# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:28:00 2021
#   Inital geometry file: a 88 line input string
#   Ligand name: ~{N}-[2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-3-yl]ethyl]-3-methyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)NCCN2C(=O)CSC2=O
#
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
 SYZ  SYZ  ~{N}-[2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-3-yl]ethyl]-3-methyl-benzamide  ligand  33  19  .  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_SYZ
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
 SYZ  N1   N  NR5   0  -0.517  -36.9665   2.1134   1.1054
 SYZ  C4   C  CR16  0  -0.291  -38.3057   8.9508   1.7786
 SYZ  C5   C  CR6   0  -0.009  -37.5989   7.9640   1.0996
 SYZ  C6   C  CR16  0  -0.351  -36.5626   8.3301   0.2419
 SYZ  C7   C  C     0   0.526  -37.9537   6.5351   1.3569
 SYZ  C8   C  CH2   0  -0.292  -37.9806   4.2629   0.4474
 SYZ  C10  C  CR5   0   0.600  -36.7200   1.2633   0.0548
 SYZ  O2   O  O     0  -0.404  -37.7654   2.1729   3.2525
 SYZ  C12  C  CR5   0   0.405  -37.4778   1.5592   2.2617
 SYZ  S    S  S2    0   0.077  -37.6540  -0.1865   2.0999
 SYZ  C11  C  CH2   0  -0.692  -37.0311  -0.1697   0.4064
 SYZ  O1   O  O     0  -0.417  -36.3042   1.6212  -1.0180
 SYZ  C9   C  CH2   0  -0.328  -36.7464   3.5465   0.9968
 SYZ  N    N  NH1   0  -0.647  -37.7480   5.6810   0.3366
 SYZ  O    O  O     0  -0.483  -38.4161   6.1789   2.4311
 SYZ  C3   C  CR16  0  -0.228  -37.9922  10.2861   1.5740
 SYZ  C2   C  CR16  0  -0.292  -36.9624  10.6397   0.7150
 SYZ  C1   C  CR6   0   0.117  -36.2275   9.6651   0.0418
 SYZ  C    C  CH3   0  -0.723  -35.0978  10.0512  -0.8675
 SYZ  H2   H  HCR6  0   0.252  -35.9754   7.5722  -0.2644
 SYZ  H3   H  HCH2  0   0.269  -38.2258   3.8825  -0.5434
 SYZ  H4   H  HCH2  0   0.259  -38.8381   4.0814   1.0952
 SYZ  H5   H  HCH2  0   0.338  -37.7779  -0.5629  -0.2826
 SYZ  H6   H  HCH2  0   0.283  -36.4915   3.9300   1.9829
 SYZ  H7   H  HCH2  0   0.280  -35.8905   3.7065   0.3432
 SYZ  H8   H  HNH1  0   0.413  -37.4344   6.0314  -0.5529
 SYZ  H9   H  HCR6  0   0.260  -38.5505  11.0539   2.0931
 SYZ  H10  H  HCR6  0   0.255  -36.7200  11.6862   0.5712
 SYZ  H11  H  HCH3  0   0.250  -34.3413  10.6271  -0.3331
 SYZ  H12  H  HCH3  0   0.246  -34.6114   9.1758  -1.2951
 SYZ  H13  H  HCH3  0   0.250  -35.4502  10.6730  -1.6919
 SYZ  H14  H  HCH2  0   0.339  -36.1284  -0.7742   0.3217
 SYZ  H1   H  HCR6  0   0.258  -39.1050   8.6803   2.4555

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
 SYZ  O1   C10  double    1.205  0.020  1.205
 SYZ  C    C1   single    1.501  0.020  1.501
 SYZ  C10  C11  single    1.508  0.020  1.508
 SYZ  C10  N1   single    1.374  0.020  1.374
 SYZ  C1   C2   aromatic  1.394  0.020  1.394
 SYZ  C1   C6   aromatic  1.391  0.020  1.391
