CH2   0  -0.415   0.6167   0.0147  -1.1350
 LIM  C7J   C  CH2   0  -0.413  -0.2370  -0.0836   0.1226
 LIM  C8J   C  CH2   0  -0.412   0.5740   0.0026   1.4092
 LIM  C9J   C  CH2   0  -0.412  -0.2875  -0.0545   2.6648
 LIM  C0X   C  CH2   0  -0.412   0.5194   0.0138   3.9553
 LIM  C1X   C  CH2   0  -0.411  -0.3489  -0.0149   5.2073
 LIM  C2X   C  CH2   0  -0.412   0.4548   0.0183   6.5013
 LIM  C3X   C  CH2   0  -0.406  -0.4188   0.0150   7.7498
 LIM  C4X   C  CH2   0  -0.419   0.3789   0.0400   9.0481
 LIM  C5X   C  CH3   0  -0.662  -0.5103   0.0436  10.2841
 LIM  O1J   O  O     0  -0.434  -0.4464   1.3843  -7.4568
 LIM  O2J   O  O     0  -0.391  -1.2670  -0.1435  -5.0489
 LIM  O3J   O  OH1   0  -0.588   0.4733  -0.3523  -8.5121
 LIM  H2J1  H  HCH2  0   0.314   1.7743   0.2946  -6.0219
 LIM  H2J2  H  HCH2  0   0.317   1.0637  -1.2691  -6.3254
 LIM  H4J1  H  HCH2  0   0.275   1.2262   0.9403  -3.6778
 LIM  H4J2  H  HCH2  0   0.270   1.4457  -0.7802  -3.6462
 LIM  H5J1  H  HCH2  0   0.223  -0.7531  -1.0369  -2.4177
 LIM  H5J2  H  HCH2  0   0.224  -0.9527   0.7024  -2.4341
 LIM  H6J1  H  HCH2  0   0.212   1.1637   0.9641  -1.1297
 LIM  H6J2  H  HCH2  0   0.212   1.3778  -0.7733  -1.1200
 LIM  H7J1  H  HCH2  0   0.208  -0.7945  -1.0270   0.1088
 LIM  H7J2  H  HCH2  0   0.208  -0.9898   0.7125   0.1133
 LIM  H8J1  H  HCH2  0   0.207   1.1578   0.9302   1.4108
 LIM  H8J2  H  HCH2  0   0.207   1.3041  -0.8141   1.4332
 LIM  H9J1  H  HCH2  0   0.206  -0.8792  -0.9771   2.6563
 LIM  H9J2  H  HCH2  0   0.206  -1.0112   0.7681   2.6450
 LIM  H0X1  H  HCH2  0   0.206   1.1281   0.9252   3.9563
 LIM  H0X2  H  HCH2  0   0.206   1.2270  -0.8224   3.9856
 LIM  H1X1  H  HCH2  0   0.206  -0.9750  -0.9145   5.1931
 LIM  H1X2  H  HCH2  0   0.206  -1.0408   0.8346   5.1876
 LIM  H2X1  H  HCH2  0   0.206   1.0965   0.9068   6.5088
 LIM  H2X2  H  HCH2  0   0.206   1.1313  -0.8433   6.5304
 LIM  H3X1  H  HCH2  0   0.205  -1.0631  -0.8717   7.7389
 LIM  H3X2  H  HCH2  0   0.205  -1.0937   0.8782   7.7230
 LIM  H4X1  H  HCH2  0   0.210   1.0268   0.9222   9.0580
 LIM  H4X2  H  HCH2  0   0.210   1.0471  -0.8264   9.0786
 LIM  H5X1  H  HCH3  0   0.225   0.0756   0.0592  11.2040
 LIM  H5X2  H  HCH3  0   0.215  -1.1646   0.9174  10.2943
 LIM  H5X3  H  HCH3  0   0.215  -1.1457  -0.8437  10.3126
 LIM  HO3   H  HOH1  0   0.482   0.0993   0.0729  -9.2993

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  1.505  0.020  1.505
