# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:29:18 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-(5-chlorothiophen-2-yl)-N-(pyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(CC(=O)Nc2cccnc2)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
 UGV  UGV  2-(5-chlorothiophen-2-yl)-N-(pyridin-3-yl)acetamide  ligand  25  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UGV
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
 UGV  N1   N   N     0  -0.391   6.6766   1.0697  17.4015
 UGV  C4   C   CH2   0  -0.655   8.7934  -0.9529  22.4726
 UGV  C5   C   C     0   0.571   8.5241  -0.3381  21.1144
 UGV  C6   C   CR6   0   0.295   6.6131   0.2974  19.6623
 UGV  C7   C   CR16  0  -0.245   5.2224   0.3992  19.6493
 UGV  C8   C   CR16  0  -0.308   4.5843   0.8356  18.5054
 UGV  C10  C   CR16  0  -0.115   7.2990   0.6510  18.4967
 UGV  O    O   O     0  -0.453   9.4307  -0.0855  20.3434
 UGV  C3   C   CR5   0  -0.135  10.0641  -0.4906  23.1016
 UGV  C2   C   CR15  0  -0.231  10.2542  -0.1952  24.4176
 UGV  C1   C   CR15  0  -0.137  11.6010   0.1195  24.7459
 UGV  S    S   S2    0   0.282  11.5474  -0.3806  22.2225
 UGV  C    C   CR5   0  -0.261  12.4033   0.0413  23.6546
 UGV  CL   CL  CL    0  -0.089  14.0817   0.3663  23.5858
 UGV  N    N   NH1   0  -0.749   7.2115  -0.1541  20.8403
 UGV  C9   C   CR16  0  -0.084   5.3552   1.1614  17.3990
 UGV  H1   H   HCH2  0   0.293   7.9745  -0.7719  23.1705
 UGV  H2   H   HCH2  0   0.315   8.8256  -2.0376  22.3153
 UGV  H3   H   HCR6  0   0.289   4.6481   0.1352  20.5295
 UGV  H4   H   HCR6  0   0.277   3.5071   0.9207  18.4718
 UGV  H5   H   HCR6  0   0.283   8.3753   0.5958  18.4431
 UGV  H6   H   HCR5  0   0.271   9.4530  -0.2115  25.1431
 UGV  H7   H   HCR5  0   0.284  11.9430   0.3902  25.7336
 UGV  H8   H   HNH1  0   0.425   6.5648  -0.3859  21.5797
 UGV  H9   H   HCR6  0   0.265   4.8890   1.5067  16.4836

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
 UGV  N1   C9   aromatic  1.325  0.020  1.325
 UGV  N1   C10  aromatic  1.327  0.020  1.327
 UGV  C9   C8   aromatic  1.387  0.020  1.387
 UGV  C10  C6   aromatic  1.398  0.020  1.398
 UGV  C8   C7   aromatic  1.381  0.020  1.381
 UGV  C6   C7   aromatic  1.394  0.020  1.394
 UGV  C6   N    single    1.396  0.020  1.396
 UGV  N    C5   single    1.353  0.020  1.353
 UGV  O    C5   double    1.217  0.020  1.217
 UGV  C5   C4   single    1.515  0.020  1.515
 UGV  S    C3   aromatic  1.728  0.020  1.728
 UGV  S    C    aromatic  1.721  0.020  1.721
 UGV  C4   C3   single    1.491  0.020  1.491
 UGV  C3   C2   aromatic  1.362  0.020  1.362
 UGV  C    CL   single    1.711  0.020  1.711
 UGV  C    C1   aromatic  1.357  0.020  1.357
 UGV  C2   C1   aromatic  1.421  0.020  1.421
 UGV  C4   H1   single    0.970  0.020  1.090
 UGV  C4   H2   single    0.970  0.020  1.090
 UGV  C7   H3   single    0.930  0.020  1.080
 UGV  C8   H4   single    0.930  0.020  1.080
 UGV  C10  H5   single    0.930  0.020  1.080
 UGV  C2   H6   single    0.930  0.020  1.080
 UGV  C1   H7   single    0.930  0.020  1.080
 UGV  N    H8   single    0.860  0.020  1.020
 UGV  C9   H9   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
 UGV  C9   N1   C10  119.42  3.000
 UGV  H2   C4   H1   106.14  3.000
 UGV  H2   C4   C3   110.01  3.000
 UGV  H1   C4   C3   108.56  3.000
 UGV  H2   C4   C5   106.14  3.000
 UGV  H1   C4   C5   111.88  3.000
 UGV  C3   C4   C5   113.81  3.000
 UGV  N    C5   O    124.48  3.000
