# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 06:25:26 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C1NN=C(N1)[C@@H]2COc3ccccc3O2
#
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
 2JX  2JX  5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione  ligand  25  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2JX
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
 2JX  C2   C  CR5   0   0.350  -3.3744   0.3453   0.1453
 2JX  N3   N  NR15  0  -0.629  -2.1014   0.6293  -0.2331
 2JX  S1   S  S1    0  -0.402  -4.7029   1.3514   0.1621
 2JX  C4   C  CR5   0   0.451  -1.3406  -0.4879  -0.0805
 2JX  N5   N  N     0  -0.242  -2.0519  -1.4637   0.3718
 2JX  N6   N  NR15  0  -0.452  -3.2884  -0.9456   0.5013
 2JX  C7   C  CH1   0  -0.079   0.1008  -0.5645  -0.4369
 2JX  C8   C  CH2   0  -0.191   0.7777  -1.7900   0.1523
 2JX  O9   O  O2    0  -0.478   2.1389  -1.7943  -0.2288
 2JX  C10  C  CR6   0   0.323   2.7727  -0.6028  -0.0987
 2JX  C11  C  CR6   0   0.309   2.0658   0.5917   0.0489
 2JX  O12  O  O2    0  -0.489   0.7053   0.6127   0.0661
 2JX  C13  C  CR16  0  -0.355   2.7486   1.7925   0.1807
 2JX  C14  C  CR16  0  -0.267   4.1347   1.8088   0.1640
 2JX  C15  C  CR16  0  -0.261   4.8404   0.6230   0.0010
 2JX  C16  C  CR16  0  -0.364   4.1612  -0.5789  -0.1251
 2JX  H1   H  HNR5  0   0.446  -1.7973   1.5322  -0.5670
 2JX  H2   H  HNR5  0   0.443  -4.0479  -1.5170   0.8390
 2JX  H3   H  HCH1  0   0.299   0.1951  -0.5887  -1.5314
 2JX  H4   H  HCH2  0   0.255   0.6812  -1.7866   1.2429
 2JX  H5   H  HCH2  0   0.275   0.3330  -2.7041  -0.2354
 2JX  H6   H  HCR6  0   0.271   2.1836   2.7089   0.2981
 2JX  H7   H  HCR6  0   0.259   4.6600   2.7485   0.2690
 2JX  H8   H  HCR6  0   0.259   5.9218   0.6291  -0.0199
 2JX  H9   H  HCR6  0   0.270   4.7008  -1.5099  -0.2461

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
 2JX  S1   C2   double    1.667  0.020  1.667
 2JX  C2   N6   single    1.342  0.020  1.342
 2JX  C2   N3   single    1.358  0.020  1.358
 2JX  N6   N5   single    1.347  0.020  1.347
 2JX  N3   C4   single    1.360  0.020  1.360
 2JX  N5   C4   double    1.289  0.020  1.289
 2JX  C4   C7   single    1.487  0.020  1.487
 2JX  C7   C8   single    1.519  0.020  1.519
 2JX  C7   O12  single    1.416  0.020  1.416
 2JX  C8   O9   single    1.414  0.020  1.414
 2JX  O12  C11  single    1.361  0.020  1.361
 2JX  O9   C10  single    1.356  0.020  1.356
 2JX  C11  C10  aromatic  1.396  0.020  1.396
 2JX  C11  C13  aromatic  1.388  0.020  1.388
 2JX  C10  C16  aromatic  1.389  0.020  1.389
 2JX  C13  C14  aromatic  1.386  0.020  1.386
 2JX  C16  C15  aromatic  1.386  0.020  1.386
 2JX  C14  C15  aromatic  1.390  0.020  1.390
 2JX  N3   H1   single    0.860  0.020  1.020
 2JX  N6   H2   single    0.860  0.020  1.020
 2JX  C7   H3   single    0.970  0.020  1.090
 2JX  C8   H4   single    0.970  0.020  1.090
 2JX  C8   H5   single    0.970  0.020  1.090
 2JX  C13  H6   single    0.930  0.020  1.080
 2JX  C14  H7   single    0.930  0.020  1.080
 2JX  C15  H8   single    0.930  0.020  1.080
 2JX  C16  H9   single    0.930  0.020  1.080

