# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 06:30:21 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccccc1Nc2nc(Nc3ccc(cc3)N4CCN(C)CC4)ncc2Cl
#
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
 6H3  6H3  N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide  ligand  61  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6H3
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
 6H3  C18   C   CR6   0  -0.258    2.2306   1.9669  -0.1508
 6H3  C13   C   CR6   0   0.337   -2.2824  -0.3549  -0.0716
 6H3  C12   C   CR16  0  -0.296   -2.9295   0.8240  -0.4486
 6H3  C17   C   CR16  0   0.035    0.9476   2.4380  -0.2466
 6H3  C15   C   CR6   0   0.618    0.1248   0.3500  -0.0735
 6H3  C11   C   CR16  0  -0.316   -4.3118   0.8821  -0.4886
 6H3  C10   C   CR16  0  -0.342   -3.0763  -1.4531   0.2535
 6H3  C22   C   CR6   0   0.334    4.0634  -1.2767   0.1702
 6H3  C20   C   CR6   0   0.642    2.3963   0.5676  -0.0120
 6H3  N02   N   NT    0  -0.412   -9.3177  -0.0136   0.2837
 6H3  C03   C   CH2   0  -0.284   -8.5641   1.1969   0.0365
 6H3  C04   C   CH2   0  -0.306   -7.1179   1.0265   0.4552
 6H3  C05   C   CH2   0  -0.278   -8.7220  -1.1182  -0.4368
 6H3  C06   C   CH2   0  -0.313   -7.2774  -1.3233  -0.0209
 6H3  N07   N   NT    0  -0.514   -6.5126  -0.1103  -0.2267
 6H3  C08   C   CR6   0   0.344   -5.1187  -0.2103  -0.1515
 6H3  C09   C   CR16  0  -0.345   -4.4597  -1.3851   0.2227
 6H3  N14   N   NH1   0  -0.767   -0.8987  -0.5367  -0.0188
 6H3  N16   N   N     0  -0.490   -0.1210   1.6472  -0.2109
 6H3  CL19  CL  CL    0  -0.115    3.5864   3.0360  -0.2132
 6H3  N21   N   NH1   0  -0.765    3.6409   0.0467   0.0700
 6H3  C23   C   CR16  0  -0.312    3.2806  -2.3241   0.6572
 6H3  C24   C   CR16  0  -0.248    3.8172  -3.5982   0.7633
 6H3  C25   C   CR16  0  -0.278    5.1287  -3.8559   0.3920
 6H3  C26   C   CR16  0  -0.264    5.9091  -2.8203  -0.0975
 6H3  C27   C   CR6   0   0.245    5.3888  -1.5408  -0.2142
 6H3  N28   N   NH1   0  -0.766    6.1749  -0.4833  -0.7272
 6H3  C29   C   C     0   0.537    7.2965  -0.0118  -0.1119
 6H3  C30   C   CH2   0  -0.583    8.0139   1.0678  -0.8920
 6H3  C31   C   CH3   0  -0.658    9.2454   1.6102  -0.1909
 6H3  O32   O   O     0  -0.463    7.6640  -0.4184   0.9727
 6H3  N33   N   N     0  -0.527    1.3347  -0.2126   0.0255
 6H3  H1    H   HCR6  0   0.278   -2.3607   1.6979  -0.7214
 6H3  H2    H   HCR6  0   0.289    0.7671   3.5016  -0.3571
 6H3  H3    H   HCR6  0   0.259   -4.7657   1.8088  -0.8153
 6H3  H4    H   HCR6  0   0.265   -2.6083  -2.3833   0.5556
 6H3  H5    H   HCH3  0   0.192  -10.8908   0.3895  -1.1008
 6H3  H6    H   HCH3  0   0.233  -11.2634  -0.7654   0.1899
 6H3  H7    H   HCH3  0   0.233  -11.1451   0.9560   0.5568
 6H3  H9    H   HCH2  0   0.192   -8.6010   1.4910  -1.0273
 6H3  H10   H   HCH2  0   0.239   -9.0005   2.0176   0.6110
 6H3  H11   H   HCH2  0   0.252   -6.5823   1.9415   0.2093
 6H3  H12   H   HCH2  0   0.212   -7.0645   0.8988   1.5470
 6H3  H13   H   HCH2  0   0.239   -9.2788  -2.0325  -0.2181
