# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:09:31 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 5-nitro-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]cnc2c1
#
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
 2ZM  2ZM  '5-nitro-1H-benzimidazole '  ligand  17  12  .  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_2ZM
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
 2ZM  O1   O  O     -1  -0.386   2.8537   1.3584  -0.0475
 2ZM  N2   N  N      1   0.329   2.5122   0.1976  -0.0199
 2ZM  O3   O  O      0  -0.386   3.2932  -0.7267   0.0010
 2ZM  C4   C  CR6    0   0.242   1.0931  -0.1003  -0.0117
 2ZM  C5   C  CR16   0  -0.294   0.6891  -1.4443   0.0285
 2ZM  C6   C  CR16   0  -0.288  -0.6497  -1.7690   0.0383
 2ZM  C7   C  CR56   0   0.370  -1.5575  -0.7146   0.0067
 2ZM  N8   N  NR15   0  -0.658  -2.9160  -0.6608   0.0053
 2ZM  C9   C  CR15   0   0.118  -3.2661   0.6506  -0.0349
 2ZM  N10  N  N      0  -0.450  -2.2477   1.4589  -0.0595
 2ZM  C11  C  CR56   0   0.147  -1.1501   0.6329  -0.0343
 2ZM  C12  C  CR16   0  -0.351   0.1985   0.9562  -0.0437
 2ZM  H1   H  HCR6   0   0.296   1.4239  -2.2346   0.0524
 2ZM  H2   H  HCR6   0   0.287  -0.9693  -2.8014   0.0702
 2ZM  H3   H  HNR5   0   0.432  -3.5550  -1.4403   0.0297
 2ZM  H4   H  HCR5   0   0.297  -4.3029   0.9513  -0.0438
 2ZM  H6   H  HCR6   0   0.297   0.5206   1.9871  -0.0753

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
 2ZM  C9   N8   aromatic  1.358  0.020  1.358
 2ZM  C9   N10  aromatic  1.300  0.020  1.300
 2ZM  N8   C7   aromatic  1.360  0.020  1.360
 2ZM  N10  C11  aromatic  1.374  0.020  1.374
 2ZM  C7   C11  aromatic  1.408  0.020  1.408
 2ZM  C7   C6   aromatic  1.392  0.020  1.392
 2ZM  C11  C12  aromatic  1.387  0.020  1.387
 2ZM  C6   C5   aromatic  1.378  0.020  1.378
 2ZM  C12  C4   aromatic  1.385  0.020  1.385
 2ZM  C5   C4   aromatic  1.404  0.020  1.404
 2ZM  C4   N2   single    1.450  0.020  1.450
 2ZM  N2   O3   double    1.210  0.020  1.210
 2ZM  N2   O1   single    1.210  0.020  1.210
 2ZM  C5   H1   single    0.930  0.020  1.080
 2ZM  C6   H2   single    0.930  0.020  1.080
 2ZM  N8   H3   single    0.860  0.020  1.020
 2ZM  C9   H4   single    0.930  0.020  1.080
 2ZM  C12  H6   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
 2ZM  C4   N2   O3   118.33  3.000
 2ZM  O3   N2   O1   123.42  3.000
 2ZM  C4   N2   O1   118.25  3.000
 2ZM  C12  C4   C5   123.03  3.000
 2ZM  C5   C4   N2   118.58  3.000
 2ZM  C12  C4   N2   118.39  3.000
 2ZM  H1   C5   C6   119.26  3.000
 2ZM  H1   C5   C4   120.37  3.000
 2ZM  C6   C5   C4   120.36  3.000
