# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:20:54 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 2-chloro-N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(Nc3ncc(Cl)c(Oc4ccccc4NC(=O)CCl)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
 5KW  5KW  2-chloro-N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}acetamide  ligand  57  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_5KW
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
 5KW  C01  C   CH3   0  -0.529   8.4534   1.6142  -1.3503
 5KW  N02  N   NT    0  -0.400   8.3486   0.7512  -0.1907
 5KW  C03  C   CH2   0  -0.321   7.6341   1.3528   0.9181
 5KW  C04  C   CH2   0  -0.321   6.1236   1.4288   0.7188
 5KW  C05  C   CH2   0  -0.324   7.7727  -0.5486  -0.4758
 5KW  C06  C   CH2   0  -0.313   6.2667  -0.5223  -0.7042
 5KW  N07  N   NT    0  -0.512   5.5876   0.1123   0.4222
 5KW  C08  C   CR6   0   0.361   4.2047  -0.0513   0.4995
 5KW  C09  C   CR16  0  -0.333   3.6301  -1.3229   0.3455
 5KW  C10  C   CR16  0  -0.269   2.2678  -1.5262   0.4562
 5KW  C11  C   CR16  0  -0.356   3.3325   1.0091   0.7688
 5KW  C12  C   CR16  0  -0.294   1.9640   0.8055   0.8722
 5KW  C13  C   CR6   0   0.306   1.4120  -0.4582   0.7161
 5KW  N14  N   NH1   0  -0.753   0.0263  -0.6181   0.8837
 5KW  C15  C   CR6   0   0.592  -0.8238  -1.2836   0.0722
 5KW  N16  N   N     0  -0.458  -0.3548  -1.9733  -0.9632
 5KW  C17  C   CR16  0   0.022  -1.2586  -2.5566  -1.7378
 5KW  C18  C   CR6   0  -0.247  -2.6163  -2.4584  -1.5167
 5KW  CL1  CL  CL    0  -0.101  -3.7742  -3.1955  -2.5494
 5KW  C20  C   CR6   0   0.616  -2.9957  -1.7149  -0.3950
 5KW  O21  O   O2    0  -0.490  -4.3006  -1.5750  -0.1507
 5KW  C22  C   CR6   0   0.341  -4.7174  -0.8285   0.9321
 5KW  C23  C   CR16  0  -0.325  -5.3954  -1.4831   1.9443
 5KW  C24  C   CR16  0  -0.255  -5.8795  -0.7567   3.0227
 5KW  C25  C   CR16  0  -0.261  -5.6859   0.6159   3.0784
 5KW  C26  C   CR16  0  -0.286  -5.0191   1.2663   2.0507
 5KW  C27  C   CR6   0   0.292  -4.5305   0.5522   0.9649
 5KW  N28  N   NH1   0  -0.734  -3.8509   1.1990  -0.0848
 5KW  C29  C   C     0   0.542  -2.6504   1.8031   0.0929
 5KW  C30  C   CH2   0  -0.590  -1.9923   2.1750  -1.2247
 5KW  O31  O   O     0  -0.439  -2.1428   2.0047   1.1728
 5KW  N32  N   N     0  -0.491  -2.1181  -1.1638   0.3953
 5KW  H1   H   HCH3  0   0.200   7.4996   1.9092  -1.8080
 5KW  H2   H   HCH3  0   0.233   8.9748   2.5315  -1.0716
 5KW  H3   H   HCH3  0   0.233   9.0460   1.1190  -2.1209
 5KW  H5   H   HCH2  0   0.233   7.8365   0.7637   1.8187
 5KW  H6   H   HCH2  0   0.241   8.0208   2.3584   1.0987
 5KW  H7   H   HCH2  0   0.252   5.6815   1.8012   1.6443
 5KW  H8   H   HCH2  0   0.214   5.8798   2.1565  -0.0712
 5KW  H9   H   HCH2  0   0.241   8.2618  -0.9799  -1.3520
 5KW  H10  H   HCH2  0   0.233   7.9842  -1.2114   0.3701
