# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 17:46:20 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: methyl 2-[[[(2~{S})-2-[[3-(trifluoromethyloxy)phenyl]carbamoyl]pyrrolidin-1-yl]carbonylamino]methyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccccc1CNC(=O)N2CCC[C@H]2C(=O)Nc3cccc(OC(F)(F)F)c3
#
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
 5W5  5W5  'methyl 2-[[[(2~{S})-2-[[3-(trifluoromethyloxy)phenyl]carbamoyl]pyrrolidin-1-yl]carbonylamino]methyl]benzoate'  ligand  55  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5W5
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
 5W5  C2   C  C     0   0.770  -1.9841  -0.1458   0.5411
 5W5  C3   C  C     0   0.550   0.7895   0.8502   0.7644
 5W5  C13  C  CR6   0   0.394   3.1218   0.1664   0.2477
 5W5  C14  C  CR6   0   0.110  -5.1909  -1.7925   0.9153
 5W5  C15  C  CR16  0  -0.406   4.0996   0.3030  -0.7410
 5W5  C16  C  CH2   0  -0.357  -3.6961  -1.8139   1.1198
 5W5  C18  C  CR6   0   0.333   5.3678  -0.1936  -0.5176
 5W5  C22  C  CH2   0  -0.299  -2.4435   2.2543   1.1410
 5W5  C24  C  CH2   0  -0.473  -0.3134   3.0873   0.4579
 5W5  C25  C  CH2   0  -0.475  -1.7844   3.4831   0.5291
 5W5  C26  C  CR16  0  -0.244   4.7324  -0.9624   1.6326
 5W5  C27  C  CR16  0  -0.254  -7.1692  -0.9811  -0.2197
 5W5  C28  C  CR16  0  -0.312   3.4476  -0.4735   1.4450
 5W5  C29  C  CR16  0  -0.316   5.7124  -0.8312   0.6613
 5W5  C30  C  CR16  0  -0.311  -6.0148  -2.5031   1.7789
 5W5  N1   N  NR5   0  -0.523  -1.6369   1.1638   0.6152
 5W5  C4   C  CR15  0  -0.175  -0.3605   1.5931   0.0975
 5W5  C5   C  CT    0   1.073   7.0928   0.9865  -1.5658
 5W5  N8   N  NH1   0  -0.701  -3.1628  -0.4739   1.1378
 5W5  C9   C  CR6   0  -0.037  -5.7850  -1.0293  -0.0952
 5W5  O10  O  O2    0  -0.525   6.3085  -0.0976  -1.5381
 5W5  O11  O  O     0  -0.456   0.7480   0.5149   1.9310
 5W5  O12  O  O     0  -0.539  -1.2765  -0.9587  -0.0454
 5W5  O17  O  O     0  -0.436  -4.1000  -0.8361  -1.7695
 5W5  F19  F  F     0  -0.298   7.8184   1.1297  -0.4557
 5W5  F20  F  F     0  -0.277   7.9200   0.8582  -2.5911
 5W5  F21  F  F     0  -0.299   6.4028   2.1184  -1.7230
 5W5  O23  O  O2    0  -0.446  -5.2623   0.9755  -1.1711
 5W5  C31  C  CH3   0  -0.431  -4.5284   1.7728  -2.1030
 5W5  C32  C  CR16  0  -0.259  -7.9768  -1.7152   0.6382
 5W5  C33  C  CR16  0  -0.236  -7.3967  -2.4797   1.6382
 5W5  H1   H  HCR6  0   0.291   3.8584   0.7810  -1.6830
 5W5  H2   H  HCH2  0   0.259  -3.4720  -2.3418   2.0511
 5W5  H3   H  HCH2  0   0.273  -3.2066  -2.3685   0.3206
 5W5  H4   H  HCH2  0   0.249  -2.4088   2.2893   2.2351
 5W5  H5   H  HCH2  0   0.251  -3.4879   2.1551   0.8406
 5W5  H6   H  HCH2  0   0.268   0.2556   3.6596  -0.2727
