# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:06:29 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4,5-bis(4-methoxyphenyl)-2-thiophen-2-yl-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2[nH]c(nc2c3ccc(OC)cc3)c4sccc4
#
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
 PF4  PF4  4,5-bis(4-methoxyphenyl)-2-thiophen-2-yl-1H-imidazole  ligand  44  26  .  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_PF4
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
 PF4  C7    C  CR16  0  -0.294  -0.7910   2.9626   0.4622
 PF4  C9    C  CR5   0   0.499   2.3711   0.2524  -0.0695
 PF4  C13   C  CR16  0  -0.326  -3.1010   2.2270  -0.8620
 PF4  C20   C  CR6   0   0.376  -2.6794  -3.5958   0.2445
 PF4  C8    C  CR16  0  -0.301  -2.0295   1.3587  -0.8003
 PF4  C18   C  CR15  0  -0.231   4.5858   1.4286   0.1372
 PF4  C16   C  CR16  0  -0.325  -2.7720  -2.4281   1.0082
 PF4  C26   C  CH3   0  -0.437  -3.6166  -5.6979  -0.3310
 PF4  O24   O  O2    0  -0.468  -3.6710  -4.4894   0.4016
 PF4  C15   C  CR16  0  -0.371  -1.5933  -3.7642  -0.6105
 PF4  C10   C  CR16  0  -0.293  -0.6245  -2.7727  -0.6984
 PF4  C11   C  CR16  0  -0.284  -1.7981  -1.4561   0.9170
 PF4  C5    C  CR6   0  -0.012  -0.7062  -1.6056   0.0554
 PF4  C2    C  CR5   0   0.314   0.3293  -0.5798  -0.0276
 PF4  N6    N  NR15  0  -0.685   1.6601  -0.8975  -0.0445
 PF4  C14   C  CR5   0  -0.277   3.8150   0.3178  -0.0740
 PF4  S19   S  S2    0   0.230   4.7998  -1.0670  -0.3745
 PF4  C23   C  CR15  0  -0.467   6.2391  -0.1550  -0.2025
 PF4  C22   C  CR15  0  -0.166   5.9741   1.1541   0.0630
 PF4  N4    N  N     0  -0.459   1.5713   1.2920  -0.0864
 PF4  C1    C  CR5   0   0.090   0.2983   0.8007  -0.0680
 PF4  C3    C  CR6   0  -0.006  -0.8534   1.7030  -0.1265
 PF4  C12   C  CR16  0  -0.371  -1.8589   3.8491   0.4063
 PF4  C17   C  CR6   0   0.369  -3.0283   3.4835  -0.2557
 PF4  O21   O  O2    0  -0.470  -4.1189   4.2650  -0.3675
 PF4  C25   C  CH3   0  -0.436  -4.0907   5.5508   0.2189
 PF4  H7    H  HCR6  0   0.250   0.1088   3.2646   0.9830
 PF4  H13   H  HCR6  0   0.261  -4.0005   1.9431  -1.3944
 PF4  H8    H  HCR6  0   0.253  -2.1067   0.4017  -1.3004
 PF4  H18   H  HCR5  0   0.264   4.1687   2.4030   0.3466
 PF4  H16   H  HCR6  0   0.266  -3.6082  -2.2985   1.6839
 PF4  H26   H  HCH3  0   0.261  -4.4889  -6.2763  -0.0370
 PF4  H26A  H  HCH3  0   0.230  -3.6578  -5.5234  -1.4093
 PF4  H26B  H  HCH3  0   0.230  -2.7175  -6.2751  -0.1008
 PF4  H15   H  HCR6  0   0.282  -1.4864  -4.6503  -1.2212
 PF4  H10   H  HCR6  0   0.260   0.2001  -2.9184  -1.3858
 PF4  H11   H  HCR6  0   0.257  -1.8792  -0.5690   1.5321
 PF4  H23   H  HCR5  0   0.302   7.1990  -0.6352  -0.3120
 PF4  H22   H  HCR5  0   0.272   6.7440   1.8982   0.2056
 PF4  H12   H  HCR6  0   0.277  -1.7598   4.8140   0.8856
 PF4  H25   H  HCH3  0   0.259  -5.0575   6.0047   0.0158
 PF4  H25A  H  HCH3  0   0.228  -3.9451   5.5037   1.3014
 PF4  H25B  H  HCH3  0   0.228  -3.3091   6.1806  -0.2145
 PF4  HN6   H  HNR5  0   0.422   2.0266  -1.8338   0.0471

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
