# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 11:23:34 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2~{S})-~{N}1-(1-methylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(NC(=O)N2CCC[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
 8RT  8RT  (2~{S})-~{N}1-(1-methylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide  ligand  53  32  .  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_8RT
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
 8RT  C2   C  CT    0   1.073  -7.2158   0.4358   0.6815
 8RT  C41  C  CR56  0  -0.015   5.4934  -0.6906  -0.0416
 8RT  C42  C  CR16  0  -0.342   6.5093   0.2275  -0.3285
 8RT  C44  C  CR16  0  -0.273   7.8049  -0.2322  -0.4569
 8RT  C46  C  CR16  0  -0.278   8.1082  -1.5958  -0.3014
 8RT  C48  C  CR16  0  -0.313   7.1251  -2.5225  -0.0141
 8RT  C12  C  CR16  0  -0.243  -4.0604  -0.6509  -2.2265
 8RT  C14  C  CR16  0  -0.318  -5.1874  -0.8139  -1.4364
 8RT  C18  C  C     0   0.551  -0.6479   1.5389  -0.4486
 8RT  C20  C  CR15  0  -0.173   0.2323   2.3634   0.4828
 8RT  C23  C  CH2   0  -0.298   2.4294   3.2866   0.0452
 8RT  C26  C  CH2   0  -0.476   1.4979   4.3993   0.5092
 8RT  C29  C  CH2   0  -0.472   0.1147   3.8613   0.1625
 8RT  F1   F  F     0  -0.299  -7.7958   0.5677  -0.5130
 8RT  F3   F  F     0  -0.299  -6.7834   1.6476   1.0350
 8RT  F4   F  F     0  -0.276  -8.1362   0.0519   1.5512
 8RT  O5   O  O2    0  -0.525  -6.2436  -0.4840   0.6875
 8RT  C6   C  CR6   0   0.333  -5.1560  -0.2884  -0.1569
 8RT  C7   C  CR16  0  -0.407  -4.0513   0.3752   0.3370
 8RT  C9   C  CR6   0   0.395  -2.9212   0.5315  -0.4692
 8RT  C10  C  CR16  0  -0.314  -2.9333   0.0142  -1.7659
 8RT  N16  N  NH1   0  -0.752  -1.8407   1.2024   0.1029
 8RT  O19  O  O     0  -0.455  -0.3131   1.2795  -1.5866
 8RT  N22  N  NR5   0  -0.534   1.6319   2.0881   0.2625
 8RT  C32  C  C     0   0.753   2.0867   0.8167   0.3770
 8RT  O33  O  O     0  -0.532   1.3524  -0.1003   0.7312
 8RT  N34  N  NH1   0  -0.793   3.4017   0.6320   0.0736
 8RT  C36  C  CR5   0   0.193   4.0805  -0.5825   0.1547
 8RT  C37  C  CR15  0  -0.074   3.6182  -1.8438   0.4176
 8RT  N39  N  NR5   0  -0.526   4.6703  -2.7306   0.3978
 8RT  C40  C  CR56  0   0.377   5.8160  -2.0565   0.1155
 8RT  H2   H  HCR6  0   0.249   8.6017   0.4660  -0.6778
 8RT  H3   H  HCR6  0   0.251   9.1337  -1.9252  -0.4081
 8RT  H4   H  HCR6  0   0.265   7.3656  -3.5712   0.1078
 8RT  H5   H  HCH3  0   0.250   4.8433  -4.7081  -0.2843
 8RT  H6   H  HCH3  0   0.251   5.2146  -4.4714   1.4309
 8RT  H7   H  HCH3  0   0.264   3.5435  -4.4005   0.8711