 5W5  H7   H  HCH2  0   0.254   0.1539   3.2299   1.4349
 5W5  H8   H  HCH2  0   0.244  -2.1803   3.6645  -0.4723
 5W5  H9   H  HCH2  0   0.261  -1.9499   4.3804   1.1235
 5W5  H10  H  HCR6  0   0.272   4.9713  -1.4634   2.5613
 5W5  H11  H  HCR6  0   0.266  -7.6242  -0.3851  -1.0007
 5W5  H12  H  HCR6  0   0.288   2.7125  -0.6038   2.2210
 5W5  H13  H  HCR6  0   0.280   6.7061  -1.2309   0.8118
 5W5  H14  H  HCR6  0   0.261  -5.5676  -3.0752   2.5830
 5W5  H15  H  HCR5  0   0.277  -0.3139   1.4627  -0.9896
 5W5  H16  H  HNH1  0   0.421   1.7489   1.0075  -0.9996
 5W5  H17  H  HNH1  0   0.406  -3.5552   0.1492   1.8256
 5W5  H18  H  HCH3  0   0.249  -4.6803   1.4319  -3.1269
 5W5  H19  H  HCH3  0   0.255  -4.9110   2.7837  -1.9971
 5W5  H20  H  HCH3  0   0.235  -3.4621   1.7618  -1.8749
 5W5  H21  H  HCR6  0   0.264  -9.0525  -1.6821   0.5259
 5W5  H22  H  HCR6  0   0.264  -8.0165  -3.0470   2.3202
 5W5  N6   N  NH1   0  -0.751   1.8604   0.6813  -0.0509
 5W5  C7   C  C     0   0.517  -4.9444  -0.3080  -1.0918

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
 5W5  C22  C25  single    1.523  0.020  1.523
 5W5  C22  N1   single    1.455  0.020  1.455
 5W5  C25  C24  single    1.525  0.020  1.525
 5W5  N8   C16  single    1.442  0.020  1.442
 5W5  N8   C2   single    1.361  0.020  1.361
 5W5  C16  C14  single    1.509  0.020  1.509
 5W5  O17  C7   double    1.205  0.020  1.205
 5W5  C14  C30  aromatic  1.389  0.020  1.389
 5W5  C14  C9   aromatic  1.399  0.020  1.399
 5W5  N1   C2   single    1.357  0.020  1.357
 5W5  N1   C4   single    1.443  0.020  1.443
 5W5  O23  C7   single    1.325  0.020  1.325
 5W5  O23  C31  single    1.429  0.020  1.429
 5W5  C7   C9   single    1.490  0.020  1.490
 5W5  C30  C33  aromatic  1.389  0.020  1.389
 5W5  C24  C4   single    1.538  0.020  1.538
 5W5  C9   C27  aromatic  1.391  0.020  1.391
 5W5  C2   O12  double    1.227  0.020  1.227
 5W5  C33  C32  aromatic  1.386  0.020  1.386
 5W5  C27  C32  aromatic  1.388  0.020  1.388
 5W5  C4   C3   single    1.523  0.020  1.523
 5W5  O11  C3   double    1.215  0.020  1.215
 5W5  C3   N6   single    1.356  0.020  1.356
 5W5  N6   C13  single    1.395  0.020  1.395
 5W5  C28  C13  aromatic  1.396  0.020  1.396
 5W5  C28  C26  aromatic  1.387  0.020  1.387
 5W5  C13  C15  aromatic  1.397  0.020  1.397
 5W5  C26  C29  aromatic  1.386  0.020  1.386
 5W5  C15  C18  aromatic  1.380  0.020  1.380
 5W5  C29  C18  aromatic  1.384  0.020  1.384
 5W5  C18  O10  single    1.391  0.020  1.391
 5W5  F20  C5   single    1.324  0.020  1.324
 5W5  O10  C5   single    1.338  0.020  1.338
 5W5  C5   F19  single    1.334  0.020  1.334
 5W5  C5   F21  single    1.335  0.020  1.335
