# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 20:57:47 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: benzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(OCc1ccccc1)[C@H]2C[C@]3(CN2)C(=O)Nc4ccccc34
#
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
 09A  09A  'benzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  42  24  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_09A
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
 09A  C22  C  CR16  0  -0.261   6.1410   1.8508  -0.5085
 09A  C5   C  CR16  0  -0.262  -4.0497   2.9582   0.9745
 09A  C21  C  CR16  0  -0.241   5.3780   1.5184  -1.6197
 09A  C23  C  CR16  0  -0.242   6.0231   1.1069   0.6595
 09A  C8   C  CR16  0  -0.268  -4.9586   2.8433  -0.0694
 09A  C3   C  CR16  0  -0.349  -3.0678   1.9850   1.1636
 09A  C20  C  CR16  0  -0.293   4.4962   0.4471  -1.5604
 09A  C24  C  CR16  0  -0.285   5.1435   0.0354   0.7143
 09A  C6   C  CR16  0  -0.306  -4.9159   1.7641  -0.9507
 09A  C1   C  CR56  0   0.139  -3.0141   0.9138   0.2970
 09A  C19  C  CR6   0   0.078   4.3730  -0.3032  -0.3952
 09A  C17  C  CR56  0   0.367  -3.9337   0.8142  -0.7461
 09A  C14  C  CR5   0   0.577  -2.6014  -1.0205  -0.9819
 09A  C9   C  C     0   0.581   1.2070  -1.7807   0.4884
 09A  C4   C  CH2   0  -0.464  -0.5952  -0.0007   0.1892
 09A  C13  C  CH2   0  -0.301  -2.2203  -1.2147   1.4918
 09A  C7   C  CR15  0  -0.186   0.0346  -1.0805   1.1254
 09A  C2   C  C     0  -0.331  -2.1087  -0.2760   0.2564
 09A  C18  C  CH2   0  -0.252   3.4046  -1.4425  -0.3236
 09A  N16  N  NR15  0  -0.744  -3.6698  -0.3396  -1.4747
 09A  N10  N  NR15  0  -0.576  -1.0126  -2.0064   1.5058
 09A  O12  O  O     0  -0.445   1.2307  -2.9439   0.1755
 09A  O11  O  O2    0  -0.449   2.2103  -0.9382   0.3019
 09A  H1   H  HCR6  0   0.260   6.8293   2.6847  -0.5524
 09A  H2   H  HCR6  0   0.255  -4.1021   3.8067   1.6434
 09A  H3   H  HCR6  0   0.259   5.4698   2.0915  -2.5331
 09A  H4   H  HCR6  0   0.259   6.6199   1.3600   1.5262
 09A  H5   H  HCR6  0   0.259  -5.7154   3.6046  -0.2063
 09A  H6   H  HCR6  0   0.253  -2.3577   2.0751   1.9771
 09A  H7   H  HCR6  0   0.256   3.9019   0.1900  -2.4294
 09A  H8   H  HCR6  0   0.256   5.0603  -0.5460   1.6252
 09A  H9   H  HCR6  0   0.268  -5.6255   1.6801  -1.7631
 09A  H10  H  HCH2  0   0.275  -0.3676   0.9996   0.5551
 09A  H11  H  HCH2  0   0.273  -0.2241  -0.0568  -0.8344
 09A  H12  H  HCH2  0   0.253  -2.2695  -0.5928   2.3904
 09A  H13  H  HCH2  0   0.270  -3.1103  -1.8440   1.4786
 09A  H14  H  HCR5  0   0.288   0.3999  -0.5704   2.0223
 09A  H15  H  HCH2  0   0.257   3.1684  -1.8216  -1.3195
 09A  H16  H  HCH2  0   0.256   3.8067  -2.2656   0.2702
 09A  H17  H  HNR5  0   0.411  -4.1832  -0.6323  -2.2926
 09A  H18  H  HNR5  0   0.356  -1.0864  -2.7403   0.8100
 09A  O15  O  O     0  -0.451  -2.1365  -2.0455  -1.4389

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
 09A  N10  C7   single    1.449  0.020  1.449
 09A  N10  C13  single    1.444  0.020  1.444
 09A  C3   C5   aromatic  1.395  0.020  1.395
 09A  C3   C1   aromatic  1.379  0.020  1.379
 09A  C5   C8   aromatic  1.389  0.020  1.389
 09A  C7   C4   single    1.562  0.020  1.562
 09A  C7   C9   single    1.507  0.020  1.507
 09A  C13  C2   single    1.556  0.020  1.556
 09A  C4   C2   single    1.540  0.020  1.540
 09A  C1   C2   single    1.496  0.020  1.496
 09A  C1   C17  aromatic  1.394  0.020  1.394
