# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:11:30 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  18  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  -0.247  -3.3044  -0.4341   0.1065
 6R7  CAB  C  C      0   0.496  -2.1823  -0.9087   0.0637
 6R7  OAC  O  OH1    0  -0.694  -1.9502  -2.2013   0.0336
 6R7  CAD  C  CR6    0  -0.157  -0.9694  -0.0746   0.0452
 6R7  CAE  C  CR16   0  -0.245   0.2997  -0.6408  -0.0016
 6R7  CAF  C  CR6    0   0.183   1.4133   0.1732  -0.0192
 6R7  NAK  N  N      1   0.343   2.7279  -0.4248  -0.0700
 6R7  OAM  O  O      0  -0.347   2.8107  -1.6314  -0.0324
 6R7  OAL  O  O     -1  -0.388   3.6837   0.3126  -0.1484
 6R7  CAG  C  CR16   0  -0.241   1.2904   1.5635   0.0109
 6R7  CAH  C  CR16   0  -0.271   0.0434   2.1319   0.0624
 6R7  CAI  C  CR6    0   0.370  -1.1064   1.3300   0.0787
 6R7  OAJ  O  OH1    0  -0.640  -2.2763   1.9374   0.1276
 6R7  H1   H  HOH1   0   0.458  -2.7821  -2.6995   0.0561
 6R7  H2   H  HCR6   0   0.296   0.4093  -1.7151  -0.0265
 6R7  H3   H  HCR6   0   0.297   2.1644   2.1982  -0.0018
 6R7  H4   H  HCR6   0   0.302  -0.0684   3.2074   0.0878
 6R7  H5   H  HOH1   0   0.487  -2.9864   1.2577   0.1349

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  double    1.219  0.020  1.219
 6R7  OAC  CAB  single    1.314  0.020  1.314
 6R7  CAB  CAD  single    1.472  0.020  1.472
 6R7  OAJ  CAI  single    1.319  0.020  1.319
 6R7  CAD  CAI  aromatic  1.412  0.020  1.412
 6R7  CAD  CAE  aromatic  1.391  0.020  1.391
 6R7  CAI  CAH  aromatic  1.402  0.020  1.402
 6R7  CAE  CAF  aromatic  1.379  0.020  1.379
 6R7  CAH  CAG  aromatic  1.371  0.020  1.371
 6R7  CAF  CAG  aromatic  1.396  0.020  1.396
 6R7  CAF  NAK  single    1.445  0.020  1.445
 6R7  OAL  NAK  single    1.210  0.020  1.210
 6R7  NAK  OAM  double    1.210  0.020  1.210
 6R7  OAC  H1   single    0.850  0.020  0.980
 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  114.31  3.000
 6R7  CAD  CAB  OAA  122.57  3.000
 6R7  OAC  CAB  OAA  123.13  3.000
 6R7  H1   OAC  CAB  110.69  3.000
 6R7  CAI  CAD  CAE  119.64  3.000
 6R7  CAE  CAD  CAB  121.45  3.000
 6R7  CAI  CAD  CAB  118.91  3.000
 6R7  H2   CAE  CAF  120.31  3.000
 6R7  H2   CAE  CAD  119.89  3.000
 6R7  CAF  CAE  CAD  119.80  3.000
 6R7  CAG  CAF  NAK  119.54  3.000
 6R7  NAK  CAF  CAE  119.38  3.000
 6R7  CAG  CAF  CAE  121.09  3.000
 6R7  OAL  NAK  OAM  123.76  3.000
 6R7  OAM  NAK  CAF  118.29  3.000
 6R7  OAL  NAK  CAF  117.95  3.000
 6R7  H3   CAG  CAH  119.52  3.000
 6R7  H3   CAG  CAF  120.91  3.000
 6R7  CAH  CAG  CAF  119.58  3.000
 6R7  H4   CAH  CAI  118.93  3.000
 6R7  H4   CAH  CAG  120.46  3.000
 6R7  CAI  CAH  CAG  120.61  3.000
 6R7  OAJ  CAI  CAH  117.67  3.000
 6R7  CAH  CAI  CAD  119.29  3.000
 6R7  OAJ  CAI  CAD  123.04  3.000
 6R7  H5   OAJ  CAI  108.81  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  CONST_20  H1   OAC  CAB  CAD  180.00   0.0  0
 6R7  Var_01    CAI  CAD  CAB  OAA    0.03  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
 6R7  plan-3  H1   0.020

