# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:54:03 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(O)CCN(C1)c2nc(cc(c2C#N)C(F)(F)F)N3C[C@H](O)[C@@H](O)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
 A4J  A4J  6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile  ligand  45  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A4J
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
 A4J  N3   N  NT    0  -0.508  -2.3641   0.5139   0.0869
 A4J  C4   C  CH2   0  -0.288   2.9461  -2.0433   0.1195
 A4J  N2   N  N     0  -0.525  -0.3535  -0.5275  -0.0778
 A4J  C7   C  CR6   0  -0.160   1.7045   0.6906  -0.2706
 A4J  C6   C  CR6   0   0.564   0.9743  -0.5300  -0.1709
 A4J  C9   C  CR16  0  -0.529  -0.3887   1.8737   0.0190
 A4J  C13  C  CH1   0   0.010  -4.6439   1.0030  -0.0646
 A4J  C8   C  CR6   0  -0.037   0.9654   1.8859  -0.1392
 A4J  C16  C  CSP   0  -0.011   3.0720   0.7418  -0.6183
 A4J  C1   C  CH3   0  -0.675   1.2016  -5.3902   0.3278
 A4J  C2   C  CR5   0   0.160   1.7403  -4.0834  -0.2281
 A4J  C3   C  CH2   0  -0.480   2.9013  -3.4960   0.5745
 A4J  N1   N  NR5   0  -0.509   1.5470  -1.7446  -0.1753
 A4J  C5   C  CH2   0  -0.229   0.7246  -2.9494  -0.1701
 A4J  C10  C  CR6   0   0.595  -1.0324   0.6071   0.0026
 A4J  C11  C  CH2   0  -0.291  -3.0622  -0.7586   0.1569
 A4J  C12  C  CH1   0   0.005  -4.4697  -0.3540   0.5952
 A4J  C14  C  CH2   0  -0.315  -3.2697   1.6480   0.1333
 A4J  O1   O  OH1   0  -0.662  -5.7011   1.7141   0.5114
 A4J  O2   O  OH1   0  -0.663  -5.4750  -1.2395   0.1920
 A4J  F1   F  F     0  -0.292   0.8848   4.2384   0.0480
 A4J  F2   F  F     0  -0.310   2.6684   3.2526   0.7255
 A4J  F3   F  F     0  -0.312   2.2527   3.4052  -1.3826
 A4J  N4   N  NS    0  -0.273   4.1811   0.8188  -0.9353
 A4J  H9   H  HCH2  0   0.256   3.3320  -1.3860   0.8995
 A4J  H8   H  HCH2  0   0.249   3.5777  -1.9298  -0.7625
 A4J  H12  H  HCR6  0   0.293  -0.9571   2.7817   0.1465
 A4J  H2   H  HCH1  0   0.228  -4.8062   0.8417  -1.1399
 A4J  H3   H  HCH3  0   0.238   0.3378  -5.7302  -0.2454
 A4J  H5   H  HCH3  0   0.237   1.9630  -6.1714   0.2857
 A4J  H4   H  HCH3  0   0.229   0.8956  -5.2833   1.3685
 A4J  H7   H  HCH2  0   0.261   3.8450  -4.0155   0.4003
 A4J  H6   H  HCH2  0   0.246   2.6824  -3.5554   1.6429
 A4J  H11  H  HCH2  0   0.255   0.0371  -2.9704  -1.0168
 A4J  H10  H  HCH2  0   0.240   0.1231  -3.0119   0.7410
 A4J  H14  H  HCH2  0   0.241  -3.0942  -1.2490  -0.8218
 A4J  H13  H  HCH2  0   0.260  -2.5747  -1.4397   0.8545
 A4J  H1   H  HCH1  0   0.225  -4.4760  -0.2086   1.6853
 A4J  H16  H  HCH2  0   0.249  -3.2275   2.1584   1.1019
 A4J  H15  H  HCH2  0   0.263  -3.0452   2.3788  -0.6462
 A4J  H17  H  HOH1  0   0.459  -5.9035   2.4701  -0.0477
 A4J  H18  H  HOH1  0   0.458  -5.4255  -2.0296   0.7386
 A4J  H19  H  HOH1  0   0.447   2.8380  -4.8381  -1.6515
 A4J  C15  C  CT    0   1.077   1.6906   3.2036  -0.1853
 A4J  O3   O  OH1   0  -0.674   2.1034  -4.2179  -1.5927

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
 A4J  O3   C2   single    1.418  0.020  1.418
 A4J  C1   C2   single    1.519  0.020  1.519
 A4J  C2   C5   single    1.523  0.020  1.523
 A4J  C2   C3   single    1.529  0.020  1.529
 A4J  C5   N1   single    1.459  0.020  1.459
 A4J  C3   C4   single    1.523  0.020  1.523
 A4J  N4   C16  triple    1.156  0.020  1.156
