# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:04:03 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-(4-methylpiperidin-1-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)c2cc(nc(N)n2)c3ccc(cc3)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
 KK3  KK3  4-(4-methylpiperidin-1-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine  ligand  43  24  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KK3
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
 KK3  C1   C  CH2   0  -0.312  -4.8206  -0.4764   0.5133
 KK3  C3   C  CH2   0  -0.416  -5.6504   0.2666  -0.5262
 KK3  C7   C  CH1   0  -0.254  -5.6834   1.7768  -0.2777
 KK3  C8   C  CH3   0  -0.643  -6.5836   2.1453   0.8992
 KK3  C9   C  CH2   0  -0.410  -4.2545   2.2955  -0.0985
 KK3  C10  C  CH2   0  -0.300  -3.4632   1.4871   0.9235
 KK3  N2   N  NT    0  -0.494  -3.4779   0.0764   0.5886
 KK3  C4   C  CR6   0   0.604  -2.3873  -0.6438   0.2558
 KK3  C5   C  CR16  0  -0.468  -1.0727  -0.1197   0.2981
 KK3  N3   N  N     0  -0.525  -2.5790  -1.9114  -0.1114
 KK3  C2   C  CR6   0   0.540  -1.5130  -2.6409  -0.4177
 KK3  N4   N  NH2   0  -0.805  -1.7369  -3.9423  -0.7209
 KK3  N1   N  N     0  -0.517  -0.2460  -2.2340  -0.4290
 KK3  C6   C  CR6   0   0.292  -0.0481  -0.9646  -0.0699
 KK3  C11  C  CR6   0   0.075   1.3616  -0.5091  -0.0616
 KK3  C12  C  CR16  0  -0.252   2.3874  -1.4394   0.0847
 KK3  C13  C  CR16  0  -0.243   3.7127  -1.0399   0.1116
 KK3  C14  C  CR6   0  -0.197   4.0365   0.3037  -0.0192
 KK3  C15  C  CT    0   1.049   5.4635   0.7517  -0.0443
 KK3  F1   F  F     0  -0.310   6.2884  -0.1401   0.5201
 KK3  F2   F  F     0  -0.308   5.8997   0.9396  -1.2973
 KK3  F3   F  F     0  -0.306   5.6374   1.9100   0.6017
 KK3  C16  C  CR16  0  -0.229   3.0232   1.2410  -0.1831
 KK3  C17  C  CR16  0  -0.286   1.7014   0.8355  -0.2032
 KK3  H1   H  HCH2  0   0.224  -5.2824  -0.4019   1.5038
 KK3  H2   H  HCH2  0   0.274  -4.7562  -1.5315   0.2694
 KK3  H3   H  HCH2  0   0.225  -5.2305   0.0643  -1.5157
 KK3  H4   H  HCH2  0   0.226  -6.6650  -0.1396  -0.5298
 KK3  H5   H  HCH1  0   0.234  -6.1023   2.2555  -1.1676
 KK3  H6   H  HCH3  0   0.209  -6.2555   1.7065   1.8430
 KK3  H7   H  HCH3  0   0.223  -6.6157   3.2265   1.0413
 KK3  H8   H  HCH3  0   0.223  -7.6058   1.8059   0.7261
 KK3  H9   H  HCH2  0   0.226  -3.7243   2.2583  -1.0545
 KK3  H10  H  HCH2  0   0.228  -4.2660   3.3433   0.2112
 KK3  H11  H  HCH2  0   0.249  -2.4488   1.8680   0.9817
 KK3  H12  H  HCH2  0   0.232  -3.8845   1.6116   1.9261
 KK3  H13  H  HCR6  0   0.232  -0.8598   0.8813   0.6313
 KK3  H14  H  HNH2  0   0.369  -2.6744  -4.2221  -0.9443
 KK3  H15  H  HNH2  0   0.368  -1.0023  -4.4534  -1.1752
 KK3  H16  H  HCR6  0   0.250   2.1453  -2.4875   0.1863
 KK3  H17  H  HCR6  0   0.250   4.4805  -1.7901   0.2369
 KK3  H18  H  HCR6  0   0.245   3.2527   2.2919  -0.2994
 KK3  H19  H  HCR6  0   0.231   0.9323   1.5806  -0.3552

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
 KK3  N4   C2   single    1.355  0.020  1.355
 KK3  C2   N3   aromatic  1.328  0.020  1.328
 KK3  C2   N1   aromatic  1.331  0.020  1.331
 KK3  N3   C4   aromatic  1.334  0.020  1.334
 KK3  C1   C3   single    1.524  0.020  1.524
 KK3  C1   N2   single    1.454  0.020  1.454
 KK3  N1   C6   aromatic  1.334  0.020  1.334
 KK3  C3   C7   single    1.531  0.020  1.531
 KK3  C4   N2   single    1.349  0.020  1.349
 KK3  C4   C5   aromatic  1.416  0.020  1.416
 KK3  N2   C10  single    1.450  0.020  1.450