 2ZM  H2   C6   C7   122.10  3.000
 2ZM  H2   C6   C5   120.83  3.000
 2ZM  C7   C6   C5   117.07  3.000
 2ZM  C11  C7   N8   104.54  3.000
 2ZM  C11  C7   C6   122.48  3.000
 2ZM  N8   C7   C6   132.98  3.000
 2ZM  H3   N8   C9   125.72  3.000
 2ZM  H3   N8   C7   127.07  3.000
 2ZM  C9   N8   C7   107.21  3.000
 2ZM  H4   C9   N10  125.37  3.000
 2ZM  H4   C9   N8   121.12  3.000
 2ZM  N10  C9   N8   113.51  3.000
 2ZM  C11  N10  C9   104.57  3.000
 2ZM  C12  C11  N10  129.54  3.000
 2ZM  C12  C11  C7   120.30  3.000
 2ZM  N10  C11  C7   110.16  3.000
 2ZM  H6   C12  C11  120.83  3.000
 2ZM  H6   C12  C4   122.41  3.000
 2ZM  C11  C12  C4   116.76  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
 2ZM  CONST_01  N10  C11  C12  C4  180.00  0.0  0
 2ZM  CONST_02  C7   C11  C12  C4    0.00  0.0  0
 2ZM  CONST_03  C7   C6   C5   C4    0.00  0.0  0
 2ZM  CONST_04  N8   C7   C6   C5  180.00  0.0  0
 2ZM  CONST_05  C11  C7   C6   C5    0.00  0.0  0
 2ZM  CONST_06  C11  C12  C4   C5    0.00  0.0  0
 2ZM  CONST_07  C9   N8   C7   C6  180.00  0.0  0
 2ZM  CONST_08  N10  C11  C7   C6  180.00  0.0  0
 2ZM  CONST_09  C12  C11  C7   C6    0.00  0.0  0
 2ZM  CONST_10  C12  C4   C5   C6    0.00  0.0  0
 2ZM  CONST_11  N10  C9   N8   C7    0.00  0.0  0
 2ZM  CONST_12  C9   N10  C11  C7    0.00  0.0  0
 2ZM  CONST_13  C11  N10  C9   N8    0.00  0.0  0
 2ZM  CONST_14  N10  C11  C7   N8    0.00  0.0  0
 2ZM  CONST_15  C12  C11  C7   N8  180.00  0.0  0
 2ZM  CONST_16  C11  C7   N8   C9    0.00  0.0  0
 2ZM  CONST_17  C12  C11  N10  C9  180.00  0.0  0
 2ZM  CONST_18  C11  C12  C4   N2  180.00  0.0  0
 2ZM  CONST_19  C6   C5   C4   N2  180.00  0.0  0
 2ZM  CONST_20  H2   C6   C5   C4  180.00  0.0  0
 2ZM  CONST_21  H6   C12  C4   C5  180.00  0.0  0
 2ZM  CONST_22  H3   N8   C7   C6    0.00  0.0  0
 2ZM  CONST_23  H4   C9   N8   C7  180.00  0.0  0
 2ZM  CONST_24  H1   C5   C6   C7  180.00  0.0  0
 2ZM  CONST_25  C12  C4   N2   O1    0.00  0.0  0
 2ZM  CONST_26  C5   C4   N2   O1  180.00  0.0  0
 2ZM  CONST_27  C12  C4   N2   O3  180.00  0.0  0
 2ZM  CONST_28  C5   C4   N2   O3    0.00  0.0  0

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
 2ZM  plan-1  N2   0.020
 2ZM  plan-1  C4   0.020
 2ZM  plan-1  C5   0.020
 2ZM  plan-1  C6   0.020
 2ZM  plan-1  C7   0.020
 2ZM  plan-1  N8   0.020
 2ZM  plan-1  C9   0.020
 2ZM  plan-1  N10  0.020
 2ZM  plan-1  C11  0.020
 2ZM  plan-1  C12  0.020
 2ZM  plan-1  H1   0.020
 2ZM  plan-1  H2   0.020
 2ZM  plan-1  H3   0.020
 2ZM  plan-1  H4   0.020
 2ZM  plan-1  H6   0.020
 2ZM  plan-2  O1   0.020
 2ZM  plan-2  N2   0.020
 2ZM  plan-2  O3   0.020
 2ZM  plan-2  C4   0.020

