# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:09:30 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-cyclohexyl-4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)c2n[nH]cc2c3ccnc(NC4CCCCC4)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
 EK3  EK3  N-cyclohexyl-4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridin-2-amine  ligand  46  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EK3
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
 EK3  F    F  F     0  -0.315  -6.1824  -2.1532  -1.0043
 EK3  C1   C  CR6   0   0.517  -5.2246  -1.2414  -0.7725
 EK3  C6   C  CR16  0  -0.401  -5.5842  -0.0032  -0.2763
 EK3  C5   C  CR16  0  -0.275  -4.5880   0.9305  -0.0362
 EK3  C4   C  CR6   0   0.030  -3.2479   0.6354  -0.2872
 EK3  C3   C  CR16  0  -0.283  -2.9268  -0.6226  -0.7968
 EK3  C2   C  CR16  0  -0.398  -3.9097  -1.5694  -1.0398
 EK3  C7   C  CR5   0   0.257  -2.2091   1.6454  -0.0547
 EK3  C9   C  CR5   0  -0.161  -0.8762   1.4761   0.4010
 EK3  C8   C  CR15  0   0.015  -0.3526   2.7524   0.3845
 EK3  N2   N  NR15  0  -0.424  -1.3311   3.5613  -0.0371
 EK3  N1   N  N     0  -0.285  -2.4558   2.9198  -0.3148
 EK3  C10  C  CR6   0   0.134  -0.1800   0.2695   0.8515
 EK3  C14  C  CR16  0  -0.418  -0.7902  -0.6409   1.7216
 EK3  C13  C  CR16  0  -0.058  -0.0530  -1.7359   2.1251
 EK3  N3   N  N     0  -0.474   1.1903  -1.9909   1.7378
 EK3  C12  C  CR6   0   0.511   1.7801  -1.1327   0.8988
 EK3  C11  C  CR16  0  -0.479   1.1199   0.0243   0.4429
 EK3  N4   N  NH1   0  -0.672   3.0283  -1.4698   0.4921
 EK3  C15  C  CH1   0  -0.066   3.9184  -0.6426  -0.2901
 EK3  C20  C  CH2   0  -0.429   4.6799   0.3765   0.5610
 EK3  C19  C  CH2   0  -0.438   5.6236   1.2192  -0.2917
 EK3  C18  C  CH2   0  -0.432   6.5882   0.3389  -1.0799
 EK3  C17  C  CH2   0  -0.438   5.8334  -0.6837  -1.9224
 EK3  C16  C  CH2   0  -0.434   4.8885  -1.5256  -1.0705
 EK3  H5   H  HCR6  0   0.281  -6.6218   0.2301  -0.0778
 EK3  H4   H  HCR6  0   0.262  -4.8606   1.8994   0.3608
 EK3  H3   H  HCR6  0   0.266  -1.8987  -0.8715  -1.0228
 EK3  H2   H  HCR6  0   0.281  -3.6537  -2.5423  -1.4381
 EK3  H6   H  HCR5  0   0.296   0.6176   3.1236   0.6710
 EK3  H1   H  HNR5  0   0.426  -1.2815   4.5608  -0.1561
 EK3  H9   H  HCR6  0   0.249  -1.7951  -0.4887   2.0885
 EK3  H8   H  HCR6  0   0.253  -0.4918  -2.4554   2.8090
 EK3  H7   H  HCR6  0   0.260   1.6046   0.7104  -0.2382
 EK3  H10  H  HNH1  0   0.373   3.4345  -2.2574   0.9739
 EK3  H11  H  HCH1  0   0.230   3.3154  -0.1011  -1.0276
 EK3  H20  H  HCH2  0   0.233   3.9738   1.0166   1.0970
 EK3  H21  H  HCH2  0   0.214   5.2558  -0.1631   1.3219
 EK3  H19  H  HCH2  0   0.213   5.0378   1.8296  -0.9878
 EK3  H18  H  HCH2  0   0.231   6.1749   1.9173   0.3425
 EK3  H17  H  HCH2  0   0.230   7.2284   0.9543  -1.7163
 EK3  H16  H  HCH2  0   0.211   7.2519  -0.1849  -0.3832
 EK3  H15  H  HCH2  0   0.215   5.2549  -0.1626  -2.6930
 EK3  H14  H  HCH2  0   0.233   6.5341  -1.3347  -2.4499
