# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:16:12 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-phenyl-1,2,5-thiadiazolidin-3-one 1,1-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CN(c2ccccc2)[S](=O)(=O)N1
#
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
 T2D  T2D  '5-phenyl-1,2,5-thiadiazolidin-3-one 1,1-dioxide'  ligand  22  14  .  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_T2D
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
 T2D  C1    C  CR16  0  -0.261  -1.1856  -1.3323   2.2266
 T2D  C2    C  CR16  0  -0.253  -2.2189  -1.5403   3.1271
 T2D  C3    C  CR16  0  -0.245  -2.9855  -2.6972   3.0559
 T2D  C4    C  CR16  0  -0.253  -2.7131  -3.6527   2.0865
 T2D  C5    C  CR16  0  -0.262  -1.6695  -3.4589   1.1922
 T2D  C6    C  CR6   0   0.285  -0.9087  -2.2996   1.2664
 T2D  N7    N  N     0  -0.731   0.1499  -2.1247   0.3280
 T2D  S8    S  S     0   1.549  -0.2738  -1.4196  -1.1109
 T2D  N9    N  NC1   0  -0.806   1.3224  -1.1263  -1.4931
 T2D  C10   C  C     0   0.565   2.2197  -1.2862  -0.4751
 T2D  C11   C  CH2   0  -0.386   1.4867  -1.7459   0.7613
 T2D  O12   O  O     0  -0.414   3.4023  -1.0767  -0.5537
 T2D  O13   O  OS    0  -0.614  -0.8435  -2.3902  -2.0163
 T2D  O14   O  OS    0  -0.615  -0.9999  -0.1799  -0.9312
 T2D  H1    H  HCR6  0   0.276  -0.5970  -0.4250   2.2773
 T2D  H2    H  HCR6  0   0.268  -2.4318  -0.7922   3.8789
 T2D  H3    H  HCR6  0   0.267  -3.7938  -2.8526   3.7581
 T2D  H4    H  HCR6  0   0.267  -3.3072  -4.5550   2.0308
 T2D  H5    H  HCR6  0   0.274  -1.4384  -4.2065   0.4449
 T2D  H9    H  HNC1  0   0.460   1.5782  -0.7817  -2.4129
 T2D  H111  H  HCH2  0   0.323   1.9933  -2.6036   1.2035
 T2D  H112  H  HCH2  0   0.305   1.4868  -0.9270   1.4868

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
 T2D  C1   C2    aromatic  1.386  0.020  1.386
 T2D  C1   C6    aromatic  1.391  0.020  1.391
 T2D  C1   H1    single    0.930  0.020  1.080
 T2D  C2   C3    aromatic  1.390  0.020  1.390
 T2D  C2   H2    single    0.930  0.020  1.080
 T2D  C3   C4    aromatic  1.388  0.020  1.388
 T2D  C3   H3    single    0.930  0.020  1.080
 T2D  C4   C5    aromatic  1.388  0.020  1.388
 T2D  C4   H4    single    0.930  0.020  1.080
 T2D  C5   C6    aromatic  1.389  0.020  1.389
 T2D  C5   H5    single    0.930  0.020  1.080
 T2D  C6   N7    single    1.425  0.020  1.425
 T2D  N7   S8    single    1.657  0.020  1.657
 T2D  N7   C11   single    1.455  0.020  1.455
 T2D  S8   N9    single    1.667  0.020  1.667
 T2D  S8   O13   double    1.444  0.020  1.444
 T2D  S8   O14   double    1.448  0.020  1.448
 T2D  N9   C10   single    1.366  0.020  1.366
 T2D  N9   H9    single    0.860  0.020  1.020
 T2D  C10  C11   single    1.509  0.020  1.509
 T2D  C10  O12   double    1.204  0.020  1.204
 T2D  C11  H111  single    0.970  0.020  1.090
 T2D  C11  H112  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
 T2D  H1    C1   C6    120.46  3.000
 T2D  H1    C1   C2    120.04  3.000
 T2D  C6    C1   C2    119.50  3.000
 T2D  H2    C2   C3    120.19  3.000
