# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:29:25 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-(5-cyanopyrazin-2-yl)-3-isoquinolin-3-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cnc(cn1)C#N)Nc2cc3ccccc3cn2
#
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
 H4K  H4K  1-(5-cyanopyrazin-2-yl)-3-isoquinolin-3-ylurea  ligand  32  22  .  2021-08-11  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_H4K
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
 H4K  N4   N  NS    0  -0.238  -8.0585   0.2445  -0.8490
 H4K  C6   C  CSP   0   0.063  -6.9470   0.0652  -0.6069
 H4K  C4   C  CR6   0   0.132  -5.5627  -0.1428  -0.3195
 H4K  N2   N  N     0  -0.344  -5.2417  -1.1772   0.4656
 H4K  C3   C  CR16  0  -0.160  -3.9765  -1.3590   0.7232
 H4K  C5   C  CR16  0  -0.040  -4.5938   0.6975  -0.8407
 H4K  N3   N  N     0  -0.379  -3.3073   0.5158  -0.5852
 H4K  C2   C  CR6   0   0.518  -2.9822  -0.4999   0.1933
 H4K  N1   N  NH1   0  -0.771  -1.6804  -0.7766   0.5004
 H4K  C1   C  C     0   0.724  -0.5533  -0.0223   0.1918
 H4K  O    O  O     0  -0.442  -0.5902   1.1034  -0.2397
 H4K  N5   N  NH1   0  -0.772   0.5908  -0.7267   0.4540
 H4K  C7   C  CR6   0   0.504   1.8834  -0.2065   0.3482
 H4K  N6   N  N     0  -0.413   2.0725   1.0496   0.7930
 H4K  C15  C  CR16  0  -0.093   3.2764   1.5490   0.7389
 H4K  C14  C  CR66  0  -0.004   4.4063   0.8449   0.2687
 H4K  C9   C  CR66  0   0.234   4.2047  -0.4829  -0.1758
 H4K  C8   C  CR16  0  -0.455   2.8942  -0.9972  -0.1378
 H4K  C13  C  CR16  0  -0.302   5.6992   1.4120   0.2382
 H4K  C12  C  CR16  0  -0.260   6.7563   0.6766  -0.2217
 H4K  C11  C  CR16  0  -0.242   6.5582  -0.6499  -0.6667
 H4K  C10  C  CR16  0  -0.313   5.3153  -1.2213  -0.6472
 H4K  H2   H  HCR6  0   0.301  -3.7050  -2.1960   1.3571
 H4K  H3   H  HCR6  0   0.300  -4.8612   1.5314  -1.4786
 H4K  H1   H  HNH1  0   0.429  -1.5368  -1.6172   1.0415
 H4K  H4   H  HNH1  0   0.421   0.5248  -1.7316   0.5192
 H4K  H10  H  HCR6  0   0.271   3.4006   2.5672   1.0974
 H4K  H5   H  HCR6  0   0.277   2.6922  -2.0006  -0.4914
 H4K  H9   H  HCR6  0   0.262   5.8413   2.4293   0.5817
 H4K  H8   H  HCR6  0   0.265   7.7494   1.1048  -0.2467
 H4K  H7   H  HCR6  0   0.267   7.4058  -1.2187  -1.0263
 H4K  H6   H  HCR6  0   0.262   5.1695  -2.2384  -0.9892

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
 H4K  C10  C11  aromatic  1.368  0.020  1.368
 H4K  C10  C9   aromatic  1.415  0.020  1.415
 H4K  C11  C12  aromatic  1.413  0.020  1.413
 H4K  O    C1   double    1.206  0.020  1.206
 H4K  C8   C9   aromatic  1.408  0.020  1.408
 H4K  C8   C7   aromatic  1.372  0.020  1.372
 H4K  C9   C14  aromatic  1.415  0.020  1.415
 H4K  C12  C13  aromatic  1.367  0.020  1.367
 H4K  C1   N1   single    1.391  0.020  1.391
 H4K  C1   N5   single    1.369  0.020  1.369
 H4K  N1   C2   single    1.366  0.020  1.366
 H4K  C7   N5   single    1.397  0.020  1.397
 H4K  C7   N6   aromatic  1.346  0.020  1.346
 H4K  C14  C13  aromatic  1.412  0.020  1.412
