# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:44:13 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: ~{N}-(2-thiophen-2-ylethyl)pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCc1sccc1)c2ccncc2
#
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
 SZA  SZA  ~{N}-(2-thiophen-2-ylethyl)pyridine-4-carboxamide  ligand  28  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 GRAND
;

data_comp_SZA
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
 SZA  C4   C  CH2   0  -0.513  15.0960  11.4532  -41.1729
 SZA  C5   C  CH2   0  -0.299  13.7885  11.9334  -41.8211
 SZA  C6   C  C     0   0.549  14.2511  13.2104  -43.8588
 SZA  N1   N  N     0  -0.399  15.3586  12.9879  -47.9948
 SZA  C7   C  CR6   0   0.054  14.6158  13.0946  -45.3088
 SZA  C8   C  CR16  0  -0.363  14.0804  12.1369  -46.1614
 SZA  C9   C  CR16  0  -0.056  14.4808  12.1310  -47.4901
 SZA  C10  C  CR16  0  -0.057  15.8650  13.9033  -47.1758
 SZA  C11  C  CR16  0  -0.337  15.5215  14.0059  -45.8376
 SZA  O    O  O     0  -0.469  14.2602  14.2979  -43.3061
 SZA  N    N  NH1   0  -0.631  13.9206  12.0563  -43.2531
 SZA  C2   C  CR5   0  -0.144  16.2521  12.3256  -41.5295
 SZA  C1   C  CR15  0  -0.234  17.1124  12.1856  -42.5786
 SZA  S    S  S2    0   0.197  16.5533  13.8026  -40.6973
 SZA  C3   C  CR15  0  -0.470  17.8318  14.2264  -41.7579
 SZA  C    C  CR15  0  -0.179  18.0185  13.2737  -42.7111
 SZA  H1   H  HCH2  0   0.264  14.9478  11.4033  -40.0920
 SZA  H2   H  HCH2  0   0.262  15.3083  10.4350  -41.5065
 SZA  H3   H  HCH2  0   0.255  13.4929  12.8975  -41.4125
 SZA  H4   H  HCH2  0   0.265  12.9916  11.2229  -41.5988
 SZA  H5   H  HCR6  0   0.278  13.3489  11.4132  -45.8269
 SZA  H6   H  HCR6  0   0.271  14.0683  11.3972  -48.1731
 SZA  H7   H  HCR6  0   0.270  16.5830  14.5931  -47.6047
 SZA  H8   H  HCR6  0   0.273  15.9647  14.7737  -45.2193
 SZA  H9   H  HNH1  0   0.406  14.0558  11.1967  -43.7617
 SZA  H10  H  HCR5  0   0.257  17.0916  11.3326  -43.2434
 SZA  H11  H  HCR5  0   0.289  18.3816  15.1439  -41.6149
 SZA  H12  H  HCR5  0   0.261  18.7753  13.3398  -43.4796

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
 SZA  N1   C10  aromatic  1.329  0.020  1.329
 SZA  N1   C9   aromatic  1.327  0.020  1.327
 SZA  C10  C11  aromatic  1.385  0.020  1.385
 SZA  C9   C8   aromatic  1.388  0.020  1.388
 SZA  C11  C7   aromatic  1.389  0.020  1.389
 SZA  C8   C7   aromatic  1.389  0.020  1.389
 SZA  C7   C6   single    1.500  0.020  1.500
 SZA  C6   O    double    1.220  0.020  1.220
 SZA  C6   N    single    1.345  0.020  1.345
 SZA  N    C5   single    1.443  0.020  1.443
 SZA  C5   C4   single    1.536  0.020  1.536
 SZA  C4   C2   single    1.492  0.020  1.492
 SZA  C2   C1   aromatic  1.364  0.020  1.364
 SZA  C2   S    aromatic  1.722  0.020  1.722
 SZA  C1   C    aromatic  1.422  0.020  1.422
 SZA  C    C3   aromatic  1.361  0.020  1.361
 SZA  S    C3   aromatic  1.714  0.020  1.714
 SZA  C4   H1   single    0.970  0.020  1.090
 SZA  C4   H2   single    0.970  0.020  1.090
 SZA  C5   H3   single    0.970  0.020  1.090
 SZA  C5   H4   single    0.970  0.020  1.090
 SZA  C8   H5   single    0.930  0.020  1.080
 SZA  C9   H6   single    0.930  0.020  1.080
 SZA  C10  H7   single    0.930  0.020  1.080
 SZA  C11  H8   single    0.930  0.020  1.080
 SZA  N    H9   single    0.890  0.020  1.040
 SZA  C1   H10  single    0.930  0.020  1.080
 SZA  C3   H11  single    0.930  0.020  1.080
 SZA  C    H12  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
 SZA  H2   C4   H1   106.62  3.000
 SZA  H2   C4   C2   108.76  3.000
 SZA  H1   C4   C2   111.63  3.000
 SZA  H2   C4   C5   109.14  3.000
 SZA  H1   C4   C5   108.44  3.000
