# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 01:46:06 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  47  18  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.410  160.7635  163.9808  201.2863
 8Z9  O1   O  OC    -1  -0.605  160.9357  165.1275  200.8261
 8Z9  O2   O  O      0  -0.626  160.2004  163.0268  200.7087
 8Z9  C2   C  CH2    0  -0.582  161.2869  163.6843  202.7082
 8Z9  C3   C  CH2    0  -0.410  161.9756  164.8366  203.4223
 8Z9  C4   C  CH2    0  -0.417  162.3970  164.5176  204.8540
 8Z9  C5   C  CH2    0  -0.495  163.4775  163.4382  204.9693
 8Z9  C6   C  C1     0  -0.213  163.9629  163.2973  206.3783
 8Z9  C7   C  C1     0  -0.206  163.7580  162.2795  207.2137
 8Z9  C8   C  CH2    0  -0.497  163.0279  160.9997  206.9500
 8Z9  C9   C  CH2    0  -0.440  163.8880  159.7691  207.2517
 8Z9  CA   C  CH2    0  -0.424  165.1446  159.6535  206.3921
 8Z9  CB   C  CH2    0  -0.432  164.8974  159.5210  204.8914
 8Z9  CC   C  CH2    0  -0.410  164.1747  158.2425  204.4848
 8Z9  CD   C  CH2    0  -0.412  163.9706  158.1297  202.9785
 8Z9  CE   C  CH2    0  -0.414  163.3614  156.7975  202.5577
 8Z9  CF   C  CH2    0  -0.424  163.0112  156.7073  201.0748
 8Z9  CG   C  CH3    0  -0.664  164.2128  156.8120  200.1448
 8Z9  H2   H  HCH2   0   0.210  160.4414  163.3349  203.3137
 8Z9  H3   H  HCH2   0   0.217  161.9581  162.8212  202.6423
 8Z9  H4   H  HCH2   0   0.198  162.8540  165.1563  202.8524
 8Z9  H5   H  HCH2   0   0.208  161.3047  165.6992  203.4428
 8Z9  H6   H  HCH2   0   0.216  162.7662  165.4329  205.3277
 8Z9  H7   H  HCH2   0   0.208  161.5230  164.2083  205.4371
 8Z9  H8   H  HCH2   0   0.234  163.1044  162.4868  204.5856
 8Z9  H9   H  HCH2   0   0.221  164.3193  163.7201  204.3269
 8Z9  H10  H  H      0   0.224  164.5146  164.1533  206.7596
 8Z9  H11  H  H      0   0.222  164.1700  162.3662  208.2169
 8Z9  H12  H  HCH2   0   0.237  162.1436  160.9613  207.5951
 8Z9  H13  H  HCH2   0   0.231  162.6515  160.9600  205.9259
 8Z9  H14  H  HCH2   0   0.224  163.2716  158.8725  207.1433
 8Z9  H15  H  HCH2   0   0.221  164.1865  159.7991  208.3043
 8Z9  H16  H  HCH2   0   0.214  165.7243  158.7899  206.7333
 8Z9  H17  H  HCH2   0   0.217  165.7777  160.5283  206.5680
 8Z9  H18  H  HCH2   0   0.215  165.8628  159.5541  204.3768
 8Z9  H19  H  HCH2   0   0.211  163.2014  158.1826  204.9817
 8Z9  H20  H  HCH2   0   0.209  164.9328  158.2771  202.4779
 8Z9  H21  H  HCH2   0   0.204  163.3261  158.9489  202.6392
 8Z9  H22  H  HCH2   0   0.213  162.4546  156.6194  203.1449
 8Z9  H23  H  HCH2   0   0.204  164.0526  155.9877  202.8166
