# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 16:59:06 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-[6-(1-benzothiophen-2-yl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ncnc2cc(sc12)c3sc4ccccc4c3
#
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
 OBW  OBW  '2-[6-(1-benzothiophen-2-yl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid'  ligand  33  23  .  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_OBW
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
 OBW  N1   N  N     0  -0.429  -3.4294   1.8741  -0.0289
 OBW  C2   C  CR6   0   0.110  -2.7353   0.7525  -0.0163
 OBW  C4   C  CR56  0   0.353  -0.7340   2.0627  -0.0327
 OBW  C5   C  CR15  0  -0.266   0.6877   1.9698  -0.0332
 OBW  C6   C  CR5   0  -0.150   1.1227   0.6797  -0.0173
 OBW  O1   O  OH1   0  -0.580  -7.3812  -1.2634   0.0010
 OBW  C    C  C     0   0.570  -6.0932  -1.5526   0.0036
 OBW  O    O  O     0  -0.428  -5.6384  -2.6671   0.0097
 OBW  C1   C  CH2   0  -0.677  -5.2583  -0.2999  -0.0027
 OBW  S    S  S2    0   0.100  -3.5230  -0.8030   0.0002
 OBW  C15  C  CR16  0   0.040  -2.7569   3.0292  -0.0431
 OBW  N    N  N     0  -0.435  -1.4541   3.1922  -0.0463
 OBW  S2   S  S2    0   0.263  -0.1869  -0.4747  -0.0004
 OBW  C3   C  CR56  0  -0.234  -1.3409   0.8023  -0.0168
 OBW  C7   C  CR5   0  -0.173   2.4852   0.2042  -0.0124
 OBW  S1   S  S2    0   0.236   3.8012   1.3498   0.0043
 OBW  C14  C  CR56  0  -0.221   4.9670   0.0694   0.0013
 OBW  C9   C  CR56  0   0.246   4.3448  -1.1917  -0.0117
 OBW  C8   C  CR15  0  -0.269   2.9215  -1.0835  -0.0196
 OBW  C13  C  CR16  0  -0.278   6.3522   0.2036   0.0105
 OBW  C12  C  CR16  0  -0.264   7.1151  -0.9486   0.0070
 OBW  C11  C  CR16  0  -0.253   6.5137  -2.2145  -0.0056
 OBW  C10  C  CR16  0  -0.316   5.1411  -2.3440  -0.0151
 OBW  H1   H  HCR5  0   0.285   1.3359   2.8348  -0.0469
 OBW  H2   H  HOH1  0   0.491  -7.9118  -2.0751   0.0046
 OBW  H3   H  HCH2  0   0.333  -5.4827   0.2996  -0.8858
 OBW  H4   H  HCH2  0   0.333  -5.4832   0.3077   0.8746
 OBW  H5   H  HCR6  0   0.268  -3.3654   3.9261  -0.0533
 OBW  H6   H  HCR5  0   0.280   2.2646  -1.9433  -0.0310
 OBW  H7   H  HCR6  0   0.274   6.8199   1.1792   0.0199
 OBW  H8   H  HCR6  0   0.267   8.1941  -0.8702   0.0140
 OBW  H9   H  HCR6  0   0.264   7.1376  -3.0982  -0.0081
 OBW  H10  H  HCR6  0   0.262   4.6785  -3.3226  -0.0249

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
 OBW  N    C15  aromatic  1.313  0.020  1.313
 OBW  N    C4   aromatic  1.340  0.020  1.340
 OBW  S1   C14  aromatic  1.732  0.020  1.732
 OBW  S1   C7   aromatic  1.745  0.020  1.745
 OBW  C15  N1   aromatic  1.337  0.020  1.337
 OBW  C5   C4   aromatic  1.425  0.020  1.425
 OBW  C5   C6   aromatic  1.362  0.020  1.362
 OBW  C13  C14  aromatic  1.392  0.020  1.392
 OBW  C13  C12  aromatic  1.382  0.020  1.382
 OBW  C4   C3   aromatic  1.399  0.020  1.399
 OBW  C14  C9   aromatic  1.406  0.020  1.406
 OBW  C12  C11  aromatic  1.402  0.020  1.402
 OBW  C6   C7   single    1.443  0.020  1.443
 OBW  C6   S2   aromatic  1.746  0.020  1.746
 OBW  N1   C2   aromatic  1.319  0.020  1.319
 OBW  C7   C8   aromatic  1.360  0.020  1.360
 OBW  C3   C2   aromatic  1.395  0.020  1.395
 OBW  C3   S2   aromatic  1.721  0.020  1.721
 OBW  C9   C8   aromatic  1.427  0.020  1.427
 OBW  C9   C10  aromatic  1.401  0.020  1.401