 6H3  H14   H   HCH2  0   0.192   -8.7663  -0.9645  -1.5296
 6H3  H15   H   HCH2  0   0.208   -7.2470  -1.6554   1.0285
 6H3  H16   H   HCH2  0   0.249   -6.8575  -2.1258  -0.6294
 6H3  H17   H   HCR6  0   0.269   -5.0128  -2.2685   0.5096
 6H3  H18   H   HNH1  0   0.408   -0.5959  -1.4862   0.1363
 6H3  H19   H   HNH1  0   0.396    4.3954   0.7074  -0.0467
 6H3  H20   H   HCR6  0   0.284    2.2616  -2.1442   0.9574
 6H3  H21   H   HCR6  0   0.261    3.1958  -4.3976   1.1457
 6H3  H22   H   HCR6  0   0.259    5.5388  -4.8533   0.4753
 6H3  H23   H   HCR6  0   0.267    6.9283  -3.0043  -0.4108
 6H3  H24   H   HNH1  0   0.414    5.9719  -0.1557  -1.6613
 6H3  H25   H   HCH2  0   0.272    8.2787   0.6615  -1.8725
 6H3  H26   H   HCH2  0   0.266    7.3034   1.8754  -1.0929
 6H3  H27   H   HCH3  0   0.230    9.9895   0.8324  -0.0235
 6H3  H28   H   HCH3  0   0.236    9.7073   2.3842  -0.8026
 6H3  H29   H   HCH3  0   0.230    8.9984   2.0529   0.7732
 6H3  C01   C   CH3   0  -0.518  -10.7159   0.1499  -0.0403

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
 6H3  C01  N02   single    1.445  0.020  1.445
 6H3  C05  N02   single    1.447  0.020  1.447
 6H3  C05  C06   single    1.517  0.020  1.517
 6H3  N02  C03   single    1.447  0.020  1.447
 6H3  C03  C04   single    1.515  0.020  1.515
 6H3  C06  N07   single    1.449  0.020  1.449
 6H3  N07  C04   single    1.457  0.020  1.457
 6H3  N07  C08   single    1.400  0.020  1.400
 6H3  C26  C25   aromatic  1.386  0.020  1.386
 6H3  C26  C27   aromatic  1.386  0.020  1.386
 6H3  C25  C24   aromatic  1.387  0.020  1.387
 6H3  C11  C08   aromatic  1.399  0.020  1.399
 6H3  C11  C12   aromatic  1.384  0.020  1.384
 6H3  C08  C09   aromatic  1.398  0.020  1.398
 6H3  N28  C27   single    1.414  0.020  1.414
 6H3  N28  C29   single    1.363  0.020  1.363
 6H3  C31  C30   single    1.517  0.020  1.517
 6H3  C27  C22   aromatic  1.405  0.020  1.405
 6H3  C12  C13   aromatic  1.397  0.020  1.397
 6H3  C24  C23   aromatic  1.387  0.020  1.387
 6H3  C09  C10   aromatic  1.385  0.020  1.385
 6H3  C30  C29   single    1.513  0.020  1.513
 6H3  C29  O32   double    1.215  0.020  1.215
 6H3  C22  C23   aromatic  1.395  0.020  1.395
 6H3  C22  N21   single    1.393  0.020  1.393
 6H3  C13  C10   aromatic  1.394  0.020  1.394
 6H3  C13  N14   single    1.397  0.020  1.397
 6H3  N21  C20   single    1.352  0.020  1.352
 6H3  N33  C20   aromatic  1.318  0.020  1.318
 6H3  N33  C15   aromatic  1.338  0.020  1.338
 6H3  N14  C15   single    1.355  0.020  1.355
 6H3  C20  C18   aromatic  1.416  0.020  1.416
 6H3  C15  N16   aromatic  1.327  0.020  1.327
 6H3  C18  C17   aromatic  1.370  0.020  1.370
 6H3  C18  CL19  single    1.728  0.020  1.728
 6H3  N16  C17   aromatic  1.330  0.020  1.330
 6H3  C12  H1    single    0.930  0.020  1.080
 6H3  C17  H2    single    0.930  0.020  1.080
 6H3  C11  H3    single    0.930  0.020  1.080
 6H3  C10  H4    single    0.930  0.020  1.080
 6H3  C01  H5    single    0.970  0.020  1.090
 6H3  C01  H6    single    0.970  0.020  1.090
 6H3  C01  H7    single    0.970  0.020  1.090