 09A  C9   O12  double    1.205  0.020  1.205
 09A  C9   O11  single    1.323  0.020  1.323
 09A  C2   C14  single    1.527  0.020  1.527
 09A  C8   C6   aromatic  1.394  0.020  1.394
 09A  O11  C18  single    1.439  0.020  1.439
 09A  C24  C23  aromatic  1.387  0.020  1.387
 09A  C24  C19  aromatic  1.393  0.020  1.393
 09A  C23  C22  aromatic  1.390  0.020  1.390
 09A  C17  C6   aromatic  1.382  0.020  1.382
 09A  C17  N16  single    1.390  0.020  1.390
 09A  C18  C19  single    1.497  0.020  1.497
 09A  C19  C20  aromatic  1.391  0.020  1.391
 09A  C14  N16  single    1.359  0.020  1.359
 09A  C14  O15  double    1.215  0.020  1.215
 09A  C22  C21  aromatic  1.388  0.020  1.388
 09A  C20  C21  aromatic  1.389  0.020  1.389
 09A  C22  H1   single    0.930  0.020  1.080
 09A  C5   H2   single    0.930  0.020  1.080
 09A  C21  H3   single    0.930  0.020  1.080
 09A  C23  H4   single    0.930  0.020  1.080
 09A  C8   H5   single    0.930  0.020  1.080
 09A  C3   H6   single    0.930  0.020  1.080
 09A  C20  H7   single    0.930  0.020  1.080
 09A  C24  H8   single    0.930  0.020  1.080
 09A  C6   H9   single    0.930  0.020  1.080
 09A  C4   H10  single    0.970  0.020  1.090
 09A  C4   H11  single    0.970  0.020  1.090
 09A  C13  H12  single    0.970  0.020  1.090
 09A  C13  H13  single    0.970  0.020  1.090
 09A  C7   H14  single    0.970  0.020  1.090
 09A  C18  H15  single    0.970  0.020  1.090
 09A  C18  H16  single    0.970  0.020  1.090
 09A  N16  H17  single    0.860  0.020  1.020
 09A  N10  H18  single    0.890  0.020  1.040

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
 09A  H1   C22  C23  120.04  3.000
 09A  H1   C22  C21  120.10  3.000
 09A  C23  C22  C21  119.86  3.000
 09A  H2   C5   C3   119.83  3.000
 09A  H2   C5   C8   119.87  3.000
 09A  C3   C5   C8   120.30  3.000
 09A  H3   C21  C20  119.90  3.000
 09A  H3   C21  C22  120.14  3.000
 09A  C20  C21  C22  119.97  3.000
 09A  H4   C23  C24  119.90  3.000
 09A  H4   C23  C22  120.07  3.000
 09A  C24  C23  C22  120.03  3.000
 09A  H5   C8   C6   119.08  3.000
 09A  H5   C8   C5   119.64  3.000
 09A  C6   C8   C5   121.28  3.000
 09A  H6   C3   C1   120.72  3.000
 09A  H6   C3   C5   120.32  3.000
 09A  C1   C3   C5   118.95  3.000
 09A  H7   C20  C19  119.67  3.000
 09A  H7   C20  C21  119.80  3.000
 09A  C19  C20  C21  120.53  3.000
 09A  H8   C24  C19  119.78  3.000
 09A  H8   C24  C23  119.75  3.000
 09A  C19  C24  C23  120.47  3.000
 09A  H9   C6   C17  121.61  3.000
 09A  H9   C6   C8   120.98  3.000
 09A  C17  C6   C8   117.41  3.000
 09A  C2   C1   C17  108.80  3.000
 09A  C17  C1   C3   120.00  3.000
 09A  C2   C1   C3   131.19  3.000
 09A  C18  C19  C24  120.32  3.000
 09A  C18  C19  C20  120.51  3.000
 09A  C24  C19  C20  119.15  3.000
 09A  N16  C17  C1   109.04  3.000
 09A  N16  C17  C6   128.91  3.000
 09A  C1   C17  C6   122.05  3.000
 09A  O15  C14  N16  125.95  3.000
 09A  O15  C14  C2   126.38  3.000
 09A  N16  C14  C2   107.66  3.000
 09A  O11  C9   O12  124.27  3.000
 09A  O11  C9   C7   110.71  3.000
 09A  O12  C9   C7   125.01  3.000
 09A  H11  C4   H10  106.95  3.000
 09A  H11  C4   C2   111.49  3.000
 09A  H10  C4   C2   110.79  3.000
 09A  H11  C4   C7   112.95  3.000
 09A  H10  C4   C7   110.45  3.000
 09A  C2   C4   C7   104.28  3.000
 09A  H13  C13  H12  107.54  3.000
 09A  H13  C13  N10  111.50  3.000
 09A  H12  C13  N10  109.95  3.000
 09A  H13  C13  C2   113.41  3.000
 09A  H12  C13  C2   108.21  3.000
