# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:24:22 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: (3~{a}~{S},8~{a}~{S})-6-(phenylcarbonyl)-2,3,3~{a},7,8,8~{a}-hexahydropyrrolo[3,4-d]azepin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC[C@H]2C=CN(CC[C@H]12)C(=O)c3ccccc3
#
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
 LXJ  LXJ  (3~{a}~{S},8~{a}~{S})-6-(phenylcarbonyl)-2,3,3~{a},7,8,8~{a}-hexahydropyrrolo[3,4-d]azepin-1-one  ligand  35  19  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LXJ
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
 LXJ  N1   N  NH1   0  -0.636  18.7538  -27.8048  -12.2304
 LXJ  C4   C  CH2   0  -0.236  18.7087  -26.7574  -11.2322
 LXJ  C5   C  C     0   0.572  18.5270  -27.3848  -13.4870
 LXJ  C6   C  CH1   0  -0.414  18.2709  -25.8891  -13.4156
 LXJ  C7   C  CH2   0  -0.427  17.2556  -25.3550  -14.4030
 LXJ  C8   C  CH2   0  -0.323  17.1131  -23.8402  -14.3221
 LXJ  C10  C  CR16  0  -0.257  13.9404  -23.9332  -14.6021
 LXJ  C13  C  CR16  0  -0.244  13.0230  -21.5484  -15.6875
 LXJ  N    N  NT    0  -0.494  16.5626  -23.3283  -13.0652
 LXJ  C    C  C     0   0.528  15.3815  -22.6602  -12.9726
 LXJ  O    O  O     0  -0.471  15.0771  -22.0327  -11.9705
 LXJ  C1   C  C1    0  -0.035  17.4320  -23.2368  -11.9486
 LXJ  C11  C  CR16  0  -0.241  12.9909  -23.9507  -15.6140
 LXJ  C12  C  CR16  0  -0.253  12.5376  -22.7593  -16.1643
 LXJ  C14  C  CR16  0  -0.274  13.9548  -21.5276  -14.6601
 LXJ  C2   C  C1    0  -0.256  18.0782  -24.2854  -11.4524
 LXJ  C3   C  CH1   0  -0.303  17.8911  -25.6817  -11.9483
 LXJ  C9   C  CR6   0  -0.081  14.4328  -22.7210  -14.1262
 LXJ  O1   O  O     0  -0.488  18.5487  -28.0697  -14.4957
 LXJ  H1   H  HNH1  0   0.399  19.0601  -28.7423  -12.0215
 LXJ  H2   H  HCH2  0   0.260  18.2346  -27.1034  -10.3146
 LXJ  H3   H  HCH2  0   0.238  19.7128  -26.3976  -10.9832
 LXJ  H4   H  HCH1  0   0.283  19.2403  -25.4055  -13.6069
 LXJ  H5   H  HCH2  0   0.240  16.2868  -25.8334  -14.2389
 LXJ  H6   H  HCH2  0   0.255  17.5638  -25.6016  -15.4211
 LXJ  H7   H  HCH2  0   0.264  18.0929  -23.3777  -14.4656
 LXJ  H8   H  HCH2  0   0.280  16.4884  -23.4914  -15.1407
 LXJ  H10  H  HCR6  0   0.263  12.6720  -20.6171  -16.1121
 LXJ  H11  H  H     0   0.267  17.5654  -22.2482  -11.5267
 LXJ  H12  H  HCR6  0   0.264  12.6074  -24.8968  -15.9725
 LXJ  H13  H  HCR6  0   0.263  11.8049  -22.7738  -16.9601
 LXJ  H14  H  HCR6  0   0.264  14.3216  -20.5807  -14.2848
 LXJ  H15  H  H     0   0.259  18.7694  -24.1114  -10.6357
 LXJ  H16  H  HCH1  0   0.273  16.8308  -25.9495  -11.8484
 LXJ  H9   H  HCR6  0   0.264  14.2852  -24.8684  -14.1785

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
 LXJ  C12  C13  aromatic  1.389  0.020  1.389
 LXJ  C12  C11  aromatic  1.389  0.020  1.389
 LXJ  C13  C14  aromatic  1.387  0.020  1.387