 6H3  C03  H9    single    0.970  0.020  1.090
 6H3  C03  H10   single    0.970  0.020  1.090
 6H3  C04  H11   single    0.970  0.020  1.090
 6H3  C04  H12   single    0.970  0.020  1.090
 6H3  C05  H13   single    0.970  0.020  1.090
 6H3  C05  H14   single    0.970  0.020  1.090
 6H3  C06  H15   single    0.970  0.020  1.090
 6H3  C06  H16   single    0.970  0.020  1.090
 6H3  C09  H17   single    0.930  0.020  1.080
 6H3  N14  H18   single    0.860  0.020  1.020
 6H3  N21  H19   single    0.860  0.020  1.020
 6H3  C23  H20   single    0.930  0.020  1.080
 6H3  C24  H21   single    0.930  0.020  1.080
 6H3  C25  H22   single    0.930  0.020  1.080
 6H3  C26  H23   single    0.930  0.020  1.080
 6H3  N28  H24   single    0.860  0.020  1.020
 6H3  C30  H25   single    0.970  0.020  1.090
 6H3  C30  H26   single    0.970  0.020  1.090
 6H3  C31  H27   single    0.970  0.020  1.090
 6H3  C31  H28   single    0.970  0.020  1.090
 6H3  C31  H29   single    0.970  0.020  1.090

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
 6H3  CL19  C18  C20  121.55  3.000
 6H3  CL19  C18  C17  121.30  3.000
 6H3  C20   C18  C17  117.15  3.000
 6H3  N14   C13  C10  116.94  3.000
 6H3  N14   C13  C12  125.39  3.000
 6H3  C10   C13  C12  117.66  3.000
 6H3  H1    C12  C11  119.06  3.000
 6H3  H1    C12  C13  120.54  3.000
 6H3  C11   C12  C13  120.40  3.000
 6H3  H2    C17  N16  116.88  3.000
 6H3  H2    C17  C18  120.02  3.000
 6H3  N16   C17  C18  123.10  3.000
 6H3  N33   C15  N16  125.88  3.000
 6H3  N16   C15  N14  120.24  3.000
 6H3  N33   C15  N14  113.88  3.000
 6H3  H3    C11  C08  119.95  3.000
 6H3  H3    C11  C12  117.62  3.000
 6H3  C08   C11  C12  122.42  3.000
 6H3  H4    C10  C09  118.64  3.000
 6H3  H4    C10  C13  119.69  3.000
 6H3  C09   C10  C13  121.66  3.000
 6H3  C27   C22  C23  118.92  3.000
 6H3  C23   C22  N21  124.62  3.000
 6H3  C27   C22  N21  116.43  3.000
 6H3  N33   C20  N21  120.78  3.000
 6H3  N33   C20  C18  119.57  3.000
 6H3  N21   C20  C18  119.65  3.000
 6H3  C05   N02  C03  109.82  3.000
 6H3  C03   N02  C01  111.78  3.000
 6H3  C05   N02  C01  111.91  3.000
 6H3  H10   C03  H9   107.04  3.000
 6H3  H10   C03  C04  108.68  3.000
 6H3  H9    C03  C04  109.14  3.000
 6H3  H10   C03  N02  109.30  3.000
 6H3  H9    C03  N02  111.71  3.000
 6H3  C04   C03  N02  110.84  3.000
 6H3  H12   C04  H11  107.33  3.000
 6H3  H12   C04  N07  110.71  3.000
 6H3  H11   C04  N07  110.22  3.000
 6H3  H12   C04  C03  109.48  3.000
 6H3  H11   C04  C03  108.22  3.000
 6H3  N07   C04  C03  110.78  3.000
 6H3  H14   C05  H13  107.10  3.000
 6H3  H14   C05  C06  109.16  3.000
 6H3  H13   C05  C06  108.50  3.000
 6H3  H14   C05  N02  111.71  3.000
 6H3  H13   C05  N02  109.22  3.000
 6H3  C06   C05  N02  111.02  3.000
 6H3  H16   C06  H15  107.40  3.000
 6H3  H16   C06  N07  109.48  3.000
 6H3  H15   C06  N07  111.93  3.000
 6H3  H16   C06  C05  108.23  3.000
 6H3  H15   C06  C05  109.16  3.000
 6H3  N07   C06  C05  110.52  3.000
 6H3  C08   N07  C06  117.28  3.000
 6H3  C08   N07  C04  116.38  3.000
