# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:47:20 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(/C=C/C#N)cc(C)c1Nc2ccnc(Nc3ccc(cc3)C#N)n2
#
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
 T27  T27  4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile  ligand  46  28  .  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_T27
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
 T27  C1   C  CR6   0   0.149   3.2002   0.2670   1.0406
 T27  N2   N  N     0  -0.490  -2.0512  -1.1353  -0.1322
 T27  C3   C  CR6   0   0.189   5.2689   0.2508  -0.2251
 T27  C4   C  CR16  0  -0.399   4.6286   0.9264  -1.2626
 T27  C5   C  CR6   0   0.126   3.2850   1.2670  -1.1864
 T27  C6   C  CR6   0   0.170   2.5796   0.9279  -0.0294
 T27  C7   C  CH3   0  -0.730   2.4493  -0.0446   2.3003
 T27  C2   C  CR16  0  -0.409   4.5389  -0.0721   0.9198
 T27  C8   C  CH3   0  -0.726   2.6066   1.9778  -2.3186
 T27  N1   N  NH1   0  -0.735   1.2220   1.2995   0.0703
 T27  C9   C  CR16  0  -0.002  -0.8320  -1.6640  -0.2572
 T27  C10  C  CR16  0  -0.435   0.3285  -0.9353  -0.2123
 T27  C11  C  CR6   0   0.521   0.1746   0.4502  -0.0110
 T27  N3   N  N     0  -0.520  -1.0329   0.9931   0.1028
 T27  C12  C  CR6   0   0.610  -2.0809   0.1774   0.0340
 T27  N4   N  NH1   0  -0.770  -3.2838   0.8261   0.1524
 T27  C13  C  CR6   0  -0.022  -7.2856  -0.3625   0.1602
 T27  C14  C  CR16  0  -0.229  -6.2907  -1.3321   0.0437
 T27  C15  C  CR16  0  -0.305  -4.9543  -0.9826   0.0348
 T27  C16  C  CR6   0   0.389  -4.5804   0.3637   0.1445
 T27  C17  C  CR16  0  -0.348  -5.5897   1.3345   0.2614
 T27  C18  C  CR16  0  -0.230  -6.9191   0.9817   0.2697
 T27  N5   N  NS    0  -0.264  -9.7713  -1.0385   0.1725
 T27  C19  C  CSP   0   0.046  -8.6579  -0.7363   0.1669
 T27  C20  C  C1    0  -0.355   7.4486  -0.7375   0.4866
 T27  C21  C  C1    0  -0.207   6.6791  -0.0738  -0.3890
 T27  N6   N  NS    0  -0.270   9.9325  -1.2000   0.0020
 T27  C22  C  CSP   0   0.086   8.8174  -0.9884   0.2107
 T27  H4   H  HCR6  0   0.260   5.1884   1.1857  -2.1539
 T27  H7   H  HCH3  0   0.254   1.7057  -0.8286   2.1476
 T27  H7A  H  HCH3  0   0.256   3.1276  -0.3857   3.0802
 T27  H7B  H  HCH3  0   0.252   1.9177   0.8316   2.6720
 T27  H2   H  HCR6  0   0.258   5.0176  -0.5784   1.7491
 T27  H8   H  HCH3  0   0.252   1.7136   1.4439  -2.6454
 T27  H8A  H  HCH3  0   0.254   2.2923   2.9829  -2.0320
 T27  H8B  H  HCH3  0   0.255   3.2743   2.0727  -3.1730
 T27  HN1  H  HNH1  0   0.400   0.9927   2.2836   0.0675
 T27  H9   H  HCR6  0   0.272  -0.7908  -2.7368  -0.4066
 T27  H10  H  HCR6  0   0.286   1.2922  -1.4055  -0.3391
 T27  HN4  H  HNH1  0   0.412  -3.1805   1.8250   0.2565
 T27  H14  H  HCR6  0   0.278  -6.5613  -2.3762  -0.0407
 T27  H15  H  HCR6  0   0.300  -4.2032  -1.7486  -0.0557
 T27  H17  H  HCR6  0   0.282  -5.3207   2.3801   0.3460
 T27  H18  H  HCR6  0   0.281  -7.6765   1.7482   0.3599