 UGV  O    C5   C4   121.33  3.000
 UGV  N    C5   C4   114.15  3.000
 UGV  N    C6   C10  125.09  3.000
 UGV  N    C6   C7   117.32  3.000
 UGV  C10  C6   C7   117.59  3.000
 UGV  H3   C7   C8   120.34  3.000
 UGV  H3   C7   C6   120.21  3.000
 UGV  C8   C7   C6   119.45  3.000
 UGV  H4   C8   C9   120.69  3.000
 UGV  H4   C8   C7   120.74  3.000
 UGV  C9   C8   C7   118.57  3.000
 UGV  H5   C10  C6   121.19  3.000
 UGV  H5   C10  N1   116.29  3.000
 UGV  C6   C10  N1   122.52  3.000
 UGV  S    C3   C2   110.98  3.000
 UGV  C2   C3   C4   126.42  3.000
 UGV  S    C3   C4   122.46  3.000
 UGV  H6   C2   C1   123.40  3.000
 UGV  H6   C2   C3   122.80  3.000
 UGV  C1   C2   C3   113.79  3.000
 UGV  H7   C1   C    124.26  3.000
 UGV  H7   C1   C2   124.54  3.000
 UGV  C    C1   C2   111.20  3.000
 UGV  C    S    C3    91.10  3.000
 UGV  CL   C    S    120.07  3.000
 UGV  CL   C    C1   126.98  3.000
 UGV  S    C    C1   112.92  3.000
 UGV  H8   N    C6   114.69  3.000
 UGV  H8   N    C5   116.22  3.000
 UGV  C6   N    C5   129.09  3.000
 UGV  H9   C9   C8   120.63  3.000
 UGV  H9   C9   N1   116.92  3.000
 UGV  C8   C9   N1   122.45  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
 UGV  CONST_01  C7   C8   C9   N1     0.00   0.0  0
 UGV  CONST_02  C7   C6   C10  N1     0.00   0.0  0
 UGV  CONST_03  C9   N1   C10  C6     0.00   0.0  0
 UGV  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 UGV  CONST_05  C10  N1   C9   C8     0.00   0.0  0
 UGV  CONST_06  C10  C6   C7   C8     0.00   0.0  0
 UGV  CONST_07  C1   C    S    C3     0.00   0.0  0
 UGV  CONST_08  C    C1   C2   C3     0.00   0.0  0
 UGV  CONST_09  C    S    C3   C2     0.00   0.0  0
 UGV  CONST_10  S    C    C1   C2     0.00   0.0  0
 UGV  CONST_11  S    C3   C2   C1     0.00   0.0  0
 UGV  CONST_12  N    C6   C10  N1   180.00   0.0  0
 UGV  CONST_13  C    S    C3   C4   180.00   0.0  0
 UGV  CONST_14  C1   C2   C3   C4   180.00   0.0  0
 UGV  CONST_15  N    C6   C7   C8   180.00   0.0  0
 UGV  CONST_16  CL   C    S    C3   180.00   0.0  0
 UGV  CONST_17  CL   C    C1   C2   180.00   0.0  0
 UGV  CONST_18  H4   C8   C9   N1   180.00   0.0  0
 UGV  CONST_19  H9   C9   C8   C7   180.00   0.0  0
 UGV  CONST_20  H5   C10  C6   C7   180.00   0.0  0
 UGV  CONST_21  H3   C7   C6   C10  180.00   0.0  0
 UGV  CONST_22  H7   C1   C2   C3   180.00   0.0  0
 UGV  CONST_23  H6   C2   C3   S    180.00   0.0  0
 UGV  CONST_24  C10  C6   N    C5     0.00   0.0  0
 UGV  CONST_25  C7   C6   N    C5   180.00   0.0  0
 UGV  CONST_26  H8   N    C6   C7     0.00   0.0  0
 UGV  CONST_27  C6   N    C5   C4   180.00   0.0  0
 UGV  CONST_28  O    C5   N    C6     0.00   0.0  0
 UGV  Var_01    S    C3   C4   C5   -44.98  30.0  2
 UGV  Var_02    C3   C4   C5   O     34.77  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
 UGV  plan-1  C4   0.020
 UGV  plan-1  C3   0.020
 UGV  plan-1  C2   0.020
 UGV  plan-1  C1   0.020
 UGV  plan-1  S    0.020
 UGV  plan-1  C    0.020
 UGV  plan-1  CL   0.020
 UGV  plan-1  H6   0.020
 UGV  plan-1  H7   0.020
 UGV  plan-2  N1   0.020
 UGV  plan-2  C6   0.020
 UGV  plan-2  C7   0.020
 UGV  plan-2  C8   0.020
 UGV  plan-2  C10  0.020
 UGV  plan-2  N    0.020
 UGV  plan-2  C9   0.020
 UGV  plan-2  H3   0.020
 UGV  plan-2  H4   0.020
 UGV  plan-2  H5   0.020
 UGV  plan-2  H9   0.020
 UGV  plan-3  C4   0.020
 UGV  plan-3  C5   0.020
 UGV  plan-3  C6   0.020
 UGV  plan-3  O    0.020
 UGV  plan-3  N    0.020
 UGV  plan-3  H8   0.020

