# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:12:31 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl prop-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(Nc3ncc(Cl)c(Nc4ccccc4OC(=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
 T92  T92  '2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl prop-2-enoate'  ligand  58  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T92
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
 T92  C01   C   CH3   0  -0.518  10.3945   0.0182  -0.4641
 T92  N02   N   NT    0  -0.413   9.0085   0.0509  -0.0586
 T92  C03   C   CH2   0  -0.277   8.2750   1.1031  -0.7289
 T92  C04   C   CH2   0  -0.313   6.8434   1.1693  -0.2303
 T92  C05   C   CH2   0  -0.283   8.3547  -1.2215  -0.2787
 T92  C06   C   CH2   0  -0.306   6.9249  -1.1875   0.2223
 T92  N07   N   NT    0  -0.513   6.1824  -0.1063  -0.4132
 T92  C08   C   CR6   0   0.339   4.7921  -0.1356  -0.2471
 T92  C09   C   CR16  0  -0.310   4.0700  -1.2879  -0.5871
 T92  C10   C   CR16  0  -0.343   2.6997  -1.3435  -0.4487
 T92  C11   C   CR16  0  -0.342   4.0549   0.9513   0.2214
 T92  C12   C   CR16  0  -0.304   2.6700   0.9077   0.3485
 T92  C13   C   CR6   0   0.336   1.9670  -0.2484   0.0248
 T92  N14   N   NH1   0  -0.768   0.5872  -0.4243   0.1383
 T92  C15   C   CR6   0   0.613  -0.3967   0.4148   0.5460
 T92  N16   N   N     0  -0.491  -0.1139   1.6744   0.8594
 T92  C17   C   CR16  0   0.039  -1.1467   2.4213   1.2373
 T92  C18   C   CR6   0  -0.255  -2.4280   1.9417   1.3186
 T92  CL19  CL  CL    0  -0.116  -3.7392   2.9548   1.8049
 T92  C20   C   CR6   0   0.631  -2.6294   0.5837   0.9814
 T92  N21   N   NH1   0  -0.769  -3.8637   0.0356   1.0529
 T92  C22   C   CR6   0   0.290  -4.2128  -1.2926   0.7820
 T92  C23   C   CR16  0  -0.284  -3.4522  -2.3832   1.1970
 T92  C24   C   CR16  0  -0.257  -3.8794  -3.6747   0.9296
 T92  C25   C   CR16  0  -0.265  -5.0787  -3.9007   0.2684
 T92  C26   C   CR16  0  -0.311  -5.8516  -2.8235  -0.1383
 T92  C27   C   CR6   0   0.308  -5.4129  -1.5379   0.1151
 T92  O28   O   O2    0  -0.502  -6.2038  -0.4680  -0.2513
 T92  C29   C   C     0   0.554  -5.9230   0.1472  -1.4220
 T92  C30   C   C1    0  -0.334  -6.8351   1.2836  -1.6388
 T92  C31   C   C2    0  -0.447  -6.7557   2.0202  -2.7420
 T92  O32   O   O     0  -0.411  -5.0438  -0.2152  -2.1539
 T92  N33   N   N     0  -0.515  -1.6074  -0.1498   0.5887
 T92  H1    H   HCH3  0   0.192  10.5284  -0.1833  -1.5384
 T92  H2    H   HCH3  0   0.233  10.8733   0.9730  -0.2409
 T92  H3    H   HCH3  0   0.233  10.9254  -0.7592   0.0877
 T92  H5    H   HCH2  0   0.239   8.7560   2.0627  -0.5261
 T92  H6    H   HCH2  0   0.192   8.2723   0.9652  -1.8246
 T92  H7    H   HCH2  0   0.207   6.8434   1.4862   0.8243
 T92  H8    H   HCH2  0   0.249   6.3158   1.9357  -0.8005
 T92  H9    H   HCH2  0   0.192   8.3575  -1.5032  -1.3463
 T92  H10   H   HCH2  0   0.239   8.8958  -2.0027   0.2606
 T92  H11   H   HCH2  0   0.251   6.4604  -2.1458  -0.0040
