# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:45:36 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-[4-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2cc(Nc3cc(C)[nH]n3)nc(Oc4ccc(NC(=O)C=C)cc4)n2
#
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
 563  563  N-[4-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide  ligand  58  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_563
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
 563  C4   C  CR6   0   0.598  -2.4251   1.0028  -0.1987
 563  C5   C  CR16  0  -0.546  -2.2546  -0.3927  -0.1428
 563  C6   C  CR6   0   0.504  -0.9496  -0.8576  -0.0694
 563  N1   N  N     0  -0.529   0.1091  -0.0265  -0.0592
 563  N3   N  N     0  -0.525  -1.3610   1.8215  -0.2017
 563  CAN  C  CH2   0  -0.314  -3.7917   2.9957  -0.5837
 563  CAL  C  CH2   0  -0.328  -4.9496   3.6172   0.1878
 563  NBE  N  NT    0  -0.401  -6.2021   2.8991   0.0515
 563  CAC  C  CH3   0  -0.529  -6.8343   3.0609  -1.2425
 563  CAM  C  CH2   0  -0.319  -5.9995   1.5153   0.4268
 563  CAO  C  CH2   0  -0.314  -4.8718   0.8157  -0.3304
 563  NBF  N  NT    0  -0.503  -3.6442   1.5874  -0.2385
 563  NAT  N  NH1   0  -0.753  -0.5991  -2.1709  -0.0105
 563  CBA  C  CR5   0   0.513  -1.3888  -3.3041   0.0077
 563  CAJ  C  CR15  0  -0.587  -0.8858  -4.6211   0.0674
 563  CAX  C  CR5   0   0.418  -2.0088  -5.4185   0.0657
 563  CAB  C  CH3   0  -0.730  -2.1587  -6.8955   0.1356
 563  NAU  N  NR15  0  -0.472  -3.0550  -4.5802   0.0066
 563  NAP  N  N     0  -0.335  -2.7059  -3.2875  -0.0301
 563  C2   C  CR6   0   0.561  -0.1834   1.2468  -0.1275
 563  OAV  O  O2    0  -0.505   0.8325   2.1342  -0.1288
 563  CAZ  C  CR6   0   0.351   2.1230   1.6729   0.0004
 563  CAI  C  CR16  0  -0.302   2.9138   1.5282  -1.1234
 563  CAG  C  CR16  0  -0.318   4.2411   1.1366  -1.0084
 563  CAH  C  CR16  0  -0.293   2.6495   1.4224   1.2574
 563  CAF  C  CR16  0  -0.353   3.9685   1.0287   1.3779
 563  CAY  C  CR6   0   0.375   4.7828   0.8793   0.2514
 563  NAS  N  NH1   0  -0.759   6.1035   0.4858   0.4811
 563  CAW  C  C     0   0.539   7.0959   0.2299  -0.4098
 563  OAD  O  O     0  -0.469   6.9683   0.3134  -1.6201
 563  CAE  C  C1    0  -0.338   8.3713  -0.1662   0.2401
 563  CAA  C  C2    0  -0.467   9.4559  -0.4447  -0.4736
 563  H1   H  HCR6  0   0.295  -3.0728  -1.0882  -0.1663
 563  H2   H  HCH2  0   0.231  -3.9535   3.0943  -1.6648
 563  H3   H  HCH2  0   0.273  -2.8721   3.5224  -0.3475
 563  H4   H  HCH2  0   0.237  -4.6862   3.6499   1.2501
 563  H5   H  HCH2  0   0.245  -5.0835   4.6497  -0.1423
 563  H7   H  HCH3  0   0.201  -6.2849   2.6333  -2.0918
 563  H8   H  HCH3  0   0.234  -7.8202   2.5932  -1.2252
 563  H9   H  HCH3  0   0.234  -6.9756   4.1231  -1.4469
 563  H10  H  HCH2  0   0.238  -5.7694   1.4781   1.4967
 563  H11  H  HCH2  0   0.247  -6.9244   0.9540   0.2778
 563  H12  H  HCH2  0   0.262  -4.7375  -0.1663   0.1162
