# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 06:02:04 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: N-{5-[(3S)-3-(2-hydroxypropan-2-yl)pyrrolidin-1-yl]-2-(trifluoromethyl)pyridin-3-yl}-6-(1-methyl-1H-pyrazol-4-yl)pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cccc(n2)C(=O)Nc3cc(cnc3C(F)(F)F)N4CC[C@@H](C4)C(C)(C)O
#
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
 YXD  YXD  N-{5-[(3S)-3-(2-hydroxypropan-2-yl)pyrrolidin-1-yl]-2-(trifluoromethyl)pyridin-3-yl}-6-(1-methyl-1H-pyrazol-4-yl)pyridine-2-carboxamide  ligand  59  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YXD
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
 YXD  N1   N  N     0  -0.390   0.3814  -4.9275  18.2221
 YXD  N3   N  NR5   0  -0.265   7.9058  -5.7489  15.5319
 YXD  C4   C  CT    0   1.048   2.3089  -5.0388  16.8090
 YXD  C5   C  CR16  0  -0.189  -0.3128  -4.5282  19.2625
 YXD  C6   C  CR6   0   0.368   0.2161  -3.6622  20.2453
 YXD  C7   C  CH2   0  -0.276  -1.8998  -3.6392  21.5178
 YXD  C8   C  CH2   0  -0.479  -2.3111  -2.7805  22.7050
 YXD  C10  C  CT    0   0.223  -0.9933  -1.5994  24.6107
 YXD  C13  C  CH2   0  -0.246   0.0509  -2.5360  22.4337
 YXD  C15  C  CR16  0  -0.301   6.2061  -0.6878  18.8884
 YXD  C17  C  CR16  0  -0.341   8.0598  -1.6277  17.7024
 YXD  C20  C  CR15  0   0.058   7.0639  -4.9833  16.2347
 YXD  C21  C  CH3   0  -0.506   7.6202  -7.0153  14.9009
 YXD  C22  C  CR15  0  -0.100   9.0663  -4.0882  16.1137
 YXD  F2   F  F     0  -0.293   1.5189  -5.8157  16.0774
 YXD  F    F  F     0  -0.326   3.4000  -5.7742  17.1179
 YXD  F1   F  F     0  -0.317   2.7445  -4.0539  16.0073
 YXD  C3   C  CR6   0  -0.149   1.6235  -4.5144  18.0367
 YXD  N2   N  NT    0  -0.536  -0.5053  -3.2806  21.3160
 YXD  C9   C  CH1   0  -0.286  -1.0224  -2.6709  23.5161
 YXD  O1   O  OH1   0  -0.676   0.3297  -1.6595  25.1290
 YXD  C11  C  CH3   0  -0.687  -1.2842  -0.1917  24.0917
 YXD  C14  C  CR16  0  -0.326   1.5381  -3.2321  20.0529
 YXD  C2   C  CR6   0   0.374   2.2544  -3.6440  18.9403
 YXD  N    N  NH1   0  -0.785   3.5670  -3.2188  18.7282
 YXD  C1   C  C     0   0.519   4.0826  -1.9992  19.0247
 YXD  O    O  O     0  -0.436   3.4902  -1.0986  19.5853
 YXD  C    C  CR6   0   0.122   5.5072  -1.8414  18.5737
 YXD  N5   N  N     0  -0.496   6.0263  -2.8403  17.8733
 YXD  C18  C  CR6   0   0.238   7.2765  -2.7544  17.4285
 YXD  C16  C  CR16  0  -0.142   7.5166  -0.5937  18.4393
 YXD  C19  C  CR5   0  -0.168   7.7783  -3.8712  16.6438
 YXD  N4   N  N     0  -0.271   9.1270  -5.2236  15.4489
 YXD  H1   H  HCR6  0   0.272  -1.3243  -4.9078  19.3414
 YXD  H2   H  HCH2  0   0.249  -2.4972  -3.4256  20.6288
 YXD  H3   H  HCH2  0   0.236  -2.0076  -4.7071  21.7400
 YXD  H4   H  HCH2  0   0.245  -2.6370  -1.7984  22.3557
 YXD  H5   H  HCH2  0   0.256  -3.1333  -3.2258  23.2636
 YXD  H6   H  HCH2  0   0.248   1.0033  -2.9633  22.7535
 YXD  H7   H  HCH2  0   0.234   0.2366  -1.4929  22.1541
