# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:21:56 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  58  22  .  2021-08-05  2021-08-05  
;
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  -5.2980   0.7232   0.0402
 4XW  C2   C  C1    0  -0.163  -5.6657   0.0403   1.3356
 4XW  C3   C  C1    0  -0.243  -5.2139  -1.1490   1.7256
 4XW  C4   C  CH2   0  -0.467  -4.3198  -1.9966   0.8742
 4XW  C5   C  CH1   0  -0.227  -4.3115  -1.5012  -0.5674
 4XW  C6   C  CH1   0  -0.210  -4.0628   0.0198  -0.5991
 4XW  C7   C  CH2   0  -0.432  -2.7464   0.4765   0.0486
 4XW  C8   C  CH2   0  -0.403  -1.4518  -0.0263  -0.5873
 4XW  C9   C  CH1   0  -0.218  -0.1983   0.7083  -0.0943
 4XW  C10  C  CH2   0  -0.400   1.0577  -0.0386  -0.5513
 4XW  C11  C  CH2   0  -0.430   2.3631   0.4662   0.0544
 4XW  C12  C  CH2   0  -0.399   3.5564  -0.3849  -0.3626
 4XW  C13  C  CH1   0  -0.231   4.9069   0.0980   0.1724
 4XW  C14  C  CH2   0  -0.565   6.0161  -0.7663  -0.4221
 4XW  C15  C  C     0   0.543   7.4075  -0.2477  -0.1834
 4XW  C16  C  CH3   0  -0.675  -5.0471   2.2074   0.3417
 4XW  C17  C  CH3   0  -0.641  -6.4954   0.6769  -0.9245
 4XW  C18  C  CH3   0  -0.671  -3.4185  -2.3551  -1.4639
 4XW  C19  C  CH3   0  -0.668  -0.1674   2.1657  -0.5474
 4XW  C20  C  CH3   0  -0.668   4.9521   0.0778   1.6978
 4XW  O21  O  OH1   0  -0.595   8.3204  -1.2127  -0.2546
 4XW  O22  O  O     0  -0.447   7.6937   0.9079   0.0130
 4XW  H1   H  H     0   0.226  -6.3437   0.5873   1.9868
 4XW  H2   H  H     0   0.228  -5.5131  -1.5425   2.6920
 4XW  H3   H  HCH2  0   0.227  -3.3011  -2.0093   1.2833
 4XW  H4   H  HCH2  0   0.236  -4.6575  -3.0374   0.9102
 4XW  H5   H  HCH1  0   0.224  -5.3276  -1.6506  -0.9449
 4XW  H6   H  HCH1  0   0.207  -4.0227   0.3333  -1.6519
 4XW  H7   H  HCH2  0   0.232  -2.7254   1.5657   0.0051
 4XW  H8   H  HCH2  0   0.213  -2.7380   0.2272   1.1150
 4XW  H9   H  HCH2  0   0.218  -1.3157  -1.0882  -0.3755
 4XW  H10  H  HCH2  0   0.199  -1.5130   0.0606  -1.6792
 4XW  H11  H  HCH1  0   0.202  -0.2148   0.6885   1.0042
 4XW  H12  H  HCH2  0   0.212   0.9466  -1.0990  -0.2985
 4XW  H13  H  HCH2  0   0.203   1.1203   0.0039  -1.6455
 4XW  H14  H  HCH2  0   0.214   2.5461   1.5040  -0.2410
 4XW  H15  H  HCH2  0   0.214   2.2637   0.4714   1.1442
 4XW  H16  H  HCH2  0   0.208   3.3945  -1.4218  -0.0442
 4XW  H17  H  HCH2  0   0.218   3.6020  -0.4096  -1.4570
 4XW  H18  H  HCH1  0   0.224   5.0559   1.1283  -0.1676
 4XW  H19  H  HCH2  0   0.261   5.9376  -1.7951  -0.0604
 4XW  H20  H  HCH2  0   0.286   5.8970  -0.8262  -1.5109
 4XW  H21  H  HCH3  0   0.232  -4.3169   2.3595   1.1357
 4XW  H22  H  HCH3  0   0.226  -4.6965   2.7359  -0.5478
 4XW  H23  H  HCH3  0   0.230  -5.9757   2.6852   0.6618
 4XW  H24  H  HCH3  0   0.225  -7.3768   1.1342  -0.4705
 4XW  H25  H  HCH3  0   0.222  -6.2671   1.2325  -1.8375
 4XW  H26  H  HCH3  0   0.229  -6.7706  -0.3377  -1.2105