 H4K  C14  C15  aromatic  1.412  0.020  1.412
 H4K  N6   C15  aromatic  1.305  0.020  1.305
 H4K  C2   C3   aromatic  1.417  0.020  1.417
 H4K  C2   N3   aromatic  1.320  0.020  1.320
 H4K  C3   N2   aromatic  1.304  0.020  1.304
 H4K  N3   C5   aromatic  1.324  0.020  1.324
 H4K  N2   C4   aromatic  1.338  0.020  1.338
 H4K  C5   C4   aromatic  1.384  0.020  1.384
 H4K  C4   C6   single    1.429  0.020  1.429
 H4K  C6   N4   triple    1.152  0.020  1.152
 H4K  C3   H2   single    0.930  0.020  1.080
 H4K  C5   H3   single    0.930  0.020  1.080
 H4K  N1   H1   single    0.860  0.020  1.020
 H4K  N5   H4   single    0.860  0.020  1.020
 H4K  C15  H10  single    0.930  0.020  1.080
 H4K  C8   H5   single    0.930  0.020  1.080
 H4K  C13  H9   single    0.930  0.020  1.080
 H4K  C12  H8   single    0.930  0.020  1.080
 H4K  C11  H7   single    0.930  0.020  1.080
 H4K  C10  H6   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
 H4K  C4   C6   N4   180.00  3.000
 H4K  C5   C4   N2   121.49  3.000
 H4K  C5   C4   C6   120.92  3.000
 H4K  N2   C4   C6   117.59  3.000
 H4K  C3   N2   C4   117.17  3.000
 H4K  H2   C3   C2   120.73  3.000
 H4K  H2   C3   N2   117.77  3.000
 H4K  C2   C3   N2   121.51  3.000
 H4K  H3   C5   N3   117.32  3.000
 H4K  H3   C5   C4   121.08  3.000
 H4K  N3   C5   C4   121.60  3.000
 H4K  C2   N3   C5   117.29  3.000
 H4K  N1   C2   N3   121.54  3.000
 H4K  N3   C2   C3   120.94  3.000
 H4K  N1   C2   C3   117.51  3.000
 H4K  H1   N1   C1   117.06  3.000
 H4K  H1   N1   C2   115.13  3.000
 H4K  C1   N1   C2   127.78  3.000
 H4K  N5   C1   O    125.05  3.000
 H4K  N5   C1   N1   110.84  3.000
 H4K  O    C1   N1   124.11  3.000
 H4K  H4   N5   C7   115.86  3.000
 H4K  H4   N5   C1   118.04  3.000
 H4K  C7   N5   C1   124.55  3.000
 H4K  C8   C7   N6   123.46  3.000
 H4K  N6   C7   N5   116.90  3.000
 H4K  C8   C7   N5   119.58  3.000
 H4K  C15  N6   C7   118.24  3.000
 H4K  H10  C15  C14  119.06  3.000
 H4K  H10  C15  N6   116.78  3.000
 H4K  C14  C15  N6   124.16  3.000
 H4K  C13  C14  C9   120.04  3.000
 H4K  C13  C14  C15  122.66  3.000
 H4K  C9   C14  C15  117.30  3.000
 H4K  C10  C9   C8   123.30  3.000
 H4K  C8   C9   C14  117.83  3.000
 H4K  C10  C9   C14  118.87  3.000
 H4K  H5   C8   C9   120.20  3.000
 H4K  H5   C8   C7   120.81  3.000
 H4K  C9   C8   C7   118.98  3.000
 H4K  H9   C13  C12  120.69  3.000
 H4K  H9   C13  C14  119.37  3.000
 H4K  C12  C13  C14  119.95  3.000
 H4K  H8   C12  C11  119.54  3.000
 H4K  H8   C12  C13  120.31  3.000
 H4K  C11  C12  C13  120.15  3.000
 H4K  H7   C11  C10  119.78  3.000
 H4K  H7   C11  C12  119.22  3.000
 H4K  C10  C11  C12  120.99  3.000
 H4K  H6   C10  C11  120.67  3.000
 H4K  H6   C10  C9   119.33  3.000
 H4K  C11  C10  C9   120.00  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
 H4K  CONST_01  C2   C3   N2   C4     0.00  0.0  0
 H4K  CONST_02  C2   N3   C5   C4     0.00  0.0  0
 H4K  CONST_03  N3   C2   C3   N2     0.00  0.0  0
 H4K  CONST_04  N3   C5   C4   N2     0.00  0.0  0
