# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 19:55:44 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-cyanobenzyl (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=C1Nc2ccccc2[C@@]13CN[C@H](C3)C(=O)OCc4ccc(cc4)C#N
#
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
 09B  09B  '4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  43  26  .  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_09B
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
 09B  C13  C  CR16  0  -0.261  -4.3649   3.2024   1.0837
 09B  C14  C  CR16  0  -0.268  -5.1333   3.2792  -0.0707
 09B  C2   C  CR16  0  -0.224   5.6164  -0.1489   0.7377
 09B  C3   C  CR16  0  -0.224   4.7167   0.8499  -1.2768
 09B  C12  C  CR16  0  -0.350  -3.5143   2.1162   1.2929
 09B  C5   C  CR16  0  -0.278   4.6023  -1.0903   0.7124
 09B  C6   C  CR16  0  -0.275   3.7103  -0.0989  -1.2874
 09B  C15  C  CR16  0  -0.306  -5.0768   2.2836  -1.0447
 09B  C1   C  CR6   0  -0.004   5.6707   0.8233  -0.2598
 09B  C11  C  CR56  0   0.138  -3.4497   1.1251   0.3362
 09B  C8   C  CR6   0   0.090   3.6445  -1.0750  -0.2970
 09B  C10  C  CR56  0   0.366  -4.2273   1.2178  -0.8169
 09B  C18  C  CR5   0   0.578  -3.0649  -0.7273  -1.0678
 09B  C24  C  C     0   0.585   0.3034  -2.1503   0.4892
 09B  C21  C  CH2   0  -0.462  -1.1481  -0.0485   0.4421
 09B  C20  C  CH2   0  -0.293  -3.0339  -1.1651   1.4111
 09B  C22  C  CR15  0  -0.180  -0.7448  -1.3449   1.2147
 09B  C16  C  C     0  -0.337  -2.6730  -0.1518   0.2914
 09B  C9   C  CH2   0  -0.250   2.5307  -2.0773  -0.3007
 09B  N7   N  NS    0  -0.248   7.5545   2.5856  -0.2212
 09B  N17  N  NR15  0  -0.744  -3.9844   0.1087  -1.6189
 09B  N19  N  NR15  0  -0.582  -1.9484  -2.1172   1.4549
 09B  O23  O  O     0  -0.450  -2.6421  -1.7512  -1.5661
 09B  O26  O  O2    0  -0.450   1.4325  -1.4628   0.3899
 09B  H1   H  HCR6  0   0.255  -4.4255   3.9884   1.8244
 09B  H2   H  HCR6  0   0.259  -5.7893   4.1266  -0.2220
 09B  H3   H  HCR6  0   0.286   6.3596  -0.1674   1.5226
 09B  H4   H  HCR6  0   0.285   4.7663   1.6043  -2.0497
 09B  H5   H  HCR6  0   0.254  -2.9117   2.0599   2.1918
 09B  H6   H  HCR6  0   0.275   4.5605  -1.8463   1.4859
 09B  H7   H  HCR6  0   0.274   2.9732  -0.0797  -2.0801
 09B  H8   H  HCR6  0   0.267  -5.6764   2.3479  -1.9432
 09B  H9   H  HCH2  0   0.275  -0.8868   0.8314   1.0286
 09B  H10  H  HCH2  0   0.272  -0.6471   0.0565  -0.5206
 09B  H11  H  HCH2  0   0.252  -3.0946  -0.6166   2.3557
 09B  H12  H  HCH2  0   0.268  -3.9919  -1.6618   1.2575
 09B  H13  H  HCR5  0   0.288  -0.3089  -1.0404   2.1719
 09B  H14  H  HCH2  0   0.264   2.2350  -2.3305  -1.3201
 09B  H15  H  HCH2  0   0.264   2.8267  -2.9949   0.2102
 09B  H16  H  HNR5  0   0.411  -4.4049  -0.0475  -2.5227
 09B  H17  H  HNR5  0   0.359  -2.0682  -2.7986   0.7149
 09B  O25  O  O     0  -0.441   0.1509  -3.2620   0.0534
 09B  C4   C  CSP   0   0.059   6.7145   1.7972  -0.2413

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
 09B  N19  C22  single    1.450  0.020  1.450
 09B  N19  C20  single    1.445  0.020  1.445
 09B  C12  C13  aromatic  1.395  0.020  1.395
 09B  C12  C11  aromatic  1.379  0.020  1.379
 09B  C13  C14  aromatic  1.389  0.020  1.389
 09B  C22  C21  single    1.562  0.020  1.562
 09B  C22  C24  single    1.508  0.020  1.508
 09B  C20  C16  single    1.553  0.020  1.553
 09B  C21  C16  single    1.536  0.020  1.536
 09B  C11  C16  single    1.495  0.020  1.495
 09B  C11  C10  aromatic  1.394  0.020  1.394
