# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:02:28 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (3S)-1-[(2-fluorophenoxy)acetyl]-N-(pyridin-2-yl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1OCC(=O)N2CC[C@@H](C2)C(=O)Nc3ccccn3
#
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
 L7W  L7W  "(3S)-1-[(2-fluorophenoxy)acetyl]-N-(pyridin-2-yl)pyrrolidine-3-carboxamide"
  ligand  43  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L7W
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
 L7W  O2   O  O     0  -0.486  -82.7434   -0.1915  32.9991
 L7W  C10  C  C     0   0.492  -82.8255   -1.4085  32.8968
 L7W  C11  C  CH2   0  -0.339  -83.7519   -2.0153  31.8455
 L7W  O1   O  O2    0  -0.474  -83.2148   -3.1239  31.1613
 L7W  C12  C  CR6   0   0.243  -82.0923   -2.9498  30.4332
 L7W  C17  C  CR16  0  -0.347  -81.5590   -1.7276  30.0417
 L7W  C16  C  CR16  0  -0.255  -80.4001   -1.6851  29.2727
 L7W  C15  C  CR16  0  -0.259  -79.7635   -2.8520  28.8861
 L7W  C14  C  CR16  0  -0.405  -80.2854   -4.0810  29.2760
 L7W  C13  C  CR6   0   0.455  -81.4296   -4.1127  30.0388
 L7W  F    F  F     0  -0.313  -81.9335   -5.2938  30.4291
 L7W  N2   N  NT    0  -0.461  -82.1430   -2.2436  33.6913
 L7W  C8   C  CH2   0  -0.268  -81.2315   -1.7110  34.7009
 L7W  C7   C  CH2   0  -0.465  -80.6173   -2.9573  35.3191
 L7W  C9   C  CH2   0  -0.230  -82.3136   -3.6891  33.8098
 L7W  C6   C  CH1   0  -0.452  -81.7459   -3.9882  35.1931
 L7W  C5   C  C     0   0.581  -81.2401   -5.4083  35.3318
 L7W  O    O  O     0  -0.449  -80.7016   -5.9978  34.4143
 L7W  N1   N  NH1   0  -0.712  -81.4082   -5.9300  36.5750
 L7W  C4   C  CR6   0   0.483  -81.0074   -7.1650  37.0804
 L7W  C    C  CR16  0  -0.369  -80.4070   -8.1742  36.3248
 L7W  N    N  N     0  -0.448  -81.2647   -7.2963  38.3764
 L7W  C3   C  CR16  0  -0.063  -80.9352   -8.4292  38.9808
 L7W  C2   C  CR16  0  -0.335  -80.3327   -9.4926  38.3308
 L7W  C1   C  CR16  0  -0.149  -80.0712   -9.3486  36.9759
 L7W  H1   H  HCH2  0   0.276  -84.0507   -1.2175  31.1603
 L7W  H2   H  HCH2  0   0.297  -84.6584   -2.3815  32.3332
 L7W  H3   H  HCR6  0   0.292  -82.0340   -0.7972  30.3216
 L7W  H4   H  HCR6  0   0.264  -80.0014   -0.7238  28.9781
 L7W  H5   H  HCR6  0   0.264  -78.8638   -2.8166  28.2875
 L7W  H6   H  HCR6  0   0.281  -79.8059   -5.0094  28.9936
 L7W  H7   H  HCH2  0   0.257  -80.4852   -1.0566  34.2504
 L7W  H8   H  HCH2  0   0.246  -81.7823   -1.1290  35.4443
 L7W  H9   H  HCH2  0   0.256  -79.7477   -3.2823  34.7438
 L7W  H10  H  HCH2  0   0.271  -80.3031   -2.7956  36.3489
 L7W  H11  H  HCH2  0   0.269  -83.3600   -3.9833  33.7303
 L7W  H12  H  HCH2  0   0.254  -81.7432   -4.2223  33.0492
 L7W  H13  H  HCH1  0   0.291  -82.5045   -3.7776  35.9522
 L7W  H14  H  HNH1  0   0.412  -81.8574   -5.3475  37.2680
 L7W  H15  H  HCR6  0   0.289  -80.2104   -8.0513  35.2733
 L7W  H16  H  HCR6  0   0.266  -81.1644   -8.4893  40.0388
 L7W  H17  H  HCR6  0   0.268  -80.0813  -10.3971  38.8663
 L7W  H18  H  HCR6  0   0.274  -79.6051  -10.1505  36.4182

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
 L7W  C16  C15  aromatic  1.384  0.020  1.384
 L7W  C16  C17  aromatic  1.392  0.020  1.392
