# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:29:49 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[C@@H](C1)N(Cc2ccccc2C(F)(F)F)c3ccc(C#N)c(Cl)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
 GKK  GKK  2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile  ligand  46  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GKK
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
 GKK  CL1  CL  CL    0  -0.100   4.7667  -0.8371  -0.1876
 GKK  C1   C   CH3   0  -0.512   3.4187   4.0859  -0.7693
 GKK  C2   C   CH2   0  -0.267   2.0452   3.4556   1.1448
 GKK  C3   C   CH2   0  -0.490   0.9950   2.3847   1.4023
 GKK  C4   C   CH1   0  -0.127   0.3512   2.1809   0.0131
 GKK  C5   C   CH2   0  -0.297   1.3413   2.8468  -0.9718
 GKK  C9   C   CR16  0  -0.225  -2.4956  -0.4506   2.8980
 GKK  C10  C   CR16  0  -0.253  -3.7563  -0.9828   2.6962
 GKK  C8   C   CR16  0  -0.294  -1.7651   0.0331   1.8219
 GKK  C7   C   CR6   0   0.098  -2.2676   0.0040   0.5274
 GKK  C6   C   CH2   0  -0.425  -1.4469   0.5858  -0.6143
 GKK  N1   N   NT    0  -0.417   2.5264   3.1198  -0.1821
 GKK  C12  C   CR6   0  -0.242  -3.5465  -0.5423   0.3342
 GKK  C13  C   CT    0   1.061  -4.1440  -0.6372  -1.0387
 GKK  C14  C   CR6   0   0.374   0.8174  -0.2348  -0.3529
 GKK  C15  C   CR16  0  -0.320   0.3535  -1.5598  -0.5183
 GKK  N2   N   NT    0  -0.518  -0.0526   0.8133  -0.3027
 GKK  C16  C   CR16  0  -0.251   1.2287  -2.6176  -0.5821
 GKK  C17  C   CR6   0   0.037   2.6087  -2.4282  -0.4778
 GKK  C18  C   CSP   0   0.036   3.4973  -3.5307  -0.5375
 GKK  N3   N   NS    0  -0.258   4.2019  -4.4431  -0.5884
 GKK  C19  C   CR6   0  -0.058   3.0673  -1.1192  -0.3111
 GKK  C20  C   CR16  0  -0.284   2.2126  -0.0447  -0.2504
 GKK  C11  C   CR16  0  -0.283  -4.2768  -1.0301   1.4121
 GKK  F1   F   F     0  -0.316  -4.1645   0.5477  -1.6681
 GKK  F2   F   F     0  -0.317  -3.4518  -1.4781  -1.8276
 GKK  F3   F   F     0  -0.296  -5.4018  -1.0820  -1.0251
 GKK  H1   H   HCH3  0   0.235   4.2950   4.2232  -0.1350
 GKK  H1A  H   HCH3  0   0.235   3.7655   3.7333  -1.7415
 GKK  H1B  H   HCH3  0   0.194   2.9474   5.0698  -0.9165
 GKK  H2   H   HCH2  0   0.200   1.5919   4.4607   1.1780
 GKK  H2A  H   HCH2  0   0.242   2.8591   3.4367   1.8717
 GKK  H3   H   HCH2  0   0.252   1.4676   1.4696   1.7621
 GKK  H3A  H   HCH2  0   0.260   0.2570   2.6863   2.1445
 GKK  H4   H   HCH1  0   0.284  -0.5707   2.7564  -0.0136
 GKK  H5   H   HCH2  0   0.253   1.5751   2.2199  -1.8358
 GKK  H5A  H   HCH2  0   0.232   0.8883   3.7734  -1.3573
 GKK  H10  H   HCR6  0   0.269  -4.3355  -1.3628   3.5268
 GKK  H8   H   HCR6  0   0.281  -0.7788   0.4349   2.0059
 GKK  H6   H   HCH2  0   0.273  -1.5092  -0.0406  -1.5050
 GKK  H6A  H   HCH2  0   0.304  -1.8793   1.5434  -0.9040
 GKK  H15  H   HCR6  0   0.272  -0.7001  -1.7839  -0.5852