 8Z9  H24  H  HCH2   0   0.209  162.2889  157.4917  200.8279
 8Z9  H25  H  HCH2   0   0.217  162.5004  155.7585  200.8902
 8Z9  H26  H  HCH3   0   0.225  163.9173  156.6768  199.1037
 8Z9  H27  H  HCH3   0   0.220  164.7039  157.7830  200.2185
 8Z9  H28  H  HCH3   0   0.213  164.9580  156.0482  200.3775
 8Z9  H29  H  HCH2   0   0.215  164.3397  160.3888  204.5237
 8Z9  H30  H  HCH2   0   0.203  164.7494  157.3794  204.8402

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  1.523  0.020  1.523
 8Z9  O2  C1   deloc   1.249  0.020  1.249
 8Z9  CF  CE   single  1.526  0.020  1.526
 8Z9  C1  O1   deloc   1.248  0.020  1.248
 8Z9  C1  C2   single  1.544  0.020  1.544
 8Z9  C2  C3   single  1.521  0.020  1.521
 8Z9  CE  CD   single  1.524  0.020  1.524
 8Z9  CD  CC   single  1.524  0.020  1.524
 8Z9  C3  C4   single  1.526  0.020  1.526
 8Z9  CC  CB   single  1.524  0.020  1.524
 8Z9  CB  CA   single  1.527  0.020  1.527
 8Z9  C4  C5   single  1.532  0.020  1.532
 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  1.497  0.020  1.497
 8Z9  C8  C9   single  1.531  0.020  1.531
 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   115.59  3.000
 8Z9  C2   C1  O1   118.00  3.000
 8Z9  O2   C1  O1   126.41  3.000
 8Z9  H3   C2  H2   104.75  3.000
 8Z9  H3   C2  C3   110.35  3.000
 8Z9  H2   C2  C3   109.34  3.000
 8Z9  H3   C2  C1   107.68  3.000
 8Z9  H2   C2  C1   107.95  3.000
 8Z9  C3   C2  C1   116.14  3.000
 8Z9  H5   C3  H4   105.78  3.000
 8Z9  H5   C3  C4   108.48  3.000
 8Z9  H4   C3  C4   109.14  3.000
 8Z9  H5   C3  C2   109.20  3.000
 8Z9  H4   C3  C2   109.89  3.000
 8Z9  C4   C3  C2   114.03  3.000
 8Z9  H7   C4  H6   105.95  3.000
 8Z9  H7   C4  C5   108.89  3.000
 8Z9  H6   C4  C5   108.59  3.000
 8Z9  H7   C4  C3   109.76  3.000
 8Z9  H6   C4  C3   108.92  3.000
 8Z9  C5   C4  C3   114.38  3.000
 8Z9  H9   C5  H8   106.30  3.000
 8Z9  H9   C5  C6   109.08  3.000
 8Z9  H8   C5  C6   111.08  3.000
 8Z9  H9   C5  C4   108.45  3.000
 8Z9  H8   C5  C4   110.28  3.000
 8Z9  C6   C5  C4   111.47  3.000
 8Z9  H10  C6  C7   117.34  3.000
 8Z9  H10  C6  C5   114.87  3.000
 8Z9  C7   C6  C5   127.74  3.000
 8Z9  H11  C7  C8   114.53  3.000
 8Z9  H11  C7  C6   117.33  3.000
 8Z9  C8   C7  C6   128.14  3.000
 8Z9  H13  C8  H12  105.83  3.000
 8Z9  H13  C8  C9   110.44  3.000
 8Z9  H12  C8  C9   108.01  3.000
 8Z9  H13  C8  C7   111.38  3.000
 8Z9  H12  C8  C7   108.67  3.000
 8Z9  C9   C8  C7   112.24  3.000
 8Z9  H15  C9  H14  105.76  3.000
 8Z9  H15  C9  CA   108.60  3.000
 8Z9  H14  C9  CA   110.25  3.000
