# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:26:53 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-phenyl-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1cncc1c2ccccc2
#
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
 PIM  PIM  '5-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 GRAND
;

data_comp_PIM
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
 PIM  N1   N  NR15  0  -0.628  -0.9921   0.2414   1.7983
 PIM  C2   C  CR15  0   0.084  -0.5755   0.1291   3.0733
 PIM  N3   N  N     0  -0.435   0.6950  -0.1816   3.1384
 PIM  C4   C  CR15  0  -0.256   1.1132  -0.2662   1.8445
 PIM  C5   C  CR5   0   0.300   0.0782  -0.0032   0.9798
 PIM  C6   C  CR6   0   0.077   0.0174   0.0146  -0.4757
 PIM  C7   C  CR16  0  -0.326   1.1915   0.1719  -1.2181
 PIM  C8   C  CR16  0  -0.236   1.1578   0.1745  -2.6030
 PIM  C9   C  CR16  0  -0.269  -0.0496   0.0314  -3.2762
 PIM  C10  C  CR16  0  -0.238  -1.2220  -0.1204  -2.5487
 PIM  C11  C  CR16  0  -0.314  -1.1903  -0.1335  -1.1618
 PIM  HN1  H  HNR5  0   0.421  -1.9205   0.5091   1.5110
 PIM  H2   H  HCR5  0   0.281  -1.2374   0.2858   3.9107
 PIM  H4   H  HCR5  0   0.259   2.1290  -0.5300   1.5915
 PIM  H7   H  HCR6  0   0.253   2.1375   0.3080  -0.7087
 PIM  H8   H  HCR6  0   0.260   2.0778   0.3006  -3.1593
 PIM  H9   H  HCR6  0   0.258  -0.0756   0.0394  -4.3578
 PIM  H10  H  HCR6  0   0.260  -2.1680  -0.2379  -3.0611
 PIM  H11  H  HCR6  0   0.248  -2.1171  -0.2799  -0.6201

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
 PIM  N1   C2   aromatic  1.346  0.020  1.346
 PIM  N1   C5   aromatic  1.369  0.020  1.369
 PIM  N1   HN1  single    0.860  0.020  1.020
 PIM  C2   N3   aromatic  1.310  0.020  1.310
 PIM  C2   H2   single    0.930  0.020  1.080
 PIM  N3   C4   aromatic  1.362  0.020  1.362
 PIM  C4   C5   aromatic  1.374  0.020  1.374
 PIM  C4   H4   single    0.930  0.020  1.080
 PIM  C5   C6   single    1.457  0.020  1.457
 PIM  C6   C7   aromatic  1.398  0.020  1.398
 PIM  C6   C11  aromatic  1.397  0.020  1.397
 PIM  C7   C8   aromatic  1.385  0.020  1.385
 PIM  C7   H7   single    0.930  0.020  1.080
 PIM  C8   C9   aromatic  1.390  0.020  1.390
 PIM  C8   H8   single    0.930  0.020  1.080
 PIM  C9   C10  aromatic  1.388  0.020  1.388
 PIM  C9   H9   single    0.930  0.020  1.080
 PIM  C10  C11  aromatic  1.387  0.020  1.387
 PIM  C10  H10  single    0.930  0.020  1.080
 PIM  C11  H11  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
 PIM  HN1  N1   C5   126.65  3.000
 PIM  HN1  N1   C2   125.25  3.000
 PIM  C5   N1   C2   108.02  3.000
 PIM  H2   C2   N3   126.23  3.000
 PIM  H2   C2   N1   122.23  3.000
 PIM  N3   C2   N1   111.54  3.000
 PIM  C4   N3   C2   105.39  3.000
 PIM  H4   C4   C5   127.45  3.000
 PIM  H4   C4   N3   121.78  3.000
 PIM  C5   C4   N3   110.76  3.000
 PIM  C6   C5   C4   131.49  3.000
 PIM  C6   C5   N1   124.22  3.000
 PIM  C4   C5   N1   104.28  3.000
 PIM  C11  C6   C7   118.51  3.000
 PIM  C11  C6   C5   121.70  3.000
 PIM  C7   C6   C5   119.79  3.000
 PIM  H7   C7   C8   119.42  3.000
 PIM  H7   C7   C6   119.86  3.000
 PIM  C8   C7   C6   120.71  3.000
 PIM  H8   C8   C9   120.09  3.000
 PIM  H8   C8   C7   119.56  3.000
 PIM  C9   C8   C7   120.34  3.000
 PIM  H9   C9   C10  120.30  3.000
 PIM  H9   C9   C8   120.29  3.000
 PIM  C10  C9   C8   119.42  3.000
 PIM  H10  C10  C11  119.49  3.000
 PIM  H10  C10  C9   120.13  3.000
 PIM  C11  C10  C9   120.38  3.000
 PIM  H11  C11  C10  118.79  3.000
 PIM  H11  C11  C6   120.56  3.000
 PIM  C10  C11  C6   120.64  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
 PIM  CONST_01  C4   N3   C2   N1    0.00  0.0  0
 PIM  CONST_02  N3   C4   C5   N1    0.00  0.0  0
 PIM  CONST_05  C4   C5   N1   C2    0.00  0.0  0
 PIM  CONST_06  C6   C5   N1   C2  180.00  0.0  0
 PIM  CONST_07  C5   C4   N3   C2    0.00  0.0  0
 PIM  CONST_08  C5   N1   C2   N3    0.00  0.0  0
 PIM  CONST_09  C6   C5   C4   N3  180.00  0.0  0
 PIM  CONST_12  C8   C7   C6   C5  180.00  0.0  0
 PIM  CONST_13  C10  C11  C6   C5  180.00  0.0  0
 PIM  CONST_14  C9   C8   C7   C6    0.00  0.0  0
 PIM  CONST_15  C9   C10  C11  C6    0.00  0.0  0
 PIM  CONST_16  C10  C11  C6   C7    0.00  0.0  0
 PIM  CONST_17  C10  C9   C8   C7    0.00  0.0  0
 PIM  CONST_18  C11  C6   C7   C8    0.00  0.0  0
 PIM  CONST_19  C11  C10  C9   C8    0.00  0.0  0
 PIM  CONST_20  H4   C4   C5   N1  180.00  0.0  0
 PIM  CONST_21  HN1  N1   C2   N3  180.00  0.0  0
 PIM  CONST_22  H2   C2   N3   C4  180.00  0.0  0
 PIM  CONST_23  H7   C7   C6   C5    0.00  0.0  0
 PIM  CONST_24  H11  C11  C6   C5    0.00  0.0  0
 PIM  CONST_25  H8   C8   C7   C6  180.00  0.0  0
 PIM  CONST_26  H10  C10  C11  C6  180.00  0.0  0
 PIM  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
 PIM  plan-1  N1   0.020
 PIM  plan-1  C2   0.020
 PIM  plan-1  N3   0.020
 PIM  plan-1  C4   0.020
 PIM  plan-1  C5   0.020
 PIM  plan-1  C6   0.020
 PIM  plan-1  HN1  0.020
 PIM  plan-1  H2   0.020
 PIM  plan-1  H4   0.020
 PIM  plan-2  C5   0.020
 PIM  plan-2  C6   0.020
 PIM  plan-2  C7   0.020
 PIM  plan-2  C8   0.020
 PIM  plan-2  C9   0.020
 PIM  plan-2  C10  0.020
 PIM  plan-2  C11  0.020
 PIM  plan-2  H7   0.020
 PIM  plan-2  H8   0.020
 PIM  plan-2  H9   0.020
 PIM  plan-2  H10  0.020
 PIM  plan-2  H11  0.020

