# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:05:11 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-{2-[4-(2-aminoethyl)piperazin-1-yl]pyridin-4-yl}-N-(3-chloro-4-methylphenyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Nc2nccc(n2)c3ccnc(c3)N4CCN(CCN)CC4)cc1Cl
#
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
 WAI  WAI  4-{2-[4-(2-aminoethyl)piperazin-1-yl]pyridin-4-yl}-N-(3-chloro-4-methylphenyl)pyrimidin-2-amine  ligand  56  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WAI
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
 WAI  C1    C   CR6   0   0.168  -2.8480   0.0266  -1.1754
 WAI  C2    C   CR16  0  -0.453  -1.7304  -0.0294  -1.9885
 WAI  C3    C   CR6   0   0.567  -1.8603   0.2445  -3.3643
 WAI  N4    N   N     0  -0.470  -3.0519   0.5297  -3.8938
 WAI  C5    C   CR16  0  -0.052  -4.1126   0.5835  -3.1023
 WAI  C6    C   CR16  0  -0.435  -4.0825   0.3489  -1.7417
 WAI  C7    C   CR6   0   0.295  -2.7158  -0.2636   0.2716
 WAI  C8    C   CR16  0  -0.395  -3.8151  -0.5847   1.0673
 WAI  C9    C   CR16  0   0.012  -3.5508  -0.8377   2.3993
 WAI  N10   N   N     0  -0.462  -2.3342  -0.7872   2.9230
 WAI  C11   C   CR6   0   0.609  -1.3523  -0.4777   2.0827
 WAI  N12   N   N     0  -0.493  -1.4964  -0.2156   0.7828
 WAI  N13   N   NH1   0  -0.777  -0.0665  -0.4024   2.5237
 WAI  C14   C   CR6   0   0.353   0.4912  -0.5870   3.7821
 WAI  C15   C   CR16  0  -0.303   1.8787  -0.4326   3.8673
 WAI  C16   C   CR6   0  -0.093   2.5234  -0.5937   5.0778
 WAI  C17   C   CR6   0   0.148   1.8506  -0.9130   6.2553
 WAI  C18   C   CR16  0  -0.304   0.4725  -1.0596   6.1406
 WAI  C19   C   CR16  0  -0.293  -0.2126  -0.9050   4.9442
 WAI  C20   C   CH3   0  -0.720   2.5557  -1.0872   7.5650
 WAI  CL24  CL  CL    0  -0.129   4.2478  -0.3866   5.1139
 WAI  N34   N   NT    0  -0.511  -0.7847   0.2517  -4.2130
 WAI  C35   C   CH2   0  -0.302   0.5116  -0.2201  -3.7673
 WAI  C36   C   CH2   0  -0.288   1.6266   0.3505  -4.6243
 WAI  N37   N   NT    0  -0.428   1.4065   0.0789  -6.0290
 WAI  C38   C   CH2   0  -0.291   0.1531   0.6824  -6.4321
 WAI  C39   C   CH2   0  -0.297  -1.0024   0.1022  -5.6426
 WAI  C48   C   CH2   0  -0.267   2.5185   0.4996  -6.8603
 WAI  C49   C   CH2   0  -0.292   3.6984  -0.4606  -6.7889
 WAI  N52   N   NH2   0  -0.802   4.7677   0.0032  -7.6604
 WAI  H2    H   HCR6  0   0.271  -0.7830  -0.2983  -1.5483
 WAI  H5    H   HCR6  0   0.260  -5.0521   0.8310  -3.5849
 WAI  H6    H   HCR6  0   0.260  -4.9888   0.4254  -1.1588
 WAI  H8    H   HCR6  0   0.277  -4.8209  -0.6512   0.6822
 WAI  H9    H   HCR6  0   0.279  -4.3558  -1.0963   3.0778
 WAI  H13   H   HNH1  0   0.412   0.5868  -0.1713   1.7896
 WAI  H15   H   HCR6  0   0.287   2.4510  -0.1847   2.9819
 WAI  H18   H   HCR6  0   0.258  -0.0964  -1.3061   7.0291
 WAI  H19   H   HCR6  0   0.288  -1.2819  -1.0312   4.9202
