# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 01:06:05 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (1S,4R,7aR)-4-butoxy-1-[(1R)-1-formylpropyl]-2,4,5,6,7,7a-hexahydro-1H-isoindole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCO[C@@H]1CCC[C@H]2[C@H](NC(=C12)C(O)=O)[C@@H](CC)C=O
#
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
 LK5  LK5  '(1S,4R,7aR)-4-butoxy-1-[(1R)-1-formylpropyl]-2,4,5,6,7,7a-hexahydro-1H-isoindole-3-carboxylic acid'  ligand  49  22  .  2021-08-12  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK5
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
 LK5  C1    C  CH3   0  -0.660   6.6503  -1.3827  -1.8992
 LK5  C3    C  CH2   0  -0.429   5.8397  -1.0941  -0.6433
 LK5  C4    C  CH2   0  -0.451   4.3836  -0.7655  -0.9498
 LK5  C5    C  CH2   0  -0.125   3.5889  -0.4767   0.3088
 LK5  O4    O  O2    0  -0.502   2.2491  -0.2115  -0.0416
 LK5  C6    C  CH1   0  -0.010   1.4865   0.4136   0.9730
 LK5  C7    C  CH2   0  -0.480   1.2730  -0.4846   2.2006
 LK5  C8    C  CH2   0  -0.440   0.4412  -1.7217   1.8763
 LK5  C9    C  CH2   0  -0.430  -0.9099  -1.3586   1.2615
 LK5  C10   C  CR15  0  -0.299  -0.6990  -0.5177  -0.0066
 LK5  C11   C  CR5   0   0.037   0.1405   0.6720   0.3852
 LK5  C12   C  CR5   0   0.154  -0.6550   1.7504   0.4262
 LK5  C13   C  C     0   0.480  -0.2922   3.1018   0.8940
 LK5  O3    O  O     0  -0.432   0.8342   3.4764   1.1171
 LK5  O2    O  OH1   0  -0.595  -1.3596   3.8780   1.0333
 LK5  N1    N  NR15  0  -0.673  -1.9774   1.4615   0.0607
 LK5  C14   C  CR15  0  -0.041  -1.9379   0.1662  -0.6164
 LK5  C15   C  CH1   0  -0.389  -3.2591  -0.5984  -0.5026
 LK5  C16   C  CH2   0  -0.434  -4.4351   0.2359  -1.0359
 LK5  C2    C  CH3   0  -0.669  -5.7777  -0.4766  -0.9421
 LK5  C17   C  C1    0   0.197  -3.1529  -1.8468  -1.3307
 LK5  O1    O  O     0  -0.375  -3.3177  -2.9735  -0.9337
 LK5  H11   H  HCH3  0   0.228   7.6922  -1.5975  -1.6603
 LK5  H12   H  HCH3  0   0.217   6.2503  -2.2430  -2.4390
 LK5  H13   H  HCH3  0   0.218   6.6352  -0.5304  -2.5806
 LK5  H31   H  HCH2  0   0.217   5.8864  -1.9564   0.0286
 LK5  H32   H  HCH2  0   0.216   6.2954  -0.2605  -0.1005
 LK5  H41   H  HCH2  0   0.219   4.3346   0.1002  -1.6177
 LK5  H42   H  HCH2  0   0.219   3.9245  -1.6038  -1.4838
 LK5  H51   H  HCH2  0   0.197   3.6579  -1.3347   0.9909
 LK5  H52   H  HCH2  0   0.193   4.0252   0.3838   0.8370
 LK5  H6    H  HCH1  0   0.239   1.9795   1.3392   1.2873
 LK5  H71   H  HCH2  0   0.247   2.2342  -0.7693   2.6370
 LK5  H72   H  HCH2  0   0.236   0.7621   0.1154   2.9598
 LK5  H81   H  HCH2  0   0.223   0.9911  -2.3677   1.1849
 LK5  H82   H  HCH2  0   0.239   0.2864  -2.3056   2.7861
 LK5  H91   H  HCH2  0   0.240  -1.4659  -2.2702   1.0329
 LK5  H92   H  HCH2  0   0.226  -1.5051  -0.7951   1.9880
 LK5  H10   H  HCR5  0   0.262  -0.2037  -1.1457  -0.7529
 LK5  HO2   H  HOH1  0   0.489  -1.0894   4.7615   1.3263
 LK5  HN1   H  HNR5  0   0.374  -2.4340   2.1852  -0.4766
 LK5  H14   H  HCR5  0   0.244  -1.7285   0.3254  -1.6860
 LK5  H15   H  HCH1  0   0.260  -3.4535  -0.8680   0.5388
 LK5  H161  H  HCH2  0   0.248  -4.4815   1.1592  -0.4558
 LK5  H162  H  HCH2  0   0.231  -4.2363   0.5283  -2.0722
 LK5  H21   H  HCH3  0   0.227  -5.9803  -0.8015   0.0796
 LK5  H22   H  HCH3  0   0.240  -6.5853   0.1906  -1.2431
 LK5  H23   H  HCH3  0   0.226  -5.8279  -1.3561  -1.5859
 LK5  H17   H  H     0   0.190  -2.9161  -1.6570  -2.3967

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