 YXD  H8   H  HCR6  0   0.276   5.7484   0.1047  19.4622
 YXD  H9   H  HCR6  0   0.274   9.0763  -1.5604  17.3392
 YXD  H10  H  HCR5  0   0.290   6.0350  -5.2623  16.3914
 YXD  H11  H  HCH3  0   0.263   8.2446  -7.7983  15.3265
 YXD  H12  H  HCH3  0   0.262   6.5763  -7.2649  15.0669
 YXD  H13  H  HCH3  0   0.263   7.8042  -6.9521  13.8305
 YXD  H14  H  HCR5  0   0.262   9.9431  -3.4632  16.1968
 YXD  H15  H  HCH1  0   0.250  -0.8617  -3.6362  24.0118
 YXD  H16  H  HCH3  0   0.231  -1.9405  -1.2445  26.5309
 YXD  H17  H  HCH3  0   0.229  -3.0253  -1.9298  25.3295
 YXD  H18  H  HCH3  0   0.231  -1.8121  -2.9547  26.1015
 YXD  H19  H  HOH1  0   0.442   0.4057  -1.0165  25.8425
 YXD  H20  H  HCH3  0   0.235  -1.1654   0.5319  24.9019
 YXD  H21  H  HCH3  0   0.235  -0.6096   0.1034  23.2875
 YXD  H22  H  HCH3  0   0.227  -2.3068  -0.0948  23.7277
 YXD  H23  H  HCR6  0   0.299   2.0028  -2.5784  20.7734
 YXD  H24  H  HNH1  0   0.419   4.2149  -3.8182  18.2311
 YXD  H25  H  HCR6  0   0.280   8.1082   0.2846  18.6608
 YXD  C12  C  CH3   0  -0.673  -2.0014  -1.9562  25.7037

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
 YXD  C21  N3   single    1.443  0.020  1.443
 YXD  N3   N4   aromatic  1.332  0.020  1.332
 YXD  N3   C20  aromatic  1.337  0.020  1.337
 YXD  N4   C22  aromatic  1.317  0.020  1.317
 YXD  C20  C19  aromatic  1.384  0.020  1.384
 YXD  C22  C19  aromatic  1.410  0.020  1.410
 YXD  F2   C4   single    1.328  0.020  1.328
 YXD  F1   C4   single    1.343  0.020  1.343
 YXD  C19  C18  single    1.454  0.020  1.454
 YXD  C4   F    single    1.352  0.020  1.352
 YXD  C4   C3   single    1.501  0.020  1.501
 YXD  C18  C17  aromatic  1.399  0.020  1.399
 YXD  C18  N5   aromatic  1.330  0.020  1.330
 YXD  C17  C16  aromatic  1.381  0.020  1.381
 YXD  N5   C    aromatic  1.326  0.020  1.326
 YXD  N1   C3   aromatic  1.322  0.020  1.322
 YXD  N1   C5   aromatic  1.313  0.020  1.313
 YXD  C3   C2   aromatic  1.404  0.020  1.404
 YXD  C16  C15  aromatic  1.389  0.020  1.389
 YXD  C    C15  aromatic  1.385  0.020  1.385
 YXD  C    C1   single    1.503  0.020  1.503
 YXD  N    C2   single    1.396  0.020  1.396
 YXD  N    C1   single    1.357  0.020  1.357
 YXD  C5   C6   aromatic  1.413  0.020  1.413
 YXD  C2   C14  aromatic  1.386  0.020  1.386
 YXD  C1   O    double    1.215  0.020  1.215
 YXD  C14  C6   aromatic  1.403  0.020  1.403
 YXD  C6   N2   single    1.346  0.020  1.346
 YXD  N2   C7   single    1.454  0.020  1.454
 YXD  N2   C13  single    1.454  0.020  1.454
 YXD  C7   C8   single    1.522  0.020  1.522
 YXD  C13  C9   single    1.530  0.020  1.530
 YXD  C8   C9   single    1.527  0.020  1.527
 YXD  C9   C10  single    1.532  0.020  1.532
 YXD  O1   C10  single    1.422  0.020  1.422
 YXD  C10  C11  single    1.528  0.020  1.528
 YXD  C10  C12  single    1.529  0.020  1.529
 YXD  C5   H1   single    0.930  0.020  1.080
 YXD  C7   H2   single    0.970  0.020  1.090