 PF4  C3   C7    aromatic  1.392  0.020  1.392
 PF4  C7   C12   aromatic  1.389  0.020  1.389
 PF4  C7   H7    single    0.930  0.020  1.080
 PF4  C14  C9    single    1.445  0.020  1.445
 PF4  C9   N6    aromatic  1.352  0.020  1.352
 PF4  C9   N4    aromatic  1.312  0.020  1.312
 PF4  C8   C13   aromatic  1.381  0.020  1.381
 PF4  C13  C17   aromatic  1.397  0.020  1.397
 PF4  C13  H13   single    0.930  0.020  1.080
 PF4  C15  C20   aromatic  1.393  0.020  1.393
 PF4  C20  O24   single    1.344  0.020  1.344
 PF4  C20  C16   aromatic  1.398  0.020  1.398
 PF4  C3   C8    aromatic  1.399  0.020  1.399
 PF4  C8   H8    single    0.930  0.020  1.080
 PF4  C22  C18   aromatic  1.417  0.020  1.417
 PF4  C18  C14   aromatic  1.368  0.020  1.368
 PF4  C18  H18   single    0.930  0.020  1.080
 PF4  C11  C16   aromatic  1.379  0.020  1.379
 PF4  C16  H16   single    0.930  0.020  1.080
 PF4  C26  O24   single    1.414  0.020  1.414
 PF4  C26  H26   single    0.970  0.020  1.090
 PF4  C26  H26A  single    0.970  0.020  1.090
 PF4  C26  H26B  single    0.970  0.020  1.090
 PF4  C10  C15   aromatic  1.389  0.020  1.389
 PF4  C15  H15   single    0.930  0.020  1.080
 PF4  C10  C5    aromatic  1.392  0.020  1.392
 PF4  C10  H10   single    0.930  0.020  1.080
 PF4  C5   C11   aromatic  1.399  0.020  1.399
 PF4  C11  H11   single    0.930  0.020  1.080
 PF4  C2   C5    single    1.460  0.020  1.460
 PF4  N6   C2    aromatic  1.368  0.020  1.368
 PF4  C2   C1    aromatic  1.381  0.020  1.381
 PF4  S19  C14   aromatic  1.726  0.020  1.726
 PF4  C23  S19   aromatic  1.713  0.020  1.713
 PF4  C22  C23   aromatic  1.362  0.020  1.362
 PF4  C23  H23   single    0.930  0.020  1.080
 PF4  C22  H22   single    0.930  0.020  1.080
 PF4  N4   C1    aromatic  1.365  0.020  1.365
 PF4  C1   C3    single    1.464  0.020  1.464
 PF4  C12  C17   aromatic  1.393  0.020  1.393
 PF4  C12  H12   single    0.930  0.020  1.080
 PF4  C17  O21   single    1.346  0.020  1.346
 PF4  O21  C25   single    1.414  0.020  1.414
 PF4  C25  H25   single    0.970  0.020  1.090
 PF4  C25  H25A  single    0.970  0.020  1.090
 PF4  C25  H25B  single    0.970  0.020  1.090
 PF4  N6   HN6   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
 PF4  H7    C7   C12   118.71  3.000
 PF4  H7    C7   C3    119.55  3.000
 PF4  C12   C7   C3    121.74  3.000
 PF4  N4    C9   C14   124.97  3.000
 PF4  N4    C9   N6    110.71  3.000
 PF4  C14   C9   N6    124.32  3.000
 PF4  H13   C13  C17   119.49  3.000
 PF4  H13   C13  C8    120.12  3.000
 PF4  C17   C13  C8    120.39  3.000
 PF4  C15   C20  O24   124.53  3.000
 PF4  O24   C20  C16   116.26  3.000
 PF4  C15   C20  C16   119.21  3.000
 PF4  H8    C8   C3    120.01  3.000
 PF4  H8    C8   C13   118.69  3.000
 PF4  C3    C8   C13   121.30  3.000
 PF4  H18   C18  C22   124.27  3.000
 PF4  H18   C18  C14   122.99  3.000
 PF4  C22   C18  C14   112.74  3.000
 PF4  H16   C16  C11   120.15  3.000
 PF4  H16   C16  C20   119.47  3.000
 PF4  C11   C16  C20   120.38  3.000
 PF4  H26B  C26  H26A  108.85  3.000
 PF4  H26B  C26  H26   108.79  3.000
