# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 01:33:06 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-fluoro-4-[(2S,3S)-3-hydroxy-2,3-dimethylpyrrolidin-1-yl]-3-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N(CC[C@]1(C)O)c2ccc(C#N)c(F)c2C
#
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
 77T  77T  2-fluoro-4-[(2S,3S)-3-hydroxy-2,3-dimethylpyrrolidin-1-yl]-3-methylbenzonitrile  ligand  35  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_77T
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
 77T  C5   C  CH2   0  -0.299  -1.7267   0.7623   1.6575
 77T  C6   C  CH2   0  -0.480  -3.2015   0.4087   1.5231
 77T  C7   C  CT    0   0.246  -3.4177   0.1687   0.0082
 77T  C8   C  CH3   0  -0.699  -4.3251   1.2177  -0.6204
 77T  C10  C  CR6   0   0.300   0.2546   0.1351   0.3662
 77T  C13  C  CR6   0  -0.191   2.9937   0.4051  -0.0922
 77T  C1   C  CH3   0  -0.673  -1.7263  -0.6190  -1.7870
 77T  C2   C  CH1   0  -0.066  -1.9910   0.2590  -0.5821
 77T  N4   N  NT    0  -0.521  -1.1306  -0.0066   0.5767
 77T  O9   O  OH1   0  -0.675  -3.9190  -1.1286  -0.2458
 77T  C11  C  CR16  0  -0.287   0.8704   1.3909   0.4074
 77T  C12  C  CR16  0  -0.242   2.2229   1.5339   0.1851
 77T  C14  C  CSP   0   0.067   4.3910   0.5026  -0.3361
 77T  N15  N  NS    0  -0.246   5.5227   0.5941  -0.5322
 77T  C16  C  CR6   0   0.569   2.3696  -0.8343  -0.1222
 77T  F17  F  F     0  -0.287   3.1309  -1.9031  -0.3740
 77T  C18  C  CR6   0  -0.133   1.0178  -1.0158   0.1087
 77T  C19  C  CH3   0  -0.722   0.4346  -2.3954   0.1067
 77T  H1   H  HCH2  0   0.209  -1.5915   1.8474   1.5355
 77T  H2   H  HCH2  0   0.251  -1.2992   0.4795   2.6200
 77T  H3   H  HCH2  0   0.246  -3.4164  -0.5112   2.0689
 77T  H4   H  HCH2  0   0.242  -3.8458   1.1922   1.9239
 77T  H5   H  HCH3  0   0.227  -3.9831   2.2259  -0.3835
 77T  H6   H  HCH3  0   0.233  -4.3505   1.1193  -1.7082
 77T  H7   H  HCH3  0   0.235  -5.3489   1.1238  -0.2506
 77T  H8   H  HCH3  0   0.240  -2.4227  -0.3651  -2.5873
 77T  H9   H  HCH3  0   0.231  -0.7212  -0.4523  -2.1756
 77T  H10  H  HCH3  0   0.234  -1.8372  -1.6773  -1.5635
 77T  H11  H  HCH1  0   0.218  -1.8397   1.3066  -0.8984
 77T  H12  H  HOH1  0   0.444  -4.8017  -1.1862   0.1348
 77T  H13  H  HCR6  0   0.270   0.2804   2.2747   0.6080
 77T  H14  H  HCR6  0   0.289   2.6871   2.5100   0.2119
 77T  H15  H  HCH3  0   0.254   0.3703  -2.7994  -0.9049
 77T  H16  H  HCH3  0   0.256   1.0394  -3.0841   0.6963
 77T  H17  H  HCH3  0   0.260  -0.5693  -2.3701   0.5208

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
 77T  C1   C2   single    1.514  0.020  1.514
 77T  O9   C7   single    1.414  0.020  1.414
 77T  C12  C11  aromatic  1.378  0.020  1.378
 77T  C12  C13  aromatic  1.395  0.020  1.395
 77T  C11  C10  aromatic  1.399  0.020  1.399
 77T  N15  C14  triple    1.152  0.020  1.152
 77T  C14  C13  single    1.422  0.020  1.422
 77T  C13  C16  aromatic  1.388  0.020  1.388
 77T  C10  N4   single    1.408  0.020  1.408
 77T  C10  C18  aromatic  1.405  0.020  1.405
 77T  N4   C2   single    1.468  0.020  1.468
 77T  N4   C5   single    1.454  0.020  1.454
 77T  C16  C18  aromatic  1.383  0.020  1.383
 77T  C16  F17  single    1.336  0.020  1.336
 77T  C2   C7   single    1.547  0.020  1.547
 77T  C18  C19  single    1.498  0.020  1.498
 77T  C7   C8   single    1.523  0.020  1.523
 77T  C7   C6   single    1.549  0.020  1.549
 77T  C5   C6   single    1.523  0.020  1.523
 77T  C5   H1   single    0.970  0.020  1.090
 77T  C5   H2   single    0.970  0.020  1.090
 77T  C6   H3   single    0.970  0.020  1.090
 77T  C6   H4   single    0.970  0.020  1.090
 77T  C8   H5   single    0.970  0.020  1.090
 77T  C8   H6   single    0.970  0.020  1.090
 77T  C8   H7   single    0.970  0.020  1.090
 77T  C1   H8   single    0.970  0.020  1.090
 77T  C1   H9   single    0.970  0.020  1.090
 77T  C1   H10  single    0.970  0.020  1.090
 77T  C2   H11  single    0.970  0.020  1.090
 77T  O9   H12  single    0.850  0.020  0.980
 77T  C11  H13  single    0.930  0.020  1.080
 77T  C12  H14  single    0.930  0.020  1.080