 LXJ  C11  C10  aromatic  1.388  0.020  1.388
 LXJ  C14  C9   aromatic  1.392  0.020  1.392
 LXJ  O1   C5   double    1.219  0.020  1.219
 LXJ  C7   C8   single    1.524  0.020  1.524
 LXJ  C7   C6   single    1.514  0.020  1.514
 LXJ  C10  C9   aromatic  1.392  0.020  1.392
 LXJ  C8   N    single    1.464  0.020  1.464
 LXJ  C9   C    single    1.495  0.020  1.495
 LXJ  C5   C6   single    1.519  0.020  1.519
 LXJ  C5   N1   single    1.344  0.020  1.344
 LXJ  C6   C3   single    1.530  0.020  1.530
 LXJ  N    C    single    1.360  0.020  1.360
 LXJ  N    C1   single    1.418  0.020  1.418
 LXJ  C    O    double    1.221  0.020  1.221
 LXJ  N1   C4   single    1.448  0.020  1.448
 LXJ  C3   C4   single    1.529  0.020  1.529
 LXJ  C3   C2   single    1.493  0.020  1.493
 LXJ  C1   C2   double    1.328  0.020  1.328
 LXJ  N1   H1   single    0.860  0.020  1.020
 LXJ  C4   H2   single    0.970  0.020  1.090
 LXJ  C4   H3   single    0.970  0.020  1.090
 LXJ  C6   H4   single    0.970  0.020  1.090
 LXJ  C7   H5   single    0.970  0.020  1.090
 LXJ  C7   H6   single    0.970  0.020  1.090
 LXJ  C8   H7   single    0.970  0.020  1.090
 LXJ  C8   H8   single    0.970  0.020  1.090
 LXJ  C10  H9   single    0.930  0.020  1.080
 LXJ  C13  H10  single    0.930  0.020  1.080
 LXJ  C1   H11  single    0.930  0.020  1.080
 LXJ  C11  H12  single    0.930  0.020  1.080
 LXJ  C12  H13  single    0.930  0.020  1.080
 LXJ  C14  H14  single    0.930  0.020  1.080
 LXJ  C2   H15  single    0.930  0.020  1.080
 LXJ  C3   H16  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
 LXJ  H1   N1   C5   122.38  3.000
 LXJ  H1   N1   C4   122.65  3.000
 LXJ  C5   N1   C4   114.41  3.000
 LXJ  H3   C4   H2   108.17  3.000
 LXJ  H3   C4   C3   111.44  3.000
 LXJ  H2   C4   C3   112.66  3.000
 LXJ  H3   C4   N1   111.46  3.000
 LXJ  H2   C4   N1   111.39  3.000
 LXJ  C3   C4   N1   101.70  3.000
 LXJ  O1   C5   C6   126.50  3.000
 LXJ  C6   C5   N1   106.99  3.000
 LXJ  O1   C5   N1   126.49  3.000
 LXJ  H4   C6   C3   109.02  3.000
 LXJ  H4   C6   C7   108.81  3.000
 LXJ  C3   C6   C7   114.29  3.000
 LXJ  H4   C6   C5   106.03  3.000
 LXJ  C3   C6   C5   102.73  3.000
 LXJ  C7   C6   C5   115.46  3.000
 LXJ  H6   C7   H5   106.94  3.000
 LXJ  H6   C7   C8   107.49  3.000
 LXJ  H5   C7   C8   110.14  3.000
 LXJ  H6   C7   C6   109.83  3.000
 LXJ  H5   C7   C6   110.01  3.000
 LXJ  C8   C7   C6   112.27  3.000
 LXJ  H8   C8   H7   106.28  3.000
 LXJ  H8   C8   N    108.55  3.000
 LXJ  H7   C8   N    107.56  3.000
 LXJ  H8   C8   C7   109.43  3.000
 LXJ  H7   C8   C7   109.26  3.000
 LXJ  N    C8   C7   115.36  3.000
 LXJ  H9   C10  C9   120.36  3.000
 LXJ  H9   C10  C11  119.49  3.000
 LXJ  C9   C10  C11  120.15  3.000
 LXJ  H10  C13  C14  119.71  3.000
 LXJ  H10  C13  C12  120.15  3.000
 LXJ  C14  C13  C12  120.14  3.000