 5W5  C15  H1   single    0.930  0.020  1.080
 5W5  C16  H2   single    0.970  0.020  1.090
 5W5  C16  H3   single    0.970  0.020  1.090
 5W5  C22  H4   single    0.970  0.020  1.090
 5W5  C22  H5   single    0.970  0.020  1.090
 5W5  C24  H6   single    0.970  0.020  1.090
 5W5  C24  H7   single    0.970  0.020  1.090
 5W5  C25  H8   single    0.970  0.020  1.090
 5W5  C25  H9   single    0.970  0.020  1.090
 5W5  C26  H10  single    0.930  0.020  1.080
 5W5  C27  H11  single    0.930  0.020  1.080
 5W5  C28  H12  single    0.930  0.020  1.080
 5W5  C29  H13  single    0.930  0.020  1.080
 5W5  C30  H14  single    0.930  0.020  1.080
 5W5  C4   H15  single    0.970  0.020  1.090
 5W5  N6   H16  single    0.860  0.020  1.020
 5W5  N8   H17  single    0.860  0.020  1.020
 5W5  C31  H18  single    0.970  0.020  1.090
 5W5  C31  H19  single    0.970  0.020  1.090
 5W5  C31  H20  single    0.970  0.020  1.090
 5W5  C32  H21  single    0.930  0.020  1.080
 5W5  C33  H22  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
 5W5  O12  C2   N8   123.31  3.000
 5W5  O12  C2   N1   121.19  3.000
 5W5  N8   C2   N1   115.49  3.000
 5W5  O11  C3   N6   124.74  3.000
 5W5  N6   C3   C4   113.19  3.000
 5W5  O11  C3   C4   121.97  3.000
 5W5  N6   C13  C28  124.32  3.000
 5W5  C28  C13  C15  119.23  3.000
 5W5  N6   C13  C15  116.44  3.000
 5W5  C9   C14  C30  118.45  3.000
 5W5  C9   C14  C16  121.76  3.000
 5W5  C30  C14  C16  119.74  3.000
 5W5  H1   C15  C18  120.26  3.000
 5W5  H1   C15  C13  120.17  3.000
 5W5  C18  C15  C13  119.56  3.000
 5W5  H3   C16  H2   106.68  3.000
 5W5  H3   C16  N8   108.43  3.000
 5W5  H2   C16  N8   111.22  3.000
 5W5  H3   C16  C14  110.67  3.000
 5W5  H2   C16  C14  108.98  3.000
 5W5  N8   C16  C14  110.78  3.000
 5W5  O10  C18  C29  119.23  3.000
 5W5  O10  C18  C15  118.54  3.000
 5W5  C29  C18  C15  122.17  3.000
 5W5  H5   C22  H4   107.95  3.000
 5W5  H5   C22  N1   111.28  3.000
 5W5  H4   C22  N1   111.56  3.000
 5W5  H5   C22  C25  112.15  3.000
 5W5  H4   C22  C25  111.22  3.000
 5W5  N1   C22  C25  102.69  3.000
 5W5  H7   C24  H6   107.94  3.000
 5W5  H7   C24  C4   110.46  3.000
 5W5  H6   C24  C4   111.69  3.000
 5W5  H7   C24  C25  109.69  3.000
 5W5  H6   C24  C25  113.52  3.000
 5W5  C4   C24  C25  103.50  3.000
 5W5  H9   C25  H8   107.98  3.000
 5W5  H9   C25  C24  112.70  3.000
 5W5  H8   C25  C24  110.49  3.000
 5W5  H9   C25  C22  112.32  3.000
 5W5  H8   C25  C22  110.22  3.000
 5W5  C24  C25  C22  103.11  3.000
 5W5  H10  C26  C29  119.29  3.000
 5W5  H10  C26  C28  118.93  3.000
 5W5  C29  C26  C28  121.78  3.000
 5W5  H11  C27  C32  119.50  3.000
 5W5  H11  C27  C9   120.13  3.000
 5W5  C32  C27  C9   120.36  3.000
 5W5  H12  C28  C26  119.48  3.000
