# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:41:55 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 2-(thiophen-2-yl)-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1ccnc1c2sccc2
#
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
 JG4  JG4  2-(thiophen-2-yl)-1H-imidazole  ligand  16  10  .  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_JG4
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
 JG4  C01   C  CR15  0  -0.167   2.5644   1.2341  -0.0245
 JG4  C02   C  CR15  0  -0.228   1.1654   1.4590  -0.0501
 JG4  C03   C  CR5   0  -0.246   0.4410   0.2991  -0.0062
 JG4  S04   S  S2    0   0.227   1.4840  -1.0730   0.0716
 JG4  C05   C  CR15  0  -0.467   2.8848  -0.0877   0.0389
 JG4  C06   C  CR5   0   0.480  -1.0013   0.1796  -0.0157
 JG4  N07   N  NR15  0  -0.632  -1.6723  -0.9945  -0.0764
 JG4  C08   C  CR15  0  -0.101  -3.0059  -0.7135  -0.0707
 JG4  C09   C  CR15  0  -0.216  -3.0843   0.6491  -0.0054
 JG4  N10   N  N     0  -0.450  -1.8362   1.1937   0.0287
 JG4  H011  H  HCR5  0   0.272   3.3019   2.0228  -0.0524
 JG4  H021  H  HCR5  0   0.263   0.7084   2.4367  -0.1029
 JG4  H051  H  HCR5  0   0.301   3.8636  -0.5405   0.0700
 JG4  H071  H  HNR5  0   0.423  -1.2788  -1.9216  -0.1323
 JG4  H081  H  HCR5  0   0.289  -3.7562  -1.4836  -0.1139
 JG4  H091  H  HCR5  0   0.253  -3.9728   1.2605   0.0203

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
 JG4  N10  C09   aromatic  1.362  0.020  1.362
 JG4  N10  C06   aromatic  1.314  0.020  1.314
 JG4  S04  C05   aromatic  1.713  0.020  1.713
 JG4  S04  C03   aromatic  1.725  0.020  1.725
 JG4  C09  C08   aromatic  1.366  0.020  1.366
 JG4  C05  C01   aromatic  1.362  0.020  1.362
 JG4  C03  C06   single    1.447  0.020  1.447
 JG4  C03  C02   aromatic  1.368  0.020  1.368
 JG4  C06  N07   aromatic  1.354  0.020  1.354
 JG4  C01  C02   aromatic  1.417  0.020  1.417
 JG4  C08  N07   aromatic  1.363  0.020  1.363
 JG4  C01  H011  single    0.930  0.020  1.080
 JG4  C02  H021  single    0.930  0.020  1.080
 JG4  C05  H051  single    0.930  0.020  1.080
 JG4  N07  H071  single    0.860  0.020  1.020
 JG4  C08  H081  single    0.930  0.020  1.080
 JG4  C09  H091  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
 JG4  H011  C01  C05  123.33  3.000
 JG4  H011  C01  C02  123.89  3.000
 JG4  C05   C01  C02  112.78  3.000
 JG4  H021  C02  C03  123.00  3.000
 JG4  H021  C02  C01  124.20  3.000
 JG4  C03   C02  C01  112.80  3.000
 JG4  C06   C03  S04  122.49  3.000
 JG4  C06   C03  C02  126.68  3.000
 JG4  S04   C03  C02  110.83  3.000
 JG4  C05   S04  C03   92.07  3.000
 JG4  H051  C05  S04  120.00  3.000
 JG4  H051  C05  C01  128.48  3.000
 JG4  S04   C05  C01  111.53  3.000
 JG4  N10   C06  N07  110.85  3.000
 JG4  N07   C06  C03  124.46  3.000
 JG4  N10   C06  C03  124.69  3.000
 JG4  H071  N07  C08  124.85  3.000
 JG4  H071  N07  C06  127.32  3.000
 JG4  C08   N07  C06  107.82  3.000
 JG4  H081  C08  C09  132.49  3.000
 JG4  H081  C08  N07  122.32  3.000
 JG4  C09   C08  N07  105.19  3.000
 JG4  H091  C09  N10  121.83  3.000
 JG4  H091  C09  C08  127.85  3.000
 JG4  N10   C09  C08  110.32  3.000
 JG4  C09   N10  C06  105.83  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
 JG4  CONST_01  C03   S04  C05  C01    0.00  0.0  0
 JG4  CONST_02  S04   C03  C02  C01    0.00  0.0  0
 JG4  CONST_03  C06   C03  C02  C01  180.00  0.0  0
 JG4  CONST_04  C05   S04  C03  C02    0.00  0.0  0
 JG4  CONST_05  N10   C06  C03  C02    0.00  0.0  0
 JG4  CONST_06  N07   C06  C03  C02  180.00  0.0  0
 JG4  CONST_07  S04   C05  C01  C02    0.00  0.0  0
 JG4  CONST_08  C09   N10  C06  C03  180.00  0.0  0
 JG4  CONST_09  C08   N07  C06  C03  180.00  0.0  0
 JG4  CONST_10  C05   C01  C02  C03    0.00  0.0  0
 JG4  CONST_11  N10   C06  C03  S04  180.00  0.0  0
 JG4  CONST_12  N07   C06  C03  S04    0.00  0.0  0
 JG4  CONST_13  C06   C03  S04  C05  180.00  0.0  0
 JG4  CONST_14  C08   C09  N10  C06    0.00  0.0  0
 JG4  CONST_15  C09   C08  N07  C06    0.00  0.0  0
 JG4  CONST_16  C09   N10  C06  N07    0.00  0.0  0
 JG4  CONST_17  N10   C09  C08  N07    0.00  0.0  0
 JG4  CONST_18  N10   C06  N07  C08    0.00  0.0  0
 JG4  CONST_19  H051  C05  C01  C02  180.00  0.0  0
 JG4  CONST_20  H071  N07  C06  C03    0.00  0.0  0
 JG4  CONST_21  H011  C01  C02  C03  180.00  0.0  0
 JG4  CONST_22  H021  C02  C03  S04  180.00  0.0  0
 JG4  CONST_23  H091  C09  N10  C06  180.00  0.0  0
 JG4  CONST_24  H081  C08  N07  C06  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
 JG4  plan-1  C01   0.020
 JG4  plan-1  C02   0.020
 JG4  plan-1  C03   0.020
 JG4  plan-1  S04   0.020
 JG4  plan-1  C05   0.020
 JG4  plan-1  C06   0.020
 JG4  plan-1  H011  0.020
 JG4  plan-1  H021  0.020
 JG4  plan-1  H051  0.020
 JG4  plan-2  C03   0.020
 JG4  plan-2  C06   0.020
 JG4  plan-2  N07   0.020
 JG4  plan-2  C08   0.020
 JG4  plan-2  C09   0.020
 JG4  plan-2  N10   0.020
 JG4  plan-2  H071  0.020
 JG4  plan-2  H081  0.020
 JG4  plan-2  H091  0.020

