# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:19:46 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-(4-methylpiperazin-1-yl)-2-[(5Z)-4-oxo-2-thioxo-5-(2,3,6-trichlorobenzylidene)-1,3-thiazolidin-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)NC(=O)CN2C(=S)S\C(=C/c3c(Cl)ccc(Cl)c3Cl)C2=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
 SVB  SVB  N-(4-methylpiperazin-1-yl)-2-[(5Z)-4-oxo-2-thioxo-5-(2,3,6-trichlorobenzylidene)-1,3-thiazolidin-3-yl]acetamide  ligand  45  28  .  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_SVB
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
 SVB  CL1  CL  CL    0  -0.086  -4.7910  -2.8730   0.0423
 SVB  C1   C   CR6   0  -0.108  -4.9615  -1.1651   0.2065
 SVB  C2   C   CR6   0   0.200  -3.8423  -0.4071   0.5494
 SVB  C3   C   C1    0  -0.250  -2.5548  -1.0780   0.7747
 SVB  C4   C   CR5   0  -0.252  -1.4746  -0.8990   0.0167
 SVB  S5   S   S2    0   0.254  -1.3295   0.1405  -1.3784
 SVB  C6   C   CR5   0   0.031   0.3190  -0.3564  -1.6513
 SVB  N7   N   NR5   0  -0.484   0.7065  -1.2911  -0.7406
 SVB  C8   C   CH2   0  -0.468   2.0562  -1.7915  -0.7098
 SVB  C9   C   CR5   0   0.681  -0.2012  -1.6152   0.2557
 SVB  O10  O   O     0  -0.392   0.0268  -2.3753   1.1597
 SVB  S11  S   S1    0  -0.170   1.2316   0.2536  -2.8550
 SVB  C12  C   CR6   0  -0.083  -4.0026   0.9740   0.6841
 SVB  CL2  CL  CL    0  -0.059  -2.6746   1.9445   1.1756
 SVB  C13  C   CR6   0   0.028  -5.2405   1.5673   0.4546
 SVB  CL3  CL  CL    0  -0.077  -5.4374   3.2661   0.6190
 SVB  C14  C   CR16  0  -0.236  -6.3293   0.7888   0.0988
 SVB  C15  C   CR16  0  -0.189  -6.1941  -0.5822  -0.0232
 SVB  H1   H   H     0   0.322  -2.4975  -1.7958   1.5867
 SVB  H3   H   HCH2  0   0.330   2.0663  -2.7125  -0.1260
 SVB  H4   H   HCH2  0   0.312   2.3765  -2.0368  -1.7217
 SVB  H6   H   HCR6  0   0.306  -7.2886   1.2533  -0.0812
 SVB  H7   H   HCR6  0   0.303  -7.0460  -1.1875  -0.2985
 SVB  C5   C   C     0   0.552   2.9707  -0.7695  -0.0425
 SVB  N1   N   NH1   0  -0.494   4.2666  -0.9482  -0.3435
 SVB  H8   H   HNH1  0   0.400   4.5396  -1.6840  -0.9871
 SVB  N2   N   NT    0  -0.292   5.2477  -0.2070   0.2759
 SVB  C11  C   CH2   0  -0.284   6.0274   0.5725  -0.6729
 SVB  C7   C   CH2   0  -0.292   7.0142   1.4387   0.0866
 SVB  N3   N   NT    0  -0.413   7.8751   0.6278   0.9242
 SVB  C17  C   CH2   0  -0.290   7.0833  -0.1497   1.8565
 SVB  C18  C   CH2   0  -0.289   6.0980  -1.0338   1.1182
 SVB  C10  C   CH3   0  -0.520   8.8574   1.4356   1.6108
 SVB  O1   O   O     0  -0.455   2.5303   0.0783   0.7061
 SVB  H2   H   HCH2  0   0.209   6.5696  -0.0734  -1.3807
 SVB  H5   H   HCH2  0   0.251   5.3512   1.2070  -1.2469
 SVB  H9   H   HCH2  0   0.244   7.6257   1.9893  -0.6315