 LIM  C1J  O1J   double  1.204  0.020  1.204
 LIM  C1J  O3J   single  1.326  0.020  1.326
 LIM  C2J  C3J   single  1.516  0.020  1.516
 LIM  C2J  H2J1  single  0.970  0.020  1.090
 LIM  C2J  H2J2  single  0.970  0.020  1.090
 LIM  C3J  C4J   single  1.501  0.020  1.501
 LIM  C3J  O2J   double  1.207  0.020  1.207
 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  1.524  0.020  1.524
 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  1.524  0.020  1.524
 LIM  C1X  H1X1  single  0.970  0.020  1.090
 LIM  C1X  H1X2  single  0.970  0.020  1.090
 LIM  C2X  C3X   single  1.524  0.020  1.524
 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
 LIM  O3J  HO3   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
 LIM  O3J   C1J  O1J   123.62  3.000
 LIM  O3J   C1J  C2J   112.12  3.000
 LIM  O1J   C1J  C2J   124.21  3.000
 LIM  H2J2  C2J  H2J1  105.73  3.000
 LIM  H2J2  C2J  C3J   107.29  3.000
 LIM  H2J1  C2J  C3J   110.53  3.000
 LIM  H2J2  C2J  C1J   111.25  3.000
 LIM  H2J1  C2J  C1J   108.20  3.000
 LIM  C3J   C2J  C1J   113.57  3.000
 LIM  O2J   C3J  C4J   123.42  3.000
 LIM  O2J   C3J  C2J   121.38  3.000
 LIM  C4J   C3J  C2J   115.16  3.000
 LIM  H4J2  C4J  H4J1  104.50  3.000
 LIM  H4J2  C4J  C5J   110.96  3.000
 LIM  H4J1  C4J  C5J   110.83  3.000
 LIM  H4J2  C4J  C3J   107.86  3.000
 LIM  H4J1  C4J  C3J   106.78  3.000
 LIM  C5J   C4J  C3J   115.26  3.000
 LIM  H5J2  C5J  H5J1  106.34  3.000
 LIM  H5J2  C5J  C6J   109.39  3.000
 LIM  H5J1  C5J  C6J   109.42  3.000
 LIM  H5J2  C5J  C4J   109.83  3.000
 LIM  H5J1  C5J  C4J   109.70  3.000
 LIM  C6J   C5J  C4J   112.00  3.000
 LIM  H6J2  C6J  H6J1  106.04  3.000
 LIM  H6J2  C6J  C7J   109.36  3.000
 LIM  H6J1  C6J  C7J   109.37  3.000
 LIM  H6J2  C6J  C5J   109.53  3.000
 LIM  H6J1  C6J  C5J   109.44  3.000
 LIM  C7J   C6J  C5J   112.86  3.000
 LIM  H7J2  C7J  H7J1  106.01  3.000
 LIM  H7J2  C7J  C8J   109.38  3.000
 LIM  H7J1  C7J  C8J   109.28  3.000
 LIM  H7J2  C7J  C6J   109.34  3.000
 LIM  H7J1  C7J  C6J   109.29  3.000
 LIM  C8J   C7J  C6J   113.28  3.000
 LIM  H8J2  C8J  H8J1  106.02  3.000
 LIM  H8J2  C8J  C9J   109.31  3.000
 LIM  H8J1  C8J  C9J   109.37  3.000
 LIM  H8J2  C8J  C7J   109.33  3.000
 LIM  H8J1  C8J  C7J   109.43  3.000
 LIM  C9J   C8J  C7J   113.13  3.000
 LIM  H9J2  C9J  H9J1  105.98  3.000
 LIM  H9J2  C9J  C0X   109.35  3.000
 LIM  H9J1  C9J  C0X   109.28  3.000