 L7W  C15  C14  aromatic  1.391  0.020  1.391
 L7W  C17  C12  aromatic  1.390  0.020  1.390
 L7W  C14  C13  aromatic  1.375  0.020  1.375
 L7W  C12  C13  aromatic  1.395  0.020  1.395
 L7W  C12  O1   single    1.349  0.020  1.349
 L7W  C13  F    single    1.342  0.020  1.342
 L7W  O1   C11  single    1.409  0.020  1.409
 L7W  C11  C10  single    1.527  0.020  1.527
 L7W  O2   C10  double    1.224  0.020  1.224
 L7W  C10  N2   single    1.340  0.020  1.340
 L7W  N2   C9   single    1.460  0.020  1.460
 L7W  N2   C8   single    1.461  0.020  1.461
 L7W  O    C5   double    1.216  0.020  1.216
 L7W  C9   C6   single    1.525  0.020  1.525
 L7W  C8   C7   single    1.521  0.020  1.521
 L7W  C5   C6   single    1.514  0.020  1.514
 L7W  C5   N1   single    1.359  0.020  1.359
 L7W  C    C1   aromatic  1.384  0.020  1.384
 L7W  C    C4   aromatic  1.396  0.020  1.396
 L7W  C6   C7   single    1.534  0.020  1.534
 L7W  C1   C2   aromatic  1.387  0.020  1.387
 L7W  N1   C4   single    1.393  0.020  1.393
 L7W  C4   N    aromatic  1.328  0.020  1.328
 L7W  C2   C3   aromatic  1.384  0.020  1.384
 L7W  N    C3   aromatic  1.326  0.020  1.326
 L7W  C11  H1   single    0.970  0.020  1.090
 L7W  C11  H2   single    0.970  0.020  1.090
 L7W  C17  H3   single    0.930  0.020  1.080
 L7W  C16  H4   single    0.930  0.020  1.080
 L7W  C15  H5   single    0.930  0.020  1.080
 L7W  C14  H6   single    0.930  0.020  1.080
 L7W  C8   H7   single    0.970  0.020  1.090
 L7W  C8   H8   single    0.970  0.020  1.090
 L7W  C7   H9   single    0.970  0.020  1.090
 L7W  C7   H10  single    0.970  0.020  1.090
 L7W  C9   H11  single    0.970  0.020  1.090
 L7W  C9   H12  single    0.970  0.020  1.090
 L7W  C6   H13  single    0.970  0.020  1.090
 L7W  N1   H14  single    0.860  0.020  1.020
 L7W  C    H15  single    0.930  0.020  1.080
 L7W  C3   H16  single    0.930  0.020  1.080
 L7W  C2   H17  single    0.930  0.020  1.080
 L7W  C1   H18  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
 L7W  N2   C10  C11  118.02  3.000
 L7W  N2   C10  O2   122.42  3.000
 L7W  C11  C10  O2   119.56  3.000
 L7W  H2   C11  H1   107.31  3.000
 L7W  H2   C11  O1   105.62  3.000
 L7W  H1   C11  O1   111.96  3.000
 L7W  H2   C11  C10  109.22  3.000
 L7W  H1   C11  C10  107.90  3.000
 L7W  O1   C11  C10  114.57  3.000
 L7W  C12  O1   C11  118.53  3.000
 L7W  C13  C12  C17  118.10  3.000
 L7W  C13  C12  O1   116.11  3.000
 L7W  C17  C12  O1   125.78  3.000
 L7W  H3   C17  C16  118.86  3.000
 L7W  H3   C17  C12  121.01  3.000
 L7W  C16  C17  C12  120.14  3.000
 L7W  H4   C16  C15  120.24  3.000
 L7W  H4   C16  C17  118.98  3.000
 L7W  C15  C16  C17  120.77  3.000
 L7W  H5   C15  C14  119.76  3.000
 L7W  H5   C15  C16  120.64  3.000
 L7W  C14  C15  C16  119.60  3.000
 L7W  H6   C14  C13  119.57  3.000
 L7W  H6   C14  C15  121.23  3.000
 L7W  C13  C14  C15  119.20  3.000
 L7W  F    C13  C14  119.60  3.000
 L7W  F    C13  C12  118.22  3.000
 L7W  C14  C13  C12  122.18  3.000
 L7W  C9   N2   C8   112.19  3.000
 L7W  C8   N2   C10  120.04  3.000
 L7W  C9   N2   C10  127.28  3.000
 L7W  H8   C8   H7   107.85  3.000
 L7W  H8   C8   C7   111.31  3.000
 L7W  H7   C8   C7   112.55  3.000
 L7W  H8   C8   N2   110.47  3.000
 L7W  H7   C8   N2   111.13  3.000