 4XW  H27  H  HCH3  0   0.229  -3.9081  -3.3061  -1.6816
 4XW  H28  H  HCH3  0   0.223  -3.2184  -1.8639  -2.4175
 4XW  H29  H  HCH3  0   0.219  -2.4601  -2.5920  -1.0059
 4XW  H30  H  HCH3  0   0.227  -1.0558   2.7152  -0.2350
 4XW  H31  H  HCH3  0   0.230   0.6916   2.6992  -0.1393
 4XW  H32  H  HCH3  0   0.210  -0.1076   2.2294  -1.6372
 4XW  H33  H  HCH3  0   0.232   5.9286   0.3757   2.0812
 4XW  H34  H  HCH3  0   0.235   4.2200   0.7605   2.1288
 4XW  H35  H  HCH3  0   0.215   4.7357  -0.9236   2.0793
 4XW  H36  H  HOH1  0   0.477   9.2077  -0.8362  -0.1544

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  1.527  0.020  1.527
 4XW  C10  C9   single  1.531  0.020  1.531
 4XW  C10  C11  single  1.525  0.020  1.525
 4XW  C14  C15  single  1.504  0.020  1.504
 4XW  C14  C13  single  1.527  0.020  1.527
 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  double  1.207  0.020  1.207
 4XW  C15  O21  single  1.330  0.020  1.330
 4XW  C13  C20  single  1.526  0.020  1.526
 4XW  C8   C7   single  1.527  0.020  1.527
 4XW  C7   C6   single  1.536  0.020  1.536
 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  1.526  0.020  1.526
 4XW  C5   C4   single  1.524  0.020  1.524
 4XW  C2   C3   double  1.331  0.020  1.331
 4XW  C4   C3   single  1.498  0.020  1.498
 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
 4XW  O21  H36  single  0.850  0.020  0.980

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  106.23  3.000
 4XW  C16  C1   C6   112.79  3.000
 4XW  C17  C1   C6   110.25  3.000
 4XW  C6   C1   C2   109.93  3.000
 4XW  C16  C1   C2   107.97  3.000
 4XW  C17  C1   C2   109.56  3.000
 4XW  H1   C2   C3   119.06  3.000
 4XW  H1   C2   C1   115.98  3.000
 4XW  C3   C2   C1   124.96  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   105.24  3.000
 4XW  H4   C4   C5   109.98  3.000
 4XW  H3   C4   C5   110.55  3.000
 4XW  H4   C4   C3   109.59  3.000
 4XW  H3   C4   C3   110.41  3.000
 4XW  C5   C4   C3   110.91  3.000
 4XW  H5   C5   C18  105.32  3.000
 4XW  H5   C5   C6   106.11  3.000
 4XW  C18  C5   C6   116.46  3.000
 4XW  H5   C5   C4   106.07  3.000
 4XW  C18  C5   C4   112.14  3.000
 4XW  C6   C5   C4   109.94  3.000
 4XW  H6   C6   C7   106.72  3.000
 4XW  H6   C6   C5   107.88  3.000
 4XW  C7   C6   C5   115.01  3.000
 4XW  H6   C6   C1   107.04  3.000
 4XW  C5   C6   C1   108.00  3.000
 4XW  C7   C6   C1   111.83  3.000
 4XW  H8   C7   H7   105.43  3.000
 4XW  H8   C7   C8   108.90  3.000
 4XW  H7   C7   C8   107.21  3.000
 4XW  H8   C7   C6   110.45  3.000
 4XW  H7   C7   C6   107.26  3.000
 4XW  C8   C7   C6   116.92  3.000
 4XW  H10  C8   H9   106.09  3.000
 4XW  H10  C8   C9   109.11  3.000
 4XW  H9   C8   C9   107.55  3.000
 4XW  H10  C8   C7   109.94  3.000
 4XW  H9   C8   C7   110.20  3.000
 4XW  C9   C8   C7   113.64  3.000
 4XW  H11  C9   C19  108.31  3.000
