# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:08:36 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-phenyl-4-(3-phenyl-1H-pyrazol-4-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1cc(c2ccnc(Nc3ccccc3)n2)c(n1)c4ccccc4
#
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
 7KW  7KW  N-phenyl-4-(3-phenyl-1H-pyrazol-4-yl)pyrimidin-2-amine  ligand  39  24  .  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_7KW
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
 7KW  C1   C  CR16  0  -0.264   1.6544   3.8172   0.7446
 7KW  C6   C  CR16  0  -0.246   1.2449   2.7314   1.5093
 7KW  C5   C  CR16  0  -0.278   1.7127   1.4588   1.2223
 7KW  C4   C  CR6   0   0.069   2.5965   1.2504   0.1644
 7KW  C3   C  CR16  0  -0.294   3.0126   2.3463  -0.5901
 7KW  C2   C  CR16  0  -0.247   2.5420   3.6207  -0.3043
 7KW  C7   C  CR5   0   0.254   3.1285  -0.0873  -0.1315
 7KW  C9   C  CR5   0  -0.170   2.4782  -1.3515  -0.1484
 7KW  C8   C  CR15  0   0.022   3.4878  -2.2472  -0.4467
 7KW  N2   N  NR15  0  -0.426   4.6007  -1.5278  -0.5931
 7KW  N1   N  N     0  -0.277   4.4146  -0.2278  -0.4022
 7KW  C10  C  CR6   0   0.215   1.0713  -1.6894   0.0188
 7KW  C14  C  CR16  0  -0.404   0.6706  -2.9669   0.4285
 7KW  C13  C  CR16  0   0.002  -0.6866  -3.1744   0.5380
 7KW  N3   N  N     0  -0.469  -1.5928  -2.2328   0.2938
 7KW  C12  C  CR6   0   0.595  -1.1116  -1.0542  -0.0835
 7KW  N4   N  NH1   0  -0.773  -1.9531  -0.0159  -0.3499
 7KW  C15  C  CR6   0   0.363  -3.3384   0.0910  -0.3263
 7KW  C20  C  CR16  0  -0.355  -3.8711   1.3362  -0.6856
 7KW  C19  C  CR16  0  -0.245  -5.2377   1.5484  -0.6927
 7KW  C18  C  CR16  0  -0.279  -6.1126   0.5266  -0.3429
 7KW  N9   N  N     0  -0.480   0.1778  -0.7499  -0.2447
 7KW  C17  C  CR16  0  -0.244  -5.5879  -0.7067   0.0120
 7KW  C16  C  CR16  0  -0.317  -4.2179  -0.9367   0.0251
 7KW  H1   H  HCR6  0   0.255   1.2852   4.8101   0.9668
 7KW  H2   H  HCR6  0   0.255   2.8673   4.4597  -0.9061
 7KW  H6   H  HCR6  0   0.255   0.5625   2.8761   2.3369
 7KW  H3   H  HCR6  0   0.249   3.7002   2.2001  -1.4134
 7KW  H5   H  HCR6  0   0.247   1.3969   0.6256   1.8357
 7KW  HA   H  HNR5  0   0.429   5.5201  -1.8748  -0.8174
 7KW  H8   H  HCR5  0   0.303   3.4751  -3.3154  -0.5899
 7KW  H14  H  HCR6  0   0.270   1.3785  -3.7486   0.6613
 7KW  H13  H  HCR6  0   0.272  -1.0712  -4.1399   0.8466
 7KW  H4   H  HNH1  0   0.403  -1.4590   0.8211  -0.6209
 7KW  H20  H  HCR6  0   0.265  -3.2037   2.1446  -0.9622
 7KW  H16  H  HCR6  0   0.283  -3.8383  -1.9045   0.3078
 7KW  H19  H  HCR6  0   0.257  -5.6190   2.5209  -0.9763
 7KW  H18  H  HCR6  0   0.252  -7.1818   0.6912  -0.3479
 7KW  H17  H  HCR6  0   0.254  -6.2516  -1.5168   0.2874

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