 5W5  H12  C28  C13  120.94  3.000
 5W5  C26  C28  C13  119.58  3.000
 5W5  H13  C29  C26  121.14  3.000
 5W5  H13  C29  C18  121.17  3.000
 5W5  C26  C29  C18  117.68  3.000
 5W5  H14  C30  C33  119.65  3.000
 5W5  H14  C30  C14  119.13  3.000
 5W5  C33  C30  C14  121.22  3.000
 5W5  C4   N1   C22  113.41  3.000
 5W5  C4   N1   C2   119.60  3.000
 5W5  C22  N1   C2   126.96  3.000
 5W5  H15  C4   N1   110.99  3.000
 5W5  H15  C4   C24  110.29  3.000
 5W5  N1   C4   C24  103.42  3.000
 5W5  H15  C4   C3   110.14  3.000
 5W5  C24  C4   C3   110.38  3.000
 5W5  N1   C4   C3   111.46  3.000
 5W5  F21  C5   F20  108.30  3.000
 5W5  F21  C5   F19  106.74  3.000
 5W5  F20  C5   F19  108.37  3.000
 5W5  F21  C5   O10  112.73  3.000
 5W5  F19  C5   O10  112.86  3.000
 5W5  F20  C5   O10  107.68  3.000
 5W5  H17  N8   C16  116.04  3.000
 5W5  H17  N8   C2   119.17  3.000
 5W5  C16  N8   C2   122.59  3.000
 5W5  C7   C9   C27  119.00  3.000
 5W5  C27  C9   C14  120.42  3.000
 5W5  C7   C9   C14  120.51  3.000
 5W5  C5   O10  C18  117.86  3.000
 5W5  C31  O23  C7   117.16  3.000
 5W5  H20  C31  H19  109.48  3.000
 5W5  H20  C31  H18  109.25  3.000
 5W5  H19  C31  H18  109.50  3.000
 5W5  H20  C31  O23  111.10  3.000
 5W5  H19  C31  O23  105.95  3.000
 5W5  H18  C31  O23  111.50  3.000
 5W5  H21  C32  C33  120.52  3.000
 5W5  H21  C32  C27  119.87  3.000
 5W5  C33  C32  C27  119.61  3.000
 5W5  H22  C33  C32  120.27  3.000
 5W5  H22  C33  C30  119.80  3.000
 5W5  C32  C33  C30  119.92  3.000
 5W5  H16  N6   C13  114.86  3.000
 5W5  H16  N6   C3   115.94  3.000
 5W5  C13  N6   C3   129.15  3.000
 5W5  O23  C7   O17  124.00  3.000
 5W5  O23  C7   C9   111.95  3.000
 5W5  O17  C7   C9   124.02  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
 5W5  CONST_01  C29  C26  C28  C13     0.00   0.0  0
 5W5  CONST_02  C29  C18  C15  C13     0.00   0.0  0
 5W5  CONST_03  C32  C33  C30  C14     0.00   0.0  0
 5W5  CONST_04  C32  C27  C9   C14     0.00   0.0  0
 5W5  CONST_05  C26  C28  C13  C15     0.00   0.0  0
 5W5  CONST_06  C26  C29  C18  C15     0.00   0.0  0
 5W5  CONST_07  C28  C13  C15  C18     0.00   0.0  0
 5W5  CONST_08  C28  C26  C29  C18     0.00   0.0  0
 5W5  CONST_09  C30  C14  C9   C27     0.00   0.0  0
 5W5  CONST_10  C30  C33  C32  C27     0.00   0.0  0
 5W5  CONST_11  C33  C30  C14  C9      0.00   0.0  0
 5W5  CONST_12  C33  C32  C27  C9      0.00   0.0  0
 5W5  CONST_13  O10  C18  C15  C13   180.00   0.0  0
 5W5  CONST_14  C33  C30  C14  C16   180.00   0.0  0
 5W5  CONST_15  C27  C9   C14  C16   180.00   0.0  0
 5W5  CONST_16  N6   C13  C15  C18   180.00   0.0  0
 5W5  CONST_17  N6   C13  C28  C26   180.00   0.0  0
 5W5  CONST_18  O10  C18  C29  C26   180.00   0.0  0
