# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:45:55 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-[(2-{[4-(2,4-dichlorophenyl)-5-(4-methyl-1H-imidazol-2-yl)pyrimidin-2-yl]amino}ethyl)amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c[nH]c(n1)c2cnc(NCCNc3ccc(cn3)C#N)nc2c4ccc(Cl)cc4Cl
#
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
 65C  65C  6-[(2-{[4-(2,4-dichlorophenyl)-5-(4-methyl-1H-imidazol-2-yl)pyrimidin-2-yl]amino}ethyl)amino]pyridine-3-carbonitrile  ligand  50  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_65C
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
 65C  C2   C   CR15  0  -0.143  -5.0443  -3.5817   0.7303
 65C  C3   C   CR5   0   0.381  -3.4184  -2.2045   0.2122
 65C  C4   C   CR6   0  -0.101  -2.0799  -1.6304   0.1644
 65C  C5   C   CR6   0   0.253  -1.8407  -0.2520   0.1777
 65C  C6   C   CR6   0   0.609   0.3964  -0.6031   0.0129
 65C  N7   N   N     0  -0.458   0.2849  -1.9341   0.0041
 65C  C9   C   CR6   0   0.536   6.4821  -0.2579  -0.0218
 65C  C10  C   CR16  0  -0.033   8.7223  -0.7202  -0.0812
 65C  C11  C   CR6   0  -0.119   9.0699   0.6087   0.1624
 65C  C12  C   CR16  0  -0.122   8.0292   1.5344   0.3216
 65C  C13  C   CR16  0  -0.401   6.7300   1.1096   0.2334
 65C  C14  C   CSP   0   0.034  10.4306   0.9953   0.2484
 65C  C21  C   CR16  0  -0.312  -3.3946   1.0339   1.6249
 65C  C19  C   CR6   0  -0.058  -4.9969   2.5527   0.7250
 65C  C18  C   CR16  0  -0.159  -4.5763   2.2640  -0.5634
 65C  C17  C   CR6   0  -0.068  -3.5543   1.3456  -0.7323
 65C  CL   CL  CL    0  -0.118  -3.0408   0.9560  -2.3340
 65C  C20  C   CR16  0  -0.190  -4.4174   1.9466   1.8273
 65C  C16  C   CR6   0   0.130  -2.9495   0.7205   0.3479
 65C  N2   N   N     0  -0.448  -0.6287   0.2563   0.0977
 65C  C15  C   CR16  0  -0.014  -0.9384  -2.4212   0.0767
 65C  N    N   NR15  0  -0.615  -3.7168  -3.3211   0.9147
 65C  N1   N   N     0  -0.434  -4.4773  -1.7460  -0.4118
 65C  C1   C   CR5   0   0.119  -5.5024  -2.5916  -0.0968
 65C  C    C   CH3   0  -0.741  -6.8790  -2.3944  -0.6287
 65C  N3   N   NH1   0  -0.668   1.6263  -0.0672  -0.0525
 65C  C7   C   CH2   0  -0.280   2.8259  -0.8423  -0.2424
 65C  C8   C   CH2   0  -0.294   4.0373   0.0279   0.0500
 65C  N4   N   NH1   0  -0.655   5.2389  -0.7468  -0.1341
 65C  N5   N   N     0  -0.457   7.4808  -1.1423  -0.1708
 65C  N6   N   NS    0  -0.267  11.5398   1.3062   0.3213
 65C  H1   H   HCR5  0   0.281  -5.5360  -4.4206   1.1930
 65C  H2   H   HCR6  0   0.283   9.4985  -1.4671  -0.2076
 65C  H3   H   HCR6  0   0.288   8.2476   2.5761   0.5142
 65C  H4   H   HCR6  0   0.290   5.9200   1.8132   0.3578
 65C  H5   H   HCR6  0   0.273  -2.9367   0.5541   2.4802
 65C  H6   H   HCR6  0   0.301  -5.0372   2.7392  -1.4180
