# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 10:47:49 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(Nc3ncc(Cl)c(Oc4ccccc4NC(=O)C=C)n3)cc2
#
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
 6H4  6H4  N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide  ligand  58  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6H4
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
 6H4  C10   C   CR16  0  -0.335  -1.7706   1.1188  -0.9252
 6H4  C11   C   CR16  0  -0.348  -3.3669  -0.9517  -0.0781
 6H4  C12   C   CR16  0  -0.295  -1.9951  -1.1446  -0.2000
 6H4  C13   C   CR6   0   0.340  -1.1702  -0.1062  -0.6177
 6H4  C15   C   CR6   0   0.622   1.1128  -1.0707  -0.2999
 6H4  C17   C   CR16  0   0.036   1.6818  -2.9022   0.8887
 6H4  C18   C   CR6   0  -0.254   3.0218  -2.6471   0.6969
 6H4  C20   C   CR6   0   0.618   3.3201  -1.5188  -0.0759
 6H4  N02   N   NT    0  -0.400  -8.1409   0.8009   0.4255
 6H4  C03   C   CH2   0  -0.321  -7.6530  -0.3701  -0.2778
 6H4  C04   C   CH2   0  -0.320  -6.1837  -0.6882  -0.0152
 6H4  C05   C   CH2   0  -0.326  -7.2773   1.9264   0.1226
 6H4  C06   C   CH2   0  -0.313  -5.8033   1.6625   0.4002
 6H4  N07   N   NT    0  -0.511  -5.3578   0.4681  -0.3119
 6H4  C08   C   CR6   0   0.348  -3.9769   0.2660  -0.3866
 6H4  C09   C   CR16  0  -0.317  -3.1335   1.2992  -0.8209
 6H4  N14   N   NH1   0  -0.765   0.2137  -0.1889  -0.7899
 6H4  N16   N   N     0  -0.473   0.7205  -2.1252   0.4061
 6H4  CL19  CL  CL    0  -0.101   4.2548  -3.6435   1.3579
 6H4  O21   O   O2    0  -0.491   4.6065  -1.2237  -0.2773
 6H4  C22   C   CR6   0   0.339   4.9462  -0.0840  -0.9776
 6H4  C23   C   CR16  0  -0.326   5.6243  -0.2399  -2.1728
 6H4  C24   C   CR16  0  -0.256   6.0329   0.8834  -2.8775
 6H4  C25   C   CR16  0  -0.261   5.7625   2.1504  -2.3807
 6H4  C26   C   CR16  0  -0.291   5.0963   2.2968  -1.1730
 6H4  C27   C   CR6   0   0.293   4.6827   1.1819  -0.4554
 6H4  N28   N   NH1   0  -0.751   3.9972   1.3114   0.7650
 6H4  C29   C   C     0   0.527   2.7441   1.8380   0.8421
 6H4  C30   C   C1    0  -0.327   2.0778   1.6068   2.1470
 6H4  C31   C   C2    0  -0.463   0.7837   1.8564   2.3113
 6H4  O32   O   O     0  -0.465   2.2143   2.4267  -0.0832
 6H4  N33   N   N     0  -0.494   2.3870  -0.7693  -0.5863
 6H4  H1    H   HCR6  0   0.261  -1.1598   1.9472  -1.2666
 6H4  H2    H   HCR6  0   0.266  -3.9525  -1.7904   0.2718
 6H4  H3    H   HCR6  0   0.277  -1.5815  -2.1073   0.0535
 6H4  H4    H   HCR6  0   0.295   1.3717  -3.7676   1.4638
 6H4  H5    H   HCH3  0   0.200  -7.4435   0.2981   2.4101
 6H4  H6    H   HCH3  0   0.233  -8.7311   1.4973   2.2990
 6H4  H7    H   HCH3  0   0.233  -9.0832  -0.2002   1.9934
 6H4  H9    H   HCH2  0   0.241  -8.2605  -1.2371  -0.0090
 6H4  H10   H   HCH2  0   0.233  -7.7849  -0.2035  -1.3521
 6H4  H11   H   HCH2  0   0.211  -6.0473  -1.0330   1.0222
 6H4  H12   H   HCH2  0   0.251  -5.8952  -1.5156  -0.6662
