# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:29:40 2021
#   Inital geometry file: a 64 line input string
#   Ligand name: ~{N}-[(~{E})-thiophen-2-ylmethylideneamino]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N/N=C/c1sccc1)C2CC2
#
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
 SZ7  SZ7  ~{N}-[(~{E})-thiophen-2-ylmethylideneamino]cyclopropanecarboxamide  ligand  23  13  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SZ7
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
 SZ7  C4   C  C1    0  -0.036  24.7712  16.6750  -17.8207
 SZ7  C5   C  C     0   0.586  25.5129  16.0252  -14.4499
 SZ7  C6   C  CH1   0  -0.428  24.9007  14.6866  -14.2918
 SZ7  N1   N  NH1   0  -0.507  25.4245  16.6163  -15.6750
 SZ7  C7   C  CH2   0  -0.462  24.2824  14.3662  -12.9530
 SZ7  C8   C  CH2   0  -0.462  25.5670  13.7319  -13.3319
 SZ7  O    O  O     0  -0.483  26.0820  16.6105  -13.5418
 SZ7  N    N  N     0  -0.202  24.8131  16.0389  -16.7188
 SZ7  C2   C  CR5   0  -0.217  24.1280  16.0953  -18.9740
 SZ7  C1   C  CR15  0  -0.234  23.9976  16.6586  -20.2148
 SZ7  S    S  S2    0   0.235  23.4067  14.5287  -18.9216
 SZ7  C3   C  CR15  0  -0.459  22.9345  14.6376  -20.5654
 SZ7  C    C  CR15  0  -0.175  23.3114  15.8194  -21.1286
 SZ7  H1   H  H     0   0.260  25.2072  17.6665  -17.9529
 SZ7  H2   H  HCH1  0   0.293  24.4306  14.2539  -15.1624
 SZ7  H3   H  HNH1  0   0.399  25.8460  17.5355  -15.7781
 SZ7  H4   H  HCH2  0   0.265  23.3822  13.7665  -12.9707
 SZ7  H5   H  HCH2  0   0.260  24.2978  15.1411  -12.1983
 SZ7  H6   H  HCH2  0   0.265  25.5655  12.6881  -13.6162
 SZ7  H7   H  HCH2  0   0.259  26.4699  14.0671  -12.8388
 SZ7  H8   H  HCR5  0   0.272  24.3814  17.6392  -20.4601
 SZ7  H9   H  HCR5  0   0.301  22.4022  13.8221  -21.0303
 SZ7  H10  H  HCR5  0   0.273  23.1079  16.0822  -22.1563

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
 SZ7  C   C3   aromatic  1.362  0.020  1.362
 SZ7  C   C1   aromatic  1.418  0.020  1.418
 SZ7  C3  S    aromatic  1.714  0.020  1.714
 SZ7  C1  C2   aromatic  1.369  0.020  1.369
 SZ7  S   C2   aromatic  1.725  0.020  1.725
 SZ7  C2  C4   single    1.442  0.020  1.442
 SZ7  C4  N    double    1.273  0.020  1.273
 SZ7  N   N1   single    1.340  0.020  1.340
 SZ7  N1  C5   single    1.363  0.020  1.363
 SZ7  C8  C6   single    1.509  0.020  1.509
 SZ7  C8  C7   single    1.482  0.020  1.482
 SZ7  C5  C6   single    1.480  0.020  1.480
 SZ7  C5  O    double    1.221  0.020  1.221
 SZ7  C6  C7   single    1.509  0.020  1.509
 SZ7  C4  H1   single    0.930  0.020  1.080
 SZ7  C6  H2   single    0.970  0.020  1.090
 SZ7  N1  H3   single    0.860  0.020  1.020
 SZ7  C7  H4   single    0.970  0.020  1.090
 SZ7  C7  H5   single    0.970  0.020  1.090
 SZ7  C8  H6   single    0.970  0.020  1.090
 SZ7  C8  H7   single    0.970  0.020  1.090
 SZ7  C1  H8   single    0.930  0.020  1.080
 SZ7  C3  H9   single    0.930  0.020  1.080
 SZ7  C   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
