# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 00:47:08 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-[3-({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(Oc4cccc(NC(=O)C=C)c4)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
 56G  56G  N-[3-({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_56G
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
 56G  C4   C  CR6   0   0.598   1.9600  -1.1298  -0.1139
 56G  C5   C  CR16  0  -0.545   1.9424   0.2769  -0.1448
 56G  C6   C  CR6   0   0.506   0.7694   0.8933   0.2635
 56G  N1   N  N     0  -0.531  -0.3101   0.1927   0.6589
 56G  N3   N  N     0  -0.525   0.8740  -1.8184   0.2722
 56G  CAN  C  CH2   0  -0.308   4.2695  -1.2721  -0.9770
 56G  CAL  C  CH2   0  -0.275   5.4841  -1.9490  -0.3653
 56G  NBE  N  NT    0  -0.414   5.4429  -3.3806  -0.5709
 56G  CAC  C  CH3   0  -0.519   6.6294  -4.0281  -0.0599
 56G  CAM  C  CH2   0  -0.283   4.2373  -3.9321   0.0115
 56G  CAO  C  CH2   0  -0.310   3.0025  -3.2978  -0.5993
 56G  NBF  N  NT    0  -0.508   3.0480  -1.8530  -0.4571
 56G  NAT  N  NH1   0  -0.754   0.5789   2.2394   0.3081
 56G  CBA  C  CR5   0   0.514   1.4449   3.2736   0.0102
 56G  CAI  C  CR15  0  -0.586   1.1204   4.6401   0.1407
 56G  CAX  C  CR5   0   0.419   2.2596   5.3034  -0.2594
 56G  CAB  C  CH3   0  -0.729   2.5738   6.7548  -0.3231
 56G  NAU  N  NR15  0  -0.473   3.1440   4.3495  -0.5877
 56G  NAP  N  N     0  -0.337   2.6741   3.1048  -0.4346
 56G  C2   C  CR6   0   0.561  -0.1711  -1.1076   0.6255
 56G  OAV  O  O2    0  -0.508  -1.2177  -1.8694   1.0057
 56G  CAZ  C  CR6   0   0.398  -2.4222  -1.2632   1.2834
 56G  CAH  C  CR16  0  -0.387  -3.2612  -0.9450   0.2267
 56G  CAG  C  CR16  0  -0.336  -2.7827  -1.0585   2.6017
 56G  CAE  C  CR16  0  -0.245  -4.0353  -0.5166   2.8609
 56G  CAF  C  CR16  0  -0.353  -4.8918  -0.1844   1.8283
 56G  CAY  C  CR6   0   0.381  -4.5133  -0.3959   0.4983
 56G  NAS  N  NH1   0  -0.762  -5.4367  -0.0348  -0.4831
 56G  CAW  C  C     0   0.542  -5.3367  -0.1245  -1.8360
 56G  OAD  O  O     0  -0.467  -4.3622  -0.5663  -2.4214
 56G  CAK  C  C1    0  -0.337  -6.5435   0.3727  -2.5432
 56G  CAA  C  C2    0  -0.466  -6.6174   0.3725  -3.8692
 56G  H1   H  HCR6  0   0.294   2.7775   0.8693  -0.4694
 56G  H2   H  HCH2  0   0.262   4.3260  -0.2113  -0.7521
 56G  H3   H  HCH2  0   0.237   4.2961  -1.3793  -2.0677
 56G  H4   H  HCH2  0   0.245   6.3804  -1.5416  -0.8389
 56G  H5   H  HCH2  0   0.197   5.5372  -1.6900   0.7068
 56G  H7   H  HCH3  0   0.194   6.7582  -3.9030   1.0265
 56G  H8   H  HCH3  0   0.235   6.5884  -5.0981  -0.2681
 56G  H9   H  HCH3  0   0.234   7.5164  -3.6237  -0.5497
 56G  H10  H  HCH2  0   0.243   4.2067  -5.0078  -0.1772
 56G  H11  H  HCH2  0   0.197   4.2106  -3.7949   1.1069
 56G  H12  H  HCH2  0   0.231   2.9464  -3.5555  -1.6639
 56G  H13  H  HCH2  0   0.273   2.1108  -3.6839  -0.1165