 6H4  H13   H   HCH2  0   0.233  -7.3925   2.1723  -0.9384
 6H4  H14   H   HCH2  0   0.241  -7.6028   2.7989   0.6932
 6H4  H15   H   HCH2  0   0.253  -5.2346   2.5305   0.0714
 6H4  H16   H   HCH2  0   0.216  -5.6283   1.5572   1.4813
 6H4  H17   H   HCR6  0   0.262  -3.5430   2.2607  -1.1012
 6H4  H18   H   HNH1  0   0.411   0.6448   0.6225  -1.2084
 6H4  H19   H   HCR6  0   0.278   5.8235  -1.2346  -2.5495
 6H4  H20   H   HCR6  0   0.268   6.5610   0.7639  -3.8138
 6H4  H21   H   HCR6  0   0.266   6.0784   3.0289  -2.9270
 6H4  H22   H   HCR6  0   0.273   4.9055   3.2829  -0.7725
 6H4  H23   H   HNH1  0   0.411   4.3480   0.7964   1.5588
 6H4  H24   H   H     0   0.276   2.6647   1.1896   2.9579
 6H4  H26   H   H     0   0.259   0.1753   2.2571   1.5108
 6H4  H27   H   H     0   0.265   0.2914   1.6588   3.2532
 6H4  C01   C   CH3   0  -0.529  -8.3404   0.5854   1.8448

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
 6H4  C01  N02   single    1.449  0.020  1.449
 6H4  C05  N02   single    1.451  0.020  1.451
 6H4  C05  C06   single    1.523  0.020  1.523
 6H4  N02  C03   single    1.450  0.020  1.450
 6H4  C06  N07   single    1.460  0.020  1.460
 6H4  C03  C04   single    1.526  0.020  1.526
 6H4  C04  N07   single    1.452  0.020  1.452
 6H4  N07  C08   single    1.398  0.020  1.398
 6H4  C26  C25   aromatic  1.387  0.020  1.387
 6H4  C26  C27   aromatic  1.389  0.020  1.389
 6H4  C08  C09   aromatic  1.403  0.020  1.403
 6H4  C08  C11   aromatic  1.396  0.020  1.396
 6H4  C25  C24   aromatic  1.387  0.020  1.387
 6H4  C09  C10   aromatic  1.379  0.020  1.379
 6H4  O32  C29   double    1.218  0.020  1.218
 6H4  C30  C29   single    1.483  0.020  1.483
 6H4  C30  C31   double    1.328  0.020  1.328
 6H4  C29  N28   single    1.361  0.020  1.361
 6H4  C11  C12   aromatic  1.391  0.020  1.391
 6H4  N28  C27   single    1.406  0.020  1.406
 6H4  C10  C13   aromatic  1.398  0.020  1.398
 6H4  C27  C22   aromatic  1.395  0.020  1.395
 6H4  C24  C23   aromatic  1.388  0.020  1.388
 6H4  C12  C13   aromatic  1.390  0.020  1.390
 6H4  C13  N14   single    1.397  0.020  1.397
 6H4  C22  C23   aromatic  1.383  0.020  1.383
 6H4  C22  O21   single    1.380  0.020  1.380
 6H4  N14  C15   single    1.351  0.020  1.351
 6H4  N33  C15   aromatic  1.340  0.020  1.340
 6H4  N33  C20   aromatic  1.301  0.020  1.301
 6H4  C15  N16   aromatic  1.328  0.020  1.328
 6H4  O21  C20   single    1.335  0.020  1.335
 6H4  C20  C18   aromatic  1.400  0.020  1.400
 6H4  N16  C17   aromatic  1.327  0.020  1.327
 6H4  C18  C17   aromatic  1.377  0.020  1.377
 6H4  C18  CL19  single    1.718  0.020  1.718
 6H4  C10  H1    single    0.930  0.020  1.080
 6H4  C11  H2    single    0.930  0.020  1.080
 6H4  C12  H3    single    0.930  0.020  1.080
 6H4  C17  H4    single    0.930  0.020  1.080
 6H4  C01  H5    single    0.970  0.020  1.090
 6H4  C01  H6    single    0.970  0.020  1.090
 6H4  C01  H7    single    0.970  0.020  1.090