 L7W  C7   C8   N2   103.54  3.000
 L7W  H10  C7   H9   108.22  3.000
 L7W  H10  C7   C6   112.94  3.000
 L7W  H9   C7   C6   110.04  3.000
 L7W  H10  C7   C8   112.29  3.000
 L7W  H9   C7   C8   110.57  3.000
 L7W  C6   C7   C8   102.72  3.000
 L7W  H12  C9   H11  108.63  3.000
 L7W  H12  C9   C6   110.01  3.000
 L7W  H11  C9   C6   111.76  3.000
 L7W  H12  C9   N2   111.49  3.000
 L7W  H11  C9   N2   111.93  3.000
 L7W  C6   C9   N2   102.96  3.000
 L7W  H13  C6   C5   110.42  3.000
 L7W  H13  C6   C9   109.49  3.000
 L7W  C5   C6   C9   113.05  3.000
 L7W  H13  C6   C7   108.90  3.000
 L7W  C5   C6   C7   112.15  3.000
 L7W  C9   C6   C7   102.51  3.000
 L7W  N1   C5   O    123.98  3.000
 L7W  N1   C5   C6   113.74  3.000
 L7W  O    C5   C6   122.24  3.000
 L7W  H14  N1   C4   112.96  3.000
 L7W  H14  N1   C5   117.46  3.000
 L7W  C4   N1   C5   129.54  3.000
 L7W  N    C4   C    122.68  3.000
 L7W  N    C4   N1   112.70  3.000
 L7W  C    C4   N1   124.61  3.000
 L7W  H15  C    C1   120.79  3.000
 L7W  H15  C    C4   121.64  3.000
 L7W  C1   C    C4   117.58  3.000
 L7W  C3   N    C4   118.78  3.000
 L7W  H16  C3   C2   120.50  3.000
 L7W  H16  C3   N    116.09  3.000
 L7W  C2   C3   N    123.41  3.000
 L7W  H17  C2   C1   121.80  3.000
 L7W  H17  C2   C3   120.76  3.000
 L7W  C1   C2   C3   117.44  3.000
 L7W  H18  C1   C2   120.50  3.000
 L7W  H18  C1   C    119.39  3.000
 L7W  C2   C1   C    120.11  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
 L7W  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 L7W  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 L7W  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 L7W  CONST_04  C14  C13  C12  C17     0.00   0.0  0
 L7W  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 L7W  CONST_06  C13  C12  C17  C16     0.00   0.0  0
 L7W  CONST_07  C2   C1   C    C4      0.00   0.0  0
 L7W  CONST_08  C2   C3   N    C4      0.00   0.0  0
 L7W  CONST_09  C3   C2   C1   C       0.00   0.0  0
 L7W  CONST_10  C3   N    C4   C       0.00   0.0  0
 L7W  CONST_11  C1   C    C4   N       0.00   0.0  0
 L7W  CONST_12  C1   C2   C3   N       0.00   0.0  0
 L7W  CONST_13  C16  C17  C12  O1    180.00   0.0  0
 L7W  CONST_14  C14  C13  C12  O1    180.00   0.0  0
 L7W  CONST_15  F    C13  C12  C17   180.00   0.0  0
 L7W  CONST_16  F    C13  C14  C15   180.00   0.0  0
 L7W  CONST_17  C1   C    C4   N1    180.00   0.0  0
 L7W  CONST_18  C3   N    C4   N1    180.00   0.0  0
 L7W  CONST_19  H4   C16  C17  C12   180.00   0.0  0
 L7W  CONST_20  H6   C14  C13  C12   180.00   0.0  0
 L7W  CONST_21  H5   C15  C16  C17   180.00   0.0  0
 L7W  CONST_22  H6   C14  C15  C16   180.00   0.0  0
 L7W  CONST_23  H3   C17  C16  C15   180.00   0.0  0
 L7W  CONST_24  H4   C16  C15  C14   180.00   0.0  0
 L7W  CONST_25  H5   C15  C14  C13   180.00   0.0  0
 L7W  CONST_26  H3   C17  C12  C13   180.00   0.0  0
 L7W  CONST_27  H18  C1   C    C4    180.00   0.0  0
 L7W  CONST_28  H16  C3   N    C4    180.00   0.0  0
 L7W  CONST_29  H17  C2   C1   C     180.00   0.0  0
 L7W  CONST_30  H15  C    C4   N     180.00   0.0  0
 L7W  CONST_31  H17  C2   C3   N     180.00   0.0  0
 L7W  CONST_32  H18  C1   C2   C3    180.00   0.0  0