 PF4  H26A  C26  H26   108.76  3.000
 PF4  H26B  C26  O24   111.94  3.000
 PF4  H26A  C26  O24   111.91  3.000
 PF4  H26   C26  O24   106.48  3.000
 PF4  C26   O24  C20   118.64  3.000
 PF4  H15   C15  C10   118.70  3.000
 PF4  H15   C15  C20   121.53  3.000
 PF4  C10   C15  C20   119.77  3.000
 PF4  H10   C10  C5    120.08  3.000
 PF4  H10   C10  C15   118.36  3.000
 PF4  C5    C10  C15   121.55  3.000
 PF4  H11   C11  C5    119.74  3.000
 PF4  H11   C11  C16   119.15  3.000
 PF4  C5    C11  C16   121.10  3.000
 PF4  C2    C5   C11   120.90  3.000
 PF4  C2    C5   C10   121.11  3.000
 PF4  C11   C5   C10   117.98  3.000
 PF4  C1    C2   N6    104.68  3.000
 PF4  C1    C2   C5    133.46  3.000
 PF4  N6    C2   C5    121.83  3.000
 PF4  HN6   N6   C2    124.56  3.000
 PF4  HN6   N6   C9    126.83  3.000
 PF4  C2    N6   C9    108.31  3.000
 PF4  S19   C14  C18   110.90  3.000
 PF4  S19   C14  C9    122.30  3.000
 PF4  C18   C14  C9    126.80  3.000
 PF4  C23   S19  C14    91.99  3.000
 PF4  H23   C23  C22   128.38  3.000
 PF4  H23   C23  S19   120.03  3.000
 PF4  C22   C23  S19   111.59  3.000
 PF4  H22   C22  C23   123.31  3.000
 PF4  H22   C22  C18   123.91  3.000
 PF4  C23   C22  C18   112.77  3.000
 PF4  C1    N4   C9    106.46  3.000
 PF4  C3    C1   N4    120.76  3.000
 PF4  C3    C1   C2    129.39  3.000
 PF4  N4    C1   C2    109.83  3.000
 PF4  C1    C3   C8    121.94  3.000
 PF4  C1    C3   C7    120.37  3.000
 PF4  C8    C3   C7    117.66  3.000
 PF4  H12   C12  C17   121.44  3.000
 PF4  H12   C12  C7    118.74  3.000
 PF4  C17   C12  C7    119.81  3.000
 PF4  O21   C17  C12   124.56  3.000
 PF4  O21   C17  C13   116.35  3.000
 PF4  C12   C17  C13   119.09  3.000
 PF4  C25   O21  C17   118.51  3.000
 PF4  H25B  C25  H25A  108.80  3.000
 PF4  H25B  C25  H25   108.73  3.000
 PF4  H25A  C25  H25   108.75  3.000
 PF4  H25B  C25  O21   111.95  3.000
 PF4  H25A  C25  O21   111.98  3.000
 PF4  H25   C25  O21   106.53  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
 PF4  CONST_01  C13  C8   C3   C7      0.00   0.0  0
 PF4  CONST_04  C13  C17  C12  C7      0.00   0.0  0
 PF4  CONST_05  C22  C18  C14  C9    180.00   0.0  0
 PF4  CONST_06  C23  S19  C14  C9    180.00   0.0  0
 PF4  CONST_07  C5   C2   N6   C9    180.00   0.0  0
 PF4  CONST_08  C1   C2   N6   C9      0.00   0.0  0
 PF4  CONST_09  C2   C1   N4   C9      0.00   0.0  0
 PF4  CONST_10  C3   C1   N4   C9    180.00   0.0  0
 PF4  CONST_11  C1   C3   C8   C13   180.00   0.0  0
 PF4  CONST_12  C5   C10  C15  C20     0.00   0.0  0
 PF4  CONST_13  C5   C11  C16  C20     0.00   0.0  0
 PF4  CONST_14  C12  C17  C13  C8      0.00   0.0  0
 PF4  CONST_15  C12  C7   C3   C8      0.00   0.0  0
 PF4  CONST_18  S19  C23  C22  C18     0.00   0.0  0
 PF4  CONST_19  N6   C9   C14  C18   180.00   0.0  0
 PF4  CONST_20  N4   C9   C14  C18     0.00   0.0  0
 PF4  CONST_21  C23  S19  C14  C18     0.00   0.0  0
 PF4  CONST_22  C10  C15  C20  C16     0.00   0.0  0
 PF4  CONST_23  C10  C5   C11  C16     0.00   0.0  0
 PF4  CONST_24  C2   C5   C11  C16   180.00   0.0  0
 PF4  CONST_25  C11  C16  C20  C15     0.00   0.0  0
