# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:53:40 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-phenyl-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1ccnc1c2ccccc2
#
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
 PIY  PIY  '2-phenyl-1H-imidazole    '  ligand  19  11  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PIY
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
 PIY  N1   N  NR15  0  -0.632  -1.8274   1.0318   0.0206
 PIY  C2   C  CR5   0   0.456  -1.0287  -0.0603  -0.0298
 PIY  N3   N  N     0  -0.453  -1.7524  -1.1559  -0.0966
 PIY  C4   C  CR15  0  -0.103  -3.1223   0.6106  -0.0154
 PIY  C5   C  CR15  0  -0.212  -3.0524  -0.7522  -0.0886
 PIY  C6   C  CR6   0   0.048   0.4317  -0.0179  -0.0118
 PIY  C7   C  CR16  0  -0.294   1.1461  -1.2176   0.0266
 PIY  C8   C  CR16  0  -0.238   2.5310  -1.2125   0.0435
 PIY  C9   C  CR16  0  -0.264   3.2285  -0.0105   0.0224
 PIY  C10  C  CR16  0  -0.237   2.5264   1.1864  -0.0166
 PIY  C11  C  CR16  0  -0.308   1.1395   1.1846  -0.0355
 PIY  H4   H  HCR5  0   0.288  -3.9512   1.2967   0.0119
 PIY  H5   H  HCR5  0   0.251  -3.8689  -1.4554  -0.1378
 PIY  H7   H  HCR6  0   0.253   0.6068  -2.1554   0.0456
 PIY  H8   H  HCR6  0   0.259   3.0693  -2.1509   0.0745
 PIY  H9   H  HCR6  0   0.260   4.3103  -0.0072   0.0368
 PIY  H10  H  HCR6  0   0.261   3.0587   2.1284  -0.0367
 PIY  H11  H  HCR6  0   0.243   0.6222   2.1353  -0.0738
 PIY  HN1  H  HNR5  0   0.423  -1.5398   1.9953   0.0846

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
 PIY  C2   N1   aromatic  1.354  0.020  1.354
 PIY  N1   C4   aromatic  1.362  0.020  1.362
 PIY  C6   C2   single    1.461  0.020  1.461
 PIY  C2   N3   aromatic  1.315  0.020  1.315
 PIY  N3   C5   aromatic  1.361  0.020  1.361
 PIY  C4   C5   aromatic  1.367  0.020  1.367
 PIY  C4   H4   single    0.930  0.020  1.080
 PIY  C5   H5   single    0.930  0.020  1.080
 PIY  C7   C6   aromatic  1.397  0.020  1.397
 PIY  C11  C6   aromatic  1.396  0.020  1.396
 PIY  C8   C7   aromatic  1.385  0.020  1.385
 PIY  C7   H7   single    0.930  0.020  1.080
 PIY  C9   C8   aromatic  1.390  0.020  1.390
 PIY  C8   H8   single    0.930  0.020  1.080
 PIY  C9   C10  aromatic  1.388  0.020  1.388
 PIY  C9   H9   single    0.930  0.020  1.080
 PIY  C10  C11  aromatic  1.387  0.020  1.387
 PIY  C10  H10  single    0.930  0.020  1.080
 PIY  C11  H11  single    0.930  0.020  1.080
 PIY  N1   HN1  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
 PIY  HN1  N1   C4   124.66  3.000
 PIY  HN1  N1   C2   127.25  3.000
 PIY  C4   N1   C2   108.08  3.000
 PIY  C6   C2   N3   125.10  3.000
 PIY  N3   C2   N1   110.45  3.000
 PIY  C6   C2   N1   124.46  3.000
 PIY  C5   N3   C2   106.16  3.000
 PIY  H4   C4   C5   132.57  3.000
