# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:55:29 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-[(2S)-2-(3-fluorophenyl)pyrrolidin-1-yl]-2,2-dimethylpropan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C(=O)N1CCC[C@H]1c2cccc(F)c2
#
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
 M5J  M5J  1-[(2S)-2-(3-fluorophenyl)pyrrolidin-1-yl]-2,2-dimethylpropan-1-one  ligand  38  18  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M5J
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
 M5J  C1   C  CR16  0  -0.227   3.5241  -0.1184  -1.3795
 M5J  C10  C  CH2   0  -0.297  -1.5841   1.6290   1.1086
 M5J  C11  C  CH1   0  -0.114   0.1762   1.4497  -0.5335
 M5J  C12  C  CH3   0  -0.625  -2.8409  -2.3765  -0.7169
 M5J  C13  C  CH3   0  -0.645  -4.0151  -0.2314  -0.3413
 M5J  C14  C  CH3   0  -0.652  -2.6091  -1.2783   1.4873
 M5J  C15  C  CT    0  -0.241  -2.7354  -1.0176  -0.0179
 M5J  C2   C  CR16  0  -0.334   2.3512   0.6185  -1.4767
 M5J  C3   C  CR16  0  -0.428   3.7755  -0.9048  -0.2640
 M5J  C4   C  CR16  0  -0.464   1.6558  -0.1926   0.6716
 M5J  C5   C  CR6   0   0.185   1.4102   0.5883  -0.4539
 M5J  C6   C  CR6   0   0.541   2.8251  -0.9217   0.7393
 M5J  C8   C  CH2   0  -0.461  -1.0888   3.0254   0.7691
 M5J  C9   C  CH2   0  -0.475   0.3221   2.7499   0.2718
 M5J  F18  F  F     0  -0.319   3.0481  -1.6776   1.8293
 M5J  N16  N  NT    0  -0.493  -1.0100   0.8118   0.0422
 M5J  O17  O  O     0  -0.491  -0.9626  -0.6859  -1.6010
 M5J  H1   H  HCR6  0   0.266   4.2487  -0.0878  -2.1822
 M5J  H2   H  HCH2  0   0.242  -1.2060   1.3174   2.0870
 M5J  H3   H  HCH2  0   0.260  -2.6671   1.5684   1.1357
 M5J  H4   H  HCH1  0   0.263  -0.0143   1.6895  -1.5838
 M5J  H5   H  HCH3  0   0.223  -3.6955  -2.9202  -0.3108
 M5J  H6   H  HCH3  0   0.229  -2.9954  -2.2735  -1.7901
 M5J  H7   H  HCH3  0   0.228  -1.9531  -2.9900  -0.5600
 M5J  H8   H  HCH3  0   0.238  -4.8837  -0.7925   0.0078
 M5J  H9   H  HCH3  0   0.238  -4.0578   0.7497   0.1290
 M5J  H10  H  HCH3  0   0.236  -4.1243  -0.0903  -1.4178
 M5J  H11  H  HCH3  0   0.233  -1.6634  -1.7682   1.7271
 M5J  H12  H  HCH3  0   0.244  -2.6827  -0.3826   2.0989
 M5J  H13  H  HCH3  0   0.238  -3.4113  -1.9460   1.8051
 M5J  H14  H  HCR6  0   0.251   2.1653   1.2211  -2.3575
 M5J  H15  H  HCR6  0   0.276   4.6813  -1.4903  -0.1777
 M5J  H16  H  HCR6  0   0.265   0.9459  -0.2419   1.4885
 M5J  H17  H  HCH2  0   0.241  -1.7025   3.4568  -0.0246
 M5J  H18  H  HCH2  0   0.254  -1.1196   3.6950   1.6276
 M5J  H19  H  HCH2  0   0.244   0.9938   2.6014   1.1203
 M5J  H20  H  HCH2  0   0.262   0.7388   3.5496  -0.3390
 M5J  C7   C  C     0   0.609  -1.5101  -0.2806  -0.5828

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
 M5J  C9   C8   single    1.521  0.020  1.521
 M5J  C9   C11  single    1.536  0.020  1.536
 M5J  C8   C10  single    1.520  0.020  1.520
 M5J  C11  C5   single    1.507  0.020  1.507
 M5J  C11  N16  single    1.465  0.020  1.465
 M5J  C2   C5   aromatic  1.390  0.020  1.390