 SYZ  C11  S    single    1.805  0.020  1.805
 SYZ  C2   C3   aromatic  1.387  0.020  1.387
 SYZ  C6   C5   aromatic  1.394  0.020  1.394
 SYZ  C9   N1   single    1.454  0.020  1.454
 SYZ  C9   C8   single    1.529  0.020  1.529
 SYZ  N1   C12  single    1.380  0.020  1.380
 SYZ  C3   C4   aromatic  1.387  0.020  1.387
 SYZ  N    C8   single    1.441  0.020  1.441
 SYZ  N    C7   single    1.346  0.020  1.346
 SYZ  C5   C4   aromatic  1.391  0.020  1.391
 SYZ  C5   C7   single    1.495  0.020  1.495
 SYZ  C7   O    double    1.223  0.020  1.223
 SYZ  S    C12  single    1.762  0.020  1.762
 SYZ  C12  O2   double    1.201  0.020  1.201
 SYZ  C4   H1   single    0.930  0.020  1.080
 SYZ  C6   H2   single    0.930  0.020  1.080
 SYZ  C8   H3   single    0.970  0.020  1.090
 SYZ  C8   H4   single    0.970  0.020  1.090
 SYZ  C11  H5   single    0.970  0.020  1.090
 SYZ  C9   H6   single    0.970  0.020  1.090
 SYZ  C9   H7   single    0.970  0.020  1.090
 SYZ  N    H8   single    0.860  0.020  1.020
 SYZ  C3   H9   single    0.930  0.020  1.080
 SYZ  C2   H10  single    0.930  0.020  1.080
 SYZ  C    H11  single    0.970  0.020  1.090
 SYZ  C    H12  single    0.970  0.020  1.090
 SYZ  C    H13  single    0.970  0.020  1.090
 SYZ  C11  H14  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
 SYZ  C9   N1   C12  120.96  3.000
 SYZ  C12  N1   C10  117.29  3.000
 SYZ  C9   N1   C10  121.71  3.000
 SYZ  H1   C4   C3   120.01  3.000
 SYZ  H1   C4   C5   120.23  3.000
 SYZ  C3   C4   C5   119.75  3.000
 SYZ  C7   C5   C6   122.24  3.000
 SYZ  C7   C5   C4   118.28  3.000
 SYZ  C6   C5   C4   119.45  3.000
 SYZ  H2   C6   C1   118.25  3.000
 SYZ  H2   C6   C5   120.42  3.000
 SYZ  C1   C6   C5   121.31  3.000
 SYZ  O    C7   N    122.60  3.000
 SYZ  O    C7   C5   121.31  3.000
 SYZ  N    C7   C5   116.09  3.000
 SYZ  H4   C8   H3   107.78  3.000
 SYZ  H4   C8   N    109.66  3.000
 SYZ  H3   C8   N    108.06  3.000
 SYZ  H4   C8   C9   110.09  3.000
 SYZ  H3   C8   C9   110.18  3.000
 SYZ  N    C8   C9   111.00  3.000
 SYZ  O1   C10  C11  124.13  3.000
 SYZ  C11  C10  N1   111.89  3.000
 SYZ  O1   C10  N1   123.99  3.000
 SYZ  S    C12  O2   123.94  3.000
 SYZ  O2   C12  N1   125.08  3.000
 SYZ  S    C12  N1   110.97  3.000
 SYZ  C11  S    C12   92.43  3.000
 SYZ  H14  C11  H5   108.57  3.000
 SYZ  H14  C11  S    110.71  3.000
 SYZ  H5   C11  S    110.71  3.000
 SYZ  H14  C11  C10  109.76  3.000
 SYZ  H5   C11  C10  109.69  3.000
 SYZ  S    C11  C10  107.39  3.000
 SYZ  H7   C9   H6   107.94  3.000
 SYZ  H7   C9   C8   110.49  3.000
 SYZ  H6   C9   C8   110.46  3.000
 SYZ  H7   C9   N1   107.98  3.000
 SYZ  H6   C9   N1   108.36  3.000
 SYZ  C8   C9   N1   111.49  3.000
 SYZ  H8   N    C8   117.44  3.000
 SYZ  H8   N    C7   119.78  3.000
 SYZ  C8   N    C7   122.77  3.000
