# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:01:15 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: hexadecanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC=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
 PLY  PLY  'hexadecanal              '  ligand  49  17  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PLY
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
 PLY  C1   C  C1    0   0.188  -8.9047  -0.2656  -0.2437
 PLY  O2   O  O     0  -0.383  -9.8364  -0.2639   0.5233
 PLY  C2   C  CH2   0  -0.546  -7.6606   0.5503  -0.1001
 PLY  C3   C  CH2   0  -0.437  -6.4087  -0.3298  -0.1411
 PLY  C4   C  CH2   0  -0.411  -5.1263   0.4907  -0.0895
 PLY  C5   C  CH2   0  -0.414  -3.8698  -0.3705  -0.1150
 PLY  C6   C  CH2   0  -0.413  -2.5853   0.4474  -0.0664
 PLY  C7   C  CH2   0  -0.412  -1.3252  -0.4090  -0.0893
 PLY  C8   C  CH2   0  -0.412  -0.0419   0.4108  -0.0422
 PLY  C9   C  CH2   0  -0.412   1.2205  -0.4423  -0.0616
 PLY  CA   C  CH2   0  -0.412   2.5021   0.3804  -0.0179
 PLY  CB   C  CH2   0  -0.412   3.7665  -0.4698  -0.0355
 PLY  CC   C  CH2   0  -0.411   5.0460   0.3563   0.0050
 PLY  CD   C  CH2   0  -0.412   6.3132  -0.4899  -0.0094
 PLY  CE   C  CH2   0  -0.406   7.5894   0.3416   0.0264
 PLY  CF   C  CH2   0  -0.419   8.8610  -0.4985   0.0160
 PLY  CG   C  CH3   0  -0.662  10.1255   0.3490   0.0511
 PLY  H11  H  H     0   0.181  -8.9201  -0.9093  -1.1432
 PLY  H21  H  HCH2  0   0.248  -7.6997   1.1421   0.8162
 PLY  H22  H  HCH2  0   0.260  -7.6314   1.2447  -0.9485
 PLY  H31  H  HCH2  0   0.227  -6.4170  -0.9365  -1.0524
 PLY  H32  H  HCH2  0   0.232  -6.4286  -1.0317   0.6978
 PLY  H41  H  HCH2  0   0.215  -5.1262   1.1083   0.8152
 PLY  H42  H  HCH2  0   0.215  -5.1086   1.1875  -0.9345
 PLY  H51  H  HCH2  0   0.210  -3.8721  -0.9907  -1.0183
 PLY  H52  H  HCH2  0   0.210  -3.8899  -1.0666   0.7309
 PLY  H61  H  HCH2  0   0.208  -2.5846   1.0692   0.8361
 PLY  H62  H  HCH2  0   0.208  -2.5660   1.1431  -0.9129
 PLY  H71  H  HCH2  0   0.207  -1.3255  -1.0317  -0.9913
 PLY  H72  H  HCH2  0   0.207  -1.3437  -1.1041   0.7577
 PLY  H81  H  HCH2  0   0.206  -0.0434   1.0354   0.8585
 PLY  H82  H  HCH2  0   0.206  -0.0232   1.1045  -0.8905
 PLY  H91  H  HCH2  0   0.206   1.2217  -1.0681  -0.9615
 PLY  H92  H  HCH2  0   0.206   1.2036  -1.1345   0.7878
 PLY  HA1  H  HCH2  0   0.206   2.4998   1.0079   0.8808
 PLY  HA2  H  HCH2  0   0.206   2.5186   1.0714  -0.8683
 PLY  HB1  H  HCH2  0   0.206   3.7684  -1.0985  -0.9333
 PLY  HB2  H  HCH2  0   0.206   3.7518  -1.1595   0.8161
 PLY  HC1  H  HCH2  0   0.206   5.0420   0.9872   0.9012
 PLY  HC2  H  HCH2  0   0.206   5.0603   1.0441  -0.8482
 PLY  HD1  H  HCH2  0   0.206   6.3169  -1.1229  -0.9041
 PLY  HD2  H  HCH2  0   0.206   6.3018  -1.1750   0.8458
 PLY  HE1  H  HCH2  0   0.205   7.5837   0.9769   0.9196
 PLY  HE2  H  HCH2  0   0.206   7.6015   1.0257  -0.8299
 PLY  HF1  H  HCH2  0   0.210   8.8680  -1.1336  -0.8756
 PLY  HF2  H  HCH2  0   0.210   8.8511  -1.1793   0.8729
 PLY  HG1  H  HCH3  0   0.215  10.1568   0.9699   0.9487
 PLY  HG2  H  HCH3  0   0.225  11.0257  -0.2668   0.0448