 M5J  C2   C1   aromatic  1.389  0.020  1.389
 M5J  C5   C4   aromatic  1.392  0.020  1.392
 M5J  C1   C3   aromatic  1.388  0.020  1.388
 M5J  C10  N16  single    1.461  0.020  1.461
 M5J  N16  C7   single    1.354  0.020  1.354
 M5J  C4   C6   aromatic  1.380  0.020  1.380
 M5J  C3   C6   aromatic  1.382  0.020  1.382
 M5J  O17  C7   double    1.225  0.020  1.225
 M5J  C7   C15  single    1.537  0.020  1.537
 M5J  C12  C15  single    1.532  0.020  1.532
 M5J  C6   F18  single    1.345  0.020  1.345
 M5J  C15  C14  single    1.533  0.020  1.533
 M5J  C15  C13  single    1.536  0.020  1.536
 M5J  C1   H1   single    0.930  0.020  1.080
 M5J  C10  H2   single    0.970  0.020  1.090
 M5J  C10  H3   single    0.970  0.020  1.090
 M5J  C11  H4   single    0.970  0.020  1.090
 M5J  C12  H5   single    0.970  0.020  1.090
 M5J  C12  H6   single    0.970  0.020  1.090
 M5J  C12  H7   single    0.970  0.020  1.090
 M5J  C13  H8   single    0.970  0.020  1.090
 M5J  C13  H9   single    0.970  0.020  1.090
 M5J  C13  H10  single    0.970  0.020  1.090
 M5J  C14  H11  single    0.970  0.020  1.090
 M5J  C14  H12  single    0.970  0.020  1.090
 M5J  C14  H13  single    0.970  0.020  1.090
 M5J  C2   H14  single    0.930  0.020  1.080
 M5J  C3   H15  single    0.930  0.020  1.080
 M5J  C4   H16  single    0.930  0.020  1.080
 M5J  C8   H17  single    0.970  0.020  1.090
 M5J  C8   H18  single    0.970  0.020  1.090
 M5J  C9   H19  single    0.970  0.020  1.090
 M5J  C9   H20  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
 M5J  H1   C1   C3   119.41  3.000
 M5J  H1   C1   C2   119.92  3.000
 M5J  C3   C1   C2   120.66  3.000
 M5J  H3   C10  H2   107.86  3.000
 M5J  H3   C10  N16  112.28  3.000
 M5J  H2   C10  N16  110.95  3.000
 M5J  H3   C10  C8   112.46  3.000
 M5J  H2   C10  C8   110.41  3.000
 M5J  N16  C10  C8   102.87  3.000
 M5J  H4   C11  N16  109.38  3.000
 M5J  H4   C11  C9   109.52  3.000
 M5J  N16  C11  C9   103.85  3.000
 M5J  H4   C11  C5   108.58  3.000
 M5J  N16  C11  C5   113.17  3.000
 M5J  C9   C11  C5   112.22  3.000
 M5J  H7   C12  H6   108.09  3.000
 M5J  H7   C12  H5   107.68  3.000
 M5J  H6   C12  H5   107.62  3.000
 M5J  H7   C12  C15  112.17  3.000
 M5J  H6   C12  C15  112.06  3.000
 M5J  H5   C12  C15  109.03  3.000
 M5J  H10  C13  H9   107.80  3.000
 M5J  H10  C13  H8   107.60  3.000
 M5J  H9   C13  H8   107.09  3.000
 M5J  H10  C13  C15  110.93  3.000
 M5J  H9   C13  C15  113.76  3.000
 M5J  H8   C13  C15  109.41  3.000
 M5J  H13  C14  H12  106.89  3.000
 M5J  H13  C14  H11  107.36  3.000
 M5J  H12  C14  H11  107.74  3.000
 M5J  H13  C14  C15  109.24  3.000
 M5J  H12  C14  C15  114.00  3.000
 M5J  H11  C14  C15  111.31  3.000
 M5J  C7   C15  C14  112.13  3.000
 M5J  C14  C15  C13  111.25  3.000
 M5J  C7   C15  C13  109.95  3.000
 M5J  C13  C15  C12  107.49  3.000
 M5J  C14  C15  C12  107.63  3.000
 M5J  C7   C15  C12  108.21  3.000
 M5J  H14  C2   C5   119.61  3.000
 M5J  H14  C2   C1   119.81  3.000
 M5J  C5   C2   C1   120.58  3.000
