# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:39:12 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-(4-chlorophenyl)-~{N}-pyrimidin-2-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CC(=O)Nc2ncccn2)cc1
#
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
 QKZ  QKZ  2-(4-chlorophenyl)-~{N}-pyrimidin-2-yl-ethanamide  ligand  27  17  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QKZ
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
 QKZ  N1   N   N     0  -0.415  -10.0057  7.2982  -97.8588
 QKZ  C4   C   CH2   0  -0.671   -6.1625  8.8016  -96.2966
 QKZ  C5   C   C     0   0.539   -7.3486  8.0989  -96.9384
 QKZ  C6   C   CR6   0   0.599   -9.7854  8.4738  -97.2966
 QKZ  C7   C   CR16  0  -0.009  -11.2545  7.0600  -98.2421
 QKZ  C8   C   CR16  0  -0.359  -12.2783  7.9729  -98.0690
 QKZ  C10  C   CR16  0  -0.296   -6.3272  8.4823  -93.8062
 QKZ  O    O   O     0  -0.426   -7.2410  6.9997  -97.4313
 QKZ  C3   C   CR6   0   0.133   -5.7896  8.0847  -95.0264
 QKZ  C2   C   CR16  0  -0.301   -4.9394  6.9833  -95.0549
 QKZ  C1   C   CR16  0  -0.197   -4.6257  6.2930  -93.8938
 QKZ  C11  C   CR16  0  -0.197   -6.0246  7.8035  -92.6348
 QKZ  C    C   CR6   0  -0.053   -5.1751  6.7103  -92.6916
 QKZ  CL   CL  CL    0  -0.131   -4.7888  5.8535  -91.2340
 QKZ  N    N   NH1   0  -0.707   -8.5137  8.8115  -96.8649
 QKZ  N2   N   N     0  -0.446  -10.6870  9.4276  -97.0781
 QKZ  C9   C   CR16  0  -0.013  -11.9254  9.1694  -97.4649
 QKZ  H1   H   HCH2  0   0.302   -5.3373  8.7655  -97.0094
 QKZ  H2   H   HCH2  0   0.287   -6.3685  9.8534  -96.0952
 QKZ  H3   H   HCR6  0   0.280  -11.4397  6.0980  -98.7062
 QKZ  H4   H   HCR6  0   0.285  -13.2898  7.7670  -98.3844
 QKZ  H6   H   HCR6  0   0.264   -4.5070  6.6574  -95.9924
 QKZ  H7   H   HCR6  0   0.280   -3.9595  5.4417  -93.9281
 QKZ  H8   H   HCR6  0   0.281   -6.4474  8.1254  -91.6929
 QKZ  H9   H   HNH1  0   0.420   -8.4678  9.7274  -96.4435
 QKZ  H10  H   HCR6  0   0.284  -12.6618  9.9443  -97.2858
 QKZ  H5   H   HCR6  0   0.264   -6.9909  9.3371  -93.7584

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
 QKZ  C7   N1   aromatic  1.328  0.020  1.328
 QKZ  C7   C8   aromatic  1.383  0.020  1.383
 QKZ  N1   C6   aromatic  1.322  0.020  1.322
 QKZ  C8   C9   aromatic  1.386  0.020  1.386
 QKZ  O    C5   double    1.209  0.020  1.209
 QKZ  C6   N    single    1.385  0.020  1.385
 QKZ  C6   N2   aromatic  1.331  0.020  1.331
 QKZ  C9   N2   aromatic  1.323  0.020  1.323
 QKZ  C5   N    single    1.368  0.020  1.368
 QKZ  C5   C4   single    1.521  0.020  1.521
 QKZ  C4   C3   single    1.505  0.020  1.505
 QKZ  C3   C2   aromatic  1.392  0.020  1.392
 QKZ  C3   C10  aromatic  1.391  0.020  1.391
 QKZ  C2   C1   aromatic  1.387  0.020  1.387
 QKZ  C10  C11  aromatic  1.387  0.020  1.387
 QKZ  C1   C    aromatic  1.386  0.020  1.386
 QKZ  C11  C    aromatic  1.386  0.020  1.386
 QKZ  C    CL   single    1.734  0.020  1.734
 QKZ  C4   H1   single    0.970  0.020  1.090
 QKZ  C4   H2   single    0.970  0.020  1.090
 QKZ  C7   H3   single    0.930  0.020  1.080
 QKZ  C8   H4   single    0.930  0.020  1.080
 QKZ  C10  H5   single    0.930  0.020  1.080
 QKZ  C2   H6   single    0.930  0.020  1.080
 QKZ  C1   H7   single    0.930  0.020  1.080
 QKZ  C11  H8   single    0.930  0.020  1.080
 QKZ  N    H9   single    0.860  0.020  1.020
 QKZ  C9   H10  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
 QKZ  C7   N1   C6   116.05  3.000
 QKZ  H2   C4   H1   107.19  3.000
 QKZ  H2   C4   C3   110.50  3.000
 QKZ  H1   C4   C3   110.37  3.000
 QKZ  H2   C4   C5   112.10  3.000
 QKZ  H1   C4   C5   107.40  3.000
 QKZ  C3   C4   C5   109.22  3.000
 QKZ  N    C5   O    124.83  3.000