 5KW  H11  H   HCH2  0   0.217   6.0257  -0.0006  -1.6423
 5KW  H12  H   HCH2  0   0.255   5.9258  -1.5492  -0.8208
 5KW  H13  H   HCR6  0   0.262   4.2576  -2.1864   0.1700
 5KW  H14  H   HCR6  0   0.261   1.8769  -2.5289   0.3545
 5KW  H15  H   HCR6  0   0.268   3.7014   2.0184   0.8840
 5KW  H16  H   HCR6  0   0.254   1.3168   1.6547   1.0569
 5KW  H17  H   HNH1  0   0.406  -0.4261   0.0025   1.5385
 5KW  H18  H   HCR6  0   0.295  -0.8885  -3.1235  -2.5849
 5KW  H19  H   HCR6  0   0.279  -5.5374  -2.5545   1.8878
 5KW  H20  H   HCR6  0   0.270  -6.4056  -1.2669   3.8180
 5KW  H21  H   HCR6  0   0.267  -6.0640   1.1854   3.9165
 5KW  H22  H   HCR6  0   0.275  -4.8867   2.3393   2.0805
 5KW  H23  H   HNH1  0   0.418  -4.1869   1.0530  -1.0260
 5KW  H24  H   HCH2  0   0.313  -1.6873   1.2693  -1.7510
 5KW  H25  H   HCH2  0   0.325  -2.6855   2.7160  -1.8681
 5KW  CL2  CL  CL    0  -0.116  -0.5548   3.1768  -0.9715

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
 5KW  C03  N02  single    1.450  0.020  1.450
 5KW  C03  C04  single    1.525  0.020  1.525
 5KW  N02  C05  single    1.450  0.020  1.450
 5KW  N02  C01  single    1.449  0.020  1.449
 5KW  C05  C06  single    1.523  0.020  1.523
 5KW  C04  N07  single    1.452  0.020  1.452
 5KW  C25  C26  aromatic  1.387  0.020  1.387
 5KW  C25  C24  aromatic  1.387  0.020  1.387
 5KW  N07  C06  single    1.460  0.020  1.460
 5KW  N07  C08  single    1.395  0.020  1.395
 5KW  C26  C27  aromatic  1.388  0.020  1.388
 5KW  C11  C08  aromatic  1.399  0.020  1.399
 5KW  C11  C12  aromatic  1.387  0.020  1.387
 5KW  O31  C29  double    1.210  0.020  1.210
 5KW  C08  C09  aromatic  1.404  0.020  1.404
 5KW  C24  C23  aromatic  1.387  0.020  1.387
 5KW  C29  C30  single    1.519  0.020  1.519
 5KW  C29  N28  single    1.356  0.020  1.356
 5KW  C12  C13  aromatic  1.388  0.020  1.388
 5KW  C27  N28  single    1.408  0.020  1.408
 5KW  C27  C22  aromatic  1.394  0.020  1.394
 5KW  C09  C10  aromatic  1.382  0.020  1.382
 5KW  C23  C22  aromatic  1.383  0.020  1.383
 5KW  C13  C10  aromatic  1.393  0.020  1.393
 5KW  C13  N14  single    1.405  0.020  1.405
 5KW  C22  O21  single    1.380  0.020  1.380
 5KW  N14  C15  single    1.351  0.020  1.351
 5KW  N32  C15  aromatic  1.339  0.020  1.339
 5KW  N32  C20  aromatic  1.303  0.020  1.303
 5KW  C15  N16  aromatic  1.330  0.020  1.330
 5KW  O21  C20  single    1.335  0.020  1.335
 5KW  C20  C18  aromatic  1.398  0.020  1.398
 5KW  N16  C17  aromatic  1.326  0.020  1.326
 5KW  C18  C17  aromatic  1.379  0.020  1.379
 5KW  C18  CL1  single    1.718  0.020  1.718
 5KW  C01  H1   single    0.970  0.020  1.090
 5KW  C01  H2   single    0.970  0.020  1.090
 5KW  C01  H3   single    0.970  0.020  1.090
 5KW  C03  H5   single    0.970  0.020  1.090
 5KW  C03  H6   single    0.970  0.020  1.090
 5KW  C04  H7   single    0.970  0.020  1.090
