# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:26:57 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (4-nitrophenyl)methyl carbamimidothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)SCc1ccc(cc1)[N+]([O-])=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
 8SJ  8SJ  '(4-nitrophenyl)methyl carbamimidothioate'  ligand  23  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8SJ
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
 8SJ  N1  N  N      1   0.331   4.0011  -0.0136  -0.3689
 8SJ  N3  N  N      0  -0.642  -4.3920   0.0001   1.2291
 8SJ  C4  C  CR16   0  -0.251   1.9109  -1.1956   0.1257
 8SJ  C5  C  CR6    0   0.241   2.5920   0.0060  -0.0085
 8SJ  C6  C  CR16   0  -0.250   1.9628   1.2258   0.1916
 8SJ  C7  C  CR16   0  -0.280   0.6205   1.2342   0.5284
 8SJ  C8  C  C      0   0.284  -4.1330  -0.0765  -0.0112
 8SJ  C2  C  CR6    0   0.110  -0.0878   0.0447   0.6709
 8SJ  C3  C  CR16   0  -0.273   0.5705  -1.1656   0.4643
 8SJ  O1  O  O     -1  -0.378   4.5322  -1.0876  -0.5284
 8SJ  O2  O  O      0  -0.378   4.5712   1.0447  -0.4930
 8SJ  S1  S  S2     0   0.016  -2.4456  -0.0915  -0.5682
 8SJ  N2  N  NH2    0  -0.806  -5.0012  -0.2138  -1.0520
 8SJ  H1  H  H      0   0.335  -5.3948   0.0018   1.3968
 8SJ  H2  H  HCR6   0   0.299   2.4059  -2.1429  -0.0301
 8SJ  H3  H  HCR6   0   0.300   2.4981   2.1581   0.0879
 8SJ  H4  H  HCR6   0   0.277   0.1213   2.1813   0.6874
 8SJ  H5  H  HCH2   0   0.302  -1.8212  -0.7685   1.6525
 8SJ  H6  H  HCH2   0   0.300  -1.8369   0.9929   1.4919
 8SJ  H7  H  HCR6   0   0.277   0.0314  -2.0981   0.5718
 8SJ  H8  H  HNH2   0   0.399  -5.9705  -0.0038  -0.8716
 8SJ  H9  H  HNH2   0   0.400  -4.6990   0.0339  -1.9805
 8SJ  C1  C  CH2    0  -0.611  -1.5482   0.0633   1.0051

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
 8SJ  C1  C2  single    1.498  0.020  1.498
 8SJ  C1  S1  single    1.818  0.020  1.818
 8SJ  C2  C7  aromatic  1.392  0.020  1.392
 8SJ  C2  C3  aromatic  1.393  0.020  1.393
 8SJ  C7  C6  aromatic  1.384  0.020  1.384
 8SJ  C3  C4  aromatic  1.383  0.020  1.383
 8SJ  S1  C8  single    1.777  0.020  1.777
 8SJ  C6  C5  aromatic  1.387  0.020  1.387
 8SJ  C4  C5  aromatic  1.388  0.020  1.388
 8SJ  C5  N1  single    1.455  0.020  1.455
 8SJ  N1  O1  single    1.209  0.020  1.209
 8SJ  N1  O2  double    1.208  0.020  1.208
 8SJ  C8  N3  double    1.269  0.020  1.269
 8SJ  C8  N2  single    1.362  0.020  1.362
 8SJ  N3  H1  single    0.890  0.020  1.040
 8SJ  C4  H2  single    0.930  0.020  1.080
 8SJ  C6  H3  single    0.930  0.020  1.080
 8SJ  C7  H4  single    0.930  0.020  1.080
 8SJ  C1  H5  single    0.970  0.020  1.090
 8SJ  C1  H6  single    0.970  0.020  1.090
 8SJ  C3  H7  single    0.930  0.020  1.080
 8SJ  N2  H8  single    0.890  0.020  1.040
 8SJ  N2  H9  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