 T27  H20  H  H     0   0.321   7.0837  -1.1130   1.4339
 T27  H21  H  H     0   0.290   7.1303   0.2636  -1.3159

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
 T27  C1   C6   aromatic  1.402  0.020  1.402
 T27  C1   C7   single    1.499  0.020  1.499
 T27  C1   C2   aromatic  1.386  0.020  1.386
 T27  N2   C9   aromatic  1.335  0.020  1.335
 T27  N2   C12  aromatic  1.324  0.020  1.324
 T27  C3   C4   aromatic  1.394  0.020  1.394
 T27  C3   C2   aromatic  1.396  0.020  1.396
 T27  C3   C21  single    1.456  0.020  1.456
 T27  C4   C5   aromatic  1.388  0.020  1.388
 T27  C5   C6   aromatic  1.397  0.020  1.397
 T27  C5   C8   single    1.499  0.020  1.499
 T27  C6   N1   single    1.411  0.020  1.411
 T27  N1   C11  single    1.351  0.020  1.351
 T27  C9   C10  aromatic  1.371  0.020  1.371
 T27  C10  C11  aromatic  1.409  0.020  1.409
 T27  C11  N3   aromatic  1.329  0.020  1.329
 T27  N3   C12  aromatic  1.330  0.020  1.330
 T27  C12  N4   single    1.372  0.020  1.372
 T27  N4   C16  single    1.377  0.020  1.377
 T27  C13  C14  aromatic  1.394  0.020  1.394
 T27  C13  C18  aromatic  1.398  0.020  1.398
 T27  C13  C19  single    1.422  0.020  1.422
 T27  C14  C15  aromatic  1.381  0.020  1.381
 T27  C15  C16  aromatic  1.402  0.020  1.402
 T27  C16  C17  aromatic  1.405  0.020  1.405
 T27  C17  C18  aromatic  1.375  0.020  1.375
 T27  N5   C19  triple    1.154  0.020  1.154
 T27  C20  C21  double    1.341  0.020  1.341
 T27  C20  C22  single    1.419  0.020  1.419
 T27  N6   C22  triple    1.154  0.020  1.154
 T27  C4   H4   single    0.930  0.020  1.080
 T27  C7   H7   single    0.970  0.020  1.090
 T27  C7   H7A  single    0.970  0.020  1.090
 T27  C7   H7B  single    0.970  0.020  1.090
 T27  C2   H2   single    0.930  0.020  1.080
 T27  C8   H8   single    0.970  0.020  1.090
 T27  C8   H8A  single    0.970  0.020  1.090
 T27  C8   H8B  single    0.970  0.020  1.090
 T27  N1   HN1  single    0.860  0.020  1.020
 T27  C9   H9   single    0.930  0.020  1.080
 T27  C10  H10  single    0.930  0.020  1.080
 T27  N4   HN4  single    0.860  0.020  1.020
 T27  C14  H14  single    0.930  0.020  1.080
 T27  C15  H15  single    0.930  0.020  1.080
 T27  C17  H17  single    0.930  0.020  1.080
 T27  C18  H18  single    0.930  0.020  1.080
 T27  C20  H20  single    0.930  0.020  1.080
 T27  C21  H21  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
 T27  C2   C1   C7   120.40  3.000
 T27  C2   C1   C6   118.44  3.000
 T27  C7   C1   C6   121.15  3.000
 T27  C12  N2   C9   115.16  3.000
 T27  C21  C3   C2   123.17  3.000
 T27  C21  C3   C4   117.98  3.000
 T27  C2   C3   C4   118.85  3.000
 T27  H4   C4   C5   119.10  3.000
 T27  H4   C4   C3   119.39  3.000
 T27  C5   C4   C3   121.51  3.000
 T27  C8   C5   C6   120.81  3.000
 T27  C8   C5   C4   120.86  3.000
 T27  C6   C5   C4   118.33  3.000
 T27  N1   C6   C5   118.71  3.000
 T27  N1   C6   C1   119.73  3.000
 T27  C5   C6   C1   121.53  3.000
 T27  H7B  C7   H7A  108.14  3.000
