# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 09:20:35 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: retinol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C\CO)/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
 RTL  RTL  'retinol                  '  ligand  51  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RTL
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
 RTL  C1    C  CT    0  -0.144   0.5979   4.6754  -7.6841
 RTL  C2    C  CH2   0  -0.413   0.8639   6.1493  -8.0114
 RTL  C3    C  CH2   0  -0.446  -0.3400   7.0285  -7.7372
 RTL  C4    C  CH2   0  -0.477  -0.6604   6.9790  -6.2553
 RTL  C5    C  C     0   0.017  -0.6611   5.5849  -5.6898
 RTL  C6    C  C     0   0.125  -0.1441   4.5328  -6.3527
 RTL  C7    C  C1    0  -0.318  -0.2671   3.1559  -5.8536
 RTL  C8    C  C1    0  -0.257  -1.4151   2.5927  -5.4437
 RTL  C9    C  C     0   0.119  -1.5700   1.2244  -4.9767
 RTL  C10   C  C1    0  -0.304  -2.8107   0.8088  -4.6271
 RTL  C11   C  C1    0  -0.256  -3.1961  -0.4960  -4.1546
 RTL  C12   C  C1    0  -0.287  -4.4653  -0.8008  -3.8202
 RTL  C13   C  C     0   0.140  -4.9331  -2.0946  -3.3414
 RTL  C14   C  C1    0  -0.316  -6.2443  -2.2336  -3.0769
 RTL  C15   C  CH2   0  -0.203  -6.9696  -3.4582  -2.6306
 RTL  O1    O  OH1   0  -0.668  -7.7672  -3.1211  -1.5121
 RTL  C16   C  CH3   0  -0.656   1.9588   3.9671  -7.6223
 RTL  C17   C  CH3   0  -0.634  -0.2326   4.0313  -8.8014
 RTL  C18   C  CH3   0  -0.729  -1.2660   5.5144  -4.3163
 RTL  C19   C  CH3   0  -0.762  -0.3478   0.3593  -4.9125
 RTL  C20   C  CH3   0  -0.759  -3.9162  -3.1874  -3.1874
 RTL  H21   H  HCH2  0   0.219   1.7040   6.5087  -7.4059
 RTL  H22   H  HCH2  0   0.224   1.1807   6.2285  -9.0554
 RTL  H31   H  HCH2  0   0.229  -0.1460   8.0572  -8.0483
 RTL  H32   H  HCH2  0   0.219  -1.2031   6.6872  -8.3161
 RTL  H41   H  HCH2  0   0.231   0.0581   7.5898  -5.6939
 RTL  H42   H  HCH2  0   0.236  -1.6374   7.4322  -6.0561
 RTL  H7    H  H     0   0.249   0.6296   2.5445  -5.8780
 RTL  H8    H  H     0   0.236  -2.3240   3.1877  -5.4704
 RTL  H10   H  H     0   0.236  -3.6180   1.5326  -4.7110
 RTL  H11   H  H     0   0.253  -2.4293  -1.2572  -4.0700
 RTL  H12   H  H     0   0.238  -5.2231  -0.0269  -3.9156
 RTL  H14   H  H     0   0.242  -6.8836  -1.3681  -3.2349
 RTL  H151  H  HCH2  0   0.211  -7.5941  -3.8107  -3.4639
 RTL  H152  H  HCH2  0   0.207  -6.2775  -4.2745  -2.3986
 RTL  HO1   H  HOH1  0   0.451  -8.3630  -3.8563  -1.3409
 RTL  H161  H  HCH3  0   0.227   1.8673   2.8828  -7.5538
 RTL  H162  H  HCH3  0   0.230   2.5270   4.1830  -8.5299
 RTL  H163  H  HCH3  0   0.226   2.5473   4.3156  -6.7714
 RTL  H171  H  HCH3  0   0.226  -0.4381   2.9813  -8.5868
