# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:02:41 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-[(2S,3S)-2-ethyl-3-hydroxy-5-oxopyrrolidin-1-yl]-2-(trifluoromethyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]1[C@@H](O)CC(=O)N1c2ccc(C#N)c(c2)C(F)(F)F
#
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
 97A  97A  4-[(2S,3S)-2-ethyl-3-hydroxy-5-oxopyrrolidin-1-yl]-2-(trifluoromethyl)benzonitrile  ligand  34  21  .  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_97A
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
 97A  C5   C  CH1   0   0.009  -4.0293   0.3742   0.2670
 97A  C8   C  CH2   0  -0.614  -3.9399  -0.8189   1.2074
 97A  C13  C  CR16  0  -0.273  -0.1040  -1.8611  -0.7731
 97A  C15  C  CR6   0   0.033   2.1654  -1.0579  -0.7042
 97A  C20  C  CT    0   1.078   2.7348   1.1455   0.3531
 97A  C1   C  CH3   0  -0.677  -3.0267   2.8512  -1.2458
 97A  C2   C  CH2   0  -0.442  -2.2360   1.5528  -1.1583
 97A  C3   C  CH1   0  -0.064  -2.5576   0.7788   0.1109
 97A  O7   O  OH1   0  -0.668  -4.5225  -0.0068  -0.9900
 97A  C9   C  C     0   0.537  -2.6416  -1.4778   0.8204
 97A  O10  O  O     0  -0.457  -2.2929  -2.6143   1.0560
 97A  N11  N  NT    0  -0.606  -1.8817  -0.5259   0.1911
 97A  C12  C  CR6   0   0.405  -0.5346  -0.7140  -0.1133
 97A  C14  C  CR16  0  -0.256   1.2373  -2.0312  -1.0612
 97A  C16  C  CSP   0   0.019   3.5361  -1.2716  -1.0356
 97A  N17  N  NS    0  -0.236   4.6342  -1.4741  -1.3179
 97A  C18  C  CR6   0  -0.165   1.7346   0.0987  -0.0435
 97A  C19  C  CR16  0  -0.379   0.3974   0.2601   0.2537
 97A  F21  F  F     0  -0.311   3.3880   1.6209  -0.7138
 97A  F22  F  F     0  -0.291   2.1693   2.1831   0.9666
 97A  F23  F  F     0  -0.310   3.6569   0.6442   1.1831
 97A  H1   H  HCH1  0   0.245  -4.6040   1.1985   0.7004
 97A  H2   H  HCH2  0   0.286  -3.8514  -0.4889   2.2475
 97A  H3   H  HCH2  0   0.288  -4.7858  -1.5036   1.1473
 97A  H4   H  HCR6  0   0.290  -0.8104  -2.6145  -1.0870
 97A  H5   H  HCH3  0   0.234  -4.0953   2.6685  -1.3564
 97A  H6   H  HCH3  0   0.223  -2.8810   3.4681  -0.3576
 97A  H7   H  HCH3  0   0.238  -2.7021   3.4356  -2.1063
 97A  H8   H  HCH2  0   0.240  -2.4270   0.9279  -2.0316
 97A  H9   H  HCH2  0   0.242  -1.1707   1.7924  -1.1773
 97A  H10  H  HCH1  0   0.268  -2.2858   1.3885   0.9818
 97A  H11  H  HOH1  0   0.474  -5.4459  -0.2600  -0.8904
 97A  H12  H  HCR6  0   0.313   1.5665  -2.9199  -1.5813
 97A  H13  H  HCR6  0   0.325   0.0625   1.1377   0.7888

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
 97A  C5   C8   single    1.522  0.020  1.522
 97A  C5   O7   single    1.403  0.020  1.403
 97A  C5   C3   single    1.534  0.020  1.534
 97A  O10  C9   double    1.212  0.020  1.212
