# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:34:21 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-(5-fluoro-2-{methyl[3-(methylamino)propyl]amino}pyrimidin-4-yl)-N-[(imidazo[1,2-a]pyridin-3-yl)methyl]azetidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCN(C)c1ncc(F)c(n1)N2CC(C2)C(=O)NCc3cnc4ccccn34
#
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
 CJ4  CJ4  1-(5-fluoro-2-{methyl[3-(methylamino)propyl]amino}pyrimidin-4-yl)-N-[(imidazo[1,2-a]pyridin-3-yl)methyl]azetidine-3-carboxamide  ligand  58  31  .  2022-07-24  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_CJ4
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
 CJ4  C01  C  CH3   0  -0.518   -9.4827   3.3695  -1.4151
 CJ4  C03  C  CH2   0  -0.257   -7.5871   2.5353  -0.1825
 CJ4  C04  C  CH2   0  -0.449   -6.1091   2.1852  -0.2485
 CJ4  C05  C  CH2   0  -0.295   -5.5994   1.6567   1.0870
 CJ4  C07  C  CH3   0  -0.510   -3.2384   2.3729   1.4652
 CJ4  C08  C  CR6   0   0.631   -3.7357   0.1499   0.6405
 CJ4  C10  C  CR16  0  -0.166   -4.1503  -1.8992  -0.2200
 CJ4  C11  C  CR6   0   0.303   -2.8164  -2.1869  -0.2188
 CJ4  C13  C  CR6   0   0.408   -1.9290  -1.2043   0.2553
 CJ4  C16  C  C     0  -0.232    0.3212  -2.3350  -0.2569
 CJ4  C17  C  C     0  -0.490    1.4809  -1.4203   0.2071
 CJ4  C18  C  C     0  -0.222    0.4086  -0.4017   0.6596
 CJ4  C19  C  C     0   0.602    2.3905  -0.9434  -0.8974
 CJ4  C22  C  CH2   0  -0.363    4.7131  -0.9049  -1.7104
 CJ4  C23  C  CR5   0   0.245    6.0275  -0.7131  -1.0530
 CJ4  C24  C  CR15  0  -0.229    7.1890  -1.4400  -1.1052
 CJ4  C26  C  CR56  0   0.522    7.6155   0.1593   0.2283
 CJ4  C27  C  CR16  0  -0.396    8.1534   1.0995   1.1310
 CJ4  C28  C  CR16  0  -0.155    7.3726   2.1314   1.5611
 CJ4  C29  C  CR16  0  -0.390    6.0353   2.2582   1.1049
 CJ4  C30  C  CR16  0   0.033    5.5200   1.3511   0.2382
 CJ4  F12  F  F     0  -0.315   -2.3555  -3.3823  -0.6448
 CJ4  N02  N  NH1   0  -0.591   -8.0820   3.0043  -1.4617
 CJ4  N06  N  NT    0  -0.485   -4.1845   1.3452   1.0882
 CJ4  N09  N  N     0  -0.490   -4.6377  -0.7340   0.2008
 CJ4  N14  N  N     0  -0.515   -2.4137  -0.0435   0.6810
 CJ4  N15  N  N     0  -0.481   -0.6067  -1.3812   0.3294
 CJ4  N21  N  NH1   0  -0.647    3.6884  -1.2483  -0.7408
 CJ4  N25  N  N     0  -0.478    8.1599  -0.9084  -0.3273
 CJ4  N31  N  N     0  -0.551    6.3042   0.3200  -0.1889
 CJ4  O20  O  O     0  -0.491    1.9578  -0.3252  -1.8594
 CJ4  H1   H  HCH3  0   0.220  -10.0903   2.4856  -1.2109
 CJ4  H2   H  HCH3  0   0.191   -9.7289   4.1174  -0.6475
 CJ4  H3   H  HCH3  0   0.230   -9.7958   3.7672  -2.3806
 CJ4  H4   H  HCH2  0   0.214   -8.1578   1.6431   0.0973
 CJ4  H5   H  HCH2  0   0.184   -7.7541   3.2674   0.6259
 CJ4  H6   H  HCH2  0   0.228   -5.9459   1.4317  -1.0225
 CJ4  H7   H  HCH2  0   0.221   -5.5335   3.0725  -0.5339
 CJ4  H8   H  HCH2  0   0.242   -5.7736   2.3972   1.8703
 CJ4  H9   H  HCH2  0   0.243   -6.1627   0.7669   1.3695