 6H4  C03  H9    single    0.970  0.020  1.090
 6H4  C03  H10   single    0.970  0.020  1.090
 6H4  C04  H11   single    0.970  0.020  1.090
 6H4  C04  H12   single    0.970  0.020  1.090
 6H4  C05  H13   single    0.970  0.020  1.090
 6H4  C05  H14   single    0.970  0.020  1.090
 6H4  C06  H15   single    0.970  0.020  1.090
 6H4  C06  H16   single    0.970  0.020  1.090
 6H4  C09  H17   single    0.930  0.020  1.080
 6H4  N14  H18   single    0.860  0.020  1.020
 6H4  C23  H19   single    0.930  0.020  1.080
 6H4  C24  H20   single    0.930  0.020  1.080
 6H4  C25  H21   single    0.930  0.020  1.080
 6H4  C26  H22   single    0.930  0.020  1.080
 6H4  N28  H23   single    0.860  0.020  1.020
 6H4  C30  H24   single    0.930  0.020  1.080
 6H4  C31  H26   single    0.930  0.020  1.080
 6H4  C31  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
 6H4  H1    C10  C09  118.73  3.000
 6H4  H1    C10  C13  119.78  3.000
 6H4  C09   C10  C13  121.49  3.000
 6H4  H2    C11  C08  120.75  3.000
 6H4  H2    C11  C12  117.08  3.000
 6H4  C08   C11  C12  122.17  3.000
 6H4  H3    C12  C13  120.67  3.000
 6H4  H3    C12  C11  118.79  3.000
 6H4  C13   C12  C11  120.53  3.000
 6H4  N14   C13  C12  125.49  3.000
 6H4  N14   C13  C10  116.75  3.000
 6H4  C12   C13  C10  117.75  3.000
 6H4  N33   C15  N16  124.95  3.000
 6H4  N16   C15  N14  120.95  3.000
 6H4  N33   C15  N14  114.10  3.000
 6H4  H4    C17  N16  116.94  3.000
 6H4  H4    C17  C18  119.99  3.000
 6H4  N16   C17  C18  123.06  3.000
 6H4  CL19  C18  C20  121.81  3.000
 6H4  CL19  C18  C17  122.50  3.000
 6H4  C20   C18  C17  115.69  3.000
 6H4  N33   C20  O21  120.30  3.000
 6H4  O21   C20  C18  117.83  3.000
 6H4  N33   C20  C18  121.87  3.000
 6H4  C05   N02  C03  108.96  3.000
 6H4  C03   N02  C01  113.65  3.000
 6H4  C05   N02  C01  113.69  3.000
 6H4  H10   C03  H9   107.17  3.000
 6H4  H10   C03  C04  108.45  3.000
 6H4  H9    C03  C04  109.13  3.000
 6H4  H10   C03  N02  108.20  3.000
 6H4  H9    C03  N02  109.54  3.000
 6H4  C04   C03  N02  114.13  3.000
 6H4  H12   C04  H11  106.96  3.000
 6H4  H12   C04  N07  109.36  3.000
 6H4  H11   C04  N07  111.79  3.000
 6H4  H12   C04  C03  108.05  3.000
 6H4  H11   C04  C03  110.27  3.000
 6H4  N07   C04  C03  110.28  3.000
 6H4  H14   C05  H13  107.19  3.000
 6H4  H14   C05  C06  109.36  3.000
 6H4  H13   C05  C06  108.50  3.000
 6H4  H14   C05  N02  109.47  3.000
 6H4  H13   C05  N02  108.30  3.000
 6H4  C06   C05  N02  113.81  3.000
 6H4  H16   C06  H15  106.86  3.000
 6H4  H16   C06  N07  110.63  3.000
 6H4  H15   C06  N07  110.22  3.000
 6H4  H16   C06  C05  110.47  3.000
 6H4  H15   C06  C05  108.21  3.000
 6H4  N07   C06  C05  110.37  3.000
 6H4  C08   N07  C06  116.48  3.000
 6H4  C08   N07  C04  117.25  3.000
 6H4  C06   N07  C04  112.23  3.000
 6H4  C09   C08  N07  120.27  3.000
 6H4  C09   C08  C11  116.62  3.000
 6H4  N07   C08  C11  123.09  3.000
 6H4  H17   C09  C08  120.49  3.000
 6H4  H17   C09  C10  118.08  3.000
