# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 03:14:21 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (5S,6S,9R,13R)-2,3-didehydro-5,6,7,8,9,10,11,12,13,14-decahydroretinoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC[C@@H](C)CC(O)=O)CC[C@H]1[C@@H](C)CC=CC1(C)C
#
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
 4XW  4XW  '(5S,6S,9R,13R)-2,3-didehydro-5,6,7,8,9,10,11,12,13,14-decahydroretinoic acid'  ligand  57  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4XW
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
 4XW  C1   C  CT     0  -0.106  -5.3102   0.7417   0.0344
 4XW  C2   C  C1     0  -0.163  -5.6805   0.0687   1.3343
 4XW  C3   C  C1     0  -0.243  -5.2363  -1.1215   1.7301
 4XW  C4   C  CH2    0  -0.467  -4.3498  -1.9801   0.8820
 4XW  C5   C  CH1    0  -0.227  -4.3392  -1.4922  -0.5622
 4XW  C6   C  CH1    0  -0.210  -4.0800   0.0268  -0.6021
 4XW  C7   C  CH2    0  -0.431  -2.7600   0.4780   0.0421
 4XW  C8   C  CH2    0  -0.402  -1.4699  -0.0382  -0.5921
 4XW  C9   C  CH1    0  -0.217  -0.2091   0.6870  -0.1038
 4XW  C10  C  CH2    0  -0.398   1.0384  -0.0762  -0.5564
 4XW  C11  C  CH2    0  -0.428   2.3541   0.4206   0.0340
 4XW  C12  C  CH2    0  -0.392   3.5321  -0.4594  -0.3683
 4XW  C13  C  CH1    0  -0.211   4.8999   0.0019   0.1405
 4XW  C14  C  CH2    0  -0.554   5.9976  -0.8828  -0.4434
 4XW  C15  C  C      0   0.403   7.4443  -0.4318  -0.1804
 4XW  C16  C  CH3    0  -0.675  -5.0500   2.2261   0.3272
 4XW  C17  C  CH3    0  -0.641  -6.5090   0.6977  -0.9287
 4XW  C18  C  CH3    0  -0.671  -3.4534  -2.3573  -1.4551
 4XW  C19  C  CH3    0  -0.668  -0.1629   2.1410  -0.5661
 4XW  C20  C  CH3    0  -0.669   4.9585   0.0132   1.6653
 4XW  O21  O  OC    -1  -0.628   8.3106  -1.3313  -0.1329
 4XW  O22  O  O      0  -0.613   7.6545   0.7943  -0.0797
 4XW  H1   H  H      0   0.226  -6.3530   0.6245   1.9838
 4XW  H2   H  H      0   0.228  -5.5359  -1.5071   2.6996
 4XW  H3   H  HCH2   0   0.227  -3.3308  -1.9992   1.2902
 4XW  H4   H  HCH2   0   0.236  -4.6956  -3.0180   0.9234
 4XW  H5   H  HCH1   0   0.224  -5.3567  -1.6365  -0.9379
 4XW  H6   H  HCH1   0   0.207  -4.0385   0.3347  -1.6566
 4XW  H7   H  HCH2   0   0.232  -2.7307   1.5669  -0.0082
 4XW  H8   H  HCH2   0   0.212  -2.7525   0.2352   1.1100
 4XW  H9   H  HCH2   0   0.217  -1.3420  -1.1002  -0.3759
 4XW  H10  H  HCH2   0   0.199  -1.5312   0.0443  -1.6844
 4XW  H11  H  HCH1   0   0.201  -0.2254   0.6746   0.9948
 4XW  H12  H  HCH2   0   0.210   0.9183  -1.1324  -0.2902
 4XW  H13  H  HCH2   0   0.201   1.0953  -0.0484  -1.6516
 4XW  H14  H  HCH2   0   0.209   2.5522   1.4492  -0.2837
 4XW  H15  H  HCH2   0   0.210   2.2591   0.4511   1.1239
 4XW  H16  H  HCH2   0   0.197   3.3511  -1.4856  -0.0249
 4XW  H17  H  HCH2   0   0.206   3.5666  -0.5137  -1.4626
