# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:43:18 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1,3-dimethyl-5-(methylamino)-6-nitro-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc2N(C)C(=O)N(C)c2cc1[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
 8SV  8SV  1,3-dimethyl-5-(methylamino)-6-nitro-1,3-dihydro-2H-benzimidazol-2-one  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SV
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
 8SV  N1   N  NH1    0  -0.668   2.5646  -1.6707   0.0463
 8SV  N3   N  NR5    0  -0.586  -2.1330   1.1987  -0.0414
 8SV  C4   C  CR56   0   0.423  -0.9152  -0.6826   0.0030
 8SV  C5   C  CR56   0   0.338  -0.8364   0.7238  -0.0225
 8SV  C6   C  CR16   0  -0.405   0.3684   1.3479  -0.0229
 8SV  C7   C  CR6    0   0.181   1.5389   0.5546   0.0020
 8SV  C8   C  CH3    0  -0.535  -2.5059   2.5888  -0.0673
 8SV  C1   C  CH3    0  -0.538   2.5092  -3.1094   0.0746
 8SV  C2   C  CR6    0   0.399   1.4826  -0.8762   0.0268
 8SV  C3   C  CR16   0  -0.483   0.1995  -1.4770   0.0276
 8SV  O1   O  O     -1  -0.419   2.7533   2.4756  -0.0274
 8SV  O2   O  O      0  -0.449   3.8229   0.6355   0.0287
 8SV  C9   C  CR5    0   0.666  -3.0101   0.1473  -0.0286
 8SV  N4   N  NR5    0  -0.590  -2.2382  -1.0069  -0.0013
 8SV  O3   O  O      0  -0.483  -4.2232   0.1964  -0.0386
 8SV  H1   H  HNH1   0   0.412   3.4652  -1.2259   0.0538
 8SV  H2   H  HCR6   0   0.304   0.4442   2.4247  -0.0412
 8SV  H3   H  HCH3   0   0.270  -3.5889   2.6666  -0.0780
 8SV  H4   H  HCH3   0   0.257  -2.1272   3.1049   0.8150
 8SV  H5   H  HCH3   0   0.257  -2.1120   3.0765  -0.9590
 8SV  H6   H  HCH3   0   0.260  -2.4487  -2.8690   0.9230
 8SV  H7   H  HCH3   0   0.274  -3.8510  -2.3037   0.0058
 8SV  H8   H  HCH3   0   0.260  -2.4262  -2.9061  -0.8511
 8SV  H9   H  HCH3   0   0.241   1.9997  -3.4854   0.9651
 8SV  H10  H  HCH3   0   0.241   2.0065  -3.5192  -0.8045
 8SV  H11  H  HCH3   0   0.271   3.5285  -3.4840   0.0854
 8SV  H12  H  HCR6   0   0.304   0.1021  -2.5522   0.0485
 8SV  N2   N  N      1   0.338   2.7668   1.2579   0.0009
 8SV  C10  C  CH3    0  -0.538  -2.7663  -2.3479   0.0204

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
 8SV  C1   N1   single    1.440  0.020  1.440
 8SV  O2   N2   double    1.226  0.020  1.226
 8SV  N1   C2   single    1.342  0.020  1.342
 8SV  N2   O1   single    1.218  0.020  1.218
 8SV  N2   C7   single    1.415  0.020  1.415
 8SV  C2   C7   aromatic  1.432  0.020  1.432
 8SV  C2   C3   aromatic  1.417  0.020  1.417
 8SV  C7   C6   aromatic  1.414  0.020  1.414
 8SV  C3   C4   aromatic  1.369  0.020  1.369
