# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 03:48:51 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: retinal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C\C=O)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(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
 RET  RET  'retinal                  '  ligand  49  21  .  2016-02-03  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RET
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
 RET  C1    C  CT    0  -0.175   -5.5986  13.1546  53.0554
 RET  C2    C  CH2   0  -0.415   -4.9341  11.8804  53.5998
 RET  C3    C  CH2   0  -0.448   -3.5568  12.1357  54.1744
 RET  C4    C  CH2   0  -0.495   -2.6500  12.6418  53.0710
 RET  C5    C  C     0   0.032   -3.2902  13.6513  52.1627
 RET  C6    C  C     0   0.168   -4.6174  13.9309  52.1725
 RET  C7    C  C1    0  -0.281   -5.0798  15.0132  51.3099
 RET  C8    C  C1    0  -0.301   -6.2443  15.6932  51.3274
 RET  C9    C  C     0   0.150   -6.5746  16.7816  50.4273
 RET  C10   C  C1    0  -0.314   -7.7744  17.3964  50.5997
 RET  C11   C  C1    0  -0.225   -8.3035  18.4864  49.8354
 RET  C12   C  C1    0  -0.300   -9.5100  19.0402  50.0919
 RET  C13   C  C     0   0.173  -10.0947  20.1400  49.3576
 RET  C14   C  C1    0  -0.423  -11.3151  20.5889  49.7523
 RET  C15   C  C1    0   0.131  -12.0572  21.6728  49.1440
 RET  O1    O  O     0  -0.420  -13.1523  22.0365  49.5333
 RET  C16   C  CH3   0  -0.647   -6.8169  12.6787  52.2476
 RET  C17   C  CH3   0  -0.648   -6.0633  14.0124  54.2428
 RET  C18   C  CH3   0  -0.757   -2.2950  14.3444  51.2661
 RET  C19   C  CH3   0  -0.769   -5.5881  17.1681  49.3679
 RET  C20   C  CH3   0  -0.763   -9.3166  20.7104  48.2095
 RET  H21   H  HCH2  0   0.227   -5.5970  11.4356  54.3471
 RET  H22   H  HCH2  0   0.221   -4.8436  11.1480  52.7893
 RET  H31   H  HCH2  0   0.223   -3.6085  12.8683  54.9839
 RET  H32   H  HCH2  0   0.233   -3.1455  11.2238  54.6120
 RET  H41   H  HCH2  0   0.247   -1.7393  13.0826  53.4900
 RET  H42   H  HCH2  0   0.242   -2.2991  11.8035  52.4546
 RET  H7    H  H     0   0.246   -4.3603  15.3363  50.5679
 RET  H8    H  H     0   0.233   -7.0109  15.4646  52.0558
 RET  H10   H  H     0   0.243   -8.4096  17.0310  51.4022
 RET  H11   H  H     0   0.266   -7.7074  18.8784  49.0201
 RET  H12   H  H     0   0.248  -10.1002  18.6427  50.9124
 RET  H14   H  H     0   0.254  -11.7972  20.1065  50.5973
 RET  H15   H  H     0   0.185  -11.5891  22.1805  48.2856
 RET  H161  H  HCH3  0   0.231   -7.4793  13.4828  51.9354
 RET  H162  H  HCH3  0   0.224   -6.5027  12.1400  51.3519
 RET  H163  H  HCH3  0   0.225   -7.4097  11.9923  52.8561
 RET  H171  H  HCH3  0   0.233   -6.5643  14.9278  53.9331
 RET  H172  H  HCH3  0   0.223   -6.7683  13.4508  54.8604
 RET  H173  H  HCH3  0   0.229   -5.2261  14.3054  54.8775
 RET  H181  H  HCH3  0   0.246   -2.6164  14.4014  50.2260
 RET  H182  H  HCH3  0   0.250   -2.0939  15.3653  51.5989
 RET  H183  H  HCH3  0   0.253   -1.3435  13.8134  51.2777
 RET  H191  H  HCH3  0   0.260   -5.9196  18.0074  48.7635
 RET  H192  H  HCH3  0   0.250   -4.6295  17.4424  49.8120
 RET  H193  H  HCH3  0   0.251   -5.3958  16.3314  48.6937
 RET  H201  H  HCH3  0   0.262   -9.8189  21.5289  47.7040
 RET  H202  H  HCH3  0   0.259   -8.3494  21.0807  48.5526
 RET  H203  H  HCH3  0   0.259   -9.1163  19.9375  47.4664

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
 RET  C1   C2    single  1.537  0.020  1.537
 RET  C1   C6    single  1.531  0.020  1.531
 RET  C1   C16   single  1.537  0.020  1.537