 4XW  H18  H  HCH1   0   0.196   5.0691   1.0239  -0.2153
 4XW  H19  H  HCH2   0   0.197   5.8643  -1.9129  -0.0954
 4XW  H20  H  HCH2   0   0.222   5.8710  -0.9257  -1.5338
 4XW  H21  H  HCH3   0   0.232  -4.3174   2.3786   1.1190
 4XW  H22  H  HCH3   0   0.226  -4.6981   2.7479  -0.5659
 4XW  H23  H  HCH3   0   0.230  -5.9752   2.7107   0.6465
 4XW  H24  H  HCH3   0   0.225  -7.3877   1.1606  -0.4752
 4XW  H25  H  HCH3   0   0.222  -6.2793   1.2493  -1.8437
 4XW  H26  H  HCH3   0   0.229  -6.7892  -0.3165  -1.2113
 4XW  H27  H  HCH3   0   0.228  -3.9493  -3.3066  -1.6661
 4XW  H28  H  HCH3   0   0.223  -3.2520  -1.8732  -2.4119
 4XW  H29  H  HCH3   0   0.219  -2.4956  -2.5975  -0.9975
 4XW  H30  H  HCH3   0   0.226  -1.0489   2.7002  -0.2638
 4XW  H31  H  HCH3   0   0.230   0.6980   2.6694  -0.1553
 4XW  H32  H  HCH3   0   0.210  -0.0945   2.1970  -1.6559
 4XW  H33  H  HCH3   0   0.227   5.9460   0.3105   2.0183
 4XW  H34  H  HCH3   0   0.223   4.2380   0.7086   2.0987
 4XW  H35  H  HCH3   0   0.203   4.7409  -0.9795   2.0703

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
 4XW  C19  C9   single  1.526  0.020  1.526
 4XW  C10  C9   single  1.531  0.020  1.531
 4XW  C10  C11  single  1.525  0.020  1.525
 4XW  C14  C15  single  1.538  0.020  1.538
 4XW  C14  C13  single  1.526  0.020  1.526
 4XW  C9   C8   single  1.534  0.020  1.534
 4XW  C12  C11  single  1.524  0.020  1.524
 4XW  C12  C13  single  1.531  0.020  1.531
 4XW  C15  O22  deloc   1.248  0.020  1.248
 4XW  C15  O21  deloc   1.250  0.020  1.250
 4XW  C13  C20  single  1.526  0.020  1.526
 4XW  C8   C7   single  1.527  0.020  1.527
 4XW  C7   C6   single  1.537  0.020  1.537
 4XW  C17  C1   single  1.538  0.020  1.538
 4XW  C16  C1   single  1.535  0.020  1.535
 4XW  C6   C1   single  1.559  0.020  1.559
 4XW  C6   C5   single  1.541  0.020  1.541
 4XW  C1   C2   single  1.510  0.020  1.510
 4XW  C18  C5   single  1.527  0.020  1.527
 4XW  C5   C4   single  1.524  0.020  1.524
 4XW  C2   C3   double  1.331  0.020  1.331
 4XW  C4   C3   single  1.497  0.020  1.497
 4XW  C2   H1   single  0.930  0.020  1.080
 4XW  C3   H2   single  0.930  0.020  1.080
 4XW  C4   H3   single  0.970  0.020  1.090
 4XW  C4   H4   single  0.970  0.020  1.090
 4XW  C5   H5   single  0.970  0.020  1.090
 4XW  C6   H6   single  0.970  0.020  1.090
 4XW  C7   H7   single  0.970  0.020  1.090
 4XW  C7   H8   single  0.970  0.020  1.090
 4XW  C8   H9   single  0.970  0.020  1.090
 4XW  C8   H10  single  0.970  0.020  1.090
 4XW  C9   H11  single  0.970  0.020  1.090
 4XW  C10  H12  single  0.970  0.020  1.090
 4XW  C10  H13  single  0.970  0.020  1.090
 4XW  C11  H14  single  0.970  0.020  1.090
 4XW  C11  H15  single  0.970  0.020  1.090
 4XW  C12  H16  single  0.970  0.020  1.090
