# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:37:03 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: (2R)-1',4'-dihydro-2'H-spiro[pyrrolidine-2,3'-quinolin]-2'-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ccccc2C[C@]13CCCN3
#
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
 W2M  W2M  (2R)-1',4'-dihydro-2'H-spiro[pyrrolidine-2,3'-quinolin]-2'-one  ligand  29  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W2M
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
 W2M  N1   N  NR15  0  -0.607  23.3089  41.3969  -25.6058
 W2M  C4   C  CR16  0  -0.258  26.1727  35.9936  -26.2831
 W2M  C5   C  CR16  0  -0.268  27.3585  36.4132  -25.6961
 W2M  C6   C  CR16  0  -0.318  27.4450  37.6698  -25.1139
 W2M  C7   C  CH2   0  -0.465  23.9670  39.0284  -25.5884
 W2M  C8   C  CR5   0  -0.030  24.4270  40.4744  -25.7701
 W2M  C10  C  CH2   0  -0.445  24.3277  42.0039  -27.6610
 W2M  C    C  C     0   0.526  25.5225  40.7792  -24.7546
 W2M  C11  C  CH2   0  -0.467  25.0016  40.7136  -27.2065
 W2M  C9   C  CH2   0  -0.322  22.9935  41.9308  -26.9279
 W2M  C2   C  CR6   0   0.070  25.1277  38.0878  -25.6811
 W2M  C3   C  CR16  0  -0.337  25.0667  36.8354  -26.2732
 W2M  C1   C  CR6   0   0.356  26.3321  38.5026  -25.1116
 W2M  N    N  NH1   0  -0.729  26.3952  39.7679  -24.5243
 W2M  H1   H  HNR5  0   0.352  23.6076  42.1636  -25.0140
 W2M  H3   H  HCR6  0   0.254  26.1086  35.0186  -26.7478
 W2M  H4   H  HCR6  0   0.259  28.2260  35.7664  -25.6984
 W2M  H5   H  HCR6  0   0.269  28.3745  38.0039  -24.6687
 W2M  H6   H  HCH2  0   0.264  23.4859  38.9293  -24.6087
 W2M  H7   H  HCH2  0   0.262  23.2083  38.7925  -26.3371
 W2M  H8   H  HCH2  0   0.230  24.8926  42.8773  -27.3254
 W2M  H9   H  HCH2  0   0.237  24.2284  42.0664  -28.7453
 W2M  H10  H  HCH2  0   0.247  24.7112  39.8836  -27.8554
 W2M  H11  H  HCH2  0   0.257  26.0907  40.7688  -27.2344
 W2M  H12  H  HCH2  0   0.242  22.4850  42.8906  -26.8349
 W2M  H13  H  HCH2  0   0.220  22.3138  41.2511  -27.4513
 W2M  H14  H  HCR6  0   0.253  24.1371  36.5126  -26.7268
 W2M  H15  H  HNH1  0   0.407  27.1934  39.9815  -23.9420
 W2M  O    O  O     0  -0.460  25.6396  41.8632  -24.2100

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
 W2M  C10  C11  single    1.525  0.020  1.525
 W2M  C10  C9   single    1.524  0.020  1.524
 W2M  C11  C8   single    1.565  0.020  1.565
 W2M  C9   N1   single    1.460  0.020  1.460
 W2M  C4   C3   aromatic  1.390  0.020  1.390
 W2M  C4   C5   aromatic  1.388  0.020  1.388
 W2M  C3   C2   aromatic  1.387  0.020  1.387
 W2M  C5   C6   aromatic  1.388  0.020  1.388
 W2M  C8   N1   single    1.459  0.020  1.459
 W2M  C8   C7   single    1.528  0.020  1.528
 W2M  C8   C    single    1.525  0.020  1.525
 W2M  C2   C7   single    1.497  0.020  1.497
 W2M  C2   C1   aromatic  1.395  0.020  1.395
 W2M  C6   C1   aromatic  1.390  0.020  1.390
 W2M  C1   N    single    1.396  0.020  1.396
 W2M  C    N    single    1.356  0.020  1.356
 W2M  C    O    double    1.219  0.020  1.219
 W2M  N1   H1   single    0.890  0.020  1.040
 W2M  C4   H3   single    0.930  0.020  1.080
 W2M  C5   H4   single    0.930  0.020  1.080
 W2M  C6   H5   single    0.930  0.020  1.080
 W2M  C7   H6   single    0.970  0.020  1.090
 W2M  C7   H7   single    0.970  0.020  1.090
 W2M  C10  H8   single    0.970  0.020  1.090
 W2M  C10  H9   single    0.970  0.020  1.090
 W2M  C11  H10  single    0.970  0.020  1.090
 W2M  C11  H11  single    0.970  0.020  1.090
 W2M  C9   H12  single    0.970  0.020  1.090
 W2M  C9   H13  single    0.970  0.020  1.090
 W2M  C3   H14  single    0.930  0.020  1.080
 W2M  N    H15  single    0.860  0.020  1.020