 65C  H7   H   HCR6  0   0.287  -4.7535   2.1787   2.8280
 65C  H8   H   HCR6  0   0.272  -1.0238  -3.5032   0.0487
 65C  H9   H   HNR5  0   0.417  -3.0963  -3.8352   1.5202
 65C  H11  H   HCH3  0   0.237  -6.9088  -2.4975  -1.7151
 65C  H12  H   HCH3  0   0.238  -7.5700  -3.1239  -0.2085
 65C  H13  H   HCH3  0   0.238  -7.2556  -1.3983  -0.3902
 65C  H14  H   HNH1  0   0.400   1.6704   0.9321  -0.1746
 65C  H15  H   HCH2  0   0.256   2.8159  -1.6966   0.4366
 65C  H16  H   HCH2  0   0.247   2.8921  -1.2382  -1.2618
 65C  H17  H   HCH2  0   0.251   4.0411   0.8893  -0.6262
 65C  H18  H   HCH2  0   0.253   3.9712   0.4162   1.0719
 65C  H19  H   HNH1  0   0.399   5.1628  -1.7455  -0.2516
 65C  CL1  CL  CL    0  -0.116  -6.2760   3.6952   0.9528

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
 65C  N7   C15  aromatic  1.319  0.020  1.319
 65C  N7   C6   aromatic  1.336  0.020  1.336
 65C  N3   C6   single    1.343  0.020  1.343
 65C  N3   C7   single    1.441  0.020  1.441
 65C  C15  C4   aromatic  1.391  0.020  1.391
 65C  C6   N2   aromatic  1.340  0.020  1.340
 65C  C7   C8   single    1.520  0.020  1.520
 65C  C4   C3   single    1.457  0.020  1.457
 65C  C4   C5   aromatic  1.399  0.020  1.399
 65C  C8   N4   single    1.441  0.020  1.441
 65C  N2   C5   aromatic  1.317  0.020  1.317
 65C  N1   C3   aromatic  1.312  0.020  1.312
 65C  N1   C1   aromatic  1.366  0.020  1.366
 65C  C3   N    aromatic  1.353  0.020  1.353
 65C  C5   C16  single    1.485  0.020  1.485
 65C  C1   C    single    1.489  0.020  1.489
 65C  C1   C2   aromatic  1.369  0.020  1.369
 65C  N    C2   aromatic  1.365  0.020  1.365
 65C  N4   C9   single    1.341  0.020  1.341
 65C  C16  C21  aromatic  1.388  0.020  1.388
 65C  C16  C17  aromatic  1.387  0.020  1.387
 65C  C21  C20  aromatic  1.386  0.020  1.386
 65C  C9   C13  aromatic  1.413  0.020  1.413
 65C  C9   N5   aromatic  1.342  0.020  1.342
 65C  C13  C12  aromatic  1.370  0.020  1.370
 65C  CL   C17  single    1.727  0.020  1.727
 65C  N5   C10  aromatic  1.314  0.020  1.314
 65C  C17  C18  aromatic  1.384  0.020  1.384
 65C  C20  C19  aromatic  1.385  0.020  1.385
 65C  C12  C11  aromatic  1.402  0.020  1.402
 65C  C10  C11  aromatic  1.395  0.020  1.395
 65C  C18  C19  aromatic  1.386  0.020  1.386
 65C  C19  CL1  single    1.730  0.020  1.730
 65C  C11  C14  single    1.417  0.020  1.417
 65C  C14  N6   triple    1.154  0.020  1.154
 65C  C2   H1   single    0.930  0.020  1.080
 65C  C10  H2   single    0.930  0.020  1.080
 65C  C12  H3   single    0.930  0.020  1.080
 65C  C13  H4   single    0.930  0.020  1.080
 65C  C21  H5   single    0.930  0.020  1.080
 65C  C18  H6   single    0.930  0.020  1.080
 65C  C20  H7   single    0.930  0.020  1.080
 65C  C15  H8   single    0.930  0.020  1.080