 7KW  C1   C2   aromatic  1.388  0.020  1.388
 7KW  C1   C6   aromatic  1.390  0.020  1.390
 7KW  C2   C3   aromatic  1.388  0.020  1.388
 7KW  C3   C4   aromatic  1.394  0.020  1.394
 7KW  C4   C5   aromatic  1.394  0.020  1.394
 7KW  C4   C7   single    1.470  0.020  1.470
 7KW  C5   C6   aromatic  1.386  0.020  1.386
 7KW  C7   C9   aromatic  1.422  0.020  1.422
 7KW  C7   N1   aromatic  1.322  0.020  1.322
 7KW  C9   C8   aromatic  1.382  0.020  1.382
 7KW  C9   C10  single    1.457  0.020  1.457
 7KW  C8   N2   aromatic  1.333  0.020  1.333
 7KW  N2   N1   aromatic  1.327  0.020  1.327
 7KW  C10  C14  aromatic  1.400  0.020  1.400
 7KW  C10  N9   aromatic  1.323  0.020  1.323
 7KW  C14  C13  aromatic  1.377  0.020  1.377
 7KW  C13  N3   aromatic  1.329  0.020  1.329
 7KW  N3   C12  aromatic  1.328  0.020  1.328
 7KW  C12  N4   single    1.363  0.020  1.363
 7KW  C12  N9   aromatic  1.335  0.020  1.335
 7KW  N4   C15  single    1.390  0.020  1.390
 7KW  C15  C20  aromatic  1.401  0.020  1.401
 7KW  C15  C16  aromatic  1.398  0.020  1.398
 7KW  C20  C19  aromatic  1.383  0.020  1.383
 7KW  C19  C18  aromatic  1.390  0.020  1.390
 7KW  C18  C17  aromatic  1.387  0.020  1.387
 7KW  C17  C16  aromatic  1.389  0.020  1.389
 7KW  C1   H1   single    0.930  0.020  1.080
 7KW  C2   H2   single    0.930  0.020  1.080
 7KW  C6   H6   single    0.930  0.020  1.080
 7KW  C3   H3   single    0.930  0.020  1.080
 7KW  C5   H5   single    0.930  0.020  1.080
 7KW  N2   HA   single    0.860  0.020  1.020
 7KW  C8   H8   single    0.930  0.020  1.080
 7KW  C14  H14  single    0.930  0.020  1.080
 7KW  C13  H13  single    0.930  0.020  1.080
 7KW  N4   H4   single    0.860  0.020  1.020
 7KW  C20  H20  single    0.930  0.020  1.080
 7KW  C16  H16  single    0.930  0.020  1.080
 7KW  C19  H19  single    0.930  0.020  1.080
 7KW  C18  H18  single    0.930  0.020  1.080
 7KW  C17  H17  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
 7KW  H1   C1   C2   120.20  3.000
 7KW  H1   C1   C6   120.21  3.000
 7KW  C2   C1   C6   119.58  3.000
 7KW  H6   C6   C5   119.60  3.000
 7KW  H6   C6   C1   120.14  3.000
 7KW  C5   C6   C1   120.26  3.000
 7KW  H5   C5   C4   120.01  3.000
 7KW  H5   C5   C6   119.43  3.000
 7KW  C4   C5   C6   120.56  3.000
 7KW  C7   C4   C3   119.90  3.000
 7KW  C7   C4   C5   121.22  3.000
 7KW  C3   C4   C5   118.84  3.000
 7KW  H3   C3   C2   119.73  3.000
 7KW  H3   C3   C4   119.67  3.000
 7KW  C2   C3   C4   120.60  3.000
 7KW  H2   C2   C3   119.68  3.000
 7KW  H2   C2   C1   120.17  3.000
 7KW  C3   C2   C1   120.15  3.000
 7KW  N1   C7   C9   110.38  3.000
 7KW  N1   C7   C4   119.35  3.000
 7KW  C9   C7   C4   130.25  3.000
 7KW  C10  C9   C8   125.45  3.000