 8Z9  H15  C9  C8   108.70  3.000
 8Z9  H14  C9  C8   108.84  3.000
 8Z9  CA   C9  C8   114.34  3.000
 8Z9  H17  CA  H16  105.92  3.000
 8Z9  H17  CA  CB   108.74  3.000
 8Z9  H16  CA  CB   108.88  3.000
 8Z9  H17  CA  C9   108.98  3.000
 8Z9  H16  CA  C9   108.66  3.000
 8Z9  CB   CA  C9   115.26  3.000
 8Z9  H29  CB  H18  105.50  3.000
 8Z9  H29  CB  CC   109.50  3.000
 8Z9  H18  CB  CC   108.56  3.000
 8Z9  H29  CB  CA   110.10  3.000
 8Z9  H18  CB  CA   108.46  3.000
 8Z9  CC   CB  CA   114.33  3.000
 8Z9  H30  CC  H19  106.02  3.000
 8Z9  H30  CC  CD   109.41  3.000
 8Z9  H19  CC  CD   109.00  3.000
 8Z9  H30  CC  CB   109.00  3.000
 8Z9  H19  CC  CB   110.28  3.000
 8Z9  CD   CC  CB   112.91  3.000
 8Z9  H21  CD  H20  105.94  3.000
 8Z9  H21  CD  CE   109.43  3.000
 8Z9  H20  CD  CE   110.05  3.000
 8Z9  H21  CD  CC   109.23  3.000
 8Z9  H20  CD  CC   108.92  3.000
 8Z9  CE   CD  CC   113.02  3.000
 8Z9  H23  CE  H22  105.99  3.000
 8Z9  H23  CE  CF   109.30  3.000
 8Z9  H22  CE  CF   108.75  3.000
 8Z9  H23  CE  CD   109.18  3.000
 8Z9  H22  CE  CD   108.98  3.000
 8Z9  CF   CE  CD   114.31  3.000
 8Z9  H25  CF  H24  106.00  3.000
 8Z9  H25  CF  CG   108.97  3.000
 8Z9  H24  CF  CG   109.49  3.000
 8Z9  H25  CF  CE   108.82  3.000
 8Z9  H24  CF  CE   109.16  3.000
 8Z9  CG   CF  CE   114.09  3.000
 8Z9  H28  CG  H27  107.52  3.000
 8Z9  H28  CG  H26  107.55  3.000
 8Z9  H27  CG  H26  107.27  3.000
 8Z9  H28  CG  CF   111.11  3.000
 8Z9  H27  CG  CF   112.03  3.000
 8Z9  H26  CG  CF   111.14  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  Var_01  C8   C7  C6  C5      2.01   0.0  2
 8Z9  Var_02  C4   C3  C2  C1    176.43  30.0  3
 8Z9  Var_03  C3   C2  C1  O1     -0.11  30.0  3
 8Z9  Var_04  C3   C2  C1  O2    179.95  30.0  3
 8Z9  Var_05  C5   C4  C3  C2     65.33  30.0  3
 8Z9  Var_06  C6   C5  C4  C3    172.91  30.0  3
 8Z9  Var_07  C7   C6  C5  C4    110.11  30.0  3
 8Z9  Var_08  C9   C8  C7  C6    124.97  30.0  1
 8Z9  Var_09  CA   C9  C8  C7    -62.19  30.0  3
 8Z9  Var_10  CB   CA  C9  C8    -61.70  30.0  2
 8Z9  Var_11  CC   CB  CA  C9    -64.69  30.0  2
 8Z9  Var_12  CD   CC  CB  CA   -178.80  30.0  1
 8Z9  Var_13  CE   CD  CC  CB    174.84  30.0  2
 8Z9  Var_14  CF   CE  CD  CC    174.02  30.0  1
 8Z9  Var_15  CG   CF  CE  CD     63.22  30.0  1
 8Z9  Var_16  H11  C7  C6  C5   -178.40   0.0  2
 8Z9  Var_17  H10  C6  C7  C8    179.48   0.0  2
 8Z9  Var_18  H4   C3  C2  C1    -60.68  30.0  3
 8Z9  Var_19  H5   C3  C2  C1     54.92  30.0  3
 8Z9  Var_20  H2   C2  C1  O1    123.04  30.0  3
