# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 07:37:15 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S},4~{R})-~{N}1-(1-aminocarbonylindol-3-yl)-4-fluoranyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)n1cc(NC(=O)N2C[C@H](F)C[C@H]2C(=O)Nc3cccc(OC(F)(F)F)c3)c4ccccc14
#
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
 8S5  8S5  (2~{S},4~{R})-~{N}1-(1-aminocarbonylindol-3-yl)-4-fluoranyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide  ligand  54  35  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8S5
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
 8S5  C4   C  CH1   0   0.157   0.4938  -4.5786   0.8085
 8S5  C14  C  CR16  0  -0.268   7.1979   1.2370   1.7199
 8S5  C5   C  CH2   0  -0.342   1.3604  -3.3768   1.1183
 8S5  C6   C  C     0   0.770   1.5332  -1.2710  -0.2480
 8S5  C11  C  CR56  0  -0.027   4.7750   0.3038   0.7825
 8S5  C7   C  CR5   0   0.236   3.5293   0.0858   0.0960
 8S5  C8   C  CR15  0  -0.079   3.3895   1.0798  -0.8170
 8S5  C10  C  CR56  0   0.376   5.3604   1.4555   0.2284
 8S5  C12  C  CR16  0  -0.335   5.4167  -0.3899   1.8089
 8S5  C13  C  CR16  0  -0.262   6.6290   0.0832   2.2711
 8S5  N1   N  NT    0  -0.541   0.8891  -2.3878   0.1637
 8S5  N2   N  NH1   0  -0.801   2.7107  -0.9948   0.3854
 8S5  C3   C  CH2   0  -0.532  -0.8203  -3.9638   0.3806
 8S5  N3   N  NR5   0  -0.636   4.4984   1.9272  -0.7470
 8S5  C1   C  C     0   0.551  -1.3957  -1.5803  -0.1858
 8S5  C2   C  CH1   0  -0.178  -0.3988  -2.7130  -0.4071
 8S5  F1   F  F     0  -0.379   1.0483  -5.2712  -0.2688
 8S5  N4   N  NH2   0  -0.835   3.6152   3.5185  -2.1765
 8S5  O2   O  O     0  -0.486   5.8054   3.5779  -1.6143
 8S5  C15  C  CR16  0  -0.287   6.5811   1.9375   0.6982
 8S5  O3   O  O     0  -0.521   1.0807  -0.5587  -1.1357
 8S5  N5   N  NH1   0  -0.748  -2.2693  -1.4210  -1.2078
 8S5  C16  C  CR6   0   0.391  -3.3441  -0.5387  -1.3173
 8S5  C17  C  CR16  0  -0.343  -4.0417  -0.5391  -2.5278
 8S5  C18  C  CR16  0  -0.242  -5.1154   0.3096  -2.7215
 8S5  C19  C  CR16  0  -0.323  -5.5302   1.1731  -1.7164
 8S5  C20  C  CR6   0   0.347  -4.8327   1.1531  -0.5242
 8S5  O4   O  O2    0  -0.526  -5.1881   2.0478   0.4814
 8S5  C21  C  CT    0   1.073  -6.0995   1.6541   1.3785
 8S5  F2   F  F     0  -0.277  -6.2635   2.6417   2.2445
 8S5  F3   F  F     0  -0.299  -7.2834   1.3792   0.8269
 8S5  F4   F  F     0  -0.299  -5.7266   0.5633   2.0507
 8S5  C22  C  CR16  0  -0.382  -3.7486   0.3224  -0.2971
 8S5  H1   H  HCH1  0   0.258   0.4079  -5.2697   1.6460
 8S5  H2   H  HCR6  0   0.258   8.1485   1.5911   2.0966
 8S5  H3   H  HCH2  0   0.269   1.2021  -3.0568   2.1527
 8S5  H4   H  HCH2  0   0.275   2.4190  -3.6100   0.9865
 8S5  H5   H  HCR5  0   0.305   2.6185   1.2327  -1.5479
 8S5  H6   H  HCR6  0   0.249   4.9836  -1.2824   2.2438
 8S5  H7   H  HCR6  0   0.257   7.1447  -0.4413   3.0644