 WAI  H201  H   HCH3  0   0.248   3.3173  -1.8663   7.5108
 WAI  H202  H   HCH3  0   0.248   3.0581  -0.1699   7.8765
 WAI  H203  H   HCH3  0   0.250   1.8497  -1.3622   8.3468
 WAI  H351  H   HCH2  0   0.257   0.6974   0.1032  -2.7452
 WAI  H352  H   HCH2  0   0.226   0.5563  -1.3173  -3.7831
 WAI  H361  H   HCH2  0   0.248   2.5614  -0.1044  -4.2933
 WAI  H362  H   HCH2  0   0.198   1.7097   1.4347  -4.4339
 WAI  H381  H   HCH2  0   0.243  -0.0197   0.4791  -7.4912
 WAI  H382  H   HCH2  0   0.196   0.1652   1.7794  -6.3091
 WAI  H391  H   HCH2  0   0.219  -1.1199  -0.9600  -5.8976
 WAI  H392  H   HCH2  0   0.263  -1.9204   0.6096  -5.9241
 WAI  H481  H   HCH2  0   0.227   2.1668   0.5343  -7.8959
 WAI  H482  H   HCH2  0   0.193   2.8608   1.5181  -6.6128
 WAI  H491  H   HCH2  0   0.219   4.0906  -0.4999  -5.7699
 WAI  H492  H   HCH2  0   0.194   3.3358  -1.4709  -7.0228
 WAI  H521  H   HNH2  0   0.349   5.5754  -0.5956  -7.5489
 WAI  H522  H   HNH2  0   0.339   4.4832  -0.1027  -8.6266

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
 WAI  C1   C2    aromatic  1.383  0.020  1.383
 WAI  C1   C6    aromatic  1.396  0.020  1.396
 WAI  C1   C7    single    1.482  0.020  1.482
 WAI  C2   C3    aromatic  1.409  0.020  1.409
 WAI  C2   H2    single    0.930  0.020  1.080
 WAI  C3   N4    aromatic  1.335  0.020  1.335
 WAI  C3   N34   single    1.370  0.020  1.370
 WAI  N4   C5    aromatic  1.325  0.020  1.325
 WAI  C5   C6    aromatic  1.381  0.020  1.381
 WAI  C5   H5    single    0.930  0.020  1.080
 WAI  C6   H6    single    0.930  0.020  1.080
 WAI  C7   C8    aromatic  1.395  0.020  1.395
 WAI  C7   N12   aromatic  1.323  0.020  1.323
 WAI  C8   C9    aromatic  1.381  0.020  1.381
 WAI  C8   H8    single    0.930  0.020  1.080
 WAI  C9   N10   aromatic  1.325  0.020  1.325
 WAI  C9   H9    single    0.930  0.020  1.080
 WAI  N10  C11   aromatic  1.329  0.020  1.329
 WAI  C11  N12   aromatic  1.334  0.020  1.334
 WAI  C11  N13   single    1.361  0.020  1.361
 WAI  N13  C14   single    1.389  0.020  1.389
 WAI  N13  H13   single    0.860  0.020  1.020
 WAI  C14  C15   aromatic  1.399  0.020  1.399
 WAI  C14  C19   aromatic  1.395  0.020  1.395
 WAI  C15  C16   aromatic  1.381  0.020  1.381
 WAI  C15  H15   single    0.930  0.020  1.080
 WAI  C16  C17   aromatic  1.393  0.020  1.393
 WAI  C16  CL24  single    1.737  0.020  1.737
 WAI  C17  C18   aromatic  1.391  0.020  1.391
 WAI  C17  C20   single    1.498  0.020  1.498
 WAI  C18  C19   aromatic  1.387  0.020  1.387
 WAI  C18  H18   single    0.930  0.020  1.080
 WAI  C19  H19   single    0.930  0.020  1.080
 WAI  C20  H201  single    0.970  0.020  1.090
 WAI  C20  H202  single    0.970  0.020  1.090
 WAI  C20  H203  single    0.970  0.020  1.090
 WAI  N34  C35   single    1.450  0.020  1.450
 WAI  N34  C39   single    1.454  0.020  1.454
 WAI  C35  C36   single    1.518  0.020  1.518
