# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:02:58 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-oxoretinol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C\CO)/C=C/C=C(C)/C=C/C1=C(C)C(=O)CCC1(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
 OXR  OXR  '4-oxoretinol             '  ligand  50  22  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OXR
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
 OXR  O2    O  O     0  -0.425  24.8756   -8.5519  40.6770
 OXR  C4    C  C     0   0.383  24.1099   -9.2948  41.2675
 OXR  C3    C  CH2   0  -0.572  24.5456  -10.6617  41.7121
 OXR  C2    C  CH2   0  -0.429  23.3906  -11.6409  41.7110
 OXR  C1    C  CT    0  -0.183  22.2043  -11.1518  42.5413
 OXR  C17   C  CH3   0  -0.643  22.5333  -11.2063  44.0414
 OXR  C16   C  CH3   0  -0.638  21.0270  -12.0943  42.2598
 OXR  C5    C  C     0  -0.112  22.7429   -8.8533  41.6090
 OXR  C18   C  CH3   0  -0.738  22.4599   -7.4057  41.3230
 OXR  C6    C  C     0   0.188  21.8537   -9.7115  42.1719
 OXR  C7    C  C1    0  -0.326  20.4925   -9.3204  42.5334
 OXR  C8    C  C1    0  -0.252  19.6466   -8.6145  41.7642
 OXR  C9    C  C     0   0.116  18.2696   -8.3011  42.1022
 OXR  C19   C  CH3   0  -0.764  17.7291   -8.7923  43.4105
 OXR  C10   C  C1    0  -0.294  17.5547   -7.5761  41.2088
 OXR  C11   C  C1    0  -0.260  16.1827   -7.1539  41.3222
 OXR  C12   C  C1    0  -0.280  15.5904   -6.3901  40.3830
 OXR  C13   C  C     0   0.137  14.2147   -5.9140  40.4088
 OXR  C20   C  CH3   0  -0.760  13.3493   -6.3346  41.5599
 OXR  C14   C  C1    0  -0.315  13.8110   -5.1169  39.4038
 OXR  C15   C  CH2   0  -0.203  12.4849   -4.4578  39.2289
 OXR  O1    O  OH1   0  -0.674  12.0804   -4.6214  37.8836
 OXR  H31   H  HCH2  0   0.266  24.9624  -10.5565  42.7204
 OXR  H32   H  HCH2  0   0.266  25.3643  -11.0046  41.0774
 OXR  H21   H  HCH2  0   0.243  23.7174  -12.6140  42.0860
 OXR  H22   H  HCH2  0   0.239  23.0584  -11.8025  40.6806
 OXR  H171  H  HCH3  0   0.237  23.3843  -10.5769  44.3042
 OXR  H172  H  HCH3  0   0.238  21.6880  -10.8791  44.6487
 OXR  H173  H  HCH3  0   0.236  22.7682  -12.2317  44.3340
 OXR  H161  H  HCH3  0   0.235  21.3400  -13.1260  42.4340
 OXR  H162  H  HCH3  0   0.230  20.1701  -11.9012  42.9049
 OXR  H163  H  HCH3  0   0.233  20.6918  -12.0152  41.2244
 OXR  H181  H  HCH3  0   0.242  22.1914   -7.2393  40.2774
 OXR  H182  H  HCH3  0   0.246  21.6438   -7.0245  41.9320
 OXR  H183  H  HCH3  0   0.245  23.3406   -6.7957  41.5196
 OXR  H7    H  H     0   0.263  20.1295   -9.7189  43.4758
 OXR  H8    H  H     0   0.255  19.9818   -8.2675  40.7920
 OXR  H191  H  HCH3  0   0.249  18.3044   -8.3881  44.2461
