# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:24:54 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  22  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  -0.646  -1.2183   1.5346  -1.3646
 6R8  O11  O  OH1    0  -0.603  -3.0185  -0.8785  -0.7350
 6R8  C10  C  C      0   0.529  -1.9829  -1.3472  -0.0460
 6R8  O12  O  O      0  -0.429  -1.9275  -2.4739   0.3799
 6R8  C01  C  CT     0   0.281  -1.1851   1.1645  -0.0095
 6R8  C02  C  CH2    0  -0.515  -0.0303   1.9496   0.6180
 6R8  C03  C  C1     0  -0.229   1.3245   1.4002   0.3828
 6R8  C04  C  C      0   0.309   1.4799   0.0869   0.1974
 6R8  C05  C  C1     0  -0.290   0.3478  -0.8149   0.1720
 6R8  C06  C  C      0  -0.049  -0.9017  -0.3390   0.0888
 6R8  N07  N  N      1   0.331   2.8109  -0.4686   0.0369
 6R8  O08  O  O      0  -0.382   3.7577   0.2812   0.0642
 6R8  O09  O  O     -1  -0.377   2.9007  -1.6647  -0.1181
 6R8  N13  N  NH2    0  -0.810  -2.3863   1.6137   0.6614
 6R8  H1   H  HOH1   0   0.452  -1.9067   1.0365  -1.8206
 6R8  H2   H  HOH1   0   0.494  -3.7053  -1.5568  -0.8265
 6R8  H3   H  HCH2   0   0.296  -0.0875   2.9868   0.2855
 6R8  H4   H  H      0   0.319   2.1701   2.0724   0.4329
 6R8  H5   H  H      0   0.302   0.5207  -1.8820   0.1931
 6R8  H7   H  HNH2   0   0.362  -3.2145   1.1639   0.2932
 6R8  H8   H  HNH2   0   0.357  -2.3483   1.3896   1.6481
 6R8  H6   H  HCH2   0   0.297  -0.1588   1.9812   1.7078

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  double  1.206  0.020  1.206
 6R8  N13  C01  single  1.447  0.020  1.447
 6R8  C10  O11  single  1.329  0.020  1.329
 6R8  C10  C06  single  1.484  0.020  1.484
 6R8  C06  C01  single  1.533  0.020  1.533
 6R8  C06  C05  double  1.340  0.020  1.340
 6R8  C01  O14  single  1.405  0.020  1.405
 6R8  C01  C02  single  1.531  0.020  1.531
 6R8  C05  C04  single  1.448  0.020  1.448
 6R8  C02  C03  single  1.481  0.020  1.481
 6R8  C04  C03  double  1.335  0.020  1.335
 6R8  C04  N07  single  1.451  0.020  1.451
 6R8  O09  N07  single  1.209  0.020  1.209
 6R8  N07  O08  double  1.208  0.020  1.208
 6R8  O14  H1   single  0.850  0.020  0.980
 6R8  O11  H2   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  109.68  3.000
 6R8  H2   O11  C10  110.74  3.000
 6R8  C06  C10  O12  124.69  3.000
 6R8  C06  C10  O11  112.03  3.000
 6R8  O12  C10  O11  123.25  3.000
 6R8  N13  C01  C06  115.35  3.000
 6R8  C06  C01  C02  109.70  3.000
 6R8  N13  C01  C02  106.08  3.000
 6R8  C02  C01  O14  106.14  3.000
 6R8  C06  C01  O14  108.93  3.000
 6R8  N13  C01  O14  110.23  3.000
 6R8  H6   C02  H3   105.61  3.000
 6R8  H6   C02  C03  106.00  3.000
 6R8  H3   C02  C03  110.63  3.000
 6R8  H6   C02  C01  109.47  3.000
 6R8  H3   C02  C01  108.85  3.000
 6R8  C03  C02  C01  115.77  3.000
 6R8  H4   C03  C04  121.79  3.000
 6R8  H4   C03  C02  118.52  3.000
 6R8  C04  C03  C02  119.56  3.000
 6R8  N07  C04  C05  118.48  3.000
 6R8  N07  C04  C03  119.90  3.000
 6R8  C05  C04  C03  121.61  3.000
 6R8  H5   C05  C06  120.06  3.000
 6R8  H5   C05  C04  119.31  3.000
 6R8  C06  C05  C04  120.61  3.000
 6R8  C05  C06  C01  121.66  3.000
 6R8  C05  C06  C10  116.34  3.000
 6R8  C01  C06  C10  121.70  3.000
 6R8  O09  N07  O08  123.95  3.000
 6R8  O08  N07  C04  118.61  3.000
 6R8  O09  N07  C04  117.44  3.000
 6R8  H8   N13  H7   106.68  3.000
 6R8  H8   N13  C01  110.60  3.000
 6R8  H7   N13  C01  111.88  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  CONST_01  H2   O11  C10  C06  180.00   0.0  0
 6R8  Var_01    C04  C05  C06  C01    1.18  30.0  1
 6R8  Var_02    C04  C03  C02  C01  -28.56  30.0  1
 6R8  Var_03    C05  C04  C03  C02    2.26  30.0  1
 6R8  Var_04    C06  C05  C04  C03   12.30  30.0  1
 6R8  Var_05    C01  C06  C10  O11   24.05  30.0  2
 6R8  Var_06    O09  N07  C04  C03  179.44  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-1  H2   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