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
 2JX  N6   C2   S1   128.99  3.000
 2JX  N6   C2   N3   102.41  3.000
 2JX  S1   C2   N3   128.59  3.000
 2JX  H1   N3   C4   127.10  3.000
 2JX  H1   N3   C2   124.16  3.000
 2JX  C4   N3   C2   108.74  3.000
 2JX  C7   C4   N5   125.45  3.000
 2JX  C7   C4   N3   123.89  3.000
 2JX  N5   C4   N3   110.63  3.000
 2JX  N6   N5   C4   104.42  3.000
 2JX  H2   N6   N5   120.37  3.000
 2JX  H2   N6   C2   125.83  3.000
 2JX  N5   N6   C2   113.79  3.000
 2JX  H3   C7   O12  109.61  3.000
 2JX  H3   C7   C8   109.29  3.000
 2JX  O12  C7   C8   110.05  3.000
 2JX  H3   C7   C4   108.85  3.000
 2JX  O12  C7   C4   106.62  3.000
 2JX  C8   C7   C4   112.37  3.000
 2JX  H5   C8   H4   108.75  3.000
 2JX  H5   C8   O9   107.16  3.000
 2JX  H4   C8   O9   110.70  3.000
 2JX  H5   C8   C7   110.95  3.000
 2JX  H4   C8   C7   110.16  3.000
 2JX  O9   C8   C7   109.09  3.000
 2JX  C10  O9   C8   114.94  3.000
 2JX  C16  C10  C11  119.57  3.000
 2JX  C16  C10  O9   118.73  3.000
 2JX  C11  C10  O9   121.70  3.000
 2JX  C13  C11  O12  118.52  3.000
 2JX  C13  C11  C10  120.09  3.000
 2JX  O12  C11  C10  121.39  3.000
 2JX  C11  O12  C7   114.18  3.000
 2JX  H6   C13  C14  120.87  3.000
 2JX  H6   C13  C11  119.07  3.000
 2JX  C14  C13  C11  120.07  3.000
 2JX  H7   C14  C15  120.41  3.000
 2JX  H7   C14  C13  119.64  3.000
 2JX  C15  C14  C13  119.95  3.000
 2JX  H8   C15  C16  119.54  3.000
 2JX  H8   C15  C14  120.34  3.000
 2JX  C16  C15  C14  120.11  3.000
 2JX  H9   C16  C15  120.76  3.000
 2JX  H9   C16  C10  119.04  3.000
 2JX  C15  C16  C10  120.20  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
 2JX  CONST_01  C14  C13  C11  C10    0.00   0.0  0
 2JX  CONST_02  C14  C15  C16  C10    0.00   0.0  0
 2JX  CONST_03  C15  C16  C10  C11    0.00   0.0  0
 2JX  CONST_04  C15  C14  C13  C11    0.00   0.0  0
 2JX  CONST_05  C16  C10  C11  C13    0.00   0.0  0
 2JX  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 2JX  CONST_07  C4   N5   N6   C2     0.00   0.0  0
 2JX  CONST_08  N5   C4   N3   C2     0.00   0.0  0
 2JX  CONST_09  C7   C4   N3   C2   180.00   0.0  0
 2JX  CONST_10  N5   N6   C2   N3     0.00   0.0  0
 2JX  CONST_11  N6   N5   C4   N3     0.00   0.0  0
 2JX  CONST_12  N6   C2   N3   C4     0.00   0.0  0
 2JX  CONST_13  C7   C4   N5   N6   180.00   0.0  0
 2JX  CONST_14  N5   N6   C2   S1   180.00   0.0  0
 2JX  CONST_15  C4   N3   C2   S1   180.00   0.0  0
 2JX  CONST_16  H9   C16  C10  O9     0.00   0.0  0
 2JX  CONST_17  H6   C13  C11  C10  180.00   0.0  0
 2JX  CONST_18  H8   C15  C16  C10  180.00   0.0  0
 2JX  CONST_19  H7   C14  C13  C11  180.00   0.0  0
 2JX  CONST_20  H2   N6   C2   N3   180.00   0.0  0
 2JX  CONST_21  H1   N3   C4   N5   180.00   0.0  0
 2JX  Var_01    C10  C11  O12  C7   -16.61  30.0  1
 2JX  Var_02    C11  C10  O9   C8   -16.35  30.0  1
 2JX  Var_03    H4   C8   O9   C10  -75.94  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
 2JX  chir_01  C7  C4  C8  O12  positiv

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
 2JX  plan-1  C2   0.020
 2JX  plan-1  N3   0.020
 2JX  plan-1  S1   0.020
 2JX  plan-1  C4   0.020
 2JX  plan-1  N5   0.020
 2JX  plan-1  N6   0.020
 2JX  plan-1  C7   0.020
 2JX  plan-1  H1   0.020
 2JX  plan-1  H2   0.020
 2JX  plan-2  O9   0.020
 2JX  plan-2  C10  0.020
 2JX  plan-2  C11  0.020
 2JX  plan-2  O12  0.020
 2JX  plan-2  C13  0.020
 2JX  plan-2  C14  0.020
 2JX  plan-2  C15  0.020
 2JX  plan-2  C16  0.020
 2JX  plan-2  H6   0.020
 2JX  plan-2  H7   0.020
 2JX  plan-2  H8   0.020
 2JX  plan-2  H9   0.020