 4XW  C12  H17  single  0.970  0.020  1.090
 4XW  C13  H18  single  0.970  0.020  1.090
 4XW  C14  H19  single  0.970  0.020  1.090
 4XW  C14  H20  single  0.970  0.020  1.090
 4XW  C16  H21  single  0.970  0.020  1.090
 4XW  C16  H22  single  0.970  0.020  1.090
 4XW  C16  H23  single  0.970  0.020  1.090
 4XW  C17  H24  single  0.970  0.020  1.090
 4XW  C17  H25  single  0.970  0.020  1.090
 4XW  C17  H26  single  0.970  0.020  1.090
 4XW  C18  H27  single  0.970  0.020  1.090
 4XW  C18  H28  single  0.970  0.020  1.090
 4XW  C18  H29  single  0.970  0.020  1.090
 4XW  C19  H30  single  0.970  0.020  1.090
 4XW  C19  H31  single  0.970  0.020  1.090
 4XW  C19  H32  single  0.970  0.020  1.090
 4XW  C20  H33  single  0.970  0.020  1.090
 4XW  C20  H34  single  0.970  0.020  1.090
 4XW  C20  H35  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
 4XW  C17  C1   C16  106.21  3.000
 4XW  C16  C1   C6   112.80  3.000
 4XW  C17  C1   C6   110.26  3.000
 4XW  C6   C1   C2   109.92  3.000
 4XW  C16  C1   C2   107.96  3.000
 4XW  C17  C1   C2   109.58  3.000
 4XW  H1   C2   C3   119.07  3.000
 4XW  H1   C2   C1   115.97  3.000
 4XW  C3   C2   C1   124.95  3.000
 4XW  H2   C3   C4   117.75  3.000
 4XW  H2   C3   C2   119.42  3.000
 4XW  C4   C3   C2   122.82  3.000
 4XW  H4   C4   H3   105.23  3.000
 4XW  H4   C4   C5   109.97  3.000
 4XW  H3   C4   C5   110.57  3.000
 4XW  H4   C4   C3   109.58  3.000
 4XW  H3   C4   C3   110.41  3.000
 4XW  C5   C4   C3   110.93  3.000
 4XW  H5   C5   C18  105.30  3.000
 4XW  H5   C5   C6   106.10  3.000
 4XW  C18  C5   C6   116.47  3.000
 4XW  H5   C5   C4   106.06  3.000
 4XW  C18  C5   C4   112.13  3.000
 4XW  C6   C5   C4   109.95  3.000
 4XW  H6   C6   C7   106.71  3.000
 4XW  H6   C6   C5   107.89  3.000
 4XW  C7   C6   C5   115.02  3.000
 4XW  H6   C6   C1   107.04  3.000
 4XW  C5   C6   C1   107.98  3.000
 4XW  C7   C6   C1   111.85  3.000
 4XW  H8   C7   H7   105.44  3.000
 4XW  H8   C7   C8   108.92  3.000
 4XW  H7   C7   C8   107.19  3.000
 4XW  H8   C7   C6   110.46  3.000
 4XW  H7   C7   C6   107.27  3.000
 4XW  C8   C7   C6   116.89  3.000
 4XW  H10  C8   H9   106.08  3.000
 4XW  H10  C8   C9   109.11  3.000
 4XW  H9   C8   C9   107.50  3.000
 4XW  H10  C8   C7   109.92  3.000
 4XW  H9   C8   C7   110.21  3.000
 4XW  C9   C8   C7   113.71  3.000
 4XW  H11  C9   C19  108.31  3.000
 4XW  H11  C9   C10  107.58  3.000
 4XW  C19  C9   C10  111.14  3.000
 4XW  H11  C9   C8   107.50  3.000
 4XW  C10  C9   C8   109.87  3.000
 4XW  C19  C9   C8   112.25  3.000
 4XW  H13  C10  H12  105.82  3.000
 4XW  H13  C10  C11  109.48  3.000
 4XW  H12  C10  C11  108.33  3.000
 4XW  H13  C10  C9   108.95  3.000
 4XW  H12  C10  C9   108.62  3.000
 4XW  C11  C10  C9   115.22  3.000
 4XW  H15  C11  H14  106.17  3.000
 4XW  H15  C11  C12  110.24  3.000
