# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 08:08:55 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (1R,4S,7aS)-1-[(1E)-1-formylprop-1-en-1-yl]-4-methoxy-2,4,5,6,7,7a-hexahydro-1H-isoindole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CCC[C@@H]2[C@@H](NC(=C12)C(O)=O)C(=C/C)\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
 LK7  LK7  '(1R,4S,7aS)-1-[(1E)-1-formylprop-1-en-1-yl]-4-methoxy-2,4,5,6,7,7a-hexahydro-1H-isoindole-3-carboxylic acid'  ligand  38  19  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK7
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
 LK7  C1    C  CH3   0  -0.722  -4.3270   0.8194  -1.3373
 LK7  C2    C  C1    0  -0.234  -3.7950   0.1982  -0.0988
 LK7  C3    C  C     0   0.028  -2.5628  -0.2803   0.1432
 LK7  C4    C  C1    0   0.111  -2.3689  -0.7900   1.5075
 LK7  O1    O  O     0  -0.389  -1.3410  -1.2241   1.9758
 LK7  C5    C  CR15  0  -0.145  -1.4545  -0.2888  -0.8816
 LK7  N1    N  NR15  0  -0.671  -0.6871  -1.5385  -0.8996
 LK7  C6    C  CR5   0   0.153   0.5514  -1.2926  -0.3006
 LK7  C7    C  C     0   0.471   1.4348  -2.4180   0.0533
 LK7  O2    O  O     0  -0.433   2.4846  -2.3198   0.6434
 LK7  O3    O  OH1   0  -0.598   0.9363  -3.5807  -0.3517
 LK7  C8    C  CR5   0   0.093   0.8171   0.0117  -0.1688
 LK7  C9    C  CR15  0  -0.278  -0.3591   0.7986  -0.6830
 LK7  C10   C  CH2   0  -0.422  -0.6993   1.9914   0.2066
 LK7  C11   C  CH2   0  -0.442   0.5606   2.7909   0.5250
 LK7  C12   C  CH2   0  -0.478   1.6140   1.9045   1.1801
 LK7  C13   C  CH1   0  -0.023   2.0394   0.7424   0.2782
 LK7  O4    O  O2    0  -0.494   2.6875   1.1821  -0.9080
 LK7  C14   C  CH3   0  -0.402   3.9250   1.8122  -0.6916
 LK7  H11   H  HCH3  0   0.264  -4.6329   1.8464  -1.1253
 LK7  H12   H  HCH3  0   0.252  -3.6244   0.8429  -2.1660
 LK7  H13A  H  HCH3  0   0.262  -5.2288   0.2942  -1.6577
 LK7  H2    H  H     0   0.267  -4.5124   0.1476   0.7168
 LK7  H4    H  H     0   0.190  -3.2863  -0.7450   2.1248
 LK7  H5    H  HCR5  0   0.254  -1.9146  -0.1486  -1.8598
 LK7  HN1   H  HNR5  0   0.368  -1.1874  -2.3491  -0.5645
 LK7  HO3   H  HOH1  0   0.488   1.5309  -4.3020  -0.0963
 LK7  H9    H  HCR5  0   0.260  -0.0977   1.1960  -1.6725
 LK7  H101  H  HCH2  0   0.235  -1.4457   2.6228  -0.2817
 LK7  H102  H  HCH2  0   0.222  -1.1427   1.6512   1.1460
 LK7  H111  H  HCH2  0   0.222   0.9635   3.2383  -0.3886
 LK7  H112  H  HCH2  0   0.238   0.3112   3.6213   1.1889
 LK7  H121  H  HCH2  0   0.243   2.4856   2.4923   1.4784
 LK7  H122  H  HCH2  0   0.235   1.2123   1.4780   2.1050
 LK7  H13   H  HCH1  0   0.233   2.7123   0.0865   0.8400
 LK7  H141  H  HCH3  0   0.206   3.8265   2.8116  -0.2547
 LK7  H142  H  HCH3  0   0.202   4.5794   1.2221  -0.0383
 LK7  H143  H  HCH3  0   0.235   4.4150   1.9170  -1.6597