 LK5  C1   C3    single  1.522  0.020  1.522
 LK5  C1   H11   single  0.970  0.020  1.090
 LK5  C1   H12   single  0.970  0.020  1.090
 LK5  C1   H13   single  0.970  0.020  1.090
 LK5  C3   C4    single  1.524  0.020  1.524
 LK5  C3   H31   single  0.970  0.020  1.090
 LK5  C3   H32   single  0.970  0.020  1.090
 LK5  C4   C5    single  1.516  0.020  1.516
 LK5  C4   H41   single  0.970  0.020  1.090
 LK5  C4   H42   single  0.970  0.020  1.090
 LK5  C5   O4    single  1.410  0.020  1.410
 LK5  C5   H51   single  0.970  0.020  1.090
 LK5  C5   H52   single  0.970  0.020  1.090
 LK5  O4   C6    single  1.415  0.020  1.415
 LK5  C6   C7    single  1.536  0.020  1.536
 LK5  C6   C11   single  1.491  0.020  1.491
 LK5  C6   H6    single  0.970  0.020  1.090
 LK5  C7   C8    single  1.526  0.020  1.526
 LK5  C7   H71   single  0.970  0.020  1.090
 LK5  C7   H72   single  0.970  0.020  1.090
 LK5  C8   C9    single  1.528  0.020  1.528
 LK5  C8   H81   single  0.970  0.020  1.090
 LK5  C8   H82   single  0.970  0.020  1.090
 LK5  C9   C10   single  1.536  0.020  1.536
 LK5  C9   H91   single  0.970  0.020  1.090
 LK5  C9   H92   single  0.970  0.020  1.090
 LK5  C10  C14   single  1.541  0.020  1.541
 LK5  C10  C11   single  1.508  0.020  1.508
 LK5  C10  H10   single  0.970  0.020  1.090
 LK5  C11  C12   double  1.341  0.020  1.341
 LK5  C12  N1    single  1.402  0.020  1.402
 LK5  C12  C13   single  1.475  0.020  1.475
 LK5  C13  O3    double  1.208  0.020  1.208
 LK5  C13  O2    single  1.327  0.020  1.327
 LK5  O2   HO2   single  0.850  0.020  0.980
 LK5  N1   C14   single  1.462  0.020  1.462
 LK5  N1   HN1   single  0.890  0.020  1.040
 LK5  C14  C15   single  1.531  0.020  1.531
 LK5  C14  H14   single  0.970  0.020  1.090
 LK5  C15  C17   single  1.502  0.020  1.502
 LK5  C15  C16   single  1.537  0.020  1.537
 LK5  C15  H15   single  0.970  0.020  1.090
 LK5  C16  C2    single  1.523  0.020  1.523
 LK5  C16  H161  single  0.970  0.020  1.090
 LK5  C16  H162  single  0.970  0.020  1.090
 LK5  C2   H21   single  0.970  0.020  1.090
 LK5  C2   H22   single  0.970  0.020  1.090
 LK5  C2   H23   single  0.970  0.020  1.090
 LK5  C17  O1    double  1.206  0.020  1.206
 LK5  C17  H17   single  0.930  0.020  1.080

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
 LK5  H13   C1   H12   107.56  3.000
 LK5  H13   C1   H11   107.70  3.000
 LK5  H12   C1   H11   107.65  3.000
 LK5  H13   C1   C3    111.08  3.000
 LK5  H12   C1   C3    111.24  3.000
 LK5  H11   C1   C3    111.43  3.000
 LK5  H32   C3   H31   106.14  3.000
 LK5  H32   C3   C4    109.48  3.000
 LK5  H31   C3   C4    109.53  3.000
 LK5  H32   C3   C1    109.38  3.000
 LK5  H31   C3   C1    109.54  3.000
 LK5  C4    C3   C1    112.57  3.000
 LK5  H42   C4   H41   106.81  3.000
 LK5  H42   C4   C5    109.33  3.000
 LK5  H41   C4   C5    109.42  3.000
 LK5  H42   C4   C3    109.49  3.000
 LK5  H41   C4   C3    109.64  3.000
 LK5  C5    C4   C3    112.02  3.000
 LK5  H52   C5   H51   106.73  3.000
 LK5  H52   C5   O4    110.43  3.000
 LK5  H51   C5   O4    111.16  3.000
 LK5  H52   C5   C4    109.86  3.000
 LK5  H51   C5   C4    109.51  3.000
 LK5  O4    C5   C4    109.12  3.000
 LK5  C6    O4   C5    114.65  3.000
 LK5  H6    C6   C11   111.90  3.000
 LK5  H6    C6   C7    109.12  3.000
 LK5  C11   C6   C7    106.91  3.000
 LK5  H6    C6   O4    109.67  3.000
 LK5  C11   C6   O4    106.29  3.000
 LK5  C7    C6   O4    112.93  3.000
 LK5  H72   C7   H71   106.04  3.000
 LK5  H72   C7   C8    109.73  3.000
