# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 14:40:49 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  37  19  .  2021-08-12  2021-08-12  
;
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  -0.721  -4.3625   0.8939  -1.3509
 LK7  C2    C  C1     0  -0.241  -3.8330   0.2528  -0.1206
 LK7  C3    C  C      0   0.031  -2.6043  -0.2400   0.1124
 LK7  C4    C  C1     0   0.108  -2.4204  -0.7626   1.4742
 LK7  O1    O  O      0  -0.385  -1.4009  -1.2040   1.9517
 LK7  C5    C  CR15   0  -0.135  -1.4998  -0.2540  -0.9177
 LK7  N1    N  NR15   0  -0.661  -0.7323  -1.4966  -0.9404
 LK7  C6    C  CR5    0   0.106   0.5147  -1.2742  -0.3566
 LK7  C7    C  C      0   0.346   1.3316  -2.4873   0.0284
 LK7  O2    O  O      0  -0.583   2.4797  -2.2996   0.4739
 LK7  O3    O  OC    -1  -0.603   0.7635  -3.5872  -0.1294
 LK7  C8    C  CR5    0   0.041   0.7833   0.0321  -0.2387
 LK7  C9    C  CR15   0  -0.270  -0.3984   0.8323  -0.7326
 LK7  C10   C  CH2    0  -0.418  -0.7244   2.0155   0.1738
 LK7  C11   C  CH2    0  -0.439   0.5429   2.8083   0.4818
 LK7  C12   C  CH2    0  -0.470   1.5991   1.9142   1.1234
 LK7  C13   C  CH1    0  -0.020   2.0057   0.7491   0.2163
 LK7  O4    O  O2     0  -0.499   2.6840   1.2015  -0.9566
 LK7  C14   C  CH3    0  -0.398   3.9357   1.7864  -0.7133
 LK7  H11   H  HCH3   0   0.261  -4.6562   1.9222  -1.1277
 LK7  H12   H  HCH3   0   0.251  -3.6611   0.9187  -2.1806
 LK7  H13A  H  HCH3   0   0.259  -5.2708   0.3827  -1.6756
 LK7  H2    H  H      0   0.263  -4.5502   0.1997   0.6952
 LK7  H4    H  H      0   0.183  -3.3443  -0.7181   2.0835
 LK7  H5    H  HCR5   0   0.236  -1.9723  -0.1107  -1.8908
 LK7  HN1   H  HNR5   0   0.350  -1.2032  -2.3314  -0.6253
 LK7  H9    H  HCR5   0   0.231  -0.1661   1.2442  -1.7249
 LK7  H101  H  HCH2   0   0.223  -1.4782   2.6572  -0.2912
 LK7  H102  H  HCH2   0   0.213  -1.1506   1.6646   1.1178
 LK7  H111  H  HCH2   0   0.215   0.9394   3.2530  -0.4363
 LK7  H112  H  HCH2   0   0.229   0.3058   3.6411   1.1481
 LK7  H121  H  HCH2   0   0.231   2.4735   2.5012   1.4176
 LK7  H122  H  HCH2   0   0.224   1.2012   1.4892   2.0508
 LK7  H13   H  HCH1   0   0.218   2.6630   0.0709   0.7695
 LK7  H141  H  HCH3   0   0.200   3.8669   2.7825  -0.2613
 LK7  H142  H  HCH3   0   0.195   4.5627   1.1667  -0.0595
 LK7  H143  H  HCH3   0   0.229   4.4469   1.8917  -1.6711

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  1.485  0.020  1.485
 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  1.470  0.020  1.470
 LK7  C3   C5    single  1.510  0.020  1.510
 LK7  C4   O1    double  1.209  0.020  1.209
 LK7  C4   H4    single  0.930  0.020  1.080
 LK7  C5   C9    single  1.558  0.020  1.558
 LK7  C5   N1    single  1.461  0.020  1.461
 LK7  C5   H5    single  0.970  0.020  1.090
 LK7  N1   C6    single  1.395  0.020  1.395
 LK7  N1   HN1   single  0.890  0.020  1.040
 LK7  C6   C8    double  1.339  0.020  1.339
 LK7  C6   C7    single  1.512  0.020  1.512
 LK7  C7   O2    deloc   1.246  0.020  1.246
 LK7  C7   O3    deloc   1.248  0.020  1.248
 LK7  C8   C13   single  1.488  0.020  1.488
 LK7  C8   C9    single  1.510  0.020  1.510
 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  1.532  0.020  1.532
 LK7  C12  H121  single  0.970  0.020  1.090
 LK7  C12  H122  single  0.970  0.020  1.090