 65C  N    H9   single    0.860  0.020  1.020
 65C  C    H11  single    0.970  0.020  1.090
 65C  C    H12  single    0.970  0.020  1.090
 65C  C    H13  single    0.970  0.020  1.090
 65C  N3   H14  single    0.860  0.020  1.020
 65C  C7   H15  single    0.970  0.020  1.090
 65C  C7   H16  single    0.970  0.020  1.090
 65C  C8   H17  single    0.970  0.020  1.090
 65C  C8   H18  single    0.970  0.020  1.090
 65C  N4   H19  single    0.860  0.020  1.020

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
 65C  H1   C2   C1   132.08  3.000
 65C  H1   C2   N    122.32  3.000
 65C  C1   C2   N    105.60  3.000
 65C  N1   C3   N    110.95  3.000
 65C  N    C3   C4   123.02  3.000
 65C  N1   C3   C4   126.02  3.000
 65C  C15  C4   C5   114.85  3.000
 65C  C5   C4   C3   123.02  3.000
 65C  C15  C4   C3   122.12  3.000
 65C  N2   C5   C16  116.20  3.000
 65C  C16  C5   C4   121.25  3.000
 65C  N2   C5   C4   122.49  3.000
 65C  N3   C6   N2   116.59  3.000
 65C  N2   C6   N7   125.13  3.000
 65C  N3   C6   N7   118.28  3.000
 65C  C15  N7   C6   116.44  3.000
 65C  N5   C9   N4   116.13  3.000
 65C  N5   C9   C13  121.81  3.000
 65C  N4   C9   C13  122.06  3.000
 65C  H2   C10  N5   116.55  3.000
 65C  H2   C10  C11  119.87  3.000
 65C  N5   C10  C11  123.59  3.000
 65C  C14  C11  C12  121.72  3.000
 65C  C14  C11  C10  120.64  3.000
 65C  C12  C11  C10  117.63  3.000
 65C  H3   C12  C13  120.11  3.000
 65C  H3   C12  C11  120.41  3.000
 65C  C13  C12  C11  119.48  3.000
 65C  H4   C13  C12  120.13  3.000
 65C  H4   C13  C9   121.31  3.000
 65C  C12  C13  C9   118.57  3.000
 65C  N6   C14  C11  180.00  3.000
 65C  H5   C21  C16  119.42  3.000
 65C  H5   C21  C20  119.27  3.000
 65C  C16  C21  C20  121.31  3.000
 65C  C20  C19  C18  121.45  3.000
 65C  C18  C19  CL1  118.97  3.000
 65C  C20  C19  CL1  119.57  3.000
 65C  H6   C18  C17  120.66  3.000
 65C  H6   C18  C19  120.94  3.000
 65C  C17  C18  C19  118.40  3.000
 65C  C16  C17  CL   119.42  3.000
 65C  CL   C17  C18  118.84  3.000
 65C  C16  C17  C18  121.73  3.000
 65C  H7   C20  C19  120.85  3.000
 65C  H7   C20  C21  120.41  3.000
 65C  C19  C20  C21  118.74  3.000
 65C  C17  C16  C21  118.35  3.000
 65C  C17  C16  C5   122.12  3.000
 65C  C21  C16  C5   119.53  3.000
 65C  C6   N2   C5   117.41  3.000
 65C  H8   C15  N7   116.09  3.000
 65C  H8   C15  C4   120.23  3.000
 65C  N7   C15  C4   123.68  3.000
 65C  H9   N    C3   126.67  3.000
 65C  H9   N    C2   125.62  3.000
 65C  C3   N    C2   107.57  3.000
 65C  C1   N1   C3   106.25  3.000
 65C  C    C1   N1   121.98  3.000
 65C  C    C1   C2   128.39  3.000
 65C  N1   C1   C2   109.63  3.000
 65C  H13  C    H12  107.95  3.000
 65C  H13  C    H11  107.11  3.000
 65C  H12  C    H11  107.65  3.000