 T92  H12   H   HCH2  0   0.211   6.9214  -1.0719   1.3168
 T92  H13   H   HCR6  0   0.261   4.5822  -2.1552  -0.9830
 T92  H14   H   HCR6  0   0.265   2.1822  -2.2545  -0.7277
 T92  H15   H   HCR6  0   0.265   4.5494   1.8678   0.5133
 T92  H16   H   HCR6  0   0.282   2.1522   1.7783   0.7158
 T92  H17   H   HNH1  0   0.408   0.2509  -1.3460  -0.0969
 T92  H18   H   HCR6  0   0.289  -0.9382   3.4553   1.4896
 T92  H19   H   HNH1  0   0.405  -4.6172   0.6555   1.3102
 T92  H20   H   HCR6  0   0.275  -2.5287  -2.2214   1.7318
 T92  H21   H   HCR6  0   0.265  -3.2750  -4.5100   1.2573
 T92  H22   H   HCR6  0   0.267  -5.4152  -4.9092   0.0712
 T92  H23   H   HCR6  0   0.277  -6.7924  -2.9766  -0.6512
 T92  H24   H   H     0   0.291  -7.5687   1.4952  -0.8714
 T92  H26   H   H     0   0.274  -6.0286   1.8179  -3.5175
 T92  H27   H   H     0   0.275  -7.4251   2.8536  -2.9017

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
 T92  N02  C01   single    1.444  0.020  1.444
 T92  N02  C05   single    1.447  0.020  1.447
 T92  N02  C03   single    1.447  0.020  1.447
 T92  C05  C06   single    1.515  0.020  1.515
 T92  C03  C04   single    1.517  0.020  1.517
 T92  C06  N07   single    1.457  0.020  1.457
 T92  C04  N07   single    1.448  0.020  1.448
 T92  N07  C08   single    1.401  0.020  1.401
 T92  O32  C29   double    1.200  0.020  1.200
 T92  C08  C09   aromatic  1.402  0.020  1.402
 T92  C08  C11   aromatic  1.394  0.020  1.394
 T92  C09  C10   aromatic  1.378  0.020  1.378
 T92  C25  C26   aromatic  1.387  0.020  1.387
 T92  C25  C24   aromatic  1.388  0.020  1.388
 T92  C26  C27   aromatic  1.382  0.020  1.382
 T92  C29  C30   single    1.473  0.020  1.473
 T92  C29  O28   single    1.352  0.020  1.352
 T92  C31  C30   double    1.329  0.020  1.329
 T92  C11  C12   aromatic  1.391  0.020  1.391
 T92  C10  C13   aromatic  1.400  0.020  1.400
 T92  C24  C23   aromatic  1.386  0.020  1.386
 T92  C27  O28   single    1.380  0.020  1.380
 T92  C27  C22   aromatic  1.395  0.020  1.395
 T92  C12  C13   aromatic  1.391  0.020  1.391
 T92  C13  N14   single    1.396  0.020  1.396
 T92  C23  C22   aromatic  1.393  0.020  1.393
 T92  C22  N21   single    1.400  0.020  1.400
 T92  N14  C15   single    1.356  0.020  1.356
 T92  N33  C15   aromatic  1.337  0.020  1.337
 T92  N33  C20   aromatic  1.318  0.020  1.318
 T92  C15  N16   aromatic  1.328  0.020  1.328
 T92  N21  C20   single    1.352  0.020  1.352
 T92  C20  C18   aromatic  1.414  0.020  1.414
 T92  N16  C17   aromatic  1.329  0.020  1.329
 T92  C18  C17   aromatic  1.371  0.020  1.371
 T92  C18  CL19  single    1.727  0.020  1.727
 T92  C01  H1    single    0.970  0.020  1.090
 T92  C01  H2    single    0.970  0.020  1.090
 T92  C01  H3    single    0.970  0.020  1.090
 T92  C03  H5    single    0.970  0.020  1.090
 T92  C03  H6    single    0.970  0.020  1.090
 T92  C04  H7    single    0.970  0.020  1.090
 T92  C04  H8    single    0.970  0.020  1.090