 SYZ  H9   C3   C2   119.96  3.000
 SYZ  H9   C3   C4   119.72  3.000
 SYZ  C2   C3   C4   120.32  3.000
 SYZ  H10  C2   C1   119.54  3.000
 SYZ  H10  C2   C3   119.64  3.000
 SYZ  C1   C2   C3   120.82  3.000
 SYZ  C    C1   C2   120.64  3.000
 SYZ  C2   C1   C6   118.33  3.000
 SYZ  C    C1   C6   121.03  3.000
 SYZ  H13  C    H12  107.81  3.000
 SYZ  H13  C    H11  107.05  3.000
 SYZ  H12  C    H11  107.88  3.000
 SYZ  H13  C    C1   111.18  3.000
 SYZ  H12  C    C1   111.55  3.000
 SYZ  H11  C    C1   111.17  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
 SYZ  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 SYZ  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 SYZ  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 SYZ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 SYZ  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 SYZ  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 SYZ  CONST_07  C11  C10  N1   C12     0.00   0.0  0
 SYZ  CONST_08  C    C1   C6   C5    180.00   0.0  0
 SYZ  CONST_09  C1   C6   C5   C7    180.00   0.0  0
 SYZ  CONST_10  C3   C4   C5   C7    180.00   0.0  0
 SYZ  CONST_11  C    C1   C2   C3    180.00   0.0  0
 SYZ  CONST_12  O1   C10  N1   C12   180.00   0.0  0
 SYZ  CONST_13  C9   N1   C10  C11   180.00   0.0  0
 SYZ  CONST_14  H10  C2   C3   C4    180.00   0.0  0
 SYZ  CONST_15  H2   C6   C5   C4    180.00   0.0  0
 SYZ  CONST_16  H9   C3   C4   C5    180.00   0.0  0
 SYZ  CONST_17  H1   C4   C5   C6    180.00   0.0  0
 SYZ  CONST_18  C9   N1   C10  O1      0.00   0.0  0
 SYZ  CONST_19  C8   N    C7   C5    180.00   0.0  0
 SYZ  CONST_20  H8   N    C7   C5      0.00   0.0  0
 SYZ  CONST_21  O    C7   N    C8      0.00   0.0  0
 SYZ  Var_01    S    C11  C10  N1      1.28  30.0  1
 SYZ  Var_02    S    C12  N1   C10     1.49  30.0  1
 SYZ  Var_03    N    C7   C5   C4    150.64  30.0  2
 SYZ  Var_04    C10  N1   C9   C8     87.64  30.0  3
 SYZ  Var_05    H11  C    C1   C6   -121.48  30.0  2
 SYZ  Var_06    N    C8   C9   N1   -179.65  30.0  3
 SYZ  Var_07    C9   C8   N    C7    -86.66  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
 SYZ  plan-1  C4   0.020
 SYZ  plan-1  C5   0.020
 SYZ  plan-1  C6   0.020
 SYZ  plan-1  C7   0.020
 SYZ  plan-1  C3   0.020
 SYZ  plan-1  C2   0.020
 SYZ  plan-1  C1   0.020
 SYZ  plan-1  C    0.020
 SYZ  plan-1  H2   0.020
 SYZ  plan-1  H9   0.020
 SYZ  plan-1  H10  0.020
 SYZ  plan-1  H1   0.020
 SYZ  plan-2  C5   0.020
 SYZ  plan-2  C7   0.020
 SYZ  plan-2  C8   0.020
 SYZ  plan-2  N    0.020
 SYZ  plan-2  O    0.020
 SYZ  plan-2  H8   0.020
 SYZ  plan-3  N1   0.020
 SYZ  plan-3  C10  0.020
 SYZ  plan-3  C12  0.020
 SYZ  plan-3  C11  0.020
 SYZ  plan-3  O1   0.020
 SYZ  plan-3  C9   0.020
 SYZ  plan-4  N1   0.020
 SYZ  plan-4  O2   0.020
 SYZ  plan-4  C12  0.020
 SYZ  plan-4  S    0.020