 8S5  H8   H  HNH1  0   0.424   2.9997  -1.5648   1.1630
 8S5  H9   H  HCH2  0   0.292  -1.4401  -4.6413  -0.2040
 8S5  H10  H  HCH2  0   0.277  -1.3772  -3.6838   1.2768
 8S5  H11  H  HCH1  0   0.290  -0.3057  -2.9405  -1.4741
 8S5  H12  H  HNH2  0   0.416   2.6802   3.2982  -1.8791
 8S5  H13  H  HNH2  0   0.415   3.7157   4.3728  -2.6995
 8S5  H14  H  HCR6  0   0.276   7.0443   2.8189   0.2855
 8S5  H15  H  HNH1  0   0.423  -2.1117  -1.9982  -2.0206
 8S5  H16  H  HCR6  0   0.281  -3.7335  -1.2041  -3.3256
 8S5  H17  H  HCR6  0   0.274  -5.6364   0.3006  -3.6691
 8S5  H18  H  HCR6  0   0.280  -6.3598   1.8500  -1.8675
 8S5  H19  H  HCR6  0   0.301  -3.2274   0.3611   0.6455
 8S5  O1   O  O     0  -0.454  -1.4110  -0.9437   0.8482
 8S5  C9   C  C     0   0.682   4.7041   3.0690  -1.5263

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
 8S5  F1   C4   single    1.396  0.020  1.396
 8S5  N4   C9   single    1.346  0.020  1.346
 8S5  C5   C4   single    1.514  0.020  1.514
 8S5  C5   N1   single    1.453  0.020  1.453
 8S5  C4   C3   single    1.513  0.020  1.513
 8S5  C8   C7   aromatic  1.357  0.020  1.357
 8S5  C8   N3   aromatic  1.397  0.020  1.397
 8S5  N2   C7   single    1.386  0.020  1.386
 8S5  N2   C6   single    1.365  0.020  1.365
 8S5  C9   N3   single    1.398  0.020  1.398
 8S5  C9   O2   double    1.216  0.020  1.216
 8S5  C7   C11  aromatic  1.439  0.020  1.439
 8S5  N3   C10  aromatic  1.385  0.020  1.385
 8S5  C11  C10  aromatic  1.406  0.020  1.406
 8S5  C11  C12  aromatic  1.395  0.020  1.395
 8S5  C10  C15  aromatic  1.394  0.020  1.394
 8S5  N1   C6   single    1.353  0.020  1.353
 8S5  N1   C2   single    1.446  0.020  1.446
 8S5  C12  C13  aromatic  1.381  0.020  1.381
 8S5  C15  C14  aromatic  1.384  0.020  1.384
 8S5  C6   O3   double    1.225  0.020  1.225
 8S5  C3   C2   single    1.537  0.020  1.537
 8S5  C13  C14  aromatic  1.400  0.020  1.400
 8S5  C2   C1   single    1.525  0.020  1.525
 8S5  O1   C1   double    1.214  0.020  1.214
 8S5  C1   N5   single    1.354  0.020  1.354
 8S5  N5   C16  single    1.395  0.020  1.395
 8S5  C16  C17  aromatic  1.397  0.020  1.397
 8S5  C16  C22  aromatic  1.395  0.020  1.395
 8S5  C17  C18  aromatic  1.382  0.020  1.382
 8S5  C22  C20  aromatic  1.385  0.020  1.385
 8S5  C18  C19  aromatic  1.389  0.020  1.389
 8S5  C20  C19  aromatic  1.381  0.020  1.381
 8S5  C20  O4   single    1.392  0.020  1.392
 8S5  F3   C21  single    1.335  0.020  1.335
 8S5  O4   C21  single    1.338  0.020  1.338
 8S5  C21  F4   single    1.334  0.020  1.334
 8S5  C21  F2   single    1.324  0.020  1.324
 8S5  C4   H1   single    0.970  0.020  1.090
 8S5  C14  H2   single    0.930  0.020  1.080
 8S5  C5   H3   single    0.970  0.020  1.090
 8S5  C5   H4   single    0.970  0.020  1.090
 8S5  C8   H5   single    0.930  0.020  1.080