 SZ7  H1   C4  C2  116.52  3.000
 SZ7  H1   C4  N   123.08  3.000
 SZ7  C2   C4  N   120.40  3.000
 SZ7  O    C5  N1  119.39  3.000
 SZ7  O    C5  C6  123.14  3.000
 SZ7  N1   C5  C6  117.46  3.000
 SZ7  H2   C6  C8  116.85  3.000
 SZ7  H2   C6  C7  116.86  3.000
 SZ7  C8   C6  C7   58.82  3.000
 SZ7  H2   C6  C5  117.14  3.000
 SZ7  C7   C6  C5  117.13  3.000
 SZ7  C8   C6  C5  117.22  3.000
 SZ7  H3   N1  N   119.98  3.000
 SZ7  H3   N1  C5  117.16  3.000
 SZ7  N    N1  C5  122.86  3.000
 SZ7  H5   C7  H4  114.86  3.000
 SZ7  H5   C7  C8  118.20  3.000
 SZ7  H4   C7  C8  118.67  3.000
 SZ7  H5   C7  C6  117.46  3.000
 SZ7  H4   C7  C6  116.36  3.000
 SZ7  C8   C7  C6   60.59  3.000
 SZ7  H7   C8  H6  114.82  3.000
 SZ7  H7   C8  C7  118.31  3.000
 SZ7  H6   C8  C7  118.62  3.000
 SZ7  H7   C8  C6  117.54  3.000
 SZ7  H6   C8  C6  116.27  3.000
 SZ7  C7   C8  C6   60.60  3.000
 SZ7  N1   N   C4  118.28  3.000
 SZ7  S    C2  C1  111.18  3.000
 SZ7  S    C2  C4  121.81  3.000
 SZ7  C1   C2  C4  127.01  3.000
 SZ7  H8   C1  C   124.22  3.000
 SZ7  H8   C1  C2  123.03  3.000
 SZ7  C    C1  C2  112.75  3.000
 SZ7  C3   S   C2   91.63  3.000
 SZ7  H9   C3  C   127.87  3.000
 SZ7  H9   C3  S   120.08  3.000
 SZ7  C    C3  S   112.05  3.000
 SZ7  H10  C   C3  123.53  3.000
 SZ7  H10  C   C1  124.08  3.000
 SZ7  C3   C   C1  112.39  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
 SZ7  CONST_01  C3   C   C1  C2    0.00   0.0  0
 SZ7  CONST_02  C    C3  S   C2    0.00   0.0  0
 SZ7  CONST_03  S    C3  C   C1    0.00   0.0  0
 SZ7  CONST_04  C3   S   C2  C1    0.00   0.0  0
 SZ7  CONST_05  C    C1  C2  S     0.00   0.0  0
 SZ7  CONST_06  C    C1  C2  C4  180.00   0.0  0
 SZ7  CONST_07  C3   S   C2  C4  180.00   0.0  0
 SZ7  CONST_08  H10  C   C1  C2  180.00   0.0  0
 SZ7  CONST_09  H9   C3  S   C2  180.00   0.0  0
 SZ7  CONST_10  H8   C1  C2  S   180.00   0.0  0
 SZ7  CONST_11  N    N1  C5  C6    0.00   0.0  0
 SZ7  CONST_12  H3   N1  C5  C6  180.00   0.0  0
 SZ7  CONST_13  N    N1  C5  O   180.00   0.0  0
 SZ7  Var_01    C7   C8  C6  C5  106.75  30.0  1
 SZ7  Var_02    H4   C7  C8  C6  105.83  30.0  1
 SZ7  Var_03    C8   C6  C5  N1  147.27  30.0  3
 SZ7  Var_04    C1   C2  C4  N   179.56  30.0  3
 SZ7  Var_05    C2   C4  N   N1  179.84   0.0  2
 SZ7  Var_06    C5   N1  N   C4  179.37  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SZ7  chir_01  C6  C8  C5  C7  both

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
 SZ7  plan-1  C4   0.020
 SZ7  plan-1  C2   0.020
 SZ7  plan-1  C1   0.020
 SZ7  plan-1  S    0.020
 SZ7  plan-1  C3   0.020
 SZ7  plan-1  C    0.020
 SZ7  plan-1  H8   0.020
 SZ7  plan-1  H9   0.020
 SZ7  plan-1  H10  0.020
 SZ7  plan-2  C5   0.020
 SZ7  plan-2  C6   0.020
 SZ7  plan-2  N1   0.020
 SZ7  plan-2  O    0.020
 SZ7  plan-2  N    0.020
 SZ7  plan-2  H3   0.020
 SZ7  plan-3  C4   0.020
 SZ7  plan-3  N1   0.020
 SZ7  plan-3  N    0.020
 SZ7  plan-3  C2   0.020
 SZ7  plan-3  H1   0.020