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
 W2M  H1   N1   C9   108.40  3.000
 W2M  H1   N1   C8   108.56  3.000
 W2M  C9   N1   C8   107.14  3.000
 W2M  H3   C4   C3   120.11  3.000
 W2M  H3   C4   C5   120.31  3.000
 W2M  C3   C4   C5   119.59  3.000
 W2M  H4   C5   C6   119.49  3.000
 W2M  H4   C5   C4   120.22  3.000
 W2M  C6   C5   C4   120.29  3.000
 W2M  H5   C6   C1   120.10  3.000
 W2M  H5   C6   C5   120.34  3.000
 W2M  C1   C6   C5   119.56  3.000
 W2M  H7   C7   H6   106.77  3.000
 W2M  H7   C7   C2   111.14  3.000
 W2M  H6   C7   C2   109.81  3.000
 W2M  H7   C7   C8   109.39  3.000
 W2M  H6   C7   C8   108.90  3.000
 W2M  C2   C7   C8   110.72  3.000
 W2M  C11  C8   C    108.48  3.000
 W2M  C    C8   C7   109.04  3.000
 W2M  C11  C8   C7   111.36  3.000
 W2M  C    C8   N1   110.44  3.000
 W2M  C7   C8   N1   110.75  3.000
 W2M  C11  C8   N1   106.74  3.000
 W2M  H9   C10  H8   107.85  3.000
 W2M  H9   C10  C9   113.66  3.000
 W2M  H8   C10  C9   110.07  3.000
 W2M  H9   C10  C11  112.65  3.000
 W2M  H8   C10  C11  110.87  3.000
 W2M  C9   C10  C11  101.70  3.000
 W2M  N    C    O    121.73  3.000
 W2M  O    C    C8   122.99  3.000
 W2M  N    C    C8   115.25  3.000
 W2M  H11  C11  H10  106.77  3.000
 W2M  H11  C11  C10  113.00  3.000
 W2M  H10  C11  C10  110.38  3.000
 W2M  H11  C11  C8   113.43  3.000
 W2M  H10  C11  C8   109.34  3.000
 W2M  C10  C11  C8   103.92  3.000
 W2M  H13  C9   H12  107.32  3.000
 W2M  H13  C9   C10  110.08  3.000
 W2M  H12  C9   C10  114.03  3.000
 W2M  H13  C9   N1   109.88  3.000
 W2M  H12  C9   N1   110.21  3.000
 W2M  C10  C9   N1   105.31  3.000
 W2M  C1   C2   C3   118.73  3.000
 W2M  C1   C2   C7   117.21  3.000
 W2M  C3   C2   C7   124.05  3.000
 W2M  H14  C3   C2   119.05  3.000
 W2M  H14  C3   C4   119.95  3.000
 W2M  C2   C3   C4   121.00  3.000
 W2M  N    C1   C2   118.69  3.000
 W2M  N    C1   C6   120.49  3.000
 W2M  C2   C1   C6   120.82  3.000
 W2M  H15  N    C1   118.00  3.000
 W2M  H15  N    C    116.65  3.000
 W2M  C1   N    C    125.14  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
 W2M  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 W2M  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 W2M  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 W2M  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 W2M  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 W2M  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 W2M  CONST_07  C1   N    C    C8     0.00   0.0  0
 W2M  CONST_08  C1   N    C    O    180.00   0.0  0
 W2M  CONST_09  H5   C6   C5   C4   180.00   0.0  0
 W2M  CONST_10  H14  C3   C4   C5   180.00   0.0  0
 W2M  CONST_11  H3   C4   C5   C6   180.00   0.0  0
 W2M  CONST_12  H4   C5   C4   C3   180.00   0.0  0
 W2M  CONST_13  H15  N    C    C8   180.00   0.0  0
 W2M  Var_01    C11  C10  C9   N1    39.56  30.0  1
 W2M  Var_02    C    N    C1   C6   161.99  30.0  1
 W2M  Var_03    C9   C10  C11  C8   -30.52  30.0  1
 W2M  Var_04    C10  C9   N1   C8   -33.04  30.0  1
 W2M  Var_05    C3   C2   C7   C8  -143.00  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
 W2M  chir_01  C8  N1  C7  C  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
 W2M  plan-1  C8   0.020
 W2M  plan-1  C    0.020
 W2M  plan-1  C1   0.020
 W2M  plan-1  N    0.020
 W2M  plan-1  H15  0.020
 W2M  plan-1  O    0.020
 W2M  plan-2  C4   0.020
 W2M  plan-2  C5   0.020
 W2M  plan-2  C6   0.020
 W2M  plan-2  C7   0.020
 W2M  plan-2  C2   0.020
 W2M  plan-2  C3   0.020
 W2M  plan-2  C1   0.020
 W2M  plan-2  N    0.020
 W2M  plan-2  H3   0.020
 W2M  plan-2  H4   0.020
 W2M  plan-2  H5   0.020
 W2M  plan-2  H14  0.020