 8S5  C12  H6   single    0.930  0.020  1.080
 8S5  C13  H7   single    0.930  0.020  1.080
 8S5  N2   H8   single    0.860  0.020  1.020
 8S5  C3   H9   single    0.970  0.020  1.090
 8S5  C3   H10  single    0.970  0.020  1.090
 8S5  C2   H11  single    0.970  0.020  1.090
 8S5  N4   H12  single    0.890  0.020  1.040
 8S5  N4   H13  single    0.890  0.020  1.040
 8S5  C15  H14  single    0.930  0.020  1.080
 8S5  N5   H15  single    0.860  0.020  1.020
 8S5  C17  H16  single    0.930  0.020  1.080
 8S5  C18  H17  single    0.930  0.020  1.080
 8S5  C19  H18  single    0.930  0.020  1.080
 8S5  C22  H19  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
 8S5  H1   C4   F1   108.06  3.000
 8S5  H1   C4   C3   114.01  3.000
 8S5  F1   C4   C3   109.18  3.000
 8S5  H1   C4   C5   113.05  3.000
 8S5  C3   C4   C5   103.45  3.000
 8S5  F1   C4   C5   108.94  3.000
 8S5  H2   C14  C15  118.88  3.000
 8S5  H2   C14  C13  119.32  3.000
 8S5  C15  C14  C13  121.80  3.000
 8S5  H4   C5   H3   108.47  3.000
 8S5  H4   C5   N1   112.36  3.000
 8S5  H3   C5   N1   112.02  3.000
 8S5  H4   C5   C4   111.15  3.000
 8S5  H3   C5   C4   110.05  3.000
 8S5  N1   C5   C4   102.72  3.000
 8S5  O3   C6   N2   122.49  3.000
 8S5  O3   C6   N1   121.64  3.000
 8S5  N2   C6   N1   115.87  3.000
 8S5  C12  C11  C10  120.38  3.000
 8S5  C12  C11  C7   132.36  3.000
 8S5  C10  C11  C7   107.25  3.000
 8S5  N2   C7   C8   130.60  3.000
 8S5  N2   C7   C11  121.99  3.000
 8S5  C8   C7   C11  107.41  3.000
 8S5  H5   C8   N3   121.18  3.000
 8S5  H5   C8   C7   129.53  3.000
 8S5  N3   C8   C7   109.20  3.000
 8S5  C15  C10  N3   131.67  3.000
 8S5  C15  C10  C11  121.00  3.000
 8S5  N3   C10  C11  107.31  3.000
 8S5  H6   C12  C13  119.93  3.000
 8S5  H6   C12  C11  121.41  3.000
 8S5  C13  C12  C11  118.66  3.000
 8S5  H7   C13  C12  119.85  3.000
 8S5  H7   C13  C14  119.65  3.000
 8S5  C12  C13  C14  120.49  3.000
 8S5  C2   N1   C6   119.30  3.000
 8S5  C2   N1   C5   113.28  3.000
 8S5  C6   N1   C5   127.38  3.000
 8S5  H8   N2   C7   115.67  3.000
 8S5  H8   N2   C6   119.43  3.000
 8S5  C7   N2   C6   124.76  3.000
 8S5  H10  C3   H9   108.06  3.000
 8S5  H10  C3   C2   110.60  3.000
 8S5  H9   C3   C2   112.80  3.000
 8S5  H10  C3   C4   108.37  3.000
 8S5  H9   C3   C4   113.18  3.000
 8S5  C2   C3   C4   103.74  3.000
 8S5  C10  N3   C9   125.41  3.000
 8S5  C10  N3   C8   108.83  3.000
 8S5  C9   N3   C8   125.76  3.000
 8S5  N5   C1   C2   113.56  3.000
 8S5  N5   C1   O1   124.95  3.000
 8S5  C2   C1   O1   121.41  3.000
 8S5  H11  C2   C1   110.56  3.000
 8S5  H11  C2   C3   110.71  3.000
 8S5  C1   C2   C3   110.54  3.000
 8S5  H11  C2   N1   110.84  3.000
 8S5  C1   C2   N1   110.97  3.000
 8S5  C3   C2   N1   103.00  3.000
 8S5  H13  N4   H12  115.62  3.000
 8S5  H13  N4   C9   116.98  3.000
 8S5  H12  N4   C9   122.44  3.000