 563  H13  H  HCH2  0   0.237  -5.1419   0.6565  -1.3815
 563  H14  H  HNH1  0   0.406   0.3956  -2.3308   0.0290
 563  H15  H  HCR5  0   0.269   0.1442  -4.9367   0.1062
 563  H16  H  HCH3  0   0.261  -2.4595  -7.2161   1.1338
 563  H17  H  HCH3  0   0.258  -2.9113  -7.2541  -0.5665
 563  H18  H  HCH3  0   0.261  -1.2163  -7.3834  -0.1020
 563  H19  H  HNR5  0   0.415  -4.0313  -4.8259  -0.0120
 563  H20  H  HCR6  0   0.272   2.5032   1.7287  -2.1048
 563  H21  H  HCR6  0   0.286   4.8356   1.0364  -1.9008
 563  H22  H  HCR6  0   0.274   2.0383   1.5380   2.1432
 563  H23  H  HCR6  0   0.277   4.3721   0.8337   2.3645
 563  H24  H  HNH1  0   0.420   6.3429   0.3714   1.4543
 563  H25  H  H     0   0.275   8.4009  -0.2225   1.3227
 563  H27  H  H     0   0.265  10.3810  -0.7308   0.0066
 563  H28  H  H     0   0.262   9.4566  -0.3956  -1.5546

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
 563  CAC  NBE  single    1.449  0.020  1.449
 563  CAL  NBE  single    1.450  0.020  1.450
 563  CAL  CAN  single    1.524  0.020  1.524
 563  NBE  CAM  single    1.448  0.020  1.448
 563  CAN  NBF  single    1.457  0.020  1.457
 563  CAH  CAF  aromatic  1.382  0.020  1.382
 563  CAH  CAZ  aromatic  1.386  0.020  1.386
 563  CAF  CAY  aromatic  1.398  0.020  1.398
 563  NBF  C4   single    1.353  0.020  1.353
 563  NBF  CAO  single    1.453  0.020  1.453
 563  CAM  CAO  single    1.528  0.020  1.528
 563  N3   C4   aromatic  1.343  0.020  1.343
 563  N3   C2   aromatic  1.313  0.020  1.313
 563  OAV  CAZ  single    1.377  0.020  1.377
 563  OAV  C2   single    1.349  0.020  1.349
 563  C4   C5   aromatic  1.407  0.020  1.407
 563  CAZ  CAI  aromatic  1.382  0.020  1.382
 563  C2   N1   aromatic  1.308  0.020  1.308
 563  CAY  NAS  single    1.397  0.020  1.397
 563  CAY  CAG  aromatic  1.395  0.020  1.395
 563  C5   C6   aromatic  1.387  0.020  1.387
 563  NAS  CAW  single    1.358  0.020  1.358
 563  N1   C6   aromatic  1.346  0.020  1.346
 563  C6   NAT  single    1.361  0.020  1.361
 563  CAI  CAG  aromatic  1.389  0.020  1.389
 563  CAW  OAD  double    1.220  0.020  1.220
 563  CAW  CAE  single    1.485  0.020  1.485
 563  CAE  CAA  double    1.328  0.020  1.328
 563  NAT  CBA  single    1.381  0.020  1.381
 563  CBA  CAJ  aromatic  1.411  0.020  1.411
 563  CBA  NAP  aromatic  1.318  0.020  1.318
 563  CAJ  CAX  aromatic  1.377  0.020  1.377
 563  NAP  NAU  aromatic  1.339  0.020  1.339
 563  CAX  NAU  aromatic  1.342  0.020  1.342
 563  CAX  CAB  single    1.486  0.020  1.486
 563  C5   H1   single    0.930  0.020  1.080
 563  CAN  H2   single    0.970  0.020  1.090
 563  CAN  H3   single    0.970  0.020  1.090
 563  CAL  H4   single    0.970  0.020  1.090
 563  CAL  H5   single    0.970  0.020  1.090
 563  CAC  H7   single    0.970  0.020  1.090
 563  CAC  H8   single    0.970  0.020  1.090
 563  CAC  H9   single    0.970  0.020  1.090