 6H3  C06   N07  C04  111.56  3.000
 6H3  C09   C08  N07  122.95  3.000
 6H3  C09   C08  C11  116.66  3.000
 6H3  N07   C08  C11  120.37  3.000
 6H3  H17   C09  C08  121.10  3.000
 6H3  H17   C09  C10  117.70  3.000
 6H3  C08   C09  C10  121.19  3.000
 6H3  H18   N14  C15  113.29  3.000
 6H3  H18   N14  C13  115.20  3.000
 6H3  C15   N14  C13  131.42  3.000
 6H3  C15   N16  C17  115.79  3.000
 6H3  H19   N21  C20  115.39  3.000
 6H3  H19   N21  C22  113.79  3.000
 6H3  C20   N21  C22  130.53  3.000
 6H3  H20   C23  C24  119.87  3.000
 6H3  H20   C23  C22  120.17  3.000
 6H3  C24   C23  C22  119.96  3.000
 6H3  H21   C24  C25  120.01  3.000
 6H3  H21   C24  C23  118.92  3.000
 6H3  C25   C24  C23  121.07  3.000
 6H3  H22   C25  C26  120.18  3.000
 6H3  H22   C25  C24  120.61  3.000
 6H3  C26   C25  C24  119.21  3.000
 6H3  H23   C26  C27  119.09  3.000
 6H3  H23   C26  C25  120.37  3.000
 6H3  C27   C26  C25  120.54  3.000
 6H3  N28   C27  C26  120.81  3.000
 6H3  N28   C27  C22  118.89  3.000
 6H3  C26   C27  C22  120.30  3.000
 6H3  H24   N28  C29  118.06  3.000
 6H3  H24   N28  C27  117.78  3.000
 6H3  C29   N28  C27  123.52  3.000
 6H3  O32   C29  C30  123.75  3.000
 6H3  O32   C29  N28  122.40  3.000
 6H3  C30   C29  N28  113.84  3.000
 6H3  H26   C30  H25  105.46  3.000
 6H3  H26   C30  C31  110.36  3.000
 6H3  H25   C30  C31  110.51  3.000
 6H3  H26   C30  C29  108.27  3.000
 6H3  H25   C30  C29  108.18  3.000
 6H3  C31   C30  C29  113.69  3.000
 6H3  H29   C31  H28  107.72  3.000
 6H3  H29   C31  H27  108.00  3.000
 6H3  H28   C31  H27  107.70  3.000
 6H3  H29   C31  C30  111.73  3.000
 6H3  H28   C31  C30  109.80  3.000
 6H3  H27   C31  C30  111.72  3.000
 6H3  C20   N33  C15  118.51  3.000
 6H3  H7    C01  H6   107.87  3.000
 6H3  H7    C01  H5   107.69  3.000
 6H3  H6    C01  H5   107.82  3.000
 6H3  H7    C01  N02  109.97  3.000
 6H3  H6    C01  N02  110.08  3.000
 6H3  H5    C01  N02  113.23  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
 6H3  CONST_01  C15   N33  C20  C18      0.00   0.0  0
 6H3  CONST_02  C15   N16  C17  C18      0.00   0.0  0
 6H3  CONST_03  C08   C11  C12  C13      0.00   0.0  0
 6H3  CONST_04  C08   C09  C10  C13      0.00   0.0  0
 6H3  CONST_05  C09   C08  C11  C12      0.00   0.0  0
 6H3  CONST_06  C09   C10  C13  C12      0.00   0.0  0
 6H3  CONST_07  N33   C20  C18  C17      0.00   0.0  0
 6H3  CONST_08  N33   C15  N16  C17      0.00   0.0  0
 6H3  CONST_09  C10   C09  C08  C11      0.00   0.0  0
 6H3  CONST_10  C10   C13  C12  C11      0.00   0.0  0
 6H3  CONST_11  C25   C26  C27  C22      0.00   0.0  0
 6H3  CONST_12  C25   C24  C23  C22      0.00   0.0  0
 6H3  CONST_13  N16   C15  N33  C20      0.00   0.0  0
 6H3  CONST_14  N16   C17  C18  C20      0.00   0.0  0
 6H3  CONST_15  C26   C25  C24  C23      0.00   0.0  0
 6H3  CONST_16  C26   C27  C22  C23      0.00   0.0  0
 6H3  CONST_17  C27   C26  C25  C24      0.00   0.0  0
 6H3  CONST_18  C27   C22  C23  C24      0.00   0.0  0
 6H3  CONST_19  N07   C08  C11  C12    180.00   0.0  0
 6H3  CONST_20  N07   C08  C09  C10    180.00   0.0  0
