# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 20 09:07:49 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (6Z)-hexadec-6-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC\C=C/CCCCC(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
 8Z9  8Z9  "Sapienic acid"  ligand  48  18  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8Z9
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
 8Z9  C1   C  C     0   0.529  160.5991  163.3870  201.4403
 8Z9  O1   O  OH1   0  -0.592  161.4512  163.8337  200.5196
 8Z9  O2   O  O     0  -0.439  159.4314  163.1923  201.2097
 8Z9  C2   C  CH2   0  -0.553  161.2679  163.1678  202.7680
 8Z9  C3   C  CH2   0  -0.440  161.8878  164.4460  203.3419
 8Z9  C4   C  CH2   0  -0.420  162.3790  164.2690  204.7748
 8Z9  C5   C  CH2   0  -0.504  163.5086  163.2476  204.9209
 8Z9  C6   C  C1    0  -0.216  164.0435  163.2041  206.3186
 8Z9  C7   C  C1    0  -0.199  163.8654  162.2383  207.2199
 8Z9  C8   C  CH2   0  -0.504  163.1133  160.9562  207.0484
 8Z9  C9   C  CH2   0  -0.439  163.9517  159.7225  207.3948
 8Z9  CA   C  CH2   0  -0.421  165.2249  159.5644  206.5661
 8Z9  CB   C  CH2   0  -0.439  165.0236  159.5714  205.0529
 8Z9  CC   C  CH2   0  -0.411  164.0978  158.4826  204.5259
 8Z9  CD   C  CH2   0  -0.413  163.9461  158.5271  203.0101
 8Z9  CE   C  CH2   0  -0.414  163.0415  157.4274  202.4676
 8Z9  CF   C  CH2   0  -0.424  162.7984  157.4992  200.9625
 8Z9  CG   C  CH3   0  -0.665  164.0522  157.2889  200.1227
 8Z9  H1   H  HOH1  0   0.477  160.9862  163.9727  199.6808
 8Z9  H2   H  HCH2  0   0.256  160.5240  162.7690  203.4588
 8Z9  H3   H  HCH2  0   0.271  162.0359  162.3991  202.6406
 8Z9  H4   H  HCH2  0   0.233  162.7163  164.7763  202.7108
 8Z9  H5   H  HCH2  0   0.240  161.1440  165.2469  203.3253
 8Z9  H6   H  HCH2  0   0.233  162.7216  165.2388  205.1462
 8Z9  H7   H  HCH2  0   0.222  161.5429  163.9729  205.4156
 8Z9  H8   H  HCH2  0   0.237  163.1577  162.2613  204.6118
 8Z9  H9   H  HCH2  0   0.228  164.3165  163.5172  204.2320
 8Z9  H10  H  H     0   0.228  164.6103  164.0800  206.6241
 8Z9  H11  H  H     0   0.224  164.3104  162.3805  208.2021
 8Z9  H12  H  HCH2  0   0.239  162.2414  160.9691  207.7114
 8Z9  H13  H  HCH2  0   0.233  162.7146  160.8665  206.0360
 8Z9  H14  H  HCH2  0   0.223  163.3222  158.8351  207.2875
 8Z9  H15  H  HCH2  0   0.222  164.2275  159.7647  208.4530
 8Z9  H16  H  HCH2  0   0.215  165.7141  158.6300  206.8589
 8Z9  H17  H  HCH2  0   0.216  165.9253  160.3634  206.8269
