# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 14:27:00 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(morpholin-4-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(cc(n1)c2ccc(cc2)C(F)(F)F)N3CCOCC3
#
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
 KK2  KK2  4-(morpholin-4-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine  ligand  38  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KK2
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
 KK2  C1   C  CH2   0  -0.320   5.0527  -0.0401   0.3900
 KK2  C2   C  CH2   0  -0.191   6.0926   0.7897  -0.3363
 KK2  O1   O  O2    0  -0.481   5.9892   2.1573  -0.0095
 KK2  C3   C  CH2   0  -0.182   4.7167   2.6482  -0.3566
 KK2  C4   C  CH2   0  -0.322   3.6007   1.9055   0.3591
 KK2  N2   N  NT    0  -0.513   3.7205   0.4784   0.1242
 KK2  C6   C  CR6   0   0.605   2.6491  -0.3492   0.0669
 KK2  C5   C  CR16  0  -0.503   1.3192   0.1271   0.0782
 KK2  N1   N  N     0  -0.524   2.8941  -1.6550  -0.0128
 KK2  C7   C  CR6   0   0.531   1.8511  -2.4751  -0.1082
 KK2  N4   N  NH2   0  -0.825   2.1234  -3.7926  -0.2475
 KK2  N3   N  N     0  -0.522   0.5673  -2.1228  -0.1073
 KK2  C8   C  CR6   0   0.307   0.3159  -0.8170  -0.0063
 KK2  C9   C  CR6   0   0.061  -1.1190  -0.4348   0.0090
 KK2  C10  C  CR16  0  -0.264  -2.0919  -1.3963  -0.2615
 KK2  C11  C  CR16  0  -0.258  -3.4379  -1.0717  -0.2599
 KK2  C12  C  CR6   0  -0.210  -3.8377   0.2290   0.0177
 KK2  C13  C  CT    0   1.053  -5.2898   0.5836   0.0724
 KK2  F1   F  F     0  -0.305  -6.0435  -0.2339  -0.6699
 KK2  F2   F  F     0  -0.314  -5.7658   0.5175   1.3259
 KK2  F3   F  F     0  -0.308  -5.5217   1.8300  -0.3576
 KK2  C14  C  CR16  0  -0.250  -2.8806   1.1973   0.2984
 KK2  C15  C  CR16  0  -0.322  -1.5373   0.8658   0.2917
 KK2  H1   H  HCH2  0   0.274   5.1176  -1.0732   0.0607
 KK2  H2   H  HCH2  0   0.235   5.2478  -0.0230   1.4699
 KK2  H3   H  HCH2  0   0.245   7.0901   0.4562  -0.0486
 KK2  H4   H  HCH2  0   0.208   5.9841   0.6442  -1.4202
 KK2  H5   H  HCH2  0   0.247   4.6811   3.7035  -0.0830
 KK2  H6   H  HCH2  0   0.209   4.5588   2.5741  -1.4416
 KK2  H7   H  HCH2  0   0.241   3.6300   2.1189   1.4345
 KK2  H8   H  HCH2  0   0.267   2.6588   2.2859  -0.0284
 KK2  H9   H  HCR6  0   0.270   1.0946   1.1762   0.1630
 KK2  H10  H  HNH2  0   0.390   3.0521  -4.1103  -0.0296
 KK2  H11  H  HNH2  0   0.390   1.3774  -4.4466  -0.0847
 KK2  H12  H  HCR6  0   0.265  -1.7896  -2.4101  -0.4806
 KK2  H13  H  HCR6  0   0.273  -4.1631  -1.8442  -0.4774
 KK2  H14  H  HCR6  0   0.277  -3.1664   2.2157   0.5252
 KK2  H15  H  HCR6  0   0.265  -0.8218   1.6437   0.5182

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
 KK2  C15  C14  aromatic  1.384  0.020  1.384
 KK2  C15  C9   aromatic  1.395  0.020  1.395
 KK2  C14  C12  aromatic  1.390  0.020  1.390
 KK2  C1   N2   single    1.454  0.020  1.454
 KK2  C1   C2   single    1.516  0.020  1.516
 KK2  F3   C13  single    1.339  0.020  1.339
 KK2  N2   C6   single    1.355  0.020  1.355
 KK2  N2   C4   single    1.451  0.020  1.451
 KK2  N1   C6   aromatic  1.331  0.020  1.331
 KK2  N1   C7   aromatic  1.330  0.020  1.330
 KK2  C6   C5   aromatic  1.413  0.020  1.413
 KK2  N4   C7   single    1.353  0.020  1.353