 97A  C8   C9   single    1.506  0.020  1.506
 97A  C9   N11  single    1.371  0.020  1.371
 97A  C13  C14  aromatic  1.382  0.020  1.382
 97A  C13  C12  aromatic  1.392  0.020  1.392
 97A  C14  C15  aromatic  1.391  0.020  1.391
 97A  N11  C3   single    1.472  0.020  1.472
 97A  N11  C12  single    1.394  0.020  1.394
 97A  C3   C2   single    1.521  0.020  1.521
 97A  C12  C19  aromatic  1.397  0.020  1.397
 97A  F21  C20  single    1.338  0.020  1.338
 97A  C15  C16  single    1.426  0.020  1.426
 97A  C15  C18  aromatic  1.400  0.020  1.400
 97A  F23  C20  single    1.338  0.020  1.338
 97A  C16  N17  triple    1.152  0.020  1.152
 97A  C19  C18  aromatic  1.379  0.020  1.379
 97A  C18  C20  single    1.501  0.020  1.501
 97A  C20  F22  single    1.331  0.020  1.331
 97A  C2   C1   single    1.523  0.020  1.523
 97A  C5   H1   single    0.970  0.020  1.090
 97A  C8   H2   single    0.970  0.020  1.090
 97A  C8   H3   single    0.970  0.020  1.090
 97A  C13  H4   single    0.930  0.020  1.080
 97A  C1   H5   single    0.970  0.020  1.090
 97A  C1   H6   single    0.970  0.020  1.090
 97A  C1   H7   single    0.970  0.020  1.090
 97A  C2   H8   single    0.970  0.020  1.090
 97A  C2   H9   single    0.970  0.020  1.090
 97A  C3   H10  single    0.970  0.020  1.090
 97A  O7   H11  single    0.850  0.020  0.980
 97A  C14  H12  single    0.930  0.020  1.080
 97A  C19  H13  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
 97A  H1   C5   O7   112.01  3.000
 97A  H1   C5   C3   110.20  3.000
 97A  O7   C5   C3   108.52  3.000
 97A  H1   C5   C8   112.13  3.000
 97A  C3   C5   C8   102.32  3.000
 97A  O7   C5   C8   111.19  3.000
 97A  H3   C8   H2   107.73  3.000
 97A  H3   C8   C9   112.33  3.000
 97A  H2   C8   C9   107.83  3.000
 97A  H3   C8   C5   114.38  3.000
 97A  H2   C8   C5   110.82  3.000
 97A  C9   C8   C5   103.58  3.000
 97A  H4   C13  C14  119.24  3.000
 97A  H4   C13  C12  120.71  3.000
 97A  C14  C13  C12  120.03  3.000
 97A  C18  C15  C16  121.95  3.000
 97A  C18  C15  C14  119.58  3.000
 97A  C16  C15  C14  118.46  3.000
 97A  F23  C20  F22  107.39  3.000
 97A  F22  C20  F21  107.32  3.000
 97A  F23  C20  F21  106.93  3.000
 97A  F22  C20  C18  112.47  3.000
 97A  F23  C20  C18  111.21  3.000
 97A  F21  C20  C18  111.24  3.000
 97A  H7   C1   H6   107.44  3.000
 97A  H7   C1   H5   107.58  3.000
 97A  H6   C1   H5   107.96  3.000
 97A  H7   C1   C2   110.36  3.000
 97A  H6   C1   C2   111.47  3.000
 97A  H5   C1   C2   111.85  3.000
 97A  H9   C2   H8   106.42  3.000
 97A  H9   C2   C3   109.42  3.000
 97A  H8   C2   C3   109.85  3.000
 97A  H9   C2   C1   108.57  3.000
 97A  H8   C2   C1   110.58  3.000
 97A  C3   C2   C1   111.84  3.000
 97A  H10  C3   N11  109.61  3.000
 97A  H10  C3   C2   109.09  3.000
