# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:08:09 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-{4-[(4-imidazo[1,2-a]pyridin-3-ylpyrimidin-2-yl)amino]piperidin-1-yl}-N-methylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN1CCC(CC1)Nc2nccc(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
 JNO  JNO  2-{4-[(4-imidazo[1,2-a]pyridin-3-ylpyrimidin-2-yl)amino]piperidin-1-yl}-N-methylacetamide  ligand  50  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JNO
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
 JNO  C01   C  CH3   0  -0.512  -8.5675   1.8309  -1.4205
 JNO  N02   N  NH1   0  -0.622  -7.7920   1.0546  -0.4827
 JNO  C03   C  C     0   0.516  -6.7450   0.3075  -0.8562
 JNO  O04   O  O     0  -0.495  -6.3463   0.2586  -2.0106
 JNO  C05   C  CH2   0  -0.393  -6.1271  -0.5210   0.2610
 JNO  N06   N  NT    0  -0.409  -4.7157  -0.7251   0.0718
 JNO  C07   C  CH2   0  -0.284  -4.2203  -1.8072   0.9035
 JNO  C08   C  CH2   0  -0.454  -2.7594  -2.1040   0.6078
 JNO  C09   C  CH1   0  -0.056  -1.9057  -0.8578   0.8007
 JNO  C10   C  CH2   0  -0.436  -2.4855   0.2869  -0.0276
 JNO  C11   C  CH2   0  -0.292  -3.9565   0.4932   0.2940
 JNO  N12   N  NH1   0  -0.670  -0.5316  -1.1562   0.4610
 JNO  C13   C  CR6   0   0.594   0.5256  -0.4016   0.8125
 JNO  N14   N  N     0  -0.497   1.7005  -0.7397   0.2716
 JNO  C15   C  CR6   0   0.270   2.7682  -0.0305   0.6197
 JNO  C16   C  CR16  0  -0.420   2.6701   1.0278   1.5264
 JNO  C17   C  CR16  0  -0.011   1.4028   1.2932   2.0126
 JNO  N18   N  N     0  -0.466   0.3251   0.6086   1.6688
 JNO  C19   C  CR5   0   0.235   4.0187  -0.4838   0.0370
 JNO  N20   N  N     0  -0.578   5.1520   0.2671  -0.2047
 JNO  C21   C  CR16  0   0.028   5.3885   1.6093  -0.1192
 JNO  C22   C  CR16  0  -0.384   6.6070   2.0973  -0.4631
 JNO  C23   C  CR16  0  -0.150   7.6249   1.2274  -0.9225
 JNO  C24   C  CR16  0  -0.402   7.3770  -0.1082  -1.0446
 JNO  C25   C  CR56  0   0.530   6.1093  -0.6073  -0.6931
 JNO  N26   N  N     0  -0.466   5.6366  -1.8433  -0.7644
 JNO  C27   C  CR15  0  -0.199   4.3673  -1.7659  -0.3342
 JNO  H01   H  HCH3  0   0.237  -7.9670   2.6081  -1.8946
 JNO  H01A  H  HCH3  0   0.237  -8.9961   1.2047  -2.2036
 JNO  H01B  H  HCH3  0   0.249  -9.3806   2.3087  -0.8817
 JNO  HN02  H  HNH1  0   0.403  -8.0585   1.0742   0.4870
 JNO  H05   H  HCH2  0   0.220  -6.3667  -0.0796   1.2435
 JNO  H05A  H  HCH2  0   0.277  -6.6303  -1.4935   0.2376
 JNO  H07   H  HCH2  0   0.193  -4.3346  -1.5793   1.9784
 JNO  H07A  H  HCH2  0   0.244  -4.8183  -2.7002   0.7082
 JNO  H08   H  HCH2  0   0.247  -2.4120  -2.9098   1.2583
