# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:43:57 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: hexadecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(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
 PLM  PLM  'hexadecanoic acid        '  ligand  49  18  .  2012-06-15  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PLM
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
 PLM  C1   C  C      0   0.401  -45.1618  67.0291   -5.6534
 PLM  O1   O  OC    -1  -0.622  -45.7066  65.9454   -5.3555
 PLM  O2   O  O      0  -0.610  -44.1443  67.1761   -6.3618
 PLM  C2   C  CH2    0  -0.559  -45.7899  68.3017   -5.0500
 PLM  C3   C  CH2    0  -0.408  -45.5837  69.5817   -5.8471
 PLM  C4   C  CH2    0  -0.423  -46.1885  70.8022   -5.1636
 PLM  C5   C  CH2    0  -0.425  -46.0001  72.1100   -5.9297
 PLM  C6   C  CH2    0  -0.424  -46.6967  72.1803   -7.2890
 PLM  C7   C  CH2    0  -0.413  -48.2128  72.0386   -7.2145
 PLM  C8   C  CH2    0  -0.413  -48.9076  72.2316   -8.5573
 PLM  C9   C  CH2    0  -0.419  -50.4213  72.0710   -8.4626
 PLM  CA   C  CH2    0  -0.419  -51.1748  72.3391   -9.7623
 PLM  CB   C  CH2    0  -0.413  -50.8673  71.3569  -10.8866
 PLM  CC   C  CH2    0  -0.413  -51.7055  71.6047  -12.1353
 PLM  CD   C  CH2    0  -0.419  -51.3967  70.6262  -13.2625
 PLM  CE   C  CH2    0  -0.413  -52.1785  70.8774  -14.5492
 PLM  CF   C  CH2    0  -0.423  -53.6818  70.6507  -14.4303
 PLM  CG   C  CH3    0  -0.657  -54.4113  70.8518  -15.7518
 PLM  H21  H  HCH2   0   0.197  -46.8595  68.1356   -4.8897
 PLM  H22  H  HCH2   0   0.211  -45.3650  68.4360   -4.0460
 PLM  H31  H  HCH2   0   0.199  -44.5149  69.7500   -6.0039
 PLM  H32  H  HCH2   0   0.203  -46.0179  69.4580   -6.8446
 PLM  H41  H  HCH2   0   0.206  -47.2536  70.6301   -4.9763
 PLM  H42  H  HCH2   0   0.211  -45.7328  70.9119   -4.1737
 PLM  H51  H  HCH2   0   0.211  -46.3630  72.9377   -5.3117
 PLM  H52  H  HCH2   0   0.211  -44.9286  72.2862   -6.0697
 PLM  H61  H  HCH2   0   0.213  -46.4537  73.1424   -7.7516
 PLM  H62  H  HCH2   0   0.209  -46.2924  71.4173   -7.9616
 PLM  H71  H  HCH2   0   0.211  -48.4764  71.0529   -6.8178
 PLM  H72  H  HCH2   0   0.203  -48.6073  72.7664   -6.4960
 PLM  H81  H  HCH2   0   0.203  -48.6738  73.2277   -8.9503
 PLM  H82  H  HCH2   0   0.211  -48.4965  71.5182   -9.2783
 PLM  H91  H  HCH2   0   0.205  -50.6549  71.0604   -8.1091
 PLM  H92  H  HCH2   0   0.213  -50.7969  72.7517   -7.6917
 PLM  HA1  H  HCH2   0   0.213  -52.2501  72.3121   -9.5584
 PLM  HA2  H  HCH2   0   0.204  -50.9597  73.3579  -10.1038
 PLM  HB1  H  HCH2   0   0.211  -49.8066  71.4079  -11.1515
 PLM  HB2  H  HCH2   0   0.204  -51.0413  70.3353  -10.5296
 PLM  HC1  H  HCH2   0   0.210  -52.7657  71.5506  -11.8689
 PLM  HC2  H  HCH2   0   0.204  -51.5349  72.6275  -12.4905
 PLM  HD1  H  HCH2   0   0.214  -50.3257  70.6736  -13.4837
 PLM  HD2  H  HCH2   0   0.204  -51.5868  69.6041  -12.9165
 PLM  HE1  H  HCH2   0   0.204  -51.9932  71.9014  -14.8935
 PLM  HE2  H  HCH2   0   0.213  -51.7874  70.2224  -15.3347
 PLM  HF1  H  HCH2   0   0.208  -53.8634  69.6359  -14.0619
 PLM  HF2  H  HCH2   0   0.215  -54.1054  71.3242  -13.6807