 CJ4  H10  H  HCH3  0   0.232   -2.7033   2.1221   2.3835
 CJ4  H11  H  HCH3  0   0.235   -2.4952   2.5487   0.6872
 CJ4  H12  H  HCH3  0   0.241   -3.7797   3.3011   1.6320
 CJ4  H13  H  HCR6  0   0.276   -4.8628  -2.6374  -0.5763
 CJ4  H14  H  H     0   0.251    0.2302  -2.4322  -1.3407
 CJ4  H15  H  H     0   0.259    0.3100  -3.3260   0.1957
 CJ4  H16  H  H     0   0.295    2.0346  -1.8462   1.0430
 CJ4  H17  H  H     0   0.254    0.4433  -0.1218   1.7128
 CJ4  H18  H  H     0   0.245    0.3582   0.5033   0.0505
 CJ4  H19  H  HCH2  0   0.274    4.3977  -0.0004  -2.2346
 CJ4  H20  H  HCH2  0   0.283    4.8168  -1.6878  -2.4659
 CJ4  H21  H  HCR5  0   0.264    7.3513  -2.3360  -1.6871
 CJ4  H22  H  HCR6  0   0.280    9.1757   0.9778   1.4606
 CJ4  H23  H  HCR6  0   0.275    7.7702   2.8608   2.2532
 CJ4  H24  H  HCR6  0   0.281    5.4125   3.0730   1.4435
 CJ4  H25  H  HCR6  0   0.305    4.5119   1.3982  -0.1442
 CJ4  H26  H  HNH1  0   0.340   -7.5436   3.8157  -1.7401
 CJ4  H28  H  HNH1  0   0.409    3.9620  -1.8246   0.0394

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
 CJ4  C05  C04  single    1.524  0.020  1.524
 CJ4  C05  N06  single    1.449  0.020  1.449
 CJ4  C04  C03  single    1.520  0.020  1.520
 CJ4  N02  C03  single    1.450  0.020  1.450
 CJ4  N02  C01  single    1.448  0.020  1.448
 CJ4  N06  C07  single    1.447  0.020  1.447
 CJ4  N06  C08  single    1.353  0.020  1.353
 CJ4  N09  C08  aromatic  1.337  0.020  1.337
 CJ4  N09  C10  aromatic  1.331  0.020  1.331
 CJ4  C08  N14  aromatic  1.337  0.020  1.337
 CJ4  C10  C11  aromatic  1.365  0.020  1.365
 CJ4  N14  C13  aromatic  1.328  0.020  1.328
 CJ4  C11  C13  aromatic  1.406  0.020  1.406
 CJ4  C11  F12  single    1.350  0.020  1.350
 CJ4  C13  N15  single    1.336  0.020  1.336
 CJ4  N15  C18  single    1.449  0.020  1.449
 CJ4  N15  C16  single    1.454  0.020  1.454
 CJ4  C18  C17  single    1.547  0.020  1.547
 CJ4  C16  C17  single    1.548  0.020  1.548
 CJ4  C17  C19  single    1.508  0.020  1.508
 CJ4  C29  C28  aromatic  1.419  0.020  1.419
 CJ4  C29  C30  aromatic  1.356  0.020  1.356
 CJ4  C28  C27  aromatic  1.364  0.020  1.364
 CJ4  C30  N31  aromatic  1.364  0.020  1.364
 CJ4  C19  O20  double    1.223  0.020  1.223
 CJ4  C19  N21  single    1.342  0.020  1.342
 CJ4  C27  C26  aromatic  1.410  0.020  1.410
 CJ4  N21  C22  single    1.452  0.020  1.452
 CJ4  N31  C26  aromatic  1.385  0.020  1.385
 CJ4  N31  C23  aromatic  1.375  0.020  1.375
 CJ4  C26  N25  aromatic  1.321  0.020  1.321
 CJ4  C23  C22  single    1.482  0.020  1.482
 CJ4  C23  C24  aromatic  1.371  0.020  1.371
 CJ4  N25  C24  aromatic  1.353  0.020  1.353
 CJ4  C01  H1   single    0.970  0.020  1.090
 CJ4  C01  H2   single    0.970  0.020  1.090
 CJ4  C01  H3   single    0.970  0.020  1.090
 CJ4  C03  H4   single    0.970  0.020  1.090
 CJ4  C03  H5   single    0.970  0.020  1.090
 CJ4  C04  H6   single    0.970  0.020  1.090
