# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 19:09:46 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 4-[1-cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2n(cnc2c3ccc(F)cc3)C4CCCCC4
#
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
 0CK  0CK  4-[1-cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine  ligand  45  25  .  2022-07-22  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_0CK
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
 0CK  C7   C  CR5   0   0.285  -0.3820   0.3371   0.0285
 0CK  N2   N  NR5   0  -0.464  -1.5890   0.9896  -0.0493
 0CK  C8   C  CR15  0   0.091  -1.3121   2.3047  -0.1460
 0CK  N3   N  N     0  -0.454  -0.0272   2.5445  -0.1232
 0CK  C9   C  CR5   0   0.081   0.5773   1.3275  -0.0135
 0CK  C10  C  CR16  0  -0.382  -0.9007  -1.8641   1.0924
 0CK  C11  C  CR16  0  -0.016  -0.6504  -3.2266   1.0879
 0CK  N4   N  N     0  -0.450   0.1707  -3.8100   0.2334
 0CK  C12  C  CR6   0   0.539   0.7663  -3.0037  -0.6557
 0CK  N5   N  N     0  -0.451   0.5854  -1.6836  -0.7518
 0CK  C13  C  CR6   0   0.180  -0.2387  -1.1191   0.1203
 0CK  C14  C  CH2   0  -0.434  -3.7068   0.6966   1.1769
 0CK  C15  C  CH1   0  -0.106  -2.9284   0.4066  -0.1032
 0CK  C16  C  CH2   0  -0.427  -3.6912   0.8716  -1.3412
 0CK  C17  C  CH2   0  -0.440  -5.0678   0.2140  -1.3890
 0CK  C18  C  CH2   0  -0.433  -5.8612   0.4834  -0.1149
 0CK  C19  C  CH2   0  -0.438  -5.0854   0.0450   1.1227
 0CK  C1   C  CR16  0  -0.400   4.0426   0.1532   0.9174
 0CK  C2   C  CR6   0   0.512   4.7997   1.0982   0.2521
 0CK  C3   C  CR16  0  -0.401   4.2194   2.1104  -0.4868
 0CK  C4   C  CR16  0  -0.282   2.8362   2.1656  -0.5650
 0CK  C5   C  CR6   0   0.036   2.0353   1.2219   0.0800
 0CK  C6   C  CR16  0  -0.295   2.6613   0.2255   0.8305
 0CK  H1   H  HCR5  0   0.288  -2.0840   3.0536  -0.2356
 0CK  H2   H  HCR6  0   0.277  -1.5462  -1.4125   1.8312
 0CK  H3   H  HCR6  0   0.274  -1.1288  -3.8714   1.8173
 0CK  H4   H  HNH2  0   0.397   1.8877  -4.5253  -1.4061
 0CK  H5   H  HNH2  0   0.397   2.1878  -2.9865  -2.1072
 0CK  H6   H  HCH2  0   0.248  -3.1480   0.3328   2.0429
 0CK  H7   H  HCH2  0   0.231  -3.8151   1.7790   1.3023
 0CK  H8   H  HCH1  0   0.266  -2.7900  -0.6732  -0.1877
 0CK  H9   H  HCH2  0   0.226  -3.8134   1.9589  -1.3218
 0CK  H10  H  HCH2  0   0.251  -3.1187   0.6270  -2.2385
 0CK  H11  H  HCH2  0   0.239  -5.6131   0.5783  -2.2620
 0CK  H12  H  HCH2  0   0.220  -4.9490  -0.8658  -1.5266
 0CK  H13  H  HCH2  0   0.215  -6.0801   1.5539  -0.0442
 0CK  H14  H  HCH2  0   0.234  -6.8242  -0.0303  -0.1565
 0CK  H15  H  HCH2  0   0.219  -4.9702  -1.0440   1.1166
 0CK  H16  H  HCH2  0   0.239  -5.6409   0.2923   2.0294
 0CK  H17  H  HCR6  0   0.279   4.5206  -0.6201   1.5043
 0CK  H18  H  HCR6  0   0.278   4.8329   2.8431  -0.9943
 0CK  H19  H  HCR6  0   0.258   2.3724   2.9548  -1.1416
 0CK  H20  H  HCR6  0   0.255   2.0724  -0.4981   1.3768