 09B  C24  O25  double    1.204  0.020  1.204
 09B  C24  O26  single    1.326  0.020  1.326
 09B  C16  C18  single    1.527  0.020  1.527
 09B  C14  C15  aromatic  1.394  0.020  1.394
 09B  O26  C9   single    1.435  0.020  1.435
 09B  C5   C2   aromatic  1.384  0.020  1.384
 09B  C5   C8   aromatic  1.392  0.020  1.392
 09B  C10  C15  aromatic  1.382  0.020  1.382
 09B  C10  N17  single    1.390  0.020  1.390
 09B  C2   C1   aromatic  1.394  0.020  1.394
 09B  C9   C8   single    1.498  0.020  1.498
 09B  C18  N17  single    1.359  0.020  1.359
 09B  C18  O23  double    1.215  0.020  1.215
 09B  C8   C6   aromatic  1.392  0.020  1.392
 09B  C1   C4   single    1.428  0.020  1.428
 09B  C1   C3   aromatic  1.395  0.020  1.395
 09B  C4   N7   triple    1.152  0.020  1.152
 09B  C6   C3   aromatic  1.383  0.020  1.383
 09B  C13  H1   single    0.930  0.020  1.080
 09B  C14  H2   single    0.930  0.020  1.080
 09B  C2   H3   single    0.930  0.020  1.080
 09B  C3   H4   single    0.930  0.020  1.080
 09B  C12  H5   single    0.930  0.020  1.080
 09B  C5   H6   single    0.930  0.020  1.080
 09B  C6   H7   single    0.930  0.020  1.080
 09B  C15  H8   single    0.930  0.020  1.080
 09B  C21  H9   single    0.970  0.020  1.090
 09B  C21  H10  single    0.970  0.020  1.090
 09B  C20  H11  single    0.970  0.020  1.090
 09B  C20  H12  single    0.970  0.020  1.090
 09B  C22  H13  single    0.970  0.020  1.090
 09B  C9   H14  single    0.970  0.020  1.090
 09B  C9   H15  single    0.970  0.020  1.090
 09B  N17  H16  single    0.860  0.020  1.020
 09B  N19  H17  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
 09B  H1   C13  C12  119.81  3.000
 09B  H1   C13  C14  119.86  3.000
 09B  C12  C13  C14  120.33  3.000
 09B  H2   C14  C15  119.09  3.000
 09B  H2   C14  C13  119.66  3.000
 09B  C15  C14  C13  121.26  3.000
 09B  H3   C2   C1   120.31  3.000
 09B  H3   C2   C5   120.35  3.000
 09B  C1   C2   C5   119.33  3.000
 09B  H4   C3   C1   120.22  3.000
 09B  H4   C3   C6   120.43  3.000
 09B  C1   C3   C6   119.35  3.000
 09B  H5   C12  C11  120.80  3.000
 09B  H5   C12  C13  120.25  3.000
 09B  C11  C12  C13  118.95  3.000
 09B  H6   C5   C8   119.96  3.000
 09B  H6   C5   C2   119.37  3.000
 09B  C8   C5   C2   120.67  3.000
 09B  H7   C6   C8   120.08  3.000
 09B  H7   C6   C3   119.27  3.000
 09B  C8   C6   C3   120.65  3.000
 09B  H8   C15  C10  121.55  3.000
 09B  H8   C15  C14  121.02  3.000
 09B  C10  C15  C14  117.43  3.000
 09B  C3   C1   C2   120.56  3.000
 09B  C3   C1   C4   119.77  3.000
 09B  C2   C1   C4   119.67  3.000
 09B  C16  C11  C10  108.77  3.000
 09B  C10  C11  C12  120.00  3.000
 09B  C16  C11  C12  131.22  3.000
 09B  C9   C8   C6   120.16  3.000
 09B  C6   C8   C5   119.43  3.000
 09B  C9   C8   C5   120.40  3.000
 09B  N17  C10  C11  109.07  3.000
 09B  N17  C10  C15  128.88  3.000
 09B  C11  C10  C15  122.05  3.000
 09B  O23  C18  N17  125.98  3.000
 09B  O23  C18  C16  126.40  3.000
 09B  N17  C18  C16  107.62  3.000
 09B  O26  C24  O25  124.03  3.000
 09B  O26  C24  C22  110.56  3.000
 09B  O25  C24  C22  125.41  3.000
 09B  H10  C21  H9   106.70  3.000
 09B  H10  C21  C16  112.09  3.000
 09B  H9   C21  C16  110.21  3.000
 09B  H10  C21  C22  113.45  3.000
 09B  H9   C21  C22  110.01  3.000
 09B  C16  C21  C22  104.42  3.000
 09B  H12  C20  H11  107.54  3.000
 09B  H12  C20  N19  111.37  3.000
 09B  H11  C20  N19  110.24  3.000
 09B  H12  C20  C16  113.58  3.000
 09B  H11  C20  C16  107.96  3.000
 09B  N19  C20  C16  106.10  3.000