 T27  H7B  C7   H7   107.03  3.000
 T27  H7A  C7   H7   107.44  3.000
 T27  H7B  C7   C1   111.33  3.000
 T27  H7A  C7   C1   110.80  3.000
 T27  H7   C7   C1   111.91  3.000
 T27  H2   C2   C3   120.33  3.000
 T27  H2   C2   C1   118.33  3.000
 T27  C3   C2   C1   121.33  3.000
 T27  H8B  C8   H8A  107.61  3.000
 T27  H8B  C8   H8   108.05  3.000
 T27  H8A  C8   H8   107.08  3.000
 T27  H8B  C8   C5   110.88  3.000
 T27  H8A  C8   C5   111.63  3.000
 T27  H8   C8   C5   111.39  3.000
 T27  HN1  N1   C11  115.86  3.000
 T27  HN1  N1   C6   118.33  3.000
 T27  C11  N1   C6   125.18  3.000
 T27  H9   C9   C10  119.89  3.000
 T27  H9   C9   N2   116.08  3.000
 T27  C10  C9   N2   124.03  3.000
 T27  H10  C10  C11  122.87  3.000
 T27  H10  C10  C9   121.35  3.000
 T27  C11  C10  C9   115.78  3.000
 T27  N3   C11  C10  120.90  3.000
 T27  N3   C11  N1   116.26  3.000
 T27  C10  C11  N1   122.84  3.000
 T27  C12  N3   C11  117.46  3.000
 T27  N4   C12  N3   113.36  3.000
 T27  N4   C12  N2   119.97  3.000
 T27  N3   C12  N2   126.67  3.000
 T27  HN4  N4   C16  115.42  3.000
 T27  HN4  N4   C12  112.78  3.000
 T27  C16  N4   C12  131.80  3.000
 T27  C19  C13  C18  120.36  3.000
 T27  C19  C13  C14  120.41  3.000
 T27  C18  C13  C14  119.23  3.000
 T27  H14  C14  C15  119.06  3.000
 T27  H14  C14  C13  119.95  3.000
 T27  C15  C14  C13  121.00  3.000
 T27  H15  C15  C16  120.26  3.000
 T27  H15  C15  C14  119.70  3.000
 T27  C16  C15  C14  120.04  3.000
 T27  C17  C16  C15  118.59  3.000
 T27  C17  C16  N4   116.35  3.000
 T27  C15  C16  N4   125.06  3.000
 T27  H17  C17  C18  119.17  3.000
 T27  H17  C17  C16  119.67  3.000
 T27  C18  C17  C16  121.16  3.000
 T27  H18  C18  C17  119.71  3.000
 T27  H18  C18  C13  120.31  3.000
 T27  C17  C18  C13  119.98  3.000
 T27  N5   C19  C13  180.00  3.000
 T27  H20  C20  C22  115.73  3.000
 T27  H20  C20  C21  123.34  3.000
 T27  C22  C20  C21  120.94  3.000
 T27  H21  C21  C20  118.23  3.000
 T27  H21  C21  C3   115.44  3.000
 T27  C20  C21  C3   126.32  3.000
 T27  N6   C22  C20  180.00  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
 T27  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 T27  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 T27  CONST_03  C11  C10  C9   N2      0.00   0.0  0
 T27  CONST_04  C11  N3   C12  N2      0.00   0.0  0
 T27  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 T27  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 T27  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 T27  CONST_08  C2   C1   C6   C5      0.00   0.0  0
 T27  CONST_09  N3   C12  N2   C9      0.00   0.0  0
 T27  CONST_10  N3   C11  C10  C9      0.00   0.0  0
 T27  CONST_11  C12  N2   C9   C10     0.00   0.0  0
 T27  CONST_12  C12  N3   C11  C10     0.00   0.0  0
 T27  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 T27  CONST_14  C16  C17  C18  C13     0.00   0.0  0
 T27  CONST_15  C17  C18  C13  C14     0.00   0.0  0
