# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:10:12 2021
#   Inital geometry file: a 54 line input string
#   Ligand name: 2H-1,3-benzodioxole-5-carbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=S)c1ccc2OCOc2c1
#
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
 TJV  TJV  2H-1,3-benzodioxole-5-carbothioamide  ligand  19  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJV
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
 TJV  C4  C  CR16  0  -0.380  41.7746  26.6516  26.0556
 TJV  C5  C  CR6   0   0.057  41.6970  25.7909  24.9405
 TJV  C6  C  C     0   0.145  42.8072  24.8606  24.6411
 TJV  C7  C  CH2   0   0.073  39.2907  29.0185  27.0500
 TJV  S   S  S1    0  -0.372  42.5635  23.3951  23.8803
 TJV  N   N  NH2   0  -0.733  44.0128  25.2472  25.0266
 TJV  C   C  CR16  0  -0.289  40.5805  25.8216  24.1109
 TJV  C3  C  CR56  0   0.318  40.7198  27.4973  26.2675
 TJV  O   O  O     0  -0.484  40.5508  28.3952  27.2638
 TJV  O1  O  O     0  -0.477  38.7351  28.4427  25.8709
 TJV  C2  C  CR56  0   0.312  39.6159  27.5264  25.4274
 TJV  C1  C  CR16  0  -0.328  39.5178  26.6976  24.3360
 TJV  H1  H  HCR6  0   0.283  42.6098  26.6309  26.7434
 TJV  H2  H  HCH2  0   0.245  39.4271  30.0922  26.9063
 TJV  H3  H  HNH2  0   0.416  44.8078  24.6483  24.8712
 TJV  H4  H  HNH2  0   0.424  44.1991  26.1712  25.3831
 TJV  H5  H  HCR6  0   0.265  40.5397  25.1515  23.2636
 TJV  H6  H  HCR6  0   0.282  38.6600  26.7181  23.6784
 TJV  H8  H  HCH2  0   0.245  38.6311  28.8262  27.8990

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
 TJV  S   C6  double    1.669  0.020  1.669
 TJV  C   C1  aromatic  1.395  0.020  1.395
 TJV  C   C5  aromatic  1.391  0.020  1.391
 TJV  C1  C2  aromatic  1.374  0.020  1.374
 TJV  C6  C5  single    1.479  0.020  1.479
 TJV  C6  N   single    1.324  0.020  1.324
 TJV  C5  C4  aromatic  1.411  0.020  1.411
 TJV  C2  O1  single    1.346  0.020  1.346
 TJV  C2  C3  aromatic  1.387  0.020  1.387
 TJV  C4  C3  aromatic  1.369  0.020  1.369
 TJV  O1  C7  single    1.425  0.020  1.425
 TJV  C3  O   single    1.352  0.020  1.352
 TJV  C7  O   single    1.422  0.020  1.422
 TJV  C4  H1  single    0.930  0.020  1.080
 TJV  C7  H2  single    0.970  0.020  1.090
 TJV  N   H3  single    0.860  0.020  1.020
 TJV  N   H4  single    0.860  0.020  1.020
 TJV  C   H5  single    0.930  0.020  1.080
 TJV  C1  H6  single    0.930  0.020  1.080
 TJV  C7  H8  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
 TJV  H1  C4  C3  120.55  3.000
 TJV  H1  C4  C5  122.22  3.000
 TJV  C3  C4  C5  117.19  3.000
 TJV  C   C5  C6  119.70  3.000
 TJV  C6  C5  C4  120.16  3.000
 TJV  C   C5  C4  120.13  3.000
 TJV  N   C6  S   121.48  3.000
 TJV  N   C6  C5  116.17  3.000
 TJV  S   C6  C5  122.34  3.000
 TJV  H8  C7  H2  110.54  3.000
 TJV  H8  C7  O1  109.67  3.000
 TJV  H2  C7  O1  109.71  3.000
 TJV  H8  C7  O   109.94  3.000
 TJV  H2  C7  O   109.89  3.000
 TJV  O1  C7  O   107.03  3.000
 TJV  H4  N   H3  116.99  3.000
 TJV  H4  N   C6  122.63  3.000
 TJV  H3  N   C6  120.01  3.000
 TJV  H5  C   C1  119.14  3.000
 TJV  H5  C   C5  118.94  3.000
 TJV  C1  C   C5  121.92  3.000
 TJV  C2  C3  O   109.45  3.000
 TJV  O   C3  C4  128.38  3.000
 TJV  C2  C3  C4  122.17  3.000
 TJV  C3  O   C7  106.92  3.000
 TJV  C2  O1  C7  107.01  3.000
 TJV  C1  C2  O1  128.72  3.000
 TJV  O1  C2  C3  109.59  3.000
 TJV  C1  C2  C3  121.68  3.000
 TJV  H6  C1  C2  121.90  3.000
 TJV  H6  C1  C   121.20  3.000
 TJV  C2  C1  C   116.90  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
 TJV  CONST_01  C1  C   C5  C4    0.00   0.0  0
 TJV  CONST_02  C1  C2  C3  C4    0.00   0.0  0
 TJV  CONST_03  C2  C1  C   C5    0.00   0.0  0
 TJV  CONST_04  C2  C3  C4  C5    0.00   0.0  0
 TJV  CONST_05  C3  C2  C1  C     0.00   0.0  0
 TJV  CONST_06  C3  C4  C5  C     0.00   0.0  0
 TJV  CONST_07  C1  C   C5  C6  180.00   0.0  0
 TJV  CONST_08  C3  C4  C5  C6  180.00   0.0  0
 TJV  CONST_09  H5  C   C5  C4  180.00   0.0  0
 TJV  CONST_10  H6  C1  C   C5  180.00   0.0  0
 TJV  CONST_11  H1  C4  C5  C   180.00   0.0  0
 TJV  Var_01    C1  C2  O1  C7  178.93  30.0  1
 TJV  Var_02    C2  C3  O   C7    0.05  30.0  1
 TJV  Var_03    O1  C7  O   C3   -0.33  30.0  1
 TJV  Var_04    S   C6  C5  C4  150.40  30.0  3
 TJV  Var_05    H3  N   C6  C5  178.57  30.0  2

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
 TJV  plan-1  C5  0.020
 TJV  plan-1  C6  0.020
 TJV  plan-1  S   0.020
 TJV  plan-1  N   0.020
 TJV  plan-2  C4  0.020
 TJV  plan-2  C5  0.020
 TJV  plan-2  C6  0.020
 TJV  plan-2  C   0.020
 TJV  plan-2  C3  0.020
 TJV  plan-2  O   0.020
 TJV  plan-2  O1  0.020
 TJV  plan-2  C2  0.020
 TJV  plan-2  C1  0.020
 TJV  plan-2  H1  0.020
 TJV  plan-2  H5  0.020
 TJV  plan-2  H6  0.020