 8Z9  H18  H  HCH2  0   0.216  166.0015  159.4654  204.5726
 8Z9  H19  H  HCH2  0   0.211  163.1075  158.5747  204.9835
 8Z9  H20  H  HCH2  0   0.211  164.9368  158.4599  202.5501
 8Z9  H21  H  HCH2  0   0.203  163.5414  159.5040  202.7187
 8Z9  H22  H  HCH2  0   0.213  162.0781  157.4768  202.9851
 8Z9  H23  H  HCH2  0   0.204  163.4692  156.4501  202.7186
 8Z9  H24  H  HCH2  0   0.208  162.3506  158.4670  200.7157
 8Z9  H25  H  HCH2  0   0.218  162.0559  156.7449  200.6884
 8Z9  H26  H  HCH3  0   0.225  163.8174  157.2840  199.0576
 8Z9  H27  H  HCH3  0   0.220  164.7914  158.0734  200.2885
 8Z9  H28  H  HCH3  0   0.213  164.5264  156.3345  200.3602
 8Z9  H29  H  HCH2  0   0.221  164.6445  160.5478  204.7355
 8Z9  H30  H  HCH2  0   0.205  164.4810  157.5008  204.8266

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
 8Z9  CG  CF   single  1.524  0.020  1.524
 8Z9  O2  C1   double  1.206  0.020  1.206
 8Z9  CF  CE   single  1.526  0.020  1.526
 8Z9  C1  O1   single  1.332  0.020  1.332
 8Z9  C1  C2   single  1.503  0.020  1.503
 8Z9  C2  C3   single  1.532  0.020  1.532
 8Z9  CE  CD   single  1.524  0.020  1.524
 8Z9  CD  CC   single  1.524  0.020  1.524
 8Z9  C3  C4   single  1.525  0.020  1.525
 8Z9  CC  CB   single  1.523  0.020  1.523
 8Z9  CB  CA   single  1.527  0.020  1.527
 8Z9  C4  C5   single  1.530  0.020  1.530
 8Z9  C5  C6   single  1.497  0.020  1.497
 8Z9  CA  C9   single  1.527  0.020  1.527
 8Z9  C6  C7   double  1.333  0.020  1.333
 8Z9  C8  C7   single  1.496  0.020  1.496
 8Z9  C8  C9   single  1.531  0.020  1.531
 8Z9  O1  H1   single  0.850  0.020  0.980
 8Z9  C2  H2   single  0.970  0.020  1.090
 8Z9  C2  H3   single  0.970  0.020  1.090
 8Z9  C3  H4   single  0.970  0.020  1.090
 8Z9  C3  H5   single  0.970  0.020  1.090
 8Z9  C4  H6   single  0.970  0.020  1.090
 8Z9  C4  H7   single  0.970  0.020  1.090
 8Z9  C5  H8   single  0.970  0.020  1.090
 8Z9  C5  H9   single  0.970  0.020  1.090
 8Z9  C6  H10  single  0.930  0.020  1.080
 8Z9  C7  H11  single  0.930  0.020  1.080
 8Z9  C8  H12  single  0.970  0.020  1.090
 8Z9  C8  H13  single  0.970  0.020  1.090
 8Z9  C9  H14  single  0.970  0.020  1.090
 8Z9  C9  H15  single  0.970  0.020  1.090
 8Z9  CA  H16  single  0.970  0.020  1.090
 8Z9  CA  H17  single  0.970  0.020  1.090
 8Z9  CB  H18  single  0.970  0.020  1.090
 8Z9  CC  H19  single  0.970  0.020  1.090
 8Z9  CD  H20  single  0.970  0.020  1.090
 8Z9  CD  H21  single  0.970  0.020  1.090