 SVB  H10  H   HCH2  0   0.197   6.4559   2.1858   0.6772
 SVB  H11  H   HCH2  0   0.243   7.7470  -0.7803   2.4520
 SVB  H12  H   HCH2  0   0.197   6.5311   0.4966   2.5606
 SVB  H13  H   HCH2  0   0.253   5.4730  -1.5637   1.8380
 SVB  H14  H   HCH2  0   0.209   6.6460  -1.7846   0.5279
 SVB  H15  H   HCH3  0   0.193   8.4073   2.1738   2.2929
 SVB  H16  H   HCH3  0   0.235   9.5205   0.7996   2.1987
 SVB  H17  H   HCH3  0   0.235   9.4681   1.9790   0.8884

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
 SVB  CL3  C13  single    1.718  0.020  1.718
 SVB  CL2  C12  single    1.717  0.020  1.717
 SVB  C13  C12  aromatic  1.392  0.020  1.392
 SVB  C13  C14  aromatic  1.385  0.020  1.385
 SVB  C12  C2   aromatic  1.397  0.020  1.397
 SVB  C14  C15  aromatic  1.383  0.020  1.383
 SVB  C15  C1   aromatic  1.383  0.020  1.383
 SVB  C2   C1   aromatic  1.395  0.020  1.395
 SVB  C2   C3   single    1.469  0.020  1.469
 SVB  C1   CL1  single    1.724  0.020  1.724
 SVB  S5   C4   single    1.746  0.020  1.746
 SVB  S5   C6   single    1.743  0.020  1.743
 SVB  C3   C4   double    1.332  0.020  1.332
 SVB  C4   C9   single    1.480  0.020  1.480
 SVB  C6   S11  double    1.629  0.020  1.629
 SVB  C6   N7   single    1.361  0.020  1.361
 SVB  C9   N7   single    1.386  0.020  1.386
 SVB  C9   O10  double    1.203  0.020  1.203
 SVB  N7   C8   single    1.440  0.020  1.440
 SVB  C3   H1   single    0.930  0.020  1.080
 SVB  C8   H3   single    0.970  0.020  1.090
 SVB  C8   H4   single    0.970  0.020  1.090
 SVB  C14  H6   single    0.930  0.020  1.080
 SVB  C15  H7   single    0.930  0.020  1.080
 SVB  C8   C5   single    1.525  0.020  1.525
 SVB  C5   N1   single    1.342  0.020  1.342
 SVB  N1   H8   single    0.860  0.020  1.020
 SVB  N1   N2   single    1.377  0.020  1.377
 SVB  N2   C11  single    1.455  0.020  1.455
 SVB  C11  C7   single    1.517  0.020  1.517
 SVB  C7   N3   single    1.449  0.020  1.449
 SVB  N3   C17  single    1.449  0.020  1.449
 SVB  C17  C18  single    1.516  0.020  1.516
 SVB  C18  N2   single    1.455  0.020  1.455
 SVB  N3   C10  single    1.445  0.020  1.445
 SVB  C5   O1   double    1.214  0.020  1.214
 SVB  C11  H2   single    0.970  0.020  1.090
 SVB  C11  H5   single    0.970  0.020  1.090
 SVB  C7   H9   single    0.970  0.020  1.090
 SVB  C7   H10  single    0.970  0.020  1.090
 SVB  C17  H11  single    0.970  0.020  1.090
 SVB  C17  H12  single    0.970  0.020  1.090
 SVB  C18  H13  single    0.970  0.020  1.090
 SVB  C18  H14  single    0.970  0.020  1.090
 SVB  C10  H15  single    0.970  0.020  1.090
 SVB  C10  H16  single    0.970  0.020  1.090
 SVB  C10  H17  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
