# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:06:39 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-(4-methylbenzyl)-4-thiophen-2-yl-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Cn2cnc(c2)c3sccc3)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
 654  654  1-(4-methylbenzyl)-4-thiophen-2-yl-1H-imidazole  ligand  32  18  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_654
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
 654  S1T   S  S2    0   0.201   1.4889   0.0909  -3.1123
 654  C2T   C  CR5   0  -0.251  -0.1512  -0.3810  -2.8512
 654  C3T   C  CR15  0  -0.239  -0.6168  -1.1110  -3.9098
 654  C4T   C  CR15  0  -0.171   0.3541  -1.2884  -4.9313
 654  C5T   C  CR15  0  -0.472   1.5418  -0.6930  -4.6382
 654  C1I   C  CR5   0   0.137  -0.8661  -0.0146  -1.6451
 654  N2I   N  N     0  -0.464  -2.1674  -0.3908  -1.4501
 654  C3I   C  CR15  0  -0.097  -0.4253   0.7105  -0.5665
 654  N4I   N  NR5   0  -0.398  -1.4841   0.7736   0.2899
 654  C5I   C  CR15  0   0.095  -2.5000   0.0960  -0.2845
 654  C1    C  CH2   0  -0.402  -1.4956   1.4146   1.5921
 654  C2    C  CR6   0   0.102  -0.5499   0.7512   2.5566
 654  C3    C  CR16  0  -0.292   0.5448   1.4396   3.0641
 654  C4    C  CR16  0  -0.282   1.4213   0.8246   3.9484
 654  C5    C  CR16  0  -0.268  -0.7478  -0.5690   2.9502
 654  C6    C  CR16  0  -0.287   0.1299  -1.1814   3.8305
 654  C7    C  CR6   0   0.088   1.2290  -0.4952   4.3470
 654  C8    C  CH3   0  -0.722   2.1635  -1.1513   5.3210
 654  H3TC  H  HCR5  0   0.258  -1.6209  -1.5078  -3.9524
 654  H4TC  H  HCR5  0   0.265   0.1741  -1.8378  -5.8443
 654  H5TC  H  HCR5  0   0.295   2.4443  -0.6720  -5.2289
 654  H3IC  H  HCR5  0   0.296   0.5233   1.1715  -0.3422
 654  H5IC  H  HCR5  0   0.288  -3.4635  -0.0049   0.1932
 654  HC11  H  HCH2  0   0.289  -2.5220   1.3745   1.9580
 654  HC12  H  HCH2  0   0.287  -1.2378   2.4669   1.4689
 654  HC3   H  HCR6  0   0.254   0.7202   2.4664   2.7649
 654  HC4   H  HCR6  0   0.249   2.2691   1.3821   4.3295
 654  HC5   H  HCR6  0   0.252  -1.5929  -1.1285   2.5649
 654  HC6   H  HCR6  0   0.250  -0.0423  -2.2104   4.1232
 654  HC81  H  HCH3  0   0.250   1.9211  -0.8674   6.3470
 654  HC82  H  HCH3  0   0.244   2.1057  -2.2375   5.2616
 654  HC83  H  HCH3  0   0.245   3.1978  -0.8580   5.1423

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
 654  S1T  C2T   aromatic  1.726  0.020  1.726
 654  S1T  C5T   aromatic  1.716  0.020  1.716
 654  C2T  C3T   aromatic  1.368  0.020  1.368
 654  C2T  C1I   single    1.449  0.020  1.449
 654  C3T  C4T   aromatic  1.420  0.020  1.420
 654  C3T  H3TC  single    0.930  0.020  1.080
 654  C4T  C5T   aromatic  1.361  0.020  1.361
 654  C4T  H4TC  single    0.930  0.020  1.080
 654  C5T  H5TC  single    0.930  0.020  1.080
 654  C1I  N2I   aromatic  1.368  0.020  1.368
 654  C1I  C3I   aromatic  1.372  0.020  1.372
 654  N2I  C5I   aromatic  1.306  0.020  1.306
 654  C3I  N4I   aromatic  1.363  0.020  1.363
 654  C3I  H3IC  single    0.930  0.020  1.080
 654  N4I  C5I   aromatic  1.349  0.020  1.349
