# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:13:05 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[1-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-1,3,4-oxadiazole-2(3H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)n2cnc3ccc(cc23)C4=NNC(=S)O4
#
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
 3HT  3HT  5-[1-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-1,3,4-oxadiazole-2(3H)-thione  ligand  35  23  .  2022-07-22  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_3HT
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
 3HT  C4    C  CR16  0  -0.340  -4.5537   0.5483  -1.1252
 3HT  C5    C  CR16  0  -0.259  -3.6589  -0.5005  -1.0487
 3HT  C6    C  CR6   0   0.271  -2.7242  -0.5440  -0.0197
 3HT  C7    C  CR16  0  -0.264  -2.6821   0.4751   0.9175
 3HT  C8    C  CR16  0  -0.382  -3.5644   1.5431   0.8345
 3HT  C10   C  CR15  0   0.111  -2.1488  -2.9470   0.1649
 3HT  C13   C  CR16  0  -0.302   1.3297  -3.2138   0.2067
 3HT  C15   C  CR6   0  -0.043   1.7931  -0.8381   0.0091
 3HT  C17   C  CR56  0   0.356  -0.4473  -1.5736   0.0758
 3HT  C21   C  CR5   0   0.397   4.7344   1.1477  -0.1710
 3HT  S22   S  S1    0  -0.331   6.3688   1.3129  -0.1966
 3HT  N20   N  NR15  0  -0.453   3.7592   2.0507  -0.2358
 3HT  N19   N  N     0  -0.232   2.5271   1.4993  -0.1817
 3HT  O32   O  O     0  -0.414   4.0814  -0.0315  -0.0720
 3HT  C18   C  CR5   0   0.501   2.7569   0.2414  -0.0836
 3HT  C14   C  CR16  0  -0.294   2.2304  -2.1724   0.1238
 3HT  C16   C  CR16  0  -0.314   0.4390  -0.5175  -0.0187
 3HT  C12   C  CR56  0   0.143  -0.0307  -2.9129   0.1796
 3HT  N11   N  N     0  -0.456  -1.1210  -3.7424   0.2317
 3HT  N9    N  NR5   0  -0.617  -1.8215  -1.6299   0.0698
 3HT  C3    C  CR6   0   0.393  -4.5132   1.5824  -0.1859
 3HT  O2    O  O2    0  -0.466  -5.4171   2.5621  -0.3424
 3HT  C1    C  CH3   0  -0.440  -5.4334   3.6263   0.5901
 3HT  H4    H  HCR6  0   0.275  -5.2849   0.5799  -1.9226
 3HT  H5    H  HCR6  0   0.280  -3.6850  -1.2844  -1.7947
 3HT  H7    H  HCR6  0   0.284  -1.9671   0.4418   1.7296
 3HT  H8    H  HCR6  0   0.290  -3.5009   2.3213   1.5820
 3HT  H10   H  HCR5  0   0.302  -3.1828  -3.2600   0.1902
 3HT  H13   H  HCR6  0   0.270   1.6717  -4.2367   0.2889
 3HT  HN20  H  HNR5  0   0.454   3.8764   3.0502  -0.3130
 3HT  H14   H  HCR6  0   0.268   3.2884  -2.3940   0.1472
 3HT  H16   H  HCR6  0   0.286   0.1050   0.5075  -0.1125
 3HT  H1    H  HCH3  0   0.263  -6.2403   4.2887   0.2873
 3HT  H1A   H  HCH3  0   0.232  -5.6289   3.2741   1.6058
 3HT  H1B   H  HCH3  0   0.232  -4.4960   4.1880   0.5838

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
 3HT  C3   C4    aromatic  1.398  0.020  1.398
 3HT  C4   C5    aromatic  1.381  0.020  1.381
 3HT  C4   H4    single    0.930  0.020  1.080
 3HT  C5   C6    aromatic  1.391  0.020  1.391
 3HT  C5   H5    single    0.930  0.020  1.080
 3HT  C7   C6    aromatic  1.385  0.020  1.385
 3HT  C6   N9    single    1.415  0.020  1.415
 3HT  C8   C7    aromatic  1.388  0.020  1.388
 3HT  C7   H7    single    0.930  0.020  1.080
 3HT  C3   C8    aromatic  1.394  0.020  1.394
 3HT  C8   H8    single    0.930  0.020  1.080
 3HT  N9   C10   aromatic  1.361  0.020  1.361
 3HT  C10  N11   aromatic  1.301  0.020  1.301
 3HT  C10  H10   single    0.930  0.020  1.080