 OXR  H192  H  HCH3  0   0.258  16.6891   -8.5195  43.5674
 OXR  H193  H  HCH3  0   0.246  17.7970   -9.8802  43.4783
 OXR  H10   H  H     0   0.244  18.0638   -7.2668  40.2994
 OXR  H11   H  H     0   0.255  15.6179   -7.4657  42.1931
 OXR  H12   H  H     0   0.243  16.1814   -6.0823  39.5238
 OXR  H201  H  HCH3  0   0.248  13.7175   -5.9153  42.4984
 OXR  H202  H  HCH3  0   0.254  12.3148   -6.0207  41.4475
 OXR  H203  H  HCH3  0   0.244  13.3545   -7.4198  41.6737
 OXR  H14   H  H     0   0.246  14.5380   -4.8724  38.6329
 OXR  H151  H  HCH2  0   0.218  12.5946   -3.3928  39.4772
 OXR  H152  H  HCH2  0   0.211  11.7397   -4.8610  39.9231
 OXR  HO1   H  HOH1  0   0.455  11.3425   -4.0263  37.7234

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
 OXR  O2   C4    double  1.219  0.020  1.219
 OXR  C4   C3    single  1.502  0.020  1.502
 OXR  C4   C5    single  1.477  0.020  1.477
 OXR  C3   C2    single  1.514  0.020  1.514
 OXR  C3   H31   single  0.970  0.020  1.090
 OXR  C3   H32   single  0.970  0.020  1.090
 OXR  C2   C1    single  1.528  0.020  1.528
 OXR  C2   H21   single  0.970  0.020  1.090
 OXR  C2   H22   single  0.970  0.020  1.090
 OXR  C1   C17   single  1.537  0.020  1.537
 OXR  C1   C16   single  1.534  0.020  1.534
 OXR  C1   C6    single  1.528  0.020  1.528
 OXR  C17  H171  single  0.970  0.020  1.090
 OXR  C17  H172  single  0.970  0.020  1.090
 OXR  C17  H173  single  0.970  0.020  1.090
 OXR  C16  H161  single  0.970  0.020  1.090
 OXR  C16  H162  single  0.970  0.020  1.090
 OXR  C16  H163  single  0.970  0.020  1.090
 OXR  C5   C18   single  1.502  0.020  1.502
 OXR  C5   C6    double  1.358  0.020  1.358
 OXR  C18  H181  single  0.970  0.020  1.090
 OXR  C18  H182  single  0.970  0.020  1.090
 OXR  C18  H183  single  0.970  0.020  1.090
 OXR  C6   C7    single  1.462  0.020  1.462
 OXR  C7   C8    double  1.344  0.020  1.344
 OXR  C7   H7    single  0.930  0.020  1.080
 OXR  C8   C9    single  1.452  0.020  1.452
 OXR  C8   H8    single  0.930  0.020  1.080
 OXR  C9   C19   single  1.498  0.020  1.498
 OXR  C9   C10   double  1.355  0.020  1.355
 OXR  C19  H191  single  0.970  0.020  1.090
 OXR  C19  H192  single  0.970  0.020  1.090
 OXR  C19  H193  single  0.970  0.020  1.090
 OXR  C10  C11   single  1.440  0.020  1.440
 OXR  C10  H10   single  0.930  0.020  1.080
 OXR  C11  C12   double  1.348  0.020  1.348
 OXR  C11  H11   single  0.930  0.020  1.080
 OXR  C12  C13   single  1.456  0.020  1.456
 OXR  C12  H12   single  0.930  0.020  1.080
 OXR  C13  C20   single  1.500  0.020  1.500
 OXR  C13  C14   double  1.345  0.020  1.345
 OXR  C20  H201  single  0.970  0.020  1.090
 OXR  C20  H202  single  0.970  0.020  1.090
 OXR  C20  H203  single  0.970  0.020  1.090
