# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 20:33:34 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  48  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   6.6822  -1.2997  -1.8910
 LK5  C3    C  CH2    0  -0.429   5.8693  -1.0462  -0.6289
 LK5  C4    C  CH2    0  -0.450   4.4056  -0.7439  -0.9261
 LK5  C5    C  CH2    0  -0.118   3.6050  -0.4913   0.3373
 LK5  O4    O  O2     0  -0.507   2.2634  -0.2456  -0.0073
 LK5  C6    C  CH1    0  -0.003   1.4809   0.3451   1.0217
 LK5  C7    C  CH2    0  -0.474   1.2853  -0.5927   2.2219
 LK5  C8    C  CH2    0  -0.437   0.4555  -1.8246   1.8670
 LK5  C9    C  CH2    0  -0.423  -0.9032  -1.4571   1.2682
 LK5  C10   C  CR15   0  -0.286  -0.7019  -0.5757   0.0285
 LK5  C11   C  CR5    0  -0.026   0.1349   0.6113   0.4466
 LK5  C12   C  CR5    0   0.108  -0.6553   1.6918   0.5278
 LK5  C13   C  C      0   0.357  -0.3411   3.1078   0.9604
 LK5  O3    O  O      0  -0.579   0.7513   3.3152   1.5205
 LK5  O2    O  OC    -1  -0.601  -1.2182   3.9534   0.6931
 LK5  N1    N  NR15   0  -0.663  -1.9722   1.3958   0.1572
 LK5  C14   C  CR15   0  -0.033  -1.9438   0.1271  -0.5568
 LK5  C15   C  CH1    0  -0.386  -3.2651  -0.6423  -0.4622
 LK5  C16   C  CH2    0  -0.432  -4.4457   0.2114  -0.9517
 LK5  C2    C  CH3    0  -0.669  -5.7896  -0.5003  -0.8694
 LK5  C17   C  C1     0   0.198  -3.1643  -1.8567  -1.3374
 LK5  O1    O  O      0  -0.379  -3.3201  -3.0002  -0.9858
 LK5  H11   H  HCH3   0   0.227   7.7290  -1.4971  -1.6585
 LK5  H12   H  HCH3   0   0.217   6.2977  -2.1593  -2.4430
 LK5  H13   H  HCH3   0   0.217   6.6480  -0.4377  -2.5593
 LK5  H31   H  HCH2   0   0.215   5.9359  -1.9164   0.0311
 LK5  H32   H  HCH2   0   0.215   6.3092  -0.2110  -0.0757
 LK5  H41   H  HCH2   0   0.216   4.3374   0.1305  -1.5810
 LK5  H42   H  HCH2   0   0.217   3.9631  -1.5829  -1.4728
 LK5  H51   H  HCH2   0   0.189   3.6941  -1.3597   1.0050
 LK5  H52   H  HCH2   0   0.186   4.0283   0.3673   0.8804
 LK5  H6    H  HCH1   0   0.227   1.9530   1.2735   1.3581
 LK5  H71   H  HCH2   0   0.233   2.2473  -0.8906   2.6497
 LK5  H72   H  HCH2   0   0.227   0.7745  -0.0172   3.0000
 LK5  H81   H  HCH2   0   0.215   1.0066  -2.4464   1.1538
 LK5  H82   H  HCH2   0   0.230   0.3118  -2.4386   2.7593
 LK5  H91   H  HCH2   0   0.227  -1.4512  -2.3700   1.0209
 LK5  H92   H  HCH2   0   0.216  -1.4994  -0.9196   2.0137
 LK5  H10   H  HCR5   0   0.237  -0.2157  -1.1846  -0.7411
 LK5  HN1   H  HNR5   0   0.355  -2.4401   2.1548  -0.3159
 LK5  H14   H  HCR5   0   0.224  -1.7383   0.3119  -1.6247
 LK5  H15   H  HCH1   0   0.254  -3.4508  -0.9524   0.5697
 LK5  H161  H  HCH2   0   0.246  -4.4816   1.1129  -0.3376
 LK5  H162  H  HCH2   0   0.227  -4.2577   0.5423  -1.9784
 LK5  H21   H  HCH3   0   0.226  -5.9842  -0.8575   0.1432
 LK5  H22   H  HCH3   0   0.238  -6.5988   0.1775  -1.1416
 LK5  H23   H  HCH3   0   0.225  -5.8477  -1.3591  -1.5400