 8SV  C6   C5   aromatic  1.357  0.020  1.357
 8SV  C4   C5   aromatic  1.409  0.020  1.409
 8SV  C4   N4   single    1.362  0.020  1.362
 8SV  C5   N3   single    1.381  0.020  1.381
 8SV  N4   C10  single    1.441  0.020  1.441
 8SV  N4   C9   single    1.389  0.020  1.389
 8SV  N3   C9   single    1.369  0.020  1.369
 8SV  N3   C8   single    1.439  0.020  1.439
 8SV  C9   O3   double    1.214  0.020  1.214
 8SV  N1   H1   single    0.860  0.020  1.020
 8SV  C6   H2   single    0.930  0.020  1.080
 8SV  C8   H3   single    0.970  0.020  1.090
 8SV  C8   H4   single    0.970  0.020  1.090
 8SV  C8   H5   single    0.970  0.020  1.090
 8SV  C10  H6   single    0.970  0.020  1.090
 8SV  C10  H7   single    0.970  0.020  1.090
 8SV  C10  H8   single    0.970  0.020  1.090
 8SV  C1   H9   single    0.970  0.020  1.090
 8SV  C1   H10  single    0.970  0.020  1.090
 8SV  C1   H11  single    0.970  0.020  1.090
 8SV  C3   H12  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
 8SV  H1   N1   C2   117.43  3.000
 8SV  H1   N1   C1   118.47  3.000
 8SV  C2   N1   C1   124.09  3.000
 8SV  C9   N3   C8   125.15  3.000
 8SV  C8   N3   C5   125.14  3.000
 8SV  C9   N3   C5   109.71  3.000
 8SV  N4   C4   C3   130.75  3.000
 8SV  N4   C4   C5   106.98  3.000
 8SV  C3   C4   C5   122.28  3.000
 8SV  C6   C5   C4   120.59  3.000
 8SV  C4   C5   N3   106.92  3.000
 8SV  C6   C5   N3   132.49  3.000
 8SV  H2   C6   C7   120.11  3.000
 8SV  H2   C6   C5   121.40  3.000
 8SV  C7   C6   C5   118.48  3.000
 8SV  N2   C7   C2   122.05  3.000
 8SV  C2   C7   C6   121.88  3.000
 8SV  N2   C7   C6   116.07  3.000
 8SV  H5   C8   H4   108.95  3.000
 8SV  H5   C8   H3   108.68  3.000
 8SV  H4   C8   H3   108.69  3.000
 8SV  H5   C8   N3   110.68  3.000
 8SV  H4   C8   N3   110.65  3.000
 8SV  H3   C8   N3   109.13  3.000
 8SV  H11  C1   H10  108.09  3.000
 8SV  H11  C1   H9   108.11  3.000
 8SV  H10  C1   H9   108.19  3.000
 8SV  H11  C1   N1   107.98  3.000
 8SV  H10  C1   N1   112.13  3.000
 8SV  H9   C1   N1   112.20  3.000
 8SV  C3   C2   C7   117.34  3.000
 8SV  C3   C2   N1   118.62  3.000
 8SV  C7   C2   N1   124.04  3.000
 8SV  H12  C3   C2   120.26  3.000
 8SV  H12  C3   C4   120.31  3.000
 8SV  C2   C3   C4   119.43  3.000
 8SV  O3   C9   N4   126.10  3.000
 8SV  O3   C9   N3   127.50  3.000
 8SV  N4   C9   N3   106.40  3.000
 8SV  C9   N4   C10  124.74  3.000
 8SV  C9   N4   C4   110.00  3.000
 8SV  C10  N4   C4   125.26  3.000
 8SV  O2   N2   O1   121.17  3.000
 8SV  O1   N2   C7   119.16  3.000
 8SV  O2   N2   C7   119.68  3.000
 8SV  H8   C10  H7   108.79  3.000
 8SV  H8   C10  H6   109.07  3.000
