# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:57:15 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-{3-[(2S)-1-acetylpyrrolidin-2-yl]phenyl}-N-(3-chlorophenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@H]1c2cccc(CC(=O)Nc3cccc(Cl)c3)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
 H5D  H5D  2-{3-[(2S)-1-acetylpyrrolidin-2-yl]phenyl}-N-(3-chlorophenyl)acetamide  ligand  46  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5D
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
 H5D  N1   N   NH1   0  -0.749   2.6484   0.8654   0.2901
 H5D  C4   C   CH2   0  -0.471  -3.4380  -2.2097  -0.5324
 H5D  C5   C   CH1   0  -0.108  -3.6273  -0.9689   0.3558
 H5D  C6   C   CR6   0   0.187  -2.8877   0.2292  -0.1826
 H5D  C7   C   CR16  0  -0.317  -3.4051   0.9909  -1.2256
 H5D  C8   C   CR16  0  -0.231  -2.6790   2.0538  -1.7415
 H5D  C10  C   CR6   0   0.166  -0.8885   1.6039  -0.1969
 H5D  C13  C   CR6   0   0.384   3.8554   0.2927  -0.1133
 H5D  C15  C   CR16  0  -0.249   5.4442  -0.5286  -1.7182
 H5D  C17  C   CR6   0  -0.024   5.9760  -0.5940   0.5938
 H5D  CL   CL  CL    0  -0.125   7.0697  -0.9860   1.8803
 H5D  C16  C   CR16  0  -0.237   6.3451  -0.8535  -0.7166
 H5D  C14  C   CR16  0  -0.309   4.2083   0.0378  -1.4397
 H5D  C18  C   CR16  0  -0.313   4.7541  -0.0304   0.9072
 H5D  C12  C   C     0   0.561   1.5743   1.2321  -0.4569
 H5D  O1   O   O     0  -0.451   1.4926   1.0765  -1.6591
 H5D  C11  C   CH2   0  -0.697   0.4757   1.9050   0.3503
 H5D  C9   C   CR16  0  -0.320  -1.4239   2.3602  -1.2328
 H5D  C19  C   CR16  0  -0.373  -1.6320   0.5466   0.3198
 H5D  C3   C   CH2   0  -0.471  -4.7486  -2.9720  -0.3897
 H5D  C2   C   CH2   0  -0.274  -5.7797  -1.8537  -0.3383
 H5D  N    N   NT    0  -0.474  -5.0763  -0.7993   0.3837
 H5D  C1   C   C     0   0.514  -5.6465   0.1593   1.1384
 H5D  O    O   O     0  -0.501  -4.9728   0.9175   1.8253
 H5D  C    C   CH3   0  -0.795  -7.1518   0.2484   1.0872
 H5D  H1   H   HNH1  0   0.421   2.5667   1.0229   1.2830
 H5D  H3   H   HCH2  0   0.260  -2.5615  -2.7829  -0.2335
 H5D  H4   H   HCH1  0   0.259  -3.2651  -1.1800   1.3678
 H5D  H5   H   HCR6  0   0.246  -4.3845   0.7655  -1.6311
 H5D  H6   H   HCR6  0   0.252  -3.0950   2.6491  -2.5444
 H5D  H7   H   HCR6  0   0.271   5.7110  -0.7198  -2.7491
 H5D  H8   H   HCR6  0   0.279   7.3037  -1.2947  -0.9505
 H5D  H9   H   HCR6  0   0.286   3.5397   0.2734  -2.2501
 H5D  H10  H   HCR6  0   0.293   4.4934   0.1588   1.9411
 H5D  H11  H   HCH2  0   0.306   0.6731   2.9809   0.3072
 H5D  H12  H   HCH2  0   0.284   0.5396   1.6237   1.4032
 H5D  H13  H   HCR6  0   0.247  -0.8658   3.1964  -1.6354
 H5D  H14  H   HCR6  0   0.242  -1.2250  -0.0397   1.1377
 H5D  H15  H   HCH2  0   0.254  -4.9287  -3.6666  -1.2093
 H5D  H16  H   HCH2  0   0.242  -4.7658  -3.5406   0.5424
 H5D  H17  H   HCH2  0   0.240  -6.0537  -1.5241  -1.3455
 H5D  H18  H   HCH2  0   0.260  -6.6917  -2.1509   0.1772