 PLY  HG3  H  HCH3  0   0.215  10.1756   1.0160  -0.8119

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
 PLY  C1  O2   double  1.207  0.020  1.207
 PLY  C1  C2   single  1.495  0.020  1.495
 PLY  C1  H11  single  0.930  0.020  1.080
 PLY  C2  C3   single  1.531  0.020  1.531
 PLY  C2  H21  single  0.970  0.020  1.090
 PLY  C2  H22  single  0.970  0.020  1.090
 PLY  C3  C4   single  1.523  0.020  1.523
 PLY  C3  H31  single  0.970  0.020  1.090
 PLY  C3  H32  single  0.970  0.020  1.090
 PLY  C4  C5   single  1.523  0.020  1.523
 PLY  C4  H41  single  0.970  0.020  1.090
 PLY  C4  H42  single  0.970  0.020  1.090
 PLY  C5  C6   single  1.524  0.020  1.524
 PLY  C5  H51  single  0.970  0.020  1.090
 PLY  C5  H52  single  0.970  0.020  1.090
 PLY  C6  C7   single  1.524  0.020  1.524
 PLY  C6  H61  single  0.970  0.020  1.090
 PLY  C6  H62  single  0.970  0.020  1.090
 PLY  C7  C8   single  1.524  0.020  1.524
 PLY  C7  H71  single  0.970  0.020  1.090
 PLY  C7  H72  single  0.970  0.020  1.090
 PLY  C8  C9   single  1.524  0.020  1.524
 PLY  C8  H81  single  0.970  0.020  1.090
 PLY  C8  H82  single  0.970  0.020  1.090
 PLY  C9  CA   single  1.524  0.020  1.524
 PLY  C9  H91  single  0.970  0.020  1.090
 PLY  C9  H92  single  0.970  0.020  1.090
 PLY  CA  CB   single  1.524  0.020  1.524
 PLY  CA  HA1  single  0.970  0.020  1.090
 PLY  CA  HA2  single  0.970  0.020  1.090
 PLY  CB  CC   single  1.524  0.020  1.524
 PLY  CB  HB1  single  0.970  0.020  1.090
 PLY  CB  HB2  single  0.970  0.020  1.090
 PLY  CC  CD   single  1.524  0.020  1.524
 PLY  CC  HC1  single  0.970  0.020  1.090
 PLY  CC  HC2  single  0.970  0.020  1.090
 PLY  CD  CE   single  1.524  0.020  1.524
 PLY  CD  HD1  single  0.970  0.020  1.090
 PLY  CD  HD2  single  0.970  0.020  1.090
 PLY  CE  CF   single  1.524  0.020  1.524
 PLY  CE  HE1  single  0.970  0.020  1.090
 PLY  CE  HE2  single  0.970  0.020  1.090
 PLY  CF  CG   single  1.523  0.020  1.523
 PLY  CF  HF1  single  0.970  0.020  1.090
 PLY  CF  HF2  single  0.970  0.020  1.090
 PLY  CG  HG1  single  0.970  0.020  1.090
 PLY  CG  HG2  single  0.970  0.020  1.090
 PLY  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
 PLY  H11  C1  C2   114.04  3.000
 PLY  H11  C1  O2   120.46  3.000
 PLY  C2   C1  O2   125.50  3.000
 PLY  H22  C2  H21  107.88  3.000
 PLY  H22  C2  C3   108.76  3.000
 PLY  H21  C2  C3   111.32  3.000
 PLY  H22  C2  C1   107.06  3.000
 PLY  H21  C2  C1   110.29  3.000
 PLY  C3   C2  C1   111.37  3.000
 PLY  H32  C3  H31  106.41  3.000
 PLY  H32  C3  C4   109.57  3.000
 PLY  H31  C3  C4   109.45  3.000
 PLY  H32  C3  C2   109.47  3.000
 PLY  H31  C3  C2   109.55  3.000
 PLY  C4   C3  C2   112.21  3.000
 PLY  H42  C4  H41  106.17  3.000
 PLY  H42  C4  C5   109.47  3.000
 PLY  H41  C4  C5   109.42  3.000
 PLY  H42  C4  C3   109.27  3.000
 PLY  H41  C4  C3   109.37  3.000
 PLY  C5   C4  C3   112.91  3.000
 PLY  H52  C5  H51  106.07  3.000
 PLY  H52  C5  C6   109.38  3.000
 PLY  H51  C5  C6   109.38  3.000
 PLY  H52  C5  C4   109.34  3.000
 PLY  H51  C5  C4   109.39  3.000
 PLY  C6   C5  C4   113.04  3.000