 GKK  H16  H   HCR6  0   0.284   0.8396  -3.6188  -0.7079
 GKK  H20  H   HCR6  0   0.334   2.6377   0.9464  -0.1375
 GKK  H11  H   HCR6  0   0.274  -5.2590  -1.4555   1.2634
 GKK  H9   H   HCR6  0   0.268  -2.0726  -0.4080   3.8930

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
 GKK  CL1  C19  single    1.727  0.020  1.727
 GKK  N1   C1   single    1.440  0.020  1.440
 GKK  C1   H1   single    0.970  0.020  1.090
 GKK  C1   H1A  single    0.970  0.020  1.090
 GKK  C1   H1B  single    0.970  0.020  1.090
 GKK  C3   C2   single    1.522  0.020  1.522
 GKK  C2   N1   single    1.451  0.020  1.451
 GKK  C2   H2   single    0.970  0.020  1.090
 GKK  C2   H2A  single    0.970  0.020  1.090
 GKK  C3   C4   single    1.545  0.020  1.545
 GKK  C3   H3   single    0.970  0.020  1.090
 GKK  C3   H3A  single    0.970  0.020  1.090
 GKK  N2   C4   single    1.460  0.020  1.460
 GKK  C4   C5   single    1.547  0.020  1.547
 GKK  C4   H4   single    0.970  0.020  1.090
 GKK  C5   N1   single    1.450  0.020  1.450
 GKK  C5   H5   single    0.970  0.020  1.090
 GKK  C5   H5A  single    0.970  0.020  1.090
 GKK  C8   C9   aromatic  1.388  0.020  1.388
 GKK  C9   C10  aromatic  1.383  0.020  1.383
 GKK  C9   H9   single    0.930  0.020  1.080
 GKK  C10  C11  aromatic  1.386  0.020  1.386
 GKK  C10  H10  single    0.930  0.020  1.080
 GKK  C8   C7   aromatic  1.389  0.020  1.389
 GKK  C8   H8   single    0.930  0.020  1.080
 GKK  C6   C7   single    1.522  0.020  1.522
 GKK  C7   C12  aromatic  1.404  0.020  1.404
 GKK  N2   C6   single    1.447  0.020  1.447
 GKK  C6   H6   single    0.970  0.020  1.090
 GKK  C6   H6A  single    0.970  0.020  1.090
 GKK  C12  C13  single    1.500  0.020  1.500
 GKK  C12  C11  aromatic  1.390  0.020  1.390
 GKK  F1   C13  single    1.342  0.020  1.342
 GKK  C13  F3   single    1.334  0.020  1.334
 GKK  C13  F2   single    1.345  0.020  1.345
 GKK  C15  C14  aromatic  1.413  0.020  1.413
 GKK  C20  C14  aromatic  1.412  0.020  1.412
 GKK  C14  N2   single    1.363  0.020  1.363
 GKK  C16  C15  aromatic  1.374  0.020  1.374
 GKK  C15  H15  single    0.930  0.020  1.080
 GKK  C17  C16  aromatic  1.397  0.020  1.397
 GKK  C16  H16  single    0.930  0.020  1.080
 GKK  C18  C17  single    1.417  0.020  1.417
 GKK  C17  C19  aromatic  1.397  0.020  1.397
 GKK  N3   C18  triple    1.154  0.020  1.154
 GKK  C19  C20  aromatic  1.374  0.020  1.374
 GKK  C20  H20  single    0.930  0.020  1.080
 GKK  C11  H11  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
 GKK  H1B  C1   H1A  107.81  3.000
 GKK  H1B  C1   H1   108.02  3.000
 GKK  H1A  C1   H1   107.68  3.000
 GKK  H1B  C1   N1   112.88  3.000
 GKK  H1A  C1   N1   110.09  3.000
 GKK  H1   C1   N1   110.19  3.000
 GKK  H2A  C2   H2   107.59  3.000
 GKK  H2A  C2   N1   110.96  3.000
 GKK  H2   C2   N1   112.00  3.000