 56G  H14  H  HNH1  0   0.405  -0.3351   2.5167   0.6304
 56G  H15  H  HCR5  0   0.269   0.1932   5.0720   0.4802
 56G  H16  H  HCH3  0   0.261   3.0488   7.0957   0.5980
 56G  H17  H  HCH3  0   0.257   3.2492   6.9827  -1.1473
 56G  H18  H  HCH3  0   0.260   1.6643   7.3353  -0.4607
 56G  H19  H  HNR5  0   0.414   4.0826   4.4825  -0.9275
 56G  H20  H  HCR6  0   0.292  -2.9372  -1.1310  -0.7841
 56G  H21  H  HCR6  0   0.269  -2.1090  -1.3208   3.4068
 56G  H22  H  HCR6  0   0.268  -4.3468  -0.3489   3.8831
 56G  H23  H  HCR6  0   0.274  -5.8634   0.2385   2.0525
 56G  H24  H  HNH1  0   0.421  -6.2981   0.3520  -0.1271
 56G  H25  H  H     0   0.277  -7.3727   0.7412  -1.9500
 56G  H27  H  H     0   0.262  -5.8050   0.0119  -4.4868
 56G  H28  H  H     0   0.266  -7.4990   0.7359  -4.3781

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
 56G  CAA  CAK  double    1.328  0.020  1.328
 56G  CAK  CAW  single    1.484  0.020  1.484
 56G  CAW  NAS  single    1.359  0.020  1.359
 56G  CAW  OAD  double    1.220  0.020  1.220
 56G  CAC  NBE  single    1.445  0.020  1.445
 56G  NAS  CAY  single    1.395  0.020  1.395
 56G  CAM  NBE  single    1.448  0.020  1.448
 56G  CAM  CAO  single    1.517  0.020  1.517
 56G  NBE  CAL  single    1.447  0.020  1.447
 56G  CAY  CAF  aromatic  1.399  0.020  1.399
 56G  CAY  CAH  aromatic  1.394  0.020  1.394
 56G  CAL  CAN  single    1.519  0.020  1.519
 56G  CAF  CAE  aromatic  1.382  0.020  1.382
 56G  CAO  NBF  single    1.453  0.020  1.453
 56G  CAH  CAZ  aromatic  1.386  0.020  1.386
 56G  NBF  CAN  single    1.449  0.020  1.449
 56G  NBF  C4   single    1.351  0.020  1.351
 56G  CAE  CAG  aromatic  1.389  0.020  1.389
 56G  C4   N3   aromatic  1.343  0.020  1.343
 56G  C4   C5   aromatic  1.407  0.020  1.407
 56G  N3   C2   aromatic  1.312  0.020  1.312
 56G  CAZ  CAG  aromatic  1.382  0.020  1.382
 56G  CAZ  OAV  single    1.377  0.020  1.377
 56G  C5   C6   aromatic  1.387  0.020  1.387
 56G  C2   OAV  single    1.349  0.020  1.349
 56G  C2   N1   aromatic  1.308  0.020  1.308
 56G  C6   N1   aromatic  1.346  0.020  1.346
 56G  C6   NAT  single    1.360  0.020  1.360
 56G  NAT  CBA  single    1.381  0.020  1.381
 56G  CBA  CAI  aromatic  1.411  0.020  1.411
 56G  CBA  NAP  aromatic  1.318  0.020  1.318
 56G  CAI  CAX  aromatic  1.378  0.020  1.378
 56G  NAP  NAU  aromatic  1.339  0.020  1.339
 56G  CAX  NAU  aromatic  1.342  0.020  1.342
 56G  CAX  CAB  single    1.486  0.020  1.486
 56G  C5   H1   single    0.930  0.020  1.080
 56G  CAN  H2   single    0.970  0.020  1.090
 56G  CAN  H3   single    0.970  0.020  1.090
 56G  CAL  H4   single    0.970  0.020  1.090
 56G  CAL  H5   single    0.970  0.020  1.090
 56G  CAC  H7   single    0.970  0.020  1.090
 56G  CAC  H8   single    0.970  0.020  1.090
 56G  CAC  H9   single    0.970  0.020  1.090
 56G  CAM  H10  single    0.970  0.020  1.090