 5KW  C04  H8   single    0.970  0.020  1.090
 5KW  C05  H9   single    0.970  0.020  1.090
 5KW  C05  H10  single    0.970  0.020  1.090
 5KW  C06  H11  single    0.970  0.020  1.090
 5KW  C06  H12  single    0.970  0.020  1.090
 5KW  C09  H13  single    0.930  0.020  1.080
 5KW  C10  H14  single    0.930  0.020  1.080
 5KW  C11  H15  single    0.930  0.020  1.080
 5KW  C12  H16  single    0.930  0.020  1.080
 5KW  N14  H17  single    0.860  0.020  1.020
 5KW  C17  H18  single    0.930  0.020  1.080
 5KW  C23  H19  single    0.930  0.020  1.080
 5KW  C24  H20  single    0.930  0.020  1.080
 5KW  C25  H21  single    0.930  0.020  1.080
 5KW  C26  H22  single    0.930  0.020  1.080
 5KW  N28  H23  single    0.860  0.020  1.020
 5KW  C30  H24  single    0.970  0.020  1.090
 5KW  C30  H25  single    0.970  0.020  1.090
 5KW  C30  CL2  single    1.770  0.020  1.770

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
 5KW  H3   C01  H2   107.60  3.000
 5KW  H3   C01  H1   107.41  3.000
 5KW  H2   C01  H1   107.19  3.000
 5KW  H3   C01  N02  109.52  3.000
 5KW  H2   C01  N02  109.31  3.000
 5KW  H1   C01  N02  115.51  3.000
 5KW  C05  N02  C03  109.06  3.000
 5KW  C05  N02  C01  113.90  3.000
 5KW  C03  N02  C01  113.61  3.000
 5KW  H6   C03  H5   107.09  3.000
 5KW  H6   C03  C04  109.05  3.000
 5KW  H5   C03  C04  108.50  3.000
 5KW  H6   C03  N02  109.51  3.000
 5KW  H5   C03  N02  108.34  3.000
 5KW  C04  C03  N02  114.13  3.000
 5KW  H8   C04  H7   107.05  3.000
 5KW  H8   C04  N07  111.76  3.000
 5KW  H7   C04  N07  109.46  3.000
 5KW  H8   C04  C03  110.23  3.000
 5KW  H7   C04  C03  107.90  3.000
 5KW  N07  C04  C03  110.31  3.000
 5KW  H10  C05  H9   107.10  3.000
 5KW  H10  C05  C06  108.50  3.000
 5KW  H9   C05  C06  109.23  3.000
 5KW  H10  C05  N02  108.29  3.000
 5KW  H9   C05  N02  109.50  3.000
 5KW  C06  C05  N02  113.99  3.000
 5KW  H12  C06  H11  106.71  3.000
 5KW  H12  C06  N07  110.31  3.000
 5KW  H11  C06  N07  110.48  3.000
 5KW  H12  C06  C05  108.02  3.000
 5KW  H11  C06  C05  110.65  3.000
 5KW  N07  C06  C05  110.59  3.000
 5KW  C08  N07  C06  116.93  3.000
 5KW  C08  N07  C04  117.45  3.000
 5KW  C06  N07  C04  112.33  3.000
 5KW  C11  C08  C09  116.90  3.000
 5KW  C09  C08  N07  120.40  3.000
 5KW  C11  C08  N07  122.67  3.000
 5KW  H13  C09  C10  117.87  3.000
 5KW  H13  C09  C08  120.22  3.000
 5KW  C10  C09  C08  121.87  3.000
 5KW  H14  C10  C13  120.43  3.000
 5KW  H14  C10  C09  119.05  3.000
 5KW  C13  C10  C09  120.51  3.000
 5KW  H15  C11  C12  117.76  3.000
 5KW  H15  C11  C08  121.03  3.000
 5KW  C12  C11  C08  121.19  3.000
 5KW  H16  C12  C13  119.68  3.000
 5KW  H16  C12  C11  119.13  3.000
 5KW  C13  C12  C11  121.17  3.000
 5KW  N14  C13  C12  118.85  3.000
 5KW  N14  C13  C10  122.75  3.000
 5KW  C12  C13  C10  118.34  3.000
 5KW  H17  N14  C15  114.25  3.000
