# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 23:19:21 2022
#   Inital geometry file: a 39 line input string
#   Ligand name: (2S,4R)-1,3-thiazolidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CS[C@@H](N)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
 XJP  XJP  (2S,4R)-1,3-thiazolidine-2,4-diamine  ligand  16  7  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XJP
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
 XJP  N01   N  NH2   0  -0.787  -13.9151  21.1167   -9.1036
 XJP  C02   C  CH1   0   0.075  -13.4865  22.0491  -10.1111
 XJP  C03   C  CH2   0  -0.553  -14.6383  22.9229  -10.5838
 XJP  S04   S  S2    0  -0.049  -13.8326  24.2445  -11.5203
 XJP  C05   C  CH1   0  -0.036  -12.3030  24.1451  -10.4997
 XJP  N06   N  NH2   0  -0.774  -12.1581  25.3498   -9.7076
 XJP  N07   N  NH1   0  -0.617  -12.4825  23.0006   -9.6391
 XJP  H012  H  HNH2  0   0.353  -13.1685  20.4681   -8.8879
 XJP  H1    H  HNH2  0   0.338  -14.1149  21.6170   -8.2449
 XJP  H021  H  HCH1  0   0.223  -13.1322  21.4623  -10.9687
 XJP  H031  H  HCH2  0   0.278  -15.3176  22.3765  -11.2344
 XJP  H032  H  HCH2  0   0.262  -15.2021  23.3210   -9.7380
 XJP  H051  H  HCH1  0   0.236  -11.4764  24.0020  -11.2079
 XJP  H062  H  HNH2  0   0.346  -11.3116  25.2672   -9.1513
 XJP  H2    H  HNH2  0   0.343  -11.9945  26.1347  -10.3284
 XJP  H3    H  HNH1  0   0.361  -11.5966  22.5359   -9.4818

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
 XJP  C02  N01   single  1.438  0.020  1.438
 XJP  C03  C02   single  1.521  0.020  1.521
 XJP  S04  C03   single  1.809  0.020  1.809
 XJP  C05  S04   single  1.842  0.020  1.842
 XJP  N06  C05   single  1.449  0.020  1.449
 XJP  N07  C05   single  1.443  0.020  1.443
 XJP  C02  N07   single  1.461  0.020  1.461
 XJP  N01  H012  single  0.890  0.020  1.040
 XJP  N01  H1    single  0.890  0.020  1.040
 XJP  C02  H021  single  0.970  0.020  1.090
 XJP  C03  H031  single  0.970  0.020  1.090
 XJP  C03  H032  single  0.970  0.020  1.090
 XJP  C05  H051  single  0.970  0.020  1.090
 XJP  N06  H062  single  0.890  0.020  1.040
 XJP  N06  H2    single  0.890  0.020  1.040
 XJP  N07  H3    single  0.890  0.020  1.040

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
 XJP  H1    N01  H012  106.33  3.000
 XJP  H1    N01  C02   109.40  3.000
 XJP  H012  N01  C02   110.17  3.000
 XJP  H021  C02  N07   112.24  3.000
 XJP  H021  C02  C03   107.98  3.000
 XJP  N07   C02  C03   104.28  3.000
 XJP  H021  C02  N01   107.27  3.000
 XJP  N07   C02  N01   113.62  3.000
 XJP  C03   C02  N01   111.38  3.000
 XJP  H032  C03  H031  108.91  3.000
 XJP  H032  C03  S04   111.39  3.000
 XJP  H031  C03  S04   109.60  3.000
 XJP  H032  C03  C02   111.09  3.000
 XJP  H031  C03  C02   111.73  3.000
 XJP  S04   C03  C02   104.08  3.000
 XJP  C05   S04  C03    92.50  3.000
 XJP  H051  C05  N07   112.02  3.000
 XJP  H051  C05  N06   112.69  3.000
 XJP  N07   C05  N06   110.23  3.000
 XJP  H051  C05  S04   105.95  3.000
 XJP  N07   C05  S04   105.66  3.000
 XJP  N06   C05  S04   109.95  3.000
 XJP  H2    N06  H062  105.29  3.000
 XJP  H2    N06  C05   108.96  3.000
 XJP  H062  N06  C05   108.36  3.000
 XJP  H3    N07  C05   110.35  3.000
 XJP  H3    N07  C02   110.63  3.000
 XJP  C05   N07  C02   114.15  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
 XJP  Var_01  H031  C03  S04  C05  -149.21  30.0  1

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
 XJP  chir_01  C02  N01  C03  N07  negativ
 XJP  chir_02  C05  S04  N07  N06  positiv