 LXJ  C1   N    C    116.55  3.000
 LXJ  C1   N    C8   117.90  3.000
 LXJ  C    N    C8   123.82  3.000
 LXJ  C9   C    O    119.74  3.000
 LXJ  O    C    N    121.66  3.000
 LXJ  C9   C    N    118.59  3.000
 LXJ  H11  C1   C2   121.02  3.000
 LXJ  H11  C1   N    116.18  3.000
 LXJ  C2   C1   N    122.79  3.000
 LXJ  H12  C11  C12  120.21  3.000
 LXJ  H12  C11  C10  119.68  3.000
 LXJ  C12  C11  C10  120.10  3.000
 LXJ  H13  C12  C11  120.08  3.000
 LXJ  H13  C12  C13  120.06  3.000
 LXJ  C11  C12  C13  119.86  3.000
 LXJ  H14  C14  C9   120.04  3.000
 LXJ  H14  C14  C13  119.84  3.000
 LXJ  C9   C14  C13  120.12  3.000
 LXJ  H15  C2   C3   118.69  3.000
 LXJ  H15  C2   C1   117.71  3.000
 LXJ  C3   C2   C1   123.59  3.000
 LXJ  H16  C3   C2   108.58  3.000
 LXJ  H16  C3   C6   107.09  3.000
 LXJ  C2   C3   C6   114.47  3.000
 LXJ  H16  C3   C4   107.59  3.000
 LXJ  C2   C3   C4   115.80  3.000
 LXJ  C6   C3   C4   102.77  3.000
 LXJ  C14  C9   C    118.62  3.000
 LXJ  C    C9   C10  121.58  3.000
 LXJ  C14  C9   C10  119.60  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
 LXJ  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 LXJ  CONST_02  C13  C14  C9   C10    0.00   0.0  0
 LXJ  CONST_03  C14  C13  C12  C11    0.00   0.0  0
 LXJ  CONST_04  C14  C9   C10  C11    0.00   0.0  0
 LXJ  CONST_05  C9   C14  C13  C12    0.00   0.0  0
 LXJ  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 LXJ  CONST_07  C6   C5   N1   C4     0.00   0.0  0
 LXJ  CONST_08  C    C9   C14  C13  180.00   0.0  0
 LXJ  CONST_09  C11  C10  C9   C    180.00   0.0  0
 LXJ  CONST_10  O1   C5   N1   C4   180.00   0.0  0
 LXJ  CONST_11  H13  C12  C11  C10  180.00   0.0  0
 LXJ  CONST_12  H14  C14  C9   C10  180.00   0.0  0
 LXJ  CONST_13  H12  C11  C12  C13  180.00   0.0  0
 LXJ  CONST_14  H10  C13  C12  C11  180.00   0.0  0
 LXJ  CONST_15  H9   C10  C11  C12  180.00   0.0  0
 LXJ  CONST_16  H1   N1   C5   C6   180.00   0.0  0
 LXJ  Var_01    C3   C4   N1   C5    21.16  30.0  1
 LXJ  Var_02    N    C    C9   C10   58.17  30.0  2

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
 LXJ  chir_01  C6  C7  C5  C3  positiv
 LXJ  chir_02  C3  C6  C4  C2  negativ

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
 LXJ  plan-1  C10  0.020
 LXJ  plan-1  C13  0.020
 LXJ  plan-1  C    0.020
 LXJ  plan-1  C11  0.020
 LXJ  plan-1  C12  0.020
 LXJ  plan-1  C14  0.020
 LXJ  plan-1  C9   0.020
 LXJ  plan-1  H10  0.020
 LXJ  plan-1  H12  0.020
 LXJ  plan-1  H13  0.020
 LXJ  plan-1  H14  0.020
 LXJ  plan-1  H9   0.020
 LXJ  plan-2  C8   0.020
 LXJ  plan-2  N    0.020
 LXJ  plan-2  C    0.020
 LXJ  plan-2  O    0.020
 LXJ  plan-2  C1   0.020
 LXJ  plan-2  C9   0.020
 LXJ  plan-3  N1   0.020
 LXJ  plan-3  C4   0.020
 LXJ  plan-3  C5   0.020
 LXJ  plan-3  C6   0.020
 LXJ  plan-3  O1   0.020
 LXJ  plan-3  H1   0.020