 7KW  C10  C9   C7   130.30  3.000
 7KW  C8   C9   C7   104.16  3.000
 7KW  H8   C8   N2   122.01  3.000
 7KW  H8   C8   C9   131.48  3.000
 7KW  N2   C8   C9   106.48  3.000
 7KW  HA   N2   N1   119.81  3.000
 7KW  HA   N2   C8   126.88  3.000
 7KW  N1   N2   C8   113.31  3.000
 7KW  N2   N1   C7   105.66  3.000
 7KW  N9   C10  C14  120.86  3.000
 7KW  N9   C10  C9   117.69  3.000
 7KW  C14  C10  C9   121.44  3.000
 7KW  H14  C14  C13  121.31  3.000
 7KW  H14  C14  C10  122.41  3.000
 7KW  C13  C14  C10  116.27  3.000
 7KW  H13  C13  N3   116.18  3.000
 7KW  H13  C13  C14  120.42  3.000
 7KW  N3   C13  C14  123.39  3.000
 7KW  C12  N3   C13  115.71  3.000
 7KW  N9   C12  N4   113.53  3.000
 7KW  N9   C12  N3   125.93  3.000
 7KW  N4   C12  N3   120.54  3.000
 7KW  H4   N4   C15  115.40  3.000
 7KW  H4   N4   C12  112.47  3.000
 7KW  C15  N4   C12  132.13  3.000
 7KW  C16  C15  C20  118.60  3.000
 7KW  C16  C15  N4   125.11  3.000
 7KW  C20  C15  N4   116.29  3.000
 7KW  H20  C20  C19  119.51  3.000
 7KW  H20  C20  C15  119.61  3.000
 7KW  C19  C20  C15  120.89  3.000
 7KW  H19  C19  C18  120.31  3.000
 7KW  H19  C19  C20  119.16  3.000
 7KW  C18  C19  C20  120.52  3.000
 7KW  H18  C18  C17  120.70  3.000
 7KW  H18  C18  C19  120.60  3.000
 7KW  C17  C18  C19  118.70  3.000
 7KW  C12  N9   C10  117.81  3.000
 7KW  H17  C17  C16  118.57  3.000
 7KW  H17  C17  C18  119.91  3.000
 7KW  C16  C17  C18  121.53  3.000
 7KW  H16  C16  C17  119.91  3.000
 7KW  H16  C16  C15  120.32  3.000
 7KW  C17  C16  C15  119.77  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
 7KW  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 7KW  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 7KW  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 7KW  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 7KW  CONST_05  C7   C4   C5   C6    180.00   0.0  0
 7KW  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 7KW  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 7KW  CONST_10  C8   C9   C7   C4    180.00   0.0  0
 7KW  CONST_11  C10  C9   C7   C4      0.00   0.0  0
 7KW  CONST_12  N2   N1   C7   C4    180.00   0.0  0
 7KW  CONST_15  C7   C4   C3   C2    180.00   0.0  0
 7KW  CONST_16  N2   C8   C9   C7      0.00   0.0  0
 7KW  CONST_19  C8   N2   N1   C7      0.00   0.0  0
 7KW  CONST_20  N2   N1   C7   C9      0.00   0.0  0
 7KW  CONST_21  N1   N2   C8   C9      0.00   0.0  0
 7KW  CONST_22  C13  C14  C10  C9    180.00   0.0  0
 7KW  CONST_23  C12  N9   C10  C9    180.00   0.0  0
 7KW  CONST_24  N1   C7   C9   C8      0.00   0.0  0
 7KW  CONST_27  C10  C9   C8   N2    180.00   0.0  0
 7KW  CONST_28  C10  C9   C7   N1    180.00   0.0  0
 7KW  CONST_29  N3   C13  C14  C10     0.00   0.0  0