 65C  H13  C    C1   111.22  3.000
 65C  H12  C    C1   111.10  3.000
 65C  H11  C    C1   111.61  3.000
 65C  H14  N3   C7   118.76  3.000
 65C  H14  N3   C6   116.20  3.000
 65C  C7   N3   C6   123.65  3.000
 65C  H16  C7   H15  107.26  3.000
 65C  H16  C7   C8   109.73  3.000
 65C  H15  C7   C8   109.62  3.000
 65C  H16  C7   N3   111.55  3.000
 65C  H15  C7   N3   109.36  3.000
 65C  C8   C7   N3   109.28  3.000
 65C  H18  C8   H17  107.31  3.000
 65C  H18  C8   N4   111.10  3.000
 65C  H17  C8   N4   109.93  3.000
 65C  H18  C8   C7   109.54  3.000
 65C  H17  C8   C7   109.54  3.000
 65C  N4   C8   C7   109.40  3.000
 65C  H19  N4   C8   118.96  3.000
 65C  H19  N4   C9   116.16  3.000
 65C  C8   N4   C9   124.50  3.000
 65C  C10  N5   C9   118.92  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
 65C  CONST_01  C3   N1   C1   C2      0.00   0.0  0
 65C  CONST_02  C4   C3   N    C2    180.00   0.0  0
 65C  CONST_03  N1   C3   N    C2      0.00   0.0  0
 65C  CONST_04  N7   C15  C4   C3    180.00   0.0  0
 65C  CONST_05  N2   C5   C4   C3    180.00   0.0  0
 65C  CONST_06  C16  C5   C4   C3      0.00   0.0  0
 65C  CONST_07  C1   C2   N    C3      0.00   0.0  0
 65C  CONST_08  C6   N7   C15  C4      0.00   0.0  0
 65C  CONST_09  C1   N1   C3   C4    180.00   0.0  0
 65C  CONST_10  C6   N2   C5   C4      0.00   0.0  0
 65C  CONST_13  N7   C15  C4   C5      0.00   0.0  0
 65C  CONST_16  N7   C6   N2   C5      0.00   0.0  0
 65C  CONST_17  C20  C21  C16  C5    180.00   0.0  0
 65C  CONST_18  C18  C17  C16  C5    180.00   0.0  0
 65C  CONST_19  C16  C5   N2   C6    180.00   0.0  0
 65C  CONST_20  C11  C12  C13  C9      0.00   0.0  0
 65C  CONST_21  C11  C10  N5   C9      0.00   0.0  0
 65C  CONST_22  C13  C9   N5   C10     0.00   0.0  0
 65C  CONST_23  C13  C12  C11  C10     0.00   0.0  0
 65C  CONST_24  N5   C9   C13  C12     0.00   0.0  0
 65C  CONST_25  N5   C10  C11  C12     0.00   0.0  0
 65C  CONST_27  C18  C17  C16  C21     0.00   0.0  0
 65C  CONST_28  C18  C19  C20  C21     0.00   0.0  0
 65C  CONST_29  C16  C21  C20  C19     0.00   0.0  0
 65C  CONST_30  C16  C17  C18  C19     0.00   0.0  0
 65C  CONST_32  C20  C21  C16  C17     0.00   0.0  0
 65C  CONST_33  C20  C19  C18  C17     0.00   0.0  0
 65C  CONST_34  C15  C4   C5   C16   180.00   0.0  0
 65C  CONST_35  C15  N7   C6   N2      0.00   0.0  0
 65C  CONST_36  C15  C4   C5   N2      0.00   0.0  0
 65C  CONST_39  C1   N1   C3   N       0.00   0.0  0
 65C  CONST_40  N1   C1   C2   N       0.00   0.0  0
 65C  CONST_41  C    C1   N1   C3    180.00   0.0  0
 65C  CONST_42  N3   C6   N2   C5    180.00   0.0  0
 65C  CONST_43  CL   C17  C16  C5      0.00   0.0  0
 65C  CONST_44  N4   C9   N5   C10   180.00   0.0  0
 65C  CONST_45  N4   C9   C13  C12   180.00   0.0  0