 5KW  H17  N14  C13  116.71  3.000
 5KW  C15  N14  C13  127.25  3.000
 5KW  N32  C15  N16  125.11  3.000
 5KW  N16  C15  N14  120.10  3.000
 5KW  N32  C15  N14  114.79  3.000
 5KW  C17  N16  C15  116.28  3.000
 5KW  H18  C17  C18  119.90  3.000
 5KW  H18  C17  N16  116.99  3.000
 5KW  C18  C17  N16  123.11  3.000
 5KW  C20  C18  CL1  121.84  3.000
 5KW  CL1  C18  C17  122.46  3.000
 5KW  C20  C18  C17  115.70  3.000
 5KW  N32  C20  O21  120.20  3.000
 5KW  O21  C20  C18  117.89  3.000
 5KW  N32  C20  C18  121.91  3.000
 5KW  C22  O21  C20  119.71  3.000
 5KW  C27  C22  C23  121.16  3.000
 5KW  C23  C22  O21  117.81  3.000
 5KW  C27  C22  O21  120.93  3.000
 5KW  H19  C23  C24  120.87  3.000
 5KW  H19  C23  C22  119.64  3.000
 5KW  C24  C23  C22  119.49  3.000
 5KW  H20  C24  C25  120.34  3.000
 5KW  H20  C24  C23  119.63  3.000
 5KW  C25  C24  C23  120.03  3.000
 5KW  H21  C25  C26  119.69  3.000
 5KW  H21  C25  C24  120.22  3.000
 5KW  C26  C25  C24  120.08  3.000
 5KW  H22  C26  C27  119.26  3.000
 5KW  H22  C26  C25  120.24  3.000
 5KW  C27  C26  C25  120.49  3.000
 5KW  N28  C27  C26  121.11  3.000
 5KW  N28  C27  C22  120.16  3.000
 5KW  C26  C27  C22  118.74  3.000
 5KW  H23  N28  C29  118.76  3.000
 5KW  H23  N28  C27  117.89  3.000
 5KW  C29  N28  C27  122.31  3.000
 5KW  O31  C29  C30  123.47  3.000
 5KW  C30  C29  N28  112.28  3.000
 5KW  O31  C29  N28  124.24  3.000
 5KW  CL2  C30  H25  108.67  3.000
 5KW  CL2  C30  H24  108.16  3.000
 5KW  H25  C30  H24  107.77  3.000
 5KW  CL2  C30  C29  111.49  3.000
 5KW  H25  C30  C29  110.99  3.000
 5KW  H24  C30  C29  109.65  3.000
 5KW  C20  N32  C15  117.82  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
 5KW  CONST_01  C13  C12  C11  C08     0.00   0.0  0
 5KW  CONST_02  C13  C10  C09  C08     0.00   0.0  0
 5KW  CONST_03  C12  C11  C08  C09     0.00   0.0  0
 5KW  CONST_04  C12  C13  C10  C09     0.00   0.0  0
 5KW  CONST_05  C11  C08  C09  C10     0.00   0.0  0
 5KW  CONST_06  C11  C12  C13  C10     0.00   0.0  0
 5KW  CONST_07  C18  C20  N32  C15     0.00   0.0  0
 5KW  CONST_08  C18  C17  N16  C15     0.00   0.0  0
 5KW  CONST_09  C20  N32  C15  N16     0.00   0.0  0
 5KW  CONST_10  C20  C18  C17  N16     0.00   0.0  0
 5KW  CONST_11  N32  C15  N16  C17     0.00   0.0  0
 5KW  CONST_12  N32  C20  C18  C17     0.00   0.0  0
 5KW  CONST_13  C25  C26  C27  C22     0.00   0.0  0
 5KW  CONST_14  C25  C24  C23  C22     0.00   0.0  0
 5KW  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 5KW  CONST_16  C26  C27  C22  C23     0.00   0.0  0
 5KW  CONST_17  C27  C26  C25  C24     0.00   0.0  0
 5KW  CONST_18  C27  C22  C23  C24     0.00   0.0  0
 5KW  CONST_19  C12  C11  C08  N07   180.00   0.0  0
 5KW  CONST_20  C10  C09  C08  N07   180.00   0.0  0
 5KW  CONST_21  N14  C13  C10  C09   180.00   0.0  0
 5KW  CONST_22  N14  C13  C12  C11   180.00   0.0  0