 SVB  C15  C1   C2   121.82  3.000
 SVB  C2   C1   CL1  118.85  3.000
 SVB  C15  C1   CL1  119.33  3.000
 SVB  C12  C2   C3   122.50  3.000
 SVB  C3   C2   C1   119.53  3.000
 SVB  C12  C2   C1   117.97  3.000
 SVB  H1   C3   C4   118.17  3.000
 SVB  H1   C3   C2   117.58  3.000
 SVB  C4   C3   C2   124.20  3.000
 SVB  C9   C4   S5   110.22  3.000
 SVB  C9   C4   C3   122.73  3.000
 SVB  S5   C4   C3   127.03  3.000
 SVB  C6   S5   C4    91.95  3.000
 SVB  S11  C6   N7   126.30  3.000
 SVB  N7   C6   S5   111.11  3.000
 SVB  S11  C6   S5   122.59  3.000
 SVB  C9   N7   C8   121.14  3.000
 SVB  C8   N7   C6   121.32  3.000
 SVB  C9   N7   C6   117.06  3.000
 SVB  C5   C8   H4   112.40  3.000
 SVB  C5   C8   H3   109.04  3.000
 SVB  H4   C8   H3   107.73  3.000
 SVB  C5   C8   N7   109.79  3.000
 SVB  H4   C8   N7   109.51  3.000
 SVB  H3   C8   N7   108.28  3.000
 SVB  O10  C9   N7   124.32  3.000
 SVB  O10  C9   C4   126.17  3.000
 SVB  N7   C9   C4   109.51  3.000
 SVB  C13  C12  CL2  119.62  3.000
 SVB  C13  C12  C2   120.51  3.000
 SVB  CL2  C12  C2   119.86  3.000
 SVB  C14  C13  CL3  119.36  3.000
 SVB  C14  C13  C12  120.13  3.000
 SVB  CL3  C13  C12  120.51  3.000
 SVB  H6   C14  C15  119.87  3.000
 SVB  H6   C14  C13  119.93  3.000
 SVB  C15  C14  C13  120.20  3.000
 SVB  H7   C15  C14  120.04  3.000
 SVB  H7   C15  C1   120.59  3.000
 SVB  C14  C15  C1   119.36  3.000
 SVB  O1   C5   N1   125.56  3.000
 SVB  O1   C5   C8   121.36  3.000
 SVB  N1   C5   C8   113.05  3.000
 SVB  N2   N1   H8   118.94  3.000
 SVB  N2   N1   C5   121.03  3.000
 SVB  H8   N1   C5   119.89  3.000
 SVB  C18  N2   C11  111.65  3.000
 SVB  C18  N2   N1   111.78  3.000
 SVB  C11  N2   N1   112.15  3.000
 SVB  H5   C11  H2   107.96  3.000
 SVB  H5   C11  C7   109.55  3.000
 SVB  H2   C11  C7   109.66  3.000
 SVB  H5   C11  N2   108.83  3.000
 SVB  H2   C11  N2   111.65  3.000
 SVB  C7   C11  N2   109.16  3.000
 SVB  H10  C7   H9   107.09  3.000
 SVB  H10  C7   N3   111.71  3.000
 SVB  H9   C7   N3   109.24  3.000
 SVB  H10  C7   C11  108.98  3.000
 SVB  H9   C7   C11  108.84  3.000
 SVB  N3   C7   C11  110.87  3.000
 SVB  C10  N3   C17  111.44  3.000
 SVB  C10  N3   C7   111.44  3.000
 SVB  C17  N3   C7   110.33  3.000
 SVB  H12  C17  H11  107.12  3.000
 SVB  H12  C17  C18  109.09  3.000
 SVB  H11  C17  C18  108.89  3.000
 SVB  H12  C17  N3   111.69  3.000
 SVB  H11  C17  N3   109.17  3.000
 SVB  C18  C17  N3   110.77  3.000
 SVB  H14  C18  H13  107.92  3.000
 SVB  H14  C18  C17  109.59  3.000
 SVB  H13  C18  C17  109.54  3.000
 SVB  H14  C18  N2   111.59  3.000
 SVB  H13  C18  N2   108.86  3.000
 SVB  C17  C18  N2   109.30  3.000
 SVB  H17  C10  H16  107.88  3.000
 SVB  H17  C10  H15  107.76  3.000
 SVB  H16  C10  H15  107.79  3.000
