# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:03:11 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-cyclohexyl-4-imidazo[1,2-a]pyridin-3-yl-N-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1CCCCC1)c2nccc(n2)c3cnc4ccccn34
#
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
 JNF  JNF  N-cyclohexyl-4-imidazo[1,2-a]pyridin-3-yl-N-methylpyrimidin-2-amine  ligand  44  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 OK
;

data_comp_JNF
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
 JNF  C01   C  CH3   0  -0.528  -2.1026   1.9239   0.2740
 JNF  N02   N  NT    0  -0.495  -2.2839   0.4961   0.1114
 JNF  C03   C  CR6   0   0.634  -1.1947  -0.2793  -0.0812
 JNF  N04   N  N     0  -0.507  -0.0101   0.3383  -0.0704
 JNF  C05   C  CR6   0   0.278   1.0827  -0.3924  -0.2722
 JNF  C06   C  CR5   0   0.235   2.3195   0.3689  -0.2876
 JNF  N07   N  N     0  -0.581   3.5988  -0.0898  -0.0397
 JNF  C08   C  CR56  0   0.529   4.4500   0.9853  -0.2410
 JNF  C09   C  CR16  0  -0.401   5.8326   0.8114  -0.0488
 JNF  C10   C  CR16  0  -0.151   6.3022  -0.4029   0.3572
 JNF  C11   C  CR16  0  -0.384   5.3984  -1.4649   0.5988
 JNF  C12   C  CR16  0   0.027   4.0665  -1.2937   0.4047
 JNF  N13   N  N     0  -0.465   3.7762   2.0702  -0.5949
 JNF  C14   C  CR15  0  -0.196   2.4865   1.7000  -0.6118
 JNF  C15   C  CR16  0  -0.433   1.0019  -1.7647  -0.5059
 JNF  C16   C  CR16  0  -0.009  -0.2732  -2.3058  -0.4739
 JNF  N17   N  N     0  -0.475  -1.3656  -1.6007  -0.2573
 JNF  C18   C  CH1   0  -0.097  -3.6366  -0.0475   0.0758
 JNF  C19   C  CH2   0  -0.423  -4.4413   0.4984  -1.1046
 JNF  C20   C  CH2   0  -0.436  -5.8359  -0.1222  -1.1438
 JNF  C21   C  CH2   0  -0.431  -6.5764   0.0845   0.1729
 JNF  C22   C  CH2   0  -0.434  -5.7690  -0.4596   1.3464
 JNF  C23   C  CH2   0  -0.426  -4.3756   0.1633   1.3976
 JNF  H01   H  HCH3  0   0.237  -1.7195   2.3975  -0.6322
 JNF  H01A  H  HCH3  0   0.244  -3.0576   2.3830   0.5137
 JNF  H01B  H  HCH3  0   0.244  -1.4110   2.1507   1.0845
 JNF  H09   H  HCR6  0   0.284   6.4885   1.6524  -0.2240
 JNF  H10   H  HCR6  0   0.279   7.3615  -0.5561   0.5092
 JNF  H11   H  HCR6  0   0.285   5.7528  -2.4224   0.9505
 JNF  H12   H  HCR6  0   0.311   3.3441  -2.0668   0.6080
 JNF  H14   H  HCR5  0   0.269   1.6975   2.3866  -0.8796
 JNF  H15   H  HCR6  0   0.268   1.8502  -2.3844  -0.7482
 JNF  H16   H  HCR6  0   0.268  -0.4125  -3.3693  -0.6385
 JNF  H18   H  HCH1  0   0.256  -3.5269  -1.1216  -0.0706
 JNF  H19   H  HCH2  0   0.215  -4.5361   1.5868  -1.0293
 JNF  H19A  H  HCH2  0   0.233  -3.9081   0.2889  -2.0353
 JNF  H20   H  HCH2  0   0.231  -6.4059   0.3031  -1.9730
 JNF  H20A  H  HCH2  0   0.213  -5.7487  -1.1952  -1.3456
 JNF  H21   H  HCH2  0   0.210  -6.7555   1.1547   0.3241
 JNF  H21A  H  HCH2  0   0.229  -7.5582  -0.3933   0.1333
 JNF  H22   H  HCH2  0   0.231  -6.2902  -0.2710   2.2876
 JNF  H22A  H  HCH2  0   0.213  -5.6787  -1.5472   1.2535