 RTL  H172  H  HCH3  0   0.226  -1.1924   4.5329  -8.9362
 RTL  H173  H  HCH3  0   0.220   0.3047   4.0759  -9.7515
 RTL  H181  H  HCH3  0   0.241  -1.0092   4.6053  -3.7777
 RTL  H182  H  HCH3  0   0.233  -0.9284   6.3694  -3.7247
 RTL  H183  H  HCH3  0   0.235  -2.3566   5.5809  -4.3551
 RTL  H191  H  HCH3  0   0.256  -0.5533  -0.6472  -4.5574
 RTL  H192  H  HCH3  0   0.244   0.1195   0.2720  -5.8956
 RTL  H193  H  HCH3  0   0.244   0.4006   0.7962  -4.2482
 RTL  H201  H  HCH3  0   0.253  -4.3272  -4.0921  -2.7473
 RTL  H202  H  HCH3  0   0.245  -3.4882  -3.4596  -4.1545
 RTL  H203  H  HCH3  0   0.242  -3.0875  -2.8599  -2.5571

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
 RTL  C1   C2    single  1.533  0.020  1.533
 RTL  C1   C6    single  1.531  0.020  1.531
 RTL  C1   C16   single  1.535  0.020  1.535
 RTL  C1   C17   single  1.534  0.020  1.534
 RTL  C2   C3    single  1.516  0.020  1.516
 RTL  C2   H21   single  0.970  0.020  1.090
 RTL  C2   H22   single  0.970  0.020  1.090
 RTL  C3   C4    single  1.517  0.020  1.517
 RTL  C3   H31   single  0.970  0.020  1.090
 RTL  C3   H32   single  0.970  0.020  1.090
 RTL  C4   C5    single  1.504  0.020  1.504
 RTL  C4   H41   single  0.970  0.020  1.090
 RTL  C4   H42   single  0.970  0.020  1.090
 RTL  C5   C6    double  1.347  0.020  1.347
 RTL  C5   C18   single  1.502  0.020  1.502
 RTL  C6   C7    single  1.470  0.020  1.470
 RTL  C7   C8    double  1.343  0.020  1.343
 RTL  C7   H7    single  0.930  0.020  1.080
 RTL  C8   C9    single  1.454  0.020  1.454
 RTL  C8   H8    single  0.930  0.020  1.080
 RTL  C9   C10   double  1.354  0.020  1.354
 RTL  C9   C19   single  1.499  0.020  1.499
 RTL  C10  C11   single  1.440  0.020  1.440
 RTL  C10  H10   single  0.930  0.020  1.080
 RTL  C11  C12   double  1.347  0.020  1.347
 RTL  C11  H11   single  0.930  0.020  1.080
 RTL  C12  C13   single  1.457  0.020  1.457
 RTL  C12  H12   single  0.930  0.020  1.080
 RTL  C13  C14   double  1.345  0.020  1.345
 RTL  C13  C20   single  1.501  0.020  1.501
 RTL  C14  C15   single  1.492  0.020  1.492
 RTL  C14  H14   single  0.930  0.020  1.080
 RTL  C15  O1    single  1.415  0.020  1.415
 RTL  C15  H151  single  0.970  0.020  1.090
 RTL  C15  H152  single  0.970  0.020  1.090
 RTL  O1   HO1   single  0.850  0.020  0.980
 RTL  C16  H161  single  0.970  0.020  1.090
 RTL  C16  H162  single  0.970  0.020  1.090
 RTL  C16  H163  single  0.970  0.020  1.090
 RTL  C17  H171  single  0.970  0.020  1.090
 RTL  C17  H172  single  0.970  0.020  1.090
 RTL  C17  H173  single  0.970  0.020  1.090
 RTL  C18  H181  single  0.970  0.020  1.090
 RTL  C18  H182  single  0.970  0.020  1.090