 4XW  H14  C11  C12  109.02  3.000
 4XW  H15  C11  C10  108.65  3.000
 4XW  H14  C11  C10  110.48  3.000
 4XW  C12  C11  C10  112.11  3.000
 4XW  H17  C12  H16  105.74  3.000
 4XW  H17  C12  C13  108.58  3.000
 4XW  H16  C12  C13  108.98  3.000
 4XW  H17  C12  C11  108.44  3.000
 4XW  H16  C12  C11  109.26  3.000
 4XW  C13  C12  C11  115.40  3.000
 4XW  H18  C13  C20  108.17  3.000
 4XW  H18  C13  C14  107.79  3.000
 4XW  C20  C13  C14  111.04  3.000
 4XW  H18  C13  C12  108.14  3.000
 4XW  C20  C13  C12  111.63  3.000
 4XW  C14  C13  C12  109.93  3.000
 4XW  H20  C14  H19  105.34  3.000
 4XW  H20  C14  C15  106.83  3.000
 4XW  H19  C14  C15  109.63  3.000
 4XW  H20  C14  C13  108.63  3.000
 4XW  H19  C14  C13  109.64  3.000
 4XW  C15  C14  C13  116.18  3.000
 4XW  O22  C15  O21  125.97  3.000
 4XW  O21  C15  C14  116.58  3.000
 4XW  O22  C15  C14  117.41  3.000
 4XW  H23  C16  H22  107.45  3.000
 4XW  H23  C16  H21  107.16  3.000
 4XW  H22  C16  H21  108.10  3.000
 4XW  H23  C16  C1   109.95  3.000
 4XW  H22  C16  C1   111.13  3.000
 4XW  H21  C16  C1   112.83  3.000
 4XW  H26  C17  H25  107.87  3.000
 4XW  H26  C17  H24  107.19  3.000
 4XW  H25  C17  H24  107.63  3.000
 4XW  H26  C17  C1   112.92  3.000
 4XW  H25  C17  C1   110.23  3.000
 4XW  H24  C17  C1   110.79  3.000
 4XW  H29  C18  H28  107.71  3.000
 4XW  H29  C18  H27  106.81  3.000
 4XW  H28  C18  H27  107.47  3.000
 4XW  H29  C18  C5   112.94  3.000
 4XW  H28  C18  C5   111.63  3.000
 4XW  H27  C18  C5   110.02  3.000
 4XW  H32  C19  H31  107.53  3.000
 4XW  H32  C19  H30  107.51  3.000
 4XW  H31  C19  H30  106.77  3.000
 4XW  H32  C19  C9   110.65  3.000
 4XW  H31  C19  C9   111.80  3.000
 4XW  H30  C19  C9   112.33  3.000
 4XW  H35  C20  H34  107.45  3.000
 4XW  H35  C20  H33  107.92  3.000
 4XW  H34  C20  H33  107.20  3.000
 4XW  H35  C20  C13  110.83  3.000
 4XW  H34  C20  C13  112.10  3.000
 4XW  H33  C20  C13  111.12  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
 4XW  Var_01  C4   C3   C2   C1    -3.15  30.0  1
 4XW  Var_02  C5   C4   C3   C2   -14.66  30.0  1
 4XW  Var_03  C6   C1   C2   C3   -14.08  30.0  1
 4XW  Var_04  H24  C17  C1   C2    56.60  30.0  3
 4XW  Var_05  H21  C16  C1   C2    53.78  30.0  3
 4XW  Var_06  C9   C8   C7   C6   167.20  30.0  3
 4XW  Var_07  C12  C11  C10  C9   175.13  30.0  3
 4XW  Var_08  C13  C12  C11  C10  177.78  30.0  1
 4XW  Var_09  O22  C15  C14  C13  -31.07  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
 4XW  chir_01  C5   C6   C18  C4   negativ
 4XW  chir_02  C6   C7   C1   C5   positiv
 4XW  chir_03  C9   C8   C10  C19  negativ
 4XW  chir_04  C13  C14  C12  C20  negativ

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
 4XW  plan-1  C14  0.020
 4XW  plan-1  C15  0.020
 4XW  plan-1  O21  0.020
 4XW  plan-1  O22  0.020