 JNO  H08A  H  HCH2  0   0.226  -2.6669  -2.4542  -0.4257
 JNO  H09   H  HCH1  0   0.235  -1.9393  -0.5736   1.8569
 JNO  H10   H  HCH2  0   0.241  -1.9361   1.2097   0.1680
 JNO  H10A  H  HCH2  0   0.220  -2.3733   0.0542  -1.0910
 JNO  H11   H  HCH2  0   0.245  -4.3529   1.2902  -0.3382
 JNO  H11A  H  HCH2  0   0.193  -4.0603   0.8402   1.3381
 JNO  HN12  H  HNH1  0   0.386  -0.3643  -1.8333  -0.2667
 JNO  H16   H  HCR6  0   0.272   3.5200   1.5901   1.8805
 JNO  H17   H  HCR6  0   0.270   1.2550   2.1008   2.7217
 JNO  H21   H  HCR6  0   0.312   4.5758   2.2395   0.2039
 JNO  H22   H  HCR6  0   0.285   6.7804   3.1607  -0.3892
 JNO  H23   H  HCR6  0   0.279   8.5920   1.6290  -1.1907
 JNO  H24   H  HCR6  0   0.284   8.1217  -0.8003  -1.4119
 JNO  H27   H  HCR5  0   0.270   3.7317  -2.6363  -0.2691

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
 JNO  C01  N02   single    1.443  0.020  1.443
 JNO  N02  C03   single    1.339  0.020  1.339
 JNO  C03  O04   double    1.222  0.020  1.222
 JNO  C03  C05   single    1.522  0.020  1.522
 JNO  C05  N06   single    1.439  0.020  1.439
 JNO  N06  C07   single    1.452  0.020  1.452
 JNO  N06  C11   single    1.453  0.020  1.453
 JNO  C07  C08   single    1.520  0.020  1.520
 JNO  C08  C09   single    1.523  0.020  1.523
 JNO  C09  C10   single    1.527  0.020  1.527
 JNO  C09  N12   single    1.447  0.020  1.447
 JNO  C10  C11   single    1.520  0.020  1.520
 JNO  N12  C13   single    1.346  0.020  1.346
 JNO  C13  N14   aromatic  1.337  0.020  1.337
 JNO  C13  N18   aromatic  1.339  0.020  1.339
 JNO  N14  C15   aromatic  1.328  0.020  1.328
 JNO  C15  C16   aromatic  1.397  0.020  1.397
 JNO  C15  C19   single    1.452  0.020  1.452
 JNO  C16  C17   aromatic  1.383  0.020  1.383
 JNO  C17  N18   aromatic  1.322  0.020  1.322
 JNO  C19  N20   aromatic  1.381  0.020  1.381
 JNO  C19  C27   aromatic  1.380  0.020  1.380
 JNO  N20  C21   aromatic  1.366  0.020  1.366
 JNO  N20  C25   aromatic  1.385  0.020  1.385
 JNO  C21  C22   aromatic  1.357  0.020  1.357
 JNO  C22  C23   aromatic  1.416  0.020  1.416
 JNO  C23  C24   aromatic  1.364  0.020  1.364
 JNO  C24  C25   aromatic  1.407  0.020  1.407
 JNO  C25  N26   aromatic  1.325  0.020  1.325
 JNO  N26  C27   aromatic  1.342  0.020  1.342
 JNO  C01  H01   single    0.970  0.020  1.090
 JNO  C01  H01A  single    0.970  0.020  1.090
 JNO  C01  H01B  single    0.970  0.020  1.090
 JNO  N02  HN02  single    0.860  0.020  1.020
 JNO  C05  H05   single    0.970  0.020  1.090
 JNO  C05  H05A  single    0.970  0.020  1.090
 JNO  C07  H07   single    0.970  0.020  1.090
 JNO  C07  H07A  single    0.970  0.020  1.090