 8Z9  CE  H22  single  0.970  0.020  1.090
 8Z9  CE  H23  single  0.970  0.020  1.090
 8Z9  CF  H24  single  0.970  0.020  1.090
 8Z9  CF  H25  single  0.970  0.020  1.090
 8Z9  CG  H26  single  0.970  0.020  1.090
 8Z9  CG  H27  single  0.970  0.020  1.090
 8Z9  CG  H28  single  0.970  0.020  1.090
 8Z9  CB  H29  single  0.970  0.020  1.090
 8Z9  CC  H30  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
 8Z9  C2   C1  O2   125.19  3.000
 8Z9  C2   C1  O1   112.02  3.000
 8Z9  O2   C1  O1   122.78  3.000
 8Z9  H1   O1  C1   109.85  3.000
 8Z9  H3   C2  H2   107.19  3.000
 8Z9  H3   C2  C3   110.23  3.000
 8Z9  H2   C2  C3   110.11  3.000
 8Z9  H3   C2  C1   108.18  3.000
 8Z9  H2   C2  C1   108.02  3.000
 8Z9  C3   C2  C1   112.91  3.000
 8Z9  H5   C3  H4   106.60  3.000
 8Z9  H5   C3  C4   108.57  3.000
 8Z9  H4   C3  C4   109.49  3.000
 8Z9  H5   C3  C2   109.28  3.000
 8Z9  H4   C3  C2   110.04  3.000
 8Z9  C4   C3  C2   112.67  3.000
 8Z9  H7   C4  H6   106.29  3.000
 8Z9  H7   C4  C5   109.12  3.000
 8Z9  H6   C4  C5   109.17  3.000
 8Z9  H7   C4  C3   109.60  3.000
 8Z9  H6   C4  C3   108.49  3.000
 8Z9  C5   C4  C3   113.89  3.000
 8Z9  H9   C5  H8   106.35  3.000
 8Z9  H9   C5  C6   109.31  3.000
 8Z9  H8   C5  C6   110.67  3.000
 8Z9  H9   C5  C4   108.67  3.000
 8Z9  H8   C5  C4   109.81  3.000
 8Z9  C6   C5  C4   111.86  3.000
 8Z9  H10  C6  C7   117.61  3.000
 8Z9  H10  C6  C5   115.16  3.000
 8Z9  C7   C6  C5   127.19  3.000
 8Z9  H11  C7  C8   114.91  3.000
 8Z9  H11  C7  C6   117.46  3.000
 8Z9  C8   C7  C6   127.63  3.000
 8Z9  H13  C8  H12  105.75  3.000
 8Z9  H13  C8  C9   110.09  3.000
 8Z9  H12  C8  C9   107.96  3.000
 8Z9  H13  C8  C7   111.12  3.000
 8Z9  H12  C8  C7   108.70  3.000
 8Z9  C9   C8  C7   112.91  3.000
 8Z9  H15  C9  H14  105.75  3.000
 8Z9  H15  C9  CA   108.57  3.000
 8Z9  H14  C9  CA   110.04  3.000
 8Z9  H15  C9  C8   109.01  3.000
 8Z9  H14  C9  C8   108.45  3.000
 8Z9  CA   C9  C8   114.64  3.000
 8Z9  H17  CA  H16  105.87  3.000
 8Z9  H17  CA  CB   108.51  3.000
 8Z9  H16  CA  CB   109.15  3.000
 8Z9  H17  CA  C9   109.19  3.000
 8Z9  H16  CA  C9   108.41  3.000
 8Z9  CB   CA  C9   115.31  3.000
 8Z9  H29  CB  H18  105.58  3.000
 8Z9  H29  CB  CC   109.08  3.000
 8Z9  H18  CB  CC   108.78  3.000
 8Z9  H29  CB  CA   109.71  3.000
 8Z9  H18  CB  CA   108.46  3.000
 8Z9  CC   CB  CA   114.82  3.000
 8Z9  H30  CC  H19  106.08  3.000
 8Z9  H30  CC  CD   109.51  3.000
 8Z9  H19  CC  CD   108.85  3.000
 8Z9  H30  CC  CB   109.45  3.000