 8RT  H8   H  HCR6  0   0.272  -4.0539  -1.0549  -3.2299
 8RT  H9   H  HCR6  0   0.280  -6.0533  -1.3495  -1.8005
 8RT  H10  H  HCR5  0   0.278  -0.0443   2.1781   1.5277
 8RT  H11  H  HCH2  0   0.248   2.6964   3.4045  -1.0102
 8RT  H12  H  HCH2  0   0.253   3.3500   3.2618   0.6320
 8RT  H13  H  HCH2  0   0.248   1.5932   4.5377   1.5876
 8RT  H14  H  HCH2  0   0.262   1.7180   5.3503   0.0266
 8RT  H15  H  HCH2  0   0.254  -0.0867   4.0058  -0.9010
 8RT  H16  H  HCH2  0   0.268  -0.6891   4.3326   0.7249
 8RT  H17  H  HCR6  0   0.292  -4.0557   0.7559   1.3512
 8RT  H18  H  HCR6  0   0.289  -2.0779   0.1134  -2.4121
 8RT  H19  H  HNH1  0   0.422  -1.9749   1.4771   1.0648
 8RT  H20  H  HNH1  0   0.416   3.9184   1.3939  -0.3338
 8RT  H21  H  HCR5  0   0.289   2.6226  -2.1916   0.6267
 8RT  H1   H  HCR6  0   0.241   6.2971   1.2837  -0.4473
 8RT  C50  C  CH3   0  -0.529   4.5689  -4.1518   0.6127

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
 8RT  C46  C48  aromatic  1.381  0.020  1.381
 8RT  C46  C44  aromatic  1.406  0.020  1.406
 8RT  C48  C40  aromatic  1.396  0.020  1.396
 8RT  C44  C42  aromatic  1.381  0.020  1.381
 8RT  C50  N39  single    1.441  0.020  1.441
 8RT  C40  N39  aromatic  1.359  0.020  1.359
 8RT  C40  C41  aromatic  1.412  0.020  1.412
 8RT  C42  C41  aromatic  1.399  0.020  1.399
 8RT  N39  C37  aromatic  1.376  0.020  1.376
 8RT  C41  C36  aromatic  1.431  0.020  1.431
 8RT  C37  C36  aromatic  1.369  0.020  1.369
 8RT  C36  N34  single    1.394  0.020  1.394
 8RT  N34  C32  single    1.362  0.020  1.362
 8RT  C32  O33  double    1.227  0.020  1.227
 8RT  C32  N22  single    1.355  0.020  1.355
 8RT  C23  N22  single    1.456  0.020  1.456
 8RT  C23  C26  single    1.524  0.020  1.524
 8RT  O19  C18  double    1.214  0.020  1.214
 8RT  N22  C20  single    1.443  0.020  1.443
 8RT  F3   C2   single    1.334  0.020  1.334
 8RT  C18  C20  single    1.524  0.020  1.524
 8RT  C18  N16  single    1.356  0.020  1.356
 8RT  F4   C2   single    1.323  0.020  1.323
 8RT  C20  C29  single    1.536  0.020  1.536
 8RT  C12  C10  aromatic  1.387  0.020  1.387
 8RT  C12  C14  aromatic  1.386  0.020  1.386
 8RT  C10  C9   aromatic  1.396  0.020  1.396
 8RT  C26  C29  single    1.524  0.020  1.524
 8RT  C2   F1   single    1.334  0.020  1.334
 8RT  C2   O5   single    1.338  0.020  1.338
 8RT  C14  C6   aromatic  1.384  0.020  1.384
 8RT  C9   N16  single    1.395  0.020  1.395
 8RT  C9   C7   aromatic  1.397  0.020  1.397
 8RT  C6   C7   aromatic  1.380  0.020  1.380
 8RT  C6   O5   single    1.391  0.020  1.391
 8RT  C42  H1   single    0.930  0.020  1.080
