# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 09:48:11 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (9cis)-retinoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(/C=C/C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1
#
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
 9CR  9CR  '(9cis)-retinoic acid     '  ligand  49  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9CR
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
 9CR  C1   C  CT     0  -0.158   4.3355   0.2147  -0.8269
 9CR  C2   C  CH2    0  -0.413   4.8879   1.6289  -1.0305
 9CR  C3   C  CH2    0  -0.446   5.1299   2.3495   0.2809
 9CR  C4   C  CH2    0  -0.468   3.8181   2.4944   1.0322
 9CR  C5   C  C      0   0.004   2.9707   1.2483   1.0358
 9CR  C6   C  C      0   0.135   3.1897   0.2241   0.1886
 9CR  C7   C  C1     0  -0.294   2.3743  -0.9964   0.1693
 9CR  C8   C  C1     0  -0.293   1.0329  -1.0564   0.1654
 9CR  C9   C  C      0   0.116   0.2583  -2.2833   0.0767
 9CR  C10  C  C1     0  -0.306  -1.0963  -2.2834   0.0353
 9CR  C11  C  C1     0  -0.248  -1.9797  -1.1456   0.1107
 9CR  C12  C  C1     0  -0.284  -3.3162  -1.2586  -0.0195
 9CR  C13  C  C      0   0.169  -4.2761  -0.1636   0.0442
 9CR  C14  C  C1     0  -0.481  -5.5786  -0.4695  -0.1276
 9CR  C15  C  C      0   0.392  -6.8000   0.4167  -0.0897
 9CR  C16  C  CH3    0  -0.646   5.4518  -0.7213  -0.3428
 9CR  C17  C  CH3    0  -0.640   3.8303  -0.2841  -2.1870
 9CR  C18  C  CH3    0  -0.736   1.8741   1.2794   2.0620
 9CR  C19  C  CH3    0  -0.749   0.9997  -3.5861   0.0015
 9CR  C20  C  CH3    0  -0.773  -3.7377   1.2084   0.3243
 9CR  O1   O  O      0  -0.593  -6.6728   1.6541  -0.1964
 9CR  O2   O  OC    -1  -0.617  -7.8789  -0.2008   0.0443
 9CR  H1   H  HCH2   0   0.225   5.8058   1.5728  -1.6236
 9CR  H2   H  HCH2   0   0.220   4.1722   2.2093  -1.6247
 9CR  H3   H  HCH2   0   0.220   5.8481   1.7960   0.8922
 9CR  H4   H  HCH2   0   0.231   5.5704   3.3331   0.1039
 9CR  H5   H  HCH2   0   0.233   4.0052   2.7992   2.0663
 9CR  H6   H  HCH2   0   0.233   3.2283   3.3100   0.5944
 9CR  H7   H  H      0   0.248   2.9303  -1.9253   0.0773
 9CR  H8   H  H      0   0.242   0.4816  -0.1239   0.1954
 9CR  H9   H  H      0   0.234  -1.5899  -3.2459  -0.0701
 9CR  H10  H  H      0   0.246  -1.5515  -0.1653   0.2850
 9CR  H11  H  H      0   0.234  -3.7318  -2.2474  -0.1985
 9CR  H12  H  H      0   0.217  -5.8057  -1.5205  -0.2917
 9CR  H13  H  HCH3   0   0.225   6.2514  -0.7792  -1.0854
 9CR  H14  H  HCH3   0   0.230   5.8899  -0.3813   0.5965
 9CR  H15  H  HCH3   0   0.230   5.0891  -1.7383  -0.1825
 9CR  H16  H  HCH3   0   0.226   4.6257  -0.2058  -2.9312
 9CR  H17  H  HCH3   0   0.226   3.5099  -1.3263  -2.1586
 9CR  H18  H  HCH3   0   0.225   2.9855   0.3131  -2.5354
 9CR  H19  H  HCH3   0   0.235   2.2416   1.7162   2.9928
 9CR  H20  H  HCH3   0   0.238   1.0438   1.9111   1.7327
 9CR  H21  H  HCH3   0   0.246   1.4654   0.2965   2.2858
 9CR  H22  H  HCH3   0   0.241   1.6382  -3.7331   0.8754
 9CR  H23  H  HCH3   0   0.251   0.3134  -4.4294  -0.0559
 9CR  H24  H  HCH3   0   0.239   1.6517  -3.6252  -0.8744
 9CR  H25  H  HCH3   0   0.232  -3.0109   1.5028  -0.4366
 9CR  H26  H  HCH3   0   0.271  -4.5286   1.9479   0.3479
 9CR  H27  H  HCH3   0   0.232  -3.2094   1.2220   1.2805

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
 9CR  O1   C15  deloc   1.249  0.020  1.249
 9CR  C15  C14  single  1.510  0.020  1.510