 PLY  H62  C6  H61  106.02  3.000
 PLY  H62  C6  C7   109.31  3.000
 PLY  H61  C6  C7   109.31  3.000
 PLY  H62  C6  C5   109.33  3.000
 PLY  H61  C6  C5   109.35  3.000
 PLY  C7   C6  C5   113.27  3.000
 PLY  H72  C7  H71  106.00  3.000
 PLY  H72  C7  C8   109.36  3.000
 PLY  H71  C7  C8   109.36  3.000
 PLY  H72  C7  C6   109.33  3.000
 PLY  H71  C7  C6   109.36  3.000
 PLY  C8   C7  C6   113.18  3.000
 PLY  H82  C8  H81  105.99  3.000
 PLY  H82  C8  C9   109.29  3.000
 PLY  H81  C8  C9   109.31  3.000
 PLY  H82  C8  C7   109.33  3.000
 PLY  H81  C8  C7   109.32  3.000
 PLY  C9   C8  C7   113.34  3.000
 PLY  H92  C9  H91  106.01  3.000
 PLY  H92  C9  CA   109.37  3.000
 PLY  H91  C9  CA   109.33  3.000
 PLY  H92  C9  C8   109.33  3.000
 PLY  H91  C9  C8   109.33  3.000
 PLY  CA   C9  C8   113.21  3.000
 PLY  HA2  CA  HA1  105.98  3.000
 PLY  HA2  CA  CB   109.29  3.000
 PLY  HA1  CA  CB   109.31  3.000
 PLY  HA2  CA  C9   109.32  3.000
 PLY  HA1  CA  C9   109.33  3.000
 PLY  CB   CA  C9   113.35  3.000
 PLY  HB2  CB  HB1  106.00  3.000
 PLY  HB2  CB  CC   109.38  3.000
 PLY  HB1  CB  CC   109.35  3.000
 PLY  HB2  CB  CA   109.33  3.000
 PLY  HB1  CB  CA   109.33  3.000
 PLY  CC   CB  CA   113.20  3.000
 PLY  HC2  CC  HC1  105.99  3.000
 PLY  HC2  CC  CD   109.28  3.000
 PLY  HC1  CC  CD   109.29  3.000
 PLY  HC2  CC  CB   109.31  3.000
 PLY  HC1  CC  CB   109.32  3.000
 PLY  CD   CC  CB   113.39  3.000
 PLY  HD2  CD  HD1  106.02  3.000
 PLY  HD2  CD  CE   109.36  3.000
 PLY  HD1  CD  CE   109.36  3.000
 PLY  HD2  CD  CC   109.34  3.000
 PLY  HD1  CD  CC   109.34  3.000
 PLY  CE   CD  CC   113.16  3.000
 PLY  HE2  CE  HE1  105.96  3.000
 PLY  HE2  CE  CF   109.24  3.000
 PLY  HE1  CE  CF   109.23  3.000
 PLY  HE2  CE  CD   109.36  3.000
 PLY  HE1  CE  CD   109.34  3.000
 PLY  CF   CE  CD   113.45  3.000
 PLY  HF2  CF  HF1  106.07  3.000
 PLY  HF2  CF  CG   109.62  3.000
 PLY  HF1  CF  CG   109.66  3.000
 PLY  HF2  CF  CE   109.27  3.000
 PLY  HF1  CF  CE   109.31  3.000
 PLY  CG   CF  CE   112.71  3.000
 PLY  HG3  CG  HG2  107.60  3.000
 PLY  HG3  CG  HG1  107.52  3.000
 PLY  HG2  CG  HG1  107.59  3.000
 PLY  HG3  CG  CF   111.10  3.000
 PLY  HG2  CG  CF   111.78  3.000
 PLY  HG1  CG  CF   111.05  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
 PLY  Var_01  C4   C3  C2  C1  176.19  30.0  3
 PLY  Var_02  C3   C2  C1  O2  125.25  30.0  3
 PLY  Var_03  C5   C4  C3  C2  179.41  30.0  3
 PLY  Var_04  C6   C5  C4  C3  179.88  30.0  3
 PLY  Var_05  C7   C6  C5  C4  179.91  30.0  3
 PLY  Var_06  C8   C7  C6  C5  179.94  30.0  3
 PLY  Var_07  C9   C8  C7  C6  179.87  30.0  3
 PLY  Var_08  CA   C9  C8  C7  179.86  30.0  3
 PLY  Var_09  CB   CA  C9  C8  179.93  30.0  3
 PLY  Var_10  CC   CB  CA  C9  179.86  30.0  3
 PLY  Var_11  CD   CC  CB  CA  179.87  30.0  3
 PLY  Var_12  CE   CD  CC  CB  179.80  30.0  3
 PLY  Var_13  CF   CE  CD  CC  179.85  30.0  3
 PLY  Var_14  CG   CF  CE  CD  179.96  30.0  3
 PLY  Var_15  HG1  CG  CF  CE   59.75  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
 PLY  plan-1  C1   0.020
 PLY  plan-1  O2   0.020
 PLY  plan-1  C2   0.020
 PLY  plan-1  H11  0.020