 5W5  CONST_19  C7   C9   C14  C30   180.00   0.0  0
 5W5  CONST_20  C32  C27  C9   C7    180.00   0.0  0
 5W5  CONST_21  H10  C26  C28  C13   180.00   0.0  0
 5W5  CONST_22  H22  C33  C30  C14   180.00   0.0  0
 5W5  CONST_23  H11  C27  C9   C14   180.00   0.0  0
 5W5  CONST_24  H12  C28  C13  C15   180.00   0.0  0
 5W5  CONST_25  H13  C29  C18  C15   180.00   0.0  0
 5W5  CONST_26  H1   C15  C13  C28   180.00   0.0  0
 5W5  CONST_27  H21  C32  C33  C30   180.00   0.0  0
 5W5  CONST_28  H14  C30  C14  C9    180.00   0.0  0
 5W5  CONST_29  C4   C3   N6   C13   180.00   0.0  0
 5W5  CONST_30  O12  C2   N1   C22   180.00   0.0  0
 5W5  CONST_31  O12  C2   N1   C4      0.00   0.0  0
 5W5  CONST_32  C28  C13  N6   C3      0.00   0.0  0
 5W5  CONST_33  C15  C13  N6   C3    180.00   0.0  0
 5W5  CONST_34  N8   C2   N1   C22     0.00   0.0  0
 5W5  CONST_35  N8   C2   N1   C4    180.00   0.0  0
 5W5  CONST_36  H16  N6   C13  C15     0.00   0.0  0
 5W5  CONST_37  O11  C3   N6   C13     0.00   0.0  0
 5W5  CONST_38  N1   C2   N8   C16   180.00   0.0  0
 5W5  CONST_40  O12  C2   N8   C16     0.00   0.0  0
 5W5  Var_01    C4   C24  C25  C22    37.01  30.0  1
 5W5  Var_02    N1   C22  C25  C24   -33.08  30.0  1
 5W5  Var_03    C4   N1   C22  C25    17.37  30.0  1
 5W5  Var_04    O17  C7   C9   C14    54.50  30.0  1
 5W5  Var_05    N8   C16  C14  C30  -128.99  30.0  2
 5W5  Var_06    C14  C16  N8   C2   -140.05  30.0  3
 5W5  Var_07    F20  C5   O10  C18   178.79  30.0  3
 5W5  Var_08    H18  C31  O23  C7     62.62  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
 5W5  chir_01  C4  N1  C24  C3  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
 5W5  plan-1  C9   0.020
 5W5  plan-1  O17  0.020
 5W5  plan-1  O23  0.020
 5W5  plan-1  C7   0.020
 5W5  plan-2  C14  0.020
 5W5  plan-2  C16  0.020
 5W5  plan-2  C27  0.020
 5W5  plan-2  C30  0.020
 5W5  plan-2  C9   0.020
 5W5  plan-2  C32  0.020
 5W5  plan-2  C33  0.020
 5W5  plan-2  H11  0.020
 5W5  plan-2  H14  0.020
 5W5  plan-2  H21  0.020
 5W5  plan-2  H22  0.020
 5W5  plan-2  C7   0.020
 5W5  plan-3  C13  0.020
 5W5  plan-3  C15  0.020
 5W5  plan-3  C18  0.020
 5W5  plan-3  C26  0.020
 5W5  plan-3  C28  0.020
 5W5  plan-3  C29  0.020
 5W5  plan-3  O10  0.020
 5W5  plan-3  H1   0.020
 5W5  plan-3  H10  0.020
 5W5  plan-3  H12  0.020
 5W5  plan-3  H13  0.020
 5W5  plan-3  N6   0.020
 5W5  plan-4  C2   0.020
 5W5  plan-4  C16  0.020
 5W5  plan-4  C22  0.020
 5W5  plan-4  N1   0.020
 5W5  plan-4  C4   0.020
 5W5  plan-4  N8   0.020
 5W5  plan-4  O12  0.020
 5W5  plan-4  H17  0.020
 5W5  plan-5  C3   0.020
 5W5  plan-5  C13  0.020
 5W5  plan-5  C4   0.020
 5W5  plan-5  O11  0.020
 5W5  plan-5  H16  0.020
 5W5  plan-5  N6   0.020