 8RT  C44  H2   single    0.930  0.020  1.080
 8RT  C46  H3   single    0.930  0.020  1.080
 8RT  C48  H4   single    0.930  0.020  1.080
 8RT  C50  H5   single    0.970  0.020  1.090
 8RT  C50  H6   single    0.970  0.020  1.090
 8RT  C50  H7   single    0.970  0.020  1.090
 8RT  C12  H8   single    0.930  0.020  1.080
 8RT  C14  H9   single    0.930  0.020  1.080
 8RT  C20  H10  single    0.970  0.020  1.090
 8RT  C23  H11  single    0.970  0.020  1.090
 8RT  C23  H12  single    0.970  0.020  1.090
 8RT  C26  H13  single    0.970  0.020  1.090
 8RT  C26  H14  single    0.970  0.020  1.090
 8RT  C29  H15  single    0.970  0.020  1.090
 8RT  C29  H16  single    0.970  0.020  1.090
 8RT  C7   H17  single    0.930  0.020  1.080
 8RT  C10  H18  single    0.930  0.020  1.080
 8RT  N16  H19  single    0.860  0.020  1.020
 8RT  N34  H20  single    0.860  0.020  1.020
 8RT  C37  H21  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
 8RT  O5   C2   F4   107.63  3.000
 8RT  O5   C2   F3   112.80  3.000
 8RT  F4   C2   F3   108.34  3.000
 8RT  O5   C2   F1   112.81  3.000
 8RT  F4   C2   F1   108.35  3.000
 8RT  F3   C2   F1   106.76  3.000
 8RT  C40  C41  C36  106.46  3.000
 8RT  C36  C41  C42  134.08  3.000
 8RT  C40  C41  C42  119.46  3.000
 8RT  H1   C42  C44  119.87  3.000
 8RT  H1   C42  C41  121.32  3.000
 8RT  C44  C42  C41  118.81  3.000
 8RT  H2   C44  C46  119.32  3.000
 8RT  H2   C44  C42  119.67  3.000
 8RT  C46  C44  C42  121.01  3.000
 8RT  H3   C46  C48  119.38  3.000
 8RT  H3   C46  C44  119.26  3.000
 8RT  C48  C46  C44  121.35  3.000
 8RT  H4   C48  C40  121.41  3.000
 8RT  H4   C48  C46  121.01  3.000
 8RT  C40  C48  C46  117.58  3.000
 8RT  H8   C12  C10  118.83  3.000
 8RT  H8   C12  C14  119.32  3.000
 8RT  C10  C12  C14  121.85  3.000
 8RT  H9   C14  C6   121.18  3.000
 8RT  H9   C14  C12  121.16  3.000
 8RT  C6   C14  C12  117.64  3.000
 8RT  O19  C18  N16  124.79  3.000
 8RT  N16  C18  C20  113.18  3.000
 8RT  O19  C18  C20  121.95  3.000
 8RT  H10  C20  N22  110.96  3.000
 8RT  H10  C20  C29  110.12  3.000
 8RT  N22  C20  C29  103.20  3.000
 8RT  H10  C20  C18  110.20  3.000
 8RT  C29  C20  C18  110.85  3.000
 8RT  N22  C20  C18  111.32  3.000
 8RT  H12  C23  H11  108.35  3.000
 8RT  H12  C23  N22  111.28  3.000
 8RT  H11  C23  N22  111.47  3.000
 8RT  H12  C23  C26  111.62  3.000
 8RT  H11  C23  C26  111.34  3.000
 8RT  N22  C23  C26  102.76  3.000
 8RT  H14  C26  H13  108.03  3.000
 8RT  H14  C26  C29  113.02  3.000
 8RT  H13  C26  C29  110.41  3.000
 8RT  H14  C26  C23  112.29  3.000
 8RT  H13  C26  C23  109.88  3.000
 8RT  C29  C26  C23  103.17  3.000