 QKZ  N    C5   C4   113.64  3.000
 QKZ  O    C5   C4   121.51  3.000
 QKZ  N2   C6   N    113.34  3.000
 QKZ  N2   C6   N1   126.48  3.000
 QKZ  N    C6   N1   120.18  3.000
 QKZ  H3   C7   C8   120.87  3.000
 QKZ  H3   C7   N1   116.32  3.000
 QKZ  C8   C7   N1   122.81  3.000
 QKZ  H4   C8   C9   122.05  3.000
 QKZ  H4   C8   C7   122.10  3.000
 QKZ  C9   C8   C7   115.85  3.000
 QKZ  H5   C10  C11  118.85  3.000
 QKZ  H5   C10  C3   120.05  3.000
 QKZ  C11  C10  C3   121.09  3.000
 QKZ  C2   C3   C10  118.69  3.000
 QKZ  C10  C3   C4   120.54  3.000
 QKZ  C2   C3   C4   120.73  3.000
 QKZ  H6   C2   C1   119.00  3.000
 QKZ  H6   C2   C3   120.00  3.000
 QKZ  C1   C2   C3   121.00  3.000
 QKZ  H7   C1   C    120.57  3.000
 QKZ  H7   C1   C2   120.30  3.000
 QKZ  C    C1   C2   119.12  3.000
 QKZ  H8   C11  C    120.67  3.000
 QKZ  H8   C11  C10  120.30  3.000
 QKZ  C    C11  C10  119.02  3.000
 QKZ  CL   C    C11  119.47  3.000
 QKZ  CL   C    C1   119.46  3.000
 QKZ  C11  C    C1   121.07  3.000
 QKZ  H9   N    C6   113.16  3.000
 QKZ  H9   N    C5   117.16  3.000
 QKZ  C6   N    C5   129.68  3.000
 QKZ  C9   N2   C6   116.52  3.000
 QKZ  H10  C9   N2   116.63  3.000
 QKZ  H10  C9   C8   121.08  3.000
 QKZ  N2   C9   C8   122.30  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
 QKZ  CONST_01  C9   C8   C7   N1     0.00   0.0  0
 QKZ  CONST_02  C9   N2   C6   N1     0.00   0.0  0
 QKZ  CONST_03  C8   C7   N1   C6     0.00   0.0  0
 QKZ  CONST_04  C8   C9   N2   C6     0.00   0.0  0
 QKZ  CONST_05  N2   C6   N1   C7     0.00   0.0  0
 QKZ  CONST_06  N2   C9   C8   C7     0.00   0.0  0
 QKZ  CONST_07  C1   C2   C3   C10    0.00   0.0  0
 QKZ  CONST_08  C1   C    C11  C10    0.00   0.0  0
 QKZ  CONST_09  C    C1   C2   C3     0.00   0.0  0
 QKZ  CONST_10  C    C11  C10  C3     0.00   0.0  0
 QKZ  CONST_11  C11  C10  C3   C2     0.00   0.0  0
 QKZ  CONST_12  C11  C    C1   C2     0.00   0.0  0
 QKZ  CONST_13  C1   C2   C3   C4   180.00   0.0  0
 QKZ  CONST_14  C11  C10  C3   C4   180.00   0.0  0
 QKZ  CONST_15  N    C6   N1   C7   180.00   0.0  0
 QKZ  CONST_16  CL   C    C11  C10  180.00   0.0  0
 QKZ  CONST_17  CL   C    C1   C2   180.00   0.0  0
 QKZ  CONST_18  C9   N2   C6   N    180.00   0.0  0
 QKZ  CONST_19  H4   C8   C7   N1   180.00   0.0  0
 QKZ  CONST_20  H3   C7   N1   C6   180.00   0.0  0
 QKZ  CONST_21  H10  C9   N2   C6   180.00   0.0  0
 QKZ  CONST_22  H6   C2   C3   C10  180.00   0.0  0
 QKZ  CONST_23  H7   C1   C2   C3   180.00   0.0  0
 QKZ  CONST_24  H8   C11  C10  C3   180.00   0.0  0
 QKZ  CONST_25  H5   C10  C3   C2   180.00   0.0  0
 QKZ  CONST_26  C5   N    C6   N1     0.00   0.0  0
 QKZ  CONST_27  N2   C6   N    C5   180.00   0.0  0
 QKZ  CONST_28  H9   N    C6   N1   180.00   0.0  0
 QKZ  CONST_29  C6   N    C5   C4   180.00   0.0  0
 QKZ  CONST_30  O    C5   N    C6     0.00   0.0  0
 QKZ  Var_01    C2   C3   C4   C5    85.33  30.0  2
 QKZ  Var_02    C3   C4   C5   O    -69.42  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
 QKZ  plan-1  N1   0.020
 QKZ  plan-1  C6   0.020
 QKZ  plan-1  C7   0.020
 QKZ  plan-1  C8   0.020
 QKZ  plan-1  N    0.020
 QKZ  plan-1  N2   0.020
 QKZ  plan-1  C9   0.020
 QKZ  plan-1  H3   0.020
 QKZ  plan-1  H4   0.020
 QKZ  plan-1  H10  0.020
 QKZ  plan-2  C4   0.020
 QKZ  plan-2  C10  0.020
 QKZ  plan-2  C3   0.020
 QKZ  plan-2  C2   0.020
 QKZ  plan-2  C1   0.020
 QKZ  plan-2  C11  0.020
 QKZ  plan-2  C    0.020
 QKZ  plan-2  CL   0.020
 QKZ  plan-2  H6   0.020
 QKZ  plan-2  H7   0.020
 QKZ  plan-2  H8   0.020
 QKZ  plan-2  H5   0.020
 QKZ  plan-3  C4   0.020
 QKZ  plan-3  C5   0.020
 QKZ  plan-3  C6   0.020
 QKZ  plan-3  O    0.020
 QKZ  plan-3  N    0.020
 QKZ  plan-3  H9   0.020