 8SJ  O2  N1  O1  123.87  3.000
 8SJ  O2  N1  C5  118.08  3.000
 8SJ  O1  N1  C5  118.05  3.000
 8SJ  H1  N3  C8  111.25  3.000
 8SJ  H2  C4  C3  119.91  3.000
 8SJ  H2  C4  C5  121.37  3.000
 8SJ  C3  C4  C5  118.72  3.000
 8SJ  C6  C5  C4  121.66  3.000
 8SJ  C4  C5  N1  119.19  3.000
 8SJ  C6  C5  N1  119.15  3.000
 8SJ  H3  C6  C7  119.92  3.000
 8SJ  H3  C6  C5  121.36  3.000
 8SJ  C7  C6  C5  118.71  3.000
 8SJ  H4  C7  C2  119.87  3.000
 8SJ  H4  C7  C6  119.24  3.000
 8SJ  C2  C7  C6  120.89  3.000
 8SJ  N2  C8  S1  111.40  3.000
 8SJ  N2  C8  N3  128.50  3.000
 8SJ  S1  C8  N3  120.03  3.000
 8SJ  C3  C2  C1  120.30  3.000
 8SJ  C3  C2  C7  119.13  3.000
 8SJ  C1  C2  C7  120.56  3.000
 8SJ  H7  C3  C2  119.89  3.000
 8SJ  H7  C3  C4  119.23  3.000
 8SJ  C2  C3  C4  120.88  3.000
 8SJ  C1  S1  C8  101.35  3.000
 8SJ  H9  N2  H8  113.72  3.000
 8SJ  H9  N2  C8  119.22  3.000
 8SJ  H8  N2  C8  117.07  3.000
 8SJ  H6  C1  H5  108.67  3.000
 8SJ  H6  C1  S1  109.20  3.000
 8SJ  H5  C1  S1  109.01  3.000
 8SJ  H6  C1  C2  111.64  3.000
 8SJ  H5  C1  C2  111.56  3.000
 8SJ  S1  C1  C2  106.68  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
 8SJ  CONST_01  C7  C2  C3  C4     0.00   0.0  0
 8SJ  CONST_02  C7  C6  C5  C4     0.00   0.0  0
 8SJ  CONST_03  C2  C7  C6  C5     0.00   0.0  0
 8SJ  CONST_04  C2  C3  C4  C5     0.00   0.0  0
 8SJ  CONST_05  C3  C2  C7  C6     0.00   0.0  0
 8SJ  CONST_06  C3  C4  C5  C6     0.00   0.0  0
 8SJ  CONST_07  C7  C6  C5  N1   180.00   0.0  0
 8SJ  CONST_08  C3  C4  C5  N1   180.00   0.0  0
 8SJ  CONST_09  C1  C2  C3  C4   180.00   0.0  0
 8SJ  CONST_10  C1  C2  C7  C6   180.00   0.0  0
 8SJ  CONST_11  H3  C6  C5  C4   180.00   0.0  0
 8SJ  CONST_12  H4  C7  C6  C5   180.00   0.0  0
 8SJ  CONST_13  H7  C3  C4  C5   180.00   0.0  0
 8SJ  CONST_14  H2  C4  C5  C6   180.00   0.0  0
 8SJ  CONST_15  O1  N1  C5  C4     0.00   0.0  0
 8SJ  CONST_16  O2  N1  C5  C4   180.00   0.0  0
 8SJ  CONST_17  O1  N1  C5  C6   180.00   0.0  0
 8SJ  CONST_18  O2  N1  C5  C6     0.00   0.0  0
 8SJ  CONST_21  H1  N3  C8  S1   180.00   0.0  0
 8SJ  Var_01    S1  C1  C2  C7    96.22  30.0  2
 8SJ  Var_02    C2  C1  S1  C8   179.27  30.0  1
 8SJ  Var_03    N2  C8  S1  C1  -178.67  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
 8SJ  plan-1  N1  0.020
 8SJ  plan-1  C4  0.020
 8SJ  plan-1  C5  0.020
 8SJ  plan-1  C6  0.020
 8SJ  plan-1  C7  0.020
 8SJ  plan-1  C2  0.020
 8SJ  plan-1  C3  0.020
 8SJ  plan-1  H2  0.020
 8SJ  plan-1  H3  0.020
 8SJ  plan-1  H4  0.020
 8SJ  plan-1  H7  0.020
 8SJ  plan-1  C1  0.020
 8SJ  plan-2  N1  0.020
 8SJ  plan-2  C5  0.020
 8SJ  plan-2  O1  0.020
 8SJ  plan-2  O2  0.020
 8SJ  plan-3  N3  0.020
 8SJ  plan-3  C8  0.020
 8SJ  plan-3  S1  0.020
 8SJ  plan-3  N2  0.020
 8SJ  plan-3  H1  0.020
 8SJ  plan-3  H8  0.020
 8SJ  plan-3  H9  0.020