 T92  C05  H9    single    0.970  0.020  1.090
 T92  C05  H10   single    0.970  0.020  1.090
 T92  C06  H11   single    0.970  0.020  1.090
 T92  C06  H12   single    0.970  0.020  1.090
 T92  C09  H13   single    0.930  0.020  1.080
 T92  C10  H14   single    0.930  0.020  1.080
 T92  C11  H15   single    0.930  0.020  1.080
 T92  C12  H16   single    0.930  0.020  1.080
 T92  N14  H17   single    0.860  0.020  1.020
 T92  C17  H18   single    0.930  0.020  1.080
 T92  N21  H19   single    0.860  0.020  1.020
 T92  C23  H20   single    0.930  0.020  1.080
 T92  C24  H21   single    0.930  0.020  1.080
 T92  C25  H22   single    0.930  0.020  1.080
 T92  C26  H23   single    0.930  0.020  1.080
 T92  C30  H24   single    0.930  0.020  1.080
 T92  C31  H26   single    0.930  0.020  1.080
 T92  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
 T92  H3    C01  H2    107.85  3.000
 T92  H3    C01  H1    107.69  3.000
 T92  H2    C01  H1    107.84  3.000
 T92  H3    C01  N02   109.93  3.000
 T92  H2    C01  N02   110.11  3.000
 T92  H1    C01  N02   113.24  3.000
 T92  C05   N02  C03   109.86  3.000
 T92  C03   N02  C01   111.89  3.000
 T92  C05   N02  C01   111.77  3.000
 T92  H6    C03  H5    107.15  3.000
 T92  H6    C03  C04   109.22  3.000
 T92  H5    C03  C04   108.43  3.000
 T92  H6    C03  N02   111.72  3.000
 T92  H5    C03  N02   109.24  3.000
 T92  C04   C03  N02   110.96  3.000
 T92  H8    C04  H7    107.36  3.000
 T92  H8    C04  N07   109.39  3.000
 T92  H7    C04  N07   111.99  3.000
 T92  H8    C04  C03   108.36  3.000
 T92  H7    C04  C03   109.10  3.000
 T92  N07   C04  C03   110.53  3.000
 T92  H10   C05  H9    107.07  3.000
 T92  H10   C05  C06   108.67  3.000
 T92  H9    C05  C06   109.13  3.000
 T92  H10   C05  N02   109.26  3.000
 T92  H9    C05  N02   111.73  3.000
 T92  C06   C05  N02   110.87  3.000
 T92  H12   C06  H11   107.32  3.000
 T92  H12   C06  N07   110.74  3.000
 T92  H11   C06  N07   110.18  3.000
 T92  H12   C06  C05   109.52  3.000
 T92  H11   C06  C05   108.31  3.000
 T92  N07   C06  C05   110.68  3.000
 T92  C08   N07  C06   116.01  3.000
 T92  C08   N07  C04   117.16  3.000
 T92  C06   N07  C04   111.46  3.000
 T92  C11   C08  C09   116.74  3.000
 T92  C11   C08  N07   123.25  3.000
 T92  C09   C08  N07   119.99  3.000
 T92  H13   C09  C10   118.35  3.000
 T92  H13   C09  C08   120.24  3.000
 T92  C10   C09  C08   121.39  3.000
 T92  H14   C10  C13   119.63  3.000
 T92  H14   C10  C09   118.85  3.000
 T92  C13   C10  C09   121.51  3.000
 T92  H15   C11  C12   117.19  3.000
 T92  H15   C11  C08   120.63  3.000
 T92  C12   C11  C08   122.17  3.000
 T92  H16   C12  C13   120.52  3.000
 T92  H16   C12  C11   118.96  3.000
 T92  C13   C12  C11   120.51  3.000
 T92  N14   C13  C12   125.83  3.000
 T92  N14   C13  C10   116.51  3.000
 T92  C12   C13  C10   117.66  3.000
 T92  H17   N14  C15   113.17  3.000
 T92  H17   N14  C13   115.20  3.000
 T92  C15   N14  C13   131.60  3.000
 T92  N33   C15  N16   125.86  3.000
