# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:46:44 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: (3R)-1-(2-fluorophenyl)-3-(methylamino)pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1CCN(C1=O)c2ccccc2F
#
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
 W0G  W0G  (3R)-1-(2-fluorophenyl)-3-(methylamino)pyrrolidin-2-one  ligand  28  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_W0G
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
 W0G  N1   N  NT    0  -0.572  21.2664  45.0490  10.8010
 W0G  C4   C  C     0   0.545  20.3505  44.4839  11.6217
 W0G  C5   C  CR6   0   0.150  21.1480  46.3647  10.3162
 W0G  C6   C  CR16  0  -0.267  21.6642  47.4440  11.0216
 W0G  C7   C  CR16  0  -0.271  21.5417  48.7338  10.5251
 W0G  C8   C  CR16  0  -0.237  20.9029  48.9496   9.3110
 W0G  C10  C  CR6   0   0.529  20.5080  46.6108   9.1086
 W0G  F    F  F     0  -0.302  19.9977  45.5716   8.4359
 W0G  C9   C  CR16  0  -0.418  20.3799  47.8840   8.5911
 W0G  C3   C  CH2   0  -0.274  22.2777  44.1175  10.3162
 W0G  C2   C  CH2   0  -0.486  22.1902  42.9805  11.3297
 W0G  O    O  O     0  -0.467  19.4006  45.0541  12.1182
 W0G  C1   C  CH1   0  -0.226  20.7230  43.0142  11.7769
 W0G  N    N  NH1   0  -0.587  20.3798  42.5055  13.0756
 W0G  C    C  CH3   0  -0.525  20.5510  41.0709  13.1957
 W0G  H1   H  HCR6  0   0.274  22.1657  47.2603  11.9630
 W0G  H2   H  HCR6  0   0.267  21.9437  49.5676  11.0842
 W0G  H3   H  HCR6  0   0.273  20.8068  49.9527   8.9180
 W0G  H4   H  HCR6  0   0.285  19.8765  48.0391   7.6459
 W0G  H5   H  HCH2  0   0.247  22.0424  43.7785   9.3036
 W0G  H6   H  HCH2  0   0.262  23.2566  44.5958  10.2933
 W0G  H7   H  HCH2  0   0.261  22.4921  42.0268  10.9013
 W0G  H8   H  HCH2  0   0.249  22.8380  43.1915  12.1844
 W0G  H9   H  HCH1  0   0.275  20.1182  42.4729  11.0358
 W0G  H10  H  HNH1  0   0.346  20.9305  42.9734  13.7852
 W0G  H12  H  HCH3  0   0.236  20.2856  40.7578  14.2049
 W0G  H13  H  HCH3  0   0.226  19.8758  40.5619  12.5055
 W0G  H14  H  HCH3  0   0.203  21.5669  40.7086  12.9913

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
 W0G  F    C10  single    1.339  0.020  1.339
 W0G  C9   C10  aromatic  1.380  0.020  1.380
 W0G  C9   C8   aromatic  1.388  0.020  1.388
 W0G  C10  C5   aromatic  1.389  0.020  1.389
 W0G  C8   C7   aromatic  1.389  0.020  1.389
 W0G  C3   N1   single    1.458  0.020  1.458
 W0G  C3   C2   single    1.526  0.020  1.526
 W0G  C5   N1   single    1.407  0.020  1.407
 W0G  C5   C6   aromatic  1.389  0.020  1.389
 W0G  N1   C4   single    1.353  0.020  1.353
 W0G  C7   C6   aromatic  1.388  0.020  1.388
 W0G  C2   C1   single    1.534  0.020  1.534
 W0G  C4   C1   single    1.524  0.020  1.524
 W0G  C4   O    double    1.214  0.020  1.214
 W0G  C1   N    single    1.436  0.020  1.436
 W0G  N    C    single    1.450  0.020  1.450
 W0G  C6   H1   single    0.930  0.020  1.080
 W0G  C7   H2   single    0.930  0.020  1.080
 W0G  C8   H3   single    0.930  0.020  1.080
 W0G  C9   H4   single    0.930  0.020  1.080
 W0G  C3   H5   single    0.970  0.020  1.090
 W0G  C3   H6   single    0.970  0.020  1.090
 W0G  C2   H7   single    0.970  0.020  1.090
 W0G  C2   H8   single    0.970  0.020  1.090
 W0G  C1   H9   single    0.970  0.020  1.090
 W0G  N    H10  single    0.890  0.020  1.040
 W0G  C    H12  single    0.970  0.020  1.090
 W0G  C    H13  single    0.970  0.020  1.090
 W0G  C    H14  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
 W0G  C3   N1   C5   122.77  3.000
 W0G  C5   N1   C4   122.84  3.000