 56G  CAM  H11  single    0.970  0.020  1.090
 56G  CAO  H12  single    0.970  0.020  1.090
 56G  CAO  H13  single    0.970  0.020  1.090
 56G  NAT  H14  single    0.860  0.020  1.020
 56G  CAI  H15  single    0.930  0.020  1.080
 56G  CAB  H16  single    0.970  0.020  1.090
 56G  CAB  H17  single    0.970  0.020  1.090
 56G  CAB  H18  single    0.970  0.020  1.090
 56G  NAU  H19  single    0.860  0.020  1.020
 56G  CAH  H20  single    0.930  0.020  1.080
 56G  CAG  H21  single    0.930  0.020  1.080
 56G  CAE  H22  single    0.930  0.020  1.080
 56G  CAF  H23  single    0.930  0.020  1.080
 56G  NAS  H24  single    0.860  0.020  1.020
 56G  CAK  H25  single    0.930  0.020  1.080
 56G  CAA  H27  single    0.930  0.020  1.080
 56G  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
 56G  NBF  C4   N3   116.74  3.000
 56G  N3   C4   C5   120.59  3.000
 56G  NBF  C4   C5   122.67  3.000
 56G  H1   C5   C6   120.10  3.000
 56G  H1   C5   C4   123.25  3.000
 56G  C6   C5   C4   116.65  3.000
 56G  NAT  C6   N1   113.15  3.000
 56G  NAT  C6   C5   124.62  3.000
 56G  N1   C6   C5   122.24  3.000
 56G  C2   N1   C6   115.13  3.000
 56G  C2   N3   C4   116.34  3.000
 56G  H3   CAN  H2   107.48  3.000
 56G  H3   CAN  NBF  109.76  3.000
 56G  H2   CAN  NBF  111.17  3.000
 56G  H3   CAN  CAL  109.74  3.000
 56G  H2   CAN  CAL  108.08  3.000
 56G  NBF  CAN  CAL  110.54  3.000
 56G  H5   CAL  H4   107.10  3.000
 56G  H5   CAL  NBE  111.80  3.000
 56G  H4   CAL  NBE  109.31  3.000
 56G  H5   CAL  CAN  108.96  3.000
 56G  H4   CAL  CAN  108.37  3.000
 56G  NBE  CAL  CAN  111.16  3.000
 56G  CAM  NBE  CAC  111.76  3.000
 56G  CAM  NBE  CAL  110.08  3.000
 56G  CAC  NBE  CAL  111.70  3.000
 56G  H9   CAC  H8   107.96  3.000
 56G  H9   CAC  H7   107.80  3.000
 56G  H8   CAC  H7   107.70  3.000
 56G  H9   CAC  NBE  110.04  3.000
 56G  H8   CAC  NBE  109.95  3.000
 56G  H7   CAC  NBE  113.21  3.000
 56G  H11  CAM  H10  107.03  3.000
 56G  H11  CAM  CAO  109.14  3.000
 56G  H10  CAM  CAO  108.62  3.000
 56G  H11  CAM  NBE  111.83  3.000
 56G  H10  CAM  NBE  109.20  3.000
 56G  CAO  CAM  NBE  110.90  3.000
 56G  H13  CAO  H12  107.83  3.000
 56G  H13  CAO  NBF  109.65  3.000
 56G  H12  CAO  NBF  109.29  3.000
 56G  H13  CAO  CAM  109.94  3.000
 56G  H12  CAO  CAM  109.53  3.000
 56G  NBF  CAO  CAM  110.55  3.000
 56G  CAO  NBF  CAN  112.96  3.000
 56G  CAN  NBF  C4   123.75  3.000
 56G  CAO  NBF  C4   122.15  3.000
 56G  H14  NAT  CBA  115.57  3.000
 56G  H14  NAT  C6   114.18  3.000
 56G  CBA  NAT  C6   130.24  3.000
 56G  NAP  CBA  CAI  111.70  3.000
 56G  NAP  CBA  NAT  124.17  3.000
 56G  CAI  CBA  NAT  124.13  3.000
 56G  H15  CAI  CAX  127.59  3.000
 56G  H15  CAI  CBA  127.97  3.000
 56G  CAX  CAI  CBA  104.44  3.000
 56G  NAU  CAX  CAB  122.99  3.000
 56G  CAB  CAX  CAI  131.10  3.000
 56G  NAU  CAX  CAI  105.89  3.000