 6H4  C08   C09  C10  121.43  3.000
 6H4  H18   N14  C15  112.99  3.000
 6H4  H18   N14  C13  115.24  3.000
 6H4  C15   N14  C13  130.77  3.000
 6H4  C17   N16  C15  116.38  3.000
 6H4  C22   O21  C20  119.75  3.000
 6H4  C27   C22  C23  121.24  3.000
 6H4  C23   C22  O21  117.78  3.000
 6H4  C27   C22  O21  120.87  3.000
 6H4  H19   C23  C24  120.87  3.000
 6H4  H19   C23  C22  119.65  3.000
 6H4  C24   C23  C22  119.48  3.000
 6H4  H20   C24  C25  120.40  3.000
 6H4  H20   C24  C23  119.60  3.000
 6H4  C25   C24  C23  120.00  3.000
 6H4  H21   C25  C26  119.62  3.000
 6H4  H21   C25  C24  120.26  3.000
 6H4  C26   C25  C24  120.11  3.000
 6H4  H22   C26  C27  119.22  3.000
 6H4  H22   C26  C25  120.23  3.000
 6H4  C27   C26  C25  120.55  3.000
 6H4  N28   C27  C26  121.32  3.000
 6H4  N28   C27  C22  120.06  3.000
 6H4  C26   C27  C22  118.62  3.000
 6H4  H23   N28  C29  118.22  3.000
 6H4  H23   N28  C27  117.80  3.000
 6H4  C29   N28  C27  122.26  3.000
 6H4  O32   C29  C30  123.25  3.000
 6H4  C30   C29  N28  113.77  3.000
 6H4  O32   C29  N28  122.97  3.000
 6H4  H24   C30  C31  120.47  3.000
 6H4  H24   C30  C29  118.34  3.000
 6H4  C31   C30  C29  121.15  3.000
 6H4  H27   C31  H26  117.13  3.000
 6H4  H27   C31  C30  121.14  3.000
 6H4  H26   C31  C30  121.72  3.000
 6H4  C20   N33  C15  117.94  3.000
 6H4  H7    C01  H6   107.53  3.000
 6H4  H7    C01  H5   107.30  3.000
 6H4  H6    C01  H5   107.26  3.000
 6H4  H7    C01  N02  109.52  3.000
 6H4  H6    C01  N02  109.43  3.000
 6H4  H5    C01  N02  115.49  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
 6H4  CONST_01  C11   C08  C09  C10      0.00   0.0  0
 6H4  CONST_02  C11   C12  C13  C10      0.00   0.0  0
 6H4  CONST_03  C09   C08  C11  C12      0.00   0.0  0
 6H4  CONST_04  C09   C10  C13  C12      0.00   0.0  0
 6H4  CONST_05  C08   C09  C10  C13      0.00   0.0  0
 6H4  CONST_06  C08   C11  C12  C13      0.00   0.0  0
 6H4  CONST_07  C18   C20  N33  C15      0.00   0.0  0
 6H4  CONST_08  C18   C17  N16  C15      0.00   0.0  0
 6H4  CONST_09  N33   C15  N16  C17      0.00   0.0  0
 6H4  CONST_10  N33   C20  C18  C17      0.00   0.0  0
 6H4  CONST_11  N16   C15  N33  C20      0.00   0.0  0
 6H4  CONST_12  N16   C17  C18  C20      0.00   0.0  0
 6H4  CONST_13  C25   C26  C27  C22      0.00   0.0  0
 6H4  CONST_14  C25   C24  C23  C22      0.00   0.0  0
 6H4  CONST_15  C26   C25  C24  C23      0.00   0.0  0
 6H4  CONST_16  C26   C27  C22  C23      0.00   0.0  0
 6H4  CONST_17  C27   C26  C25  C24      0.00   0.0  0
 6H4  CONST_18  C27   C22  C23  C24      0.00   0.0  0
 6H4  CONST_19  N07   C08  C09  C10    180.00   0.0  0
 6H4  CONST_20  N07   C08  C11  C12    180.00   0.0  0
 6H4  CONST_21  N14   C13  C12  C11    180.00   0.0  0
 6H4  CONST_22  O21   C20  N33  C15    180.00   0.0  0
 6H4  CONST_23  N14   C15  N16  C17    180.00   0.0  0
 6H4  CONST_24  O21   C20  C18  C17    180.00   0.0  0
 6H4  CONST_25  N14   C15  N33  C20    180.00   0.0  0