 WAI  C35  H351  single    0.970  0.020  1.090
 WAI  C35  H352  single    0.970  0.020  1.090
 WAI  C36  N37   single    1.448  0.020  1.448
 WAI  C36  H361  single    0.970  0.020  1.090
 WAI  C36  H362  single    0.970  0.020  1.090
 WAI  N37  C38   single    1.448  0.020  1.448
 WAI  N37  C48   single    1.451  0.020  1.451
 WAI  C38  C39   single    1.515  0.020  1.515
 WAI  C38  H381  single    0.970  0.020  1.090
 WAI  C38  H382  single    0.970  0.020  1.090
 WAI  C39  H391  single    0.970  0.020  1.090
 WAI  C39  H392  single    0.970  0.020  1.090
 WAI  C48  C49   single    1.523  0.020  1.523
 WAI  C48  H481  single    0.970  0.020  1.090
 WAI  C48  H482  single    0.970  0.020  1.090
 WAI  C49  N52   single    1.455  0.020  1.455
 WAI  C49  H491  single    0.970  0.020  1.090
 WAI  C49  H492  single    0.970  0.020  1.090
 WAI  N52  H521  single    0.890  0.020  1.040
 WAI  N52  H522  single    0.890  0.020  1.040

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
 WAI  C7    C1   C6    121.35  3.000
 WAI  C7    C1   C2    119.61  3.000
 WAI  C6    C1   C2    119.04  3.000
 WAI  H2    C2   C3    121.86  3.000
 WAI  H2    C2   C1    118.68  3.000
 WAI  C3    C2   C1    119.45  3.000
 WAI  N34   C3   N4    117.00  3.000
 WAI  N34   C3   C2    122.25  3.000
 WAI  N4    C3   C2    120.74  3.000
 WAI  C5    N4   C3    119.11  3.000
 WAI  H5    C5   C6    119.73  3.000
 WAI  H5    C5   N4    115.91  3.000
 WAI  C6    C5   N4    124.36  3.000
 WAI  H6    C6   C5    120.08  3.000
 WAI  H6    C6   C1    122.64  3.000
 WAI  C5    C6   C1    117.27  3.000
 WAI  N12   C7   C8    120.96  3.000
 WAI  N12   C7   C1    116.90  3.000
 WAI  C8    C7   C1    122.14  3.000
 WAI  H8    C8   C9    120.74  3.000
 WAI  H8    C8   C7    123.05  3.000
 WAI  C9    C8   C7    116.20  3.000
 WAI  H9    C9   N10   116.32  3.000
 WAI  H9    C9   C8    120.34  3.000
 WAI  N10   C9   C8    123.34  3.000
 WAI  C11   N10  C9    115.93  3.000
 WAI  N13   C11  N12   114.00  3.000
 WAI  N13   C11  N10   120.39  3.000
 WAI  N12   C11  N10   125.60  3.000
 WAI  C11   N12  C7    117.97  3.000
 WAI  H13   N13  C14   115.44  3.000
 WAI  H13   N13  C11   112.85  3.000
 WAI  C14   N13  C11   131.71  3.000
 WAI  C19   C14  C15   118.34  3.000
 WAI  C19   C14  N13   125.62  3.000
 WAI  C15   C14  N13   116.04  3.000
 WAI  H15   C15  C16   119.78  3.000
 WAI  H15   C15  C14   119.98  3.000
 WAI  C16   C15  C14   120.24  3.000
 WAI  CL24  C16  C17   119.28  3.000
 WAI  CL24  C16  C15   117.89  3.000
 WAI  C17   C16  C15   122.83  3.000
 WAI  C20   C17  C18   121.77  3.000
 WAI  C20   C17  C16   122.58  3.000
 WAI  C18   C17  C16   115.65  3.000
 WAI  H18   C18  C19   118.25  3.000
 WAI  H18   C18  C17   118.47  3.000
 WAI  C19   C18  C17   123.29  3.000
 WAI  H19   C19  C18   119.76  3.000
 WAI  H19   C19  C14   120.59  3.000