 8SV  H7   C10  H6   108.77  3.000
 8SV  H8   C10  N4   110.50  3.000
 8SV  H7   C10  N4   109.15  3.000
 8SV  H6   C10  N4   110.53  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
 8SV  CONST_01  C7   C2   C3  C4     0.00   0.0  0
 8SV  CONST_02  C7   C6   C5  C4     0.00   0.0  0
 8SV  CONST_03  C2   C7   C6  C5     0.00   0.0  0
 8SV  CONST_04  C2   C3   C4  C5     0.00   0.0  0
 8SV  CONST_05  C3   C2   C7  C6     0.00   0.0  0
 8SV  CONST_06  C3   C4   C5  C6     0.00   0.0  0
 8SV  CONST_07  N4   C4   C5  N3     0.00   0.0  0
 8SV  CONST_08  C4   N4   C9  N3     0.00   0.0  0
 8SV  CONST_09  C9   N3   C5  C4     0.00   0.0  0
 8SV  CONST_10  C9   N4   C4  C5     0.00   0.0  0
 8SV  CONST_11  N4   C9   N3  C5     0.00   0.0  0
 8SV  CONST_12  C6   C7   C2  N1   180.00   0.0  0
 8SV  CONST_13  C4   C3   C2  N1   180.00   0.0  0
 8SV  CONST_14  N2   C7   C6  C5   180.00   0.0  0
 8SV  CONST_15  N2   C7   C2  C3   180.00   0.0  0
 8SV  CONST_16  C10  N4   C9  N3   180.00   0.0  0
 8SV  CONST_17  C8   N3   C5  C4   180.00   0.0  0
 8SV  CONST_18  O3   C9   N4  C4   180.00   0.0  0
 8SV  CONST_19  C10  N4   C4  C5   180.00   0.0  0
 8SV  CONST_20  O3   C9   N3  C5   180.00   0.0  0
 8SV  CONST_21  N4   C9   N3  C8   180.00   0.0  0
 8SV  CONST_22  H2   C6   C5  N3     0.00   0.0  0
 8SV  CONST_23  H12  C3   C4  C5   180.00   0.0  0
 8SV  CONST_24  O2   N2   C7  C6   180.00   0.0  0
 8SV  CONST_25  O1   N2   C7  C6     0.00   0.0  0
 8SV  CONST_26  C1   N1   C2  C7   180.00   0.0  0
 8SV  CONST_27  C3   C2   N1  C1     0.00   0.0  0
 8SV  CONST_28  O2   N2   C7  C2     0.00   0.0  0
 8SV  CONST_29  O1   N2   C7  C2   180.00   0.0  0
 8SV  CONST_30  O3   C9   N3  C8     0.00   0.0  0
 8SV  CONST_31  O3   C9   N4  C10    0.00   0.0  0
 8SV  CONST_32  H1   N1   C2  C7     0.00   0.0  0
 8SV  Var_01    H6   C10  N4  C4    60.69  30.0  3
 8SV  Var_02    H3   C8   N3  C5   179.99  30.0  3
 8SV  Var_03    H9   C1   N1  C2   -60.97  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
 8SV  plan-1  N1   0.020
 8SV  plan-1  N3   0.020
 8SV  plan-1  C4   0.020
 8SV  plan-1  C5   0.020
 8SV  plan-1  C6   0.020
 8SV  plan-1  C7   0.020
 8SV  plan-1  C8   0.020
 8SV  plan-1  C2   0.020
 8SV  plan-1  C3   0.020
 8SV  plan-1  C9   0.020
 8SV  plan-1  N4   0.020
 8SV  plan-1  O3   0.020
 8SV  plan-1  H2   0.020
 8SV  plan-1  H12  0.020
 8SV  plan-1  N2   0.020
 8SV  plan-1  C10  0.020
 8SV  plan-2  N1   0.020
 8SV  plan-2  C1   0.020
 8SV  plan-2  C2   0.020
 8SV  plan-2  H1   0.020
 8SV  plan-3  C7   0.020
 8SV  plan-3  O1   0.020
 8SV  plan-3  O2   0.020
 8SV  plan-3  N2   0.020

