# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:18:52 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 1-[(3,4-dichlorophenyl)methyl]imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Cn2ccnc2)cc1Cl
#
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
 JJ8  JJ8  1-[(3,4-dichlorophenyl)methyl]imidazole  ligand  22  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JJ8
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
 JJ8  CL8  CL  CL    0  -0.094   2.9485   1.6978  -0.9454
 JJ8  C3   C   CR6   0   0.024   1.7403   0.5053  -0.6571
 JJ8  C2   C   CR16  0  -0.270   0.4583   0.7041  -1.1520
 JJ8  C4   C   CR6   0  -0.016   2.0361  -0.6429   0.0651
 JJ8  CL7  CL  CL    0  -0.094   3.6190  -0.9079   0.6871
 JJ8  C5   C   CR16  0  -0.199   1.0448  -1.5896   0.2890
 JJ8  C6   C   CR16  0  -0.281  -0.2293  -1.3879  -0.2079
 JJ8  C1   C   CR6   0   0.124  -0.5330  -0.2397  -0.9342
 JJ8  C9   C   CH2   0  -0.399  -1.9190  -0.0242  -1.4837
 JJ8  N10  N   NR5   0  -0.394  -2.9222  -0.0197  -0.4412
 JJ8  C14  C   CR15  0  -0.097  -3.0698   0.9256   0.5353
 JJ8  C13  C   CR15  0  -0.216  -4.1055   0.4890   1.3097
 JJ8  N12  N   N     0  -0.456  -4.5865  -0.6979   0.8325
 JJ8  C11  C   CR15  0   0.098  -3.8518  -0.9727  -0.2137
 JJ8  H1   H   HCR6  0   0.288   0.2395   1.6047  -1.7115
 JJ8  H2   H   HCR6  0   0.291   1.2771  -2.4842   0.8504
 JJ8  H3   H   HCR6  0   0.271  -0.9889  -2.1381  -0.0263
 JJ8  H4   H   HCH2  0   0.292  -1.9685   0.9154  -2.0340
 JJ8  H5   H   HCH2  0   0.297  -2.1755  -0.8189  -2.1853
 JJ8  H6   H   HCR5  0   0.291  -2.4454   1.8021   0.5876
 JJ8  H7   H   HCR5  0   0.252  -4.5281   0.9695   2.1785
 JJ8  H8   H   HCR5  0   0.284  -3.9462  -1.8409  -0.8498

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
 JJ8  N12  C13  aromatic  1.367  0.020  1.367
 JJ8  N12  C11  aromatic  1.308  0.020  1.308
 JJ8  C13  C14  aromatic  1.365  0.020  1.365
 JJ8  C11  N10  aromatic  1.351  0.020  1.351
 JJ8  C14  N10  aromatic  1.367  0.020  1.367
 JJ8  C5   C6   aromatic  1.382  0.020  1.382
 JJ8  C5   C4   aromatic  1.389  0.020  1.389
 JJ8  N10  C9   single    1.447  0.020  1.447
 JJ8  C6   C1   aromatic  1.392  0.020  1.392
 JJ8  CL7  C4   single    1.721  0.020  1.721
 JJ8  C4   C3   aromatic  1.388  0.020  1.388
 JJ8  C1   C9   single    1.506  0.020  1.506
 JJ8  C1   C2   aromatic  1.386  0.020  1.386
 JJ8  C3   C2   aromatic  1.389  0.020  1.389
 JJ8  C3   CL8  single    1.722  0.020  1.722
 JJ8  C2   H1   single    0.930  0.020  1.080
 JJ8  C5   H2   single    0.930  0.020  1.080
 JJ8  C6   H3   single    0.930  0.020  1.080
 JJ8  C9   H4   single    0.970  0.020  1.090
 JJ8  C9   H5   single    0.970  0.020  1.090
 JJ8  C14  H6   single    0.930  0.020  1.080
 JJ8  C13  H7   single    0.930  0.020  1.080
 JJ8  C11  H8   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
 JJ8  C4   C3   C2   120.03  3.000
 JJ8  C2   C3   CL8  119.28  3.000
 JJ8  C4   C3   CL8  120.69  3.000
 JJ8  H1   C2   C1   120.20  3.000
 JJ8  H1   C2   C3   119.34  3.000
 JJ8  C1   C2   C3   120.46  3.000
 JJ8  C5   C4   CL7  119.55  3.000