 EK3  H13  H  HCH2  0   0.217   5.4714  -2.1309  -0.3652
 EK3  H12  H  HCH2  0   0.239   4.3263  -2.2218  -1.6976

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
 EK3  C18  C19  single    1.525  0.020  1.525
 EK3  C18  C17  single    1.525  0.020  1.525
 EK3  C19  C20  single    1.526  0.020  1.526
 EK3  C20  C15  single    1.531  0.020  1.531
 EK3  C17  C16  single    1.526  0.020  1.526
 EK3  F    C1   single    1.343  0.020  1.343
 EK3  C6   C1   aromatic  1.381  0.020  1.381
 EK3  C6   C5   aromatic  1.386  0.020  1.386
 EK3  C15  C16  single    1.526  0.020  1.526
 EK3  C15  N4   single    1.445  0.020  1.445
 EK3  C1   C2   aromatic  1.381  0.020  1.381
 EK3  C5   C4   aromatic  1.395  0.020  1.395
 EK3  N4   C12  single    1.355  0.020  1.355
 EK3  C2   C3   aromatic  1.386  0.020  1.386
 EK3  C12  N3   aromatic  1.337  0.020  1.337
 EK3  C12  C11  aromatic  1.408  0.020  1.408
 EK3  C4   C3   aromatic  1.395  0.020  1.395
 EK3  C4   C7   single    1.467  0.020  1.467
 EK3  N3   C13  aromatic  1.327  0.020  1.327
 EK3  C11  C10  aromatic  1.384  0.020  1.384
 EK3  C13  C14  aromatic  1.380  0.020  1.380
 EK3  C7   C9   aromatic  1.419  0.020  1.419
 EK3  C7   N1   aromatic  1.324  0.020  1.324
 EK3  C10  C14  aromatic  1.399  0.020  1.399
 EK3  C10  C9   single    1.464  0.020  1.464
 EK3  C9   C8   aromatic  1.380  0.020  1.380
 EK3  N1   N2   aromatic  1.324  0.020  1.324
 EK3  C8   N2   aromatic  1.338  0.020  1.338
 EK3  C6   H5   single    0.930  0.020  1.080
 EK3  C5   H4   single    0.930  0.020  1.080
 EK3  C3   H3   single    0.930  0.020  1.080
 EK3  C2   H2   single    0.930  0.020  1.080
 EK3  C8   H6   single    0.930  0.020  1.080
 EK3  N2   H1   single    0.860  0.020  1.020
 EK3  C14  H9   single    0.930  0.020  1.080
 EK3  C13  H8   single    0.930  0.020  1.080
 EK3  C11  H7   single    0.930  0.020  1.080
 EK3  N4   H10  single    0.860  0.020  1.020
 EK3  C15  H11  single    0.970  0.020  1.090
 EK3  C20  H20  single    0.970  0.020  1.090
 EK3  C20  H21  single    0.970  0.020  1.090
 EK3  C19  H19  single    0.970  0.020  1.090
 EK3  C19  H18  single    0.970  0.020  1.090
 EK3  C18  H17  single    0.970  0.020  1.090
 EK3  C18  H16  single    0.970  0.020  1.090
 EK3  C17  H15  single    0.970  0.020  1.090
 EK3  C17  H14  single    0.970  0.020  1.090
 EK3  C16  H13  single    0.970  0.020  1.090
 EK3  C16  H12  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
 EK3  C2   C1   C6   122.01  3.000
 EK3  C2   C1   F    118.97  3.000
 EK3  C6   C1   F    119.02  3.000
 EK3  H5   C6   C5   120.80  3.000
 EK3  H5   C6   C1   120.58  3.000
 EK3  C5   C6   C1   118.61  3.000
 EK3  H4   C5   C4   119.83  3.000
 EK3  H4   C5   C6   119.06  3.000
 EK3  C4   C5   C6   121.11  3.000
 EK3  C7   C4   C3   121.05  3.000
 EK3  C7   C4   C5   120.39  3.000
 EK3  C3   C4   C5   118.54  3.000
 EK3  H3   C3   C2   118.69  3.000
 EK3  H3   C3   C4   120.18  3.000
 EK3  C2   C3   C4   121.12  3.000
 EK3  H2   C2   C3   120.72  3.000