 GKK  H2A  C2   C3   112.94  3.000
 GKK  H2   C2   C3   110.64  3.000
 GKK  N1   C2   C3   102.75  3.000
 GKK  H3A  C3   H3   107.53  3.000
 GKK  H3A  C3   C4   111.53  3.000
 GKK  H3   C3   C4   111.50  3.000
 GKK  H3A  C3   C2   112.83  3.000
 GKK  H3   C3   C2   110.30  3.000
 GKK  C4   C3   C2   103.20  3.000
 GKK  H4   C4   N2   104.83  3.000
 GKK  H4   C4   C5   107.41  3.000
 GKK  N2   C4   C5   116.25  3.000
 GKK  H4   C4   C3   107.80  3.000
 GKK  C5   C4   C3   104.42  3.000
 GKK  N2   C4   C3   115.68  3.000
 GKK  H5A  C5   H5   107.10  3.000
 GKK  H5A  C5   N1   111.62  3.000
 GKK  H5   C5   N1   111.33  3.000
 GKK  H5A  C5   C4   108.77  3.000
 GKK  H5   C5   C4   113.15  3.000
 GKK  N1   C5   C4   104.91  3.000
 GKK  H9   C9   C8   119.58  3.000
 GKK  H9   C9   C10  120.37  3.000
 GKK  C8   C9   C10  120.05  3.000
 GKK  H10  C10  C11  119.89  3.000
 GKK  H10  C10  C9   120.74  3.000
 GKK  C11  C10  C9   119.36  3.000
 GKK  H8   C8   C7   119.78  3.000
 GKK  H8   C8   C9   118.56  3.000
 GKK  C7   C8   C9   121.67  3.000
 GKK  C12  C7   C6   122.47  3.000
 GKK  C12  C7   C8   117.77  3.000
 GKK  C6   C7   C8   119.74  3.000
 GKK  H6A  C6   H6   105.36  3.000
 GKK  H6A  C6   N2   107.54  3.000
 GKK  H6   C6   N2   108.74  3.000
 GKK  H6A  C6   C7   108.75  3.000
 GKK  H6   C6   C7   111.24  3.000
 GKK  N2   C6   C7   114.73  3.000
 GKK  C5   N1   C2   105.70  3.000
 GKK  C5   N1   C1   114.24  3.000
 GKK  C2   N1   C1   115.03  3.000
 GKK  C11  C12  C13  118.56  3.000
 GKK  C11  C12  C7   120.55  3.000
 GKK  C13  C12  C7   120.88  3.000
 GKK  F3   C13  F2   106.42  3.000
 GKK  F2   C13  F1   106.55  3.000
 GKK  F3   C13  F1   106.54  3.000
 GKK  F2   C13  C12  111.80  3.000
 GKK  F3   C13  C12  112.78  3.000
 GKK  F1   C13  C12  112.30  3.000
 GKK  C20  C14  N2   121.64  3.000
 GKK  N2   C14  C15  121.04  3.000
 GKK  C20  C14  C15  117.33  3.000
 GKK  H15  C15  C16  117.32  3.000
 GKK  H15  C15  C14  121.49  3.000
 GKK  C16  C15  C14  121.19  3.000
 GKK  C14  N2   C6   119.09  3.000
 GKK  C14  N2   C4   123.47  3.000
 GKK  C6   N2   C4   117.41  3.000
 GKK  H16  C16  C17  119.31  3.000
 GKK  H16  C16  C15  119.27  3.000
 GKK  C17  C16  C15  121.42  3.000
 GKK  C19  C17  C18  121.88  3.000
 GKK  C19  C17  C16  117.41  3.000
 GKK  C18  C17  C16  120.72  3.000
 GKK  N3   C18  C17  180.00  3.000
 GKK  C20  C19  C17  122.26  3.000
 GKK  C20  C19  CL1  118.75  3.000
 GKK  C17  C19  CL1  118.99  3.000
 GKK  H20  C20  C19  118.39  3.000
 GKK  H20  C20  C14  121.20  3.000
 GKK  C19  C20  C14  120.40  3.000
 GKK  H11  C11  C12  120.59  3.000
 GKK  H11  C11  C10  118.82  3.000
 GKK  C12  C11  C10  120.59  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
 GKK  CONST_01  C12  C7   C8   C9      0.00   0.0  0
 GKK  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 GKK  CONST_03  C7   C8   C9   C10     0.00   0.0  0