 563  CAM  H10  single    0.970  0.020  1.090
 563  CAM  H11  single    0.970  0.020  1.090
 563  CAO  H12  single    0.970  0.020  1.090
 563  CAO  H13  single    0.970  0.020  1.090
 563  NAT  H14  single    0.860  0.020  1.020
 563  CAJ  H15  single    0.930  0.020  1.080
 563  CAB  H16  single    0.970  0.020  1.090
 563  CAB  H17  single    0.970  0.020  1.090
 563  CAB  H18  single    0.970  0.020  1.090
 563  NAU  H19  single    0.860  0.020  1.020
 563  CAI  H20  single    0.930  0.020  1.080
 563  CAG  H21  single    0.930  0.020  1.080
 563  CAH  H22  single    0.930  0.020  1.080
 563  CAF  H23  single    0.930  0.020  1.080
 563  NAS  H24  single    0.860  0.020  1.020
 563  CAE  H25  single    0.930  0.020  1.080
 563  CAA  H27  single    0.930  0.020  1.080
 563  CAA  H28  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
 563  NBF  C4   N3   116.79  3.000
 563  N3   C4   C5   120.59  3.000
 563  NBF  C4   C5   122.62  3.000
 563  H1   C5   C6   120.05  3.000
 563  H1   C5   C4   123.30  3.000
 563  C6   C5   C4   116.65  3.000
 563  NAT  C6   N1   113.14  3.000
 563  NAT  C6   C5   124.62  3.000
 563  N1   C6   C5   122.24  3.000
 563  C2   N1   C6   115.13  3.000
 563  C2   N3   C4   116.35  3.000
 563  H3   CAN  H2   107.19  3.000
 563  H3   CAN  NBF  109.36  3.000
 563  H2   CAN  NBF  109.57  3.000
 563  H3   CAN  CAL  109.61  3.000
 563  H2   CAN  CAL  110.49  3.000
 563  NBF  CAN  CAL  110.55  3.000
 563  H5   CAL  H4   107.12  3.000
 563  H5   CAL  NBE  109.50  3.000
 563  H4   CAL  NBE  108.29  3.000
 563  H5   CAL  CAN  109.01  3.000
 563  H4   CAL  CAN  108.70  3.000
 563  NBE  CAL  CAN  114.00  3.000
 563  CAM  NBE  CAC  113.53  3.000
 563  CAM  NBE  CAL  109.14  3.000
 563  CAC  NBE  CAL  113.92  3.000
 563  H9   CAC  H8   107.65  3.000
 563  H9   CAC  H7   107.39  3.000
 563  H8   CAC  H7   107.30  3.000
 563  H9   CAC  NBE  109.42  3.000
 563  H8   CAC  NBE  109.40  3.000
 563  H7   CAC  NBE  115.39  3.000
 563  H11  CAM  H10  107.09  3.000
 563  H11  CAM  CAO  108.79  3.000
 563  H10  CAM  CAO  108.27  3.000
 563  H11  CAM  NBE  109.71  3.000
 563  H10  CAM  NBE  108.37  3.000
 563  CAO  CAM  NBE  114.35  3.000
 563  H13  CAO  H12  107.03  3.000
 563  H13  CAO  NBF  110.23  3.000
 563  H12  CAO  NBF  110.45  3.000
 563  H13  CAO  CAM  111.08  3.000
 563  H12  CAO  CAM  107.53  3.000
 563  NBF  CAO  CAM  110.43  3.000
 563  CAO  NBF  CAN  114.38  3.000
 563  CAO  NBF  C4   122.26  3.000
 563  CAN  NBF  C4   121.05  3.000
 563  H14  NAT  CBA  115.68  3.000
 563  H14  NAT  C6   114.14  3.000
 563  CBA  NAT  C6   130.18  3.000
 563  NAP  CBA  CAJ  111.67  3.000
 563  NAP  CBA  NAT  124.11  3.000
 563  CAJ  CBA  NAT  124.22  3.000
 563  H15  CAJ  CAX  127.56  3.000
 563  H15  CAJ  CBA  127.99  3.000
 563  CAX  CAJ  CBA  104.46  3.000
 563  NAU  CAX  CAB  122.98  3.000
 563  CAB  CAX  CAJ  131.11  3.000
