# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:44:04 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (6~{R})-6-azanyl-3-nitro-6-oxidanyl-cyclohexa-1,3-diene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@]1(O)CC=C(C=C1C(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
 6R8  6R8  '(6~{R})-6-azanyl-3-nitro-6-oxidanyl-cyclohexa-1,3-diene-1-carboxylic acid'  ligand  21  14  .  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_6R8
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
 6R8  O14  O  OH1    0  -0.677  -1.4101   1.5334  -1.3534
 6R8  O11  O  OC    -1  -0.604  -2.8789  -0.7726  -1.1212
 6R8  C10  C  C      0   0.431  -1.9943  -1.2784  -0.3827
 6R8  O12  O  O      0  -0.566  -1.9497  -2.4459   0.0246
 6R8  C01  C  CT     0   0.282  -1.1673   1.1550  -0.0210
 6R8  C02  C  CH2    0  -0.517   0.0033   1.9974   0.5026
 6R8  C03  C  C1     0  -0.248   1.3586   1.4120   0.3724
 6R8  C04  C  C      0   0.299   1.5102   0.0917   0.2395
 6R8  C05  C  C1     0  -0.351   0.3803  -0.8122   0.1171
 6R8  C06  C  C      0  -0.067  -0.8611  -0.3360  -0.0186
 6R8  N07  N  N      1   0.329   2.8508  -0.4652   0.2021
 6R8  O08  O  O      0  -0.392   3.7990   0.2832   0.2726
 6R8  O09  O  O     -1  -0.383   2.9548  -1.6671   0.1033
 6R8  N13  N  NH2    0  -0.813  -2.3220   1.5041   0.7952
 6R8  H1   H  HOH1   0   0.439  -2.0620   0.8810  -1.6720
 6R8  H3   H  HCH2   0   0.281  -0.0289   2.9848   0.0375
 6R8  H4   H  H      0   0.304   2.2077   2.0758   0.4587
 6R8  H5   H  H      0   0.275   0.5510  -1.8789   0.0800
 6R8  H7   H  HNH2   0   0.349  -3.1303   0.9743   0.4888
 6R8  H8   H  HNH2   0   0.345  -2.1597   1.2381   1.7595
 6R8  H6   H  HCH2   0   0.282  -0.1354   2.1873   1.5746

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
 6R8  O12  C10  deloc   1.237  0.020  1.237
 6R8  N13  C01  single  1.456  0.020  1.456
 6R8  C10  O11  deloc   1.258  0.020  1.258
 6R8  C10  C06  single  1.518  0.020  1.518
 6R8  C06  C01  single  1.522  0.020  1.522
 6R8  C06  C05  double  1.337  0.020  1.337
 6R8  C01  O14  single  1.406  0.020  1.406
 6R8  C01  C02  single  1.534  0.020  1.534
 6R8  C05  C04  single  1.452  0.020  1.452
 6R8  C02  C03  single  1.482  0.020  1.482
 6R8  C04  C03  double  1.336  0.020  1.336
 6R8  C04  N07  single  1.452  0.020  1.452
 6R8  O09  N07  single  1.210  0.020  1.210
 6R8  N07  O08  double  1.210  0.020  1.210
 6R8  O14  H1   single  0.850  0.020  0.980
 6R8  C02  H3   single  0.970  0.020  1.090
 6R8  C03  H4   single  0.930  0.020  1.080
 6R8  C05  H5   single  0.930  0.020  1.080
 6R8  N13  H7   single  0.890  0.020  1.040
 6R8  N13  H8   single  0.890  0.020  1.040
 6R8  C02  H6   single  0.970  0.020  1.090

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
 6R8  H1   O14  C01  104.17  3.000
 6R8  C06  C10  O12  118.68  3.000
 6R8  C06  C10  O11  114.58  3.000
 6R8  O12  C10  O11  126.71  3.000
 6R8  N13  C01  C06  113.17  3.000
 6R8  C06  C01  C02  112.57  3.000
 6R8  N13  C01  C02  106.38  3.000
 6R8  C02  C01  O14  107.90  3.000
 6R8  C06  C01  O14  107.45  3.000
 6R8  N13  C01  O14  109.25  3.000
 6R8  H6   C02  H3   104.83  3.000
 6R8  H6   C02  C03  105.65  3.000
 6R8  H3   C02  C03  110.29  3.000
 6R8  H6   C02  C01  109.38  3.000
 6R8  H3   C02  C01  109.18  3.000
 6R8  C03  C02  C01  116.80  3.000
 6R8  H4   C03  C04  121.72  3.000
 6R8  H4   C03  C02  117.94  3.000
 6R8  C04  C03  C02  120.20  3.000
 6R8  N07  C04  C05  118.52  3.000
 6R8  N07  C04  C03  119.11  3.000
 6R8  C05  C04  C03  122.37  3.000
 6R8  H5   C05  C06  119.66  3.000
 6R8  H5   C05  C04  119.62  3.000
 6R8  C06  C05  C04  120.63  3.000
 6R8  C05  C06  C01  122.41  3.000
 6R8  C05  C06  C10  119.77  3.000
 6R8  C01  C06  C10  117.23  3.000
 6R8  O09  N07  O08  123.48  3.000
 6R8  O08  N07  C04  118.99  3.000
 6R8  O09  N07  C04  117.53  3.000
 6R8  H8   N13  H7   106.15  3.000
 6R8  H8   N13  C01  110.08  3.000
 6R8  H7   N13  C01  109.72  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
 6R8  Var_01  C04  C05  C06  C01   -1.43  30.0  1
 6R8  Var_02  C04  C03  C02  C01  -21.68  30.0  1
 6R8  Var_03  C05  C04  C03  C02    4.64  30.0  1
 6R8  Var_04  C06  C05  C04  C03    7.62  30.0  1
 6R8  Var_05  C01  C06  C10  O11   26.08  30.0  2
 6R8  Var_06  O09  N07  C04  C03  178.80  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6R8  chir_01  C01  C06  O14  C02  positiv

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
 6R8  plan-1  O11  0.020
 6R8  plan-1  C10  0.020
 6R8  plan-1  O12  0.020
 6R8  plan-1  C06  0.020
 6R8  plan-2  C04  0.020
 6R8  plan-2  N07  0.020
 6R8  plan-2  O08  0.020
 6R8  plan-2  O09  0.020