 T27  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 T27  CONST_17  C18  C13  C14  C15     0.00   0.0  0
 T27  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 T27  CONST_19  C8   C5   C6   C1    180.00   0.0  0
 T27  CONST_20  C21  C3   C2   C1    180.00   0.0  0
 T27  CONST_21  C8   C5   C4   C3    180.00   0.0  0
 T27  CONST_22  C7   C1   C2   C3    180.00   0.0  0
 T27  CONST_23  N1   C6   C5   C4    180.00   0.0  0
 T27  CONST_24  C21  C3   C4   C5    180.00   0.0  0
 T27  CONST_25  C7   C1   C6   C5    180.00   0.0  0
 T27  CONST_26  N1   C6   C1   C2    180.00   0.0  0
 T27  CONST_27  C9   C10  C11  N1    180.00   0.0  0
 T27  CONST_28  C12  N3   C11  N1    180.00   0.0  0
 T27  CONST_29  N4   C12  N2   C9    180.00   0.0  0
 T27  CONST_30  N4   C12  N3   C11   180.00   0.0  0
 T27  CONST_31  C14  C15  C16  N4    180.00   0.0  0
 T27  CONST_32  C18  C17  C16  N4    180.00   0.0  0
 T27  CONST_33  C19  C13  C14  C15   180.00   0.0  0
 T27  CONST_34  C19  C13  C18  C17   180.00   0.0  0
 T27  CONST_35  H10  C10  C9   N2    180.00   0.0  0
 T27  CONST_36  H2   C2   C3   C4    180.00   0.0  0
 T27  CONST_37  H4   C4   C5   C6    180.00   0.0  0
 T27  CONST_38  H9   C9   C10  C11   180.00   0.0  0
 T27  CONST_39  H15  C15  C14  C13   180.00   0.0  0
 T27  CONST_40  H17  C17  C18  C13   180.00   0.0  0
 T27  CONST_41  H18  C18  C13  C14   180.00   0.0  0
 T27  CONST_42  H14  C14  C15  C16   180.00   0.0  0
 T27  Var_01    C11  N1   C6   C1    -74.22  30.0  2
 T27  Var_02    C16  N4   C12  N2      0.60  30.0  2
 T27  Var_03    C10  C11  N1   C6     -0.14  30.0  2
 T27  Var_04    C15  C16  N4   C12     1.69  30.0  2
 T27  Var_05    C20  C21  C3   C4   -178.70  30.0  2
 T27  Var_06    H8   C8   C5   C4    125.92  30.0  2
 T27  Var_07    H7   C7   C1   C6     70.68  30.0  2
 T27  Var_08    C22  C20  C21  C3   -179.79   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
 T27  plan-1  C1   0.020
 T27  plan-1  C3   0.020
 T27  plan-1  C4   0.020
 T27  plan-1  C5   0.020
 T27  plan-1  C6   0.020
 T27  plan-1  C7   0.020
 T27  plan-1  C2   0.020
 T27  plan-1  C8   0.020
 T27  plan-1  N1   0.020
 T27  plan-1  C21  0.020
 T27  plan-1  H4   0.020
 T27  plan-1  H2   0.020
 T27  plan-2  N2   0.020
 T27  plan-2  N1   0.020
 T27  plan-2  C9   0.020
 T27  plan-2  C10  0.020
 T27  plan-2  C11  0.020
 T27  plan-2  N3   0.020
 T27  plan-2  C12  0.020
 T27  plan-2  N4   0.020
 T27  plan-2  H9   0.020
 T27  plan-2  H10  0.020
 T27  plan-3  N4   0.020
 T27  plan-3  C13  0.020
 T27  plan-3  C14  0.020
 T27  plan-3  C15  0.020
 T27  plan-3  C16  0.020
 T27  plan-3  C17  0.020
 T27  plan-3  C18  0.020
 T27  plan-3  N5   0.020
 T27  plan-3  C19  0.020
 T27  plan-3  H14  0.020
 T27  plan-3  H15  0.020
 T27  plan-3  H17  0.020
 T27  plan-3  H18  0.020
 T27  plan-4  C3   0.020
 T27  plan-4  C20  0.020
 T27  plan-4  C21  0.020
 T27  plan-4  C22  0.020
 T27  plan-4  H20  0.020
 T27  plan-4  H21  0.020