 0CK  N1   N  NH2   0  -0.824   1.5937  -3.5751  -1.5498
 0CK  F1   F  F     0  -0.316   6.1393   1.0339   0.3340

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
 0CK  N1   C12  single    1.346  0.020  1.346
 0CK  N4   C12  aromatic  1.340  0.020  1.340
 0CK  N4   C11  aromatic  1.321  0.020  1.321
 0CK  C12  N5   aromatic  1.336  0.020  1.336
 0CK  C11  C10  aromatic  1.385  0.020  1.385
 0CK  N5   C13  aromatic  1.326  0.020  1.326
 0CK  C17  C16  single    1.526  0.020  1.526
 0CK  C17  C18  single    1.525  0.020  1.525
 0CK  C10  C13  aromatic  1.392  0.020  1.392
 0CK  C13  C7   single    1.466  0.020  1.466
 0CK  C16  C15  single    1.527  0.020  1.527
 0CK  C1   C6   aromatic  1.386  0.020  1.386
 0CK  C1   C2   aromatic  1.382  0.020  1.382
 0CK  C18  C19  single    1.525  0.020  1.525
 0CK  C6   C5   aromatic  1.396  0.020  1.396
 0CK  C7   N2   aromatic  1.374  0.020  1.374
 0CK  C7   C9   aromatic  1.380  0.020  1.380
 0CK  C15  N2   single    1.462  0.020  1.462
 0CK  C15  C14  single    1.526  0.020  1.526
 0CK  F1   C2   single    1.344  0.020  1.344
 0CK  C19  C14  single    1.526  0.020  1.526
 0CK  C2   C3   aromatic  1.381  0.020  1.381
 0CK  N2   C8   aromatic  1.347  0.020  1.347
 0CK  C5   C9   single    1.465  0.020  1.465
 0CK  C5   C4   aromatic  1.396  0.020  1.396
 0CK  C9   N3   aromatic  1.363  0.020  1.363
 0CK  C8   N3   aromatic  1.307  0.020  1.307
 0CK  C3   C4   aromatic  1.387  0.020  1.387
 0CK  C8   H1   single    0.930  0.020  1.080
 0CK  C10  H2   single    0.930  0.020  1.080
 0CK  C11  H3   single    0.930  0.020  1.080
 0CK  N1   H4   single    0.890  0.020  1.040
 0CK  N1   H5   single    0.890  0.020  1.040
 0CK  C14  H6   single    0.970  0.020  1.090
 0CK  C14  H7   single    0.970  0.020  1.090
 0CK  C15  H8   single    0.970  0.020  1.090
 0CK  C16  H9   single    0.970  0.020  1.090
 0CK  C16  H10  single    0.970  0.020  1.090
 0CK  C17  H11  single    0.970  0.020  1.090
 0CK  C17  H12  single    0.970  0.020  1.090
 0CK  C18  H13  single    0.970  0.020  1.090
 0CK  C18  H14  single    0.970  0.020  1.090
 0CK  C19  H15  single    0.970  0.020  1.090
 0CK  C19  H16  single    0.970  0.020  1.090
 0CK  C1   H17  single    0.930  0.020  1.080
 0CK  C3   H18  single    0.930  0.020  1.080
 0CK  C4   H19  single    0.930  0.020  1.080
 0CK  C6   H20  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
 0CK  C13  C7   C9   130.32  3.000
 0CK  C9   C7   N2   105.55  3.000
 0CK  C13  C7   N2   124.12  3.000
 0CK  C15  N2   C8   125.09  3.000
 0CK  C8   N2   C7   106.68  3.000
 0CK  C15  N2   C7   128.13  3.000
 0CK  H1   C8   N3   125.25  3.000
 0CK  H1   C8   N2   122.43  3.000
 0CK  N3   C8   N2   112.32  3.000
 0CK  C9   N3   C8   105.87  3.000
 0CK  C5   C9   N3   120.72  3.000
 0CK  N3   C9   C7   109.57  3.000
 0CK  C5   C9   C7   129.68  3.000
 0CK  H2   C10  C13  122.55  3.000
 0CK  H2   C10  C11  121.43  3.000