 RTL  C18  H183  single  0.970  0.020  1.090
 RTL  C19  H191  single  0.970  0.020  1.090
 RTL  C19  H192  single  0.970  0.020  1.090
 RTL  C19  H193  single  0.970  0.020  1.090
 RTL  C20  H201  single  0.970  0.020  1.090
 RTL  C20  H202  single  0.970  0.020  1.090
 RTL  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
 RTL  C17   C1   C16   108.39  3.000
 RTL  C17   C1   C6    109.39  3.000
 RTL  C16   C1   C6    110.58  3.000
 RTL  C17   C1   C2    110.01  3.000
 RTL  C16   C1   C2    107.36  3.000
 RTL  C6    C1   C2    111.06  3.000
 RTL  H22   C2   H21   106.35  3.000
 RTL  H22   C2   C3    111.14  3.000
 RTL  H21   C2   C3    108.58  3.000
 RTL  H22   C2   C1    108.88  3.000
 RTL  H21   C2   C1    109.29  3.000
 RTL  C3    C2   C1    112.41  3.000
 RTL  H32   C3   H31   106.46  3.000
 RTL  H32   C3   C4    109.89  3.000
 RTL  H31   C3   C4    110.27  3.000
 RTL  H32   C3   C2    110.49  3.000
 RTL  H31   C3   C2    110.72  3.000
 RTL  C4    C3   C2    109.00  3.000
 RTL  H42   C4   H41   105.11  3.000
 RTL  H42   C4   C5    108.34  3.000
 RTL  H41   C4   C5    108.89  3.000
 RTL  H42   C4   C3    110.64  3.000
 RTL  H41   C4   C3    110.08  3.000
 RTL  C5    C4   C3    113.43  3.000
 RTL  C18   C5   C6    124.60  3.000
 RTL  C18   C5   C4    112.79  3.000
 RTL  C6    C5   C4    122.59  3.000
 RTL  C7    C6   C5    122.18  3.000
 RTL  C7    C6   C1    115.03  3.000
 RTL  C5    C6   C1    122.78  3.000
 RTL  H7    C7   C8    118.47  3.000
 RTL  H7    C7   C6    116.80  3.000
 RTL  C8    C7   C6    124.62  3.000
 RTL  H8    C8   C9    115.73  3.000
 RTL  H8    C8   C7    118.55  3.000
 RTL  C9    C8   C7    125.72  3.000
 RTL  C19   C9   C10   123.98  3.000
 RTL  C19   C9   C8    118.04  3.000
 RTL  C10   C9   C8    117.98  3.000
 RTL  H10   C10  C11   115.45  3.000
 RTL  H10   C10  C9    117.12  3.000
 RTL  C11   C10  C9    127.43  3.000
 RTL  H11   C11  C12   119.22  3.000
 RTL  H11   C11  C10   118.20  3.000
 RTL  C12   C11  C10   122.57  3.000
 RTL  H12   C12  C13   115.92  3.000
 RTL  H12   C12  C11   118.28  3.000
 RTL  C13   C12  C11   125.80  3.000
 RTL  C20   C13  C14   124.42  3.000
 RTL  C20   C13  C12   117.57  3.000
 RTL  C14   C13  C12   118.01  3.000
 RTL  H14   C14  C15   114.27  3.000
 RTL  H14   C14  C13   117.54  3.000
 RTL  C15   C14  C13   128.15  3.000
 RTL  H152  C15  H151  106.30  3.000
 RTL  H152  C15  O1    111.50  3.000
 RTL  H151  C15  O1    110.82  3.000
 RTL  H152  C15  C14   111.60  3.000
 RTL  H151  C15  C14   108.22  3.000
 RTL  O1    C15  C14   108.37  3.000
 RTL  HO1   O1   C15   107.94  3.000
 RTL  H163  C16  H162  107.70  3.000
 RTL  H163  C16  H161  108.29  3.000
 RTL  H162  C16  H161  107.00  3.000
 RTL  H163  C16  C1    111.22  3.000