 OXR  C14  C15   single  1.491  0.020  1.491
 OXR  C14  H14   single  0.930  0.020  1.080
 OXR  C15  O1    single  1.414  0.020  1.414
 OXR  C15  H151  single  0.970  0.020  1.090
 OXR  C15  H152  single  0.970  0.020  1.090
 OXR  O1   HO1   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
 OXR  C5    C4   C3    118.18  3.000
 OXR  C5    C4   O2    120.74  3.000
 OXR  C3    C4   O2    121.04  3.000
 OXR  H32   C3   H31   106.25  3.000
 OXR  H32   C3   C2    111.63  3.000
 OXR  H31   C3   C2    110.66  3.000
 OXR  H32   C3   C4    109.36  3.000
 OXR  H31   C3   C4    107.17  3.000
 OXR  C2    C3   C4    111.53  3.000
 OXR  H22   C2   H21   106.40  3.000
 OXR  H22   C2   C1    108.84  3.000
 OXR  H21   C2   C1    109.31  3.000
 OXR  H22   C2   C3    109.13  3.000
 OXR  H21   C2   C3    110.33  3.000
 OXR  C1    C2   C3    112.63  3.000
 OXR  C6    C1   C16   111.02  3.000
 OXR  C6    C1   C17   108.58  3.000
 OXR  C16   C1   C17   108.76  3.000
 OXR  C6    C1   C2    110.39  3.000
 OXR  C16   C1   C2    107.42  3.000
 OXR  C17   C1   C2    110.66  3.000
 OXR  H173  C17  H172  107.40  3.000
 OXR  H173  C17  H171  108.03  3.000
 OXR  H172  C17  H171  107.30  3.000
 OXR  H173  C17  C1    109.93  3.000
 OXR  H172  C17  C1    111.52  3.000
 OXR  H171  C17  C1    112.45  3.000
 OXR  H163  C16  H162  107.90  3.000
 OXR  H163  C16  H161  107.94  3.000
 OXR  H162  C16  H161  107.35  3.000
 OXR  H163  C16  C1    111.43  3.000
 OXR  H162  C16  C1    112.70  3.000
 OXR  H161  C16  C1    109.34  3.000
 OXR  C6    C5   C18   124.37  3.000
 OXR  C6    C5   C4    120.87  3.000
 OXR  C18   C5   C4    114.74  3.000
 OXR  H183  C18  H182  108.03  3.000
 OXR  H183  C18  H181  106.63  3.000
 OXR  H182  C18  H181  107.36  3.000
 OXR  H183  C18  C5    110.66  3.000
 OXR  H182  C18  C5    111.87  3.000
 OXR  H181  C18  C5    112.04  3.000
 OXR  C7    C6   C5    122.90  3.000
 OXR  C7    C6   C1    113.97  3.000
 OXR  C5    C6   C1    123.08  3.000
 OXR  H7    C7   C8    118.63  3.000
 OXR  H7    C7   C6    115.33  3.000
 OXR  C8    C7   C6    125.82  3.000
 OXR  H8    C8   C9    115.62  3.000
 OXR  H8    C8   C7    119.10  3.000
 OXR  C9    C8   C7    125.25  3.000
 OXR  C10   C9   C19   124.12  3.000
 OXR  C10   C9   C8    117.55  3.000
 OXR  C19   C9   C8    118.33  3.000
 OXR  H193  C19  H192  107.49  3.000
 OXR  H193  C19  H191  106.77  3.000
 OXR  H192  C19  H191  107.51  3.000
 OXR  H193  C19  C9    111.00  3.000
 OXR  H192  C19  C9    112.90  3.000
 OXR  H191  C19  C9    110.90  3.000
 OXR  H10   C10  C11   115.38  3.000
 OXR  H10   C10  C9    117.18  3.000
 OXR  C11   C10  C9    127.43  3.000
 OXR  H11   C11  C12   119.61  3.000
 OXR  H11   C11  C10   118.38  3.000
