# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:18:56 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2Z,4E)-5-[(1R)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/[C@]1(O)C(=CC(=O)CC1(C)C)C)=C/C(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
 A9S  A9S  '(2Z,4E)-5-[(1R)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid'  ligand  38  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9S
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
 A9S  O3   O  O      0  -0.594   3.7456   1.2279   1.1387
 A9S  C10  C  C      0   0.394   4.5160   0.5079   0.4692
 A9S  O1   O  OC    -1  -0.616   5.7644   0.5720   0.4747
 A9S  C11  C  C1     0  -0.458   3.9549  -0.5532  -0.4490
 A9S  C12  C  C      0   0.141   2.6813  -0.9067  -0.7073
 A9S  C15  C  CH3    0  -0.748   2.4154  -2.0174  -1.6857
 A9S  C8   C  C1     0  -0.320   1.5216  -0.2634  -0.0903
 A9S  C9   C  C1     0  -0.235   0.2582  -0.6211  -0.3337
 A9S  C5   C  CT     0   0.164  -0.9561   0.0257   0.2793
 A9S  O4   O  OH1    0  -0.659  -0.6181   0.9206   1.3176
 A9S  C6   C  CT     0  -0.121  -1.7231   0.8490  -0.7963
 A9S  C14  C  CH3    0  -0.661  -1.9671   0.0125  -2.0583
 A9S  C13  C  CH3    0  -0.638  -0.9328   2.0949  -1.1957
 A9S  C1   C  CH2    0  -0.551  -3.0741   1.2888  -0.2213
 A9S  C4   C  C      0   0.179  -1.8493  -1.0575   0.8967
 A9S  C7   C  CH3    0  -0.721  -1.1609  -2.1858   1.5947
 A9S  C3   C  C1     0  -0.417  -3.1856  -0.9689   0.8874
 A9S  C2   C  C      0   0.402  -3.9102   0.1466   0.2785
 A9S  O2   O  O      0  -0.430  -5.1278   0.1592   0.2322
 A9S  H2   H  H      0   0.208   4.7208  -1.1116  -0.9803
 A9S  H3   H  HCH3   0   0.236   1.8628  -2.8377  -1.2223
 A9S  H4   H  HCH3   0   0.237   1.8141  -1.6700  -2.5292
 A9S  H5   H  HCH3   0   0.249   3.3434  -2.4246  -2.0836
 A9S  H6   H  H      0   0.254   1.7394   0.5480   0.5903
 A9S  H7   H  H      0   0.272   0.0412  -1.4337  -1.0192
 A9S  H8   H  HOH1   0   0.453  -0.0804   0.4568   1.9696
 A9S  H9   H  HCH3   0   0.235  -2.4217  -0.9568  -1.8488
 A9S  H10  H  HCH3   0   0.240  -2.6375   0.5525  -2.7291
 A9S  H11  H  HCH3   0   0.240  -1.0410  -0.1677  -2.6048
 A9S  H12  H  HCH3   0   0.237   0.0663   1.8381  -1.5501
 A9S  H13  H  HCH3   0   0.228  -1.4489   2.6077  -2.0102
 A9S  H14  H  HCH3   0   0.233  -0.8303   2.8048  -0.3757
 A9S  H15  H  HCH2   0   0.280  -2.9184   1.9667   0.6259
 A9S  H16  H  HCH2   0   0.262  -3.6375   1.8520  -0.9695
 A9S  H17  H  HCH3   0   0.250  -0.4099  -1.8152   2.2962
 A9S  H18  H  HCH3   0   0.260  -1.8657  -2.8024   2.1493
 A9S  H19  H  HCH3   0   0.259  -0.6283  -2.8256   0.8890
 A9S  H20  H  H      0   0.257  -3.7852  -1.7388   1.3621