 H4K  CONST_05  C5   N3   C2   C3     0.00  0.0  0
 H4K  CONST_06  C5   C4   N2   C3     0.00  0.0  0
 H4K  CONST_07  C10  C9   C8   C7   180.00  0.0  0
 H4K  CONST_08  C14  C9   C8   C7     0.00  0.0  0
 H4K  CONST_09  C14  C15  N6   C7     0.00  0.0  0
 H4K  CONST_10  C9   C8   C7   N6     0.00  0.0  0
 H4K  CONST_11  C9   C14  C15  N6     0.00  0.0  0
 H4K  CONST_12  C13  C14  C15  N6   180.00  0.0  0
 H4K  CONST_13  C10  C9   C14  C15  180.00  0.0  0
 H4K  CONST_14  C8   C9   C14  C15    0.00  0.0  0
 H4K  CONST_15  C12  C13  C14  C15  180.00  0.0  0
 H4K  CONST_16  C8   C7   N6   C15    0.00  0.0  0
 H4K  CONST_17  C11  C10  C9   C14    0.00  0.0  0
 H4K  CONST_18  C11  C12  C13  C14    0.00  0.0  0
 H4K  CONST_19  C12  C11  C10  C9     0.00  0.0  0
 H4K  CONST_20  C12  C13  C14  C9     0.00  0.0  0
 H4K  CONST_21  C11  C10  C9   C8   180.00  0.0  0
 H4K  CONST_22  C13  C14  C9   C8   180.00  0.0  0
 H4K  CONST_23  C10  C11  C12  C13    0.00  0.0  0
 H4K  CONST_24  C10  C9   C14  C13    0.00  0.0  0
 H4K  CONST_25  C3   N2   C4   C6   180.00  0.0  0
 H4K  CONST_26  N3   C5   C4   C6   180.00  0.0  0
 H4K  CONST_27  N1   C2   C3   N2   180.00  0.0  0
 H4K  CONST_28  N1   C2   N3   C5   180.00  0.0  0
 H4K  CONST_29  C9   C8   C7   N5   180.00  0.0  0
 H4K  CONST_30  C15  N6   C7   N5   180.00  0.0  0
 H4K  CONST_31  H2   C3   N2   C4   180.00  0.0  0
 H4K  CONST_32  H3   C5   C4   N2   180.00  0.0  0
 H4K  CONST_33  H10  C15  N6   C7   180.00  0.0  0
 H4K  CONST_34  H5   C8   C7   N6   180.00  0.0  0
 H4K  CONST_35  H9   C13  C14  C15    0.00  0.0  0
 H4K  CONST_36  H6   C10  C9   C14  180.00  0.0  0
 H4K  CONST_37  H8   C12  C13  C14  180.00  0.0  0
 H4K  CONST_38  H7   C11  C10  C9   180.00  0.0  0
 H4K  CONST_39  C1   N1   C2   C3   180.00  0.0  0
 H4K  CONST_40  C1   N1   C2   N3     0.00  0.0  0
 H4K  CONST_43  H1   N1   C2   C3     0.00  0.0  0
 H4K  CONST_45  O    C1   N1   C2     0.00  0.0  0
 H4K  CONST_46  C7   N5   C1   O      0.00  0.0  0
 H4K  CONST_47  N5   C1   N1   C2   180.00  0.0  0
 H4K  CONST_48  C7   N5   C1   N1   180.00  0.0  0

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
 H4K  plan-1  N4   0.020
 H4K  plan-1  C6   0.020
 H4K  plan-1  C4   0.020
 H4K  plan-1  N2   0.020
 H4K  plan-1  C3   0.020
 H4K  plan-1  C5   0.020
 H4K  plan-1  N3   0.020
 H4K  plan-1  C2   0.020
 H4K  plan-1  N1   0.020
 H4K  plan-1  H2   0.020
 H4K  plan-1  H3   0.020
 H4K  plan-2  N5   0.020
 H4K  plan-2  C7   0.020
 H4K  plan-2  N6   0.020
 H4K  plan-2  C15  0.020
 H4K  plan-2  C14  0.020
 H4K  plan-2  C9   0.020
 H4K  plan-2  C8   0.020
 H4K  plan-2  C13  0.020
 H4K  plan-2  C12  0.020
 H4K  plan-2  C11  0.020
 H4K  plan-2  C10  0.020
 H4K  plan-2  H10  0.020
 H4K  plan-2  H5   0.020
 H4K  plan-2  H9   0.020
 H4K  plan-2  H8   0.020
 H4K  plan-2  H7   0.020
 H4K  plan-2  H6   0.020
 H4K  plan-3  C2   0.020
 H4K  plan-3  N1   0.020
 H4K  plan-3  C1   0.020
 H4K  plan-3  O    0.020
 H4K  plan-3  N5   0.020
 H4K  plan-3  C7   0.020
 H4K  plan-3  H1   0.020
 H4K  plan-3  H4   0.020