 A4J  N1   C4   single    1.461  0.020  1.461
 A4J  N1   C6   single    1.343  0.020  1.343
 A4J  C16  C7   single    1.412  0.020  1.412
 A4J  F2   C15  single    1.337  0.020  1.337
 A4J  C6   C7   aromatic  1.426  0.020  1.426
 A4J  C6   N2   aromatic  1.331  0.020  1.331
 A4J  C7   C8   aromatic  1.411  0.020  1.411
 A4J  N2   C10  aromatic  1.325  0.020  1.325
 A4J  C8   C15  single    1.505  0.020  1.505
 A4J  C8   C9   aromatic  1.363  0.020  1.363
 A4J  C15  F1   single    1.332  0.020  1.332
 A4J  C15  F3   single    1.338  0.020  1.338
 A4J  C10  C9   aromatic  1.421  0.020  1.421
 A4J  C10  N3   single    1.338  0.020  1.338
 A4J  O2   C12  single    1.399  0.020  1.399
 A4J  C14  N3   single    1.452  0.020  1.452
 A4J  C14  C13  single    1.531  0.020  1.531
 A4J  N3   C11  single    1.453  0.020  1.453
 A4J  C12  C13  single    1.519  0.020  1.519
 A4J  C12  C11  single    1.529  0.020  1.529
 A4J  C13  O1   single    1.398  0.020  1.398
 A4J  C4   H9   single    0.970  0.020  1.090
 A4J  C4   H8   single    0.970  0.020  1.090
 A4J  C9   H12  single    0.930  0.020  1.080
 A4J  C13  H2   single    0.970  0.020  1.090
 A4J  C1   H3   single    0.970  0.020  1.090
 A4J  C1   H5   single    0.970  0.020  1.090
 A4J  C1   H4   single    0.970  0.020  1.090
 A4J  C3   H7   single    0.970  0.020  1.090
 A4J  C3   H6   single    0.970  0.020  1.090
 A4J  C5   H11  single    0.970  0.020  1.090
 A4J  C5   H10  single    0.970  0.020  1.090
 A4J  C11  H14  single    0.970  0.020  1.090
 A4J  C11  H13  single    0.970  0.020  1.090
 A4J  C12  H1   single    0.970  0.020  1.090
 A4J  C14  H16  single    0.970  0.020  1.090
 A4J  C14  H15  single    0.970  0.020  1.090
 A4J  O1   H17  single    0.850  0.020  0.980
 A4J  O2   H18  single    0.850  0.020  0.980
 A4J  O3   H19  single    0.850  0.020  0.980

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
 A4J  C14  N3   C11  112.51  3.000
 A4J  C11  N3   C10  122.85  3.000
 A4J  C14  N3   C10  124.64  3.000
 A4J  H8   C4   H9   108.10  3.000
 A4J  H8   C4   N1   111.73  3.000
 A4J  H9   C4   N1   111.10  3.000
 A4J  H8   C4   C3   110.97  3.000
 A4J  H9   C4   C3   111.82  3.000
 A4J  N1   C4   C3   103.13  3.000
 A4J  C10  N2   C6   121.14  3.000
 A4J  C16  C7   C8   119.96  3.000
 A4J  C8   C7   C6   116.76  3.000
 A4J  C16  C7   C6   122.98  3.000
 A4J  N1   C6   C7   123.75  3.000
 A4J  C7   C6   N2   120.94  3.000
 A4J  N1   C6   N2   115.30  3.000
 A4J  H12  C9   C10  120.86  3.000
 A4J  H12  C9   C8   121.97  3.000
 A4J  C10  C9   C8   117.17  3.000
 A4J  H2   C13  O1   111.47  3.000
 A4J  H2   C13  C14  108.71  3.000
 A4J  O1   C13  C14  114.28  3.000
 A4J  H2   C13  C12  108.10  3.000
 A4J  O1   C13  C12  111.23  3.000
 A4J  C14  C13  C12  102.55  3.000
 A4J  C15  C8   C9   119.34  3.000
 A4J  C9   C8   C7   121.56  3.000
 A4J  C15  C8   C7   119.10  3.000
 A4J  N4   C16  C7   180.00  3.000
 A4J  H4   C1   H5   107.62  3.000
 A4J  H4   C1   H3   108.05  3.000
 A4J  H5   C1   H3   107.99  3.000
 A4J  H4   C1   C2   111.39  3.000
 A4J  H5   C1   C2   110.75  3.000
 A4J  H3   C1   C2   110.89  3.000
 A4J  O3   C2   C5   106.13  3.000
 A4J  C5   C2   C3   101.55  3.000
 A4J  O3   C2   C3   110.31  3.000
 A4J  C3   C2   C1   114.06  3.000
 A4J  C5   C2   C1   112.96  3.000
 A4J  O3   C2   C1   111.18  3.000
 A4J  H6   C3   H7   107.67  3.000
 A4J  H6   C3   C2   109.91  3.000