 L7W  CONST_33  H15  C    C1   C2    180.00   0.0  0
 L7W  CONST_34  H16  C3   C2   C1    180.00   0.0  0
 L7W  CONST_35  C9   N2   C10  O2    180.00   0.0  0
 L7W  CONST_36  C8   N2   C10  O2      0.00   0.0  0
 L7W  CONST_37  C9   N2   C10  C11     0.00   0.0  0
 L7W  CONST_38  C8   N2   C10  C11   180.00   0.0  0
 L7W  CONST_39  C4   N1   C5   C6    180.00   0.0  0
 L7W  CONST_40  C    C4   N1   C5      0.00   0.0  0
 L7W  CONST_41  N    C4   N1   C5    180.00   0.0  0
 L7W  CONST_42  H14  N1   C4   C     180.00   0.0  0
 L7W  CONST_43  H14  N1   C4   N       0.00   0.0  0
 L7W  CONST_44  C4   N1   C5   O       0.00   0.0  0
 L7W  CONST_45  H14  N1   C5   C6      0.00   0.0  0
 L7W  CONST_46  H14  N1   C5   O     180.00   0.0  0
 L7W  Var_01    C6   C7   C8   N2    -31.03  30.0  1
 L7W  Var_02    C6   C9   N2   C8     14.78  30.0  1
 L7W  Var_03    C9   N2   C8   C7     10.38  30.0  1
 L7W  Var_04    C6   C9   N2   C10  -157.07  30.0  1
 L7W  Var_05    C7   C8   N2   C10  -177.11  30.0  1
 L7W  Var_06    H9   C7   C8   N2     86.35  30.0  1
 L7W  Var_07    H10  C7   C8   N2   -152.67  30.0  1
 L7W  Var_08    H11  C9   N2   C8    134.96  30.0  1
 L7W  Var_09    H12  C9   N2   C8   -103.13  30.0  1
 L7W  Var_10    H7   C8   N2   C9    131.44  30.0  1
 L7W  Var_11    H8   C8   N2   C9   -108.90  30.0  1
 L7W  Var_12    H7   C8   C7   C6   -151.13  30.0  1
 L7W  Var_13    H8   C8   C7   C6     87.66  30.0  1
 L7W  Var_14    C17  C12  O1   C11   -15.10  30.0  2
 L7W  Var_15    C13  C12  O1   C11   165.48  30.0  2
 L7W  Var_16    H11  C9   N2   C10   -36.90  30.0  1
 L7W  Var_17    H12  C9   N2   C10    85.02  30.0  1
 L7W  Var_18    H7   C8   N2   C10   -56.05  30.0  1
 L7W  Var_19    H8   C8   N2   C10    63.62  30.0  1
 L7W  Var_20    C12  O1   C11  C10   -61.36  30.0  1
 L7W  Var_21    N2   C10  C11  O1    -42.50  30.0  3
 L7W  Var_22    H1   C11  O1   C12    61.92  30.0  3
 L7W  Var_23    H2   C11  O1   C12   178.40  30.0  3
 L7W  Var_24    H1   C11  C10  N2   -167.94  30.0  2
 L7W  Var_25    H2   C11  C10  N2     75.72  30.0  2
 L7W  Var_26    O1   C11  C10  O2    138.46  30.0  2
 L7W  Var_27    H1   C11  C10  O2     13.02  30.0  2
 L7W  Var_28    H2   C11  C10  O2   -103.32  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
 L7W  chir_01  C6  C9  C5  C7  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
 L7W  plan-1  O1   0.020
 L7W  plan-1  C12  0.020
 L7W  plan-1  C17  0.020
 L7W  plan-1  C16  0.020
 L7W  plan-1  C15  0.020
 L7W  plan-1  C14  0.020
 L7W  plan-1  C13  0.020
 L7W  plan-1  F    0.020
 L7W  plan-1  H3   0.020
 L7W  plan-1  H4   0.020
 L7W  plan-1  H5   0.020
 L7W  plan-1  H6   0.020
 L7W  plan-2  N1   0.020
 L7W  plan-2  C4   0.020
 L7W  plan-2  C    0.020
 L7W  plan-2  N    0.020
 L7W  plan-2  C3   0.020
 L7W  plan-2  C2   0.020
 L7W  plan-2  C1   0.020
 L7W  plan-2  H15  0.020
 L7W  plan-2  H16  0.020
 L7W  plan-2  H17  0.020
 L7W  plan-2  H18  0.020
 L7W  plan-3  C6   0.020
 L7W  plan-3  C5   0.020
 L7W  plan-3  O    0.020
 L7W  plan-3  N1   0.020
 L7W  plan-3  C4   0.020
 L7W  plan-3  H14  0.020
 L7W  plan-4  O2   0.020
 L7W  plan-4  C10  0.020
 L7W  plan-4  C11  0.020
 L7W  plan-4  N2   0.020
 L7W  plan-4  C8   0.020
 L7W  plan-4  C9   0.020