 H5D  H19  H   HCH3  0   0.267  -7.6097  -0.6102   1.5820
 H5D  H20  H   HCH3  0   0.266  -7.4820   1.1509   1.5956
 H5D  H21  H   HCH3  0   0.260  -7.5230   0.2661   0.0620
 H5D  H2   H   HCH2  0   0.243  -3.2932  -1.9065  -1.5720

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
 H5D  CL   C17  single    1.733  0.020  1.733
 H5D  C17  C18  aromatic  1.382  0.020  1.382
 H5D  C17  C16  aromatic  1.386  0.020  1.386
 H5D  C18  C13  aromatic  1.398  0.020  1.398
 H5D  O1   C12  double    1.215  0.020  1.215
 H5D  C16  C15  aromatic  1.386  0.020  1.386
 H5D  C12  N1   single    1.359  0.020  1.359
 H5D  C12  C11  single    1.520  0.020  1.520
 H5D  C13  N1   single    1.395  0.020  1.395
 H5D  C13  C14  aromatic  1.396  0.020  1.396
 H5D  C9   C8   aromatic  1.388  0.020  1.388
 H5D  C9   C10  aromatic  1.390  0.020  1.390
 H5D  C8   C7   aromatic  1.387  0.020  1.387
 H5D  C15  C14  aromatic  1.388  0.020  1.388
 H5D  C11  C10  single    1.500  0.020  1.500
 H5D  C10  C19  aromatic  1.392  0.020  1.392
 H5D  C7   C6   aromatic  1.391  0.020  1.391
 H5D  C3   C4   single    1.523  0.020  1.523
 H5D  C3   C2   single    1.522  0.020  1.522
 H5D  C4   C5   single    1.538  0.020  1.538
 H5D  C19  C6   aromatic  1.389  0.020  1.389
 H5D  C6   C5   single    1.507  0.020  1.507
 H5D  C2   N    single    1.459  0.020  1.459
 H5D  C5   N    single    1.459  0.020  1.459
 H5D  N    C1   single    1.347  0.020  1.347
 H5D  C1   O    double    1.225  0.020  1.225
 H5D  C1   C    single    1.509  0.020  1.509
 H5D  N1   H1   single    0.860  0.020  1.020
 H5D  C4   H2   single    0.970  0.020  1.090
 H5D  C4   H3   single    0.970  0.020  1.090
 H5D  C5   H4   single    0.970  0.020  1.090
 H5D  C7   H5   single    0.930  0.020  1.080
 H5D  C8   H6   single    0.930  0.020  1.080
 H5D  C15  H7   single    0.930  0.020  1.080
 H5D  C16  H8   single    0.930  0.020  1.080
 H5D  C14  H9   single    0.930  0.020  1.080
 H5D  C18  H10  single    0.930  0.020  1.080
 H5D  C11  H11  single    0.970  0.020  1.090
 H5D  C11  H12  single    0.970  0.020  1.090
 H5D  C9   H13  single    0.930  0.020  1.080
 H5D  C19  H14  single    0.930  0.020  1.080
 H5D  C3   H15  single    0.970  0.020  1.090
 H5D  C3   H16  single    0.970  0.020  1.090
 H5D  C2   H17  single    0.970  0.020  1.090
 H5D  C2   H18  single    0.970  0.020  1.090
 H5D  C    H19  single    0.970  0.020  1.090
 H5D  C    H20  single    0.970  0.020  1.090
 H5D  C    H21  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
 H5D  H1   N1   C12  115.78  3.000
 H5D  H1   N1   C13  114.76  3.000
 H5D  C12  N1   C13  129.46  3.000
 H5D  H3   C4   H2   107.49  3.000
 H5D  H3   C4   C3   113.79  3.000
 H5D  H2   C4   C3   110.01  3.000
 H5D  H3   C4   C5   111.42  3.000
 H5D  H2   C4   C5   110.00  3.000
 H5D  C3   C4   C5   104.11  3.000
 H5D  H4   C5   N    109.46  3.000
 H5D  H4   C5   C6   108.72  3.000
 H5D  N    C5   C6   113.68  3.000