 3HT  C12  C13   aromatic  1.394  0.020  1.394
 3HT  C14  C13   aromatic  1.379  0.020  1.379
 3HT  C13  H13   single    0.930  0.020  1.080
 3HT  C16  C15   aromatic  1.392  0.020  1.392
 3HT  C18  C15   single    1.450  0.020  1.450
 3HT  C15  C14   aromatic  1.409  0.020  1.409
 3HT  N9   C17   aromatic  1.375  0.020  1.375
 3HT  C16  C17   aromatic  1.382  0.020  1.382
 3HT  C17  C12   aromatic  1.406  0.020  1.406
 3HT  S22  C21   double    1.643  0.020  1.643
 3HT  O32  C21   single    1.352  0.020  1.352
 3HT  C21  N20   single    1.331  0.020  1.331
 3HT  N20  N19   single    1.351  0.020  1.351
 3HT  N20  HN20  single    0.860  0.020  1.020
 3HT  C18  N19   double    1.282  0.020  1.282
 3HT  O32  C18   single    1.352  0.020  1.352
 3HT  C14  H14   single    0.930  0.020  1.080
 3HT  C16  H16   single    0.930  0.020  1.080
 3HT  N11  C12   aromatic  1.371  0.020  1.371
 3HT  O2   C3    single    1.342  0.020  1.342
 3HT  C1   O2    single    1.415  0.020  1.415
 3HT  C1   H1    single    0.970  0.020  1.090
 3HT  C1   H1A   single    0.970  0.020  1.090
 3HT  C1   H1B   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
 3HT  H4    C4   C3   119.54  3.000
 3HT  H4    C4   C5   120.06  3.000
 3HT  C3    C4   C5   120.40  3.000
 3HT  H5    C5   C6   120.23  3.000
 3HT  H5    C5   C4   119.75  3.000
 3HT  C6    C5   C4   120.02  3.000
 3HT  N9    C6   C7   120.16  3.000
 3HT  N9    C6   C5   119.97  3.000
 3HT  C7    C6   C5   119.86  3.000
 3HT  H7    C7   C8   119.24  3.000
 3HT  H7    C7   C6   120.33  3.000
 3HT  C8    C7   C6   120.43  3.000
 3HT  H8    C8   C3   121.73  3.000
 3HT  H8    C8   C7   118.39  3.000
 3HT  C3    C8   C7   119.88  3.000
 3HT  H10   C10  N9   120.81  3.000
 3HT  H10   C10  N11  125.27  3.000
 3HT  N9    C10  N11  113.91  3.000
 3HT  H13   C13  C12  120.95  3.000
 3HT  H13   C13  C14  120.81  3.000
 3HT  C12   C13  C14  118.25  3.000
 3HT  C16   C15  C14  121.45  3.000
 3HT  C14   C15  C18  120.26  3.000
 3HT  C16   C15  C18  118.29  3.000
 3HT  N9    C17  C12  104.91  3.000
 3HT  C12   C17  C16  122.88  3.000
 3HT  N9    C17  C16  132.20  3.000
 3HT  O32   C21  N20  103.98  3.000
 3HT  N20   C21  S22  131.30  3.000
 3HT  O32   C21  S22  124.72  3.000
 3HT  HN20  N20  N19  120.87  3.000
 3HT  HN20  N20  C21  126.21  3.000
 3HT  N19   N20  C21  112.92  3.000
 3HT  C18   N19  N20  103.88  3.000
 3HT  C18   O32  C21  107.25  3.000
 3HT  O32   C18  N19  111.97  3.000
 3HT  O32   C18  C15  120.01  3.000
 3HT  N19   C18  C15  128.02  3.000
 3HT  H14   C14  C15  119.98  3.000
 3HT  H14   C14  C13  118.87  3.000
 3HT  C15   C14  C13  121.15  3.000
 3HT  H16   C16  C17  122.13  3.000
 3HT  H16   C16  C15  121.34  3.000
 3HT  C17   C16  C15  116.53  3.000
 3HT  N11   C12  C17  110.09  3.000
 3HT  N11   C12  C13  130.17  3.000
 3HT  C17   C12  C13  119.74  3.000
 3HT  C12   N11  C10  104.85  3.000
 3HT  C17   N9   C10  106.24  3.000
 3HT  C17   N9   C6   127.32  3.000
 3HT  C10   N9   C6   126.44  3.000
 3HT  O2    C3   C8   124.35  3.000
 3HT  O2    C3   C4   116.25  3.000
 3HT  C8    C3   C4   119.39  3.000
 3HT  C1    O2   C3   118.68  3.000
 3HT  H1B   C1   H1A  108.93  3.000
 3HT  H1B   C1   H1   108.78  3.000
 3HT  H1A   C1   H1   108.82  3.000
 3HT  H1B   C1   O2   111.90  3.000
 3HT  H1A   C1   O2   111.85  3.000
