# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:59:12 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]sulfuric diamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(n1CCN[S](N)(=O)=O)[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
 2VQ  2VQ  'N-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]sulfuric diamide'  ligand  27  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 OK
;

data_comp_2VQ
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
 2VQ  S1   S  S      0   1.489  -3.2523   0.1493   0.1031
 2VQ  O1   O  OS     0  -0.661  -4.3487  -0.1921   0.9915
 2VQ  O2   O  OS     0  -0.667  -2.9411   1.5451  -0.1336
 2VQ  N5   N  NC1    0  -0.748  -1.9314  -0.5861   0.7340
 2VQ  C1   C  CH2    0  -0.280  -0.6740  -0.5596   0.0058
 2VQ  C2   C  CH2    0  -0.339   0.4645  -0.5336   1.0190
 2VQ  N3   N  N      0  -0.445   3.5915  -1.5357  -0.4663
 2VQ  C3   C  CR5    0   0.408   2.5377   0.3925  -0.1836
 2VQ  C4   C  CR15   0  -0.132   3.6627  -0.2122  -0.6830
 2VQ  C5   C  CR5    0   0.481   2.4473  -1.7502   0.1602
 2VQ  C6   C  CH3    0  -0.767   1.9672  -3.0831   0.5985
 2VQ  N2   N  NR5    0  -0.490   1.7617  -0.6064   0.3641
 2VQ  O4   O  O     -1  -0.395   1.1369   2.1328   0.1774
 2VQ  O5   O  O      0  -0.399   3.0627   2.5043  -0.6843
 2VQ  N1   N  NC2    0  -0.889  -3.4062  -0.5253  -1.3982
 2VQ  H1   H  HNC1   0   0.420  -2.1539  -1.4739   1.1701
 2VQ  H2   H  HCH2   0   0.260  -0.5785  -1.4210  -0.6602
 2VQ  H3   H  HCH2   0   0.273  -0.6347   0.3353  -0.6124
 2VQ  H4   H  HCH2   0   0.300   0.4120   0.3567   1.6373
 2VQ  H5   H  HCH2   0   0.291   0.3951  -1.3909   1.6868
 2VQ  H6   H  HCR5   0   0.299   4.4970   0.2517  -1.1849
 2VQ  H7   H  HCH3   0   0.277   1.8725  -3.1410   1.6841
 2VQ  H8   H  HCH3   0   0.270   0.9961  -3.3278   0.1671
 2VQ  H9   H  HCH3   0   0.285   2.6811  -3.8375   0.2788
 2VQ  H10  H  HNC2   0   0.418  -4.0022   0.0288  -2.0048
 2VQ  H11  H  HNC2   0   0.412  -3.7342  -1.4849  -1.3657
 2VQ  N4   N  N      1   0.328   2.2199   1.7608  -0.2275

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
 2VQ  O5  N4   double    1.213  0.020  1.213
 2VQ  O4  N4   single    1.215  0.020  1.215
 2VQ  N4  C3   single    1.405  0.020  1.405
 2VQ  C3  N2   aromatic  1.378  0.020  1.378
 2VQ  C3  C4   aromatic  1.371  0.020  1.371
 2VQ  C2  N2   single    1.455  0.020  1.455
 2VQ  C2  C1   single    1.524  0.020  1.524
 2VQ  N2  C5   aromatic  1.349  0.020  1.349
 2VQ  C4  N3   aromatic  1.343  0.020  1.343
 2VQ  C1  N5   single    1.453  0.020  1.453
 2VQ  C5  N3   aromatic  1.322  0.020  1.322
 2VQ  C5  C6   single    1.483  0.020  1.483
 2VQ  N5  S1   single    1.638  0.020  1.638
 2VQ  O2  S1   double    1.450  0.020  1.450
 2VQ  N1  S1   single    1.653  0.020  1.653
 2VQ  S1  O1   double    1.452  0.020  1.452
 2VQ  N5  H1   single    0.890  0.020  1.040
 2VQ  C1  H2   single    0.970  0.020  1.090
 2VQ  C1  H3   single    0.970  0.020  1.090
 2VQ  C2  H4   single    0.970  0.020  1.090
 2VQ  C2  H5   single    0.970  0.020  1.090
 2VQ  C4  H6   single    0.930  0.020  1.080
 2VQ  C6  H7   single    0.970  0.020  1.090
 2VQ  C6  H8   single    0.970  0.020  1.090
