# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 01:56:18 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 6-[(4-chlorophenyl)methyl]-8,9,10,11-tetrahydro[1]benzothieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CN2C(=O)n3ncnc3c4c5CCCCc5sc24)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
 8HP  8HP  6-[(4-chlorophenyl)methyl]-8,9,10,11-tetrahydro[1]benzothieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one  ligand  40  25  .  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_8HP
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
 8HP  C4   C   CR16  0  -0.308  -2.6867  -1.2596   1.3960
 8HP  C5   C   CR6   0   0.127  -2.2304   0.0096   1.0639
 8HP  C6   C   CH2   0  -0.438  -1.1964   0.6935   1.9192
 8HP  C8   C   CR6   0   0.754   0.1210   2.4681   0.8812
 8HP  C15  C   CR56  0   0.014   2.0143   0.4961  -0.0004
 8HP  C17  C   CH2   0  -0.500   4.0854  -0.6652  -1.0833
 8HP  C20  C   CH2   0  -0.477   2.7827  -3.1739   0.0146
 8HP  C21  C   CR5   0  -0.275   2.2344  -1.7930   0.1656
 8HP  C24  C   CR16  0  -0.289  -2.7662   0.6465  -0.0526
 8HP  C3   C   CR16  0  -0.195  -3.6562  -1.8940   0.6318
 8HP  C25  C   CR16  0  -0.193  -3.7299   0.0256  -0.8298
 8HP  C12  C   CR15  0   0.016   2.7452   3.8155  -0.8225
 8HP  C16  C   CR5   0   0.185   2.8002  -0.6574  -0.3143
 8HP  C2   C   CR6   0  -0.051  -4.1663  -1.2440  -0.4792
 8HP  C23  C   CR56  0   0.082   0.8788   0.1967   0.7120
 8HP  C14  C   CR56  0   0.549   2.2200   1.8700  -0.2849
 8HP  C18  C   CH2   0  -0.450   4.8001  -2.0086  -0.9476
 8HP  C19  C   CH2   0  -0.451   3.8356  -3.1809  -1.0921
 8HP  N13  N   N     0  -0.467   3.1593   2.5285  -0.9184
 8HP  N11  N   N     0  -0.244   1.6232   4.0054  -0.1822
 8HP  N10  N   N     0  -0.471   1.2808   2.7519   0.1683
 8HP  N7   N   NR6   0  -0.586  -0.0298   1.1294   1.1522
 8HP  S22  S   S2    0   0.267   0.7412  -1.4895   1.0027
 8HP  CL1  CL  CL    0  -0.124  -5.3702  -2.0263  -1.4482
 8HP  H1   H   HCR6  0   0.272  -2.2862  -1.7719   2.2624
 8HP  H2   H   HCH2  0   0.318  -1.6188   1.5706   2.4040
 8HP  H3   H   HCH2  0   0.304  -0.8514   0.0335   2.7178
 8HP  H4   H   HCH2  0   0.248   3.8734  -0.4531  -2.1360
 8HP  H5   H   HCH2  0   0.253   4.7318   0.1447  -0.7400
 8HP  H6   H   HCH2  0   0.256   3.2258  -3.5023   0.9599
 8HP  H7   H   HCH2  0   0.260   1.9862  -3.8853  -0.2150
 8HP  H8   H   HCR6  0   0.266  -2.4442   1.6437  -0.3252
 8HP  H9   H   HCR6  0   0.284  -3.9988  -2.8844   0.8979
 8HP  H10  H   HCR6  0   0.284  -4.1400   0.5296  -1.6943
 8HP  H11  H   HCR5  0   0.284   3.3006   4.6399  -1.2433
 8HP  H12  H   HCH2  0   0.243   5.5890  -2.0755  -1.6983
 8HP  H13  H   HCH2  0   0.229   5.2917  -2.0624   0.0283
 8HP  H14  H   HCH2  0   0.245   4.3802  -4.1261  -1.0663