 A4J  H7   C3   C2   112.95  3.000
 A4J  H6   C3   C4   110.49  3.000
 A4J  H7   C3   C4   112.40  3.000
 A4J  C2   C3   C4   103.41  3.000
 A4J  C5   N1   C6   120.43  3.000
 A4J  C6   N1   C4   126.36  3.000
 A4J  C5   N1   C4   111.74  3.000
 A4J  H10  C5   H11  107.39  3.000
 A4J  H10  C5   N1   111.12  3.000
 A4J  H11  C5   N1   111.62  3.000
 A4J  H10  C5   C2   110.85  3.000
 A4J  H11  C5   C2   112.10  3.000
 A4J  N1   C5   C2   103.82  3.000
 A4J  C9   C10  N2   122.14  3.000
 A4J  C9   C10  N3   120.83  3.000
 A4J  N2   C10  N3   117.02  3.000
 A4J  H13  C11  H14  107.78  3.000
 A4J  H13  C11  C12  113.18  3.000
 A4J  H14  C11  C12  110.36  3.000
 A4J  H13  C11  N3   111.29  3.000
 A4J  H14  C11  N3   111.29  3.000
 A4J  C12  C11  N3   102.97  3.000
 A4J  H1   C12  O2   111.43  3.000
 A4J  H1   C12  C11  108.93  3.000
 A4J  O2   C12  C11  114.30  3.000
 A4J  H1   C12  C13  108.16  3.000
 A4J  C11  C12  C13  102.56  3.000
 A4J  O2   C12  C13  110.97  3.000
 A4J  H15  C14  H16  108.15  3.000
 A4J  H15  C14  C13  111.98  3.000
 A4J  H16  C14  C13  110.19  3.000
 A4J  H15  C14  N3   111.82  3.000
 A4J  H16  C14  N3   111.60  3.000
 A4J  C13  C14  N3   103.10  3.000
 A4J  H17  O1   C13  108.63  3.000
 A4J  H18  O2   C12  108.61  3.000
 A4J  F3   C15  F2   107.27  3.000
 A4J  F3   C15  F1   107.09  3.000
 A4J  F2   C15  F1   107.13  3.000
 A4J  F3   C15  C8   111.21  3.000
 A4J  F1   C15  C8   112.55  3.000
 A4J  F2   C15  C8   111.32  3.000
 A4J  H19  O3   C2   108.36  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
 A4J  CONST_01  C8   C7   C6   N2      0.00   0.0  0
 A4J  CONST_02  C8   C9   C10  N2      0.00   0.0  0
 A4J  CONST_03  C10  N2   C6   C7      0.00   0.0  0
 A4J  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 A4J  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 A4J  CONST_06  C9   C10  N2   C6      0.00   0.0  0
 A4J  CONST_07  C6   N2   C10  N3    180.00   0.0  0
 A4J  CONST_08  C8   C9   C10  N3    180.00   0.0  0
 A4J  CONST_09  N1   C6   C7   C8    180.00   0.0  0
 A4J  CONST_10  C10  N2   C6   N1    180.00   0.0  0
 A4J  CONST_11  C16  C7   C6   N2    180.00   0.0  0
 A4J  CONST_12  C15  C8   C7   C6    180.00   0.0  0
 A4J  CONST_13  C16  C7   C8   C9    180.00   0.0  0
 A4J  CONST_14  N1   C6   C7   C16     0.00   0.0  0
 A4J  CONST_15  C15  C8   C9   C10   180.00   0.0  0
 A4J  CONST_16  H12  C9   C10  N3      0.00   0.0  0
 A4J  Var_01    C2   C5   N1   C4    -14.93  30.0  1
 A4J  Var_02    C7   C6   N1   C4     19.61  30.0  2
 A4J  Var_03    C14  N3   C10  N2   -177.67  30.0  2
 A4J  Var_04    C3   C4   N1   C6    155.66  30.0  1
 A4J  Var_05    C10  N3   C14  C13   168.81  30.0  1
 A4J  Var_06    N1   C4   C3   C2     31.52  30.0  1
 A4J  Var_07    C12  C11  N3   C10   166.05  30.0  1
 A4J  Var_08    F2   C15  C8   C7    -55.13  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
 A4J  chir_01  C13  C14  C12  O1   negativ
 A4J  chir_02  C2   C1   C5   C3   negativ
 A4J  chir_03  C12  O2   C13  C11  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
 A4J  plan-1  N3   0.020
 A4J  plan-1  N2   0.020
 A4J  plan-1  C7   0.020
 A4J  plan-1  C6   0.020
 A4J  plan-1  C9   0.020
 A4J  plan-1  C8   0.020
 A4J  plan-1  C16  0.020
 A4J  plan-1  N1   0.020
 A4J  plan-1  C10  0.020
 A4J  plan-1  N4   0.020
 A4J  plan-1  H12  0.020
 A4J  plan-1  C15  0.020