 OXR  C12   C11  C10   122.01  3.000
 OXR  H12   C12  C13   115.78  3.000
 OXR  H12   C12  C11   118.18  3.000
 OXR  C13   C12  C11   126.03  3.000
 OXR  C14   C13  C20   124.50  3.000
 OXR  C14   C13  C12   117.66  3.000
 OXR  C20   C13  C12   117.84  3.000
 OXR  H203  C20  H202  107.61  3.000
 OXR  H203  C20  H201  106.90  3.000
 OXR  H202  C20  H201  107.40  3.000
 OXR  H203  C20  C13   110.86  3.000
 OXR  H202  C20  C13   112.87  3.000
 OXR  H201  C20  C13   110.93  3.000
 OXR  H14   C14  C15   114.33  3.000
 OXR  H14   C14  C13   117.54  3.000
 OXR  C15   C14  C13   128.07  3.000
 OXR  H152  C15  H151  106.34  3.000
 OXR  H152  C15  O1    111.45  3.000
 OXR  H151  C15  O1    110.83  3.000
 OXR  H152  C15  C14   111.59  3.000
 OXR  H151  C15  C14   108.24  3.000
 OXR  O1    C15  C14   108.35  3.000
 OXR  HO1   O1   C15   107.84  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
 OXR  Var_01  C1    C2   C3   C4    -54.65  30.0  1
 OXR  Var_02  C1    C6   C5   C4      2.53  30.0  1
 OXR  Var_03  C6    C5   C4   C3     -7.45  30.0  1
 OXR  Var_04  C6    C1   C2   C3     48.92  30.0  1
 OXR  Var_05  C5    C4   C3   C2     33.22  30.0  1
 OXR  Var_06  C5    C6   C1   C2    -23.29  30.0  1
 OXR  Var_07  C8    C7   C6   C1   -136.83  30.0  2
 OXR  Var_08  H181  C18  C5   C4     82.81  30.0  3
 OXR  Var_09  H171  C17  C1   C2     60.58  30.0  3
 OXR  Var_10  H161  C16  C1   C2     53.37  30.0  3
 OXR  Var_11  C9    C8   C7   C6    176.09   0.0  2
 OXR  Var_12  C11   C10  C9   C8    179.68   0.0  2
 OXR  Var_13  C13   C12  C11  C10  -179.96   0.0  2
 OXR  Var_14  C15   C14  C13  C12  -177.24   0.0  2
 OXR  Var_15  C19   C9   C8   C7      0.13  30.0  2
 OXR  Var_16  C12   C11  C10  C9    177.57  30.0  2
 OXR  Var_17  C20   C13  C12  C11    -1.88  30.0  2
 OXR  Var_18  O1    C15  C14  C13  -135.63  30.0  3
 OXR  Var_19  H191  C19  C9   C8     60.02  30.0  3
 OXR  Var_20  H201  C20  C13  C12    65.34  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
 OXR  plan-1  O2   0.020
 OXR  plan-1  C4   0.020
 OXR  plan-1  C3   0.020
 OXR  plan-1  C5   0.020
 OXR  plan-2  C6   0.020
 OXR  plan-2  C7   0.020
 OXR  plan-2  C8   0.020
 OXR  plan-2  C9   0.020
 OXR  plan-2  H7   0.020
 OXR  plan-2  H8   0.020
 OXR  plan-3  C8   0.020
 OXR  plan-3  C9   0.020
 OXR  plan-3  C19  0.020
 OXR  plan-3  C10  0.020
 OXR  plan-3  C11  0.020
 OXR  plan-3  H10  0.020
 OXR  plan-4  C10  0.020
 OXR  plan-4  C11  0.020
 OXR  plan-4  C12  0.020
 OXR  plan-4  C13  0.020
 OXR  plan-4  H11  0.020
 OXR  plan-4  H12  0.020
 OXR  plan-5  C12  0.020
 OXR  plan-5  C13  0.020
 OXR  plan-5  C20  0.020
 OXR  plan-5  C14  0.020
 OXR  plan-5  C15  0.020
 OXR  plan-5  H14  0.020

