# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:54:37 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: {(2Z)-3-[(6-chloropyridin-3-yl)methyl]-1,3-thiazolidin-2-ylidene}cyanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CN2CCSC2=NC#N)cn1
#
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
 TH4  TH4  {(2Z)-3-[(6-chloropyridin-3-yl)methyl]-1,3-thiazolidin-2-ylidene}cyanamide  ligand  25  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TH4
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
 TH4  C5    C   CR16  0  -0.180  -1.7829   1.5392  -0.7826
 TH4  C6    C   CR16  0  -0.260  -3.0117   1.2525  -0.2147
 TH4  C1    C   CR6   0   0.158  -3.2847  -0.0798   0.0526
 TH4  CL7   CL  CL    0  -0.102  -4.8117  -0.4962   0.7631
 TH4  N2    N   N     0  -0.386  -2.4670  -1.0730  -0.1985
 TH4  C3    C   CR16  0  -0.075  -1.2903  -0.7832  -0.7422
 TH4  C4    C   CR6   0   0.038  -0.8885   0.5096  -1.0546
 TH4  C8    C   CH2   0  -0.432   0.4706   0.7779  -1.6429
 TH4  N9    N   NT    0  -0.423   1.4867   0.9287  -0.6149
 TH4  C13   C   CH2   0  -0.264   1.5119   2.1260   0.2099
 TH4  C12   C   CH2   0  -0.582   2.8560   2.1267   0.9169
 TH4  S11   S   S2    0   0.100   3.2395   0.3668   1.1772
 TH4  C10   C   C     0   0.413   2.2101  -0.0912  -0.1637
 TH4  N14   N   N     0  -0.492   2.1292  -1.2845  -0.6743
 TH4  C15   C   CSP   0   0.192   2.9079  -2.2429  -0.2431
 TH4  N16   N   NS    0  -0.363   3.5537  -3.1526   0.0791
 TH4  H5    H   HCR6  0   0.287  -1.5283   2.5655  -1.0168
 TH4  H6    H   HCR6  0   0.297  -3.7275   2.0304   0.0072
 TH4  H3    H   HCR6  0   0.278  -0.6354  -1.6238  -0.9419
 TH4  H8    H   HCH2  0   0.302   0.7705  -0.0272  -2.3111
 TH4  H8A   H   HCH2  0   0.302   0.4573   1.6973  -2.2290
 TH4  H13   H   HCH2  0   0.289   1.4033   3.0090  -0.4186
 TH4  H13A  H   HCH2  0   0.276   0.6889   2.1052   0.9293
 TH4  H12   H   HCH2  0   0.312   3.6402   2.5708   0.3070
 TH4  H12A  H   HCH2  0   0.315   2.8114   2.6330   1.8773

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
 TH4  C6   C5    aromatic  1.384  0.020  1.384
 TH4  C5   C4    aromatic  1.391  0.020  1.391
 TH4  C5   H5    single    0.930  0.020  1.080
 TH4  C6   C1    aromatic  1.386  0.020  1.386
 TH4  C6   H6    single    0.930  0.020  1.080
 TH4  CL7  C1    single    1.735  0.020  1.735
 TH4  C1   N2    aromatic  1.311  0.020  1.311
 TH4  N2   C3    aromatic  1.328  0.020  1.328
 TH4  C4   C3    aromatic  1.389  0.020  1.389
 TH4  C3   H3    single    0.930  0.020  1.080
 TH4  C4   C8    single    1.505  0.020  1.505
 TH4  C8   N9    single    1.453  0.020  1.453
 TH4  C8   H8    single    0.970  0.020  1.090
 TH4  C8   H8A   single    0.970  0.020  1.090
 TH4  N9   C10   single    1.329  0.020  1.329
 TH4  N9   C13   single    1.454  0.020  1.454
 TH4  C13  C12   single    1.519  0.020  1.519
 TH4  C13  H13   single    0.970  0.020  1.090
 TH4  C13  H13A  single    0.970  0.020  1.090
 TH4  S11  C12   single    1.820  0.020  1.820
 TH4  C12  H12   single    0.970  0.020  1.090
 TH4  C12  H12A  single    0.970  0.020  1.090
 TH4  C10  S11   single    1.751  0.020  1.751
 TH4  N14  C10   double    1.300  0.020  1.300
 TH4  N14  C15   single    1.308  0.020  1.308
 TH4  C15  N16   triple    1.161  0.020  1.161

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
