# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:56:50 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 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
 REA  REA  'retinoic acid            '  ligand  49  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_REA
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
 REA  C1    C  CT     0  -0.155  21.8416  29.8598  16.8998
 REA  C2    C  CH2    0  -0.411  20.6781  30.5617  16.1933
 REA  C3    C  CH2    0  -0.446  20.1727  29.7847  14.9941
 REA  C4    C  CH2    0  -0.467  19.6656  28.4253  15.4416
 REA  C5    C  C      0   0.006  20.5603  27.7311  16.4352
 REA  C6    C  C      0   0.127  21.5301  28.3759  17.1116
 REA  C7    C  C1     0  -0.315  22.4040  27.7100  18.0874
 REA  C8    C  C1     0  -0.262  21.9946  26.9543  19.1184
 REA  C9    C  C      0   0.116  22.8587  26.3110  20.0954
 REA  C10   C  C1     0  -0.304  22.2737  25.6154  21.0999
 REA  C11   C  C1     0  -0.261  22.9207  24.8927  22.1650
 REA  C12   C  C1     0  -0.281  22.2276  24.2610  23.1344
 REA  C13   C  C      0   0.151  22.7940  23.4921  24.2332
 REA  C14   C  C1     0  -0.455  21.9477  22.9896  25.1542
 REA  C15   C  C      0   0.381  22.2608  22.1991  26.4045
 REA  C16   C  CH3    0  -0.638  22.0485  30.5558  18.2506
 REA  C17   C  CH3    0  -0.642  23.1265  30.0081  16.0725
 REA  C18   C  CH3    0  -0.726  20.2501  26.2683  16.5812
 REA  C19   C  CH3    0  -0.761  24.3415  26.4584  19.9337
 REA  C20   C  CH3    0  -0.759  24.2870  23.3499  24.2827
 REA  O1    O  O      0  -0.592  23.1747  21.3510  26.3682
 REA  O2    O  OC    -1  -0.605  21.5318  22.4715  27.3808
 REA  H21   H  HCH2   0   0.218  19.8542  30.6870  16.9051
 REA  H22   H  HCH2   0   0.223  20.9935  31.5686  15.9046
 REA  H31   H  HCH2   0   0.230  19.3758  30.3346  14.4888
 REA  H32   H  HCH2   0   0.220  20.9714  29.6572  14.2588
 REA  H41   H  HCH2   0   0.231  18.6681  28.5264  15.8887
 REA  H42   H  HCH2   0   0.231  19.5246  27.7720  14.5753
 REA  H7    H  H      0   0.248  23.4672  27.9126  17.9846
 REA  H8    H  H      0   0.237  20.9280  26.8062  19.2635
 REA  H10   H  H      0   0.234  21.1865  25.5895  21.1144
 REA  H11   H  H      0   0.250  24.0041  24.8575  22.1799
 REA  H12   H  H      0   0.233  21.1417  24.3177  23.1060
 REA  H14   H  H      0   0.225  20.8924  23.2186  25.0191
 REA  H161  H  HCH3   0   0.227  22.9272  30.1850  18.7802
 REA  H162  H  HCH3   0   0.224  22.1857  31.6291  18.0993
 REA  H163  H  HCH3   0   0.223  21.1831  30.4181  18.9018
 REA  H171  H  HCH3   0   0.229  23.9785  29.5329  16.5615
 REA  H172  H  HCH3   0   0.228  23.0277  29.5642  15.0813
 REA  H173  H  HCH3   0   0.223  23.3745  31.0643  15.9448
 REA  H181  H  HCH3   0   0.244  21.0261  25.7093  17.0979
 REA  H182  H  HCH3   0   0.234  19.3168  26.1189  17.1316
 REA  H183  H  HCH3   0   0.231  20.1007  25.8166  15.5977
 REA  H191  H  HCH3   0   0.255  24.9068  25.9236  20.6925
 REA  H192  H  HCH3   0   0.242  24.6667  26.0885  18.9591
 REA  H193  H  HCH3   0   0.243  24.6374  27.5088  19.9848
 REA  H201  H  HCH3   0   0.258  24.6068  22.7668  25.1388
 REA  H202  H  HCH3   0   0.231  24.6620  22.8616  23.3802
 REA  H203  H  HCH3   0   0.230  24.7682  24.3294  24.3298

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
 REA  C1   C2    single  1.532  0.020  1.532
 REA  C1   C6    single  1.531  0.020  1.531
 REA  C1   C16   single  1.534  0.020  1.534
 REA  C1   C17   single  1.535  0.020  1.535
 REA  C2   C3    single  1.516  0.020  1.516