 7KW  CONST_30  N3   C12  N9   C10     0.00   0.0  0
 7KW  CONST_31  C12  N9   C10  C14     0.00   0.0  0
 7KW  CONST_32  C12  N3   C13  C14     0.00   0.0  0
 7KW  CONST_33  N9   C10  C14  C13     0.00   0.0  0
 7KW  CONST_34  N9   C12  N3   C13     0.00   0.0  0
 7KW  CONST_35  C18  C19  C20  C15     0.00   0.0  0
 7KW  CONST_36  C18  C17  C16  C15     0.00   0.0  0
 7KW  CONST_37  C17  C16  C15  C20     0.00   0.0  0
 7KW  CONST_38  C17  C18  C19  C20     0.00   0.0  0
 7KW  CONST_39  C16  C15  C20  C19     0.00   0.0  0
 7KW  CONST_40  C16  C17  C18  C19     0.00   0.0  0
 7KW  CONST_41  N4   C12  N9   C10   180.00   0.0  0
 7KW  CONST_42  N4   C12  N3   C13   180.00   0.0  0
 7KW  CONST_43  C19  C20  C15  N4    180.00   0.0  0
 7KW  CONST_44  C17  C16  C15  N4    180.00   0.0  0
 7KW  CONST_45  H3   C3   C2   C1    180.00   0.0  0
 7KW  CONST_46  H5   C5   C6   C1    180.00   0.0  0
 7KW  CONST_47  H2   C2   C1   C6    180.00   0.0  0
 7KW  CONST_48  H1   C1   C6   C5    180.00   0.0  0
 7KW  CONST_49  H6   C6   C5   C4    180.00   0.0  0
 7KW  CONST_50  H8   C8   C9   C7    180.00   0.0  0
 7KW  CONST_51  HA   N2   N1   C7    180.00   0.0  0
 7KW  CONST_52  H14  C14  C10  C9      0.00   0.0  0
 7KW  CONST_53  H13  C13  C14  C10   180.00   0.0  0
 7KW  CONST_54  H19  C19  C20  C15   180.00   0.0  0
 7KW  CONST_55  H17  C17  C16  C15   180.00   0.0  0
 7KW  CONST_56  H16  C16  C15  C20   180.00   0.0  0
 7KW  CONST_57  H18  C18  C19  C20   180.00   0.0  0
 7KW  CONST_58  H20  C20  C19  C18   180.00   0.0  0
 7KW  Var_01    C15  N4   C12  N3     -0.89  30.0  2
 7KW  Var_02    C20  C15  N4   C12  -179.07  30.0  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
 7KW  plan-1  C4   0.020
 7KW  plan-1  C7   0.020
 7KW  plan-1  C9   0.020
 7KW  plan-1  C8   0.020
 7KW  plan-1  N2   0.020
 7KW  plan-1  N1   0.020
 7KW  plan-1  C10  0.020
 7KW  plan-1  HA   0.020
 7KW  plan-1  H8   0.020
 7KW  plan-2  C1   0.020
 7KW  plan-2  C6   0.020
 7KW  plan-2  C5   0.020
 7KW  plan-2  C4   0.020
 7KW  plan-2  C3   0.020
 7KW  plan-2  C2   0.020
 7KW  plan-2  C7   0.020
 7KW  plan-2  H1   0.020
 7KW  plan-2  H2   0.020
 7KW  plan-2  H6   0.020
 7KW  plan-2  H3   0.020
 7KW  plan-2  H5   0.020
 7KW  plan-3  C9   0.020
 7KW  plan-3  C10  0.020
 7KW  plan-3  C14  0.020
 7KW  plan-3  C13  0.020
 7KW  plan-3  N3   0.020
 7KW  plan-3  C12  0.020
 7KW  plan-3  N4   0.020
 7KW  plan-3  N9   0.020
 7KW  plan-3  H14  0.020
 7KW  plan-3  H13  0.020
 7KW  plan-4  N4   0.020
 7KW  plan-4  C15  0.020
 7KW  plan-4  C20  0.020
 7KW  plan-4  C19  0.020
 7KW  plan-4  C18  0.020
 7KW  plan-4  C17  0.020
 7KW  plan-4  C16  0.020
 7KW  plan-4  H20  0.020
 7KW  plan-4  H16  0.020
 7KW  plan-4  H19  0.020
 7KW  plan-4  H18  0.020
 7KW  plan-4  H17  0.020