 4XW  H11  C9   C10  107.57  3.000
 4XW  C19  C9   C10  111.14  3.000
 4XW  H11  C9   C8   107.48  3.000
 4XW  C10  C9   C8   109.92  3.000
 4XW  C19  C9   C8   112.23  3.000
 4XW  H13  C10  H12  105.87  3.000
 4XW  H13  C10  C11  109.54  3.000
 4XW  H12  C10  C11  108.39  3.000
 4XW  H13  C10  C9   109.01  3.000
 4XW  H12  C10  C9   108.67  3.000
 4XW  C11  C10  C9   114.97  3.000
 4XW  H15  C11  H14  106.23  3.000
 4XW  H15  C11  C12  110.26  3.000
 4XW  H14  C11  C12  108.95  3.000
 4XW  H15  C11  C10  108.62  3.000
 4XW  H14  C11  C10  110.48  3.000
 4XW  C12  C11  C10  112.13  3.000
 4XW  H17  C12  H16  105.95  3.000
 4XW  H17  C12  C13  108.64  3.000
 4XW  H16  C12  C13  109.09  3.000
 4XW  H17  C12  C11  108.57  3.000
 4XW  H16  C12  C11  109.45  3.000
 4XW  C13  C12  C11  114.77  3.000
 4XW  H18  C13  C20  108.59  3.000
 4XW  H18  C13  C14  108.23  3.000
 4XW  C20  C13  C14  111.11  3.000
 4XW  H18  C13  C12  107.96  3.000
 4XW  C20  C13  C12  111.80  3.000
 4XW  C14  C13  C12  109.04  3.000
 4XW  H20  C14  H19  105.62  3.000
 4XW  H20  C14  C15  106.07  3.000
 4XW  H19  C14  C15  109.78  3.000
 4XW  H20  C14  C13  109.79  3.000
 4XW  H19  C14  C13  110.59  3.000
 4XW  C15  C14  C13  114.53  3.000
 4XW  O22  C15  O21  122.73  3.000
 4XW  O21  C15  C14  112.10  3.000
 4XW  O22  C15  C14  125.14  3.000
 4XW  H23  C16  H22  107.45  3.000
 4XW  H23  C16  H21  107.17  3.000
 4XW  H22  C16  H21  108.10  3.000
 4XW  H23  C16  C1   109.97  3.000
 4XW  H22  C16  C1   111.11  3.000
 4XW  H21  C16  C1   112.81  3.000
 4XW  H26  C17  H25  107.88  3.000
 4XW  H26  C17  H24  107.18  3.000
 4XW  H25  C17  H24  107.64  3.000
 4XW  H26  C17  C1   112.90  3.000
 4XW  H25  C17  C1   110.24  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   111.64  3.000
 4XW  H27  C18  C5   110.01  3.000
 4XW  H32  C19  H31  107.54  3.000
 4XW  H32  C19  H30  107.51  3.000
 4XW  H31  C19  H30  106.74  3.000
 4XW  H32  C19  C9   110.65  3.000
 4XW  H31  C19  C9   111.83  3.000
 4XW  H30  C19  C9   112.31  3.000
 4XW  H35  C20  H34  107.63  3.000
 4XW  H35  C20  H33  107.75  3.000
 4XW  H34  C20  H33  106.94  3.000
 4XW  H35  C20  C13  110.79  3.000
 4XW  H34  C20  C13  111.53  3.000
 4XW  H33  C20  C13  111.98  3.000
 4XW  H36  O21  C15  109.94  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  CONST_01  H36  O21  C15  C14  180.00   0.0  0
 4XW  Var_01    C4   C3   C2   C1    -3.14  30.0  1
 4XW  Var_02    C5   C4   C3   C2   -14.73  30.0  1
 4XW  Var_03    C6   C1   C2   C3   -14.02  30.0  1
 4XW  Var_04    H24  C17  C1   C2    56.77  30.0  3
 4XW  Var_05    H21  C16  C1   C2    53.74  30.0  3
 4XW  Var_06    C9   C8   C7   C6   167.09  30.0  1
 4XW  Var_07    C12  C11  C10  C9   175.79  30.0  3
 4XW  Var_08    C13  C12  C11  C10  177.95  30.0  1
 4XW  Var_09    O22  C15  C14  C13  -25.38  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
 4XW  plan-1  H36  0.020