 JNO  C08  H08   single    0.970  0.020  1.090
 JNO  C08  H08A  single    0.970  0.020  1.090
 JNO  C09  H09   single    0.970  0.020  1.090
 JNO  C10  H10   single    0.970  0.020  1.090
 JNO  C10  H10A  single    0.970  0.020  1.090
 JNO  C11  H11   single    0.970  0.020  1.090
 JNO  C11  H11A  single    0.970  0.020  1.090
 JNO  N12  HN12  single    0.860  0.020  1.020
 JNO  C16  H16   single    0.930  0.020  1.080
 JNO  C17  H17   single    0.930  0.020  1.080
 JNO  C21  H21   single    0.930  0.020  1.080
 JNO  C22  H22   single    0.930  0.020  1.080
 JNO  C23  H23   single    0.930  0.020  1.080
 JNO  C24  H24   single    0.930  0.020  1.080
 JNO  C27  H27   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
 JNO  H01B  C01  H01A  108.34  3.000
 JNO  H01B  C01  H01   108.32  3.000
 JNO  H01A  C01  H01   108.27  3.000
 JNO  H01B  C01  N02   108.46  3.000
 JNO  H01A  C01  N02   111.65  3.000
 JNO  H01   C01  N02   111.71  3.000
 JNO  HN02  N02  C03   119.14  3.000
 JNO  HN02  N02  C01   118.26  3.000
 JNO  C03   N02  C01   122.60  3.000
 JNO  C05   C03  O04   122.63  3.000
 JNO  C05   C03  N02   114.60  3.000
 JNO  O04   C03  N02   122.73  3.000
 JNO  H05A  C05  H05   105.93  3.000
 JNO  H05A  C05  N06   108.79  3.000
 JNO  H05   C05  N06   112.77  3.000
 JNO  H05A  C05  C03   106.32  3.000
 JNO  H05   C05  C03   110.35  3.000
 JNO  N06   C05  C03   112.27  3.000
 JNO  C11   N06  C07   111.05  3.000
 JNO  C11   N06  C05   111.94  3.000
 JNO  C07   N06  C05   111.41  3.000
 JNO  H07A  C07  H07   106.62  3.000
 JNO  H07A  C07  C08   109.38  3.000
 JNO  H07   C07  C08   109.21  3.000
 JNO  H07A  C07  N06   108.67  3.000
 JNO  H07   C07  N06   111.61  3.000
 JNO  C08   C07  N06   111.23  3.000
 JNO  H08A  C08  H08   107.41  3.000
 JNO  H08A  C08  C09   109.50  3.000
 JNO  H08   C08  C09   110.48  3.000
 JNO  H08A  C08  C07   109.10  3.000
 JNO  H08   C08  C07   109.51  3.000
 JNO  C09   C08  C07   110.76  3.000
 JNO  H09   C09  N12   108.03  3.000
 JNO  H09   C09  C10   108.49  3.000
 JNO  N12   C09  C10   112.82  3.000
 JNO  H09   C09  C08   108.51  3.000
 JNO  N12   C09  C08   109.51  3.000
 JNO  C10   C09  C08   109.38  3.000
 JNO  H10A  C10  H10   107.59  3.000
 JNO  H10A  C10  C11   109.50  3.000
 JNO  H10   C10  C11   109.54  3.000
 JNO  H10A  C10  C09   109.19  3.000
 JNO  H10   C10  C09   110.20  3.000
 JNO  C11   C10  C09   110.76  3.000
 JNO  H11A  C11  H11   106.49  3.000
 JNO  H11A  C11  C10   109.48  3.000
 JNO  H11   C11  C10   109.14  3.000
 JNO  H11A  C11  N06   111.03  3.000
 JNO  H11   C11  N06   109.50  3.000
 JNO  C10   C11  N06   111.08  3.000
 JNO  HN12  N12  C13   115.78  3.000