 LK7  C13  O4    single  1.428  0.020  1.428
 LK7  C13  H13   single  0.970  0.020  1.090
 LK7  O4   C14   single  1.403  0.020  1.403
 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   106.13  3.000
 LK7  H12   C1   H11   107.94  3.000
 LK7  H13A  C1   C2    109.94  3.000
 LK7  H12   C1   C2    114.35  3.000
 LK7  H11   C1   C2    109.45  3.000
 LK7  H2    C2   C3    117.06  3.000
 LK7  H2    C2   C1    114.04  3.000
 LK7  C3    C2   C1    128.89  3.000
 LK7  C5    C3   C4    122.48  3.000
 LK7  C5    C3   C2    123.62  3.000
 LK7  C4    C3   C2    113.90  3.000
 LK7  H4    C4   O1    120.05  3.000
 LK7  H4    C4   C3    113.01  3.000
 LK7  O1    C4   C3    126.94  3.000
 LK7  H5    C5   C9    108.69  3.000
 LK7  H5    C5   N1    108.99  3.000
 LK7  C9    C5   N1    102.91  3.000
 LK7  H5    C5   C3    106.88  3.000
 LK7  N1    C5   C3    113.75  3.000
 LK7  C9    C5   C3    115.43  3.000
 LK7  HN1   N1   C6    114.74  3.000
 LK7  HN1   N1   C5    116.98  3.000
 LK7  C6    N1   C5    109.13  3.000
 LK7  C8    C6   C7    130.68  3.000
 LK7  C7    C6   N1    117.49  3.000
 LK7  C8    C6   N1    111.83  3.000
 LK7  O3    C7   O2    126.70  3.000
 LK7  O3    C7   C6    115.40  3.000
 LK7  O2    C7   C6    117.90  3.000
 LK7  C13   C8   C9    119.17  3.000
 LK7  C9    C8   C6    109.34  3.000
 LK7  C13   C8   C6    131.43  3.000
 LK7  H9    C9   C10   106.91  3.000
 LK7  H9    C9   C8    109.18  3.000
 LK7  C10   C9   C8    112.57  3.000
 LK7  H9    C9   C5    107.67  3.000
 LK7  C10   C9   C5    117.40  3.000
 LK7  C8    C9   C5    102.86  3.000
 LK7  H102  C10  H101  106.66  3.000
 LK7  H102  C10  C11   108.43  3.000
 LK7  H101  C10  C11   110.68  3.000
 LK7  H102  C10  C9    110.33  3.000
 LK7  H101  C10  C9    110.47  3.000
 LK7  C11   C10  C9    110.20  3.000
 LK7  H112  C11  H111  106.29  3.000
 LK7  H112  C11  C12   109.91  3.000
 LK7  H111  C11  C12   109.89  3.000
 LK7  H112  C11  C10   109.81  3.000
 LK7  H111  C11  C10   110.04  3.000
 LK7  C12   C11  C10   110.81  3.000
 LK7  H122  C12  H121  105.73  3.000
 LK7  H122  C12  C13   107.63  3.000
 LK7  H121  C12  C13   110.82  3.000
 LK7  H122  C12  C11   109.40  3.000
 LK7  H121  C12  C11   110.62  3.000
 LK7  C13   C12  C11   112.37  3.000
 LK7  H13   C13  O4    109.04  3.000
 LK7  H13   C13  C12   109.36  3.000
 LK7  O4    C13  C12   111.81  3.000
 LK7  H13   C13  C8    110.44  3.000
 LK7  O4    C13  C8    106.95  3.000
 LK7  C12   C13  C8    109.24  3.000
 LK7  C14   O4   C13   114.41  3.000
 LK7  H143  C14  H142  108.04  3.000
 LK7  H143  C14  H141  107.69  3.000
 LK7  H142  C14  H141  107.66  3.000
 LK7  H143  C14  O4    107.82  3.000
 LK7  H142  C14  O4    112.18  3.000
 LK7  H141  C14  O4    113.23  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  Var_01  C8    C6   N1   C5    -14.84  30.0  1
 LK7  Var_02  C13   C8   C6   N1   -174.69  30.0  1
 LK7  Var_03  C12   C11  C10  C9    -57.19  30.0  1
 LK7  Var_04  C13   C12  C11  C10    60.21  30.0  1
 LK7  Var_05  O2    C7   C6   N1    175.66  30.0  2
 LK7  Var_06  C5    C3   C2   C1     -1.68   0.0  2
 LK7  Var_07  H141  C14  O4   C13   -73.07  30.0  3
 LK7  Var_08  H11   C1   C2   C3   -118.16  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-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