 W0G  C3   N1   C4   113.85  3.000
 W0G  C1   C4   O    127.05  3.000
 W0G  O    C4   N1   125.55  3.000
 W0G  C1   C4   N1   107.40  3.000
 W0G  C10  C5   C6   118.38  3.000
 W0G  C6   C5   N1   121.35  3.000
 W0G  C10  C5   N1   120.27  3.000
 W0G  H1   C6   C7   120.66  3.000
 W0G  H1   C6   C5   118.82  3.000
 W0G  C7   C6   C5   120.52  3.000
 W0G  H2   C7   C8   120.21  3.000
 W0G  H2   C7   C6   119.93  3.000
 W0G  C8   C7   C6   119.86  3.000
 W0G  H3   C8   C9   119.34  3.000
 W0G  H3   C8   C7   120.18  3.000
 W0G  C9   C8   C7   120.48  3.000
 W0G  C9   C10  F    119.48  3.000
 W0G  C9   C10  C5   122.16  3.000
 W0G  F    C10  C5   118.36  3.000
 W0G  H4   C9   C10  120.19  3.000
 W0G  H4   C9   C8   121.21  3.000
 W0G  C10  C9   C8   118.60  3.000
 W0G  H6   C3   H5   108.06  3.000
 W0G  H6   C3   C2   113.12  3.000
 W0G  H5   C3   C2   111.83  3.000
 W0G  H6   C3   N1   110.47  3.000
 W0G  H5   C3   N1   110.90  3.000
 W0G  C2   C3   N1   102.44  3.000
 W0G  H8   C2   H7   108.21  3.000
 W0G  H8   C2   C1   109.55  3.000
 W0G  H7   C2   C1   113.54  3.000
 W0G  H8   C2   C3   109.98  3.000
 W0G  H7   C2   C3   112.07  3.000
 W0G  C1   C2   C3   103.43  3.000
 W0G  H9   C1   N    107.68  3.000
 W0G  H9   C1   C2   108.59  3.000
 W0G  N    C1   C2   118.97  3.000
 W0G  H9   C1   C4   105.77  3.000
 W0G  N    C1   C4   112.04  3.000
 W0G  C2   C1   C4   103.02  3.000
 W0G  H10  N    C    109.57  3.000
 W0G  H10  N    C1   109.87  3.000
 W0G  C    N    C1   113.40  3.000
 W0G  H14  C    H13  107.51  3.000
 W0G  H14  C    H12  107.64  3.000
 W0G  H13  C    H12  107.52  3.000
 W0G  H14  C    N    114.86  3.000
 W0G  H13  C    N    109.63  3.000
 W0G  H12  C    N    109.41  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
 W0G  CONST_01  C8   C9   C10  C5    0.00   0.0  0
 W0G  CONST_02  C8   C7   C6   C5    0.00   0.0  0
 W0G  CONST_03  C9   C10  C5   C6    0.00   0.0  0
 W0G  CONST_04  C9   C8   C7   C6    0.00   0.0  0
 W0G  CONST_05  C10  C9   C8   C7    0.00   0.0  0
 W0G  CONST_06  C10  C5   C6   C7    0.00   0.0  0
 W0G  CONST_07  C9   C10  C5   N1  180.00   0.0  0
 W0G  CONST_08  C7   C6   C5   N1  180.00   0.0  0
 W0G  CONST_09  C1   C4   N1   C5  180.00   0.0  0
 W0G  CONST_10  C1   C4   N1   C3    0.00   0.0  0
 W0G  CONST_11  F    C10  C5   N1    0.00   0.0  0
 W0G  CONST_12  F    C10  C5   C6  180.00   0.0  0
 W0G  CONST_13  F    C10  C9   C8  180.00   0.0  0
 W0G  CONST_14  O    C4   N1   C5    0.00   0.0  0
 W0G  CONST_15  O    C4   N1   C3  180.00   0.0  0
 W0G  CONST_16  H1   C6   C5   N1    0.00   0.0  0
 W0G  CONST_17  H4   C9   C10  C5  180.00   0.0  0
 W0G  CONST_18  H2   C7   C6   C5  180.00   0.0  0
 W0G  CONST_19  H3   C8   C7   C6  180.00   0.0  0
 W0G  Var_01    C1   C2   C3   N1   29.78  30.0  1
 W0G  Var_02    C2   C3   N1   C4  -19.88  30.0  1
 W0G  Var_03    C10  C5   N1   C4  -91.27  30.0  2
 W0G  Var_04    H12  C    N    C1  179.30  30.0  3

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
 W0G  chir_01  C1  C2  C4  N  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
 W0G  plan-1  N1   0.020
 W0G  plan-1  C5   0.020
 W0G  plan-1  C6   0.020
 W0G  plan-1  C7   0.020
 W0G  plan-1  C8   0.020
 W0G  plan-1  C10  0.020
 W0G  plan-1  F    0.020
 W0G  plan-1  C9   0.020
 W0G  plan-1  H1   0.020
 W0G  plan-1  H2   0.020
 W0G  plan-1  H3   0.020
 W0G  plan-1  H4   0.020
 W0G  plan-2  N1   0.020
 W0G  plan-2  C4   0.020
 W0G  plan-2  C5   0.020
 W0G  plan-2  C3   0.020
 W0G  plan-2  O    0.020
 W0G  plan-2  C1   0.020