 JNF  H23   H  HCH2  0   0.234  -3.7936  -0.2728   2.2136
 JNF  H23A  H  HCH2  0   0.215  -4.4749   1.2323   1.6125

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
 JNF  C01  N02   single    1.448  0.020  1.448
 JNF  N02  C03   single    1.351  0.020  1.351
 JNF  N02  C18   single    1.458  0.020  1.458
 JNF  C03  N04   aromatic  1.336  0.020  1.336
 JNF  C03  N17   aromatic  1.344  0.020  1.344
 JNF  N04  C05   aromatic  1.330  0.020  1.330
 JNF  C05  C06   single    1.452  0.020  1.452
 JNF  C05  C15   aromatic  1.394  0.020  1.394
 JNF  C06  N07   aromatic  1.381  0.020  1.381
 JNF  C06  C14   aromatic  1.380  0.020  1.380
 JNF  N07  C08   aromatic  1.386  0.020  1.386
 JNF  N07  C12   aromatic  1.366  0.020  1.366
 JNF  C08  C09   aromatic  1.407  0.020  1.407
 JNF  C08  N13   aromatic  1.325  0.020  1.325
 JNF  C09  C10   aromatic  1.364  0.020  1.364
 JNF  C10  C11   aromatic  1.415  0.020  1.415
 JNF  C11  C12   aromatic  1.357  0.020  1.357
 JNF  N13  C14   aromatic  1.342  0.020  1.342
 JNF  C15  C16   aromatic  1.386  0.020  1.386
 JNF  C16  N17   aromatic  1.318  0.020  1.318
 JNF  C18  C19   single    1.529  0.020  1.529
 JNF  C18  C23   single    1.529  0.020  1.529
 JNF  C19  C20   single    1.527  0.020  1.527
 JNF  C20  C21   single    1.525  0.020  1.525
 JNF  C21  C22   single    1.525  0.020  1.525
 JNF  C22  C23   single    1.527  0.020  1.527
 JNF  C01  H01   single    0.970  0.020  1.090
 JNF  C01  H01A  single    0.970  0.020  1.090
 JNF  C01  H01B  single    0.970  0.020  1.090
 JNF  C09  H09   single    0.930  0.020  1.080
 JNF  C10  H10   single    0.930  0.020  1.080
 JNF  C11  H11   single    0.930  0.020  1.080
 JNF  C12  H12   single    0.930  0.020  1.080
 JNF  C14  H14   single    0.930  0.020  1.080
 JNF  C15  H15   single    0.930  0.020  1.080
 JNF  C16  H16   single    0.930  0.020  1.080
 JNF  C18  H18   single    0.970  0.020  1.090
 JNF  C19  H19   single    0.970  0.020  1.090
 JNF  C19  H19A  single    0.970  0.020  1.090
 JNF  C20  H20   single    0.970  0.020  1.090
 JNF  C20  H20A  single    0.970  0.020  1.090
 JNF  C21  H21   single    0.970  0.020  1.090
 JNF  C21  H21A  single    0.970  0.020  1.090
 JNF  C22  H22   single    0.970  0.020  1.090
 JNF  C22  H22A  single    0.970  0.020  1.090
 JNF  C23  H23   single    0.970  0.020  1.090
 JNF  C23  H23A  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
 JNF  H01B  C01  H01A  107.81  3.000
 JNF  H01B  C01  H01   107.73  3.000
 JNF  H01A  C01  H01   107.95  3.000
 JNF  H01B  C01  N02   111.60  3.000
 JNF  H01A  C01  N02   109.35  3.000
 JNF  H01   C01  N02   112.23  3.000
 JNF  C18   N02  C03   122.04  3.000
 JNF  C18   N02  C01   119.10  3.000
 JNF  C03   N02  C01   118.75  3.000
 JNF  N17   C03  N04   124.63  3.000
 JNF  N17   C03  N02   118.72  3.000
 JNF  N04   C03  N02   116.65  3.000
 JNF  C05   N04  C03   118.25  3.000
 JNF  C15   C05  C06   124.29  3.000