 77T  C19  H15  single    0.970  0.020  1.090
 77T  C19  H16  single    0.970  0.020  1.090
 77T  C19  H17  single    0.970  0.020  1.090

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
 77T  H2   C5   H1   107.79  3.000
 77T  H2   C5   N4   110.99  3.000
 77T  H1   C5   N4   112.87  3.000
 77T  H2   C5   C6   113.42  3.000
 77T  H1   C5   C6   109.77  3.000
 77T  N4   C5   C6   102.05  3.000
 77T  H4   C6   H3   107.79  3.000
 77T  H4   C6   C7   112.85  3.000
 77T  H3   C6   C7   109.34  3.000
 77T  H4   C6   C5   111.90  3.000
 77T  H3   C6   C5   110.02  3.000
 77T  C7   C6   C5   104.92  3.000
 77T  O9   C7   C2   108.18  3.000
 77T  C2   C7   C8   110.60  3.000
 77T  O9   C7   C8   110.28  3.000
 77T  C8   C7   C6   112.35  3.000
 77T  C2   C7   C6   103.62  3.000
 77T  O9   C7   C6   111.55  3.000
 77T  H7   C8   H6   107.91  3.000
 77T  H7   C8   H5   107.44  3.000
 77T  H6   C8   H5   107.87  3.000
 77T  H7   C8   C7   111.07  3.000
 77T  H6   C8   C7   111.27  3.000
 77T  H5   C8   C7   111.12  3.000
 77T  C18  C10  C11  120.10  3.000
 77T  C18  C10  N4   118.65  3.000
 77T  C11  C10  N4   121.25  3.000
 77T  C16  C13  C14  119.97  3.000
 77T  C16  C13  C12  118.59  3.000
 77T  C14  C13  C12  121.45  3.000
 77T  H10  C1   H9   108.43  3.000
 77T  H10  C1   H8   108.19  3.000
 77T  H9   C1   H8   106.94  3.000
 77T  H10  C1   C2   112.52  3.000
 77T  H9   C1   C2   110.86  3.000
 77T  H8   C1   C2   109.71  3.000
 77T  H11  C2   N4   108.51  3.000
 77T  H11  C2   C1   107.34  3.000
 77T  N4   C2   C1   114.89  3.000
 77T  H11  C2   C7   106.92  3.000
 77T  N4   C2   C7   103.24  3.000
 77T  C1   C2   C7   115.54  3.000
 77T  C2   N4   C10  116.13  3.000
 77T  C2   N4   C5   104.52  3.000
 77T  C10  N4   C5   117.46  3.000
 77T  H12  O9   C7   107.99  3.000
 77T  H13  C11  C12  118.72  3.000
 77T  H13  C11  C10  119.93  3.000
 77T  C12  C11  C10  121.35  3.000
 77T  H14  C12  C11  120.73  3.000
 77T  H14  C12  C13  119.89  3.000
 77T  C11  C12  C13  119.37  3.000
 77T  N15  C14  C13  180.00  3.000
 77T  C18  C16  F17  118.90  3.000
 77T  F17  C16  C13  117.52  3.000
 77T  C18  C16  C13  123.57  3.000
 77T  C19  C18  C16  120.07  3.000
 77T  C19  C18  C10  122.91  3.000
 77T  C16  C18  C10  117.01  3.000
 77T  H17  C19  H16  108.74  3.000
 77T  H17  C19  H15  107.91  3.000
 77T  H16  C19  H15  107.47  3.000
 77T  H17  C19  C18  109.75  3.000
 77T  H16  C19  C18  111.43  3.000
 77T  H15  C19  C18  111.42  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
 77T  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 77T  CONST_02  C13  C16  C18  C10    0.00   0.0  0
 77T  CONST_03  C16  C13  C12  C11    0.00   0.0  0
 77T  CONST_04  C16  C18  C10  C11    0.00   0.0  0
 77T  CONST_05  C18  C10  C11  C12    0.00   0.0  0
 77T  CONST_06  C18  C16  C13  C12    0.00   0.0  0
 77T  CONST_07  C12  C11  C10  N4   180.00   0.0  0
 77T  CONST_08  C16  C18  C10  N4   180.00   0.0  0
 77T  CONST_09  F17  C16  C18  C10  180.00   0.0  0
 77T  CONST_10  C19  C18  C16  C13  180.00   0.0  0
 77T  CONST_11  C19  C18  C10  N4     0.00   0.0  0
 77T  CONST_12  C14  C13  C12  C11  180.00   0.0  0
 77T  CONST_13  C19  C18  C10  C11  180.00   0.0  0
 77T  CONST_14  F17  C16  C13  C12  180.00   0.0  0
 77T  CONST_15  C18  C16  C13  C14  180.00   0.0  0
 77T  CONST_16  H14  C12  C11  C10  180.00   0.0  0
 77T  CONST_17  H13  C11  C12  C13  180.00   0.0  0
 77T  Var_01    C11  C10  N4   C5   -42.95  30.0  2
 77T  Var_02    C10  N4   C5   C6   177.16  30.0  1
 77T  Var_03    N4   C5   C6   C7   -31.55  30.0  1
 77T  Var_04    H15  C19  C18  C10  108.10  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
 77T  chir_01  C7  C2  C8  C6  positiv
 77T  chir_02  C2  N4  C7  C1  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
 77T  plan-1  C10  0.020
 77T  plan-1  C13  0.020
 77T  plan-1  N4   0.020
 77T  plan-1  C11  0.020
 77T  plan-1  C12  0.020
 77T  plan-1  C14  0.020
 77T  plan-1  N15  0.020
 77T  plan-1  C16  0.020
 77T  plan-1  F17  0.020
 77T  plan-1  C18  0.020
 77T  plan-1  C19  0.020
 77T  plan-1  H13  0.020
 77T  plan-1  H14  0.020