 6H3  CONST_21  N21   C20  C18  C17    180.00   0.0  0
 6H3  CONST_22  N14   C15  N16  C17    180.00   0.0  0
 6H3  CONST_23  N21   C20  N33  C15    180.00   0.0  0
 6H3  CONST_24  N14   C13  C12  C11    180.00   0.0  0
 6H3  CONST_25  N14   C15  N33  C20    180.00   0.0  0
 6H3  CONST_26  N14   C13  C10  C09    180.00   0.0  0
 6H3  CONST_27  CL19  C18  C17  N16    180.00   0.0  0
 6H3  CONST_28  N33   C20  C18  CL19   180.00   0.0  0
 6H3  CONST_29  C26   C27  C22  N21    180.00   0.0  0
 6H3  CONST_30  C24   C23  C22  N21    180.00   0.0  0
 6H3  CONST_31  N28   C27  C22  C23    180.00   0.0  0
 6H3  CONST_32  N28   C27  C26  C25    180.00   0.0  0
 6H3  CONST_33  H3    C11  C12  C13    180.00   0.0  0
 6H3  CONST_34  H17   C09  C10  C13    180.00   0.0  0
 6H3  CONST_35  H4    C10  C13  C12    180.00   0.0  0
 6H3  CONST_36  H2    C17  N16  C15    180.00   0.0  0
 6H3  CONST_37  H1    C12  C13  C10    180.00   0.0  0
 6H3  CONST_38  H23   C26  C27  C22    180.00   0.0  0
 6H3  CONST_39  H21   C24  C23  C22    180.00   0.0  0
 6H3  CONST_40  H22   C25  C24  C23    180.00   0.0  0
 6H3  CONST_41  H20   C23  C24  C25    180.00   0.0  0
 6H3  CONST_45  C30   C29  N28  C27    180.00   0.0  0
 6H3  CONST_46  O32   C29  N28  C27      0.00   0.0  0
 6H3  Var_01    C06   N07  C08  C11    172.70  30.0  2
 6H3  Var_02    N07   C06  C05  N02    -56.95  30.0  1
 6H3  Var_03    N07   C04  C03  N02     56.48  30.0  1
 6H3  Var_04    C06   C05  N02  C03     58.60  30.0  1
 6H3  Var_05    C05   N02  C03  C04    -58.31  30.0  1
 6H3  Var_06    C05   C06  N07  C04     54.86  30.0  1
 6H3  Var_07    C22   N21  C20  C18   -177.96  30.0  2
 6H3  Var_08    N33   C15  N14  C13    179.27  30.0  2
 6H3  Var_09    C15   N14  C13  C12     12.73  30.0  2
 6H3  Var_10    C27   C22  N21  C20    158.94  30.0  1
 6H3  Var_11    H5    C01  N02  C03     61.28  30.0  3
 6H3  Var_12    C31   C30  C29  N28    178.80  30.0  1
 6H3  Var_13    H27   C31  C30  C29     60.91  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
 6H3  plan-1  C13   0.020
 6H3  plan-1  C12   0.020
 6H3  plan-1  C11   0.020
 6H3  plan-1  C10   0.020
 6H3  plan-1  N07   0.020
 6H3  plan-1  C08   0.020
 6H3  plan-1  C09   0.020
 6H3  plan-1  N14   0.020
 6H3  plan-1  H1    0.020
 6H3  plan-1  H3    0.020
 6H3  plan-1  H4    0.020
 6H3  plan-1  H17   0.020
 6H3  plan-2  C22   0.020
 6H3  plan-2  N21   0.020
 6H3  plan-2  C23   0.020
 6H3  plan-2  C24   0.020
 6H3  plan-2  C25   0.020
 6H3  plan-2  C26   0.020
 6H3  plan-2  C27   0.020
 6H3  plan-2  N28   0.020
 6H3  plan-2  H20   0.020
 6H3  plan-2  H21   0.020
 6H3  plan-2  H22   0.020
 6H3  plan-2  H23   0.020
 6H3  plan-3  C18   0.020
 6H3  plan-3  C17   0.020
 6H3  plan-3  C15   0.020
 6H3  plan-3  C20   0.020
 6H3  plan-3  N14   0.020
 6H3  plan-3  N16   0.020
 6H3  plan-3  CL19  0.020
 6H3  plan-3  N21   0.020
 6H3  plan-3  N33   0.020
 6H3  plan-3  H2    0.020
 6H3  plan-4  C27   0.020
 6H3  plan-4  N28   0.020
 6H3  plan-4  C29   0.020
 6H3  plan-4  C30   0.020
 6H3  plan-4  O32   0.020
 6H3  plan-4  H24   0.020