 T92  N16   C15  N14   120.21  3.000
 T92  N33   C15  N14   113.92  3.000
 T92  C17   N16  C15   115.75  3.000
 T92  H18   C17  C18   119.97  3.000
 T92  H18   C17  N16   116.90  3.000
 T92  C18   C17  N16   123.13  3.000
 T92  C20   C18  CL19  121.50  3.000
 T92  CL19  C18  C17   121.42  3.000
 T92  C20   C18  C17   117.08  3.000
 T92  N33   C20  N21   119.87  3.000
 T92  N21   C20  C18   120.44  3.000
 T92  N33   C20  C18   119.69  3.000
 T92  H19   N21  C22   116.49  3.000
 T92  H19   N21  C20   116.49  3.000
 T92  C22   N21  C20   127.00  3.000
 T92  C27   C22  C23   118.33  3.000
 T92  C23   C22  N21   123.30  3.000
 T92  C27   C22  N21   118.30  3.000
 T92  H20   C23  C24   119.92  3.000
 T92  H20   C23  C22   119.84  3.000
 T92  C24   C23  C22   120.24  3.000
 T92  H21   C24  C25   120.09  3.000
 T92  H21   C24  C23   119.25  3.000
 T92  C25   C24  C23   120.65  3.000
 T92  H22   C25  C26   119.84  3.000
 T92  H22   C25  C24   120.51  3.000
 T92  C26   C25  C24   119.66  3.000
 T92  H23   C26  C27   119.64  3.000
 T92  H23   C26  C25   120.89  3.000
 T92  C27   C26  C25   119.47  3.000
 T92  O28   C27  C26   119.38  3.000
 T92  O28   C27  C22   118.93  3.000
 T92  C26   C27  C22   121.64  3.000
 T92  C29   O28  C27   117.63  3.000
 T92  O32   C29  C30   126.64  3.000
 T92  C30   C29  O28   110.48  3.000
 T92  O32   C29  O28   122.88  3.000
 T92  H24   C30  C31   121.37  3.000
 T92  H24   C30  C29   117.78  3.000
 T92  C31   C30  C29   120.85  3.000
 T92  H27   C31  H26   117.02  3.000
 T92  H27   C31  C30   120.87  3.000
 T92  H26   C31  C30   122.11  3.000
 T92  C20   N33  C15   118.48  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
 T92  CONST_01  C13   C10  C09  C08      0.00   0.0  0
 T92  CONST_02  C13   C12  C11  C08      0.00   0.0  0
 T92  CONST_03  C12   C11  C08  C09      0.00   0.0  0
 T92  CONST_04  C12   C13  C10  C09      0.00   0.0  0
 T92  CONST_05  C11   C08  C09  C10      0.00   0.0  0
 T92  CONST_06  C11   C12  C13  C10      0.00   0.0  0
 T92  CONST_07  C18   C20  N33  C15      0.00   0.0  0
 T92  CONST_08  C18   C17  N16  C15      0.00   0.0  0
 T92  CONST_09  C20   N33  C15  N16      0.00   0.0  0
 T92  CONST_10  C20   C18  C17  N16      0.00   0.0  0
 T92  CONST_11  N33   C15  N16  C17      0.00   0.0  0
 T92  CONST_12  N33   C20  C18  C17      0.00   0.0  0
 T92  CONST_13  C25   C26  C27  C22      0.00   0.0  0
 T92  CONST_14  C25   C24  C23  C22      0.00   0.0  0
 T92  CONST_15  C26   C25  C24  C23      0.00   0.0  0
 T92  CONST_16  C26   C27  C22  C23      0.00   0.0  0
 T92  CONST_17  C27   C26  C25  C24      0.00   0.0  0
 T92  CONST_18  C27   C22  C23  C24      0.00   0.0  0
 T92  CONST_19  C10   C09  C08  N07    180.00   0.0  0
 T92  CONST_20  C12   C11  C08  N07    180.00   0.0  0
 T92  CONST_21  N14   C13  C10  C09    180.00   0.0  0
 T92  CONST_22  N14   C13  C12  C11    180.00   0.0  0
 T92  CONST_23  C20   N33  C15  N14    180.00   0.0  0