 CJ4  C04  H7   single    0.970  0.020  1.090
 CJ4  C05  H8   single    0.970  0.020  1.090
 CJ4  C05  H9   single    0.970  0.020  1.090
 CJ4  C07  H10  single    0.970  0.020  1.090
 CJ4  C07  H11  single    0.970  0.020  1.090
 CJ4  C07  H12  single    0.970  0.020  1.090
 CJ4  C10  H13  single    0.930  0.020  1.080
 CJ4  C16  H14  single    0.970  0.020  1.090
 CJ4  C16  H15  single    0.970  0.020  1.090
 CJ4  C17  H16  single    0.970  0.020  1.090
 CJ4  C18  H17  single    0.970  0.020  1.090
 CJ4  C18  H18  single    0.970  0.020  1.090
 CJ4  C22  H19  single    0.970  0.020  1.090
 CJ4  C22  H20  single    0.970  0.020  1.090
 CJ4  C24  H21  single    0.930  0.020  1.080
 CJ4  C27  H22  single    0.930  0.020  1.080
 CJ4  C28  H23  single    0.930  0.020  1.080
 CJ4  C29  H24  single    0.930  0.020  1.080
 CJ4  C30  H25  single    0.930  0.020  1.080
 CJ4  N02  H26  single    0.890  0.020  1.040
 CJ4  N21  H28  single    0.860  0.020  1.020

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
 CJ4  H3   C01  H2   107.81  3.000
 CJ4  H3   C01  H1   107.53  3.000
 CJ4  H2   C01  H1   107.18  3.000
 CJ4  H3   C01  N02  109.95  3.000
 CJ4  H2   C01  N02  114.24  3.000
 CJ4  H1   C01  N02  109.88  3.000
 CJ4  H5   C03  H4   105.93  3.000
 CJ4  H5   C03  N02  112.35  3.000
 CJ4  H4   C03  N02  108.12  3.000
 CJ4  H5   C03  C04  109.37  3.000
 CJ4  H4   C03  C04  109.27  3.000
 CJ4  N02  C03  C04  111.59  3.000
 CJ4  H7   C04  H6   107.20  3.000
 CJ4  H7   C04  C05  109.48  3.000
 CJ4  H6   C04  C05  109.37  3.000
 CJ4  H7   C04  C03  109.61  3.000
 CJ4  H6   C04  C03  109.56  3.000
 CJ4  C05  C04  C03  111.52  3.000
 CJ4  H9   C05  H8   106.57  3.000
 CJ4  H9   C05  N06  109.20  3.000
 CJ4  H8   C05  N06  107.52  3.000
 CJ4  H9   C05  C04  109.71  3.000
 CJ4  H8   C05  C04  109.88  3.000
 CJ4  N06  C05  C04  113.69  3.000
 CJ4  H12  C07  H11  108.13  3.000
 CJ4  H12  C07  H10  108.12  3.000
 CJ4  H11  C07  H10  107.65  3.000
 CJ4  H12  C07  N06  108.70  3.000
 CJ4  H11  C07  N06  111.99  3.000
 CJ4  H10  C07  N06  112.11  3.000
 CJ4  N14  C08  N09  125.55  3.000
 CJ4  N14  C08  N06  116.48  3.000
 CJ4  N09  C08  N06  117.97  3.000
 CJ4  H13  C10  N09  117.29  3.000
 CJ4  H13  C10  C11  119.89  3.000
 CJ4  N09  C10  C11  122.83  3.000
 CJ4  F12  C11  C13  120.64  3.000
 CJ4  F12  C11  C10  121.33  3.000
 CJ4  C13  C11  C10  118.02  3.000
 CJ4  N15  C13  N14  117.33  3.000
 CJ4  N15  C13  C11  123.41  3.000
 CJ4  N14  C13  C11  119.25  3.000
 CJ4  H15  C16  H14  109.30  3.000
 CJ4  H15  C16  N15  115.00  3.000
 CJ4  H14  C16  N15  113.92  3.000
 CJ4  H15  C16  C17  114.87  3.000
 CJ4  H14  C16  C17  114.36  3.000
 CJ4  N15  C16  C17   88.26  3.000
 CJ4  H16  C17  C19  112.27  3.000
 CJ4  H16  C17  C18  112.67  3.000
 CJ4  C19  C17  C18  115.09  3.000
 CJ4  H16  C17  C16  112.32  3.000
 CJ4  C19  C17  C16  114.78  3.000
 CJ4  C18  C17  C16   87.56  3.000
 CJ4  H18  C18  H17  109.12  3.000