 9CR  C15  O2   deloc   1.250  0.020  1.250
 9CR  C14  C13  double  1.349  0.020  1.349
 9CR  C13  C12  single  1.458  0.020  1.458
 9CR  C13  C20  single  1.500  0.020  1.500
 9CR  C12  C11  double  1.348  0.020  1.348
 9CR  C11  C10  single  1.442  0.020  1.442
 9CR  C18  C5   single  1.502  0.020  1.502
 9CR  C10  C9   double  1.355  0.020  1.355
 9CR  C9   C19  single  1.501  0.020  1.501
 9CR  C9   C8   single  1.454  0.020  1.454
 9CR  C8   C7   double  1.343  0.020  1.343
 9CR  C5   C4   single  1.507  0.020  1.507
 9CR  C5   C6   double  1.347  0.020  1.347
 9CR  C4   C3   single  1.519  0.020  1.519
 9CR  C7   C6   single  1.468  0.020  1.468
 9CR  C6   C1   single  1.531  0.020  1.531
 9CR  C3   C2   single  1.516  0.020  1.516
 9CR  C1   C17  single  1.534  0.020  1.534
 9CR  C1   C2   single  1.532  0.020  1.532
 9CR  C1   C16  single  1.535  0.020  1.535
 9CR  C2   H1   single  0.970  0.020  1.090
 9CR  C2   H2   single  0.970  0.020  1.090
 9CR  C3   H3   single  0.970  0.020  1.090
 9CR  C3   H4   single  0.970  0.020  1.090
 9CR  C4   H5   single  0.970  0.020  1.090
 9CR  C4   H6   single  0.970  0.020  1.090
 9CR  C7   H7   single  0.930  0.020  1.080
 9CR  C8   H8   single  0.930  0.020  1.080
 9CR  C10  H9   single  0.930  0.020  1.080
 9CR  C11  H10  single  0.930  0.020  1.080
 9CR  C12  H11  single  0.930  0.020  1.080
 9CR  C14  H12  single  0.930  0.020  1.080
 9CR  C16  H13  single  0.970  0.020  1.090
 9CR  C16  H14  single  0.970  0.020  1.090
 9CR  C16  H15  single  0.970  0.020  1.090
 9CR  C17  H16  single  0.970  0.020  1.090
 9CR  C17  H17  single  0.970  0.020  1.090
 9CR  C17  H18  single  0.970  0.020  1.090
 9CR  C18  H19  single  0.970  0.020  1.090
 9CR  C18  H20  single  0.970  0.020  1.090
 9CR  C18  H21  single  0.970  0.020  1.090
 9CR  C19  H22  single  0.970  0.020  1.090
 9CR  C19  H23  single  0.970  0.020  1.090
 9CR  C19  H24  single  0.970  0.020  1.090
 9CR  C20  H25  single  0.970  0.020  1.090
 9CR  C20  H26  single  0.970  0.020  1.090
 9CR  C20  H27  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
 9CR  C17  C1   C16  108.71  3.000
 9CR  C16  C1   C6   109.80  3.000
 9CR  C17  C1   C6   110.09  3.000
 9CR  C16  C1   C2   110.04  3.000
 9CR  C17  C1   C2   107.52  3.000
 9CR  C6   C1   C2   110.63  3.000
 9CR  H2   C2   H1   106.31  3.000
 9CR  H2   C2   C3   108.75  3.000
 9CR  H1   C2   C3   111.06  3.000
 9CR  H2   C2   C1   108.99  3.000
 9CR  H1   C2   C1   109.09  3.000
 9CR  C3   C2   C1   112.43  3.000
 9CR  H4   C3   H3   106.35  3.000
 9CR  H4   C3   C4   110.04  3.000
 9CR  H3   C3   C4   109.82  3.000
 9CR  H4   C3   C2   110.63  3.000
 9CR  H3   C3   C2   110.36  3.000
 9CR  C4   C3   C2   109.60  3.000
 9CR  H6   C4   H5   105.18  3.000
 9CR  H6   C4   C5   108.26  3.000
 9CR  H5   C4   C5   108.92  3.000
 9CR  H6   C4   C3   109.74  3.000
 9CR  H5   C4   C3   110.27  3.000
 9CR  C5   C4   C3   114.08  3.000
 9CR  C18  C5   C6   124.34  3.000
 9CR  C6   C5   C4   122.40  3.000
 9CR  C18  C5   C4   113.26  3.000
 9CR  C7   C6   C5   123.37  3.000
 9CR  C7   C6   C1   113.70  3.000
 9CR  C5   C6   C1   122.92  3.000
 9CR  H7   C7   C8   118.21  3.000
 9CR  H7   C7   C6   115.33  3.000
 9CR  C8   C7   C6   126.31  3.000
 9CR  H8   C8   C9   117.18  3.000
 9CR  H8   C8   C7   118.01  3.000
 9CR  C9   C8   C7   124.77  3.000
 9CR  C19  C9   C10  119.48  3.000
 9CR  C19  C9   C8   118.19  3.000
 9CR  C10  C9   C8   122.32  3.000
 9CR  H9   C10  C11  115.18  3.000