 LIM  H9J2  C9J  C8J   109.29  3.000
 LIM  H9J1  C9J  C8J   109.29  3.000
 LIM  C0X   C9J  C8J   113.38  3.000
 LIM  H0X2  C0X  H0X1  106.02  3.000
 LIM  H0X2  C0X  C1X   109.32  3.000
 LIM  H0X1  C0X  C1X   109.36  3.000
 LIM  H0X2  C0X  C9J   109.34  3.000
 LIM  H0X1  C0X  C9J   109.40  3.000
 LIM  C1X   C0X  C9J   113.16  3.000
 LIM  H1X2  C1X  H1X1  105.98  3.000
 LIM  H1X2  C1X  C2X   109.35  3.000
 LIM  H1X1  C1X  C2X   109.28  3.000
 LIM  H1X2  C1X  C0X   109.29  3.000
 LIM  H1X1  C1X  C0X   109.29  3.000
 LIM  C2X   C1X  C0X   113.38  3.000
 LIM  H2X2  C2X  H2X1  106.01  3.000
 LIM  H2X2  C2X  C3X   109.30  3.000
 LIM  H2X1  C2X  C3X   109.38  3.000
 LIM  H2X2  C2X  C1X   109.32  3.000
 LIM  H2X1  C2X  C1X   109.41  3.000
 LIM  C3X   C2X  C1X   113.17  3.000
 LIM  H3X2  C3X  H3X1  105.96  3.000
 LIM  H3X2  C3X  C4X   109.28  3.000
 LIM  H3X1  C3X  C4X   109.23  3.000
 LIM  H3X2  C3X  C2X   109.35  3.000
 LIM  H3X1  C3X  C2X   109.31  3.000
 LIM  C4X   C3X  C2X   113.44  3.000
 LIM  H4X2  C4X  H4X1  106.05  3.000
 LIM  H4X2  C4X  C5X   109.62  3.000
 LIM  H4X1  C4X  C5X   109.66  3.000
 LIM  H4X2  C4X  C3X   109.29  3.000
 LIM  H4X1  C4X  C3X   109.32  3.000
 LIM  C5X   C4X  C3X   112.70  3.000
 LIM  H5X3  C5X  H5X2  107.54  3.000
 LIM  H5X3  C5X  H5X1  107.59  3.000
 LIM  H5X2  C5X  H5X1  107.62  3.000
 LIM  H5X3  C5X  C4X   111.05  3.000
 LIM  H5X2  C5X  C4X   111.07  3.000
 LIM  H5X1  C5X  C4X   111.77  3.000
 LIM  HO3   O3J  C1J   110.02  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  CONST_01  HO3   O3J  C1J  C2J   180.00   0.0  0
 LIM  Var_01    C4J   C3J  C2J  C1J  -150.88  30.0  3
 LIM  Var_02    C5J   C4J  C3J  C2J  -171.93  30.0  3
 LIM  Var_03    O1J   C1J  C2J  C3J    40.38  30.0  2
 LIM  Var_04    C6J   C5J  C4J  C3J   179.86  30.0  3
 LIM  Var_05    C7J   C6J  C5J  C4J  -179.44  30.0  3
 LIM  Var_06    C8J   C7J  C6J  C5J   179.21  30.0  3
 LIM  Var_07    C9J   C8J  C7J  C6J   178.29  30.0  3
 LIM  Var_08    C0X   C9J  C8J  C7J   179.28  30.0  3
 LIM  Var_09    C1X   C0X  C9J  C8J   178.82  30.0  3
 LIM  Var_10    C2X   C1X  C0X  C9J   178.57  30.0  3
 LIM  Var_11    C3X   C2X  C1X  C0X   178.95  30.0  3
 LIM  Var_12    C4X   C3X  C2X  C1X   179.66  30.0  3
 LIM  Var_13    C5X   C4X  C3X  C2X   179.70  30.0  3
 LIM  Var_14    H5X1  C5X  C4X  C3X   179.86  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
 LIM  plan-2  HO3  0.020