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
 A9S  O3   C10  deloc   1.249  0.020  1.249
 A9S  C10  O1   deloc   1.250  0.020  1.250
 A9S  C10  C11  single  1.511  0.020  1.511
 A9S  C11  C12  double  1.347  0.020  1.347
 A9S  C12  C15  single  1.504  0.020  1.504
 A9S  C12  C8   single  1.463  0.020  1.463
 A9S  C8   C9   double  1.335  0.020  1.335
 A9S  O4   C5   single  1.412  0.020  1.412
 A9S  C7   C4   single  1.495  0.020  1.495
 A9S  C9   C5   single  1.506  0.020  1.506
 A9S  C5   C4   single  1.534  0.020  1.534
 A9S  C5   C6   single  1.557  0.020  1.557
 A9S  C4   C3   double  1.339  0.020  1.339
 A9S  C14  C6   single  1.534  0.020  1.534
 A9S  C6   C13  single  1.529  0.020  1.529
 A9S  C6   C1   single  1.533  0.020  1.533
 A9S  C3   C2   single  1.463  0.020  1.463
 A9S  C1   C2   single  1.501  0.020  1.501
 A9S  C2   O2   double  1.219  0.020  1.219
 A9S  C11  H2   single  0.930  0.020  1.080
 A9S  C15  H3   single  0.970  0.020  1.090
 A9S  C15  H4   single  0.970  0.020  1.090
 A9S  C15  H5   single  0.970  0.020  1.090
 A9S  C8   H6   single  0.930  0.020  1.080
 A9S  C9   H7   single  0.930  0.020  1.080
 A9S  O4   H8   single  0.850  0.020  0.980
 A9S  C14  H9   single  0.970  0.020  1.090
 A9S  C14  H10  single  0.970  0.020  1.090
 A9S  C14  H11  single  0.970  0.020  1.090
 A9S  C13  H12  single  0.970  0.020  1.090
 A9S  C13  H13  single  0.970  0.020  1.090
 A9S  C13  H14  single  0.970  0.020  1.090
 A9S  C1   H15  single  0.970  0.020  1.090
 A9S  C1   H16  single  0.970  0.020  1.090
 A9S  C7   H17  single  0.970  0.020  1.090
 A9S  C7   H18  single  0.970  0.020  1.090
 A9S  C7   H19  single  0.970  0.020  1.090
 A9S  C3   H20  single  0.930  0.020  1.080

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
 A9S  C11  C10  O1   114.17  3.000
 A9S  C11  C10  O3   120.10  3.000
 A9S  O1   C10  O3   125.73  3.000
 A9S  H2   C11  C12  115.97  3.000
 A9S  H2   C11  C10  113.35  3.000
 A9S  C12  C11  C10  130.69  3.000
 A9S  C8   C12  C15  117.33  3.000
 A9S  C8   C12  C11  123.60  3.000
 A9S  C15  C12  C11  119.07  3.000
 A9S  H5   C15  H4   107.81  3.000
 A9S  H5   C15  H3   107.78  3.000
 A9S  H4   C15  H3   106.73  3.000
 A9S  H5   C15  C12  111.30  3.000
 A9S  H4   C15  C12  111.39  3.000
 A9S  H3   C15  C12  111.60  3.000
 A9S  H6   C8   C9   120.42  3.000
 A9S  H6   C8   C12  115.84  3.000
 A9S  C9   C8   C12  123.74  3.000
 A9S  H7   C9   C5   114.68  3.000
 A9S  H7   C9   C8   120.33  3.000
 A9S  C5   C9   C8   125.00  3.000
 A9S  C4   C5   C6   111.39  3.000
 A9S  C6   C5   O4   106.91  3.000
 A9S  C4   C5   O4   106.92  3.000
 A9S  C6   C5   C9   110.07  3.000
 A9S  C4   C5   C9   109.27  3.000
 A9S  O4   C5   C9   112.24  3.000