 RET  C1   C17   single  1.537  0.020  1.537
 RET  C2   C3    single  1.514  0.020  1.514
 RET  C2   H21   single  0.970  0.020  1.090
 RET  C2   H22   single  0.970  0.020  1.090
 RET  C3   C4    single  1.515  0.020  1.515
 RET  C3   H31   single  0.970  0.020  1.090
 RET  C3   H32   single  0.970  0.020  1.090
 RET  C4   C5    single  1.501  0.020  1.501
 RET  C4   H41   single  0.970  0.020  1.090
 RET  C4   H42   single  0.970  0.020  1.090
 RET  C5   C6    double  1.356  0.020  1.356
 RET  C5   C18   single  1.508  0.020  1.508
 RET  C6   C7    single  1.459  0.020  1.459
 RET  C7   C8    double  1.349  0.020  1.349
 RET  C7   H7    single  0.930  0.020  1.080
 RET  C8   C9    single  1.450  0.020  1.450
 RET  C8   H8    single  0.930  0.020  1.080
 RET  C9   C10   double  1.359  0.020  1.359
 RET  C9   C19   single  1.498  0.020  1.498
 RET  C10  C11   single  1.433  0.020  1.433
 RET  C10  H10   single  0.930  0.020  1.080
 RET  C11  C12   double  1.352  0.020  1.352
 RET  C11  H11   single  0.930  0.020  1.080
 RET  C12  C13   single  1.446  0.020  1.446
 RET  C12  H12   single  0.930  0.020  1.080
 RET  C13  C14   double  1.359  0.020  1.359
 RET  C13  C20   single  1.500  0.020  1.500
 RET  C14  C15   single  1.448  0.020  1.448
 RET  C14  H14   single  0.930  0.020  1.080
 RET  C15  O1    double  1.218  0.020  1.218
 RET  C15  H15   single  0.930  0.020  1.080
 RET  C16  H161  single  0.970  0.020  1.090
 RET  C16  H162  single  0.970  0.020  1.090
 RET  C16  H163  single  0.970  0.020  1.090
 RET  C17  H171  single  0.970  0.020  1.090
 RET  C17  H172  single  0.970  0.020  1.090
 RET  C17  H173  single  0.970  0.020  1.090
 RET  C18  H181  single  0.970  0.020  1.090
 RET  C18  H182  single  0.970  0.020  1.090
 RET  C18  H183  single  0.970  0.020  1.090
 RET  C19  H191  single  0.970  0.020  1.090
 RET  C19  H192  single  0.970  0.020  1.090
 RET  C19  H193  single  0.970  0.020  1.090
 RET  C20  H201  single  0.970  0.020  1.090
 RET  C20  H202  single  0.970  0.020  1.090
 RET  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
 RET  C17   C1   C16   109.83  3.000
 RET  C17   C1   C6    110.87  3.000
 RET  C16   C1   C6    111.21  3.000
 RET  C17   C1   C2    108.65  3.000
 RET  C16   C1   C2    105.80  3.000
 RET  C6    C1   C2    110.34  3.000
 RET  H22   C2   H21   106.48  3.000
 RET  H22   C2   C3    108.55  3.000
 RET  H21   C2   C3    111.14  3.000
 RET  H22   C2   C1    109.13  3.000
 RET  H21   C2   C1    108.50  3.000
 RET  C3    C2   C1    112.83  3.000
 RET  H32   C3   H31   106.31  3.000
 RET  H32   C3   C4    110.20  3.000
 RET  H31   C3   C4    110.10  3.000
 RET  H32   C3   C2    110.73  3.000
 RET  H31   C3   C2    110.55  3.000
 RET  C4    C3   C2    108.93  3.000
 RET  H42   C4   H41   104.86  3.000
 RET  H42   C4   C5    108.06  3.000
 RET  H41   C4   C5    108.39  3.000
 RET  H42   C4   C3    110.18  3.000
 RET  H41   C4   C3    110.70  3.000
 RET  C5    C4   C3    114.20  3.000
 RET  C18   C5   C6    123.73  3.000
 RET  C18   C5   C4    112.78  3.000
 RET  C6    C5   C4    123.47  3.000
 RET  C7    C6   C5    117.30  3.000
 RET  C7    C6   C1    120.92  3.000
 RET  C5    C6   C1    121.78  3.000
 RET  H7    C7   C8    115.61  3.000
 RET  H7    C7   C6    114.57  3.000
 RET  C8    C7   C6    129.79  3.000
 RET  H8    C8   C9    114.52  3.000
 RET  H8    C8   C7    120.93  3.000
 RET  C9    C8   C7    124.53  3.000
 RET  C19   C9   C10   123.65  3.000
 RET  C19   C9   C8    118.85  3.000
 RET  C10   C9   C8    117.50  3.000
 RET  H10   C10  C11   115.72  3.000