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
 LK7  C1   C2    single  1.484  0.020  1.484
 LK7  C1   H11   single  0.970  0.020  1.090
 LK7  C1   H12   single  0.970  0.020  1.090
 LK7  C1   H13A  single  0.970  0.020  1.090
 LK7  C2   C3    double  1.344  0.020  1.344
 LK7  C2   H2    single  0.930  0.020  1.080
 LK7  C3   C4    single  1.469  0.020  1.469
 LK7  C3   C5    single  1.509  0.020  1.509
 LK7  C4   O1    double  1.210  0.020  1.210
 LK7  C4   H4    single  0.930  0.020  1.080
 LK7  C5   C9    single  1.556  0.020  1.556
 LK7  C5   N1    single  1.467  0.020  1.467
 LK7  C5   H5    single  0.970  0.020  1.090
 LK7  N1   C6    single  1.398  0.020  1.398
 LK7  N1   HN1   single  0.890  0.020  1.040
 LK7  C6   C8    double  1.338  0.020  1.338
 LK7  C6   C7    single  1.474  0.020  1.474
 LK7  C7   O2    double  1.208  0.020  1.208
 LK7  C7   O3    single  1.328  0.020  1.328
 LK7  O3   HO3   single  0.850  0.020  0.980
 LK7  C8   C13   single  1.493  0.020  1.493
 LK7  C8   C9    single  1.506  0.020  1.506
 LK7  C9   C10   single  1.526  0.020  1.526
 LK7  C9   H9    single  0.970  0.020  1.090
 LK7  C10  C11   single  1.526  0.020  1.526
 LK7  C10  H101  single  0.970  0.020  1.090
 LK7  C10  H102  single  0.970  0.020  1.090
 LK7  C11  C12   single  1.525  0.020  1.525
 LK7  C11  H111  single  0.970  0.020  1.090
 LK7  C11  H112  single  0.970  0.020  1.090
 LK7  C12  C13   single  1.531  0.020  1.531
 LK7  C12  H121  single  0.970  0.020  1.090
 LK7  C12  H122  single  0.970  0.020  1.090
 LK7  C13  O4    single  1.421  0.020  1.421
 LK7  C13  H13   single  0.970  0.020  1.090
 LK7  O4   C14   single  1.405  0.020  1.405
 LK7  C14  H141  single  0.970  0.020  1.090
 LK7  C14  H142  single  0.970  0.020  1.090
 LK7  C14  H143  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
 LK7  H13A  C1   H12   108.70  3.000
 LK7  H13A  C1   H11   106.14  3.000
 LK7  H12   C1   H11   107.98  3.000
 LK7  H13A  C1   C2    109.86  3.000
 LK7  H12   C1   C2    114.44  3.000
 LK7  H11   C1   C2    109.39  3.000
 LK7  H2    C2   C3    116.95  3.000
 LK7  H2    C2   C1    114.14  3.000
 LK7  C3    C2   C1    128.90  3.000
 LK7  C5    C3   C4    122.11  3.000
 LK7  C5    C3   C2    123.57  3.000
 LK7  C4    C3   C2    114.31  3.000
 LK7  H4    C4   O1    120.20  3.000
 LK7  H4    C4   C3    113.23  3.000
 LK7  O1    C4   C3    126.57  3.000
 LK7  H5    C5   C9    108.76  3.000
 LK7  H5    C5   N1    108.63  3.000
 LK7  C9    C5   N1    103.22  3.000
 LK7  H5    C5   C3    107.38  3.000
 LK7  N1    C5   C3    113.41  3.000
 LK7  C9    C5   C3    115.23  3.000
 LK7  HN1   N1   C6    115.99  3.000
 LK7  HN1   N1   C5    114.87  3.000
 LK7  C6    N1   C5    107.97  3.000
 LK7  C8    C6   C7    127.00  3.000
 LK7  C7    C6   N1    119.98  3.000
 LK7  C8    C6   N1    112.95  3.000