 563  NAU  CAX  CAJ  105.90  3.000
 563  H18  CAB  H17  108.07  3.000
 563  H18  CAB  H16  107.88  3.000
 563  H17  CAB  H16  107.60  3.000
 563  H18  CAB  CAX  110.38  3.000
 563  H17  CAB  CAX  111.49  3.000
 563  H16  CAB  CAX  111.28  3.000
 563  H19  NAU  NAP  119.19  3.000
 563  H19  NAU  CAX  127.17  3.000
 563  NAP  NAU  CAX  113.64  3.000
 563  NAU  NAP  CBA  104.33  3.000
 563  OAV  C2   N3   112.80  3.000
 563  OAV  C2   N1   118.17  3.000
 563  N3   C2   N1   129.03  3.000
 563  CAZ  OAV  C2   119.04  3.000
 563  CAH  CAZ  CAI  120.09  3.000
 563  CAI  CAZ  OAV  119.69  3.000
 563  CAH  CAZ  OAV  120.13  3.000
 563  H20  CAI  CAG  119.33  3.000
 563  H20  CAI  CAZ  120.06  3.000
 563  CAG  CAI  CAZ  120.61  3.000
 563  H21  CAG  CAY  121.11  3.000
 563  H21  CAG  CAI  119.04  3.000
 563  CAY  CAG  CAI  119.86  3.000
 563  H22  CAH  CAF  119.87  3.000
 563  H22  CAH  CAZ  120.56  3.000
 563  CAF  CAH  CAZ  119.56  3.000
 563  H23  CAF  CAY  119.83  3.000
 563  H23  CAF  CAH  119.09  3.000
 563  CAY  CAF  CAH  121.07  3.000
 563  NAS  CAY  CAF  116.63  3.000
 563  NAS  CAY  CAG  124.57  3.000
 563  CAF  CAY  CAG  118.80  3.000
 563  H24  NAS  CAW  115.98  3.000
 563  H24  NAS  CAY  114.52  3.000
 563  CAW  NAS  CAY  129.50  3.000
 563  CAE  CAW  OAD  122.83  3.000
 563  CAE  CAW  NAS  113.00  3.000
 563  OAD  CAW  NAS  124.16  3.000
 563  H25  CAE  CAA  120.23  3.000
 563  H25  CAE  CAW  118.30  3.000
 563  CAA  CAE  CAW  121.48  3.000
 563  H28  CAA  H27  117.08  3.000
 563  H28  CAA  CAE  121.87  3.000
 563  H27  CAA  CAE  121.05  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
 563  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 563  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 563  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 563  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 563  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 563  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 563  CONST_07  NAU  CAX  CAJ  CBA     0.00   0.0  0
 563  CONST_08  CAX  NAU  NAP  CBA     0.00   0.0  0
 563  CONST_09  NAU  NAP  CBA  CAJ     0.00   0.0  0
 563  CONST_10  NAP  NAU  CAX  CAJ     0.00   0.0  0
 563  CONST_11  NAP  CBA  CAJ  CAX     0.00   0.0  0
 563  CONST_12  CAY  CAF  CAH  CAZ     0.00   0.0  0
 563  CONST_13  CAY  CAG  CAI  CAZ     0.00   0.0  0
 563  CONST_14  CAF  CAH  CAZ  CAI     0.00   0.0  0
 563  CONST_15  CAF  CAY  CAG  CAI     0.00   0.0  0
 563  CONST_16  CAH  CAF  CAY  CAG     0.00   0.0  0
 563  CONST_17  CAH  CAZ  CAI  CAG     0.00   0.0  0
 563  CONST_18  NBF  C4   C5   C6    180.00   0.0  0
 563  CONST_19  C2   N3   C4   NBF   180.00   0.0  0
 563  CONST_20  OAV  C2   N3   C4    180.00   0.0  0
 563  CONST_21  NAT  C6   C5   C4    180.00   0.0  0
 563  CONST_22  OAV  C2   N1   C6    180.00   0.0  0
 563  CONST_23  C2   N1   C6   NAT   180.00   0.0  0
 563  CONST_24  CAX  CAJ  CBA  NAT   180.00   0.0  0