 REA  C2   H21   single  0.970  0.020  1.090
 REA  C2   H22   single  0.970  0.020  1.090
 REA  C3   C4    single  1.518  0.020  1.518
 REA  C3   H31   single  0.970  0.020  1.090
 REA  C3   H32   single  0.970  0.020  1.090
 REA  C4   C5    single  1.507  0.020  1.507
 REA  C4   H41   single  0.970  0.020  1.090
 REA  C4   H42   single  0.970  0.020  1.090
 REA  C5   C6    double  1.347  0.020  1.347
 REA  C5   C18   single  1.502  0.020  1.502
 REA  C6   C7    single  1.469  0.020  1.469
 REA  C7   C8    double  1.342  0.020  1.342
 REA  C7   H7    single  0.930  0.020  1.080
 REA  C8   C9    single  1.454  0.020  1.454
 REA  C8   H8    single  0.930  0.020  1.080
 REA  C9   C10   double  1.355  0.020  1.355
 REA  C9   C19   single  1.499  0.020  1.499
 REA  C10  C11   single  1.441  0.020  1.441
 REA  C10  H10   single  0.930  0.020  1.080
 REA  C11  C12   double  1.349  0.020  1.349
 REA  C11  H11   single  0.930  0.020  1.080
 REA  C12  C13   single  1.456  0.020  1.456
 REA  C12  H12   single  0.930  0.020  1.080
 REA  C13  C14   double  1.348  0.020  1.348
 REA  C13  C20   single  1.501  0.020  1.501
 REA  C14  C15   single  1.512  0.020  1.512
 REA  C14  H14   single  0.930  0.020  1.080
 REA  C15  O1    deloc   1.247  0.020  1.247
 REA  C15  O2    deloc   1.248  0.020  1.248
 REA  C16  H161  single  0.970  0.020  1.090
 REA  C16  H162  single  0.970  0.020  1.090
 REA  C16  H163  single  0.970  0.020  1.090
 REA  C17  H171  single  0.970  0.020  1.090
 REA  C17  H172  single  0.970  0.020  1.090
 REA  C17  H173  single  0.970  0.020  1.090
 REA  C18  H181  single  0.970  0.020  1.090
 REA  C18  H182  single  0.970  0.020  1.090
 REA  C18  H183  single  0.970  0.020  1.090
 REA  C19  H191  single  0.970  0.020  1.090
 REA  C19  H192  single  0.970  0.020  1.090
 REA  C19  H193  single  0.970  0.020  1.090
 REA  C20  H201  single  0.970  0.020  1.090
 REA  C20  H202  single  0.970  0.020  1.090
 REA  C20  H203  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
 REA  C17   C1   C16   108.53  3.000
 REA  C17   C1   C6    109.78  3.000
 REA  C16   C1   C6    110.21  3.000
 REA  C17   C1   C2    110.06  3.000
 REA  C16   C1   C2    107.51  3.000
 REA  C6    C1   C2    110.70  3.000
 REA  H22   C2   H21   106.44  3.000
 REA  H22   C2   C3    111.05  3.000
 REA  H21   C2   C3    108.77  3.000
 REA  H22   C2   C1    108.94  3.000
 REA  H21   C2   C1    108.89  3.000
 REA  C3    C2   C1    112.54  3.000
 REA  H32   C3   H31   106.29  3.000
 REA  H32   C3   C4    109.74  3.000
 REA  H31   C3   C4    110.09  3.000
 REA  H32   C3   C2    110.39  3.000
 REA  H31   C3   C2    110.57  3.000
 REA  C4    C3   C2    109.71  3.000
 REA  H42   C4   H41   105.09  3.000
 REA  H42   C4   C5    108.88  3.000
 REA  H41   C4   C5    108.27  3.000
 REA  H42   C4   C3    110.14  3.000
 REA  H41   C4   C3    109.94  3.000
 REA  C5    C4   C3    114.12  3.000
 REA  C18   C5   C6    124.47  3.000
 REA  C18   C5   C4    112.96  3.000
 REA  C6    C5   C4    122.56  3.000
 REA  C7    C6   C5    123.01  3.000
 REA  C7    C6   C1    114.21  3.000
 REA  C5    C6   C1    122.76  3.000
 REA  H7    C7   C8    118.41  3.000
 REA  H7    C7   C6    115.75  3.000
 REA  C8    C7   C6    125.72  3.000
 REA  H8    C8   C9    115.67  3.000
 REA  H8    C8   C7    118.60  3.000
 REA  C9    C8   C7    125.72  3.000
 REA  C19   C9   C10   123.90  3.000
 REA  C19   C9   C8    118.15  3.000
 REA  C10   C9   C8    117.95  3.000
 REA  H10   C10  C11   115.29  3.000
 REA  H10   C10  C9    116.99  3.000