 8S5  H14  C15  C10  122.01  3.000
 8S5  H14  C15  C14  120.34  3.000
 8S5  C10  C15  C14  117.65  3.000
 8S5  H15  N5   C16  114.76  3.000
 8S5  H15  N5   C1   116.09  3.000
 8S5  C16  N5   C1   129.12  3.000
 8S5  C22  C16  C17  119.28  3.000
 8S5  C22  C16  N5   123.81  3.000
 8S5  C17  C16  N5   116.91  3.000
 8S5  H16  C17  C18  119.65  3.000
 8S5  H16  C17  C16  119.74  3.000
 8S5  C18  C17  C16  120.60  3.000
 8S5  H17  C18  C19  119.71  3.000
 8S5  H17  C18  C17  119.46  3.000
 8S5  C19  C18  C17  120.83  3.000
 8S5  H18  C19  C20  121.14  3.000
 8S5  H18  C19  C18  121.15  3.000
 8S5  C20  C19  C18  117.70  3.000
 8S5  C22  C20  O4   117.85  3.000
 8S5  O4   C20  C19  119.02  3.000
 8S5  C22  C20  C19  123.06  3.000
 8S5  C21  O4   C20  117.97  3.000
 8S5  F4   C21  F3   106.72  3.000
 8S5  F4   C21  F2   108.36  3.000
 8S5  F3   C21  F2   108.31  3.000
 8S5  F2   C21  O4   107.67  3.000
 8S5  F4   C21  O4   112.83  3.000
 8S5  F3   C21  O4   112.81  3.000
 8S5  H19  C22  C20  120.03  3.000
 8S5  H19  C22  C16  121.44  3.000
 8S5  C20  C22  C16  118.52  3.000
 8S5  O2   C9   N4   123.92  3.000
 8S5  O2   C9   N3   121.03  3.000
 8S5  N4   C9   N3   115.04  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
 8S5  CONST_01  N3   C10  C15  C14  180.00   0.0  0
 8S5  CONST_02  C11  C10  C15  C14    0.00   0.0  0
 8S5  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 8S5  CONST_04  N3   C8   C7   C11    0.00   0.0  0
 8S5  CONST_05  C8   N3   C10  C11    0.00   0.0  0
 8S5  CONST_06  C10  N3   C8   C7     0.00   0.0  0
 8S5  CONST_07  N3   C10  C11  C7     0.00   0.0  0
 8S5  CONST_08  C15  C10  C11  C7   180.00   0.0  0
 8S5  CONST_09  C13  C12  C11  C7   180.00   0.0  0
 8S5  CONST_10  C10  C11  C7   C8     0.00   0.0  0
 8S5  CONST_11  C12  C11  C7   C8   180.00   0.0  0
 8S5  CONST_12  C15  C10  N3   C8   180.00   0.0  0
 8S5  CONST_13  C13  C12  C11  C10    0.00   0.0  0
 8S5  CONST_14  C13  C14  C15  C10    0.00   0.0  0
 8S5  CONST_15  N3   C10  C11  C12  180.00   0.0  0
 8S5  CONST_16  C15  C10  C11  C12    0.00   0.0  0
 8S5  CONST_17  C15  C14  C13  C12    0.00   0.0  0
 8S5  CONST_18  C19  C18  C17  C16    0.00   0.0  0
 8S5  CONST_19  C19  C20  C22  C16    0.00   0.0  0
 8S5  CONST_20  C20  C22  C16  C17    0.00   0.0  0
 8S5  CONST_21  C20  C19  C18  C17    0.00   0.0  0
 8S5  CONST_22  C22  C16  C17  C18    0.00   0.0  0
 8S5  CONST_23  C22  C20  C19  C18    0.00   0.0  0
 8S5  CONST_24  C9   N3   C10  C11  180.00   0.0  0
 8S5  CONST_25  C9   N3   C8   C7   180.00   0.0  0
 8S5  CONST_26  C15  C10  N3   C9     0.00   0.0  0
 8S5  CONST_27  N2   C7   C11  C10  180.00   0.0  0
 8S5  CONST_28  N2   C7   C11  C12    0.00   0.0  0
 8S5  CONST_29  N3   C8   C7   N2   180.00   0.0  0
 8S5  CONST_30  C18  C17  C16  N5   180.00   0.0  0
 8S5  CONST_31  C20  C22  C16  N5   180.00   0.0  0