 EK3  H2   C2   C1   120.67  3.000
 EK3  C3   C2   C1   118.61  3.000
 EK3  N1   C7   C9   110.67  3.000
 EK3  N1   C7   C4   119.97  3.000
 EK3  C9   C7   C4   129.33  3.000
 EK3  C10  C9   C8   125.85  3.000
 EK3  C8   C9   C7   104.02  3.000
 EK3  C10  C9   C7   130.08  3.000
 EK3  H6   C8   N2   122.28  3.000
 EK3  H6   C8   C9   131.09  3.000
 EK3  N2   C8   C9   106.59  3.000
 EK3  H1   N2   N1   119.84  3.000
 EK3  H1   N2   C8   126.93  3.000
 EK3  N1   N2   C8   113.23  3.000
 EK3  N2   N1   C7   105.48  3.000
 EK3  C11  C10  C14  118.53  3.000
 EK3  C14  C10  C9   121.34  3.000
 EK3  C11  C10  C9   120.11  3.000
 EK3  H9   C14  C13  120.61  3.000
 EK3  H9   C14  C10  121.67  3.000
 EK3  C13  C14  C10  117.71  3.000
 EK3  H8   C13  N3   115.81  3.000
 EK3  H8   C13  C14  119.62  3.000
 EK3  N3   C13  C14  124.58  3.000
 EK3  C12  N3   C13  118.23  3.000
 EK3  N4   C12  C11  122.62  3.000
 EK3  C11  C12  N3   121.58  3.000
 EK3  N4   C12  N3   115.77  3.000
 EK3  H7   C11  C12  121.01  3.000
 EK3  H7   C11  C10  119.62  3.000
 EK3  C12  C11  C10  119.35  3.000
 EK3  H10  N4   C15  117.22  3.000
 EK3  H10  N4   C12  114.94  3.000
 EK3  C15  N4   C12  125.96  3.000
 EK3  H11  C15  C16  106.95  3.000
 EK3  H11  C15  C20  108.60  3.000
 EK3  C16  C15  C20  110.69  3.000
 EK3  H11  C15  N4   107.95  3.000
 EK3  C16  C15  N4   109.70  3.000
 EK3  C20  C15  N4   112.74  3.000
 EK3  H21  C20  H20  106.69  3.000
 EK3  H21  C20  C19  109.56  3.000
 EK3  H20  C20  C19  110.49  3.000
 EK3  H21  C20  C15  108.63  3.000
 EK3  H20  C20  C15  109.94  3.000
 EK3  C19  C20  C15  111.39  3.000
 EK3  H18  C19  H19  106.42  3.000
 EK3  H18  C19  C18  110.47  3.000
 EK3  H19  C19  C18  109.35  3.000
 EK3  H18  C19  C20  109.92  3.000
 EK3  H19  C19  C20  109.39  3.000
 EK3  C18  C19  C20  111.18  3.000
 EK3  H16  C18  H17  106.55  3.000
 EK3  H16  C18  C17  109.31  3.000
 EK3  H17  C18  C17  110.24  3.000
 EK3  H16  C18  C19  109.29  3.000
 EK3  H17  C18  C19  110.27  3.000
 EK3  C17  C18  C19  111.07  3.000
 EK3  H14  C17  H15  106.41  3.000
 EK3  H14  C17  C16  109.76  3.000
 EK3  H15  C17  C16  109.17  3.000
 EK3  H14  C17  C18  110.42  3.000
 EK3  H15  C17  C18  109.33  3.000
 EK3  C16  C17  C18  111.60  3.000
 EK3  H12  C16  H13  106.90  3.000
 EK3  H12  C16  C17  110.47  3.000
 EK3  H13  C16  C17  109.54  3.000
 EK3  H12  C16  C15  109.57  3.000
 EK3  H13  C16  C15  109.16  3.000
 EK3  C17  C16  C15  111.09  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
 EK3  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 EK3  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 EK3  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 EK3  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 EK3  CONST_05  C7   C4   C5   C6   180.00   0.0  0
 EK3  CONST_06  C2   C1   C6   C5     0.00   0.0  0
 EK3  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 EK3  CONST_10  C10  C9   C7   C4     0.00   0.0  0