 JNO  HN12  N12  C09   117.76  3.000
 JNO  C13   N12  C09   124.70  3.000
 JNO  N18   C13  N14   125.51  3.000
 JNO  N18   C13  N12   118.19  3.000
 JNO  N14   C13  N12   116.30  3.000
 JNO  C15   N14  C13   117.74  3.000
 JNO  C19   C15  C16   123.87  3.000
 JNO  C19   C15  N14   114.86  3.000
 JNO  C16   C15  N14   121.20  3.000
 JNO  H16   C16  C17   120.42  3.000
 JNO  H16   C16  C15   123.54  3.000
 JNO  C17   C16  C15   115.97  3.000
 JNO  H17   C17  N18   116.38  3.000
 JNO  H17   C17  C16   119.84  3.000
 JNO  N18   C17  C16   123.78  3.000
 JNO  C17   N18  C13   115.77  3.000
 JNO  C27   C19  N20   104.53  3.000
 JNO  C27   C19  C15   128.00  3.000
 JNO  N20   C19  C15   127.39  3.000
 JNO  C25   N20  C21   121.52  3.000
 JNO  C25   N20  C19   106.60  3.000
 JNO  C21   N20  C19   131.73  3.000
 JNO  H21   C21  C22   122.87  3.000
 JNO  H21   C21  N20   117.57  3.000
 JNO  C22   C21  N20   119.55  3.000
 JNO  H22   C22  C23   120.78  3.000
 JNO  H22   C22  C21   118.75  3.000
 JNO  C23   C22  C21   120.46  3.000
 JNO  H23   C23  C24   120.28  3.000
 JNO  H23   C23  C22   119.70  3.000
 JNO  C24   C23  C22   120.01  3.000
 JNO  H24   C24  C25   118.59  3.000
 JNO  H24   C24  C23   122.15  3.000
 JNO  C25   C24  C23   119.26  3.000
 JNO  N26   C25  C24   129.70  3.000
 JNO  N26   C25  N20   111.17  3.000
 JNO  C24   C25  N20   119.13  3.000
 JNO  C27   N26  C25   105.44  3.000
 JNO  H27   C27  N26   121.97  3.000
 JNO  H27   C27  C19   125.74  3.000
 JNO  N26   C27  C19   112.26  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
 JNO  CONST_01  C16   C15  N14  C13     0.00   0.0  0
 JNO  CONST_02  C19   C15  N14  C13   180.00   0.0  0
 JNO  CONST_03  C16   C17  N18  C13     0.00   0.0  0
 JNO  CONST_04  C17   N18  C13  N14     0.00   0.0  0
 JNO  CONST_05  C17   C16  C15  N14     0.00   0.0  0
 JNO  CONST_08  N18   C13  N14  C15     0.00   0.0  0
 JNO  CONST_09  N18   C17  C16  C15     0.00   0.0  0
 JNO  CONST_10  C21   N20  C19  C15     0.00   0.0  0
 JNO  CONST_11  C25   N20  C19  C15   180.00   0.0  0
 JNO  CONST_12  N26   C27  C19  C15   180.00   0.0  0
 JNO  CONST_15  C19   C15  C16  C17   180.00   0.0  0
 JNO  CONST_16  C22   C21  N20  C19   180.00   0.0  0
 JNO  CONST_17  C24   C25  N20  C19   180.00   0.0  0
 JNO  CONST_18  N26   C25  N20  C19     0.00   0.0  0
 JNO  CONST_19  C25   N26  C27  C19     0.00   0.0  0
 JNO  CONST_20  N26   C27  C19  N20     0.00   0.0  0
 JNO  CONST_21  C23   C22  C21  N20     0.00   0.0  0
 JNO  CONST_22  C23   C24  C25  N20     0.00   0.0  0
 JNO  CONST_23  C27   N26  C25  N20     0.00   0.0  0
 JNO  CONST_24  C27   C19  N20  C21   180.00   0.0  0