 0CK  C13  C10  C11  115.99  3.000
 0CK  H3   C11  N4   116.53  3.000
 0CK  H3   C11  C10  120.19  3.000
 0CK  N4   C11  C10  123.28  3.000
 0CK  C12  N4   C11  116.10  3.000
 0CK  N1   C12  N5   117.07  3.000
 0CK  N5   C12  N4   125.60  3.000
 0CK  N1   C12  N4   117.30  3.000
 0CK  C13  N5   C12  117.23  3.000
 0CK  N5   C13  C10  121.80  3.000
 0CK  C10  C13  C7   121.92  3.000
 0CK  N5   C13  C7   116.26  3.000
 0CK  H7   C14  H6   106.79  3.000
 0CK  H7   C14  C19  109.69  3.000
 0CK  H6   C14  C19  110.36  3.000
 0CK  H7   C14  C15  109.53  3.000
 0CK  H6   C14  C15  109.91  3.000
 0CK  C19  C14  C15  110.48  3.000
 0CK  H8   C15  C16  107.57  3.000
 0CK  H8   C15  C14  108.51  3.000
 0CK  C16  C15  C14  111.56  3.000
 0CK  H8   C15  N2   106.33  3.000
 0CK  C14  C15  N2   111.14  3.000
 0CK  C16  C15  N2   111.49  3.000
 0CK  H10  C16  H9   107.19  3.000
 0CK  H10  C16  C17  110.52  3.000
 0CK  H9   C16  C17  109.14  3.000
 0CK  H10  C16  C15  109.64  3.000
 0CK  H9   C16  C15  110.12  3.000
 0CK  C17  C16  C15  110.17  3.000
 0CK  H12  C17  H11  106.42  3.000
 0CK  H12  C17  C18  109.62  3.000
 0CK  H11  C17  C18  110.44  3.000
 0CK  H12  C17  C16  109.33  3.000
 0CK  H11  C17  C16  109.37  3.000
 0CK  C18  C17  C16  111.53  3.000
 0CK  H14  C18  H13  106.62  3.000
 0CK  H14  C18  C19  110.14  3.000
 0CK  H13  C18  C19  109.29  3.000
 0CK  H14  C18  C17  110.11  3.000
 0CK  H13  C18  C17  109.31  3.000
 0CK  C19  C18  C17  111.26  3.000
 0CK  H16  C19  H15  106.47  3.000
 0CK  H16  C19  C18  110.49  3.000
 0CK  H15  C19  C18  109.56  3.000
 0CK  H16  C19  C14  109.48  3.000
 0CK  H15  C19  C14  109.26  3.000
 0CK  C18  C19  C14  111.45  3.000
 0CK  H17  C1   C6   120.76  3.000
 0CK  H17  C1   C2   120.52  3.000
 0CK  C6   C1   C2   118.71  3.000
 0CK  F1   C2   C3   119.12  3.000
 0CK  C3   C2   C1   121.91  3.000
 0CK  F1   C2   C1   118.97  3.000
 0CK  H18  C3   C4   120.81  3.000
 0CK  H18  C3   C2   120.60  3.000
 0CK  C4   C3   C2   118.59  3.000
 0CK  H19  C4   C5   119.57  3.000
 0CK  H19  C4   C3   119.13  3.000
 0CK  C5   C4   C3   121.29  3.000
 0CK  C6   C5   C4   118.28  3.000
 0CK  C4   C5   C9   119.53  3.000
 0CK  C6   C5   C9   122.16  3.000
 0CK  H20  C6   C5   120.35  3.000
 0CK  H20  C6   C1   118.44  3.000
 0CK  C5   C6   C1   121.20  3.000
 0CK  H5   N1   H4   117.39  3.000
 0CK  H5   N1   C12  118.90  3.000
 0CK  H4   N1   C12  119.11  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
 0CK  CONST_01  C12  N5   C13  C7   180.00   0.0  0
 0CK  CONST_02  C11  C10  C13  C7   180.00   0.0  0
 0CK  CONST_03  N3   C8   N2   C7     0.00   0.0  0
 0CK  CONST_06  C8   N3   C9   C7     0.00   0.0  0
 0CK  CONST_09  C5   C9   C7   N2   180.00   0.0  0
 0CK  CONST_10  N3   C9   C7   N2     0.00   0.0  0
 0CK  CONST_11  C9   N3   C8   N2     0.00   0.0  0
 0CK  CONST_12  C13  C7   N2   C8   180.00   0.0  0
 0CK  CONST_13  C9   C7   N2   C8     0.00   0.0  0