 RET  H10   C10  C9    117.23  3.000
 RET  C11   C10  C9    127.06  3.000
 RET  H11   C11  C12   119.05  3.000
 RET  H11   C11  C10   118.27  3.000
 RET  C12   C11  C10   122.68  3.000
 RET  H12   C12  C13   116.25  3.000
 RET  H12   C12  C11   118.58  3.000
 RET  C13   C12  C11   125.17  3.000
 RET  C20   C13  C14   124.24  3.000
 RET  C20   C13  C12   117.92  3.000
 RET  C14   C13  C12   117.84  3.000
 RET  H14   C14  C15   115.60  3.000
 RET  H14   C14  C13   118.55  3.000
 RET  C15   C14  C13   125.85  3.000
 RET  H15   C15  O1    119.57  3.000
 RET  H15   C15  C14   117.04  3.000
 RET  O1    C15  C14   123.39  3.000
 RET  H163  C16  H162  107.65  3.000
 RET  H163  C16  H161  107.10  3.000
 RET  H162  C16  H161  107.74  3.000
 RET  H163  C16  C1    109.39  3.000
 RET  H162  C16  C1    110.85  3.000
 RET  H161  C16  C1    113.87  3.000
 RET  H173  C17  H172  107.73  3.000
 RET  H173  C17  H171  107.03  3.000
 RET  H172  C17  H171  107.23  3.000
 RET  H173  C17  C1    111.56  3.000
 RET  H172  C17  C1    110.18  3.000
 RET  H171  C17  C1    112.87  3.000
 RET  H183  C18  H182  106.94  3.000
 RET  H183  C18  H181  107.04  3.000
 RET  H182  C18  H181  107.22  3.000
 RET  H183  C18  C5    110.24  3.000
 RET  H182  C18  C5    111.71  3.000
 RET  H181  C18  C5    113.37  3.000
 RET  H193  C19  H192  106.81  3.000
 RET  H193  C19  H191  107.60  3.000
 RET  H192  C19  H191  107.48  3.000
 RET  H193  C19  C9    110.78  3.000
 RET  H192  C19  C9    110.81  3.000
 RET  H191  C19  C9    113.07  3.000
 RET  H203  C20  H202  106.97  3.000
 RET  H203  C20  H201  107.58  3.000
 RET  H202  C20  H201  107.51  3.000
 RET  H203  C20  C13   110.32  3.000
 RET  H202  C20  C13   110.39  3.000
 RET  H201  C20  C13   113.79  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
 RET  Var_01  C4    C3   C2   C1    -62.54  30.0  1
 RET  Var_02  C4    C5   C6   C1     -4.54  30.0  1
 RET  Var_03  C5    C6   C1   C2    -13.67  30.0  1
 RET  Var_04  C5    C4   C3   C2     42.40  30.0  1
 RET  Var_05  C6    C1   C2   C3     47.45  30.0  1
 RET  Var_06  C6    C5   C4   C3    -10.51  30.0  1
 RET  Var_07  C8    C7   C6   C1     15.93  30.0  2
 RET  Var_08  H161  C16  C1   C2    170.54  30.0  3
 RET  Var_09  H171  C17  C1   C2   -178.85  30.0  3
 RET  Var_10  H181  C18  C5   C4    133.68  30.0  3
 RET  Var_11  C9    C8   C7   C6    178.39   0.0  2
 RET  Var_12  C11   C10  C9   C8    179.88   0.0  2
 RET  Var_13  C13   C12  C11  C10   179.95   0.0  2
 RET  Var_14  C15   C14  C13  C12  -179.94   0.0  2
 RET  Var_15  C10   C9   C8   C7   -177.92  30.0  2
 RET  Var_16  C12   C11  C10  C9   -179.46  30.0  2
 RET  Var_17  C14   C13  C12  C11  -179.39  30.0  2
 RET  Var_18  O1    C15  C14  C13   179.80  30.0  2
 RET  Var_19  H191  C19  C9   C8   -178.62  30.0  3
 RET  Var_20  H201  C20  C13  C12   179.76  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
 RET  plan-1  C6   0.020
 RET  plan-1  C7   0.020
 RET  plan-1  C8   0.020
 RET  plan-1  C9   0.020
 RET  plan-1  H7   0.020
 RET  plan-1  H8   0.020
 RET  plan-2  C8   0.020
 RET  plan-2  C9   0.020
 RET  plan-2  C10  0.020
 RET  plan-2  C11  0.020
 RET  plan-2  C19  0.020
 RET  plan-2  H10  0.020
 RET  plan-3  C10  0.020
 RET  plan-3  C11  0.020
 RET  plan-3  C12  0.020
 RET  plan-3  C13  0.020
 RET  plan-3  H11  0.020
 RET  plan-3  H12  0.020
 RET  plan-4  C12  0.020
 RET  plan-4  C13  0.020
 RET  plan-4  C14  0.020
 RET  plan-4  C15  0.020
 RET  plan-4  C20  0.020
 RET  plan-4  H14  0.020
 RET  plan-5  C14  0.020
 RET  plan-5  C15  0.020
 RET  plan-5  O1   0.020
 RET  plan-5  H15  0.020