 OBW  C2   S    single    1.744  0.020  1.744
 OBW  C11  C10  aromatic  1.379  0.020  1.379
 OBW  S    C1   single    1.807  0.020  1.807
 OBW  C1   C    single    1.505  0.020  1.505
 OBW  C    O    double    1.204  0.020  1.204
 OBW  C    O1   single    1.320  0.020  1.320
 OBW  C5   H1   single    0.930  0.020  1.080
 OBW  O1   H2   single    0.850  0.020  0.980
 OBW  C1   H3   single    0.970  0.020  1.090
 OBW  C1   H4   single    0.970  0.020  1.090
 OBW  C15  H5   single    0.930  0.020  1.080
 OBW  C8   H6   single    0.930  0.020  1.080
 OBW  C13  H7   single    0.930  0.020  1.080
 OBW  C12  H8   single    0.930  0.020  1.080
 OBW  C11  H9   single    0.930  0.020  1.080
 OBW  C10  H10  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
 OBW  C15  N1   C2   118.05  3.000
 OBW  C3   C2   S    118.90  3.000
 OBW  S    C2   N1   121.40  3.000
 OBW  C3   C2   N1   119.70  3.000
 OBW  C3   C4   N    121.77  3.000
 OBW  C3   C4   C5   111.97  3.000
 OBW  N    C4   C5   126.25  3.000
 OBW  H1   C5   C6   124.52  3.000
 OBW  H1   C5   C4   123.11  3.000
 OBW  C6   C5   C4   112.37  3.000
 OBW  C7   C6   S2   119.36  3.000
 OBW  S2   C6   C5   112.77  3.000
 OBW  C7   C6   C5   127.87  3.000
 OBW  H2   O1   C    110.52  3.000
 OBW  C1   C    O    124.11  3.000
 OBW  O    C    O1   124.86  3.000
 OBW  C1   C    O1   111.03  3.000
 OBW  H4   C1   H3   107.62  3.000
 OBW  H4   C1   S    110.61  3.000
 OBW  H3   C1   S    110.61  3.000
 OBW  H4   C1   C    110.23  3.000
 OBW  H3   C1   C    110.28  3.000
 OBW  S    C1   C    107.52  3.000
 OBW  C1   S    C2   100.69  3.000
 OBW  H5   C15  N    117.01  3.000
 OBW  H5   C15  N1   115.65  3.000
 OBW  N    C15  N1   127.34  3.000
 OBW  C15  N    C4   115.38  3.000
 OBW  C3   S2   C6    90.70  3.000
 OBW  S2   C3   C4   112.19  3.000
 OBW  S2   C3   C2   130.05  3.000
 OBW  C4   C3   C2   117.76  3.000
 OBW  C8   C7   S1   112.33  3.000
 OBW  C8   C7   C6   127.95  3.000
 OBW  S1   C7   C6   119.72  3.000
 OBW  C14  S1   C7    91.28  3.000
 OBW  C13  C14  C9   121.79  3.000
 OBW  C9   C14  S1   111.42  3.000
 OBW  C13  C14  S1   126.79  3.000
 OBW  C10  C9   C8   128.99  3.000
 OBW  C10  C9   C14  119.09  3.000
 OBW  C8   C9   C14  111.92  3.000
 OBW  H6   C8   C9   123.04  3.000
 OBW  H6   C8   C7   123.90  3.000
 OBW  C9   C8   C7   113.06  3.000
 OBW  H7   C13  C12  120.88  3.000
 OBW  H7   C13  C14  121.14  3.000
 OBW  C12  C13  C14  117.98  3.000
 OBW  H8   C12  C11  119.57  3.000
 OBW  H8   C12  C13  119.36  3.000
 OBW  C11  C12  C13  121.07  3.000
 OBW  H9   C11  C10  119.84  3.000
 OBW  H9   C11  C12  119.36  3.000
 OBW  C10  C11  C12  120.80  3.000
 OBW  H10  C10  C11  120.69  3.000
 OBW  H10  C10  C9   120.06  3.000
 OBW  C11  C10  C9   119.26  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
 OBW  CONST_01  C4   N    C15  N1      0.00   0.0  0
 OBW  CONST_02  C4   C3   C2   N1      0.00   0.0  0
 OBW  CONST_03  S2   C3   C2   N1    180.00   0.0  0
 OBW  CONST_04  N    C15  N1   C2      0.00   0.0  0
 OBW  CONST_05  N    C4   C3   C2      0.00   0.0  0
 OBW  CONST_06  C5   C4   C3   C2    180.00   0.0  0
 OBW  CONST_07  C6   S2   C3   C2    180.00   0.0  0
 OBW  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 OBW  CONST_09  S2   C6   C5   C4      0.00   0.0  0
 OBW  CONST_10  C6   S2   C3   C4      0.00   0.0  0