 8Z9  H19  CC  CB   110.18  3.000
 8Z9  CD   CC  CB   112.56  3.000
 8Z9  H21  CD  H20  106.08  3.000
 8Z9  H21  CD  CE   109.22  3.000
 8Z9  H20  CD  CE   110.08  3.000
 8Z9  H21  CD  CC   109.09  3.000
 8Z9  H20  CD  CC   109.04  3.000
 8Z9  CE   CD  CC   113.08  3.000
 8Z9  H23  CE  H22  105.99  3.000
 8Z9  H23  CE  CF   109.26  3.000
 8Z9  H22  CE  CF   108.90  3.000
 8Z9  H23  CE  CD   109.29  3.000
 8Z9  H22  CE  CD   108.76  3.000
 8Z9  CF   CE  CD   114.31  3.000
 8Z9  H25  CF  H24  106.00  3.000
 8Z9  H25  CF  CG   108.99  3.000
 8Z9  H24  CF  CG   109.54  3.000
 8Z9  H25  CF  CE   108.84  3.000
 8Z9  H24  CF  CE   109.21  3.000
 8Z9  CG   CF  CE   113.95  3.000
 8Z9  H28  CG  H27  107.54  3.000
 8Z9  H28  CG  H26  107.57  3.000
 8Z9  H27  CG  H26  107.32  3.000
 8Z9  H28  CG  CF   110.98  3.000
 8Z9  H27  CG  CF   112.00  3.000
 8Z9  H26  CG  CF   111.20  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
 8Z9  CONST_01  H1   O1  C1  O2      0.00   0.0  0
 8Z9  CONST_02  H1   O1  C1  C2    180.00   0.0  0
 8Z9  Var_01    C8   C7  C6  C5      1.26   0.0  2
 8Z9  Var_02    C4   C3  C2  C1    171.39  30.0  3
 8Z9  Var_03    C3   C2  C1  O1     60.09  30.0  3
 8Z9  Var_04    C3   C2  C1  O2   -119.76  30.0  3
 8Z9  Var_05    C5   C4  C3  C2     63.34  30.0  3
 8Z9  Var_06    C6   C5  C4  C3    174.58  30.0  3
 8Z9  Var_07    C7   C6  C5  C4    107.68  30.0  3
 8Z9  Var_08    C9   C8  C7  C6    125.72  30.0  2
 8Z9  Var_09    CA   C9  C8  C7    -59.06  30.0  3
 8Z9  Var_10    CB   CA  C9  C8    -54.39  30.0  2
 8Z9  Var_11    CC   CB  CA  C9    -58.86  30.0  1
 8Z9  Var_12    CD   CC  CB  CA   -179.35  30.0  2
 8Z9  Var_13    CE   CD  CC  CB    178.99  30.0  1
 8Z9  Var_14    CF   CE  CD  CC    176.30  30.0  2
 8Z9  Var_15    CG   CF  CE  CD     64.41  30.0  1
 8Z9  Var_16    H11  C7  C6  C5   -178.67   0.0  2
 8Z9  Var_17    H10  C6  C7  C8    179.11   0.0  2
 8Z9  Var_18    H4   C3  C2  C1    -66.11  30.0  3
 8Z9  Var_19    H5   C3  C2  C1     50.61  30.0  3
 8Z9  Var_20    H2   C2  C1  O1   -177.90  30.0  3
 8Z9  Var_21    H3   C2  C1  O1    -62.18  30.0  3
 8Z9  Var_22    H2   C2  C1  O2      2.24  30.0  3
 8Z9  Var_23    H3   C2  C1  O2    117.97  30.0  3
 8Z9  Var_24    H6   C4  C3  C2   -174.87  30.0  3
 8Z9  Var_25    H7   C4  C3  C2    -59.22  30.0  3
 8Z9  Var_26    H8   C5  C4  C3    -62.14  30.0  3
 8Z9  Var_27    H9   C5  C4  C3     53.80  30.0  3
 8Z9  Var_28    H2   C2  C3  C4     50.57  30.0  1
 8Z9  Var_29    H3   C2  C3  C4    -67.49  30.0  1