 8S5  CONST_32  O4   C20  C22  C16  180.00   0.0  0
 8S5  CONST_33  O4   C20  C19  C18  180.00   0.0  0
 8S5  CONST_34  H6   C12  C13  C14  180.00   0.0  0
 8S5  CONST_35  H5   C8   C7   C11  180.00   0.0  0
 8S5  CONST_36  H14  C15  C10  C11  180.00   0.0  0
 8S5  CONST_37  H7   C13  C12  C11  180.00   0.0  0
 8S5  CONST_38  H2   C14  C15  C10  180.00   0.0  0
 8S5  CONST_39  H17  C18  C17  C16  180.00   0.0  0
 8S5  CONST_40  H19  C22  C16  C17  180.00   0.0  0
 8S5  CONST_41  H18  C19  C18  C17  180.00   0.0  0
 8S5  CONST_42  H16  C17  C18  C19  180.00   0.0  0
 8S5  CONST_43  O3   C6   N1   C5   180.00   0.0  0
 8S5  CONST_46  O3   C6   N1   C2     0.00   0.0  0
 8S5  CONST_47  C16  N5   C1   C2   180.00   0.0  0
 8S5  CONST_48  C8   C7   N2   C6     0.00   0.0  0
 8S5  CONST_49  C11  C7   N2   C6   180.00   0.0  0
 8S5  CONST_50  N1   C6   N2   C7   180.00   0.0  0
 8S5  CONST_51  C17  C16  N5   C1   180.00   0.0  0
 8S5  CONST_52  C22  C16  N5   C1     0.00   0.0  0
 8S5  CONST_53  N2   C6   N1   C5     0.00   0.0  0
 8S5  CONST_54  N4   C9   N3   C8     0.00   0.0  0
 8S5  CONST_56  C2   N1   C6   N2   180.00   0.0  0
 8S5  CONST_57  H8   N2   C7   C11    0.00   0.0  0
 8S5  CONST_58  H15  N5   C16  C17    0.00   0.0  0
 8S5  CONST_59  O3   C6   N2   C7     0.00   0.0  0
 8S5  CONST_60  C16  N5   C1   O1     0.00   0.0  0
 8S5  CONST_62  H13  N4   C9   N3   180.00   0.0  0
 8S5  Var_01    C2   N1   C5   C4    17.11  30.0  1
 8S5  Var_02    C22  C20  O4   C21  -92.03  30.0  2
 8S5  Var_03    F3   C21  O4   C20  -61.67  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
 8S5  chir_01  C4  F1  C5  C3  negativ
 8S5  chir_02  C2  N1  C1  C3  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
 8S5  plan-1  N5   0.020
 8S5  plan-1  C16  0.020
 8S5  plan-1  C17  0.020
 8S5  plan-1  C18  0.020
 8S5  plan-1  C19  0.020
 8S5  plan-1  C20  0.020
 8S5  plan-1  O4   0.020
 8S5  plan-1  C22  0.020
 8S5  plan-1  H16  0.020
 8S5  plan-1  H17  0.020
 8S5  plan-1  H18  0.020
 8S5  plan-1  H19  0.020
 8S5  plan-2  C1   0.020
 8S5  plan-2  C2   0.020
 8S5  plan-2  N5   0.020
 8S5  plan-2  C16  0.020
 8S5  plan-2  H15  0.020
 8S5  plan-2  O1   0.020
 8S5  plan-3  C14  0.020
 8S5  plan-3  C11  0.020
 8S5  plan-3  C7   0.020
 8S5  plan-3  C8   0.020
 8S5  plan-3  C10  0.020
 8S5  plan-3  C12  0.020
 8S5  plan-3  C13  0.020
 8S5  plan-3  N2   0.020
 8S5  plan-3  N3   0.020
 8S5  plan-3  N4   0.020
 8S5  plan-3  O2   0.020
 8S5  plan-3  C15  0.020
 8S5  plan-3  H2   0.020
 8S5  plan-3  H5   0.020
 8S5  plan-3  H6   0.020
 8S5  plan-3  H7   0.020
 8S5  plan-3  H12  0.020
 8S5  plan-3  H13  0.020
 8S5  plan-3  H14  0.020
 8S5  plan-3  C9   0.020
 8S5  plan-4  C5   0.020
 8S5  plan-4  C6   0.020
 8S5  plan-4  C7   0.020
 8S5  plan-4  N1   0.020
 8S5  plan-4  N2   0.020
 8S5  plan-4  C2   0.020
 8S5  plan-4  O3   0.020
 8S5  plan-4  H8   0.020