 TH4  H5    C5   C4   120.54  3.000
 TH4  H5    C5   C6   119.60  3.000
 TH4  C4    C5   C6   119.86  3.000
 TH4  H6    C6   C1   121.47  3.000
 TH4  H6    C6   C5   121.57  3.000
 TH4  C1    C6   C5   116.96  3.000
 TH4  N2    C1   CL7  116.47  3.000
 TH4  N2    C1   C6   124.65  3.000
 TH4  CL7   C1   C6   118.89  3.000
 TH4  C3    N2   C1   117.76  3.000
 TH4  H3    C3   C4   120.35  3.000
 TH4  H3    C3   N2   116.19  3.000
 TH4  C4    C3   N2   123.45  3.000
 TH4  C8    C4   C3   120.99  3.000
 TH4  C8    C4   C5   121.68  3.000
 TH4  C3    C4   C5   117.32  3.000
 TH4  H8A   C8   H8   107.28  3.000
 TH4  H8A   C8   N9   107.54  3.000
 TH4  H8    C8   N9   108.56  3.000
 TH4  H8A   C8   C4   110.45  3.000
 TH4  H8    C8   C4   110.91  3.000
 TH4  N9    C8   C4   111.93  3.000
 TH4  C10   N9   C13  115.45  3.000
 TH4  C13   N9   C8   119.92  3.000
 TH4  C10   N9   C8   122.75  3.000
 TH4  H13A  C13  H13  108.66  3.000
 TH4  H13A  C13  C12  111.09  3.000
 TH4  H13   C13  C12  110.89  3.000
 TH4  H13A  C13  N9   110.15  3.000
 TH4  H13   C13  N9   109.78  3.000
 TH4  C12   C13  N9   106.25  3.000
 TH4  H12A  C12  H12  109.56  3.000
 TH4  H12A  C12  S11  109.44  3.000
 TH4  H12   C12  S11  108.84  3.000
 TH4  H12A  C12  C13  112.05  3.000
 TH4  H12   C12  C13  112.15  3.000
 TH4  S11   C12  C13  104.63  3.000
 TH4  C10   S11  C12   91.12  3.000
 TH4  N14   C10  S11  125.25  3.000
 TH4  N14   C10  N9   122.47  3.000
 TH4  S11   C10  N9   112.27  3.000
 TH4  C15   N14  C10  120.39  3.000
 TH4  N16   C15  N14  180.00  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
 TH4  CONST_01  N2   C1   C6   C5     0.00   0.0  0
 TH4  CONST_02  N2   C3   C4   C5     0.00   0.0  0
 TH4  CONST_03  C3   C4   C5   C6     0.00   0.0  0
 TH4  CONST_04  C3   N2   C1   C6     0.00   0.0  0
 TH4  CONST_05  C4   C5   C6   C1     0.00   0.0  0
 TH4  CONST_06  C4   C3   N2   C1     0.00   0.0  0
 TH4  CONST_07  S11  C10  N9   C13    0.00   0.0  0
 TH4  CONST_08  CL7  C1   C6   C5   180.00   0.0  0
 TH4  CONST_09  C8   C4   C5   C6   180.00   0.0  0
 TH4  CONST_10  C3   N2   C1   CL7  180.00   0.0  0
 TH4  CONST_11  C8   C4   C3   N2   180.00   0.0  0
 TH4  CONST_12  S11  C10  N9   C8   180.00   0.0  0
 TH4  CONST_13  N14  C10  N9   C13  180.00   0.0  0
 TH4  CONST_14  H3   C3   C4   C5   180.00   0.0  0
 TH4  CONST_15  H5   C5   C6   C1   180.00   0.0  0
 TH4  CONST_16  H6   C6   C1   N2   180.00   0.0  0
 TH4  CONST_17  N14  C10  N9   C8     0.00   0.0  0
 TH4  CONST_18  C15  N14  C10  N9   180.00   0.0  0
 TH4  CONST_19  C15  N14  C10  S11    0.00   0.0  0
 TH4  Var_01    S11  C12  C13  N9   -32.65  30.0  1
 TH4  Var_02    C10  N9   C13  C12   28.82  30.0  1
 TH4  Var_03    N9   C8   C4   C5    92.79  30.0  2
 TH4  Var_04    N14  C10  S11  C12  171.16  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
 TH4  plan-1  C5   0.020
 TH4  plan-1  C6   0.020
 TH4  plan-1  C1   0.020
 TH4  plan-1  CL7  0.020
 TH4  plan-1  N2   0.020
 TH4  plan-1  C3   0.020
 TH4  plan-1  C4   0.020
 TH4  plan-1  C8   0.020
 TH4  plan-1  H5   0.020
 TH4  plan-1  H6   0.020
 TH4  plan-1  H3   0.020
 TH4  plan-2  C8   0.020
 TH4  plan-2  N9   0.020
 TH4  plan-2  C13  0.020
 TH4  plan-2  S11  0.020
 TH4  plan-2  C10  0.020
 TH4  plan-2  N14  0.020
 TH4  plan-2  C15  0.020