 8HP  H15  H   HCH2  0   0.231   3.3387  -3.1294  -2.0652
 8HP  O9   O   O     0  -0.449  -0.6567   3.3290   1.2140

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
 8HP  CL1  C2   single    1.732  0.020  1.732
 8HP  C25  C2   aromatic  1.388  0.020  1.388
 8HP  C25  C24  aromatic  1.385  0.020  1.385
 8HP  C2   C3   aromatic  1.385  0.020  1.385
 8HP  C24  C5   aromatic  1.393  0.020  1.393
 8HP  C3   C4   aromatic  1.388  0.020  1.388
 8HP  C5   C4   aromatic  1.389  0.020  1.389
 8HP  C5   C6   single    1.506  0.020  1.506
 8HP  C6   N7   single    1.463  0.020  1.463
 8HP  O9   C8   double    1.207  0.020  1.207
 8HP  N7   C8   single    1.374  0.020  1.374
 8HP  N7   C23  single    1.375  0.020  1.375
 8HP  C8   N10  single    1.391  0.020  1.391
 8HP  S22  C23  aromatic  1.717  0.020  1.717
 8HP  S22  C21  aromatic  1.739  0.020  1.739
 8HP  C23  C15  aromatic  1.374  0.020  1.374
 8HP  N10  N11  aromatic  1.346  0.020  1.346
 8HP  N10  C14  aromatic  1.366  0.020  1.366
 8HP  N11  C12  aromatic  1.306  0.020  1.306
 8HP  C15  C14  aromatic  1.418  0.020  1.418
 8HP  C15  C16  aromatic  1.431  0.020  1.431
 8HP  C14  N13  aromatic  1.310  0.020  1.310
 8HP  C21  C16  aromatic  1.356  0.020  1.356
 8HP  C21  C20  single    1.493  0.020  1.493
 8HP  C12  N13  aromatic  1.355  0.020  1.355
 8HP  C16  C17  single    1.498  0.020  1.498
 8HP  C20  C19  single    1.528  0.020  1.528
 8HP  C17  C18  single    1.528  0.020  1.528
 8HP  C19  C18  single    1.525  0.020  1.525
 8HP  C4   H1   single    0.930  0.020  1.080
 8HP  C6   H2   single    0.970  0.020  1.090
 8HP  C6   H3   single    0.970  0.020  1.090
 8HP  C17  H4   single    0.970  0.020  1.090
 8HP  C17  H5   single    0.970  0.020  1.090
 8HP  C20  H6   single    0.970  0.020  1.090
 8HP  C20  H7   single    0.970  0.020  1.090
 8HP  C24  H8   single    0.930  0.020  1.080
 8HP  C3   H9   single    0.930  0.020  1.080
 8HP  C25  H10  single    0.930  0.020  1.080
 8HP  C12  H11  single    0.930  0.020  1.080
 8HP  C18  H12  single    0.970  0.020  1.090
 8HP  C18  H13  single    0.970  0.020  1.090
 8HP  C19  H14  single    0.970  0.020  1.090
 8HP  C19  H15  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
 8HP  H1   C4   C3   118.85  3.000
 8HP  H1   C4   C5   120.12  3.000
 8HP  C3   C4   C5   121.03  3.000
 8HP  C24  C5   C6   120.79  3.000
 8HP  C6   C5   C4   120.31  3.000
 8HP  C24  C5   C4   118.89  3.000
 8HP  H3   C6   H2   106.50  3.000
 8HP  H3   C6   N7   108.17  3.000
 8HP  H2   C6   N7   107.65  3.000
 8HP  H3   C6   C5   110.97  3.000
 8HP  H2   C6   C5   110.65  3.000
 8HP  N7   C6   C5   112.65  3.000
 8HP  O9   C8   N7   124.74  3.000
 8HP  N7   C8   N10  113.04  3.000
 8HP  O9   C8   N10  122.22  3.000