 8RT  H16  C29  H15  108.04  3.000
 8RT  H16  C29  C26  113.57  3.000
 8RT  H15  C29  C26  110.01  3.000
 8RT  H16  C29  C20  111.78  3.000
 8RT  H15  C29  C20  110.25  3.000
 8RT  C26  C29  C20  103.14  3.000
 8RT  C6   O5   C2   117.95  3.000
 8RT  C7   C6   O5   118.44  3.000
 8RT  O5   C6   C14  119.36  3.000
 8RT  C7   C6   C14  122.13  3.000
 8RT  H17  C7   C9   120.28  3.000
 8RT  H17  C7   C6   120.05  3.000
 8RT  C9   C7   C6   119.66  3.000
 8RT  N16  C9   C10  124.47  3.000
 8RT  N16  C9   C7   116.35  3.000
 8RT  C10  C9   C7   119.18  3.000
 8RT  H18  C10  C9   121.09  3.000
 8RT  H18  C10  C12  119.37  3.000
 8RT  C9   C10  C12  119.54  3.000
 8RT  H19  N16  C9   114.76  3.000
 8RT  H19  N16  C18  115.91  3.000
 8RT  C9   N16  C18  129.33  3.000
 8RT  C32  N22  C23  126.95  3.000
 8RT  C23  N22  C20  113.39  3.000
 8RT  C32  N22  C20  119.44  3.000
 8RT  N34  C32  O33  122.73  3.000
 8RT  O33  C32  N22  121.65  3.000
 8RT  N34  C32  N22  115.62  3.000
 8RT  H20  N34  C36  115.67  3.000
 8RT  H20  N34  C32  118.88  3.000
 8RT  C36  N34  C32  125.13  3.000
 8RT  C37  C36  N34  130.52  3.000
 8RT  N34  C36  C41  122.61  3.000
 8RT  C37  C36  C41  106.88  3.000
 8RT  H21  C37  N39  120.15  3.000
 8RT  H21  C37  C36  130.41  3.000
 8RT  N39  C37  C36  109.44  3.000
 8RT  C40  N39  C37  109.14  3.000
 8RT  C37  N39  C50  125.43  3.000
 8RT  C40  N39  C50  125.42  3.000
 8RT  N39  C40  C48  130.13  3.000
 8RT  N39  C40  C41  108.08  3.000
 8RT  C48  C40  C41  121.79  3.000
 8RT  H7   C50  H6   108.27  3.000
 8RT  H7   C50  H5   108.44  3.000
 8RT  H6   C50  H5   108.59  3.000
 8RT  H7   C50  N39  109.13  3.000
 8RT  H6   C50  N39  111.06  3.000
 8RT  H5   C50  N39  111.27  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
 8RT  CONST_01  C46  C48  C40  C41    0.00   0.0  0
 8RT  CONST_02  C37  N39  C40  C41    0.00   0.0  0
 8RT  CONST_03  C46  C44  C42  C41    0.00   0.0  0
 8RT  CONST_04  N39  C37  C36  C41    0.00   0.0  0
 8RT  CONST_05  C48  C46  C44  C42    0.00   0.0  0
 8RT  CONST_06  C48  C40  C41  C42    0.00   0.0  0
 8RT  CONST_07  N39  C40  C41  C42  180.00   0.0  0
 8RT  CONST_08  C37  C36  C41  C42  180.00   0.0  0
 8RT  CONST_09  C40  C48  C46  C44    0.00   0.0  0
 8RT  CONST_10  C40  C41  C42  C44    0.00   0.0  0
 8RT  CONST_11  C36  C41  C42  C44  180.00   0.0  0
 8RT  CONST_12  N39  C40  C48  C46  180.00   0.0  0
 8RT  CONST_13  C37  N39  C40  C48  180.00   0.0  0
 8RT  CONST_14  C36  C41  C40  C48  180.00   0.0  0
 8RT  CONST_15  C7   C9   C10  C12    0.00   0.0  0
 8RT  CONST_16  C7   C6   C14  C12    0.00   0.0  0