 8Z9  Var_21  H3   C2  C1  O1   -124.37  30.0  3
 8Z9  Var_22  H2   C2  C1  O2    -56.90  30.0  3
 8Z9  Var_23  H3   C2  C1  O2     55.68  30.0  3
 8Z9  Var_24  H6   C4  C3  C2   -172.98  30.0  3
 8Z9  Var_25  H7   C4  C3  C2    -57.40  30.0  3
 8Z9  Var_26  H8   C5  C4  C3    -63.21  30.0  3
 8Z9  Var_27  H9   C5  C4  C3     52.81  30.0  3
 8Z9  Var_28  H2   C2  C3  C4     54.01  30.0  2
 8Z9  Var_29  H3   C2  C3  C4    -60.69  30.0  2
 8Z9  Var_30  H10  C6  C5  C4    -67.41  30.0  3
 8Z9  Var_31  H4   C3  C4  C5    -57.97  30.0  2
 8Z9  Var_32  H5   C3  C4  C5   -172.77  30.0  2
 8Z9  Var_33  H6   C4  C5  C6     51.04  30.0  1
 8Z9  Var_34  H7   C4  C5  C6    -63.89  30.0  1
 8Z9  Var_35  H12  C8  C7  C6   -115.65  30.0  1
 8Z9  Var_36  H13  C8  C7  C6      0.55  30.0  1
 8Z9  Var_37  H8   C5  C6  C7    -13.31  30.0  2
 8Z9  Var_38  H9   C5  C6  C7   -130.16  30.0  2
 8Z9  Var_39  H14  C9  C8  C7    174.06  30.0  3
 8Z9  Var_40  H15  C9  C8  C7     59.33  30.0  3
 8Z9  Var_41  H16  CA  C9  C8    175.81  30.0  2
 8Z9  Var_42  H17  CA  C9  C8     60.83  30.0  2
 8Z9  Var_43  H18  CB  CA  C9    174.04  30.0  2
 8Z9  Var_44  H29  CB  CA  C9     59.06  30.0  2
 8Z9  Var_45  H11  C7  C8  C9    -54.63  30.0  3
 8Z9  Var_46  H19  CC  CB  CA     59.00  30.0  1
 8Z9  Var_47  H30  CC  CB  CA    -57.00  30.0  1
 8Z9  Var_48  H12  C8  C9  CA    178.05  30.0  1
 8Z9  Var_49  H13  C8  C9  CA     62.75  30.0  1
 8Z9  Var_50  H20  CD  CC  CB     52.20  30.0  2
 8Z9  Var_51  H21  CD  CC  CB    -63.08  30.0  2
 8Z9  Var_52  H14  C9  CA  CB     61.29  30.0  3
 8Z9  Var_53  H15  C9  CA  CB    176.73  30.0  3
 8Z9  Var_54  H22  CE  CD  CC     52.13  30.0  1
 8Z9  Var_55  H23  CE  CD  CC    -63.21  30.0  1
 8Z9  Var_56  H16  CA  CB  CC     57.68  30.0  3
 8Z9  Var_57  H17  CA  CB  CC    172.65  30.0  3
 8Z9  Var_58  H24  CF  CE  CD    -59.61  30.0  1
 8Z9  Var_59  H25  CF  CE  CD   -174.87  30.0  1
 8Z9  Var_60  H18  CB  CC  CD    -57.58  30.0  3
 8Z9  Var_61  H29  CB  CC  CD     57.13  30.0  3
 8Z9  Var_62  H26  CG  CF  CE    176.29  30.0  3
 8Z9  Var_63  H27  CG  CF  CE    -63.72  30.0  3
 8Z9  Var_64  H28  CG  CF  CE     56.57  30.0  3
 8Z9  Var_65  H19  CC  CD  CE    -62.24  30.0  3
 8Z9  Var_66  H30  CC  CD  CE     53.27  30.0  3
 8Z9  Var_67  H20  CD  CE  CF    -63.96  30.0  3
 8Z9  Var_68  H21  CD  CE  CF     52.06  30.0  3
 8Z9  Var_69  H22  CE  CF  CG   -174.76  30.0  3
 8Z9  Var_70  H23  CE  CF  CG    -59.48  30.0  3
 8Z9  Var_71  H11  C7  C6  H10    -0.94   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-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