 8HP  C14  C15  C23  115.80  3.000
 8HP  C14  C15  C16  131.10  3.000
 8HP  C23  C15  C16  113.09  3.000
 8HP  H5   C17  H4   105.87  3.000
 8HP  H5   C17  C18  110.33  3.000
 8HP  H4   C17  C18  110.27  3.000
 8HP  H5   C17  C16  110.05  3.000
 8HP  H4   C17  C16  109.06  3.000
 8HP  C18  C17  C16  111.13  3.000
 8HP  H7   C20  H6   106.34  3.000
 8HP  H7   C20  C19  110.33  3.000
 8HP  H6   C20  C19  110.20  3.000
 8HP  H7   C20  C21  110.84  3.000
 8HP  H6   C20  C21  109.80  3.000
 8HP  C19  C20  C21  109.30  3.000
 8HP  S22  C21  C16  112.49  3.000
 8HP  C16  C21  C20  125.82  3.000
 8HP  S22  C21  C20  121.69  3.000
 8HP  H8   C24  C25  118.59  3.000
 8HP  H8   C24  C5   120.57  3.000
 8HP  C25  C24  C5   120.84  3.000
 8HP  H9   C3   C2   120.71  3.000
 8HP  H9   C3   C4   120.30  3.000
 8HP  C2   C3   C4   118.99  3.000
 8HP  H10  C25  C2   120.61  3.000
 8HP  H10  C25  C24  120.23  3.000
 8HP  C2   C25  C24  119.16  3.000
 8HP  H11  C12  N11  121.48  3.000
 8HP  H11  C12  N13  122.71  3.000
 8HP  N11  C12  N13  115.80  3.000
 8HP  C21  C16  C17  122.36  3.000
 8HP  C17  C16  C15  126.03  3.000
 8HP  C21  C16  C15  111.61  3.000
 8HP  CL1  C2   C25  119.37  3.000
 8HP  C25  C2   C3   121.09  3.000
 8HP  CL1  C2   C3   119.54  3.000
 8HP  S22  C23  N7   124.01  3.000
 8HP  S22  C23  C15  111.61  3.000
 8HP  N7   C23  C15  124.38  3.000
 8HP  N10  C14  N13  109.20  3.000
 8HP  N13  C14  C15  133.46  3.000
 8HP  N10  C14  C15  117.34  3.000
 8HP  H13  C18  H12  106.61  3.000
 8HP  H13  C18  C19  109.32  3.000
 8HP  H12  C18  C19  110.18  3.000
 8HP  H13  C18  C17  109.43  3.000
 8HP  H12  C18  C17  109.34  3.000
 8HP  C19  C18  C17  111.82  3.000
 8HP  H15  C19  H14  106.77  3.000
 8HP  H15  C19  C18  109.60  3.000
 8HP  H14  C19  C18  110.37  3.000
 8HP  H15  C19  C20  109.34  3.000
 8HP  H14  C19  C20  109.31  3.000
 8HP  C18  C19  C20  111.33  3.000
 8HP  C14  N13  C12  102.94  3.000
 8HP  N10  N11  C12  102.17  3.000
 8HP  N11  N10  C14  109.88  3.000
 8HP  C14  N10  C8   127.73  3.000
 8HP  N11  N10  C8   122.39  3.000
 8HP  C23  N7   C8   121.70  3.000
 8HP  C23  N7   C6   119.53  3.000
 8HP  C8   N7   C6   118.77  3.000
 8HP  C23  S22  C21   91.21  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
 8HP  CONST_01  C25  C2   C3   C4     0.00   0.0  0
 8HP  CONST_02  C25  C24  C5   C4     0.00   0.0  0
 8HP  CONST_03  C2   C25  C24  C5     0.00   0.0  0
 8HP  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 8HP  CONST_05  C21  S22  C23  C15    0.00   0.0  0
 8HP  CONST_06  N11  N10  C14  C15  180.00   0.0  0
 8HP  CONST_07  C12  N13  C14  C15  180.00   0.0  0
 8HP  CONST_08  S22  C21  C16  C15    0.00   0.0  0
 8HP  CONST_09  C23  C15  C16  C21    0.00   0.0  0
 8HP  CONST_10  C14  C15  C16  C21  180.00   0.0  0