 YXD  C7   H3   single    0.970  0.020  1.090
 YXD  C8   H4   single    0.970  0.020  1.090
 YXD  C8   H5   single    0.970  0.020  1.090
 YXD  C13  H6   single    0.970  0.020  1.090
 YXD  C13  H7   single    0.970  0.020  1.090
 YXD  C15  H8   single    0.930  0.020  1.080
 YXD  C17  H9   single    0.930  0.020  1.080
 YXD  C20  H10  single    0.930  0.020  1.080
 YXD  C21  H11  single    0.970  0.020  1.090
 YXD  C21  H12  single    0.970  0.020  1.090
 YXD  C21  H13  single    0.970  0.020  1.090
 YXD  C22  H14  single    0.930  0.020  1.080
 YXD  C9   H15  single    0.970  0.020  1.090
 YXD  C12  H16  single    0.970  0.020  1.090
 YXD  C12  H17  single    0.970  0.020  1.090
 YXD  C12  H18  single    0.970  0.020  1.090
 YXD  O1   H19  single    0.850  0.020  0.980
 YXD  C11  H20  single    0.970  0.020  1.090
 YXD  C11  H21  single    0.970  0.020  1.090
 YXD  C11  H22  single    0.970  0.020  1.090
 YXD  C14  H23  single    0.930  0.020  1.080
 YXD  N    H24  single    0.860  0.020  1.020
 YXD  C16  H25  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
 YXD  C3   N1   C5   120.85  3.000
 YXD  N4   N3   C21  120.01  3.000
 YXD  N4   N3   C20  112.59  3.000
 YXD  C21  N3   C20  127.40  3.000
 YXD  C3   C4   F1   112.36  3.000
 YXD  C3   C4   F    111.83  3.000
 YXD  F1   C4   F    105.89  3.000
 YXD  C3   C4   F2   112.55  3.000
 YXD  F    C4   F2   106.73  3.000
 YXD  F1   C4   F2   107.05  3.000
 YXD  H1   C5   C6   120.92  3.000
 YXD  H1   C5   N1   116.41  3.000
 YXD  C6   C5   N1   122.67  3.000
 YXD  C14  C6   N2   121.80  3.000
 YXD  N2   C6   C5   121.76  3.000
 YXD  C14  C6   C5   116.43  3.000
 YXD  H3   C7   H2   107.56  3.000
 YXD  H3   C7   N2   111.27  3.000
 YXD  H2   C7   N2   111.31  3.000
 YXD  H3   C7   C8   111.41  3.000
 YXD  H2   C7   C8   112.14  3.000
 YXD  N2   C7   C8   103.20  3.000
 YXD  H5   C8   H4   107.84  3.000
 YXD  H5   C8   C9   113.21  3.000
 YXD  H4   C8   C9   110.93  3.000
 YXD  H5   C8   C7   111.93  3.000
 YXD  H4   C8   C7   109.79  3.000
 YXD  C9   C8   C7   103.11  3.000
 YXD  C11  C10  O1   109.86  3.000
 YXD  C11  C10  C12  109.40  3.000
 YXD  O1   C10  C12  110.06  3.000
 YXD  C12  C10  C9   109.57  3.000
 YXD  C11  C10  C9   113.45  3.000
 YXD  O1   C10  C9   104.39  3.000
 YXD  H7   C13  H6   107.43  3.000
 YXD  H7   C13  C9   112.54  3.000
 YXD  H6   C13  C9   111.73  3.000
 YXD  H7   C13  N2   110.87  3.000
 YXD  H6   C13  N2   111.01  3.000
 YXD  C9   C13  N2   103.32  3.000
 YXD  H8   C15  C16  121.47  3.000
 YXD  H8   C15  C    121.20  3.000
 YXD  C16  C15  C    117.34  3.000
 YXD  H9   C17  C16  120.15  3.000
 YXD  H9   C17  C18  120.70  3.000
 YXD  C16  C17  C18  119.15  3.000
 YXD  H10  C20  C19  131.16  3.000
 YXD  H10  C20  N3   121.96  3.000
 YXD  C19  C20  N3   106.89  3.000
 YXD  H13  C21  H12  109.04  3.000
 YXD  H13  C21  H11  109.25  3.000
 YXD  H12  C21  H11  109.05  3.000
 YXD  H13  C21  N3   110.22  3.000