 3HT  H1    C1   O2   106.46  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
 3HT  CONST_01  C7   C8   C3   C4      0.00   0.0  0
 3HT  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 3HT  CONST_03  N9   C6   C5   C4    180.00   0.0  0
 3HT  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 3HT  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 3HT  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 3HT  CONST_09  C3   C8   C7   C6      0.00   0.0  0
 3HT  CONST_10  N11  C10  N9   C6    180.00   0.0  0
 3HT  CONST_11  C16  C17  N9   C6      0.00   0.0  0
 3HT  CONST_12  C12  C17  N9   C6    180.00   0.0  0
 3HT  CONST_15  N9   C6   C7   C8    180.00   0.0  0
 3HT  CONST_16  C16  C17  N9   C10   180.00   0.0  0
 3HT  CONST_17  C12  C17  N9   C10     0.00   0.0  0
 3HT  CONST_18  C13  C12  N11  C10   180.00   0.0  0
 3HT  CONST_19  C17  C12  N11  C10     0.00   0.0  0
 3HT  CONST_20  N9   C17  C12  C13   180.00   0.0  0
 3HT  CONST_21  C16  C17  C12  C13     0.00   0.0  0
 3HT  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 3HT  CONST_23  N9   C17  C16  C15   180.00   0.0  0
 3HT  CONST_24  C12  C17  C16  C15     0.00   0.0  0
 3HT  CONST_25  C12  C13  C14  C15     0.00   0.0  0
 3HT  CONST_26  N11  C10  N9   C17     0.00   0.0  0
 3HT  CONST_27  C14  C15  C16  C17     0.00   0.0  0
 3HT  CONST_28  C14  C13  C12  C17     0.00   0.0  0
 3HT  CONST_29  N11  C12  C13  C14   180.00   0.0  0
 3HT  CONST_30  N11  C12  C17  C16   180.00   0.0  0
 3HT  CONST_31  N9   C10  N11  C12     0.00   0.0  0
 3HT  CONST_32  N9   C17  C12  N11     0.00   0.0  0
 3HT  CONST_33  C18  C15  C14  C13   180.00   0.0  0
 3HT  CONST_34  C18  C15  C16  C17   180.00   0.0  0
 3HT  CONST_35  O2   C3   C4   C5    180.00   0.0  0
 3HT  CONST_36  O2   C3   C8   C7    180.00   0.0  0
 3HT  CONST_37  H8   C8   C3   C4    180.00   0.0  0
 3HT  CONST_38  H7   C7   C6   C5    180.00   0.0  0
 3HT  CONST_39  H4   C4   C5   C6    180.00   0.0  0
 3HT  CONST_40  H10  C10  N9   C6      0.00   0.0  0
 3HT  CONST_41  H5   C5   C6   C7    180.00   0.0  0
 3HT  CONST_42  H13  C13  C14  C15   180.00   0.0  0
 3HT  CONST_43  H16  C16  C15  C18     0.00   0.0  0
 3HT  CONST_44  H14  C14  C15  C18     0.00   0.0  0
 3HT  Var_01    C16  C15  C18  N19     0.57  30.0  2
 3HT  Var_02    H1   C1   O2   C3   -179.17  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
 3HT  plan-1  C15   0.020
 3HT  plan-1  C21   0.020
 3HT  plan-1  S22   0.020
 3HT  plan-1  N20   0.020
 3HT  plan-1  N19   0.020
 3HT  plan-1  O32   0.020
 3HT  plan-1  C18   0.020
 3HT  plan-1  HN20  0.020
 3HT  plan-2  C4    0.020
 3HT  plan-2  C5    0.020
 3HT  plan-2  C6    0.020
 3HT  plan-2  C7    0.020
 3HT  plan-2  C8    0.020
 3HT  plan-2  N9    0.020
 3HT  plan-2  C3    0.020
 3HT  plan-2  O2    0.020
 3HT  plan-2  H4    0.020
 3HT  plan-2  H5    0.020
 3HT  plan-2  H7    0.020
 3HT  plan-2  H8    0.020
 3HT  plan-3  C6    0.020
 3HT  plan-3  C10   0.020
 3HT  plan-3  C13   0.020
 3HT  plan-3  C15   0.020
 3HT  plan-3  C17   0.020
 3HT  plan-3  C18   0.020
 3HT  plan-3  C14   0.020
 3HT  plan-3  C16   0.020
 3HT  plan-3  C12   0.020
 3HT  plan-3  N11   0.020
 3HT  plan-3  N9    0.020
 3HT  plan-3  H10   0.020
 3HT  plan-3  H13   0.020
 3HT  plan-3  H14   0.020
 3HT  plan-3  H16   0.020