 PF4  CONST_26  C11  C5   C10  C15     0.00   0.0  0
 PF4  CONST_27  C2   C5   C10  C15   180.00   0.0  0
 PF4  CONST_32  N4   C1   C2   C5    180.00   0.0  0
 PF4  CONST_33  C3   C1   C2   C5      0.00   0.0  0
 PF4  CONST_34  C14  C9   N6   C2    180.00   0.0  0
 PF4  CONST_35  N4   C9   N6   C2      0.00   0.0  0
 PF4  CONST_36  S19  C14  C9   N6      0.00   0.0  0
 PF4  CONST_37  C1   N4   C9   N6      0.00   0.0  0
 PF4  CONST_38  N4   C1   C2   N6      0.00   0.0  0
 PF4  CONST_39  C3   C1   C2   N6    180.00   0.0  0
 PF4  CONST_40  C1   N4   C9   C14   180.00   0.0  0
 PF4  CONST_41  C23  C22  C18  C14     0.00   0.0  0
 PF4  CONST_42  C22  C23  S19  C14     0.00   0.0  0
 PF4  CONST_43  N4   C9   C14  S19   180.00   0.0  0
 PF4  CONST_44  C22  C18  C14  S19     0.00   0.0  0
 PF4  CONST_45  C12  C7   C3   C1    180.00   0.0  0
 PF4  CONST_46  C17  C12  C7   C3      0.00   0.0  0
 PF4  CONST_47  C17  C13  C8   C3      0.00   0.0  0
 PF4  CONST_48  O21  C17  C12  C7    180.00   0.0  0
 PF4  CONST_49  O21  C17  C13  C8    180.00   0.0  0
 PF4  CONST_50  C10  C15  C20  O24   180.00   0.0  0
 PF4  CONST_51  C11  C16  C20  O24   180.00   0.0  0
 PF4  CONST_52  H8   C8   C3   C7    180.00   0.0  0
 PF4  CONST_53  H18  C18  C14  C9      0.00   0.0  0
 PF4  CONST_54  H12  C12  C17  C13   180.00   0.0  0
 PF4  CONST_55  H10  C10  C15  C20   180.00   0.0  0
 PF4  CONST_56  H11  C11  C16  C20   180.00   0.0  0
 PF4  CONST_57  H7   C7   C3   C8    180.00   0.0  0
 PF4  CONST_58  H23  C23  C22  C18   180.00   0.0  0
 PF4  CONST_59  H15  C15  C20  C16   180.00   0.0  0
 PF4  CONST_60  H16  C16  C20  C15   180.00   0.0  0
 PF4  CONST_61  HN6  N6   C2   C5      0.00   0.0  0
 PF4  CONST_62  H22  C22  C18  C14   180.00   0.0  0
 PF4  CONST_63  H13  C13  C8   C3    180.00   0.0  0
 PF4  Var_01    C15  C20  O24  C26     0.83  30.0  1
 PF4  Var_02    H26  C26  O24  C20   178.51  30.0  3
 PF4  Var_03    H25  C25  O21  C17  -179.88  30.0  3

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
 PF4  plan-1  C9   0.020
 PF4  plan-1  C5   0.020
 PF4  plan-1  C2   0.020
 PF4  plan-1  N6   0.020
 PF4  plan-1  C14  0.020
 PF4  plan-1  N4   0.020
 PF4  plan-1  C1   0.020
 PF4  plan-1  C3   0.020
 PF4  plan-1  HN6  0.020
 PF4  plan-2  C9   0.020
 PF4  plan-2  C18  0.020
 PF4  plan-2  C14  0.020
 PF4  plan-2  S19  0.020
 PF4  plan-2  C23  0.020
 PF4  plan-2  C22  0.020
 PF4  plan-2  H18  0.020
 PF4  plan-2  H23  0.020
 PF4  plan-2  H22  0.020
 PF4  plan-3  C20  0.020
 PF4  plan-3  C16  0.020
 PF4  plan-3  O24  0.020
 PF4  plan-3  C15  0.020
 PF4  plan-3  C10  0.020
 PF4  plan-3  C11  0.020
 PF4  plan-3  C5   0.020
 PF4  plan-3  C2   0.020
 PF4  plan-3  H16  0.020
 PF4  plan-3  H15  0.020
 PF4  plan-3  H10  0.020
 PF4  plan-3  H11  0.020
 PF4  plan-4  C7   0.020
 PF4  plan-4  C13  0.020
 PF4  plan-4  C8   0.020
 PF4  plan-4  C1   0.020
 PF4  plan-4  C3   0.020
 PF4  plan-4  C12  0.020
 PF4  plan-4  C17  0.020
 PF4  plan-4  O21  0.020
 PF4  plan-4  H7   0.020
 PF4  plan-4  H13  0.020
 PF4  plan-4  H8   0.020
 PF4  plan-4  H12  0.020