 5KW  CONST_23  C20  N32  C15  N14   180.00   0.0  0
 5KW  CONST_24  C17  N16  C15  N14   180.00   0.0  0
 5KW  CONST_25  O21  C20  N32  C15   180.00   0.0  0
 5KW  CONST_26  CL1  C18  C17  N16   180.00   0.0  0
 5KW  CONST_27  O21  C20  C18  C17   180.00   0.0  0
 5KW  CONST_28  N32  C20  C18  CL1   180.00   0.0  0
 5KW  CONST_29  C26  C27  C22  O21   180.00   0.0  0
 5KW  CONST_30  C24  C23  C22  O21   180.00   0.0  0
 5KW  CONST_31  N28  C27  C22  C23   180.00   0.0  0
 5KW  CONST_32  N28  C27  C26  C25   180.00   0.0  0
 5KW  CONST_33  H15  C11  C08  N07     0.00   0.0  0
 5KW  CONST_34  H13  C09  C08  N07     0.00   0.0  0
 5KW  CONST_35  H16  C12  C11  C08   180.00   0.0  0
 5KW  CONST_36  H14  C10  C09  C08   180.00   0.0  0
 5KW  CONST_37  H18  C17  N16  C15   180.00   0.0  0
 5KW  CONST_38  H22  C26  C27  C22   180.00   0.0  0
 5KW  CONST_39  H20  C24  C23  C22   180.00   0.0  0
 5KW  CONST_40  H21  C25  C24  C23   180.00   0.0  0
 5KW  CONST_41  H19  C23  C24  C25   180.00   0.0  0
 5KW  CONST_45  O31  C29  N28  C27     0.00   0.0  0
 5KW  CONST_46  C30  C29  N28  C27   180.00   0.0  0
 5KW  Var_01    N07  C04  C03  N02    54.88  30.0  1
 5KW  Var_02    N07  C06  C05  N02   -54.27  30.0  1
 5KW  Var_03    C06  C05  N02  C03    53.59  30.0  1
 5KW  Var_04    C06  N07  C04  C03   -53.73  30.0  1
 5KW  Var_05    C05  N02  C03  C04   -53.93  30.0  1
 5KW  Var_06    C05  C06  N07  C04    53.64  30.0  1
 5KW  Var_07    C11  C08  N07  C04     3.89  30.0  2
 5KW  Var_08    C15  N14  C13  C10   -49.97  30.0  2
 5KW  Var_09    N32  C15  N14  C13  -173.43  30.0  2
 5KW  Var_10    C27  C22  O21  C20    68.12  30.0  3
 5KW  Var_11    N32  C20  O21  C22     0.89  30.0  2
 5KW  Var_12    H1   C01  N02  C03   -61.61  30.0  3
 5KW  Var_13    CL2  C30  C29  N28   171.30  30.0  3

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
 5KW  plan-1  N07  0.020
 5KW  plan-1  C08  0.020
 5KW  plan-1  C09  0.020
 5KW  plan-1  C10  0.020
 5KW  plan-1  C11  0.020
 5KW  plan-1  C12  0.020
 5KW  plan-1  C13  0.020
 5KW  plan-1  N14  0.020
 5KW  plan-1  H13  0.020
 5KW  plan-1  H14  0.020
 5KW  plan-1  H15  0.020
 5KW  plan-1  H16  0.020
 5KW  plan-2  O21  0.020
 5KW  plan-2  C22  0.020
 5KW  plan-2  C23  0.020
 5KW  plan-2  C24  0.020
 5KW  plan-2  C25  0.020
 5KW  plan-2  C26  0.020
 5KW  plan-2  C27  0.020
 5KW  plan-2  N28  0.020
 5KW  plan-2  H19  0.020
 5KW  plan-2  H20  0.020
 5KW  plan-2  H21  0.020
 5KW  plan-2  H22  0.020
 5KW  plan-3  N14  0.020
 5KW  plan-3  C15  0.020
 5KW  plan-3  N16  0.020
 5KW  plan-3  C17  0.020
 5KW  plan-3  C18  0.020
 5KW  plan-3  CL1  0.020
 5KW  plan-3  C20  0.020
 5KW  plan-3  O21  0.020
 5KW  plan-3  N32  0.020
 5KW  plan-3  H18  0.020
 5KW  plan-4  C27  0.020
 5KW  plan-4  N28  0.020
 5KW  plan-4  C29  0.020
 5KW  plan-4  C30  0.020
 5KW  plan-4  O31  0.020
 5KW  plan-4  H23  0.020