 RTL  H162  C16  C1    109.66  3.000
 RTL  H161  C16  C1    112.76  3.000
 RTL  H173  C17  H172  107.84  3.000
 RTL  H173  C17  H171  107.63  3.000
 RTL  H172  C17  H171  107.51  3.000
 RTL  H173  C17  C1    110.49  3.000
 RTL  H172  C17  C1    111.91  3.000
 RTL  H171  C17  C1    111.27  3.000
 RTL  H183  C18  H182  106.24  3.000
 RTL  H183  C18  H181  107.70  3.000
 RTL  H182  C18  H181  108.24  3.000
 RTL  H183  C18  C5    111.48  3.000
 RTL  H182  C18  C5    109.49  3.000
 RTL  H181  C18  C5    113.39  3.000
 RTL  H193  C19  H192  106.64  3.000
 RTL  H193  C19  H191  107.54  3.000
 RTL  H192  C19  H191  107.51  3.000
 RTL  H193  C19  C9    110.74  3.000
 RTL  H192  C19  C9    110.89  3.000
 RTL  H191  C19  C9    113.23  3.000
 RTL  H203  C20  H202  106.78  3.000
 RTL  H203  C20  H201  107.65  3.000
 RTL  H202  C20  H201  107.42  3.000
 RTL  H203  C20  C13   110.81  3.000
 RTL  H202  C20  C13   110.87  3.000
 RTL  H201  C20  C13   113.04  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
 RTL  Var_01  C4    C3   C2   C1     62.72  30.0  1
 RTL  Var_02  C4    C5   C6   C1      5.43  30.0  1
 RTL  Var_03  C5    C6   C1   C2      9.47  30.0  1
 RTL  Var_04  C5    C4   C3   C2    -46.39  30.0  1
 RTL  Var_05  C6    C1   C2   C3    -43.56  30.0  1
 RTL  Var_06  C6    C5   C4   C3     13.84  30.0  1
 RTL  Var_07  C8    C7   C6   C1   -129.92  30.0  2
 RTL  Var_08  H161  C16  C1   C2   -170.74  30.0  3
 RTL  Var_09  H171  C17  C1   C2   -179.74  30.0  3
 RTL  Var_10  H181  C18  C5   C4   -162.49  30.0  3
 RTL  Var_11  C9    C8   C7   C6    178.42   0.0  2
 RTL  Var_12  C11   C10  C9   C8    179.33   0.0  2
 RTL  Var_13  C13   C12  C11  C10   179.73   0.0  2
 RTL  Var_14  C15   C14  C13  C12   177.48   0.0  2
 RTL  Var_15  C10   C9   C8   C7   -178.57  30.0  2
 RTL  Var_16  C12   C11  C10  C9    179.33  30.0  2
 RTL  Var_17  C14   C13  C12  C11  -178.72  30.0  2
 RTL  Var_18  O1    C15  C14  C13   130.63  30.0  3
 RTL  Var_19  H191  C19  C9   C8   -179.76  30.0  3
 RTL  Var_20  H201  C20  C13  C12   175.11  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
 RTL  plan-1  C6   0.020
 RTL  plan-1  C7   0.020
 RTL  plan-1  C8   0.020
 RTL  plan-1  C9   0.020
 RTL  plan-1  H7   0.020
 RTL  plan-1  H8   0.020
 RTL  plan-2  C8   0.020
 RTL  plan-2  C9   0.020
 RTL  plan-2  C10  0.020
 RTL  plan-2  C11  0.020
 RTL  plan-2  C19  0.020
 RTL  plan-2  H10  0.020
 RTL  plan-3  C10  0.020
 RTL  plan-3  C11  0.020
 RTL  plan-3  C12  0.020
 RTL  plan-3  C13  0.020
 RTL  plan-3  H11  0.020
 RTL  plan-3  H12  0.020
 RTL  plan-4  C12  0.020
 RTL  plan-4  C13  0.020
 RTL  plan-4  C14  0.020
 RTL  plan-4  C15  0.020
 RTL  plan-4  C20  0.020
 RTL  plan-4  H14  0.020