 M5J  H15  C3   C6   120.74  3.000
 M5J  H15  C3   C1   121.49  3.000
 M5J  C6   C3   C1   117.77  3.000
 M5J  H16  C4   C6   119.63  3.000
 M5J  H16  C4   C5   121.31  3.000
 M5J  C6   C4   C5   119.06  3.000
 M5J  C4   C5   C2   119.19  3.000
 M5J  C4   C5   C11  120.53  3.000
 M5J  C2   C5   C11  120.20  3.000
 M5J  F18  C6   C4   118.51  3.000
 M5J  F18  C6   C3   118.76  3.000
 M5J  C4   C6   C3   122.73  3.000
 M5J  H18  C8   H17  108.31  3.000
 M5J  H18  C8   C9   113.29  3.000
 M5J  H17  C8   C9   110.80  3.000
 M5J  H18  C8   C10  112.30  3.000
 M5J  H17  C8   C10  110.00  3.000
 M5J  C9   C8   C10  102.05  3.000
 M5J  H20  C9   H19  107.47  3.000
 M5J  H20  C9   C8   113.91  3.000
 M5J  H19  C9   C8   109.94  3.000
 M5J  H20  C9   C11  111.33  3.000
 M5J  H19  C9   C11  110.52  3.000
 M5J  C8   C9   C11  103.68  3.000
 M5J  C7   N16  C11  117.97  3.000
 M5J  C7   N16  C10  130.01  3.000
 M5J  C11  N16  C10  111.19  3.000
 M5J  O17  C7   N16  119.03  3.000
 M5J  O17  C7   C15  120.20  3.000
 M5J  N16  C7   C15  120.76  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
 M5J  CONST_01  C4   C5   C2   C1      0.00   0.0  0
 M5J  CONST_02  C4   C6   C3   C1      0.00   0.0  0
 M5J  CONST_03  C6   C4   C5   C2      0.00   0.0  0
 M5J  CONST_04  C6   C3   C1   C2      0.00   0.0  0
 M5J  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 M5J  CONST_06  C5   C4   C6   C3      0.00   0.0  0
 M5J  CONST_07  C11  C5   C2   C1    180.00   0.0  0
 M5J  CONST_08  C6   C4   C5   C11   180.00   0.0  0
 M5J  CONST_09  F18  C6   C3   C1    180.00   0.0  0
 M5J  CONST_10  F18  C6   C4   C5    180.00   0.0  0
 M5J  CONST_11  H14  C2   C5   C11     0.00   0.0  0
 M5J  CONST_12  H16  C4   C5   C11     0.00   0.0  0
 M5J  CONST_13  H15  C3   C1   C2    180.00   0.0  0
 M5J  CONST_14  H1   C1   C2   C5    180.00   0.0  0
 M5J  CONST_15  O17  C7   N16  C10   180.00   0.0  0
 M5J  CONST_16  C15  C7   N16  C10     0.00   0.0  0
 M5J  CONST_17  O17  C7   N16  C11     0.00   0.0  0
 M5J  CONST_18  C15  C7   N16  C11   180.00   0.0  0
 M5J  Var_01    C11  C9   C8   C10    38.78  30.0  1
 M5J  Var_02    C8   C10  N16  C11    23.70  30.0  1
 M5J  Var_03    N16  C10  C8   C9    -38.03  30.0  1
 M5J  Var_04    N16  C7   C15  C12  -165.93  30.0  3
 M5J  Var_05    H11  C14  C15  C12    66.91  30.0  3
 M5J  Var_06    H8   C13  C15  C12    58.88  30.0  3
 M5J  Var_07    H5   C12  C15  C13   -62.45  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
 M5J  chir_01  C11  C9  C5  N16  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
 M5J  plan-1  C1   0.020
 M5J  plan-1  C11  0.020
 M5J  plan-1  C2   0.020
 M5J  plan-1  C3   0.020
 M5J  plan-1  C4   0.020
 M5J  plan-1  C5   0.020
 M5J  plan-1  C6   0.020
 M5J  plan-1  F18  0.020
 M5J  plan-1  H1   0.020
 M5J  plan-1  H14  0.020
 M5J  plan-1  H15  0.020
 M5J  plan-1  H16  0.020
 M5J  plan-2  C10  0.020
 M5J  plan-2  C11  0.020
 M5J  plan-2  C15  0.020
 M5J  plan-2  N16  0.020
 M5J  plan-2  O17  0.020
 M5J  plan-2  C7   0.020