 KK3  C6   C5   aromatic  1.378  0.020  1.378
 KK3  C6   C11  single    1.481  0.020  1.481
 KK3  C7   C8   single    1.527  0.020  1.527
 KK3  C7   C9   single    1.531  0.020  1.531
 KK3  C10  C9   single    1.525  0.020  1.525
 KK3  C11  C12  aromatic  1.393  0.020  1.393
 KK3  C11  C17  aromatic  1.394  0.020  1.394
 KK3  C12  C13  aromatic  1.384  0.020  1.384
 KK3  C17  C16  aromatic  1.383  0.020  1.383
 KK3  C13  C14  aromatic  1.388  0.020  1.388
 KK3  C16  C14  aromatic  1.390  0.020  1.390
 KK3  C14  C15  single    1.496  0.020  1.496
 KK3  F3   C15  single    1.338  0.020  1.338
 KK3  C15  F2   single    1.340  0.020  1.340
 KK3  C15  F1   single    1.340  0.020  1.340
 KK3  C1   H1   single    0.970  0.020  1.090
 KK3  C1   H2   single    0.970  0.020  1.090
 KK3  C3   H3   single    0.970  0.020  1.090
 KK3  C3   H4   single    0.970  0.020  1.090
 KK3  C7   H5   single    0.970  0.020  1.090
 KK3  C8   H6   single    0.970  0.020  1.090
 KK3  C8   H7   single    0.970  0.020  1.090
 KK3  C8   H8   single    0.970  0.020  1.090
 KK3  C9   H9   single    0.970  0.020  1.090
 KK3  C9   H10  single    0.970  0.020  1.090
 KK3  C10  H11  single    0.970  0.020  1.090
 KK3  C10  H12  single    0.970  0.020  1.090
 KK3  C5   H13  single    0.930  0.020  1.080
 KK3  N4   H14  single    0.890  0.020  1.040
 KK3  N4   H15  single    0.890  0.020  1.040
 KK3  C12  H16  single    0.930  0.020  1.080
 KK3  C13  H17  single    0.930  0.020  1.080
 KK3  C16  H18  single    0.930  0.020  1.080
 KK3  C17  H19  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
 KK3  H2   C1   H1   107.12  3.000
 KK3  H2   C1   N2   109.07  3.000
 KK3  H1   C1   N2   108.46  3.000
 KK3  H2   C1   C3   110.68  3.000
 KK3  H1   C1   C3   110.74  3.000
 KK3  N2   C1   C3   110.67  3.000
 KK3  H4   C3   H3   106.54  3.000
 KK3  H4   C3   C7   110.31  3.000
 KK3  H3   C3   C7   109.73  3.000
 KK3  H4   C3   C1   109.07  3.000
 KK3  H3   C3   C1   108.53  3.000
 KK3  C7   C3   C1   112.46  3.000
 KK3  H5   C7   C9   107.72  3.000
 KK3  H5   C7   C8   107.20  3.000
 KK3  C9   C7   C8   112.23  3.000
 KK3  H5   C7   C3   107.93  3.000
 KK3  C9   C7   C3   109.46  3.000
 KK3  C8   C7   C3   112.08  3.000
 KK3  H8   C8   H7   107.54  3.000
 KK3  H8   C8   H6   107.09  3.000
 KK3  H7   C8   H6   107.14  3.000
 KK3  H8   C8   C7   110.80  3.000
 KK3  H7   C8   C7   110.91  3.000
 KK3  H6   C8   C7   113.10  3.000
 KK3  H10  C9   H9   106.58  3.000
 KK3  H10  C9   C10  108.90  3.000
 KK3  H9   C9   C10  108.44  3.000
 KK3  H10  C9   C7   110.38  3.000
 KK3  H9   C9   C7   109.80  3.000
 KK3  C10  C9   C7   112.54  3.000
 KK3  H12  C10  H11  105.71  3.000
 KK3  H12  C10  N2   108.56  3.000
 KK3  H11  C10  N2   111.31  3.000
 KK3  H12  C10  C9   110.73  3.000
 KK3  H11  C10  C9   109.57  3.000
 KK3  N2   C10  C9   110.84  3.000
 KK3  C4   N2   C10  124.64  3.000
 KK3  C10  N2   C1   113.03  3.000
 KK3  C4   N2   C1   122.07  3.000
 KK3  N3   C4   C5   119.57  3.000
 KK3  C5   C4   N2   123.08  3.000
 KK3  N3   C4   N2   117.34  3.000
 KK3  H13  C5   C6   120.39  3.000
 KK3  H13  C5   C4   122.49  3.000
 KK3  C6   C5   C4   117.09  3.000
 KK3  C2   N3   C4   118.06  3.000
 KK3  N1   C2   N4   116.68  3.000
 KK3  N1   C2   N3   126.76  3.000
 KK3  N4   C2   N3   116.54  3.000
 KK3  H15  N4   H14  116.17  3.000
 KK3  H15  N4   C2   118.00  3.000
 KK3  H14  N4   C2   118.17  3.000
 KK3  C6   N1   C2   115.46  3.000
 KK3  C11  C6   N1   115.80  3.000
 KK3  C11  C6   C5   121.17  3.000