 654  N4I  C1    single    1.451  0.020  1.451
 654  C5I  H5IC  single    0.930  0.020  1.080
 654  C1   C2    single    1.505  0.020  1.505
 654  C1   HC11  single    0.970  0.020  1.090
 654  C1   HC12  single    0.970  0.020  1.090
 654  C2   C3    aromatic  1.389  0.020  1.389
 654  C2   C5    aromatic  1.392  0.020  1.392
 654  C3   C4    aromatic  1.389  0.020  1.389
 654  C3   HC3   single    0.930  0.020  1.080
 654  C4   C7    aromatic  1.392  0.020  1.392
 654  C4   HC4   single    0.930  0.020  1.080
 654  C5   C6    aromatic  1.386  0.020  1.386
 654  C5   HC5   single    0.930  0.020  1.080
 654  C6   C7    aromatic  1.395  0.020  1.395
 654  C6   HC6   single    0.930  0.020  1.080
 654  C7   C8    single    1.501  0.020  1.501
 654  C8   HC81  single    0.970  0.020  1.090
 654  C8   HC82  single    0.970  0.020  1.090
 654  C8   HC83  single    0.970  0.020  1.090

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
 654  C5T   S1T  C2T    92.23  3.000
 654  C1I   C2T  C3T   127.68  3.000
 654  C1I   C2T  S1T   121.69  3.000
 654  C3T   C2T  S1T   110.63  3.000
 654  H3TC  C3T  C4T   124.13  3.000
 654  H3TC  C3T  C2T   122.88  3.000
 654  C4T   C3T  C2T   112.99  3.000
 654  H4TC  C4T  C5T   123.36  3.000
 654  H4TC  C4T  C3T   123.86  3.000
 654  C5T   C4T  C3T   112.78  3.000
 654  H5TC  C5T  C4T   128.38  3.000
 654  H5TC  C5T  S1T   120.25  3.000
 654  C4T   C5T  S1T   111.38  3.000
 654  C3I   C1I  N2I   109.79  3.000
 654  C3I   C1I  C2T   128.99  3.000
 654  N2I   C1I  C2T   121.21  3.000
 654  C5I   N2I  C1I   105.48  3.000
 654  H3IC  C3I  N4I   122.20  3.000
 654  H3IC  C3I  C1I   132.21  3.000
 654  N4I   C3I  C1I   105.59  3.000
 654  C1    N4I  C5I   126.70  3.000
 654  C1    N4I  C3I   126.17  3.000
 654  C5I   N4I  C3I   107.10  3.000
 654  H5IC  C5I  N4I   122.02  3.000
 654  H5IC  C5I  N2I   125.95  3.000
 654  N4I   C5I  N2I   112.04  3.000
 654  HC12  C1   HC11  107.22  3.000
 654  HC12  C1   C2    110.44  3.000
 654  HC11  C1   C2    111.11  3.000
 654  HC12  C1   N4I   108.85  3.000
 654  HC11  C1   N4I   106.99  3.000
 654  C2    C1   N4I   112.04  3.000
 654  C5    C2   C3    118.61  3.000
 654  C5    C2   C1    120.67  3.000
 654  C3    C2   C1    120.72  3.000
 654  HC3   C3   C4    119.55  3.000
 654  HC3   C3   C2    119.75  3.000
 654  C4    C3   C2    120.70  3.000
 654  HC4   C4   C7    119.67  3.000
 654  HC4   C4   C3    119.33  3.000
 654  C7    C4   C3    121.00  3.000
 654  HC5   C5   C6    119.43  3.000
 654  HC5   C5   C2    119.99  3.000
 654  C6    C5   C2    120.58  3.000
 654  HC6   C6   C7    119.50  3.000
 654  HC6   C6   C5    119.38  3.000
 654  C7    C6   C5    121.12  3.000
 654  C8    C7   C6    121.05  3.000
 654  C8    C7   C4    120.95  3.000
 654  C6    C7   C4    117.99  3.000
 654  HC83  C8   HC82  108.04  3.000
 654  HC83  C8   HC81  107.15  3.000
 654  HC82  C8   HC81  107.39  3.000
 654  HC83  C8   C7    111.52  3.000
 654  HC82  C8   C7    111.56  3.000
 654  HC81  C8   C7    110.98  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