 T2D  H2    C2   C1    119.63  3.000
 T2D  C3    C2   C1    120.19  3.000
 T2D  H3    C3   C4    120.07  3.000
 T2D  H3    C3   C2    119.89  3.000
 T2D  C4    C3   C2    120.04  3.000
 T2D  H4    C4   C5    119.75  3.000
 T2D  H4    C4   C3    120.16  3.000
 T2D  C5    C4   C3    120.09  3.000
 T2D  H5    C5   C6    119.78  3.000
 T2D  H5    C5   C4    120.61  3.000
 T2D  C6    C5   C4    119.60  3.000
 T2D  N7    C6   C5    118.30  3.000
 T2D  N7    C6   C1    121.13  3.000
 T2D  C5    C6   C1    120.56  3.000
 T2D  C11   N7   S8    112.49  3.000
 T2D  C11   N7   C6    121.20  3.000
 T2D  S8    N7   C6    115.71  3.000
 T2D  O14   S8   O13   117.09  3.000
 T2D  O14   S8   N9    110.98  3.000
 T2D  O13   S8   N9    110.61  3.000
 T2D  O14   S8   N7    112.63  3.000
 T2D  O13   S8   N7    111.05  3.000
 T2D  N9    S8   N7     91.67  3.000
 T2D  H9    N9   C10   123.32  3.000
 T2D  H9    N9   S8    120.58  3.000
 T2D  C10   N9   S8    115.93  3.000
 T2D  O12   C10  C11   125.72  3.000
 T2D  O12   C10  N9    125.18  3.000
 T2D  C11   C10  N9    109.09  3.000
 T2D  H112  C11  H111  108.66  3.000
 T2D  H112  C11  C10   108.37  3.000
 T2D  H111  C11  C10   110.27  3.000
 T2D  H112  C11  N7    113.09  3.000
 T2D  H111  C11  N7    110.06  3.000
 T2D  C10   C11  N7    106.35  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
 T2D  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 T2D  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 T2D  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 T2D  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 T2D  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 T2D  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 T2D  CONST_07  N7   C6   C1   C2    180.00   0.0  0
 T2D  CONST_08  N7   C6   C5   C4    180.00   0.0  0
 T2D  CONST_09  C11  C10  N9   S8      0.00   0.0  0
 T2D  CONST_10  O12  C10  N9   S8    180.00   0.0  0
 T2D  CONST_11  H3   C3   C2   C1    180.00   0.0  0
 T2D  CONST_12  H5   C5   C6   C1    180.00   0.0  0
 T2D  CONST_13  H4   C4   C3   C2    180.00   0.0  0
 T2D  CONST_14  H1   C1   C2   C3    180.00   0.0  0
 T2D  CONST_15  H2   C2   C3   C4    180.00   0.0  0
 T2D  CONST_16  H9   N9   C10  C11   180.00   0.0  0
 T2D  Var_01    S8   N7   C6   C1    -92.10  30.0  2
 T2D  Var_02    N9   S8   N7   C6    165.23  30.0  1
 T2D  Var_03    C10  C11  N7   C6   -164.70  30.0  1
 T2D  Var_04    C10  N9   S8   N7    -12.63  30.0  1
 T2D  Var_05    N9   C10  C11  N7     12.11  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
 T2D  plan-1  C1   0.020
 T2D  plan-1  C2   0.020
 T2D  plan-1  C3   0.020
 T2D  plan-1  C4   0.020
 T2D  plan-1  C5   0.020
 T2D  plan-1  C6   0.020
 T2D  plan-1  N7   0.020
 T2D  plan-1  H1   0.020
 T2D  plan-1  H2   0.020
 T2D  plan-1  H3   0.020
 T2D  plan-1  H4   0.020
 T2D  plan-1  H5   0.020
 T2D  plan-2  C6   0.020
 T2D  plan-2  N7   0.020
 T2D  plan-2  S8   0.020
 T2D  plan-2  C11  0.020
 T2D  plan-3  S8   0.020
 T2D  plan-3  N9   0.020
 T2D  plan-3  C10  0.020
 T2D  plan-3  C11  0.020
 T2D  plan-3  O12  0.020
 T2D  plan-3  H9   0.020