 JNO  CONST_25  C24   C25  N20  C21     0.00   0.0  0
 JNO  CONST_26  N26   C25  N20  C21   180.00   0.0  0
 JNO  CONST_27  C24   C23  C22  C21     0.00   0.0  0
 JNO  CONST_28  C25   N20  C21  C22     0.00   0.0  0
 JNO  CONST_29  C25   C24  C23  C22     0.00   0.0  0
 JNO  CONST_30  N26   C25  C24  C23   180.00   0.0  0
 JNO  CONST_31  C27   N26  C25  C24   180.00   0.0  0
 JNO  CONST_32  C27   C19  N20  C25     0.00   0.0  0
 JNO  CONST_33  C15   N14  C13  N12   180.00   0.0  0
 JNO  CONST_34  C17   N18  C13  N12   180.00   0.0  0
 JNO  CONST_35  N14   C13  N12  C09   180.00   0.0  0
 JNO  CONST_36  N18   C13  N12  C09     0.00   0.0  0
 JNO  CONST_37  H17   C17  N18  C13   180.00   0.0  0
 JNO  CONST_38  H16   C16  C15  N14   180.00   0.0  0
 JNO  CONST_39  H27   C27  C19  C15     0.00   0.0  0
 JNO  CONST_40  H21   C21  N20  C19     0.00   0.0  0
 JNO  CONST_41  H22   C22  C21  N20   180.00   0.0  0
 JNO  CONST_42  H24   C24  C25  N20   180.00   0.0  0
 JNO  CONST_43  H23   C23  C22  C21   180.00   0.0  0
 JNO  CONST_44  HN12  N12  C13  N14     0.00   0.0  0
 JNO  CONST_45  O04   C03  N02  C01     0.00   0.0  0
 JNO  CONST_46  C05   C03  N02  C01   180.00   0.0  0
 JNO  CONST_47  HN02  N02  C03  O04   180.00   0.0  0
 JNO  Var_01    C09   C08  C07  N06    57.03  30.0  1
 JNO  Var_02    C09   C10  C11  N06   -57.05  30.0  1
 JNO  Var_03    C10   C11  N06  C07    59.71  30.0  1
 JNO  Var_04    C11   N06  C07  C08   -59.70  30.0  1
 JNO  Var_05    C07   N06  C05  C03  -163.57  30.0  3
 JNO  Var_06    N06   C05  C03  N02  -149.50  30.0  3
 JNO  Var_07    H01   C01  N02  C03   -63.16  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
 JNO  chir_01  C09  C08  C10  N12  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
 JNO  plan-1  N12   0.020
 JNO  plan-1  C13   0.020
 JNO  plan-1  N14   0.020
 JNO  plan-1  C15   0.020
 JNO  plan-1  C16   0.020
 JNO  plan-1  C17   0.020
 JNO  plan-1  N18   0.020
 JNO  plan-1  C19   0.020
 JNO  plan-1  H16   0.020
 JNO  plan-1  H17   0.020
 JNO  plan-2  C15   0.020
 JNO  plan-2  C19   0.020
 JNO  plan-2  N20   0.020
 JNO  plan-2  C21   0.020
 JNO  plan-2  C22   0.020
 JNO  plan-2  C23   0.020
 JNO  plan-2  C24   0.020
 JNO  plan-2  C25   0.020
 JNO  plan-2  N26   0.020
 JNO  plan-2  C27   0.020
 JNO  plan-2  H21   0.020
 JNO  plan-2  H22   0.020
 JNO  plan-2  H23   0.020
 JNO  plan-2  H24   0.020
 JNO  plan-2  H27   0.020
 JNO  plan-3  C09   0.020
 JNO  plan-3  N12   0.020
 JNO  plan-3  C13   0.020
 JNO  plan-3  HN12  0.020
 JNO  plan-4  C01   0.020
 JNO  plan-4  N02   0.020
 JNO  plan-4  C03   0.020
 JNO  plan-4  O04   0.020
 JNO  plan-4  C05   0.020
 JNO  plan-4  HN02  0.020