 CJ4  H18  C18  N15  113.62  3.000
 CJ4  H17  C18  N15  114.58  3.000
 CJ4  H18  C18  C17  114.49  3.000
 CJ4  H17  C18  C17  115.44  3.000
 CJ4  N15  C18  C17   88.50  3.000
 CJ4  O20  C19  N21  123.29  3.000
 CJ4  N21  C19  C17  115.21  3.000
 CJ4  O20  C19  C17  121.51  3.000
 CJ4  H20  C22  H19  106.79  3.000
 CJ4  H20  C22  N21  111.05  3.000
 CJ4  H19  C22  N21  108.21  3.000
 CJ4  H20  C22  C23  108.37  3.000
 CJ4  H19  C22  C23  111.22  3.000
 CJ4  N21  C22  C23  111.12  3.000
 CJ4  N31  C23  C24  104.58  3.000
 CJ4  C24  C23  C22  131.74  3.000
 CJ4  N31  C23  C22  123.68  3.000
 CJ4  H21  C24  N25  121.84  3.000
 CJ4  H21  C24  C23  125.96  3.000
 CJ4  N25  C24  C23  112.19  3.000
 CJ4  N31  C26  N25  110.92  3.000
 CJ4  N25  C26  C27  130.62  3.000
 CJ4  N31  C26  C27  118.46  3.000
 CJ4  H22  C27  C28  122.04  3.000
 CJ4  H22  C27  C26  118.74  3.000
 CJ4  C28  C27  C26  119.21  3.000
 CJ4  H23  C28  C29  119.48  3.000
 CJ4  H23  C28  C27  120.12  3.000
 CJ4  C29  C28  C27  120.40  3.000
 CJ4  H24  C29  C30  119.07  3.000
 CJ4  H24  C29  C28  120.67  3.000
 CJ4  C30  C29  C28  120.26  3.000
 CJ4  H25  C30  N31  117.33  3.000
 CJ4  H25  C30  C29  123.51  3.000
 CJ4  N31  C30  C29  119.16  3.000
 CJ4  H26  N02  C03  108.68  3.000
 CJ4  H26  N02  C01  108.72  3.000
 CJ4  C03  N02  C01  112.54  3.000
 CJ4  C08  N06  C07  119.79  3.000
 CJ4  C08  N06  C05  120.91  3.000
 CJ4  C07  N06  C05  119.09  3.000
 CJ4  C10  N09  C08  115.82  3.000
 CJ4  C13  N14  C08  118.54  3.000
 CJ4  C18  N15  C16   95.06  3.000
 CJ4  C16  N15  C13  134.11  3.000
 CJ4  C18  N15  C13  128.07  3.000
 CJ4  H28  N21  C22  117.43  3.000
 CJ4  H28  N21  C19  118.86  3.000
 CJ4  C22  N21  C19  123.42  3.000
 CJ4  C26  N25  C24  105.29  3.000
 CJ4  C30  N31  C26  122.51  3.000
 CJ4  C26  N31  C23  107.02  3.000
 CJ4  C30  N31  C23  130.47  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
 CJ4  CONST_01  C11  C10  N09  C08     0.00   0.0  0
 CJ4  CONST_02  C11  C13  N14  C08     0.00   0.0  0
 CJ4  CONST_03  N14  C08  N09  C10     0.00   0.0  0
 CJ4  CONST_04  N14  C13  C11  C10     0.00   0.0  0
 CJ4  CONST_05  N09  C08  N14  C13     0.00   0.0  0
 CJ4  CONST_06  N09  C10  C11  C13     0.00   0.0  0
 CJ4  CONST_07  C29  C30  N31  C23   180.00   0.0  0
 CJ4  CONST_08  C27  C26  N31  C23   180.00   0.0  0
 CJ4  CONST_09  N25  C26  N31  C23     0.00   0.0  0
 CJ4  CONST_10  C26  N25  C24  C23     0.00   0.0  0
 CJ4  CONST_11  C30  N31  C23  C24   180.00   0.0  0
 CJ4  CONST_12  C26  N31  C23  C24     0.00   0.0  0
 CJ4  CONST_13  C27  C26  N25  C24   180.00   0.0  0
 CJ4  CONST_14  N31  C26  N25  C24     0.00   0.0  0
 CJ4  CONST_15  C29  C28  C27  C26     0.00   0.0  0
 CJ4  CONST_16  C29  C30  N31  C26     0.00   0.0  0
 CJ4  CONST_17  C30  C29  C28  C27     0.00   0.0  0
 CJ4  CONST_18  C30  N31  C26  C27     0.00   0.0  0
 CJ4  CONST_19  N31  C30  C29  C28     0.00   0.0  0
 CJ4  CONST_20  N31  C26  C27  C28     0.00   0.0  0