 LK7  O3    C7   O2    123.10  3.000
 LK7  O3    C7   C6    111.73  3.000
 LK7  O2    C7   C6    125.17  3.000
 LK7  HO3   O3   C7    109.94  3.000
 LK7  C13   C8   C9    119.09  3.000
 LK7  C9    C8   C6    108.71  3.000
 LK7  C13   C8   C6    132.03  3.000
 LK7  H9    C9   C10   107.19  3.000
 LK7  H9    C9   C8    108.12  3.000
 LK7  C10   C9   C8    112.55  3.000
 LK7  H9    C9   C5    107.79  3.000
 LK7  C10   C9   C5    117.61  3.000
 LK7  C8    C9   C5    103.19  3.000
 LK7  H102  C10  H101  106.67  3.000
 LK7  H102  C10  C11   108.59  3.000
 LK7  H101  C10  C11   110.76  3.000
 LK7  H102  C10  C9    110.37  3.000
 LK7  H101  C10  C9    110.07  3.000
 LK7  C11   C10  C9    110.31  3.000
 LK7  H112  C11  H111  106.31  3.000
 LK7  H112  C11  C12   109.79  3.000
 LK7  H111  C11  C12   110.01  3.000
 LK7  H112  C11  C10   109.68  3.000
 LK7  H111  C11  C10   110.13  3.000
 LK7  C12   C11  C10   110.82  3.000
 LK7  H122  C12  H121  105.76  3.000
 LK7  H122  C12  C13   107.69  3.000
 LK7  H121  C12  C13   110.33  3.000
 LK7  H122  C12  C11   109.63  3.000
 LK7  H121  C12  C11   110.83  3.000
 LK7  C13   C12  C11   112.34  3.000
 LK7  H13   C13  O4    109.47  3.000
 LK7  H13   C13  C12   108.86  3.000
 LK7  O4    C13  C12   112.55  3.000
 LK7  H13   C13  C8    111.33  3.000
 LK7  O4    C13  C8    105.96  3.000
 LK7  C12   C13  C8    108.68  3.000
 LK7  C14   O4   C13   114.31  3.000
 LK7  H143  C14  H142  108.21  3.000
 LK7  H143  C14  H141  107.88  3.000
 LK7  H142  C14  H141  107.88  3.000
 LK7  H143  C14  O4    107.59  3.000
 LK7  H142  C14  O4    112.07  3.000
 LK7  H141  C14  O4    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
 LK7  CONST_01  HO3   O3   C7   C6    180.00   0.0  0
 LK7  Var_01    C8    C6   N1   C5    -14.41  30.0  1
 LK7  Var_02    C13   C8   C6   N1   -173.21  30.0  1
 LK7  Var_03    C12   C11  C10  C9    -56.70  30.0  1
 LK7  Var_04    C13   C12  C11  C10    60.46  30.0  1
 LK7  Var_05    O2    C7   C6   N1   -175.35  30.0  2
 LK7  Var_06    C5    C3   C2   C1     -1.33   0.0  2
 LK7  Var_07    H141  C14  O4   C13   -72.46  30.0  3
 LK7  Var_08    H11   C1   C2   C3   -118.31  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
 LK7  chir_01  C5   C3  C9  N1   negativ
 LK7  chir_02  C9   C5  C8  C10  positiv
 LK7  chir_03  C13  O4  C8  C12  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
 LK7  plan-1  C5   0.020
 LK7  plan-1  N1   0.020
 LK7  plan-1  C6   0.020
 LK7  plan-1  HN1  0.020
 LK7  plan-2  C6   0.020
 LK7  plan-2  C7   0.020
 LK7  plan-2  O2   0.020
 LK7  plan-2  O3   0.020
 LK7  plan-2  HO3  0.020
 LK7  plan-3  C1   0.020
 LK7  plan-3  C2   0.020
 LK7  plan-3  C3   0.020
 LK7  plan-3  C4   0.020
 LK7  plan-3  C5   0.020
 LK7  plan-3  H2   0.020
 LK7  plan-4  C3   0.020
 LK7  plan-4  C4   0.020
 LK7  plan-4  O1   0.020
 LK7  plan-4  H4   0.020