 KK2  C7   N3   aromatic  1.331  0.020  1.331
 KK2  C4   C3   single    1.520  0.020  1.520
 KK2  C5   C8   aromatic  1.380  0.020  1.380
 KK2  N3   C8   aromatic  1.334  0.020  1.334
 KK2  C8   C9   single    1.485  0.020  1.485
 KK2  C9   C10  aromatic  1.394  0.020  1.394
 KK2  C12  C13  single    1.496  0.020  1.496
 KK2  C12  C11  aromatic  1.389  0.020  1.389
 KK2  C13  F2   single    1.343  0.020  1.343
 KK2  C13  F1   single    1.337  0.020  1.337
 KK2  C2   O1   single    1.410  0.020  1.410
 KK2  O1   C3   single    1.407  0.020  1.407
 KK2  C10  C11  aromatic  1.385  0.020  1.385
 KK2  C1   H1   single    0.970  0.020  1.090
 KK2  C1   H2   single    0.970  0.020  1.090
 KK2  C2   H3   single    0.970  0.020  1.090
 KK2  C2   H4   single    0.970  0.020  1.090
 KK2  C3   H5   single    0.970  0.020  1.090
 KK2  C3   H6   single    0.970  0.020  1.090
 KK2  C4   H7   single    0.970  0.020  1.090
 KK2  C4   H8   single    0.970  0.020  1.090
 KK2  C5   H9   single    0.930  0.020  1.080
 KK2  N4   H10  single    0.890  0.020  1.040
 KK2  N4   H11  single    0.890  0.020  1.040
 KK2  C10  H12  single    0.930  0.020  1.080
 KK2  C11  H13  single    0.930  0.020  1.080
 KK2  C14  H14  single    0.930  0.020  1.080
 KK2  C15  H15  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
 KK2  H2   C1   H1   107.61  3.000
 KK2  H2   C1   N2   109.71  3.000
 KK2  H1   C1   N2   109.78  3.000
 KK2  H2   C1   C2   109.94  3.000
 KK2  H1   C1   C2   109.54  3.000
 KK2  N2   C1   C2   110.23  3.000
 KK2  H4   C2   H3   108.05  3.000
 KK2  H4   C2   O1   110.48  3.000
 KK2  H3   C2   O1   107.62  3.000
 KK2  H4   C2   C1   109.41  3.000
 KK2  H3   C2   C1   109.50  3.000
 KK2  O1   C2   C1   111.70  3.000
 KK2  C3   O1   C2   110.33  3.000
 KK2  H6   C3   H5   107.95  3.000
 KK2  H6   C3   C4   109.06  3.000
 KK2  H5   C3   C4   109.32  3.000
 KK2  H6   C3   O1   110.48  3.000
 KK2  H5   C3   O1   107.76  3.000
 KK2  C4   C3   O1   112.17  3.000
 KK2  H8   C4   H7   107.74  3.000
 KK2  H8   C4   N2   110.97  3.000
 KK2  H7   C4   N2   110.36  3.000
 KK2  H8   C4   C3   107.30  3.000
 KK2  H7   C4   C3   110.31  3.000
 KK2  N2   C4   C3   110.10  3.000
 KK2  C6   N2   C4   122.83  3.000
 KK2  C4   N2   C1   113.37  3.000
 KK2  C6   N2   C1   120.95  3.000
 KK2  N1   C6   C5   120.30  3.000
 KK2  C5   C6   N2   122.56  3.000
 KK2  N1   C6   N2   117.14  3.000
 KK2  H9   C5   C8   121.32  3.000
 KK2  H9   C5   C6   121.72  3.000
 KK2  C8   C5   C6   116.95  3.000
 KK2  C7   N1   C6   117.70  3.000
 KK2  N3   C7   N4   116.87  3.000
 KK2  N3   C7   N1   126.37  3.000
 KK2  N4   C7   N1   116.75  3.000
 KK2  H11  N4   H10  116.40  3.000
 KK2  H11  N4   C7   117.88  3.000
 KK2  H10  N4   C7   118.13  3.000
 KK2  C8   N3   C7   116.16  3.000
 KK2  C9   C8   N3   115.78  3.000
 KK2  C9   C8   C5   121.72  3.000
 KK2  N3   C8   C5   122.51  3.000
 KK2  C15  C9   C10  118.23  3.000
 KK2  C10  C9   C8   119.65  3.000
 KK2  C15  C9   C8   122.12  3.000
 KK2  H12  C10  C11  119.48  3.000
 KK2  H12  C10  C9   119.43  3.000
 KK2  C11  C10  C9   121.09  3.000
 KK2  H13  C11  C12  121.07  3.000
 KK2  H13  C11  C10  118.96  3.000
 KK2  C12  C11  C10  119.97  3.000
 KK2  C14  C12  C13  119.73  3.000
 KK2  C13  C12  C11  120.58  3.000