 09B  H13  C22  N19  109.50  3.000
 09B  H13  C22  C21  107.72  3.000
 09B  N19  C22  C21  108.03  3.000
 09B  H13  C22  C24  107.00  3.000
 09B  C21  C22  C24  112.63  3.000
 09B  N19  C22  C24  111.86  3.000
 09B  C20  C16  C21  101.77  3.000
 09B  C21  C16  C18  111.56  3.000
 09B  C20  C16  C18  109.65  3.000
 09B  C18  C16  C11  102.43  3.000
 09B  C21  C16  C11  117.09  3.000
 09B  C20  C16  C11  114.52  3.000
 09B  H15  C9   H14  108.41  3.000
 09B  H15  C9   O26  110.01  3.000
 09B  H14  C9   O26  109.96  3.000
 09B  H15  C9   C8   111.09  3.000
 09B  H14  C9   C8   111.03  3.000
 09B  O26  C9   C8   106.33  3.000
 09B  H16  N17  C18  123.36  3.000
 09B  H16  N17  C10  124.58  3.000
 09B  C18  N17  C10  112.02  3.000
 09B  H17  N19  C22  109.60  3.000
 09B  H17  N19  C20  109.40  3.000
 09B  C22  N19  C20  105.53  3.000
 09B  C9   O26  C24  117.75  3.000
 09B  N7   C4   C1   180.00  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
 09B  CONST_01  C10  C11  C12  C13    0.00   0.0  0
 09B  CONST_02  C10  C15  C14  C13    0.00   0.0  0
 09B  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 09B  CONST_04  C11  C10  C15  C14    0.00   0.0  0
 09B  CONST_05  C6   C8   C5   C2     0.00   0.0  0
 09B  CONST_06  C6   C3   C1   C2     0.00   0.0  0
 09B  CONST_07  C5   C2   C1   C3     0.00   0.0  0
 09B  CONST_08  C5   C8   C6   C3     0.00   0.0  0
 09B  CONST_09  C15  C14  C13  C12    0.00   0.0  0
 09B  CONST_10  C15  C10  C11  C12    0.00   0.0  0
 09B  CONST_11  C8   C5   C2   C1     0.00   0.0  0
 09B  CONST_12  C8   C6   C3   C1     0.00   0.0  0
 09B  CONST_13  C16  C18  N17  C10    0.00   0.0  0
 09B  CONST_14  C5   C2   C1   C4   180.00   0.0  0
 09B  CONST_15  C6   C3   C1   C4   180.00   0.0  0
 09B  CONST_16  C9   C8   C5   C2   180.00   0.0  0
 09B  CONST_17  C9   C8   C6   C3   180.00   0.0  0
 09B  CONST_18  O23  C18  N17  C10  180.00   0.0  0
 09B  CONST_19  H8   C15  C14  C13  180.00   0.0  0
 09B  CONST_20  H5   C12  C13  C14  180.00   0.0  0
 09B  CONST_21  H4   C3   C1   C2   180.00   0.0  0
 09B  CONST_22  H3   C2   C1   C3   180.00   0.0  0
 09B  CONST_23  H2   C14  C13  C12  180.00   0.0  0
 09B  CONST_24  H7   C6   C8   C5   180.00   0.0  0
 09B  CONST_25  H6   C5   C8   C6   180.00   0.0  0
 09B  CONST_26  H1   C13  C14  C15  180.00   0.0  0
 09B  CONST_27  H16  N17  C18  C16  180.00   0.0  0
 09B  Var_01    C16  C20  N19  C22   37.52  30.0  1
 09B  Var_02    O26  C9   C8   C5    92.77  30.0  2
 09B  Var_03    O25  C24  O26  C9     1.11  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
 09B  chir_01  C22  N19  C21  C24  positiv
 09B  chir_02  C16  C21  C11  C18  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
 09B  plan-1  C2   0.020
 09B  plan-1  C3   0.020
 09B  plan-1  C5   0.020
 09B  plan-1  C6   0.020
 09B  plan-1  C1   0.020
 09B  plan-1  C8   0.020
 09B  plan-1  C9   0.020
 09B  plan-1  N7   0.020
 09B  plan-1  H3   0.020
 09B  plan-1  H4   0.020
 09B  plan-1  H6   0.020
 09B  plan-1  H7   0.020
 09B  plan-1  C4   0.020
 09B  plan-2  C13  0.020
 09B  plan-2  C14  0.020
 09B  plan-2  C12  0.020
 09B  plan-2  C15  0.020
 09B  plan-2  C11  0.020
 09B  plan-2  C10  0.020
 09B  plan-2  C18  0.020
 09B  plan-2  C16  0.020
 09B  plan-2  N17  0.020
 09B  plan-2  O23  0.020
 09B  plan-2  H1   0.020
 09B  plan-2  H2   0.020
 09B  plan-2  H5   0.020
 09B  plan-2  H8   0.020
 09B  plan-2  H16  0.020
 09B  plan-3  C24  0.020
 09B  plan-3  C22  0.020
 09B  plan-3  O26  0.020
 09B  plan-3  O25  0.020