 654  CONST_01  C4T   C3T  C2T  S1T    0.00   0.0  0
 654  CONST_02  N2I   C1I  C2T  S1T  180.00   0.0  0
 654  CONST_03  C3I   C1I  C2T  S1T    0.00   0.0  0
 654  CONST_04  C3T   C4T  C5T  S1T    0.00   0.0  0
 654  CONST_05  C4T   C5T  S1T  C2T    0.00   0.0  0
 654  CONST_06  C5T   C4T  C3T  C2T    0.00   0.0  0
 654  CONST_07  C5I   N2I  C1I  C2T  180.00   0.0  0
 654  CONST_08  N4I   C3I  C1I  C2T  180.00   0.0  0
 654  CONST_09  C5T   S1T  C2T  C3T    0.00   0.0  0
 654  CONST_10  N2I   C1I  C2T  C3T    0.00   0.0  0
 654  CONST_11  C3I   C1I  C2T  C3T  180.00   0.0  0
 654  CONST_12  C1I   C2T  C3T  C4T  180.00   0.0  0
 654  CONST_13  C1I   C2T  S1T  C5T  180.00   0.0  0
 654  CONST_14  N4I   C5I  N2I  C1I    0.00   0.0  0
 654  CONST_15  C5I   N4I  C3I  C1I    0.00   0.0  0
 654  CONST_16  N4I   C3I  C1I  N2I    0.00   0.0  0
 654  CONST_17  C3I   N4I  C5I  N2I    0.00   0.0  0
 654  CONST_18  C5I   N2I  C1I  C3I    0.00   0.0  0
 654  CONST_19  C7    C4   C3   C2     0.00   0.0  0
 654  CONST_20  C7    C6   C5   C2     0.00   0.0  0
 654  CONST_21  C6    C5   C2   C3     0.00   0.0  0
 654  CONST_22  C6    C7   C4   C3     0.00   0.0  0
 654  CONST_23  C5    C2   C3   C4     0.00   0.0  0
 654  CONST_24  C5    C6   C7   C4     0.00   0.0  0
 654  CONST_25  C1    N4I  C3I  C1I  180.00   0.0  0
 654  CONST_26  C1    N4I  C5I  N2I  180.00   0.0  0
 654  CONST_27  C4    C3   C2   C1   180.00   0.0  0
 654  CONST_28  C6    C5   C2   C1   180.00   0.0  0
 654  CONST_29  C8    C7   C4   C3   180.00   0.0  0
 654  CONST_30  C8    C7   C6   C5   180.00   0.0  0
 654  CONST_31  H3TC  C3T  C2T  S1T  180.00   0.0  0
 654  CONST_32  H4TC  C4T  C5T  S1T  180.00   0.0  0
 654  CONST_33  H5TC  C5T  S1T  C2T  180.00   0.0  0
 654  CONST_34  H3IC  C3I  C1I  C2T    0.00   0.0  0
 654  CONST_35  H5IC  C5I  N2I  C1I  180.00   0.0  0
 654  CONST_36  HC4   C4   C3   C2   180.00   0.0  0
 654  CONST_37  HC6   C6   C5   C2   180.00   0.0  0
 654  CONST_38  HC5   C5   C2   C3   180.00   0.0  0
 654  CONST_39  HC3   C3   C2   C5   180.00   0.0  0
 654  Var_01    C2    C1   N4I  C3I  -64.05  30.0  2
 654  Var_02    C3    C2   C1   N4I  115.94  30.0  2
 654  Var_03    HC81  C8   C7   C4    80.59  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
 654  plan-1  S1T   0.020
 654  plan-1  C2T   0.020
 654  plan-1  C3T   0.020
 654  plan-1  C4T   0.020
 654  plan-1  C5T   0.020
 654  plan-1  C1I   0.020
 654  plan-1  H3TC  0.020
 654  plan-1  H4TC  0.020
 654  plan-1  H5TC  0.020
 654  plan-2  C2T   0.020
 654  plan-2  C1I   0.020
 654  plan-2  N2I   0.020
 654  plan-2  C3I   0.020
 654  plan-2  N4I   0.020
 654  plan-2  C5I   0.020
 654  plan-2  C1    0.020
 654  plan-2  H3IC  0.020
 654  plan-2  H5IC  0.020
 654  plan-3  C1    0.020
 654  plan-3  C2    0.020
 654  plan-3  C3    0.020
 654  plan-3  C4    0.020
 654  plan-3  C5    0.020
 654  plan-3  C6    0.020
 654  plan-3  C7    0.020
 654  plan-3  C8    0.020
 654  plan-3  HC3   0.020
 654  plan-3  HC4   0.020
 654  plan-3  HC5   0.020
 654  plan-3  HC6   0.020