 JNF  C15   C05  N04   121.23  3.000
 JNF  C06   C05  N04   114.41  3.000
 JNF  C14   C06  N07   104.50  3.000
 JNF  C14   C06  C05   127.66  3.000
 JNF  N07   C06  C05   127.78  3.000
 JNF  C12   N07  C08   121.38  3.000
 JNF  C12   N07  C06   131.92  3.000
 JNF  C08   N07  C06   106.57  3.000
 JNF  N13   C08  C09   129.60  3.000
 JNF  N13   C08  N07   111.20  3.000
 JNF  C09   C08  N07   119.20  3.000
 JNF  H09   C09  C10   122.15  3.000
 JNF  H09   C09  C08   118.57  3.000
 JNF  C10   C09  C08   119.29  3.000
 JNF  H10   C10  C11   119.70  3.000
 JNF  H10   C10  C09   120.36  3.000
 JNF  C11   C10  C09   119.94  3.000
 JNF  H11   C11  C12   118.73  3.000
 JNF  H11   C11  C10   120.76  3.000
 JNF  C12   C11  C10   120.51  3.000
 JNF  H12   C12  C11   122.72  3.000
 JNF  H12   C12  N07   117.66  3.000
 JNF  C11   C12  N07   119.60  3.000
 JNF  C14   N13  C08   105.43  3.000
 JNF  H14   C14  N13   122.01  3.000
 JNF  H14   C14  C06   125.68  3.000
 JNF  N13   C14  C06   112.29  3.000
 JNF  H15   C15  C16   120.32  3.000
 JNF  H15   C15  C05   123.90  3.000
 JNF  C16   C15  C05   115.71  3.000
 JNF  H16   C16  N17   116.28  3.000
 JNF  H16   C16  C15   119.82  3.000
 JNF  N17   C16  C15   123.89  3.000
 JNF  C16   N17  C03   116.24  3.000
 JNF  H18   C18  C23   107.50  3.000
 JNF  H18   C18  C19   107.52  3.000
 JNF  C23   C18  C19   111.33  3.000
 JNF  H18   C18  N02   106.10  3.000
 JNF  C23   C18  N02   112.08  3.000
 JNF  C19   C18  N02   111.95  3.000
 JNF  H19A  C19  H19   106.93  3.000
 JNF  H19A  C19  C20   110.23  3.000
 JNF  H19   C19  C20   109.06  3.000
 JNF  H19A  C19  C18   109.40  3.000
 JNF  H19   C19  C18   110.32  3.000
 JNF  C20   C19  C18   110.81  3.000
 JNF  H20A  C20  H20   106.44  3.000
 JNF  H20A  C20  C21   109.31  3.000
 JNF  H20   C20  C21   110.44  3.000
 JNF  H20A  C20  C19   109.28  3.000
 JNF  H20   C20  C19   109.74  3.000
 JNF  C21   C20  C19   111.49  3.000
 JNF  H21A  C21  H21   106.58  3.000
 JNF  H21A  C21  C22   110.34  3.000
 JNF  H21   C21  C22   109.20  3.000
 JNF  H21A  C21  C20   110.23  3.000
 JNF  H21   C21  C20   109.33  3.000
 JNF  C22   C21  C20   111.04  3.000
 JNF  H22A  C22  H22   106.49  3.000
 JNF  H22A  C22  C23   109.42  3.000
 JNF  H22   C22  C23   109.64  3.000
 JNF  H22A  C22  C21   109.44  3.000
 JNF  H22   C22  C21   110.42  3.000
 JNF  C23   C22  C21   111.31  3.000
 JNF  H23A  C23  H23   106.93  3.000
 JNF  H23A  C23  C22   108.79  3.000
 JNF  H23   C23  C22   110.38  3.000
 JNF  H23A  C23  C18   110.37  3.000
 JNF  H23   C23  C18   109.45  3.000
 JNF  C22   C23  C18   110.84  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
 JNF  CONST_01  C06  C05  N04  C03  180.00   0.0  0
 JNF  CONST_02  C15  C05  N04  C03    0.00   0.0  0
 JNF  CONST_03  C15  C16  N17  C03    0.00   0.0  0
 JNF  CONST_04  C16  N17  C03  N04    0.00   0.0  0
 JNF  CONST_07  C16  C15  C05  N04    0.00   0.0  0
 JNF  CONST_08  N17  C03  N04  C05    0.00   0.0  0