 CJ4  CONST_21  N25  C26  C27  C28   180.00   0.0  0
 CJ4  CONST_22  N25  C26  N31  C30   180.00   0.0  0
 CJ4  CONST_23  N31  C23  C24  N25     0.00   0.0  0
 CJ4  CONST_24  N15  C13  N14  C08   180.00   0.0  0
 CJ4  CONST_25  N15  C13  C11  C10   180.00   0.0  0
 CJ4  CONST_26  N06  C08  N09  C10   180.00   0.0  0
 CJ4  CONST_27  N06  C08  N14  C13   180.00   0.0  0
 CJ4  CONST_28  C30  N31  C23  C22     0.00   0.0  0
 CJ4  CONST_29  C26  N31  C23  C22   180.00   0.0  0
 CJ4  CONST_30  N25  C24  C23  C22   180.00   0.0  0
 CJ4  CONST_31  N09  C10  C11  F12   180.00   0.0  0
 CJ4  CONST_32  N14  C13  C11  F12   180.00   0.0  0
 CJ4  CONST_33  N15  C13  C11  F12     0.00   0.0  0
 CJ4  CONST_34  H13  C10  N09  C08   180.00   0.0  0
 CJ4  CONST_35  H25  C30  N31  C23     0.00   0.0  0
 CJ4  CONST_36  H23  C28  C27  C26   180.00   0.0  0
 CJ4  CONST_37  H21  C24  N25  C26   180.00   0.0  0
 CJ4  CONST_38  H24  C29  C28  C27   180.00   0.0  0
 CJ4  CONST_39  H22  C27  C28  C29   180.00   0.0  0
 CJ4  CONST_40  N09  C08  N06  C05     0.00   0.0  0
 CJ4  CONST_41  N14  C08  N06  C05   180.00   0.0  0
 CJ4  CONST_42  N09  C08  N06  C07   180.00   0.0  0
 CJ4  CONST_43  N14  C08  N06  C07     0.00   0.0  0
 CJ4  CONST_44  C22  N21  C19  C17   180.00   0.0  0
 CJ4  CONST_45  H28  N21  C19  C17     0.00   0.0  0
 CJ4  CONST_46  O20  C19  N21  C22     0.00   0.0  0
 CJ4  Var_01    C18  N15  C13  C11   172.69  30.0  2
 CJ4  Var_02    C17  C18  N15  C13  -169.25  30.0  1
 CJ4  Var_03    C17  C16  N15  C13   167.56  30.0  1
 CJ4  Var_04    N21  C22  C23  C24   111.76  30.0  2
 CJ4  Var_05    C08  N06  C05  C04   -84.23  30.0  3
 CJ4  Var_06    C23  C22  N21  C19   151.06  30.0  3
 CJ4  Var_07    H10  C07  N06  C08   -70.06  30.0  3
 CJ4  Var_08    C04  C03  N02  C01  -178.83  30.0  3
 CJ4  Var_09    N06  C05  C04  C03  -178.27  30.0  1
 CJ4  Var_10    N02  C03  C04  C05  -178.46  30.0  3
 CJ4  Var_11    H1   C01  N02  C03   -64.98  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
 CJ4  chir_01  C17  C18  C16  C19  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
 CJ4  plan-1  C08  0.020
 CJ4  plan-1  C10  0.020
 CJ4  plan-1  C11  0.020
 CJ4  plan-1  C13  0.020
 CJ4  plan-1  F12  0.020
 CJ4  plan-1  N06  0.020
 CJ4  plan-1  N09  0.020
 CJ4  plan-1  N14  0.020
 CJ4  plan-1  N15  0.020
 CJ4  plan-1  H13  0.020
 CJ4  plan-2  C22  0.020
 CJ4  plan-2  C23  0.020
 CJ4  plan-2  C24  0.020
 CJ4  plan-2  C26  0.020
 CJ4  plan-2  C27  0.020
 CJ4  plan-2  C28  0.020
 CJ4  plan-2  C29  0.020
 CJ4  plan-2  C30  0.020
 CJ4  plan-2  N25  0.020
 CJ4  plan-2  N31  0.020
 CJ4  plan-2  H21  0.020
 CJ4  plan-2  H22  0.020
 CJ4  plan-2  H23  0.020
 CJ4  plan-2  H24  0.020
 CJ4  plan-2  H25  0.020
 CJ4  plan-3  C05  0.020
 CJ4  plan-3  C07  0.020
 CJ4  plan-3  C08  0.020
 CJ4  plan-3  N06  0.020
 CJ4  plan-4  C17  0.020
 CJ4  plan-4  C19  0.020
 CJ4  plan-4  C22  0.020
 CJ4  plan-4  N21  0.020
 CJ4  plan-4  O20  0.020
 CJ4  plan-4  H28  0.020