 T92  CONST_24  C17   N16  C15  N14    180.00   0.0  0
 T92  CONST_25  N21   C20  N33  C15    180.00   0.0  0
 T92  CONST_26  CL19  C18  C17  N16    180.00   0.0  0
 T92  CONST_27  N21   C20  C18  C17    180.00   0.0  0
 T92  CONST_28  N33   C20  C18  CL19   180.00   0.0  0
 T92  CONST_29  C26   C27  C22  N21    180.00   0.0  0
 T92  CONST_30  C24   C23  C22  N21    180.00   0.0  0
 T92  CONST_31  O28   C27  C22  C23    180.00   0.0  0
 T92  CONST_32  O28   C27  C26  C25    180.00   0.0  0
 T92  CONST_33  H13   C09  C08  N07      0.00   0.0  0
 T92  CONST_34  H15   C11  C08  N07      0.00   0.0  0
 T92  CONST_35  H14   C10  C09  C08    180.00   0.0  0
 T92  CONST_36  H16   C12  C11  C08    180.00   0.0  0
 T92  CONST_37  H18   C17  N16  C15    180.00   0.0  0
 T92  CONST_38  H23   C26  C27  C22    180.00   0.0  0
 T92  CONST_39  H21   C24  C23  C22    180.00   0.0  0
 T92  CONST_40  H22   C25  C24  C23    180.00   0.0  0
 T92  CONST_41  H20   C23  C24  C25    180.00   0.0  0
 T92  Var_01    N07   C06  C05  N02     56.58  30.0  1
 T92  Var_02    N07   C04  C03  N02    -57.02  30.0  1
 T92  Var_03    C06   C05  N02  C03    -58.25  30.0  1
 T92  Var_04    C06   N07  C04  C03     55.15  30.0  1
 T92  Var_05    C05   N02  C03  C04     58.46  30.0  1
 T92  Var_06    C05   C06  N07  C04    -55.09  30.0  1
 T92  Var_07    C09   C08  N07  C04    171.24  30.0  2
 T92  Var_08    C15   N14  C13  C10   -179.54  30.0  2
 T92  Var_09    N33   C15  N14  C13   -176.38  30.0  2
 T92  Var_10    C22   N21  C20  C18   -178.47  30.0  2
 T92  Var_11    C27   C22  N21  C20   -140.94  30.0  2
 T92  Var_12    H1    C01  N02  C03    -61.70  30.0  3
 T92  Var_13    O32   C29  O28  C27      1.58  30.0  1
 T92  Var_14    C31   C30  C29  O28   -178.79  30.0  2
 T92  Var_15    H26   C31  C30  C29      0.09   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
 T92  plan-1  N07   0.020
 T92  plan-1  C08   0.020
 T92  plan-1  C09   0.020
 T92  plan-1  C10   0.020
 T92  plan-1  C11   0.020
 T92  plan-1  C12   0.020
 T92  plan-1  C13   0.020
 T92  plan-1  N14   0.020
 T92  plan-1  H13   0.020
 T92  plan-1  H14   0.020
 T92  plan-1  H15   0.020
 T92  plan-1  H16   0.020
 T92  plan-2  O28   0.020
 T92  plan-2  C29   0.020
 T92  plan-2  C30   0.020
 T92  plan-2  O32   0.020
 T92  plan-3  N21   0.020
 T92  plan-3  C22   0.020
 T92  plan-3  C23   0.020
 T92  plan-3  C24   0.020
 T92  plan-3  C25   0.020
 T92  plan-3  C26   0.020
 T92  plan-3  C27   0.020
 T92  plan-3  O28   0.020
 T92  plan-3  H20   0.020
 T92  plan-3  H21   0.020
 T92  plan-3  H22   0.020
 T92  plan-3  H23   0.020
 T92  plan-4  N14   0.020
 T92  plan-4  C15   0.020
 T92  plan-4  N16   0.020
 T92  plan-4  C17   0.020
 T92  plan-4  C18   0.020
 T92  plan-4  CL19  0.020
 T92  plan-4  C20   0.020
 T92  plan-4  N21   0.020
 T92  plan-4  N33   0.020
 T92  plan-4  H18   0.020
 T92  plan-5  C29   0.020
 T92  plan-5  C30   0.020
 T92  plan-5  C31   0.020
 T92  plan-5  H24   0.020
 T92  plan-5  H26   0.020
 T92  plan-5  H27   0.020