 SVB  H17  C10  N3   110.14  3.000
 SVB  H16  C10  N3   110.08  3.000
 SVB  H15  C10  N3   113.02  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
 SVB  CONST_01  C13  C14  C15  C1      0.00   0.0  0
 SVB  CONST_02  C13  C12  C2   C1      0.00   0.0  0
 SVB  CONST_03  C14  C13  C12  C2      0.00   0.0  0
 SVB  CONST_04  C14  C15  C1   C2      0.00   0.0  0
 SVB  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 SVB  CONST_06  C15  C1   C2   C12     0.00   0.0  0
 SVB  CONST_07  C6   N7   C9   C4      0.00   0.0  0
 SVB  CONST_08  C14  C15  C1   CL1   180.00   0.0  0
 SVB  CONST_09  C12  C2   C1   CL1   180.00   0.0  0
 SVB  CONST_10  CL2  C12  C2   C1    180.00   0.0  0
 SVB  CONST_11  CL3  C13  C12  C2    180.00   0.0  0
 SVB  CONST_12  C13  C12  C2   C3    180.00   0.0  0
 SVB  CONST_13  C15  C1   C2   C3    180.00   0.0  0
 SVB  CONST_14  C14  C13  C12  CL2   180.00   0.0  0
 SVB  CONST_15  C15  C14  C13  CL3   180.00   0.0  0
 SVB  CONST_16  C8   N7   C9   C4    180.00   0.0  0
 SVB  CONST_17  O10  C9   N7   C6    180.00   0.0  0
 SVB  CONST_18  H6   C14  C15  C1    180.00   0.0  0
 SVB  CONST_19  H7   C15  C1   C2    180.00   0.0  0
 SVB  CONST_20  O10  C9   N7   C8      0.00   0.0  0
 SVB  CONST_21  N2   N1   C5   C8    180.00   0.0  0
 SVB  CONST_22  O1   C5   N1   N2      0.00   0.0  0
 SVB  CONST_23  H8   N1   C5   C8      0.00   0.0  0
 SVB  Var_01    N3   C7   C11  N2     57.41  30.0  1
 SVB  Var_02    N3   C17  C18  N2    -57.41  30.0  1
 SVB  Var_03    C17  C18  N2   C11    57.97  30.0  1
 SVB  Var_04    C17  N3   C7   C11   -58.07  30.0  1
 SVB  Var_05    C18  N2   C11  C7    -57.89  30.0  1
 SVB  Var_06    C18  C17  N3   C7     58.01  30.0  1
 SVB  Var_07    C4   C3   C2   C1    115.26  30.0  2
 SVB  Var_08    S5   C4   C3   C2      0.07  30.0  2
 SVB  Var_09    C5   C8   N7   C6     77.59  30.0  3
 SVB  Var_10    C11  N2   N1   C5   -120.10  30.0  2
 SVB  Var_11    H15  C10  N3   C7     61.95  30.0  3
 SVB  Var_12    N1   C5   C8   N7   -160.05  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
 SVB  plan-1  C3   0.020
 SVB  plan-1  C4   0.020
 SVB  plan-1  S5   0.020
 SVB  plan-1  C6   0.020
 SVB  plan-1  N7   0.020
 SVB  plan-1  C8   0.020
 SVB  plan-1  C9   0.020
 SVB  plan-1  O10  0.020
 SVB  plan-1  S11  0.020
 SVB  plan-2  CL1  0.020
 SVB  plan-2  C1   0.020
 SVB  plan-2  C2   0.020
 SVB  plan-2  C3   0.020
 SVB  plan-2  C12  0.020
 SVB  plan-2  CL2  0.020
 SVB  plan-2  C13  0.020
 SVB  plan-2  CL3  0.020
 SVB  plan-2  C14  0.020
 SVB  plan-2  C15  0.020
 SVB  plan-2  H6   0.020
 SVB  plan-2  H7   0.020
 SVB  plan-3  C8   0.020
 SVB  plan-3  C5   0.020
 SVB  plan-3  N1   0.020
 SVB  plan-3  H8   0.020
 SVB  plan-3  N2   0.020
 SVB  plan-3  O1   0.020