 2VQ  C6  H9   single    0.970  0.020  1.090
 2VQ  N1  H10  single    0.890  0.020  1.040
 2VQ  N1  H11  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
 2VQ  N1   S1  N5   103.99  3.000
 2VQ  N1   S1  O2   105.35  3.000
 2VQ  N5   S1  O2   108.79  3.000
 2VQ  N1   S1  O1   112.92  3.000
 2VQ  O2   S1  O1   119.24  3.000
 2VQ  N5   S1  O1   105.53  3.000
 2VQ  H1   N5  C1   114.92  3.000
 2VQ  H1   N5  S1   112.44  3.000
 2VQ  C1   N5  S1   119.77  3.000
 2VQ  H3   C1  H2   107.38  3.000
 2VQ  H3   C1  C2   109.68  3.000
 2VQ  H2   C1  C2   110.68  3.000
 2VQ  H3   C1  N5   109.32  3.000
 2VQ  H2   C1  N5   111.50  3.000
 2VQ  C2   C1  N5   108.27  3.000
 2VQ  H5   C2  H4   107.06  3.000
 2VQ  H5   C2  N2   107.07  3.000
 2VQ  H4   C2  N2   109.92  3.000
 2VQ  H5   C2  C1   110.28  3.000
 2VQ  H4   C2  C1   110.89  3.000
 2VQ  N2   C2  C1   111.46  3.000
 2VQ  C5   N3  C4   106.39  3.000
 2VQ  N2   C3  C4   106.68  3.000
 2VQ  C4   C3  N4   127.12  3.000
 2VQ  N2   C3  N4   126.20  3.000
 2VQ  H6   C4  C3   127.90  3.000
 2VQ  H6   C4  N3   122.69  3.000
 2VQ  C3   C4  N3   109.41  3.000
 2VQ  N2   C5  C6   123.56  3.000
 2VQ  C6   C5  N3   124.48  3.000
 2VQ  N2   C5  N3   111.96  3.000
 2VQ  H9   C6  H8   108.23  3.000
 2VQ  H9   C6  H7   108.23  3.000
 2VQ  H8   C6  H7   107.72  3.000
 2VQ  H9   C6  C5   108.93  3.000
 2VQ  H8   C6  C5   111.91  3.000
 2VQ  H7   C6  C5   111.71  3.000
 2VQ  C5   N2  C3   105.56  3.000
 2VQ  C5   N2  C2   124.30  3.000
 2VQ  C3   N2  C2   130.13  3.000
 2VQ  H11  N1  H10  110.22  3.000
 2VQ  H11  N1  S1   112.77  3.000
 2VQ  H10  N1  S1   112.01  3.000
 2VQ  O5   N4  O4   123.87  3.000
 2VQ  O4   N4  C3   119.30  3.000
 2VQ  O5   N4  C3   116.83  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
 2VQ  CONST_01  N2   C3  C4  N3    0.00   0.0  0
 2VQ  CONST_02  C3   N2  C5  N3    0.00   0.0  0
 2VQ  CONST_03  C5   N3  C4  C3    0.00   0.0  0
 2VQ  CONST_04  C5   N2  C3  C4    0.00   0.0  0
 2VQ  CONST_05  N2   C5  N3  C4    0.00   0.0  0
 2VQ  CONST_06  C4   C3  N2  C2  180.00   0.0  0
 2VQ  CONST_07  N3   C5  N2  C2  180.00   0.0  0
 2VQ  CONST_08  N4   C3  C4  N3  180.00   0.0  0
 2VQ  CONST_09  C5   N2  C3  N4  180.00   0.0  0
 2VQ  CONST_10  C6   C5  N2  C3  180.00   0.0  0
 2VQ  CONST_11  C6   C5  N3  C4  180.00   0.0  0
 2VQ  CONST_12  H6   C4  N3  C5  180.00   0.0  0
 2VQ  CONST_13  O5   N4  C3  C4    0.00   0.0  0
 2VQ  CONST_14  O4   N4  C3  C4  180.00   0.0  0
 2VQ  CONST_15  O5   N4  C3  N2  180.00   0.0  0
 2VQ  CONST_16  O4   N4  C3  N2    0.00   0.0  0
 2VQ  Var_01    C3   N2  C2  C1   84.60  30.0  2
 2VQ  Var_02    H7   C6  C5  N3  116.84  30.0  2
 2VQ  Var_03    N2   C2  C1  N5  175.76  30.0  1
 2VQ  Var_04    C2   C1  N5  S1  147.47  30.0  1
 2VQ  Var_05    C1   N5  S1  O1  173.73  30.0  2
 2VQ  Var_06    H10  N1  S1  O1   83.60  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
 2VQ  plan-1  C2  0.020
 2VQ  plan-1  N3  0.020
 2VQ  plan-1  C3  0.020
 2VQ  plan-1  C4  0.020
 2VQ  plan-1  C5  0.020
 2VQ  plan-1  C6  0.020
 2VQ  plan-1  N2  0.020
 2VQ  plan-1  H6  0.020
 2VQ  plan-1  N4  0.020
 2VQ  plan-2  C3  0.020
 2VQ  plan-2  O4  0.020
 2VQ  plan-2  O5  0.020
 2VQ  plan-2  N4  0.020