 SZA  C2   C4   C5   112.08  3.000
 SZA  H4   C5   H3   107.59  3.000
 SZA  H4   C5   N    108.94  3.000
 SZA  H3   C5   N    108.78  3.000
 SZA  H4   C5   C4   109.41  3.000
 SZA  H3   C5   C4   110.47  3.000
 SZA  N    C5   C4   111.55  3.000
 SZA  N    C6   O    124.26  3.000
 SZA  N    C6   C7   115.40  3.000
 SZA  O    C6   C7   120.34  3.000
 SZA  C10  N1   C9   117.57  3.000
 SZA  C11  C7   C8   118.01  3.000
 SZA  C8   C7   C6   123.56  3.000
 SZA  C11  C7   C6   118.42  3.000
 SZA  H5   C8   C9   119.22  3.000
 SZA  H5   C8   C7   122.13  3.000
 SZA  C9   C8   C7   118.64  3.000
 SZA  H6   C9   C8   119.76  3.000
 SZA  H6   C9   N1   116.70  3.000
 SZA  C8   C9   N1   123.54  3.000
 SZA  H7   C10  C11  119.95  3.000
 SZA  H7   C10  N1   116.55  3.000
 SZA  C11  C10  N1   123.50  3.000
 SZA  H8   C11  C10  120.23  3.000
 SZA  H8   C11  C7   121.03  3.000
 SZA  C10  C11  C7   118.73  3.000
 SZA  H9   N    C6   118.15  3.000
 SZA  H9   N    C5   116.12  3.000
 SZA  C6   N    C5   122.85  3.000
 SZA  S    C2   C1   110.45  3.000
 SZA  S    C2   C4   121.45  3.000
 SZA  C1   C2   C4   127.79  3.000
 SZA  H10  C1   C    123.95  3.000
 SZA  H10  C1   C2   122.78  3.000
 SZA  C    C1   C2   113.27  3.000
 SZA  C3   S    C2    92.49  3.000
 SZA  H11  C3   C    128.19  3.000
 SZA  H11  C3   S    120.55  3.000
 SZA  C    C3   S    111.26  3.000
 SZA  H12  C    C3   123.47  3.000
 SZA  H12  C    C1   124.01  3.000
 SZA  C3   C    C1   112.52  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
 SZA  CONST_01  C7   C11  C10  N1     0.00   0.0  0
 SZA  CONST_02  C7   C8   C9   N1     0.00   0.0  0
 SZA  CONST_03  C10  N1   C9   C8     0.00   0.0  0
 SZA  CONST_04  C10  C11  C7   C8     0.00   0.0  0
 SZA  CONST_05  C11  C10  N1   C9     0.00   0.0  0
 SZA  CONST_06  C11  C7   C8   C9     0.00   0.0  0
 SZA  CONST_07  C3   C    C1   C2     0.00   0.0  0
 SZA  CONST_08  C    C3   S    C2     0.00   0.0  0
 SZA  CONST_09  C3   S    C2   C1     0.00   0.0  0
 SZA  CONST_10  S    C3   C    C1     0.00   0.0  0
 SZA  CONST_11  C    C1   C2   S      0.00   0.0  0
 SZA  CONST_12  C    C1   C2   C4   180.00   0.0  0
 SZA  CONST_13  C3   S    C2   C4   180.00   0.0  0
 SZA  CONST_14  C10  C11  C7   C6   180.00   0.0  0
 SZA  CONST_15  C9   C8   C7   C6   180.00   0.0  0
 SZA  CONST_16  H8   C11  C10  N1   180.00   0.0  0
 SZA  CONST_17  H5   C8   C9   N1   180.00   0.0  0
 SZA  CONST_18  H7   C10  C11  C7   180.00   0.0  0
 SZA  CONST_19  H6   C9   C8   C7   180.00   0.0  0
 SZA  CONST_20  H12  C    C1   C2   180.00   0.0  0
 SZA  CONST_21  H11  C3   S    C2   180.00   0.0  0
 SZA  CONST_22  H10  C1   C2   S    180.00   0.0  0
 SZA  CONST_23  C7   C6   N    C5   180.00   0.0  0
 SZA  CONST_24  H9   N    C6   C7     0.00   0.0  0
 SZA  CONST_25  O    C6   N    C5     0.00   0.0  0
 SZA  Var_01    C1   C2   C4   C5   -91.09  30.0  2
 SZA  Var_02    O    C6   C7   C8  -148.93  30.0  2
 SZA  Var_03    C2   C4   C5   N     54.86  30.0  3
 SZA  Var_04    C6   N    C5   C4   -93.66  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
 SZA  plan-1  C4   0.020
 SZA  plan-1  C2   0.020
 SZA  plan-1  C1   0.020
 SZA  plan-1  S    0.020
 SZA  plan-1  C3   0.020
 SZA  plan-1  C    0.020
 SZA  plan-1  H10  0.020
 SZA  plan-1  H11  0.020
 SZA  plan-1  H12  0.020
 SZA  plan-2  C6   0.020
 SZA  plan-2  N1   0.020
 SZA  plan-2  C7   0.020
 SZA  plan-2  C8   0.020
 SZA  plan-2  C9   0.020
 SZA  plan-2  C10  0.020
 SZA  plan-2  C11  0.020
 SZA  plan-2  H5   0.020
 SZA  plan-2  H6   0.020
 SZA  plan-2  H7   0.020
 SZA  plan-2  H8   0.020
 SZA  plan-3  C5   0.020
 SZA  plan-3  C6   0.020
 SZA  plan-3  C7   0.020
 SZA  plan-3  O    0.020
 SZA  plan-3  N    0.020
 SZA  plan-3  H9   0.020