 H5D  H4   C5   C4   109.72  3.000
 H5D  N    C5   C4   103.12  3.000
 H5D  C6   C5   C4   112.00  3.000
 H5D  C19  C6   C7   118.83  3.000
 H5D  C19  C6   C5   119.73  3.000
 H5D  C7   C6   C5   121.36  3.000
 H5D  H5   C7   C8   119.56  3.000
 H5D  H5   C7   C6   120.18  3.000
 H5D  C8   C7   C6   120.25  3.000
 H5D  H6   C8   C9   119.85  3.000
 H5D  H6   C8   C7   119.75  3.000
 H5D  C9   C8   C7   120.41  3.000
 H5D  C19  C10  C9   118.96  3.000
 H5D  C19  C10  C11  120.18  3.000
 H5D  C9   C10  C11  120.86  3.000
 H5D  C18  C13  C14  119.27  3.000
 H5D  C14  C13  N1   124.63  3.000
 H5D  C18  C13  N1   116.10  3.000
 H5D  H7   C15  C14  118.88  3.000
 H5D  H7   C15  C16  119.14  3.000
 H5D  C14  C15  C16  121.98  3.000
 H5D  C18  C17  C16  121.77  3.000
 H5D  C16  C17  CL   119.43  3.000
 H5D  C18  C17  CL   118.81  3.000
 H5D  H8   C16  C17  121.15  3.000
 H5D  H8   C16  C15  121.05  3.000
 H5D  C17  C16  C15  117.80  3.000
 H5D  H9   C14  C15  119.42  3.000
 H5D  H9   C14  C13  121.21  3.000
 H5D  C15  C14  C13  119.37  3.000
 H5D  H10  C18  C17  120.05  3.000
 H5D  H10  C18  C13  120.12  3.000
 H5D  C17  C18  C13  119.82  3.000
 H5D  C11  C12  O1   122.24  3.000
 H5D  C11  C12  N1   113.50  3.000
 H5D  O1   C12  N1   124.23  3.000
 H5D  H12  C11  H11  106.30  3.000
 H5D  H12  C11  C12  110.84  3.000
 H5D  H11  C11  C12  106.49  3.000
 H5D  H12  C11  C10  110.69  3.000
 H5D  H11  C11  C10  110.29  3.000
 H5D  C12  C11  C10  112.00  3.000
 H5D  H13  C9   C10  119.91  3.000
 H5D  H13  C9   C8   120.00  3.000
 H5D  C10  C9   C8   120.08  3.000
 H5D  H14  C19  C10  119.32  3.000
 H5D  H14  C19  C6   119.20  3.000
 H5D  C10  C19  C6   121.47  3.000
 H5D  H16  C3   H15  107.91  3.000
 H5D  H16  C3   C2   110.07  3.000
 H5D  H15  C3   C2   112.45  3.000
 H5D  H16  C3   C4   110.75  3.000
 H5D  H15  C3   C4   113.01  3.000
 H5D  C2   C3   C4   102.62  3.000
 H5D  H18  C2   H17  107.95  3.000
 H5D  H18  C2   N    111.52  3.000
 H5D  H17  C2   N    111.01  3.000
 H5D  H18  C2   C3   112.51  3.000
 H5D  H17  C2   C3   111.08  3.000
 H5D  N    C2   C3   102.77  3.000
 H5D  C1   N    C2   126.00  3.000
 H5D  C1   N    C5   120.92  3.000
 H5D  C2   N    C5   112.67  3.000
 H5D  C    C1   O    122.09  3.000
 H5D  C    C1   N    116.45  3.000
 H5D  O    C1   N    121.47  3.000
 H5D  H21  C    H20  108.83  3.000
 H5D  H21  C    H19  107.22  3.000
 H5D  H20  C    H19  108.28  3.000
 H5D  H21  C    C1   111.87  3.000
 H5D  H20  C    C1   109.64  3.000
 H5D  H19  C    C1   110.89  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
 H5D  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 H5D  CONST_02  C9   C10  C19  C6      0.00   0.0  0
 H5D  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 H5D  CONST_04  C10  C19  C6   C7      0.00   0.0  0
 H5D  CONST_05  C19  C10  C9   C8      0.00   0.0  0
 H5D  CONST_06  C19  C6   C7   C8      0.00   0.0  0