 KK3  N1   C6   C5   123.03  3.000
 KK3  C17  C11  C12  118.39  3.000
 KK3  C17  C11  C6   121.86  3.000
 KK3  C12  C11  C6   119.75  3.000
 KK3  H16  C12  C13  119.51  3.000
 KK3  H16  C12  C11  119.53  3.000
 KK3  C13  C12  C11  120.96  3.000
 KK3  H17  C13  C14  121.13  3.000
 KK3  H17  C13  C12  118.82  3.000
 KK3  C14  C13  C12  120.05  3.000
 KK3  C16  C14  C15  119.44  3.000
 KK3  C15  C14  C13  120.93  3.000
 KK3  C16  C14  C13  119.58  3.000
 KK3  F3   C15  F2   106.72  3.000
 KK3  F2   C15  F1   106.67  3.000
 KK3  F3   C15  F1   107.04  3.000
 KK3  F1   C15  C14  112.40  3.000
 KK3  F2   C15  C14  111.61  3.000
 KK3  F3   C15  C14  112.04  3.000
 KK3  H18  C16  C17  119.08  3.000
 KK3  H18  C16  C14  120.87  3.000
 KK3  C17  C16  C14  120.05  3.000
 KK3  H19  C17  C16  118.67  3.000
 KK3  H19  C17  C11  120.36  3.000
 KK3  C16  C17  C11  120.96  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
 KK3  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 KK3  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 KK3  CONST_03  C11  C6   C5   C4    180.00   0.0  0
 KK3  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 KK3  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 KK3  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 KK3  CONST_09  C6   C5   C4   N3      0.00   0.0  0
 KK3  CONST_10  C11  C6   N1   C2    180.00   0.0  0
 KK3  CONST_13  C13  C12  C11  C6    180.00   0.0  0
 KK3  CONST_14  C16  C17  C11  C6    180.00   0.0  0
 KK3  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 KK3  CONST_16  C14  C16  C17  C11     0.00   0.0  0
 KK3  CONST_17  C16  C17  C11  C12     0.00   0.0  0
 KK3  CONST_18  C16  C14  C13  C12     0.00   0.0  0
 KK3  CONST_19  C17  C11  C12  C13     0.00   0.0  0
 KK3  CONST_20  C17  C16  C14  C13     0.00   0.0  0
 KK3  CONST_21  C2   N3   C4   N2    180.00   0.0  0
 KK3  CONST_22  C6   C5   C4   N2    180.00   0.0  0
 KK3  CONST_23  N4   C2   N3   C4    180.00   0.0  0
 KK3  CONST_24  C6   N1   C2   N4    180.00   0.0  0
 KK3  CONST_25  C15  C14  C13  C12   180.00   0.0  0
 KK3  CONST_26  C17  C16  C14  C15   180.00   0.0  0
 KK3  CONST_27  H13  C5   C4   N2      0.00   0.0  0
 KK3  CONST_28  H16  C12  C11  C6      0.00   0.0  0
 KK3  CONST_29  H19  C17  C11  C6      0.00   0.0  0
 KK3  CONST_30  H17  C13  C12  C11   180.00   0.0  0
 KK3  CONST_31  H18  C16  C17  C11   180.00   0.0  0
 KK3  Var_01    N3   C4   N2   C1     -2.01  30.0  1
 KK3  Var_02    C9   C10  N2   C1    -58.33  30.0  1
 KK3  Var_03    C4   N2   C1   C3   -115.81  30.0  1
 KK3  Var_04    N2   C1   C3   C7    -54.80  30.0  1
 KK3  Var_05    N2   C10  C9   C7     54.40  30.0  1
 KK3  Var_06    F3   C15  C14  C13  -142.41  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
 KK3  chir_01  C7  C3  C8  C9  negativ

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
 KK3  plan-1  N2   0.020
 KK3  plan-1  C4   0.020
 KK3  plan-1  C5   0.020
 KK3  plan-1  N3   0.020
 KK3  plan-1  C2   0.020
 KK3  plan-1  N4   0.020
 KK3  plan-1  N1   0.020
 KK3  plan-1  C6   0.020
 KK3  plan-1  C11  0.020
 KK3  plan-1  H13  0.020
 KK3  plan-2  C6   0.020
 KK3  plan-2  C11  0.020
 KK3  plan-2  C12  0.020
 KK3  plan-2  C13  0.020
 KK3  plan-2  C14  0.020
 KK3  plan-2  C15  0.020
 KK3  plan-2  C16  0.020
 KK3  plan-2  C17  0.020
 KK3  plan-2  H16  0.020
 KK3  plan-2  H17  0.020
 KK3  plan-2  H18  0.020
 KK3  plan-2  H19  0.020
 KK3  plan-3  C2   0.020
 KK3  plan-3  N4   0.020
 KK3  plan-3  H14  0.020
 KK3  plan-3  H15  0.020