 LK5  H17   H  H      0   0.185  -2.9378  -1.6234  -2.3973

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  1.517  0.020  1.517
 LK5  C4   H41   single  0.970  0.020  1.090
 LK5  C4   H42   single  0.970  0.020  1.090
 LK5  C5   O4    single  1.407  0.020  1.407
 LK5  C5   H51   single  0.970  0.020  1.090
 LK5  C5   H52   single  0.970  0.020  1.090
 LK5  O4   C6    single  1.421  0.020  1.421
 LK5  C6   C7    single  1.536  0.020  1.536
 LK5  C6   C11   single  1.488  0.020  1.488
 LK5  C6   H6    single  0.970  0.020  1.090
 LK5  C7   C8    single  1.527  0.020  1.527
 LK5  C7   H71   single  0.970  0.020  1.090
 LK5  C7   H72   single  0.970  0.020  1.090
 LK5  C8   C9    single  1.530  0.020  1.530
 LK5  C8   H81   single  0.970  0.020  1.090
 LK5  C8   H82   single  0.970  0.020  1.090
 LK5  C9   C10   single  1.534  0.020  1.534
 LK5  C9   H91   single  0.970  0.020  1.090
 LK5  C9   H92   single  0.970  0.020  1.090
 LK5  C10  C14   single  1.542  0.020  1.542
 LK5  C10  C11   single  1.511  0.020  1.511
 LK5  C10  H10   single  0.970  0.020  1.090
 LK5  C11  C12   double  1.341  0.020  1.341
 LK5  C12  N1    single  1.400  0.020  1.400
 LK5  C12  C13   single  1.514  0.020  1.514
 LK5  C13  O3    deloc   1.245  0.020  1.245
 LK5  C13  O2    deloc   1.247  0.020  1.247
 LK5  N1   C14   single  1.456  0.020  1.456
 LK5  N1   HN1   single  0.890  0.020  1.040
 LK5  C14  C15   single  1.532  0.020  1.532
 LK5  C14  H14   single  0.970  0.020  1.090
 LK5  C15  C17   single  1.500  0.020  1.500
 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  1.207  0.020  1.207
 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   107.54  3.000
 LK5  H13   C1   H11   107.68  3.000
 LK5  H12   C1   H11   107.67  3.000
 LK5  H13   C1   C3    111.06  3.000
 LK5  H12   C1   C3    111.24  3.000
 LK5  H11   C1   C3    111.47  3.000
 LK5  H32   C3   H31   106.12  3.000
 LK5  H32   C3   C4    109.47  3.000
 LK5  H31   C3   C4    109.50  3.000
 LK5  H32   C3   C1    109.37  3.000
 LK5  H31   C3   C1    109.58  3.000
 LK5  C4    C3   C1    112.60  3.000
 LK5  H42   C4   H41   106.75  3.000
 LK5  H42   C4   C5    109.28  3.000
 LK5  H41   C4   C5    109.41  3.000
 LK5  H42   C4   C3    109.48  3.000
 LK5  H41   C4   C3    109.58  3.000
 LK5  C5    C4   C3    112.19  3.000
 LK5  H52   C5   H51   106.58  3.000
 LK5  H52   C5   O4    110.58  3.000
 LK5  H51   C5   O4    111.36  3.000
 LK5  H52   C5   C4    109.75  3.000
 LK5  H51   C5   C4    109.36  3.000
 LK5  O4    C5   C4    109.17  3.000
 LK5  C6    O4   C5    114.85  3.000
 LK5  H6    C6   C11   110.93  3.000
 LK5  H6    C6   C7    109.44  3.000
 LK5  C11   C6   C7    107.23  3.000
 LK5  H6    C6   O4    109.73  3.000
 LK5  C11   C6   O4    107.01  3.000
 LK5  C7    C6   O4    112.47  3.000
 LK5  H72   C7   H71   106.00  3.000
 LK5  H72   C7   C8    109.62  3.000
 LK5  H71   C7   C8    110.42  3.000