 8RT  CONST_17  C9   C10  C12  C14    0.00   0.0  0
 8RT  CONST_18  C9   C7   C6   C14    0.00   0.0  0
 8RT  CONST_19  C10  C12  C14  C6     0.00   0.0  0
 8RT  CONST_20  C10  C9   C7   C6     0.00   0.0  0
 8RT  CONST_21  N39  C40  C41  C36    0.00   0.0  0
 8RT  CONST_22  C40  N39  C37  C36    0.00   0.0  0
 8RT  CONST_23  C40  C41  C36  C37    0.00   0.0  0
 8RT  CONST_24  C50  N39  C40  C41  180.00   0.0  0
 8RT  CONST_25  N34  C36  C41  C42    0.00   0.0  0
 8RT  CONST_26  C50  N39  C40  C48    0.00   0.0  0
 8RT  CONST_27  C36  C37  N39  C50  180.00   0.0  0
 8RT  CONST_28  N16  C9   C10  C12  180.00   0.0  0
 8RT  CONST_29  O5   C6   C14  C12  180.00   0.0  0
 8RT  CONST_30  C9   C7   C6   O5   180.00   0.0  0
 8RT  CONST_31  N16  C9   C7   C6   180.00   0.0  0
 8RT  CONST_32  C40  C41  C36  N34  180.00   0.0  0
 8RT  CONST_33  N39  C37  C36  N34  180.00   0.0  0
 8RT  CONST_34  H4   C48  C40  C41  180.00   0.0  0
 8RT  CONST_35  H2   C44  C42  C41  180.00   0.0  0
 8RT  CONST_36  H21  C37  C36  C41  180.00   0.0  0
 8RT  CONST_37  H3   C46  C44  C42  180.00   0.0  0
 8RT  CONST_38  H1   C42  C44  C46  180.00   0.0  0
 8RT  CONST_39  H18  C10  C12  C14  180.00   0.0  0
 8RT  CONST_40  H17  C7   C6   C14  180.00   0.0  0
 8RT  CONST_41  H8   C12  C14  C6   180.00   0.0  0
 8RT  CONST_42  H9   C14  C6   C7   180.00   0.0  0
 8RT  CONST_43  O33  C32  N22  C20    0.00   0.0  0
 8RT  CONST_44  C9   N16  C18  C20  180.00   0.0  0
 8RT  CONST_45  O33  C32  N22  C23  180.00   0.0  0
 8RT  CONST_46  C32  N34  C36  C41  180.00   0.0  0
 8RT  CONST_47  C10  C9   N16  C18    0.00   0.0  0
 8RT  CONST_48  C7   C9   N16  C18  180.00   0.0  0
 8RT  CONST_49  C36  N34  C32  N22  180.00   0.0  0
 8RT  CONST_50  C37  C36  N34  C32    0.00   0.0  0
 8RT  CONST_51  N34  C32  N22  C20  180.00   0.0  0
 8RT  CONST_52  N34  C32  N22  C23    0.00   0.0  0
 8RT  CONST_53  H20  N34  C36  C41    0.00   0.0  0
 8RT  CONST_54  H19  N16  C9   C7     0.00   0.0  0
 8RT  CONST_55  O19  C18  N16  C9     0.00   0.0  0
 8RT  CONST_56  C36  N34  C32  O33    0.00   0.0  0
 8RT  Var_01    C26  C23  N22  C20   14.58  30.0  1
 8RT  Var_02    C23  C26  C29  C20   38.00  30.0  1
 8RT  Var_03    N22  C23  C26  C29  -32.14  30.0  1
 8RT  Var_04    C14  C6   O5   C2   -90.78  30.0  3
 8RT  Var_05    H5   C50  N39  C37  115.14  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
 8RT  chir_01  C20  N22  C18  C29  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
 8RT  plan-1  C12  0.020
 8RT  plan-1  C14  0.020
 8RT  plan-1  O5   0.020
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