 WAI  C18   C19  C14   119.64  3.000
 WAI  H203  C20  H202  107.81  3.000
 WAI  H203  C20  H201  107.94  3.000
 WAI  H202  C20  H201  107.04  3.000
 WAI  H203  C20  C17   110.62  3.000
 WAI  H202  C20  C17   111.63  3.000
 WAI  H201  C20  C17   111.61  3.000
 WAI  C39   N34  C35   113.75  3.000
 WAI  C39   N34  C3    119.41  3.000
 WAI  C35   N34  C3    120.65  3.000
 WAI  H352  C35  H351  107.66  3.000
 WAI  H352  C35  C36   109.73  3.000
 WAI  H351  C35  C36   107.06  3.000
 WAI  H352  C35  N34   110.92  3.000
 WAI  H351  C35  N34   110.17  3.000
 WAI  C36   C35  N34   111.16  3.000
 WAI  H362  C36  H361  107.01  3.000
 WAI  H362  C36  N37   111.29  3.000
 WAI  H361  C36  N37   110.27  3.000
 WAI  H362  C36  C35   109.10  3.000
 WAI  H361  C36  C35   107.54  3.000
 WAI  N37   C36  C35   111.46  3.000
 WAI  C48   N37  C38   112.52  3.000
 WAI  C48   N37  C36   112.65  3.000
 WAI  C38   N37  C36   108.87  3.000
 WAI  H382  C38  H381  107.14  3.000
 WAI  H382  C38  C39   109.32  3.000
 WAI  H381  C38  C39   108.27  3.000
 WAI  H382  C38  N37   111.93  3.000
 WAI  H381  C38  N37   109.22  3.000
 WAI  C39   C38  N37   110.82  3.000
 WAI  H392  C39  H391  107.53  3.000
 WAI  H392  C39  C38   109.31  3.000
 WAI  H391  C39  C38   109.32  3.000
 WAI  H392  C39  N34   109.48  3.000
 WAI  H391  C39  N34   110.10  3.000
 WAI  C38   C39  N34   111.03  3.000
 WAI  H482  C48  H481  106.43  3.000
 WAI  H482  C48  C49   109.35  3.000
 WAI  H481  C48  C49   108.26  3.000
 WAI  H482  C48  N37   112.16  3.000
 WAI  H481  C48  N37   107.77  3.000
 WAI  C49   C48  N37   112.59  3.000
 WAI  H492  C49  H491  106.50  3.000
 WAI  H492  C49  N52   114.09  3.000
 WAI  H491  C49  N52   107.83  3.000
 WAI  H492  C49  C48   108.31  3.000
 WAI  H491  C49  C48   110.15  3.000
 WAI  N52   C49  C48   109.89  3.000
 WAI  H522  N52  H521  105.52  3.000
 WAI  H522  N52  C49   109.36  3.000
 WAI  H521  N52  C49   109.39  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
 WAI  CONST_01  N4    C3   C2   C1      0.00   0.0  0
 WAI  CONST_02  N4    C5   C6   C1      0.00   0.0  0
 WAI  CONST_03  C9    C8   C7   C1    180.00   0.0  0
 WAI  CONST_04  C11   N12  C7   C1    180.00   0.0  0
 WAI  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 WAI  CONST_08  C5    N4   C3   C2      0.00   0.0  0
 WAI  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 WAI  CONST_10  C7    C1   C2   C3    180.00   0.0  0
 WAI  CONST_11  C6    C5   N4   C3      0.00   0.0  0
 WAI  CONST_12  C7    C1   C6   C5    180.00   0.0  0
 WAI  CONST_15  N10   C9   C8   C7      0.00   0.0  0
 WAI  CONST_16  N10   C11  N12  C7      0.00   0.0  0
 WAI  CONST_17  C11   N12  C7   C8      0.00   0.0  0
 WAI  CONST_18  C11   N10  C9   C8      0.00   0.0  0
 WAI  CONST_19  N12   C7   C8   C9      0.00   0.0  0
 WAI  CONST_20  N12   C11  N10  C9      0.00   0.0  0
 WAI  CONST_21  C17   C16  C15  C14     0.00   0.0  0