 56G  H18  CAB  H17  108.11  3.000
 56G  H18  CAB  H16  107.71  3.000
 56G  H17  CAB  H16  107.66  3.000
 56G  H18  CAB  CAX  110.47  3.000
 56G  H17  CAB  CAX  111.57  3.000
 56G  H16  CAB  CAX  111.16  3.000
 56G  H19  NAU  NAP  119.23  3.000
 56G  H19  NAU  CAX  127.09  3.000
 56G  NAP  NAU  CAX  113.68  3.000
 56G  NAU  NAP  CBA  104.29  3.000
 56G  OAV  C2   N3   112.81  3.000
 56G  OAV  C2   N1   118.15  3.000
 56G  N3   C2   N1   129.04  3.000
 56G  CAZ  OAV  C2   119.13  3.000
 56G  CAG  CAZ  CAH  122.36  3.000
 56G  CAG  CAZ  OAV  119.07  3.000
 56G  CAH  CAZ  OAV  118.48  3.000
 56G  H20  CAH  CAY  121.39  3.000
 56G  H20  CAH  CAZ  119.57  3.000
 56G  CAY  CAH  CAZ  119.05  3.000
 56G  H21  CAG  CAE  121.14  3.000
 56G  H21  CAG  CAZ  120.76  3.000
 56G  CAE  CAG  CAZ  118.10  3.000
 56G  H22  CAE  CAF  119.36  3.000
 56G  H22  CAE  CAG  119.77  3.000
 56G  CAF  CAE  CAG  120.87  3.000
 56G  H23  CAF  CAY  119.91  3.000
 56G  H23  CAF  CAE  119.67  3.000
 56G  CAY  CAF  CAE  120.42  3.000
 56G  NAS  CAY  CAF  116.79  3.000
 56G  CAF  CAY  CAH  119.20  3.000
 56G  NAS  CAY  CAH  124.01  3.000
 56G  H24  NAS  CAW  116.05  3.000
 56G  H24  NAS  CAY  114.58  3.000
 56G  CAW  NAS  CAY  129.37  3.000
 56G  CAK  CAW  OAD  122.83  3.000
 56G  OAD  CAW  NAS  124.07  3.000
 56G  CAK  CAW  NAS  113.09  3.000
 56G  H25  CAK  CAA  120.26  3.000
 56G  H25  CAK  CAW  118.35  3.000
 56G  CAA  CAK  CAW  121.39  3.000
 56G  H28  CAA  H27  117.11  3.000
 56G  H28  CAA  CAK  121.02  3.000
 56G  H27  CAA  CAK  121.87  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
 56G  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 56G  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 56G  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 56G  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 56G  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 56G  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 56G  CONST_07  NAU  CAX  CAI  CBA     0.00   0.0  0
 56G  CONST_08  CAX  NAU  NAP  CBA     0.00   0.0  0
 56G  CONST_09  NAU  NAP  CBA  CAI     0.00   0.0  0
 56G  CONST_10  NAP  NAU  CAX  CAI     0.00   0.0  0
 56G  CONST_11  NAP  CBA  CAI  CAX     0.00   0.0  0
 56G  CONST_12  CAF  CAY  CAH  CAZ     0.00   0.0  0
 56G  CONST_13  CAF  CAE  CAG  CAZ     0.00   0.0  0
 56G  CONST_14  CAE  CAF  CAY  CAH     0.00   0.0  0
 56G  CONST_15  CAE  CAG  CAZ  CAH     0.00   0.0  0
 56G  CONST_16  CAY  CAF  CAE  CAG     0.00   0.0  0
 56G  CONST_17  CAY  CAH  CAZ  CAG     0.00   0.0  0
 56G  CONST_18  NBF  C4   C5   C6    180.00   0.0  0
 56G  CONST_19  C2   N3   C4   NBF   180.00   0.0  0
 56G  CONST_20  OAV  C2   N3   C4    180.00   0.0  0
 56G  CONST_21  NAT  C6   C5   C4    180.00   0.0  0
 56G  CONST_22  OAV  C2   N1   C6    180.00   0.0  0
 56G  CONST_23  C2   N1   C6   NAT   180.00   0.0  0
 56G  CONST_24  CAX  CAI  CBA  NAT   180.00   0.0  0