 0CK  CONST_14  C5   C9   N3   C8   180.00   0.0  0
 0CK  CONST_15  C13  C7   C9   N3   180.00   0.0  0
 0CK  CONST_20  C1   C6   C5   C9   180.00   0.0  0
 0CK  CONST_21  C3   C4   C5   C9   180.00   0.0  0
 0CK  CONST_22  C12  N4   C11  C10    0.00   0.0  0
 0CK  CONST_23  C12  N5   C13  C10    0.00   0.0  0
 0CK  CONST_24  N5   C12  N4   C11    0.00   0.0  0
 0CK  CONST_25  N5   C13  C10  C11    0.00   0.0  0
 0CK  CONST_26  C13  N5   C12  N4     0.00   0.0  0
 0CK  CONST_27  C13  C10  C11  N4     0.00   0.0  0
 0CK  CONST_28  C5   C9   C7   C13    0.00   0.0  0
 0CK  CONST_29  C4   C5   C6   C1     0.00   0.0  0
 0CK  CONST_30  C4   C3   C2   C1     0.00   0.0  0
 0CK  CONST_31  C5   C6   C1   C2     0.00   0.0  0
 0CK  CONST_32  C5   C4   C3   C2     0.00   0.0  0
 0CK  CONST_33  C6   C1   C2   C3     0.00   0.0  0
 0CK  CONST_34  C6   C5   C4   C3     0.00   0.0  0
 0CK  CONST_35  C15  N2   C8   N3   180.00   0.0  0
 0CK  CONST_36  C15  N2   C7   C9   180.00   0.0  0
 0CK  CONST_37  C15  N2   C7   C13    0.00   0.0  0
 0CK  CONST_38  N1   C12  N4   C11  180.00   0.0  0
 0CK  CONST_39  N1   C12  N5   C13  180.00   0.0  0
 0CK  CONST_40  F1   C2   C3   C4   180.00   0.0  0
 0CK  CONST_41  F1   C2   C1   C6   180.00   0.0  0
 0CK  CONST_42  H2   C10  C13  C7     0.00   0.0  0
 0CK  CONST_43  H1   C8   N2   C7   180.00   0.0  0
 0CK  CONST_44  H20  C6   C5   C9     0.00   0.0  0
 0CK  CONST_45  H19  C4   C5   C9     0.00   0.0  0
 0CK  CONST_46  H3   C11  N4   C12  180.00   0.0  0
 0CK  CONST_47  H18  C3   C2   C1   180.00   0.0  0
 0CK  CONST_48  H17  C1   C2   C3   180.00   0.0  0
 0CK  CONST_49  H4   N1   C12  N4     0.00   0.0  0
 0CK  CONST_50  H5   N1   C12  N4   180.00   0.0  0
 0CK  Var_01    C17  C18  C19  C14   55.00  30.0  1
 0CK  Var_02    C18  C17  C16  C15   55.84  30.0  1
 0CK  Var_03    C18  C19  C14  C15  -55.44  30.0  1
 0CK  Var_04    C19  C18  C17  C16  -55.31  30.0  1

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
 0CK  chir_01  C15  C16  N2  C14  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
 0CK  plan-1  C7   0.020
 0CK  plan-1  N2   0.020
 0CK  plan-1  C8   0.020
 0CK  plan-1  N3   0.020
 0CK  plan-1  C9   0.020
 0CK  plan-1  C13  0.020
 0CK  plan-1  C15  0.020
 0CK  plan-1  C5   0.020
 0CK  plan-1  H1   0.020
 0CK  plan-2  C7   0.020
 0CK  plan-2  C10  0.020
 0CK  plan-2  C11  0.020
 0CK  plan-2  N4   0.020
 0CK  plan-2  C12  0.020
 0CK  plan-2  N5   0.020
 0CK  plan-2  C13  0.020
 0CK  plan-2  H2   0.020
 0CK  plan-2  H3   0.020
 0CK  plan-2  N1   0.020
 0CK  plan-3  C9   0.020
 0CK  plan-3  C1   0.020
 0CK  plan-3  C2   0.020
 0CK  plan-3  C3   0.020
 0CK  plan-3  C4   0.020
 0CK  plan-3  C5   0.020
 0CK  plan-3  C6   0.020
 0CK  plan-3  H17  0.020
 0CK  plan-3  H18  0.020
 0CK  plan-3  H19  0.020
 0CK  plan-3  H20  0.020
 0CK  plan-3  F1   0.020
 0CK  plan-4  C12  0.020
 0CK  plan-4  H4   0.020
 0CK  plan-4  H5   0.020
 0CK  plan-4  N1   0.020