 WAI  CONST_22  C17   C18  C19  C14     0.00   0.0  0
 WAI  CONST_23  C18   C19  C14  C15     0.00   0.0  0
 WAI  CONST_24  C18   C17  C16  C15     0.00   0.0  0
 WAI  CONST_25  C19   C14  C15  C16     0.00   0.0  0
 WAI  CONST_26  C19   C18  C17  C16     0.00   0.0  0
 WAI  CONST_27  N34   C3   C2   C1    180.00   0.0  0
 WAI  CONST_28  N34   C3   N4   C5    180.00   0.0  0
 WAI  CONST_29  N13   C11  N12  C7    180.00   0.0  0
 WAI  CONST_30  N13   C11  N10  C9    180.00   0.0  0
 WAI  CONST_31  C16   C15  C14  N13   180.00   0.0  0
 WAI  CONST_32  C18   C19  C14  N13   180.00   0.0  0
 WAI  CONST_33  CL24  C16  C15  C14   180.00   0.0  0
 WAI  CONST_34  C20   C17  C16  C15   180.00   0.0  0
 WAI  CONST_35  CL24  C16  C17  C18   180.00   0.0  0
 WAI  CONST_36  C20   C17  C18  C19   180.00   0.0  0
 WAI  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 WAI  CONST_38  H8    C8   C7   C1      0.00   0.0  0
 WAI  CONST_39  H6    C6   C1   C2    180.00   0.0  0
 WAI  CONST_40  H2    C2   C3   N4    180.00   0.0  0
 WAI  CONST_41  H9    C9   C8   C7    180.00   0.0  0
 WAI  CONST_42  H18   C18  C19  C14   180.00   0.0  0
 WAI  CONST_43  H19   C19  C14  C15   180.00   0.0  0
 WAI  CONST_44  H15   C15  C16  C17   180.00   0.0  0
 WAI  Var_01    C35   N34  C3   C2      9.32  30.0  2
 WAI  Var_02    C36   C35  N34  C3   -158.12  30.0  1
 WAI  Var_03    C38   C39  N34  C3    156.80  30.0  1
 WAI  Var_04    N37   C36  C35  N34   -54.40  30.0  1
 WAI  Var_05    N37   C38  C39  N34    55.99  30.0  1
 WAI  Var_06    C38   N37  C36  C35    60.00  30.0  1
 WAI  Var_07    C39   C38  N37  C36   -60.69  30.0  1
 WAI  Var_08    C14   N13  C11  N10    -0.60  30.0  2
 WAI  Var_09    C15   C14  N13  C11   179.72  30.0  2
 WAI  Var_10    C49   C48  N37  C36    76.91  30.0  3
 WAI  Var_11    H201  C20  C17  C16   -58.11  30.0  2
 WAI  Var_12    N52   C49  C48  N37   178.98  30.0  3
 WAI  Var_13    H521  N52  C49  C48   175.29  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
 WAI  plan-1  C1    0.020
 WAI  plan-1  C2    0.020
 WAI  plan-1  C3    0.020
 WAI  plan-1  N4    0.020
 WAI  plan-1  C5    0.020
 WAI  plan-1  C6    0.020
 WAI  plan-1  C7    0.020
 WAI  plan-1  N34   0.020
 WAI  plan-1  H2    0.020
 WAI  plan-1  H5    0.020
 WAI  plan-1  H6    0.020
 WAI  plan-2  C1    0.020
 WAI  plan-2  C7    0.020
 WAI  plan-2  C8    0.020
 WAI  plan-2  C9    0.020
 WAI  plan-2  N10   0.020
 WAI  plan-2  C11   0.020
 WAI  plan-2  N12   0.020
 WAI  plan-2  N13   0.020
 WAI  plan-2  H8    0.020
 WAI  plan-2  H9    0.020
 WAI  plan-3  N13   0.020
 WAI  plan-3  C14   0.020
 WAI  plan-3  C15   0.020
 WAI  plan-3  C16   0.020
 WAI  plan-3  C17   0.020
 WAI  plan-3  C18   0.020
 WAI  plan-3  C19   0.020
 WAI  plan-3  C20   0.020
 WAI  plan-3  CL24  0.020
 WAI  plan-3  H15   0.020
 WAI  plan-3  H18   0.020
 WAI  plan-3  H19   0.020