 6H4  CONST_26  N14   C13  C10  C09    180.00   0.0  0
 6H4  CONST_27  CL19  C18  C17  N16    180.00   0.0  0
 6H4  CONST_28  N33   C20  C18  CL19   180.00   0.0  0
 6H4  CONST_29  C26   C27  C22  O21    180.00   0.0  0
 6H4  CONST_30  C24   C23  C22  O21    180.00   0.0  0
 6H4  CONST_31  N28   C27  C22  C23    180.00   0.0  0
 6H4  CONST_32  N28   C27  C26  C25    180.00   0.0  0
 6H4  CONST_33  H3    C12  C13  C10    180.00   0.0  0
 6H4  CONST_34  H17   C09  C08  C11    180.00   0.0  0
 6H4  CONST_35  H1    C10  C13  C12    180.00   0.0  0
 6H4  CONST_36  H2    C11  C12  C13    180.00   0.0  0
 6H4  CONST_37  H4    C17  N16  C15    180.00   0.0  0
 6H4  CONST_38  H22   C26  C27  C22    180.00   0.0  0
 6H4  CONST_39  H20   C24  C23  C22    180.00   0.0  0
 6H4  CONST_40  H21   C25  C24  C23    180.00   0.0  0
 6H4  CONST_41  H19   C23  C24  C25    180.00   0.0  0
 6H4  CONST_45  O32   C29  N28  C27      0.00   0.0  0
 6H4  CONST_46  C30   C29  N28  C27    180.00   0.0  0
 6H4  Var_01    C06   N07  C08  C11    131.35  30.0  2
 6H4  Var_02    N07   C06  C05  N02     55.02  30.0  1
 6H4  Var_03    N07   C04  C03  N02    -54.74  30.0  1
 6H4  Var_04    C06   C05  N02  C03    -54.03  30.0  1
 6H4  Var_05    C05   N02  C03  C04     53.93  30.0  1
 6H4  Var_06    C05   C06  N07  C04    -54.24  30.0  1
 6H4  Var_07    C15   N14  C13  C10    161.98  30.0  2
 6H4  Var_08    N33   C15  N14  C13   -174.49  30.0  2
 6H4  Var_09    C27   C22  O21  C20     66.89  30.0  1
 6H4  Var_10    N33   C20  O21  C22      3.02  30.0  2
 6H4  Var_11    H5    C01  N02  C03     60.35  30.0  3
 6H4  Var_12    C31   C30  C29  N28   -168.70  30.0  2
 6H4  Var_13    H26   C31  C30  C29     -1.43   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
 6H4  plan-1  C10   0.020
 6H4  plan-1  C11   0.020
 6H4  plan-1  C12   0.020
 6H4  plan-1  C13   0.020
 6H4  plan-1  N07   0.020
 6H4  plan-1  C08   0.020
 6H4  plan-1  C09   0.020
 6H4  plan-1  N14   0.020
 6H4  plan-1  H1    0.020
 6H4  plan-1  H2    0.020
 6H4  plan-1  H3    0.020
 6H4  plan-1  H17   0.020
 6H4  plan-2  O21   0.020
 6H4  plan-2  C22   0.020
 6H4  plan-2  C23   0.020
 6H4  plan-2  C24   0.020
 6H4  plan-2  C25   0.020
 6H4  plan-2  C26   0.020
 6H4  plan-2  C27   0.020
 6H4  plan-2  N28   0.020
 6H4  plan-2  H19   0.020
 6H4  plan-2  H20   0.020
 6H4  plan-2  H21   0.020
 6H4  plan-2  H22   0.020
 6H4  plan-3  C15   0.020
 6H4  plan-3  C17   0.020
 6H4  plan-3  C18   0.020
 6H4  plan-3  C20   0.020
 6H4  plan-3  N14   0.020
 6H4  plan-3  N16   0.020
 6H4  plan-3  CL19  0.020
 6H4  plan-3  O21   0.020
 6H4  plan-3  N33   0.020
 6H4  plan-3  H4    0.020
 6H4  plan-4  C27   0.020
 6H4  plan-4  N28   0.020
 6H4  plan-4  C29   0.020
 6H4  plan-4  C30   0.020
 6H4  plan-4  O32   0.020
 6H4  plan-4  H23   0.020
 6H4  plan-5  C29   0.020
 6H4  plan-5  C30   0.020
 6H4  plan-5  C31   0.020
 6H4  plan-5  H24   0.020
 6H4  plan-5  H26   0.020
 6H4  plan-5  H27   0.020