 97A  N11  C3   C2   113.55  3.000
 97A  H10  C3   C5   107.66  3.000
 97A  C2   C3   C5   114.96  3.000
 97A  N11  C3   C5   101.61  3.000
 97A  H11  O7   C5   108.42  3.000
 97A  N11  C9   O10  125.51  3.000
 97A  N11  C9   C8   106.97  3.000
 97A  O10  C9   C8   127.46  3.000
 97A  C12  N11  C9   122.83  3.000
 97A  C12  N11  C3   123.48  3.000
 97A  C9   N11  C3   112.71  3.000
 97A  C19  C12  N11  119.55  3.000
 97A  C19  C12  C13  119.52  3.000
 97A  N11  C12  C13  120.92  3.000
 97A  H12  C14  C15  119.70  3.000
 97A  H12  C14  C13  119.79  3.000
 97A  C15  C14  C13  120.50  3.000
 97A  N17  C16  C15  180.00  3.000
 97A  C19  C18  C20  120.49  3.000
 97A  C20  C18  C15  119.72  3.000
 97A  C19  C18  C15  119.79  3.000
 97A  H13  C19  C18  120.13  3.000
 97A  H13  C19  C12  119.30  3.000
 97A  C18  C19  C12  120.56  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
 97A  CONST_01  C18  C15  C14  C13    0.00   0.0  0
 97A  CONST_02  C18  C19  C12  C13    0.00   0.0  0
 97A  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 97A  CONST_04  C12  C19  C18  C15    0.00   0.0  0
 97A  CONST_05  C19  C12  C13  C14    0.00   0.0  0
 97A  CONST_06  C19  C18  C15  C14    0.00   0.0  0
 97A  CONST_07  C14  C13  C12  N11  180.00   0.0  0
 97A  CONST_08  C18  C19  C12  N11  180.00   0.0  0
 97A  CONST_09  C3   N11  C9   C8     0.00   0.0  0
 97A  CONST_10  C12  N11  C9   C8   180.00   0.0  0
 97A  CONST_11  C16  C15  C14  C13  180.00   0.0  0
 97A  CONST_12  C14  C15  C18  C20  180.00   0.0  0
 97A  CONST_13  C12  C19  C18  C20  180.00   0.0  0
 97A  CONST_14  C19  C18  C15  C16  180.00   0.0  0
 97A  CONST_15  O10  C9   N11  C3   180.00   0.0  0
 97A  CONST_16  C12  N11  C9   O10    0.00   0.0  0
 97A  CONST_17  H13  C19  C12  C13  180.00   0.0  0
 97A  CONST_18  H4   C13  C14  C15  180.00   0.0  0
 97A  CONST_19  H12  C14  C13  C12  180.00   0.0  0
 97A  Var_01    N11  C9   C8   C5    21.67  30.0  1
 97A  Var_02    C9   N11  C12  C13   50.16  30.0  2
 97A  Var_03    F21  C20  C18  C15   59.36  30.0  2
 97A  Var_04    H5   C1   C2   C3   -66.29  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
 97A  chir_01  C5  C8   O7  C3  positiv
 97A  chir_02  C3  N11  C5  C2  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
 97A  plan-1  C13  0.020
 97A  plan-1  C15  0.020
 97A  plan-1  C20  0.020
 97A  plan-1  N11  0.020
 97A  plan-1  C12  0.020
 97A  plan-1  C14  0.020
 97A  plan-1  C16  0.020
 97A  plan-1  N17  0.020
 97A  plan-1  C18  0.020
 97A  plan-1  C19  0.020
 97A  plan-1  H4   0.020
 97A  plan-1  H12  0.020
 97A  plan-1  H13  0.020
 97A  plan-2  C8   0.020
 97A  plan-2  C3   0.020
 97A  plan-2  C9   0.020
 97A  plan-2  O10  0.020
 97A  plan-2  N11  0.020
 97A  plan-2  C12  0.020