 56G  CONST_25  NAU  NAP  CBA  NAT   180.00   0.0  0
 56G  CONST_26  CAB  CAX  CAI  CBA   180.00   0.0  0
 56G  CONST_27  NAP  NAU  CAX  CAB   180.00   0.0  0
 56G  CONST_28  CAY  CAH  CAZ  OAV   180.00   0.0  0
 56G  CONST_29  CAE  CAG  CAZ  OAV   180.00   0.0  0
 56G  CONST_30  NAS  CAY  CAH  CAZ   180.00   0.0  0
 56G  CONST_31  NAS  CAY  CAF  CAE   180.00   0.0  0
 56G  CONST_32  H1   C5   C6   N1    180.00   0.0  0
 56G  CONST_33  H19  NAU  NAP  CBA   180.00   0.0  0
 56G  CONST_34  H15  CAI  CAX  NAU   180.00   0.0  0
 56G  CONST_35  H22  CAE  CAG  CAZ   180.00   0.0  0
 56G  CONST_36  H23  CAF  CAY  CAH   180.00   0.0  0
 56G  CONST_37  H21  CAG  CAZ  CAH   180.00   0.0  0
 56G  CONST_38  H20  CAH  CAZ  CAG   180.00   0.0  0
 56G  CONST_39  CAW  NAS  CAY  CAH     0.00   0.0  0
 56G  CONST_40  CAW  NAS  CAY  CAF   180.00   0.0  0
 56G  CONST_41  H24  NAS  CAY  CAH   180.00   0.0  0
 56G  CONST_42  CAK  CAW  NAS  CAY   180.00   0.0  0
 56G  CONST_43  OAD  CAW  NAS  CAY     0.00   0.0  0
 56G  Var_01    CAM  CAO  NBF  C4   -138.16  30.0  1
 56G  Var_02    CAL  CAN  NBF  C4    138.74  30.0  1
 56G  Var_03    CAO  NBF  C4   C5   -171.35  30.0  1
 56G  Var_04    CAM  NBE  CAL  CAN   -58.48  30.0  1
 56G  Var_05    CAO  CAM  NBE  CAL    58.70  30.0  1
 56G  Var_06    NBF  CAO  CAM  NBE   -55.87  30.0  1
 56G  Var_07    NBF  CAN  CAL  NBE    55.37  30.0  1
 56G  Var_08    CBA  NAT  C6   C5     -1.51  30.0  2
 56G  Var_09    CAI  CBA  NAT  C6   -178.03  30.0  2
 56G  Var_10    CAH  CAZ  OAV  C2     81.98  30.0  3
 56G  Var_11    H7   CAC  NBE  CAL    61.95  30.0  3
 56G  Var_12    H16  CAB  CAX  CAI    92.28  30.0  2
 56G  Var_13    CAA  CAK  CAW  NAS   179.38  30.0  2
 56G  Var_14    H27  CAA  CAK  CAW    -0.02   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
 56G  plan-1  NAT  0.020
 56G  plan-1  CBA  0.020
 56G  plan-1  CAI  0.020
 56G  plan-1  CAX  0.020
 56G  plan-1  CAB  0.020
 56G  plan-1  NAU  0.020
 56G  plan-1  NAP  0.020
 56G  plan-1  H15  0.020
 56G  plan-1  H19  0.020
 56G  plan-2  C4   0.020
 56G  plan-2  C5   0.020
 56G  plan-2  C6   0.020
 56G  plan-2  N1   0.020
 56G  plan-2  N3   0.020
 56G  plan-2  NBF  0.020
 56G  plan-2  NAT  0.020
 56G  plan-2  C2   0.020
 56G  plan-2  OAV  0.020
 56G  plan-2  H1   0.020
 56G  plan-3  OAV  0.020
 56G  plan-3  CAZ  0.020
 56G  plan-3  CAH  0.020
 56G  plan-3  CAG  0.020
 56G  plan-3  CAE  0.020
 56G  plan-3  CAF  0.020
 56G  plan-3  CAY  0.020
 56G  plan-3  NAS  0.020
 56G  plan-3  H20  0.020
 56G  plan-3  H21  0.020
 56G  plan-3  H22  0.020
 56G  plan-3  H23  0.020
 56G  plan-4  CAY  0.020
 56G  plan-4  NAS  0.020
 56G  plan-4  CAW  0.020
 56G  plan-4  OAD  0.020
 56G  plan-4  CAK  0.020
 56G  plan-4  H24  0.020
 56G  plan-5  CAW  0.020
 56G  plan-5  CAK  0.020
 56G  plan-5  CAA  0.020
 56G  plan-5  H25  0.020
 56G  plan-5  H27  0.020
 56G  plan-5  H28  0.020