 PLM  HG1  H  HCH3   0   0.224  -55.4841  70.6857  -15.6474
 PLM  HG2  H  HCH3   0   0.214  -54.2699  71.8663  -16.1295
 PLM  HG3  H  HCH3   0   0.214  -54.0434  70.1641  -16.5155

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
 PLM  C1  O1   deloc   1.249  0.020  1.249
 PLM  C1  O2   deloc   1.249  0.020  1.249
 PLM  C1  C2   single  1.542  0.020  1.542
 PLM  C2  C3   single  1.522  0.020  1.522
 PLM  C2  H21  single  0.970  0.020  1.090
 PLM  C2  H22  single  0.970  0.020  1.090
 PLM  C3  C4   single  1.524  0.020  1.524
 PLM  C3  H31  single  0.970  0.020  1.090
 PLM  C3  H32  single  0.970  0.020  1.090
 PLM  C4  C5   single  1.527  0.020  1.527
 PLM  C4  H41  single  0.970  0.020  1.090
 PLM  C4  H42  single  0.970  0.020  1.090
 PLM  C5  C6   single  1.529  0.020  1.529
 PLM  C5  H51  single  0.970  0.020  1.090
 PLM  C5  H52  single  0.970  0.020  1.090
 PLM  C6  C7   single  1.525  0.020  1.525
 PLM  C6  H61  single  0.970  0.020  1.090
 PLM  C6  H62  single  0.970  0.020  1.090
 PLM  C7  C8   single  1.524  0.020  1.524
 PLM  C7  H71  single  0.970  0.020  1.090
 PLM  C7  H72  single  0.970  0.020  1.090
 PLM  C8  C9   single  1.525  0.020  1.525
 PLM  C8  H81  single  0.970  0.020  1.090
 PLM  C8  H82  single  0.970  0.020  1.090
 PLM  C9  CA   single  1.526  0.020  1.526
 PLM  C9  H91  single  0.970  0.020  1.090
 PLM  C9  H92  single  0.970  0.020  1.090
 PLM  CA  CB   single  1.524  0.020  1.524
 PLM  CA  HA1  single  0.970  0.020  1.090
 PLM  CA  HA2  single  0.970  0.020  1.090
 PLM  CB  CC   single  1.524  0.020  1.524
 PLM  CB  HB1  single  0.970  0.020  1.090
 PLM  CB  HB2  single  0.970  0.020  1.090
 PLM  CC  CD   single  1.524  0.020  1.524
 PLM  CC  HC1  single  0.970  0.020  1.090
 PLM  CC  HC2  single  0.970  0.020  1.090
 PLM  CD  CE   single  1.526  0.020  1.526
 PLM  CD  HD1  single  0.970  0.020  1.090
 PLM  CD  HD2  single  0.970  0.020  1.090
 PLM  CE  CF   single  1.525  0.020  1.525
 PLM  CE  HE1  single  0.970  0.020  1.090
 PLM  CE  HE2  single  0.970  0.020  1.090
 PLM  CF  CG   single  1.523  0.020  1.523
 PLM  CF  HF1  single  0.970  0.020  1.090
 PLM  CF  HF2  single  0.970  0.020  1.090
 PLM  CG  HG1  single  0.970  0.020  1.090
 PLM  CG  HG2  single  0.970  0.020  1.090
 PLM  CG  HG3  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
 PLM  C2   C1  O2   117.18  3.000
 PLM  C2   C1  O1   116.43  3.000
 PLM  O2   C1  O1   126.37  3.000
 PLM  H22  C2  H21  105.23  3.000
 PLM  H22  C2  C3   108.87  3.000
 PLM  H21  C2  C3   109.68  3.000
 PLM  H22  C2  C1   107.52  3.000
 PLM  H21  C2  C1   109.28  3.000
 PLM  C3   C2  C1   115.72  3.000
 PLM  H32  C3  H31  105.92  3.000
 PLM  H32  C3  C4   109.98  3.000
 PLM  H31  C3  C4   109.21  3.000
 PLM  H32  C3  C2   109.17  3.000
 PLM  H31  C3  C2   109.70  3.000
 PLM  C4   C3  C2   112.64  3.000
 PLM  H42  C4  H41  105.42  3.000
 PLM  H42  C4  C5   108.44  3.000
 PLM  H41  C4  C5   109.90  3.000
 PLM  H42  C4  C3   108.68  3.000
 PLM  H41  C4  C3   109.68  3.000
 PLM  C5   C4  C3   114.32  3.000
 PLM  H52  C5  H51  105.95  3.000
 PLM  H52  C5  C6   108.95  3.000
 PLM  H51  C5  C6   108.42  3.000
 PLM  H52  C5  C4   108.83  3.000
 PLM  H51  C5  C4   108.86  3.000