 LK5  H72   C7   C6    107.09  3.000
 LK5  H71   C7   C6    111.09  3.000
 LK5  C8    C7   C6    112.35  3.000
 LK5  H82   C8   H81   106.20  3.000
 LK5  H82   C8   C9    109.75  3.000
 LK5  H81   C8   C9    109.17  3.000
 LK5  H82   C8   C7    109.57  3.000
 LK5  H81   C8   C7    109.63  3.000
 LK5  C9    C8   C7    112.33  3.000
 LK5  H92   C9   H91   106.92  3.000
 LK5  H92   C9   C10   109.84  3.000
 LK5  H91   C9   C10   111.27  3.000
 LK5  H92   C9   C8    109.56  3.000
 LK5  H91   C9   C8    109.47  3.000
 LK5  C10   C9   C8    109.74  3.000
 LK5  H10   C10  C14   110.13  3.000
 LK5  H10   C10  C11   112.66  3.000
 LK5  C14   C10  C11   101.13  3.000
 LK5  H10   C10  C9    107.85  3.000
 LK5  C11   C10  C9    107.48  3.000
 LK5  C14   C10  C9    117.56  3.000
 LK5  C12   C11  C10   108.86  3.000
 LK5  C12   C11  C6    130.83  3.000
 LK5  C10   C11  C6    117.87  3.000
 LK5  N1    C12  C13   117.96  3.000
 LK5  C13   C12  C11   130.45  3.000
 LK5  N1    C12  C11   111.59  3.000
 LK5  O2    C13  O3    126.90  3.000
 LK5  O2    C13  C12   115.28  3.000
 LK5  O3    C13  C12   117.81  3.000
 LK5  HN1   N1   C14   115.75  3.000
 LK5  HN1   N1   C12   113.65  3.000
 LK5  C14   N1   C12   107.20  3.000
 LK5  H14   C14  C15   107.73  3.000
 LK5  H14   C14  N1    109.41  3.000
 LK5  C15   C14  N1    112.98  3.000
 LK5  H14   C14  C10   107.08  3.000
 LK5  C15   C14  C10   116.25  3.000
 LK5  N1    C14  C10   103.10  3.000
 LK5  H15   C15  C17   109.42  3.000
 LK5  H15   C15  C16   109.13  3.000
 LK5  C17   C15  C16   108.39  3.000
 LK5  H15   C15  C14   110.31  3.000
 LK5  C16   C15  C14   111.34  3.000
 LK5  C17   C15  C14   108.21  3.000
 LK5  H162  C16  H161  106.47  3.000
 LK5  H162  C16  C2    110.09  3.000
 LK5  H161  C16  C2    109.06  3.000
 LK5  H162  C16  C15   109.54  3.000
 LK5  H161  C16  C15   107.75  3.000
 LK5  C2    C16  C15   113.65  3.000
 LK5  H23   C2   H22   107.24  3.000
 LK5  H23   C2   H21   107.64  3.000
 LK5  H22   C2   H21   107.63  3.000
 LK5  H23   C2   C16   112.43  3.000
 LK5  H22   C2   C16   110.54  3.000
 LK5  H21   C2   C16   111.14  3.000
 LK5  H17   C17  O1    120.30  3.000
 LK5  H17   C17  C15   113.65  3.000
 LK5  O1    C17  C15   126.05  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  Var_01  C9   C8   C7   C6    -55.55  30.0  1
 LK5  Var_02  N1   C12  C11  C6   -163.66  30.0  1
 LK5  Var_03  C10  C9   C8   C7     56.92  30.0  1
 LK5  Var_04  C14  N1   C12  C11   -16.42  30.0  1
 LK5  Var_05  O3   C13  C12  C11   -12.08  30.0  2
 LK5  Var_06  H51  C5   O4   C6     74.92  30.0  1
 LK5  Var_07  C5   C4   C3   C1   -179.93  30.0  3
 LK5  Var_08  O4   C5   C4   C3   -178.86  30.0  3
 LK5  Var_09  H11  C1   C3   C4    179.03  30.0  3
 LK5  Var_10  H21  C2   C16  C15    55.42  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-3  C15  0.020
 LK5  plan-3  C17  0.020
 LK5  plan-3  O1   0.020
 LK5  plan-3  H17  0.020