 PIY  H4   C4   N1   122.30  3.000
 PIY  C5   C4   N1   105.14  3.000
 PIY  H5   C5   C4   127.87  3.000
 PIY  H5   C5   N3   121.95  3.000
 PIY  C4   C5   N3   110.17  3.000
 PIY  C11  C6   C7   118.76  3.000
 PIY  C11  C6   C2   122.12  3.000
 PIY  C7   C6   C2   119.12  3.000
 PIY  H7   C7   C8   120.09  3.000
 PIY  H7   C7   C6   119.34  3.000
 PIY  C8   C7   C6   120.57  3.000
 PIY  H8   C8   C9   120.05  3.000
 PIY  H8   C8   C7   119.64  3.000
 PIY  C9   C8   C7   120.31  3.000
 PIY  H9   C9   C10  120.23  3.000
 PIY  H9   C9   C8   120.28  3.000
 PIY  C10  C9   C8   119.49  3.000
 PIY  H10  C10  C11  119.52  3.000
 PIY  H10  C10  C9   120.15  3.000
 PIY  C11  C10  C9   120.33  3.000
 PIY  H11  C11  C10  118.49  3.000
 PIY  H11  C11  C6   120.98  3.000
 PIY  C10  C11  C6   120.53  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
 PIY  CONST_01  C7   C6   C2   N1  180.00  0.0  0
 PIY  CONST_02  C11  C6   C2   N1    0.00  0.0  0
 PIY  CONST_03  C5   N3   C2   N1    0.00  0.0  0
 PIY  CONST_04  N3   C5   C4   N1    0.00  0.0  0
 PIY  CONST_05  C5   C4   N1   C2    0.00  0.0  0
 PIY  CONST_06  C8   C7   C6   C2  180.00  0.0  0
 PIY  CONST_07  C10  C11  C6   C2  180.00  0.0  0
 PIY  CONST_08  C4   C5   N3   C2    0.00  0.0  0
 PIY  CONST_09  C4   N1   C2   N3    0.00  0.0  0
 PIY  CONST_10  C7   C6   C2   N3    0.00  0.0  0
 PIY  CONST_11  C11  C6   C2   N3  180.00  0.0  0
 PIY  CONST_12  C6   C2   N1   C4  180.00  0.0  0
 PIY  CONST_13  C6   C2   N3   C5  180.00  0.0  0
 PIY  CONST_14  C9   C8   C7   C6    0.00  0.0  0
 PIY  CONST_15  C9   C10  C11  C6    0.00  0.0  0
 PIY  CONST_16  C10  C11  C6   C7    0.00  0.0  0
 PIY  CONST_17  C10  C9   C8   C7    0.00  0.0  0
 PIY  CONST_18  C11  C6   C7   C8    0.00  0.0  0
 PIY  CONST_19  C11  C10  C9   C8    0.00  0.0  0
 PIY  CONST_20  H5   C5   C4   N1  180.00  0.0  0
 PIY  CONST_21  H4   C4   N1   C2  180.00  0.0  0
 PIY  CONST_22  H7   C7   C6   C2    0.00  0.0  0
 PIY  CONST_23  H11  C11  C6   C2    0.00  0.0  0
 PIY  CONST_24  HN1  N1   C2   N3  180.00  0.0  0
 PIY  CONST_25  H8   C8   C7   C6  180.00  0.0  0
 PIY  CONST_26  H10  C10  C11  C6  180.00  0.0  0
 PIY  CONST_27  H9   C9   C8   C7  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
 PIY  plan-1  N1   0.020
 PIY  plan-1  C2   0.020
 PIY  plan-1  N3   0.020
 PIY  plan-1  C4   0.020
 PIY  plan-1  C5   0.020
 PIY  plan-1  C6   0.020
 PIY  plan-1  H4   0.020
 PIY  plan-1  H5   0.020
 PIY  plan-1  HN1  0.020
 PIY  plan-2  C2   0.020
 PIY  plan-2  C6   0.020
 PIY  plan-2  C7   0.020
 PIY  plan-2  C8   0.020
 PIY  plan-2  C9   0.020
 PIY  plan-2  C10  0.020
 PIY  plan-2  C11  0.020
 PIY  plan-2  H7   0.020
 PIY  plan-2  H8   0.020
 PIY  plan-2  H9   0.020
 PIY  plan-2  H10  0.020
 PIY  plan-2  H11  0.020

