# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:19:11 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (3S)-spiro[indole-3,3'-pyrrolidin]-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ccccc2[C@]13CCNC3
#
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
 091  091  (3S)-spiro[indole-3,3'-pyrrolidin]-2(1H)-one  ligand  26  14  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_091
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
 091  C1   C  C     0  -0.314  -0.7529   0.0835   0.0732
 091  C2   C  CR56  0   0.129   0.7154   0.3672   0.0306
 091  C3   C  CR5   0   0.565  -0.7885  -1.4415   0.0975
 091  C4   C  CH2   0  -0.454  -1.5470   0.7024   1.2491
 091  C5   C  CH2   0  -0.306  -1.5303   0.6060  -1.1825
 091  C6   C  CR56  0   0.366   1.4088  -0.8410  -0.0128
 091  C7   C  CR16  0  -0.340   1.4080   1.5598   0.0075
 091  N1   N  NR15  0  -0.744   0.4949  -1.8876   0.0236
 091  O1   O  O     0  -0.457  -1.7812  -2.1394   0.1535
 091  C8   C  CH2   0  -0.323  -2.6592   1.5257   0.5693
 091  N2   N  NR15  0  -0.568  -2.8649   0.9392  -0.7444
 091  C9   C  CR16  0  -0.308   2.7882  -0.8932  -0.0770
 091  C10  C  CR16  0  -0.264   2.8016   1.5320  -0.0571
 091  C11  C  CR16  0  -0.269   3.4765   0.3189  -0.0987
 091  H1   H  HCH2  0   0.256  -1.9814  -0.0792   1.8746
 091  H2   H  HCH2  0   0.254  -0.9071   1.3114   1.8874
 091  H3   H  HCH2  0   0.247  -1.0274   1.5117  -1.5331
 091  H4   H  HCH2  0   0.263  -1.5395  -0.1040  -2.0095
 091  H5   H  HCR6  0   0.252   0.8805   2.5059   0.0416
 091  H6   H  HNR5  0   0.410   0.7434  -2.8653   0.0032
 091  H7   H  HCH2  0   0.247  -3.5859   1.5425   1.1421
 091  H8   H  HCH2  0   0.232  -2.3296   2.5610   0.4453
 091  H9   H  HNR5  0   0.349  -3.4035   0.0865  -0.6447
 091  H11  H  HCR6  0   0.266   3.3201  -1.8351  -0.1088
 091  H12  H  HCR6  0   0.253   3.3591   2.4590  -0.0747
 091  H13  H  HCR6  0   0.258   4.5574   0.3097  -0.1489

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
 091  N2   C8   single    1.453  0.020  1.453
 091  N2   C5   single    1.444  0.020  1.444
 091  C7   C10  aromatic  1.395  0.020  1.395
 091  C7   C2   aromatic  1.379  0.020  1.379
 091  C10  C11  aromatic  1.389  0.020  1.389
 091  C8   C4   single    1.542  0.020  1.542
 091  C5   C1   single    1.567  0.020  1.567
 091  C4   C1   single    1.548  0.020  1.548
 091  C2   C1   single    1.496  0.020  1.496
 091  C2   C6   aromatic  1.394  0.020  1.394
 091  C1   C3   single    1.526  0.020  1.526
 091  C11  C9   aromatic  1.394  0.020  1.394
 091  C6   C9   aromatic  1.382  0.020  1.382
 091  C6   N1   single    1.390  0.020  1.390
 091  C3   O1   double    1.215  0.020  1.215
 091  C3   N1   single    1.361  0.020  1.361
 091  C4   H1   single    0.970  0.020  1.090
 091  C4   H2   single    0.970  0.020  1.090
 091  C5   H3   single    0.970  0.020  1.090
 091  C5   H4   single    0.970  0.020  1.090
 091  C7   H5   single    0.930  0.020  1.080
 091  N1   H6   single    0.860  0.020  1.020
 091  C8   H7   single    0.970  0.020  1.090
 091  C8   H8   single    0.970  0.020  1.090
 091  N2   H9   single    0.890  0.020  1.040
 091  C9   H11  single    0.930  0.020  1.080
 091  C10  H12  single    0.930  0.020  1.080