 LK5  H71   C7   C8    110.68  3.000
 LK5  H72   C7   C6    107.38  3.000
 LK5  H71   C7   C6    110.43  3.000
 LK5  C8    C7   C6    112.34  3.000
 LK5  H82   C8   H81   106.38  3.000
 LK5  H82   C8   C9    109.69  3.000
 LK5  H81   C8   C9    109.29  3.000
 LK5  H82   C8   C7    109.49  3.000
 LK5  H81   C8   C7    109.81  3.000
 LK5  C9    C8   C7    112.02  3.000
 LK5  H92   C9   H91   106.96  3.000
 LK5  H92   C9   C10   109.91  3.000
 LK5  H91   C9   C10   110.74  3.000
 LK5  H92   C9   C8    109.62  3.000
 LK5  H91   C9   C8    109.64  3.000
 LK5  C10   C9   C8    109.92  3.000
 LK5  H10   C10  C14   110.42  3.000
 LK5  H10   C10  C11   112.22  3.000
 LK5  C14   C10  C11   101.55  3.000
 LK5  H10   C10  C9    108.12  3.000
 LK5  C11   C10  C9    107.09  3.000
 LK5  C14   C10  C9    117.34  3.000
 LK5  C12   C11  C10   108.20  3.000
 LK5  C12   C11  C6    131.52  3.000
 LK5  C10   C11  C6    117.92  3.000
 LK5  N1    C12  C13   120.22  3.000
 LK5  C13   C12  C11   126.91  3.000
 LK5  N1    C12  C11   112.70  3.000
 LK5  O2    C13  O3    123.31  3.000
 LK5  O2    C13  C12   111.80  3.000
 LK5  O3    C13  C12   124.89  3.000
 LK5  HO2   O2   C13   109.92  3.000
 LK5  HN1   N1   C14   113.61  3.000
 LK5  HN1   N1   C12   114.67  3.000
 LK5  C14   N1   C12   106.13  3.000
 LK5  H14   C14  C15   107.96  3.000
 LK5  H14   C14  N1    109.08  3.000
 LK5  C15   C14  N1    112.63  3.000
 LK5  H14   C14  C10   107.19  3.000
 LK5  C15   C14  C10   116.28  3.000
 LK5  N1    C14  C10   103.39  3.000
 LK5  H15   C15  C17   109.44  3.000
 LK5  H15   C15  C16   109.17  3.000
 LK5  C17   C15  C16   108.29  3.000
 LK5  H15   C15  C14   110.33  3.000
 LK5  C16   C15  C14   111.31  3.000
 LK5  C17   C15  C14   108.25  3.000
 LK5  H162  C16  H161  106.55  3.000
 LK5  H162  C16  C2    110.08  3.000
 LK5  H161  C16  C2    109.00  3.000
 LK5  H162  C16  C15   109.53  3.000
 LK5  H161  C16  C15   107.89  3.000
 LK5  C2    C16  C15   113.53  3.000
 LK5  H23   C2   H22   107.24  3.000
 LK5  H23   C2   H21   107.69  3.000
 LK5  H22   C2   H21   107.66  3.000
 LK5  H23   C2   C16   112.41  3.000
 LK5  H22   C2   C16   110.48  3.000
 LK5  H21   C2   C16   111.15  3.000
 LK5  H17   C17  O1    120.39  3.000
 LK5  H17   C17  C15   113.76  3.000
 LK5  O1    C17  C15   125.84  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
 LK5  CONST_01  HO2  O2   C13  C12   180.00   0.0  0
 LK5  Var_01    C9   C8   C7   C6    -55.95  30.0  1
 LK5  Var_02    N1   C12  C11  C6   -163.57  30.0  1
 LK5  Var_03    C10  C9   C8   C7     57.28  30.0  1
 LK5  Var_04    C14  N1   C12  C11   -16.44  30.0  1
 LK5  Var_05    O3   C13  C12  C11    11.92  30.0  2
 LK5  Var_06    H51  C5   O4   C6     75.17  30.0  2
 LK5  Var_07    C5   C4   C3   C1   -179.85  30.0  3
 LK5  Var_08    O4   C5   C4   C3   -178.67  30.0  3
 LK5  Var_09    H11  C1   C3   C4    178.97  30.0  3
 LK5  Var_10    H21  C2   C16  C15    55.17  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
 LK5  chir_01  C6   O4   C7   C11  positiv
 LK5  chir_02  C10  C11  C14  C9   positiv
 LK5  chir_03  C14  N1   C10  C15  negativ
 LK5  chir_04  C15  C14  C17  C16  positiv

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
 LK5  plan-1  C12  0.020
 LK5  plan-1  N1   0.020
 LK5  plan-1  C14  0.020
 LK5  plan-1  HN1  0.020
 LK5  plan-2  C12  0.020
 LK5  plan-2  C13  0.020
 LK5  plan-2  O3   0.020
 LK5  plan-2  O2   0.020
 LK5  plan-2  HO2  0.020
 LK5  plan-3  C15  0.020
 LK5  plan-3  C17  0.020
 LK5  plan-3  O1   0.020
 LK5  plan-3  H17  0.020