 8HP  CONST_11  C3   C2   C25  C24    0.00   0.0  0
 8HP  CONST_12  C3   C4   C5   C24    0.00   0.0  0
 8HP  CONST_13  C14  N10  N11  C12    0.00   0.0  0
 8HP  CONST_14  N10  C14  N13  C12    0.00   0.0  0
 8HP  CONST_15  S22  C23  C15  C16    0.00   0.0  0
 8HP  CONST_16  N10  C14  C15  C16  180.00   0.0  0
 8HP  CONST_17  N13  C14  C15  C16    0.00   0.0  0
 8HP  CONST_18  C23  S22  C21  C16    0.00   0.0  0
 8HP  CONST_19  N10  C14  C15  C23    0.00   0.0  0
 8HP  CONST_20  N13  C14  C15  C23  180.00   0.0  0
 8HP  CONST_21  S22  C23  C15  C14  180.00   0.0  0
 8HP  CONST_22  N11  C12  N13  C14    0.00   0.0  0
 8HP  CONST_23  N11  N10  C14  N13    0.00   0.0  0
 8HP  CONST_24  N10  N11  C12  N13    0.00   0.0  0
 8HP  CONST_25  N10  C8   N7   C23    0.00   0.0  0
 8HP  CONST_26  N7   C8   N10  C14    0.00   0.0  0
 8HP  CONST_27  N7   C8   N10  N11  180.00   0.0  0
 8HP  CONST_28  CL1  C2   C3   C4   180.00   0.0  0
 8HP  CONST_29  C25  C24  C5   C6   180.00   0.0  0
 8HP  CONST_30  C3   C4   C5   C6   180.00   0.0  0
 8HP  CONST_31  CL1  C2   C25  C24  180.00   0.0  0
 8HP  CONST_32  N10  C8   N7   C6   180.00   0.0  0
 8HP  CONST_33  O9   C8   N7   C23  180.00   0.0  0
 8HP  CONST_34  O9   C8   N10  C14  180.00   0.0  0
 8HP  CONST_35  O9   C8   N10  N11    0.00   0.0  0
 8HP  CONST_36  H8   C24  C5   C4   180.00   0.0  0
 8HP  CONST_37  H10  C25  C24  C5   180.00   0.0  0
 8HP  CONST_38  H9   C3   C4   C5   180.00   0.0  0
 8HP  CONST_39  H1   C4   C5   C24  180.00   0.0  0
 8HP  CONST_40  H11  C12  N13  C14  180.00   0.0  0
 8HP  CONST_41  O9   C8   N7   C6     0.00   0.0  0
 8HP  Var_01    C18  C17  C16  C15  166.83  30.0  1
 8HP  Var_02    C20  C19  C18  C17  -62.64  30.0  1
 8HP  Var_03    C18  C19  C20  C21   46.20  30.0  1
 8HP  Var_04    C19  C20  C21  C16  -16.60  30.0  1
 8HP  Var_05    C19  C18  C17  C16   43.89  30.0  1
 8HP  Var_06    N7   C6   C5   C4   125.74  30.0  2
 8HP  Var_07    C8   N7   C6   C5   105.80  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
 8HP  plan-1  C4   0.020
 8HP  plan-1  C5   0.020
 8HP  plan-1  C6   0.020
 8HP  plan-1  C24  0.020
 8HP  plan-1  C3   0.020
 8HP  plan-1  C25  0.020
 8HP  plan-1  C2   0.020
 8HP  plan-1  CL1  0.020
 8HP  plan-1  H1   0.020
 8HP  plan-1  H8   0.020
 8HP  plan-1  H9   0.020
 8HP  plan-1  H10  0.020
 8HP  plan-2  C6   0.020
 8HP  plan-2  C8   0.020
 8HP  plan-2  C15  0.020
 8HP  plan-2  C17  0.020
 8HP  plan-2  C20  0.020
 8HP  plan-2  C21  0.020
 8HP  plan-2  C12  0.020
 8HP  plan-2  C16  0.020
 8HP  plan-2  C23  0.020
 8HP  plan-2  C14  0.020
 8HP  plan-2  N13  0.020
 8HP  plan-2  N11  0.020
 8HP  plan-2  N10  0.020
 8HP  plan-2  N7   0.020
 8HP  plan-2  S22  0.020
 8HP  plan-2  H11  0.020
 8HP  plan-2  O9   0.020