 YXD  H12  C21  N3   108.96  3.000
 YXD  H11  C21  N3   110.29  3.000
 YXD  H14  C22  N4   120.02  3.000
 YXD  H14  C22  C19  128.60  3.000
 YXD  N4   C22  C19  111.38  3.000
 YXD  C2   C3   C4   122.53  3.000
 YXD  C2   C3   N1   121.71  3.000
 YXD  C4   C3   N1   115.77  3.000
 YXD  C13  N2   C7   112.74  3.000
 YXD  C13  N2   C6   123.48  3.000
 YXD  C7   N2   C6   123.68  3.000
 YXD  H15  C9   C13  107.13  3.000
 YXD  H15  C9   C10  106.84  3.000
 YXD  C13  C9   C10  115.49  3.000
 YXD  H15  C9   C8   107.49  3.000
 YXD  C10  C9   C8   116.48  3.000
 YXD  C13  C9   C8   102.86  3.000
 YXD  H19  O1   C10  108.36  3.000
 YXD  H22  C11  H21  108.07  3.000
 YXD  H22  C11  H20  106.90  3.000
 YXD  H21  C11  H20  107.48  3.000
 YXD  H22  C11  C10  111.96  3.000
 YXD  H21  C11  C10  112.46  3.000
 YXD  H20  C11  C10  109.72  3.000
 YXD  H23  C14  C2   119.60  3.000
 YXD  H23  C14  C6   120.01  3.000
 YXD  C2   C14  C6   120.39  3.000
 YXD  N    C2   C14  121.16  3.000
 YXD  C14  C2   C3   117.94  3.000
 YXD  N    C2   C3   120.90  3.000
 YXD  H24  N    C1   113.33  3.000
 YXD  H24  N    C2   119.71  3.000
 YXD  C1   N    C2   126.72  3.000
 YXD  C    C1   O    121.52  3.000
 YXD  O    C1   N    125.58  3.000
 YXD  C    C1   N    112.90  3.000
 YXD  N5   C    C1   116.78  3.000
 YXD  C1   C    C15  119.85  3.000
 YXD  N5   C    C15  123.36  3.000
 YXD  C18  N5   C    119.74  3.000
 YXD  C19  C18  N5   117.08  3.000
 YXD  N5   C18  C17  120.86  3.000
 YXD  C19  C18  C17  122.06  3.000
 YXD  H25  C16  C17  120.13  3.000
 YXD  H25  C16  C15  120.33  3.000
 YXD  C17  C16  C15  119.54  3.000
 YXD  C18  C19  C22  129.52  3.000
 YXD  C18  C19  C20  126.77  3.000
 YXD  C22  C19  C20  103.70  3.000
 YXD  C22  N4   N3   105.44  3.000
 YXD  H18  C12  H17  108.06  3.000
 YXD  H18  C12  H16  108.08  3.000
 YXD  H17  C12  H16  107.24  3.000
 YXD  H18  C12  C10  111.07  3.000
 YXD  H17  C12  C10  111.60  3.000
 YXD  H16  C12  C10  110.63  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
 YXD  CONST_01  C14  C2   C3   N1      0.00   0.0  0
 YXD  CONST_02  C14  C6   C5   N1      0.00   0.0  0
 YXD  CONST_03  C19  C22  N4   N3      0.00   0.0  0
 YXD  CONST_04  C22  C19  C20  N3      0.00   0.0  0
 YXD  CONST_05  C18  C19  C20  N3    180.00   0.0  0
 YXD  CONST_06  C2   C3   N1   C5      0.00   0.0  0
 YXD  CONST_07  C2   C14  C6   C5      0.00   0.0  0
 YXD  CONST_08  C3   N1   C5   C6      0.00   0.0  0
 YXD  CONST_09  C3   C2   C14  C6      0.00   0.0  0
 YXD  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 YXD  CONST_11  C18  N5   C    C15     0.00   0.0  0
 YXD  CONST_12  C20  C19  C18  C17   180.00   0.0  0
 YXD  CONST_13  C22  C19  C18  C17     0.00   0.0  0
 YXD  CONST_14  C    N5   C18  C17     0.00   0.0  0
 YXD  CONST_15  C    C15  C16  C17     0.00   0.0  0
 YXD  CONST_16  C22  N4   N3   C20     0.00   0.0  0
 YXD  CONST_17  N4   C22  C19  C20     0.00   0.0  0
 YXD  CONST_18  N5   C18  C19  C20     0.00   0.0  0