 OBW  CONST_11  C15  N    C4   C5    180.00   0.0  0
 OBW  CONST_12  S2   C3   C4   C5      0.00   0.0  0
 OBW  CONST_13  S1   C7   C6   C5      0.00   0.0  0
 OBW  CONST_14  C8   C7   C6   C5    180.00   0.0  0
 OBW  CONST_15  C3   S2   C6   C5      0.00   0.0  0
 OBW  CONST_16  N    C4   C5   C6    180.00   0.0  0
 OBW  CONST_17  C3   C4   C5   C6      0.00   0.0  0
 OBW  CONST_18  C14  S1   C7   C6    180.00   0.0  0
 OBW  CONST_19  C9   C8   C7   C6    180.00   0.0  0
 OBW  CONST_20  C3   C4   N    C15     0.00   0.0  0
 OBW  CONST_21  C3   C2   N1   C15     0.00   0.0  0
 OBW  CONST_22  S2   C3   C4   N     180.00   0.0  0
 OBW  CONST_23  S1   C7   C6   S2    180.00   0.0  0
 OBW  CONST_24  C8   C7   C6   S2      0.00   0.0  0
 OBW  CONST_25  C7   C6   S2   C3    180.00   0.0  0
 OBW  CONST_26  C13  C14  S1   C7    180.00   0.0  0
 OBW  CONST_27  C9   C14  S1   C7      0.00   0.0  0
 OBW  CONST_28  C14  C9   C8   C7      0.00   0.0  0
 OBW  CONST_29  C10  C9   C8   C7    180.00   0.0  0
 OBW  CONST_30  C12  C13  C14  S1    180.00   0.0  0
 OBW  CONST_31  C8   C9   C14  S1      0.00   0.0  0
 OBW  CONST_32  C10  C9   C14  S1    180.00   0.0  0
 OBW  CONST_33  C9   C8   C7   S1      0.00   0.0  0
 OBW  CONST_34  C8   C7   S1   C14     0.00   0.0  0
 OBW  CONST_35  C11  C12  C13  C14     0.00   0.0  0
 OBW  CONST_36  C11  C10  C9   C14     0.00   0.0  0
 OBW  CONST_37  C12  C13  C14  C9      0.00   0.0  0
 OBW  CONST_38  C12  C11  C10  C9      0.00   0.0  0
 OBW  CONST_39  C13  C14  C9   C8    180.00   0.0  0
 OBW  CONST_40  C11  C10  C9   C8    180.00   0.0  0
 OBW  CONST_41  C10  C9   C14  C13     0.00   0.0  0
 OBW  CONST_42  C10  C11  C12  C13     0.00   0.0  0
 OBW  CONST_43  S    C2   C3   C4    180.00   0.0  0
 OBW  CONST_44  C15  N1   C2   S     180.00   0.0  0
 OBW  CONST_45  S2   C3   C2   S       0.00   0.0  0
 OBW  CONST_46  H5   C15  N1   C2    180.00   0.0  0
 OBW  CONST_47  H6   C8   C7   C6      0.00   0.0  0
 OBW  CONST_48  H1   C5   C4   N       0.00   0.0  0
 OBW  CONST_49  H7   C13  C14  S1      0.00   0.0  0
 OBW  CONST_50  H8   C12  C13  C14   180.00   0.0  0
 OBW  CONST_51  H10  C10  C9   C14   180.00   0.0  0
 OBW  CONST_52  H9   C11  C10  C9    180.00   0.0  0
 OBW  CONST_53  H2   O1   C    O       0.00   0.0  0
 OBW  Var_01    C3   C2   S    C1    179.92  30.0  1
 OBW  Var_02    C    C1   S    C2    179.71  30.0  3
 OBW  Var_03    S    C1   C    O1   -179.96  30.0  1

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
 OBW  plan-1  N1   0.020
 OBW  plan-1  C2   0.020
 OBW  plan-1  C4   0.020
 OBW  plan-1  C5   0.020
 OBW  plan-1  C6   0.020
 OBW  plan-1  S    0.020
 OBW  plan-1  C15  0.020
 OBW  plan-1  N    0.020
 OBW  plan-1  S2   0.020
 OBW  plan-1  C3   0.020
 OBW  plan-1  C7   0.020
 OBW  plan-1  H1   0.020
 OBW  plan-1  H5   0.020
 OBW  plan-2  C6   0.020
 OBW  plan-2  C7   0.020
 OBW  plan-2  S1   0.020
 OBW  plan-2  C14  0.020
 OBW  plan-2  C9   0.020
 OBW  plan-2  C8   0.020
 OBW  plan-2  C13  0.020
 OBW  plan-2  C12  0.020
 OBW  plan-2  C11  0.020
 OBW  plan-2  C10  0.020
 OBW  plan-2  H6   0.020
 OBW  plan-2  H7   0.020
 OBW  plan-2  H8   0.020
 OBW  plan-2  H9   0.020
 OBW  plan-2  H10  0.020
 OBW  plan-3  O1   0.020
 OBW  plan-3  C    0.020
 OBW  plan-3  O    0.020
 OBW  plan-3  C1   0.020
 OBW  plan-3  H2   0.020