 REA  C11   C10  C9    127.72  3.000
 REA  H11   C11  C12   119.24  3.000
 REA  H11   C11  C10   118.38  3.000
 REA  C12   C11  C10   122.38  3.000
 REA  H12   C12  C13   115.83  3.000
 REA  H12   C12  C11   118.02  3.000
 REA  C13   C12  C11   126.15  3.000
 REA  C20   C13  C14   124.53  3.000
 REA  C20   C13  C12   117.53  3.000
 REA  C14   C13  C12   117.92  3.000
 REA  H14   C14  C15   114.42  3.000
 REA  H14   C14  C13   116.46  3.000
 REA  C15   C14  C13   129.04  3.000
 REA  O2    C15  O1    126.79  3.000
 REA  O2    C15  C14   114.31  3.000
 REA  O1    C15  C14   118.89  3.000
 REA  H163  C16  H162  107.82  3.000
 REA  H163  C16  H161  107.82  3.000
 REA  H162  C16  H161  107.46  3.000
 REA  H163  C16  C1    111.17  3.000
 REA  H162  C16  C1    109.93  3.000
 REA  H161  C16  C1    112.46  3.000
 REA  H173  C17  H172  107.93  3.000
 REA  H173  C17  H171  107.22  3.000
 REA  H172  C17  H171  107.50  3.000
 REA  H173  C17  C1    110.27  3.000
 REA  H172  C17  C1    112.00  3.000
 REA  H171  C17  C1    111.71  3.000
 REA  H183  C18  H182  106.25  3.000
 REA  H183  C18  H181  108.23  3.000
 REA  H182  C18  H181  107.44  3.000
 REA  H183  C18  C5    110.08  3.000
 REA  H182  C18  C5    110.98  3.000
 REA  H181  C18  C5    113.54  3.000
 REA  H193  C19  H192  106.67  3.000
 REA  H193  C19  H191  107.44  3.000
 REA  H192  C19  H191  107.55  3.000
 REA  H193  C19  C9    110.94  3.000
 REA  H192  C19  C9    110.95  3.000
 REA  H191  C19  C9    113.00  3.000
 REA  H203  C20  H202  106.57  3.000
 REA  H203  C20  H201  108.57  3.000
 REA  H202  C20  H201  108.11  3.000
 REA  H203  C20  C13   110.77  3.000
 REA  H202  C20  C13   110.89  3.000
 REA  H201  C20  C13   111.75  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
 REA  Var_01  C4    C3   C2   C1     60.98  30.0  1
 REA  Var_02  C4    C5   C6   C1     -2.05  30.0  1
 REA  Var_03  C5    C6   C1   C2     17.43  30.0  1
 REA  Var_04  C5    C4   C3   C2    -43.68  30.0  1
 REA  Var_05  C6    C1   C2   C3    -46.86  30.0  1
 REA  Var_06  C6    C5   C4   C3     15.54  30.0  1
 REA  Var_07  C8    C7   C6   C1    129.86  30.0  2
 REA  Var_08  H161  C16  C1   C2   -174.13  30.0  3
 REA  Var_09  H171  C17  C1   C2    178.92  30.0  3
 REA  Var_10  H181  C18  C5   C4    165.87  30.0  3
 REA  Var_11  C9    C8   C7   C6   -179.06   0.0  2
 REA  Var_12  C11   C10  C9   C8    179.39   0.0  2
 REA  Var_13  C13   C12  C11  C10   178.97   0.0  2
 REA  Var_14  C15   C14  C13  C12  -178.01   0.0  2
 REA  Var_15  C10   C9   C8   C7    177.99  30.0  2
 REA  Var_16  C12   C11  C10  C9    178.30  30.0  2
 REA  Var_17  C14   C13  C12  C11   176.41  30.0  2
 REA  Var_18  O1    C15  C14  C13   -38.69  30.0  2
 REA  Var_19  H191  C19  C9   C8   -178.46  30.0  3
 REA  Var_20  H201  C20  C13  C12   179.66  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
 REA  plan-1  C14  0.020
 REA  plan-1  C15  0.020
 REA  plan-1  O1   0.020
 REA  plan-1  O2   0.020
 REA  plan-2  C6   0.020
 REA  plan-2  C7   0.020
 REA  plan-2  C8   0.020
 REA  plan-2  C9   0.020
 REA  plan-2  H7   0.020
 REA  plan-2  H8   0.020
 REA  plan-3  C8   0.020
 REA  plan-3  C9   0.020
 REA  plan-3  C10  0.020
 REA  plan-3  C11  0.020
 REA  plan-3  C19  0.020
 REA  plan-3  H10  0.020
 REA  plan-4  C10  0.020
 REA  plan-4  C11  0.020
 REA  plan-4  C12  0.020
 REA  plan-4  C13  0.020
 REA  plan-4  H11  0.020
 REA  plan-4  H12  0.020
 REA  plan-5  C12  0.020
 REA  plan-5  C13  0.020
 REA  plan-5  C14  0.020
 REA  plan-5  C15  0.020
 REA  plan-5  C20  0.020
 REA  plan-5  H14  0.020