 PLM  C6   C5  C4   115.41  3.000
 PLM  H62  C6  H61  105.72  3.000
 PLM  H62  C6  C7   109.42  3.000
 PLM  H61  C6  C7   108.85  3.000
 PLM  H62  C6  C5   110.24  3.000
 PLM  H61  C6  C5   108.36  3.000
 PLM  C7   C6  C5   113.91  3.000
 PLM  H72  C7  H71  105.88  3.000
 PLM  H72  C7  C8   109.23  3.000
 PLM  H71  C7  C8   108.88  3.000
 PLM  H72  C7  C6   109.16  3.000
 PLM  H71  C7  C6   109.93  3.000
 PLM  C8   C7  C6   113.49  3.000
 PLM  H82  C8  H81  106.02  3.000
 PLM  H82  C8  C9   110.18  3.000
 PLM  H81  C8  C9   109.25  3.000
 PLM  H82  C8  C7   109.07  3.000
 PLM  H81  C8  C7   109.50  3.000
 PLM  C9   C8  C7   112.61  3.000
 PLM  H92  C9  H91  105.84  3.000
 PLM  H92  C9  CA   108.73  3.000
 PLM  H91  C9  CA   109.36  3.000
 PLM  H92  C9  C8   108.59  3.000
 PLM  H91  C9  C8   109.19  3.000
 PLM  CA   C9  C8   114.75  3.000
 PLM  HA2  CA  HA1  105.89  3.000
 PLM  HA2  CA  CB   109.25  3.000
 PLM  HA1  CA  CB   108.64  3.000
 PLM  HA2  CA  C9   109.38  3.000
 PLM  HA1  CA  C9   108.78  3.000
 PLM  CB   CA  C9   114.54  3.000
 PLM  HB2  CB  HB1  106.03  3.000
 PLM  HB2  CB  CC   109.33  3.000
 PLM  HB1  CB  CC   109.09  3.000
 PLM  HB2  CB  CA   109.17  3.000
 PLM  HB1  CB  CA   110.12  3.000
 PLM  CC   CB  CA   112.86  3.000
 PLM  HC2  CC  HC1  106.01  3.000
 PLM  HC2  CC  CD   109.13  3.000
 PLM  HC1  CC  CD   110.15  3.000
 PLM  HC2  CC  CB   109.37  3.000
 PLM  HC1  CC  CB   108.98  3.000
 PLM  CD   CC  CB   112.96  3.000
 PLM  HD2  CD  HD1  105.90  3.000
 PLM  HD2  CD  CE   109.32  3.000
 PLM  HD1  CD  CE   108.88  3.000
 PLM  HD2  CD  CC   109.28  3.000
 PLM  HD1  CD  CC   108.65  3.000
 PLM  CE   CD  CC   114.45  3.000
 PLM  HE2  CE  HE1  105.86  3.000
 PLM  HE2  CE  CF   108.61  3.000
 PLM  HE1  CE  CF   109.27  3.000
 PLM  HE2  CE  CD   108.86  3.000
 PLM  HE1  CE  CD   109.39  3.000
 PLM  CF   CE  CD   114.50  3.000
 PLM  HF2  CF  HF1  106.02  3.000
 PLM  HF2  CF  CG   109.15  3.000
 PLM  HF1  CF  CG   109.57  3.000
 PLM  HF2  CF  CE   110.12  3.000
 PLM  HF1  CF  CE   109.12  3.000
 PLM  CG   CF  CE   112.64  3.000
 PLM  HG3  CG  HG2  107.44  3.000
 PLM  HG3  CG  HG1  107.61  3.000
 PLM  HG2  CG  HG1  107.58  3.000
 PLM  HG3  CG  CF   111.26  3.000
 PLM  HG2  CG  CF   111.16  3.000
 PLM  HG1  CG  CF   111.60  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
 PLM  Var_01  C4   C3  C2  C1  -177.93  30.0  3
 PLM  Var_02  C3   C2  C1  O1  -153.28  30.0  3
 PLM  Var_03  C5   C4  C3  C2   179.84  30.0  3
 PLM  Var_04  C6   C5  C4  C3    64.24  30.0  3
 PLM  Var_05  C7   C6  C5  C4    60.96  30.0  3
 PLM  Var_06  C8   C7  C6  C5   174.95  30.0  3
 PLM  Var_07  C9   C8  C7  C6   179.39  30.0  3
 PLM  Var_08  CA   C9  C8  C7   176.40  30.0  3
 PLM  Var_09  CB   CA  C9  C8    64.77  30.0  3
 PLM  Var_10  CC   CB  CA  C9   176.28  30.0  3
 PLM  Var_11  CD   CC  CB  CA   179.83  30.0  3
 PLM  Var_12  CE   CD  CC  CB  -177.73  30.0  3
 PLM  Var_13  CF   CE  CD  CC   -66.25  30.0  3
 PLM  Var_14  CG   CF  CE  CD  -177.41  30.0  3
 PLM  Var_15  HG1  CG  CF  CE  -179.99  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
 PLM  plan-1  C1  0.020
 PLM  plan-1  O1  0.020
 PLM  plan-1  O2  0.020
 PLM  plan-1  C2  0.020