 09A  N10  C13  C2   106.17  3.000
 09A  H14  C7   N10  108.90  3.000
 09A  H14  C7   C4   107.67  3.000
 09A  N10  C7   C4   107.93  3.000
 09A  H14  C7   C9   107.65  3.000
 09A  C4   C7   C9   112.44  3.000
 09A  N10  C7   C9   112.12  3.000
 09A  C13  C2   C4   102.30  3.000
 09A  C4   C2   C14  111.66  3.000
 09A  C13  C2   C14  109.07  3.000
 09A  C14  C2   C1   102.39  3.000
 09A  C4   C2   C1   117.00  3.000
 09A  C13  C2   C1   114.52  3.000
 09A  H16  C18  H15  108.32  3.000
 09A  H16  C18  O11  109.47  3.000
 09A  H15  C18  O11  109.79  3.000
 09A  H16  C18  C19  111.20  3.000
 09A  H15  C18  C19  111.14  3.000
 09A  O11  C18  C19  106.91  3.000
 09A  H17  N16  C14  123.26  3.000
 09A  H17  N16  C17  124.69  3.000
 09A  C14  N16  C17  112.02  3.000
 09A  H18  N10  C7   109.57  3.000
 09A  H18  N10  C13  109.22  3.000
 09A  C7   N10  C13  104.58  3.000
 09A  C18  O11  C9   117.85  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
 09A  CONST_01  C19  C24  C23  C22    0.00   0.0  0
 09A  CONST_02  C19  C20  C21  C22    0.00   0.0  0
 09A  CONST_03  C17  C1   C3   C5     0.00   0.0  0
 09A  CONST_04  C17  C6   C8   C5     0.00   0.0  0
 09A  CONST_05  C24  C23  C22  C21    0.00   0.0  0
 09A  CONST_06  C24  C19  C20  C21    0.00   0.0  0
 09A  CONST_07  C20  C19  C24  C23    0.00   0.0  0
 09A  CONST_08  C20  C21  C22  C23    0.00   0.0  0
 09A  CONST_09  C1   C3   C5   C8     0.00   0.0  0
 09A  CONST_10  C1   C17  C6   C8     0.00   0.0  0
 09A  CONST_11  C6   C8   C5   C3     0.00   0.0  0
 09A  CONST_12  C6   C17  C1   C3     0.00   0.0  0
 09A  CONST_13  C2   C14  N16  C17    0.00   0.0  0
 09A  CONST_14  C18  C19  C20  C21  180.00   0.0  0
 09A  CONST_15  C18  C19  C24  C23  180.00   0.0  0
 09A  CONST_16  O15  C14  N16  C17  180.00   0.0  0
 09A  CONST_17  H8   C24  C23  C22  180.00   0.0  0
 09A  CONST_18  H7   C20  C21  C22  180.00   0.0  0
 09A  CONST_19  H9   C6   C8   C5   180.00   0.0  0
 09A  CONST_20  H4   C23  C22  C21  180.00   0.0  0
 09A  CONST_21  H3   C21  C22  C23  180.00   0.0  0
 09A  CONST_22  H6   C3   C5   C8   180.00   0.0  0
 09A  CONST_23  H5   C8   C5   C3   180.00   0.0  0
 09A  CONST_24  H1   C22  C21  C20  180.00   0.0  0
 09A  CONST_25  H2   C5   C8   C6   180.00   0.0  0
 09A  CONST_26  H17  N16  C14  C2   180.00   0.0  0
 09A  Var_01    C2   C13  N10  C7    39.60  30.0  1
 09A  Var_02    O11  C18  C19  C20  -97.02  30.0  2
 09A  Var_03    O12  C9   O11  C18    0.43  30.0  1

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
 09A  chir_01  C7  N10  C4  C9   positiv
 09A  chir_02  C2  C4   C1  C14  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
 09A  plan-1  C22  0.020
 09A  plan-1  C21  0.020
 09A  plan-1  C23  0.020
 09A  plan-1  C20  0.020
 09A  plan-1  C24  0.020
 09A  plan-1  C19  0.020
 09A  plan-1  C18  0.020
 09A  plan-1  H1   0.020
 09A  plan-1  H3   0.020
 09A  plan-1  H4   0.020
 09A  plan-1  H7   0.020
 09A  plan-1  H8   0.020
 09A  plan-2  C5   0.020
 09A  plan-2  C8   0.020
 09A  plan-2  C3   0.020
 09A  plan-2  C6   0.020
 09A  plan-2  C1   0.020
 09A  plan-2  C17  0.020
 09A  plan-2  C14  0.020
 09A  plan-2  C2   0.020
 09A  plan-2  N16  0.020
 09A  plan-2  H2   0.020
 09A  plan-2  H5   0.020
 09A  plan-2  H6   0.020
 09A  plan-2  H9   0.020
 09A  plan-2  H17  0.020
 09A  plan-2  O15  0.020
 09A  plan-3  C9   0.020
 09A  plan-3  C7   0.020
 09A  plan-3  O12  0.020
 09A  plan-3  O11  0.020