 JNF  CONST_09  C08  N07  C06  C05  180.00   0.0  0
 JNF  CONST_10  C12  N07  C06  C05    0.00   0.0  0
 JNF  CONST_11  N13  C14  C06  C05  180.00   0.0  0
 JNF  CONST_12  N17  C16  C15  C05    0.00   0.0  0
 JNF  CONST_13  C16  C15  C05  C06  180.00   0.0  0
 JNF  CONST_14  C09  C08  N07  C06  180.00   0.0  0
 JNF  CONST_15  N13  C08  N07  C06    0.00   0.0  0
 JNF  CONST_16  C11  C12  N07  C06  180.00   0.0  0
 JNF  CONST_17  C08  N13  C14  C06    0.00   0.0  0
 JNF  CONST_19  N13  C14  C06  N07    0.00   0.0  0
 JNF  CONST_20  C10  C09  C08  N07    0.00   0.0  0
 JNF  CONST_21  C14  N13  C08  N07    0.00   0.0  0
 JNF  CONST_22  C10  C11  C12  N07    0.00   0.0  0
 JNF  CONST_23  C14  C06  N07  C08    0.00   0.0  0
 JNF  CONST_24  C11  C12  N07  C08    0.00   0.0  0
 JNF  CONST_25  C11  C10  C09  C08    0.00   0.0  0
 JNF  CONST_26  C12  N07  C08  C09    0.00   0.0  0
 JNF  CONST_27  C14  N13  C08  C09  180.00   0.0  0
 JNF  CONST_28  C12  C11  C10  C09    0.00   0.0  0
 JNF  CONST_29  N13  C08  C09  C10  180.00   0.0  0
 JNF  CONST_30  C14  C06  N07  C12  180.00   0.0  0
 JNF  CONST_31  N13  C08  N07  C12  180.00   0.0  0
 JNF  CONST_33  C05  N04  C03  N02  180.00   0.0  0
 JNF  CONST_34  C16  N17  C03  N02  180.00   0.0  0
 JNF  CONST_35  C18  N02  C03  N04  180.00   0.0  0
 JNF  CONST_36  C18  N02  C03  N17    0.00   0.0  0
 JNF  CONST_37  H16  C16  N17  C03  180.00   0.0  0
 JNF  CONST_38  H15  C15  C05  N04  180.00   0.0  0
 JNF  CONST_39  H14  C14  C06  C05    0.00   0.0  0
 JNF  CONST_40  H12  C12  N07  C06    0.00   0.0  0
 JNF  CONST_41  H09  C09  C08  N07  180.00   0.0  0
 JNF  CONST_42  H11  C11  C12  N07  180.00   0.0  0
 JNF  CONST_43  H10  C10  C09  C08  180.00   0.0  0
 JNF  CONST_44  N04  C03  N02  C01    0.00   0.0  0
 JNF  CONST_45  N17  C03  N02  C01  180.00   0.0  0
 JNF  Var_01    C21  C20  C19  C18   55.49  30.0  1
 JNF  Var_02    C21  C22  C23  C18  -55.79  30.0  1
 JNF  Var_03    C22  C21  C20  C19  -55.66  30.0  1
 JNF  Var_04    C23  C22  C21  C20   55.75  30.0  1
 JNF  Var_05    H01  C01  N02  C03   65.69  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
 JNF  chir_01  C18  N02  C19  C23  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
 JNF  plan-1  N02  0.020
 JNF  plan-1  C03  0.020
 JNF  plan-1  N04  0.020
 JNF  plan-1  C05  0.020
 JNF  plan-1  C06  0.020
 JNF  plan-1  C15  0.020
 JNF  plan-1  C16  0.020
 JNF  plan-1  N17  0.020
 JNF  plan-1  H15  0.020
 JNF  plan-1  H16  0.020
 JNF  plan-2  C05  0.020
 JNF  plan-2  C06  0.020
 JNF  plan-2  N07  0.020
 JNF  plan-2  C08  0.020
 JNF  plan-2  C09  0.020
 JNF  plan-2  C10  0.020
 JNF  plan-2  C11  0.020
 JNF  plan-2  C12  0.020
 JNF  plan-2  N13  0.020
 JNF  plan-2  C14  0.020
 JNF  plan-2  H09  0.020
 JNF  plan-2  H10  0.020
 JNF  plan-2  H11  0.020
 JNF  plan-2  H12  0.020
 JNF  plan-2  H14  0.020
 JNF  plan-3  C01  0.020
 JNF  plan-3  N02  0.020
 JNF  plan-3  C03  0.020
 JNF  plan-3  C18  0.020