 563  CONST_25  NAU  NAP  CBA  NAT   180.00   0.0  0
 563  CONST_26  CAB  CAX  CAJ  CBA   180.00   0.0  0
 563  CONST_27  NAP  NAU  CAX  CAB   180.00   0.0  0
 563  CONST_28  CAF  CAH  CAZ  OAV   180.00   0.0  0
 563  CONST_29  CAG  CAI  CAZ  OAV   180.00   0.0  0
 563  CONST_30  NAS  CAY  CAG  CAI   180.00   0.0  0
 563  CONST_31  NAS  CAY  CAF  CAH   180.00   0.0  0
 563  CONST_32  H1   C5   C6   N1    180.00   0.0  0
 563  CONST_33  H19  NAU  NAP  CBA   180.00   0.0  0
 563  CONST_34  H15  CAJ  CAX  NAU   180.00   0.0  0
 563  CONST_35  H23  CAF  CAH  CAZ   180.00   0.0  0
 563  CONST_36  H21  CAG  CAI  CAZ   180.00   0.0  0
 563  CONST_37  H22  CAH  CAZ  CAI   180.00   0.0  0
 563  CONST_38  H20  CAI  CAZ  CAH   180.00   0.0  0
 563  CONST_39  CAW  NAS  CAY  CAG     0.00   0.0  0
 563  CONST_40  CAW  NAS  CAY  CAF   180.00   0.0  0
 563  CONST_41  H24  NAS  CAY  CAG   180.00   0.0  0
 563  CONST_42  OAD  CAW  NAS  CAY     0.00   0.0  0
 563  CONST_43  CAE  CAW  NAS  CAY   180.00   0.0  0
 563  Var_01    CAL  CAN  NBF  C4   -146.01  30.0  1
 563  Var_02    CAM  CAO  NBF  C4    146.68  30.0  1
 563  Var_03    CAN  NBF  C4   C5   -166.63  30.0  1
 563  Var_04    CAM  NBE  CAL  CAN    54.74  30.0  1
 563  Var_05    CAO  CAM  NBE  CAL   -54.53  30.0  1
 563  Var_06    NBF  CAN  CAL  NBE   -53.27  30.0  1
 563  Var_07    NBF  CAO  CAM  NBE    52.74  30.0  1
 563  Var_08    CBA  NAT  C6   C5     -0.86  30.0  2
 563  Var_09    CAJ  CBA  NAT  C6    179.80  30.0  2
 563  Var_10    CAH  CAZ  OAV  C2    -84.13  30.0  2
 563  Var_11    H7   CAC  NBE  CAL    65.65  30.0  3
 563  Var_12    H16  CAB  CAX  CAJ   102.78  30.0  2
 563  Var_13    CAA  CAE  CAW  NAS  -179.47  30.0  2
 563  Var_14    H27  CAA  CAE  CAW   179.90   0.0  2

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
 563  plan-1  NAT  0.020
 563  plan-1  CBA  0.020
 563  plan-1  CAJ  0.020
 563  plan-1  CAX  0.020
 563  plan-1  CAB  0.020
 563  plan-1  NAU  0.020
 563  plan-1  NAP  0.020
 563  plan-1  H15  0.020
 563  plan-1  H19  0.020
 563  plan-2  C4   0.020
 563  plan-2  C5   0.020
 563  plan-2  C6   0.020
 563  plan-2  N1   0.020
 563  plan-2  N3   0.020
 563  plan-2  NBF  0.020
 563  plan-2  NAT  0.020
 563  plan-2  C2   0.020
 563  plan-2  OAV  0.020
 563  plan-2  H1   0.020
 563  plan-3  OAV  0.020
 563  plan-3  CAZ  0.020
 563  plan-3  CAI  0.020
 563  plan-3  CAG  0.020
 563  plan-3  CAH  0.020
 563  plan-3  CAF  0.020
 563  plan-3  CAY  0.020
 563  plan-3  NAS  0.020
 563  plan-3  H20  0.020
 563  plan-3  H21  0.020
 563  plan-3  H22  0.020
 563  plan-3  H23  0.020
 563  plan-4  CAY  0.020
 563  plan-4  NAS  0.020
 563  plan-4  CAW  0.020
 563  plan-4  OAD  0.020
 563  plan-4  CAE  0.020
 563  plan-4  H24  0.020
 563  plan-5  CAW  0.020
 563  plan-5  CAE  0.020
 563  plan-5  CAA  0.020
 563  plan-5  H25  0.020
 563  plan-5  H27  0.020
 563  plan-5  H28  0.020