 YXD  CONST_19  N5   C18  C19  C22   180.00   0.0  0
 YXD  CONST_20  C19  C18  N5   C     180.00   0.0  0
 YXD  CONST_21  C16  C17  C18  N5      0.00   0.0  0
 YXD  CONST_22  C16  C15  C    N5      0.00   0.0  0
 YXD  CONST_23  N4   C22  C19  C18   180.00   0.0  0
 YXD  CONST_24  C19  C18  C17  C16   180.00   0.0  0
 YXD  CONST_25  N4   N3   C20  C19     0.00   0.0  0
 YXD  CONST_26  N2   C6   C5   N1    180.00   0.0  0
 YXD  CONST_27  C2   C14  C6   N2    180.00   0.0  0
 YXD  CONST_28  N    C2   C3   N1    180.00   0.0  0
 YXD  CONST_29  C5   N1   C3   C4    180.00   0.0  0
 YXD  CONST_30  C14  C2   C3   C4    180.00   0.0  0
 YXD  CONST_31  N    C2   C14  C6    180.00   0.0  0
 YXD  CONST_32  C22  N4   N3   C21   180.00   0.0  0
 YXD  CONST_33  C19  C20  N3   C21   180.00   0.0  0
 YXD  CONST_34  C18  N5   C    C1    180.00   0.0  0
 YXD  CONST_35  C16  C15  C    C1    180.00   0.0  0
 YXD  CONST_36  H14  C22  N4   N3    180.00   0.0  0
 YXD  CONST_37  H23  C14  C6   C5    180.00   0.0  0
 YXD  CONST_38  H9   C17  C16  C15   180.00   0.0  0
 YXD  CONST_39  H8   C15  C16  C17   180.00   0.0  0
 YXD  CONST_40  H10  C20  C19  C22   180.00   0.0  0
 YXD  CONST_41  H1   C5   N1   C3    180.00   0.0  0
 YXD  CONST_42  H25  C16  C15  C     180.00   0.0  0
 YXD  CONST_43  C    C1   N    C2    180.00   0.0  0
 YXD  CONST_47  O    C1   N    C2      0.00   0.0  0
 YXD  Var_01    C7   N2   C6   C5     -4.28  30.0  2
 YXD  Var_02    C8   C7   N2   C6   -170.27  30.0  1
 YXD  Var_03    C9   C13  N2   C6   -165.65  30.0  1
 YXD  Var_04    C9   C8   C7   N2    -31.85  30.0  1
 YXD  Var_05    F2   C4   C3   N1      1.97  30.0  3
 YXD  Var_06    N    C1   C    C15  -175.35  30.0  2
 YXD  Var_07    H11  C21  N3   C20  -118.62  30.0  2
 YXD  Var_08    H20  C11  C10  C9   -175.25  30.0  3
 YXD  Var_09    H16  C12  C10  C9    175.63  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
 YXD  chir_01  C9  C13  C8  C10  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
 YXD  plan-1  N3   0.020
 YXD  plan-1  C20  0.020
 YXD  plan-1  C21  0.020
 YXD  plan-1  C22  0.020
 YXD  plan-1  C18  0.020
 YXD  plan-1  C19  0.020
 YXD  plan-1  N4   0.020
 YXD  plan-1  H10  0.020
 YXD  plan-1  H14  0.020
 YXD  plan-2  N1   0.020
 YXD  plan-2  C4   0.020
 YXD  plan-2  C5   0.020
 YXD  plan-2  C6   0.020
 YXD  plan-2  C3   0.020
 YXD  plan-2  N2   0.020
 YXD  plan-2  C14  0.020
 YXD  plan-2  C2   0.020
 YXD  plan-2  N    0.020
 YXD  plan-2  H1   0.020
 YXD  plan-2  H23  0.020
 YXD  plan-3  C15  0.020
 YXD  plan-3  C17  0.020
 YXD  plan-3  C1   0.020
 YXD  plan-3  C    0.020
 YXD  plan-3  N5   0.020
 YXD  plan-3  C18  0.020
 YXD  plan-3  C16  0.020
 YXD  plan-3  C19  0.020
 YXD  plan-3  H8   0.020
 YXD  plan-3  H9   0.020
 YXD  plan-3  H25  0.020
 YXD  plan-4  C2   0.020
 YXD  plan-4  N    0.020
 YXD  plan-4  C1   0.020
 YXD  plan-4  O    0.020
 YXD  plan-4  C    0.020
 YXD  plan-4  H24  0.020