 8Z9  Var_30    H10  C6  C5  C4    -70.20  30.0  3
 8Z9  Var_31    H4   C3  C4  C5    -59.46  30.0  2
 8Z9  Var_32    H5   C3  C4  C5   -175.48  30.0  2
 8Z9  Var_33    H6   C4  C5  C6     53.17  30.0  2
 8Z9  Var_34    H7   C4  C5  C6    -62.60  30.0  2
 8Z9  Var_35    H12  C8  C7  C6   -114.52  30.0  2
 8Z9  Var_36    H13  C8  C7  C6      1.45  30.0  2
 8Z9  Var_37    H8   C5  C6  C7    -15.11  30.0  1
 8Z9  Var_38    H9   C5  C6  C7   -131.92  30.0  1
 8Z9  Var_39    H14  C9  C8  C7    177.54  30.0  3
 8Z9  Var_40    H15  C9  C8  C7     62.86  30.0  3
 8Z9  Var_41    H16  CA  C9  C8   -177.06  30.0  2
 8Z9  Var_42    H17  CA  C9  C8     68.04  30.0  2
 8Z9  Var_43    H18  CB  CA  C9    179.25  30.0  1
 8Z9  Var_44    H29  CB  CA  C9     64.39  30.0  1
 8Z9  Var_45    H11  C7  C8  C9    -54.35  30.0  3
 8Z9  Var_46    H19  CC  CB  CA     58.94  30.0  2
 8Z9  Var_47    H30  CC  CB  CA    -57.33  30.0  2
 8Z9  Var_48    H12  C8  C9  CA   -179.25  30.0  1
 8Z9  Var_49    H13  C8  C9  CA     65.76  30.0  1
 8Z9  Var_50    H20  CD  CC  CB     56.17  30.0  1
 8Z9  Var_51    H21  CD  CC  CB    -59.27  30.0  1
 8Z9  Var_52    H14  C9  CA  CB     68.15  30.0  3
 8Z9  Var_53    H15  C9  CA  CB   -176.55  30.0  3
 8Z9  Var_54    H22  CE  CD  CC     54.38  30.0  2
 8Z9  Var_55    H23  CE  CD  CC    -60.90  30.0  2
 8Z9  Var_56    H16  CA  CB  CC     63.41  30.0  3
 8Z9  Var_57    H17  CA  CB  CC    178.34  30.0  3
 8Z9  Var_58    H24  CF  CE  CD    -58.44  30.0  1
 8Z9  Var_59    H25  CF  CE  CD   -173.73  30.0  1
 8Z9  Var_60    H18  CB  CC  CD    -57.63  30.0  3
 8Z9  Var_61    H29  CB  CC  CD     57.06  30.0  3
 8Z9  Var_62    H26  CG  CF  CE    176.28  30.0  3
 8Z9  Var_63    H27  CG  CF  CE    -63.64  30.0  3
 8Z9  Var_64    H28  CG  CF  CE     56.56  30.0  3
 8Z9  Var_65    H19  CC  CD  CE    -58.56  30.0  3
 8Z9  Var_66    H30  CC  CD  CE     57.00  30.0  3
 8Z9  Var_67    H20  CD  CE  CF    -61.47  30.0  3
 8Z9  Var_68    H21  CD  CE  CF     54.63  30.0  3
 8Z9  Var_69    H22  CE  CF  CG   -173.75  30.0  3
 8Z9  Var_70    H23  CE  CF  CG    -58.41  30.0  3
 8Z9  Var_71    H11  C7  C6  H10    -0.83   0.0  2

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
 8Z9  plan-1  C1   0.020
 8Z9  plan-1  O1   0.020
 8Z9  plan-1  O2   0.020
 8Z9  plan-1  C2   0.020
 8Z9  plan-1  H1   0.020
 8Z9  plan-2  C5   0.020
 8Z9  plan-2  C6   0.020
 8Z9  plan-2  C7   0.020
 8Z9  plan-2  C8   0.020
 8Z9  plan-2  H10  0.020
 8Z9  plan-2  H11  0.020