 A9S  H8   O4   C5   109.03  3.000
 A9S  C1   C6   C13  108.66  3.000
 A9S  C1   C6   C14  108.97  3.000
 A9S  C13  C6   C14  108.16  3.000
 A9S  C1   C6   C5   109.08  3.000
 A9S  C13  C6   C5   110.91  3.000
 A9S  C14  C6   C5   111.01  3.000
 A9S  H11  C14  H10  107.19  3.000
 A9S  H11  C14  H9   107.66  3.000
 A9S  H10  C14  H9   107.56  3.000
 A9S  H11  C14  C6   111.56  3.000
 A9S  H10  C14  C6   109.49  3.000
 A9S  H9   C14  C6   113.13  3.000
 A9S  H14  C13  H13  107.44  3.000
 A9S  H14  C13  H12  108.17  3.000
 A9S  H13  C13  H12  107.53  3.000
 A9S  H14  C13  C6   112.52  3.000
 A9S  H13  C13  C6   109.47  3.000
 A9S  H12  C13  C6   111.51  3.000
 A9S  H16  C1   H15  106.47  3.000
 A9S  H16  C1   C2   109.44  3.000
 A9S  H15  C1   C2   107.00  3.000
 A9S  H16  C1   C6   110.21  3.000
 A9S  H15  C1   C6   110.02  3.000
 A9S  C2   C1   C6   113.42  3.000
 A9S  C3   C4   C7   120.85  3.000
 A9S  C3   C4   C5   122.11  3.000
 A9S  C7   C4   C5   116.93  3.000
 A9S  H19  C7   H18  108.26  3.000
 A9S  H19  C7   H17  106.18  3.000
 A9S  H18  C7   H17  108.06  3.000
 A9S  H19  C7   C4   111.43  3.000
 A9S  H18  C7   C4   111.55  3.000
 A9S  H17  C7   C4   111.12  3.000
 A9S  H20  C3   C2   116.71  3.000
 A9S  H20  C3   C4   120.09  3.000
 A9S  C2   C3   C4   123.20  3.000
 A9S  O2   C2   C3   121.24  3.000
 A9S  O2   C2   C1   122.42  3.000
 A9S  C3   C2   C1   116.29  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
 A9S  Var_01  C2   C3   C4   C5      0.87  30.0  1
 A9S  Var_02  C2   C1   C6   C5    -55.76  30.0  1
 A9S  Var_03  C3   C2   C1   C6     34.83  30.0  1
 A9S  Var_04  C4   C3   C2   C1     -6.38  30.0  1
 A9S  Var_05  H17  C7   C4   C5     49.10  30.0  3
 A9S  Var_06  H9   C14  C6   C5     51.18  30.0  3
 A9S  Var_07  H12  C13  C6   C5     56.30  30.0  3
 A9S  Var_08  C5   C9   C8   C12  -179.65   0.0  2
 A9S  Var_09  C15  C12  C11  C10   179.90   0.0  2
 A9S  Var_10  C12  C11  C10  O3     -0.16  30.0  2
 A9S  Var_11  C9   C8   C12  C11  -179.27  30.0  2
 A9S  Var_12  H3   C15  C12  C11   120.74  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A9S  chir_01  C5  C9  C4  C6  positiv

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
 A9S  plan-1  C1   0.020
 A9S  plan-1  C3   0.020
 A9S  plan-1  C2   0.020
 A9S  plan-1  O2   0.020
 A9S  plan-2  O3   0.020
 A9S  plan-2  C10  0.020
 A9S  plan-2  O1   0.020
 A9S  plan-2  C11  0.020
 A9S  plan-3  C10  0.020
 A9S  plan-3  C11  0.020
 A9S  plan-3  C12  0.020
 A9S  plan-3  C15  0.020
 A9S  plan-3  C8   0.020
 A9S  plan-3  H2   0.020
 A9S  plan-4  C12  0.020
 A9S  plan-4  C8   0.020
 A9S  plan-4  C9   0.020
 A9S  plan-4  C5   0.020
 A9S  plan-4  H6   0.020
 A9S  plan-4  H7   0.020