 H5D  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 H5D  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 H5D  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 H5D  CONST_10  C18  C13  C14  C15     0.00   0.0  0
 H5D  CONST_11  C14  C13  C18  C17     0.00   0.0  0
 H5D  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 H5D  CONST_13  C8   C7   C6   C5    180.00   0.0  0
 H5D  CONST_14  C10  C19  C6   C5    180.00   0.0  0
 H5D  CONST_15  C17  C18  C13  N1    180.00   0.0  0
 H5D  CONST_16  C15  C14  C13  N1    180.00   0.0  0
 H5D  CONST_17  C11  C10  C19  C6    180.00   0.0  0
 H5D  CONST_18  C11  C10  C9   C8    180.00   0.0  0
 H5D  CONST_19  CL   C17  C18  C13   180.00   0.0  0
 H5D  CONST_20  CL   C17  C16  C15   180.00   0.0  0
 H5D  CONST_21  H5   C7   C6   C5      0.00   0.0  0
 H5D  CONST_22  H14  C19  C6   C5      0.00   0.0  0
 H5D  CONST_23  H6   C8   C7   C6    180.00   0.0  0
 H5D  CONST_24  H13  C9   C8   C7    180.00   0.0  0
 H5D  CONST_25  H7   C15  C14  C13   180.00   0.0  0
 H5D  CONST_26  H10  C18  C17  C16   180.00   0.0  0
 H5D  CONST_27  H9   C14  C15  C16   180.00   0.0  0
 H5D  CONST_28  H8   C16  C15  C14   180.00   0.0  0
 H5D  CONST_29  O    C1   N    C5      0.00   0.0  0
 H5D  CONST_30  C    C1   N    C5    180.00   0.0  0
 H5D  CONST_31  O    C1   N    C2    180.00   0.0  0
 H5D  CONST_32  C    C1   N    C2      0.00   0.0  0
 H5D  CONST_33  C12  N1   C13  C14     0.00   0.0  0
 H5D  CONST_34  C12  N1   C13  C18   180.00   0.0  0
 H5D  CONST_35  H1   N1   C13  C14   180.00   0.0  0
 H5D  CONST_36  O1   C12  N1   C13     0.00   0.0  0
 H5D  CONST_37  C11  C12  N1   C13   180.00   0.0  0
 H5D  Var_01    N    C2   C3   C4    -35.09  30.0  1
 H5D  Var_02    C2   C3   C4   C5     37.67  30.0  1
 H5D  Var_03    C3   C2   N    C5     20.30  30.0  1
 H5D  Var_04    C9   C10  C11  C12   -85.05  30.0  2
 H5D  Var_05    C10  C11  C12  N1   -147.33  30.0  3
 H5D  Var_06    H19  C    C1   N      69.92  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
 H5D  chir_01  C5  C4  C6  N  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
 H5D  plan-1  N1   0.020
 H5D  plan-1  C13  0.020
 H5D  plan-1  C15  0.020
 H5D  plan-1  C17  0.020
 H5D  plan-1  CL   0.020
 H5D  plan-1  C16  0.020
 H5D  plan-1  C14  0.020
 H5D  plan-1  C18  0.020
 H5D  plan-1  H7   0.020
 H5D  plan-1  H8   0.020
 H5D  plan-1  H9   0.020
 H5D  plan-1  H10  0.020
 H5D  plan-2  C5   0.020
 H5D  plan-2  C6   0.020
 H5D  plan-2  C7   0.020
 H5D  plan-2  C8   0.020
 H5D  plan-2  C10  0.020
 H5D  plan-2  C11  0.020
 H5D  plan-2  C9   0.020
 H5D  plan-2  C19  0.020
 H5D  plan-2  H5   0.020
 H5D  plan-2  H6   0.020
 H5D  plan-2  H13  0.020
 H5D  plan-2  H14  0.020
 H5D  plan-3  C5   0.020
 H5D  plan-3  C2   0.020
 H5D  plan-3  N    0.020
 H5D  plan-3  C1   0.020
 H5D  plan-3  O    0.020
 H5D  plan-3  C    0.020
 H5D  plan-4  N1   0.020
 H5D  plan-4  C13  0.020
 H5D  plan-4  C12  0.020
 H5D  plan-4  O1   0.020
 H5D  plan-4  C11  0.020
 H5D  plan-4  H1   0.020