 EK3  CONST_11  C8   C9   C7   C4   180.00   0.0  0
 EK3  CONST_12  N2   N1   C7   C4   180.00   0.0  0
 EK3  CONST_15  C7   C4   C3   C2   180.00   0.0  0
 EK3  CONST_18  N2   C8   C9   C7     0.00   0.0  0
 EK3  CONST_19  C8   N2   N1   C7     0.00   0.0  0
 EK3  CONST_20  N2   N1   C7   C9     0.00   0.0  0
 EK3  CONST_21  C12  C11  C10  C9   180.00   0.0  0
 EK3  CONST_22  C13  C14  C10  C9   180.00   0.0  0
 EK3  CONST_23  N1   N2   C8   C9     0.00   0.0  0
 EK3  CONST_24  N1   C7   C9   C8     0.00   0.0  0
 EK3  CONST_27  C10  C9   C8   N2   180.00   0.0  0
 EK3  CONST_28  C10  C9   C7   N1   180.00   0.0  0
 EK3  CONST_29  N3   C12  C11  C10    0.00   0.0  0
 EK3  CONST_30  N3   C13  C14  C10    0.00   0.0  0
 EK3  CONST_31  C12  N3   C13  C14    0.00   0.0  0
 EK3  CONST_32  C12  C11  C10  C14    0.00   0.0  0
 EK3  CONST_33  C11  C12  N3   C13    0.00   0.0  0
 EK3  CONST_34  C11  C10  C14  C13    0.00   0.0  0
 EK3  CONST_35  C5   C6   C1   F    180.00   0.0  0
 EK3  CONST_36  C3   C2   C1   F    180.00   0.0  0
 EK3  CONST_37  N4   C12  C11  C10  180.00   0.0  0
 EK3  CONST_38  N4   C12  N3   C13  180.00   0.0  0
 EK3  CONST_39  C15  N4   C12  N3   180.00   0.0  0
 EK3  CONST_40  C15  N4   C12  C11    0.00   0.0  0
 EK3  CONST_41  H4   C5   C6   C1   180.00   0.0  0
 EK3  CONST_42  H3   C3   C2   C1   180.00   0.0  0
 EK3  CONST_43  H2   C2   C1   C6   180.00   0.0  0
 EK3  CONST_44  H5   C6   C5   C4   180.00   0.0  0
 EK3  CONST_45  H6   C8   C9   C7   180.00   0.0  0
 EK3  CONST_46  H1   N2   N1   C7   180.00   0.0  0
 EK3  CONST_47  H7   C11  C10  C9     0.00   0.0  0
 EK3  CONST_48  H9   C14  C10  C9     0.00   0.0  0
 EK3  CONST_49  H8   C13  C14  C10  180.00   0.0  0
 EK3  CONST_50  H10  N4   C12  N3     0.00   0.0  0
 EK3  Var_01    C18  C19  C20  C15  -55.74  30.0  1
 EK3  Var_02    C18  C17  C16  C15   55.74  30.0  1
 EK3  Var_03    C17  C18  C19  C20   55.11  30.0  1
 EK3  Var_04    C16  C17  C18  C19  -55.28  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
 EK3  chir_01  C15  C20  C16  N4  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
 EK3  plan-1  C4   0.020
 EK3  plan-1  C7   0.020
 EK3  plan-1  C9   0.020
 EK3  plan-1  C8   0.020
 EK3  plan-1  N2   0.020
 EK3  plan-1  N1   0.020
 EK3  plan-1  C10  0.020
 EK3  plan-1  H6   0.020
 EK3  plan-1  H1   0.020
 EK3  plan-2  F    0.020
 EK3  plan-2  C1   0.020
 EK3  plan-2  C6   0.020
 EK3  plan-2  C5   0.020
 EK3  plan-2  C4   0.020
 EK3  plan-2  C3   0.020
 EK3  plan-2  C2   0.020
 EK3  plan-2  C7   0.020
 EK3  plan-2  H5   0.020
 EK3  plan-2  H4   0.020
 EK3  plan-2  H3   0.020
 EK3  plan-2  H2   0.020
 EK3  plan-3  C9   0.020
 EK3  plan-3  C10  0.020
 EK3  plan-3  C14  0.020
 EK3  plan-3  C13  0.020
 EK3  plan-3  N3   0.020
 EK3  plan-3  C12  0.020
 EK3  plan-3  C11  0.020
 EK3  plan-3  N4   0.020
 EK3  plan-3  H9   0.020
 EK3  plan-3  H8   0.020
 EK3  plan-3  H7   0.020
 EK3  plan-4  C12  0.020
 EK3  plan-4  N4   0.020
 EK3  plan-4  C15  0.020
 EK3  plan-4  H10  0.020