 JJ8  CL7  C4   C3   120.74  3.000
 JJ8  C5   C4   C3   119.71  3.000
 JJ8  H2   C5   C6   120.35  3.000
 JJ8  H2   C5   C4   119.62  3.000
 JJ8  C6   C5   C4   120.03  3.000
 JJ8  H3   C6   C1   120.38  3.000
 JJ8  H3   C6   C5   119.02  3.000
 JJ8  C1   C6   C5   120.59  3.000
 JJ8  C9   C1   C6   120.60  3.000
 JJ8  C9   C1   C2   120.22  3.000
 JJ8  C6   C1   C2   119.18  3.000
 JJ8  H5   C9   H4   107.02  3.000
 JJ8  H5   C9   N10  107.62  3.000
 JJ8  H4   C9   N10  109.24  3.000
 JJ8  H5   C9   C1   110.29  3.000
 JJ8  H4   C9   C1   110.44  3.000
 JJ8  N10  C9   C1   112.06  3.000
 JJ8  C11  N10  C14  107.06  3.000
 JJ8  C14  N10  C9   126.28  3.000
 JJ8  C11  N10  C9   126.61  3.000
 JJ8  H6   C14  C13  132.25  3.000
 JJ8  H6   C14  N10  122.32  3.000
 JJ8  C13  C14  N10  105.43  3.000
 JJ8  H7   C13  N12  122.01  3.000
 JJ8  H7   C13  C14  127.70  3.000
 JJ8  N12  C13  C14  110.29  3.000
 JJ8  C11  N12  C13  105.31  3.000
 JJ8  H8   C11  N12  126.22  3.000
 JJ8  H8   C11  N10  121.87  3.000
 JJ8  N12  C11  N10  111.91  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
 JJ8  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 JJ8  CONST_02  C6   C1   C2   C3      0.00   0.0  0
 JJ8  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 JJ8  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 JJ8  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 JJ8  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 JJ8  CONST_07  C13  N12  C11  N10     0.00   0.0  0
 JJ8  CONST_08  N12  C13  C14  N10     0.00   0.0  0
 JJ8  CONST_09  C11  N12  C13  C14     0.00   0.0  0
 JJ8  CONST_10  N12  C11  N10  C14     0.00   0.0  0
 JJ8  CONST_11  C11  N10  C14  C13     0.00   0.0  0
 JJ8  CONST_12  C5   C4   C3   CL8   180.00   0.0  0
 JJ8  CONST_13  C1   C2   C3   CL8   180.00   0.0  0
 JJ8  CONST_14  C9   C1   C2   C3    180.00   0.0  0
 JJ8  CONST_15  CL7  C4   C3   C2    180.00   0.0  0
 JJ8  CONST_16  C6   C5   C4   CL7   180.00   0.0  0
 JJ8  CONST_17  C9   C1   C6   C5    180.00   0.0  0
 JJ8  CONST_18  N12  C11  N10  C9    180.00   0.0  0
 JJ8  CONST_19  C13  C14  N10  C9    180.00   0.0  0
 JJ8  CONST_20  H2   C5   C4   C3    180.00   0.0  0
 JJ8  CONST_21  H3   C6   C1   C2    180.00   0.0  0
 JJ8  CONST_22  H1   C2   C3   C4    180.00   0.0  0
 JJ8  CONST_23  H7   C13  C14  N10   180.00   0.0  0
 JJ8  CONST_24  H8   C11  N10  C14   180.00   0.0  0
 JJ8  CONST_25  H6   C14  C13  N12   180.00   0.0  0
 JJ8  Var_01    N10  C9   C1   C2   -121.47  30.0  2
 JJ8  Var_02    C11  N10  C9   C1   -109.38  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
 JJ8  plan-1  C9   0.020
 JJ8  plan-1  N10  0.020
 JJ8  plan-1  C14  0.020
 JJ8  plan-1  C13  0.020
 JJ8  plan-1  N12  0.020
 JJ8  plan-1  C11  0.020
 JJ8  plan-1  H6   0.020
 JJ8  plan-1  H7   0.020
 JJ8  plan-1  H8   0.020
 JJ8  plan-2  CL8  0.020
 JJ8  plan-2  C3   0.020
 JJ8  plan-2  C2   0.020
 JJ8  plan-2  C4   0.020
 JJ8  plan-2  CL7  0.020
 JJ8  plan-2  C5   0.020
 JJ8  plan-2  C6   0.020
 JJ8  plan-2  C1   0.020
 JJ8  plan-2  C9   0.020
 JJ8  plan-2  H1   0.020
 JJ8  plan-2  H2   0.020
 JJ8  plan-2  H3   0.020

