# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:56:59 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-nitro-2-oxidanyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(ccc1O)[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
 6R7  6R7  '5-nitro-2-oxidanyl-benzoic acid'  ligand  17  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6R7
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
 6R7  OAA  O  O      0  -0.631  -3.3125  -0.3113   0.1055
 6R7  CAB  C  C      0   0.519  -2.2077  -0.9464   0.0593
 6R7  OAC  O  OC    -1  -0.532  -2.0881  -2.1688   0.0270
 6R7  CAD  C  CR6    0  -0.283  -0.9791  -0.0741   0.0469
 6R7  CAE  C  CR16   0  -0.309   0.2837  -0.6293   0.0049
 6R7  CAF  C  CR6    0   0.235   1.4051   0.1894  -0.0039
 6R7  NAK  N  N      1   0.322   2.7155  -0.3981  -0.0467
 6R7  OAM  O  O      0  -0.401   2.8081  -1.6075  -0.0723
 6R7  OAL  O  O     -1  -0.401   3.6784   0.3400  -0.0554
 6R7  CAG  C  CR16   0  -0.257   1.2742   1.5798   0.0289
 6R7  CAH  C  CR16   0  -0.355   0.0231   2.1450   0.0714
 6R7  CAI  C  CR6    0   0.400  -1.1250   1.3337   0.0823
 6R7  OAJ  O  OH1    0  -0.628  -2.3173   1.8746   0.1250
 6R7  H2   H  HCR6   0   0.287   0.3792  -1.7059  -0.0196
 6R7  H3   H  HCR6   0   0.292   2.1446   2.2198   0.0220
 6R7  H4   H  HCR6   0   0.273  -0.0862   3.2214   0.0970
 6R7  H5   H  HOH1   0   0.470  -2.9605   1.0323   0.1251

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
 6R7  OAA  CAB  deloc     1.275  0.020  1.275
 6R7  OAC  CAB  deloc     1.229  0.020  1.229
 6R7  CAB  CAD  single    1.507  0.020  1.507
 6R7  OAJ  CAI  single    1.310  0.020  1.310
 6R7  CAD  CAI  aromatic  1.416  0.020  1.416
 6R7  CAD  CAE  aromatic  1.380  0.020  1.380
 6R7  CAI  CAH  aromatic  1.406  0.020  1.406
 6R7  CAE  CAF  aromatic  1.388  0.020  1.388
 6R7  CAH  CAG  aromatic  1.373  0.020  1.373
 6R7  CAF  CAG  aromatic  1.397  0.020  1.397
 6R7  CAF  NAK  single    1.437  0.020  1.437
 6R7  OAL  NAK  single    1.213  0.020  1.213
 6R7  NAK  OAM  double    1.213  0.020  1.213
 6R7  CAE  H2   single    0.930  0.020  1.080
 6R7  CAG  H3   single    0.930  0.020  1.080
 6R7  CAH  H4   single    0.930  0.020  1.080
 6R7  OAJ  H5   single    0.850  0.020  0.980

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
 6R7  CAD  CAB  OAC  119.76  3.000
 6R7  CAD  CAB  OAA  114.74  3.000
 6R7  OAC  CAB  OAA  125.50  3.000
 6R7  CAI  CAD  CAE  119.68  3.000
 6R7  CAE  CAD  CAB  120.89  3.000
 6R7  CAI  CAD  CAB  119.43  3.000
 6R7  H2   CAE  CAF  121.05  3.000
 6R7  H2   CAE  CAD  118.82  3.000
 6R7  CAF  CAE  CAD  120.13  3.000
 6R7  CAG  CAF  NAK  119.55  3.000
 6R7  NAK  CAF  CAE  119.72  3.000
 6R7  CAG  CAF  CAE  120.73  3.000
 6R7  OAL  NAK  OAM  123.07  3.000
 6R7  OAM  NAK  CAF  118.55  3.000
 6R7  OAL  NAK  CAF  118.38  3.000
 6R7  H3   CAG  CAH  119.36  3.000
 6R7  H3   CAG  CAF  120.93  3.000
 6R7  CAH  CAG  CAF  119.71  3.000
 6R7  H4   CAH  CAI  119.43  3.000
 6R7  H4   CAH  CAG  120.13  3.000
 6R7  CAI  CAH  CAG  120.44  3.000
 6R7  OAJ  CAI  CAH  120.35  3.000
 6R7  CAH  CAI  CAD  119.31  3.000
 6R7  OAJ  CAI  CAD  120.35  3.000
 6R7  H5   OAJ  CAI  102.95  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
 6R7  CONST_01  CAG  CAH  CAI  CAD    0.00   0.0  0
 6R7  CONST_02  CAG  CAF  CAE  CAD    0.00   0.0  0
 6R7  CONST_03  CAH  CAI  CAD  CAE    0.00   0.0  0
 6R7  CONST_04  CAH  CAG  CAF  CAE    0.00   0.0  0
 6R7  CONST_05  CAI  CAD  CAE  CAF    0.00   0.0  0
 6R7  CONST_06  CAI  CAH  CAG  CAF    0.00   0.0  0
 6R7  CONST_07  CAH  CAI  CAD  CAB  180.00   0.0  0
 6R7  CONST_08  CAF  CAE  CAD  CAB  180.00   0.0  0
 6R7  CONST_09  NAK  CAF  CAE  CAD  180.00   0.0  0
 6R7  CONST_10  OAJ  CAI  CAD  CAE  180.00   0.0  0
 6R7  CONST_11  CAH  CAG  CAF  NAK  180.00   0.0  0
 6R7  CONST_12  OAJ  CAI  CAH  CAG  180.00   0.0  0
 6R7  CONST_13  H4   CAH  CAI  CAD  180.00   0.0  0
 6R7  CONST_14  H3   CAG  CAF  CAE  180.00   0.0  0
 6R7  CONST_15  H2   CAE  CAF  CAG  180.00   0.0  0
 6R7  CONST_16  OAL  NAK  CAF  CAE  180.00   0.0  0
 6R7  CONST_17  OAM  NAK  CAF  CAE    0.00   0.0  0
 6R7  CONST_18  CAG  CAF  NAK  OAM  180.00   0.0  0
 6R7  CONST_19  CAG  CAF  NAK  OAL    0.00   0.0  0
 6R7  Var_01    CAI  CAD  CAB  OAA   -0.16  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
 6R7  plan-1  CAB  0.020
 6R7  plan-1  CAD  0.020
 6R7  plan-1  CAE  0.020
 6R7  plan-1  CAF  0.020
 6R7  plan-1  NAK  0.020
 6R7  plan-1  CAG  0.020
 6R7  plan-1  CAH  0.020
 6R7  plan-1  CAI  0.020
 6R7  plan-1  OAJ  0.020
 6R7  plan-1  H2   0.020
 6R7  plan-1  H3   0.020
 6R7  plan-1  H4   0.020
 6R7  plan-2  CAF  0.020
 6R7  plan-2  NAK  0.020
 6R7  plan-2  OAM  0.020
 6R7  plan-2  OAL  0.020
 6R7  plan-3  OAA  0.020
 6R7  plan-3  CAB  0.020
 6R7  plan-3  OAC  0.020
 6R7  plan-3  CAD  0.020