 65C  CONST_46  C14  C11  C12  C13   180.00   0.0  0
 65C  CONST_47  N5   C10  C11  C14   180.00   0.0  0
 65C  CONST_48  CL   C17  C16  C21   180.00   0.0  0
 65C  CONST_49  CL1  C19  C20  C21   180.00   0.0  0
 65C  CONST_50  C17  C18  C19  CL1   180.00   0.0  0
 65C  CONST_51  CL   C17  C18  C19   180.00   0.0  0
 65C  CONST_52  N3   C6   N7   C15   180.00   0.0  0
 65C  CONST_53  C    C1   C2   N     180.00   0.0  0
 65C  CONST_54  H8   C15  C4   C3      0.00   0.0  0
 65C  CONST_55  H1   C2   N    C3    180.00   0.0  0
 65C  CONST_56  H9   N    C3   C4      0.00   0.0  0
 65C  CONST_57  H5   C21  C16  C5      0.00   0.0  0
 65C  CONST_58  H3   C12  C13  C9    180.00   0.0  0
 65C  CONST_59  H2   C10  N5   C9    180.00   0.0  0
 65C  CONST_60  H4   C13  C12  C11   180.00   0.0  0
 65C  CONST_61  H7   C20  C19  C18   180.00   0.0  0
 65C  CONST_62  H6   C18  C19  C20   180.00   0.0  0
 65C  CONST_63  C7   N3   C6   N7      0.00   0.0  0
 65C  CONST_64  C8   N4   C9   C13     0.00   0.0  0
 65C  CONST_65  C7   N3   C6   N2    180.00   0.0  0
 65C  CONST_66  N5   C9   N4   C8    180.00   0.0  0
 65C  CONST_67  H14  N3   C6   N7    180.00   0.0  0
 65C  CONST_68  H19  N4   C9   C13   180.00   0.0  0
 65C  Var_01    H11  C    C1   C2   -115.46  30.0  2
 65C  Var_02    C8   C7   N3   C6   -167.09  30.0  3
 65C  Var_03    C7   C8   N4   C9    176.47  30.0  2
 65C  Var_04    N4   C8   C7   N3    179.77  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
 65C  plan-1  C2   0.020
 65C  plan-1  C3   0.020
 65C  plan-1  C4   0.020
 65C  plan-1  N    0.020
 65C  plan-1  N1   0.020
 65C  plan-1  C1   0.020
 65C  plan-1  C    0.020
 65C  plan-1  H1   0.020
 65C  plan-1  H9   0.020
 65C  plan-2  C3   0.020
 65C  plan-2  C4   0.020
 65C  plan-2  C5   0.020
 65C  plan-2  C6   0.020
 65C  plan-2  N7   0.020
 65C  plan-2  C16  0.020
 65C  plan-2  N2   0.020
 65C  plan-2  C15  0.020
 65C  plan-2  N3   0.020
 65C  plan-2  H8   0.020
 65C  plan-3  C9   0.020
 65C  plan-3  C10  0.020
 65C  plan-3  C11  0.020
 65C  plan-3  C12  0.020
 65C  plan-3  C13  0.020
 65C  plan-3  C14  0.020
 65C  plan-3  N4   0.020
 65C  plan-3  N5   0.020
 65C  plan-3  N6   0.020
 65C  plan-3  H2   0.020
 65C  plan-3  H3   0.020
 65C  plan-3  H4   0.020
 65C  plan-4  C5   0.020
 65C  plan-4  C21  0.020
 65C  plan-4  C19  0.020
 65C  plan-4  C18  0.020
 65C  plan-4  C17  0.020
 65C  plan-4  CL   0.020
 65C  plan-4  C20  0.020
 65C  plan-4  C16  0.020
 65C  plan-4  H5   0.020
 65C  plan-4  H6   0.020
 65C  plan-4  H7   0.020
 65C  plan-4  CL1  0.020
 65C  plan-5  C6   0.020
 65C  plan-5  N3   0.020
 65C  plan-5  C7   0.020
 65C  plan-5  H14  0.020
 65C  plan-6  C9   0.020
 65C  plan-6  C8   0.020
 65C  plan-6  N4   0.020
 65C  plan-6  H19  0.020