 9CR  H9   C10  C9   117.19  3.000
 9CR  C11  C10  C9   127.62  3.000
 9CR  H10  C11  C12  118.89  3.000
 9CR  H10  C11  C10  118.68  3.000
 9CR  C12  C11  C10  122.43  3.000
 9CR  H11  C12  C13  116.02  3.000
 9CR  H11  C12  C11  118.11  3.000
 9CR  C13  C12  C11  125.87  3.000
 9CR  C20  C13  C14  125.29  3.000
 9CR  C20  C13  C12  117.32  3.000
 9CR  C14  C13  C12  117.38  3.000
 9CR  H12  C14  C15  113.71  3.000
 9CR  H12  C14  C13  116.11  3.000
 9CR  C15  C14  C13  130.16  3.000
 9CR  O2   C15  O1   125.91  3.000
 9CR  O2   C15  C14  114.27  3.000
 9CR  O1   C15  C14  119.82  3.000
 9CR  H15  C16  H14  107.31  3.000
 9CR  H15  C16  H13  107.07  3.000
 9CR  H14  C16  H13  107.93  3.000
 9CR  H15  C16  C1   111.88  3.000
 9CR  H14  C16  C1   111.93  3.000
 9CR  H13  C16  C1   110.49  3.000
 9CR  H18  C17  H17  107.68  3.000
 9CR  H18  C17  H16  107.87  3.000
 9CR  H17  C17  H16  107.47  3.000
 9CR  H18  C17  C1   111.09  3.000
 9CR  H17  C17  C1   112.60  3.000
 9CR  H16  C17  C1   109.94  3.000
 9CR  H21  C18  H20  107.37  3.000
 9CR  H21  C18  H19  108.21  3.000
 9CR  H20  C18  H19  106.32  3.000
 9CR  H21  C18  C5   113.33  3.000
 9CR  H20  C18  C5   111.13  3.000
 9CR  H19  C18  C5   110.18  3.000
 9CR  H24  C19  H23  107.82  3.000
 9CR  H24  C19  H22  106.73  3.000
 9CR  H23  C19  H22  107.84  3.000
 9CR  H24  C19  C9   111.47  3.000
 9CR  H23  C19  C9   111.32  3.000
 9CR  H22  C19  C9   111.44  3.000
 9CR  H27  C20  H26  109.00  3.000
 9CR  H27  C20  H25  106.53  3.000
 9CR  H26  C20  H25  108.48  3.000
 9CR  H27  C20  C13  110.38  3.000
 9CR  H26  C20  C13  111.50  3.000
 9CR  H25  C20  C13  110.80  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
 9CR  Var_01  C4   C5   C6   C1      1.62  30.0  1
 9CR  Var_02  C4   C3   C2   C1    -61.38  30.0  1
 9CR  Var_03  C5   C4   C3   C2     44.09  30.0  1
 9CR  Var_04  C5   C6   C1   C2    -17.03  30.0  1
 9CR  Var_05  C6   C5   C4   C3    -15.54  30.0  1
 9CR  Var_06  C6   C1   C2   C3     46.85  30.0  1
 9CR  Var_07  C8   C7   C6   C1   -133.45  30.0  2
 9CR  Var_08  H16  C17  C1   C2     54.38  30.0  3
 9CR  Var_09  H13  C16  C1   C2    -61.11  30.0  3
 9CR  Var_10  H19  C18  C5   C4    -40.65  30.0  3
 9CR  Var_11  C9   C8   C7   C6    176.67   0.0  2
 9CR  Var_12  C11  C10  C9   C8     -2.11   0.0  2
 9CR  Var_13  C13  C12  C11  C10   179.97   0.0  2
 9CR  Var_14  C15  C14  C13  C12   178.53   0.0  2
 9CR  Var_15  C10  C9   C8   C7   -177.91  30.0  3
 9CR  Var_16  C12  C11  C10  C9    176.03  30.0  1
 9CR  Var_17  C14  C13  C12  C11   179.11  30.0  2
 9CR  Var_18  O1   C15  C14  C13    17.32  30.0  2
 9CR  Var_19  H22  C19  C9   C8     59.26  30.0  3
 9CR  Var_20  H25  C20  C13  C12    58.90  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
 9CR  plan-1  C14  0.020
 9CR  plan-1  C15  0.020
 9CR  plan-1  O1   0.020
 9CR  plan-1  O2   0.020
 9CR  plan-2  C12  0.020
 9CR  plan-2  C13  0.020
 9CR  plan-2  C14  0.020
 9CR  plan-2  C15  0.020
 9CR  plan-2  C20  0.020
 9CR  plan-2  H12  0.020
 9CR  plan-3  C10  0.020
 9CR  plan-3  C11  0.020
 9CR  plan-3  C12  0.020
 9CR  plan-3  C13  0.020
 9CR  plan-3  H10  0.020
 9CR  plan-3  H11  0.020
 9CR  plan-4  C8   0.020
 9CR  plan-4  C9   0.020
 9CR  plan-4  C10  0.020
 9CR  plan-4  C11  0.020
 9CR  plan-4  C19  0.020
 9CR  plan-4  H9   0.020
 9CR  plan-5  C6   0.020
 9CR  plan-5  C7   0.020
 9CR  plan-5  C8   0.020
 9CR  plan-5  C9   0.020
 9CR  plan-5  H7   0.020
 9CR  plan-5  H8   0.020