 GKK  CONST_04  C7   C12  C11  C10     0.00   0.0  0
 GKK  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 GKK  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 GKK  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 GKK  CONST_08  C17  C19  C20  C14     0.00   0.0  0
 GKK  CONST_09  C19  C20  C14  C15     0.00   0.0  0
 GKK  CONST_10  C19  C17  C16  C15     0.00   0.0  0
 GKK  CONST_11  C20  C14  C15  C16     0.00   0.0  0
 GKK  CONST_12  C20  C19  C17  C16     0.00   0.0  0
 GKK  CONST_13  C16  C17  C19  CL1   180.00   0.0  0
 GKK  CONST_14  C14  C20  C19  CL1   180.00   0.0  0
 GKK  CONST_15  C6   C7   C8   C9    180.00   0.0  0
 GKK  CONST_16  C13  C12  C11  C10   180.00   0.0  0
 GKK  CONST_17  C13  C12  C7   C8    180.00   0.0  0
 GKK  CONST_18  C11  C12  C7   C6    180.00   0.0  0
 GKK  CONST_19  C18  C17  C16  C15   180.00   0.0  0
 GKK  CONST_20  C16  C15  C14  N2    180.00   0.0  0
 GKK  CONST_21  C19  C20  C14  N2    180.00   0.0  0
 GKK  CONST_22  C20  C19  C17  C18   180.00   0.0  0
 GKK  CONST_23  C15  C14  N2   C4    180.00   0.0  0
 GKK  CONST_24  C20  C14  N2   C4      0.00   0.0  0
 GKK  CONST_25  H11  C11  C10  C9    180.00   0.0  0
 GKK  CONST_26  H8   C8   C9   C10   180.00   0.0  0
 GKK  CONST_27  H10  C10  C9   C8    180.00   0.0  0
 GKK  CONST_28  H9   C9   C8   C7    180.00   0.0  0
 GKK  CONST_29  H16  C16  C15  C14   180.00   0.0  0
 GKK  CONST_30  H20  C20  C14  C15   180.00   0.0  0
 GKK  CONST_31  H15  C15  C16  C17   180.00   0.0  0
 GKK  CONST_32  C15  C14  N2   C6      0.00   0.0  0
 GKK  CONST_33  C20  C14  N2   C6    180.00   0.0  0
 GKK  Var_01    C4   C5   N1   C2    -34.74  30.0  1
 GKK  Var_02    C5   N1   C2   C3     44.99  30.0  1
 GKK  Var_03    N1   C2   C3   C4    -36.30  30.0  1
 GKK  Var_04    C7   C6   N2   C4   -100.89  30.0  3
 GKK  Var_05    N2   C6   C7   C8     15.40  30.0  1
 GKK  Var_06    F1   C13  C12  C7    -54.60  30.0  2
 GKK  Var_07    H1   C1   N1   C2     58.79  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
 GKK  chir_01  C4  C3  N2  C5  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
 GKK  plan-1  C9   0.020
 GKK  plan-1  C10  0.020
 GKK  plan-1  C8   0.020
 GKK  plan-1  C7   0.020
 GKK  plan-1  C6   0.020
 GKK  plan-1  C12  0.020
 GKK  plan-1  C13  0.020
 GKK  plan-1  C11  0.020
 GKK  plan-1  H10  0.020
 GKK  plan-1  H8   0.020
 GKK  plan-1  H11  0.020
 GKK  plan-1  H9   0.020
 GKK  plan-2  CL1  0.020
 GKK  plan-2  C14  0.020
 GKK  plan-2  C15  0.020
 GKK  plan-2  N2   0.020
 GKK  plan-2  C16  0.020
 GKK  plan-2  C17  0.020
 GKK  plan-2  C18  0.020
 GKK  plan-2  N3   0.020
 GKK  plan-2  C19  0.020
 GKK  plan-2  C20  0.020
 GKK  plan-2  H15  0.020
 GKK  plan-2  H16  0.020
 GKK  plan-2  H20  0.020
 GKK  plan-3  C4   0.020
 GKK  plan-3  C6   0.020
 GKK  plan-3  C14  0.020
 GKK  plan-3  N2   0.020