 091  C11  H13  single    0.930  0.020  1.080

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
 091  C5   C1   C4   102.77  3.000
 091  C4   C1   C3   112.06  3.000
 091  C5   C1   C3   109.55  3.000
 091  C3   C1   C2   102.29  3.000
 091  C4   C1   C2   116.69  3.000
 091  C5   C1   C2   113.64  3.000
 091  C7   C2   C6   119.95  3.000
 091  C6   C2   C1   108.95  3.000
 091  C7   C2   C1   131.09  3.000
 091  O1   C3   N1   125.79  3.000
 091  N1   C3   C1   107.75  3.000
 091  O1   C3   C1   126.45  3.000
 091  H2   C4   H1   107.35  3.000
 091  H2   C4   C8   112.55  3.000
 091  H1   C4   C8   110.37  3.000
 091  H2   C4   C1   111.54  3.000
 091  H1   C4   C1   110.69  3.000
 091  C8   C4   C1   104.39  3.000
 091  H4   C5   H3   107.46  3.000
 091  H4   C5   N2   111.89  3.000
 091  H3   C5   N2   109.34  3.000
 091  H4   C5   C1   113.27  3.000
 091  H3   C5   C1   107.76  3.000
 091  N2   C5   C1   107.01  3.000
 091  C9   C6   N1   128.98  3.000
 091  N1   C6   C2   108.96  3.000
 091  C9   C6   C2   122.06  3.000
 091  H5   C7   C10  120.33  3.000
 091  H5   C7   C2   120.65  3.000
 091  C10  C7   C2   119.02  3.000
 091  H6   N1   C6   124.56  3.000
 091  H6   N1   C3   123.44  3.000
 091  C6   N1   C3   112.00  3.000
 091  H8   C8   H7   107.54  3.000
 091  H8   C8   N2   108.80  3.000
 091  H7   C8   N2   111.16  3.000
 091  H8   C8   C4   109.77  3.000
 091  H7   C8   C4   112.95  3.000
 091  N2   C8   C4   106.57  3.000
 091  H9   N2   C8   109.02  3.000
 091  H9   N2   C5   109.09  3.000
 091  C8   N2   C5   103.69  3.000
 091  H11  C9   C11  120.91  3.000
 091  H11  C9   C6   121.66  3.000
 091  C11  C9   C6   117.43  3.000
 091  H12  C10  C11  119.84  3.000
 091  H12  C10  C7   119.89  3.000
 091  C11  C10  C7   120.27  3.000
 091  H13  C11  C10  119.62  3.000
 091  H13  C11  C9   119.11  3.000
 091  C10  C11  C9   121.27  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
 091  CONST_01  C11  C10  C7   C2    0.00   0.0  0
 091  CONST_02  C11  C9   C6   C2    0.00   0.0  0
 091  CONST_03  C10  C7   C2   C6    0.00   0.0  0
 091  CONST_04  C10  C11  C9   C6    0.00   0.0  0
 091  CONST_05  C9   C11  C10  C7    0.00   0.0  0
 091  CONST_06  C9   C6   C2   C7    0.00   0.0  0
 091  CONST_07  C6   N1   C3   C1    0.00   0.0  0
 091  CONST_08  O1   C3   N1   C6  180.00   0.0  0
 091  CONST_09  H5   C7   C2   C1    0.00   0.0  0
 091  CONST_10  H12  C10  C7   C2  180.00   0.0  0
 091  CONST_11  H11  C9   C6   C2  180.00   0.0  0
 091  CONST_12  H13  C11  C9   C6  180.00   0.0  0
 091  CONST_13  H6   N1   C3   C1  180.00   0.0  0
 091  Var_01    C8   N2   C5   C1   38.27  30.0  1
 091  Var_02    N2   C8   C4   C1   24.28  30.0  1
 091  Var_03    C5   N2   C8   C4  -38.99  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
 091  chir_01  C1  C4  C2  C3  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
 091  plan-1  C1   0.020
 091  plan-1  C2   0.020
 091  plan-1  C3   0.020
 091  plan-1  C6   0.020
 091  plan-1  C7   0.020
 091  plan-1  N1   0.020
 091  plan-1  O1   0.020
 091  plan-1  C9   0.020
 091  plan-1  C10  0.020
 091  plan-1  C11  0.020
 091  plan-1  H5   0.020
 091  plan-1  H6   0.020
 091  plan-1  H11  0.020
 091  plan-1  H12  0.020
 091  plan-1  H13  0.020