 KK2  C14  C12  C11  119.64  3.000
 KK2  F3   C13  F2   106.52  3.000
 KK2  F2   C13  F1   106.76  3.000
 KK2  F3   C13  F1   107.06  3.000
 KK2  F1   C13  C12  112.46  3.000
 KK2  F2   C13  C12  111.51  3.000
 KK2  F3   C13  C12  112.16  3.000
 KK2  H14  C14  C15  118.89  3.000
 KK2  H14  C14  C12  121.07  3.000
 KK2  C15  C14  C12  120.04  3.000
 KK2  H15  C15  C14  117.98  3.000
 KK2  H15  C15  C9   120.99  3.000
 KK2  C14  C15  C9   121.03  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
 KK2  CONST_01  N3   C7   N1   C6      0.00   0.0  0
 KK2  CONST_02  N3   C8   C5   C6      0.00   0.0  0
 KK2  CONST_03  C9   C8   C5   C6    180.00   0.0  0
 KK2  CONST_04  C7   N1   C6   C5      0.00   0.0  0
 KK2  CONST_05  C7   N3   C8   C5      0.00   0.0  0
 KK2  CONST_06  C15  C9   C8   C5      0.00   0.0  0
 KK2  CONST_07  C10  C9   C8   C5    180.00   0.0  0
 KK2  CONST_08  C8   C5   C6   N1      0.00   0.0  0
 KK2  CONST_09  C8   N3   C7   N1      0.00   0.0  0
 KK2  CONST_10  C9   C8   N3   C7    180.00   0.0  0
 KK2  CONST_11  C15  C9   C8   N3    180.00   0.0  0
 KK2  CONST_12  C10  C9   C8   N3      0.00   0.0  0
 KK2  CONST_13  C14  C15  C9   C8    180.00   0.0  0
 KK2  CONST_14  C11  C10  C9   C8    180.00   0.0  0
 KK2  CONST_15  C12  C14  C15  C9      0.00   0.0  0
 KK2  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 KK2  CONST_17  C14  C15  C9   C10     0.00   0.0  0
 KK2  CONST_18  C14  C12  C11  C10     0.00   0.0  0
 KK2  CONST_19  C15  C14  C12  C11     0.00   0.0  0
 KK2  CONST_20  C15  C9   C10  C11     0.00   0.0  0
 KK2  CONST_21  C7   N1   C6   N2    180.00   0.0  0
 KK2  CONST_22  C8   C5   C6   N2    180.00   0.0  0
 KK2  CONST_23  N4   C7   N1   C6    180.00   0.0  0
 KK2  CONST_24  C8   N3   C7   N4    180.00   0.0  0
 KK2  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 KK2  CONST_26  C15  C14  C12  C13   180.00   0.0  0
 KK2  CONST_27  H9   C5   C6   N2      0.00   0.0  0
 KK2  CONST_28  H15  C15  C9   C8      0.00   0.0  0
 KK2  CONST_29  H12  C10  C9   C8      0.00   0.0  0
 KK2  CONST_30  H14  C14  C15  C9    180.00   0.0  0
 KK2  CONST_31  H13  C11  C10  C9    180.00   0.0  0
 KK2  Var_01    N1   C6   N2   C1    -13.46  30.0  2
 KK2  Var_02    C3   C4   N2   C1     50.46  30.0  1
 KK2  Var_03    C6   N2   C1   C2    147.51  30.0  1
 KK2  Var_04    C4   C3   O1   C2     59.39  30.0  1
 KK2  Var_05    N2   C1   C2   O1     55.12  30.0  1
 KK2  Var_06    N2   C4   C3   O1    -54.30  30.0  1
 KK2  Var_07    H3   C2   O1   C3   -179.91  30.0  1
 KK2  Var_08    F3   C13  C12  C11  -146.62  30.0  2

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
 KK2  plan-1  N2   0.020
 KK2  plan-1  C6   0.020
 KK2  plan-1  C5   0.020
 KK2  plan-1  N1   0.020
 KK2  plan-1  C7   0.020
 KK2  plan-1  N4   0.020
 KK2  plan-1  N3   0.020
 KK2  plan-1  C8   0.020
 KK2  plan-1  C9   0.020
 KK2  plan-1  H9   0.020
 KK2  plan-2  C8   0.020
 KK2  plan-2  C9   0.020
 KK2  plan-2  C10  0.020
 KK2  plan-2  C11  0.020
 KK2  plan-2  C12  0.020
 KK2  plan-2  C13  0.020
 KK2  plan-2  C14  0.020
 KK2  plan-2  C15  0.020
 KK2  plan-2  H12  0.020
 KK2  plan-2  H13  0.020
 KK2  plan-2  H14  0.020
 KK2  plan-2  H15  0.020
 KK2  plan-3  C7   0.020
 KK2  plan-3  N4   0.020
 KK2  plan-3  H10  0.020
 KK2  plan-3  H11  0.020

