# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:48:27 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-azanyl-3-nitro-phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1c(O)cccc1[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
 JBK  JBK  '2-azanyl-3-nitro-phenol  '  ligand  17  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JBK
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
 JBK  C10  C  CR6    0   0.273   0.3683   0.7080  -0.0159
 JBK  O01  O  O      0  -0.402  -2.7656  -0.9827   0.1119
 JBK  N02  N  N      1   0.344  -1.9833  -0.0556   0.0926
 JBK  O03  O  O     -1  -0.427  -2.3565   1.1047   0.1462
 JBK  C04  C  CR6    0   0.200  -0.5836  -0.3351   0.0028
 JBK  C05  C  CR16   0  -0.328  -0.2023  -1.6883  -0.0589
 JBK  C06  C  CR16   0  -0.274   1.1189  -2.0249  -0.1393
 JBK  C07  C  CR16   0  -0.363   2.0931  -1.0155  -0.1615
 JBK  C08  C  CR6    0   0.299   1.7353   0.3049  -0.1043
 JBK  O09  O  OH1    0  -0.637   2.6194   1.3242  -0.1240
 JBK  N11  N  NH2    0  -0.825   0.1157   2.0272   0.0181
 JBK  H1   H  HCR6   0   0.286  -0.9572  -2.4588  -0.0428
 JBK  H2   H  HCR6   0   0.267   1.4170  -3.0624  -0.1878
 JBK  H3   H  HCR6   0   0.284   3.1424  -1.2802  -0.2277
 JBK  H4   H  HOH1   0   0.484   3.5229   0.9901  -0.1522
 JBK  H5   H  HNH2   0   0.412  -0.8115   2.3624   0.2002
 JBK  H6   H  HNH2   0   0.407   0.8802   2.6672   0.1428

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
 JBK  O09  C08  single    1.349  0.020  1.349
 JBK  C08  C07  aromatic  1.369  0.020  1.369
 JBK  C08  C10  aromatic  1.428  0.020  1.428
 JBK  C07  C06  aromatic  1.403  0.020  1.403
 JBK  N11  C10  single    1.344  0.020  1.344
 JBK  C10  C04  aromatic  1.412  0.020  1.412
 JBK  C06  C05  aromatic  1.366  0.020  1.366
 JBK  C04  C05  aromatic  1.407  0.020  1.407
 JBK  C04  N02  single    1.430  0.020  1.430
 JBK  O01  N02  double    1.213  0.020  1.213
 JBK  N02  O03  single    1.220  0.020  1.220
 JBK  C05  H1   single    0.930  0.020  1.080
 JBK  C06  H2   single    0.930  0.020  1.080
 JBK  C07  H3   single    0.930  0.020  1.080
 JBK  O09  H4   single    0.850  0.020  0.980
 JBK  N11  H5   single    0.860  0.020  1.020
 JBK  N11  H6   single    0.860  0.020  1.020

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
 JBK  N11  C10  C08  117.31  3.000
 JBK  N11  C10  C04  126.74  3.000
 JBK  C08  C10  C04  115.95  3.000
 JBK  C04  N02  O03  119.21  3.000
 JBK  O03  N02  O01  121.92  3.000
 JBK  C04  N02  O01  118.86  3.000
 JBK  C05  C04  N02  117.12  3.000
 JBK  N02  C04  C10  121.07  3.000
 JBK  C05  C04  C10  121.81  3.000
 JBK  H1   C05  C06  120.12  3.000
 JBK  H1   C05  C04  119.77  3.000
 JBK  C06  C05  C04  120.11  3.000
 JBK  H2   C06  C07  119.91  3.000
 JBK  H2   C06  C05  120.40  3.000
 JBK  C07  C06  C05  119.69  3.000
 JBK  H3   C07  C08  119.40  3.000
 JBK  H3   C07  C06  119.82  3.000
 JBK  C08  C07  C06  120.78  3.000
 JBK  O09  C08  C07  123.82  3.000
 JBK  C07  C08  C10  121.67  3.000
 JBK  O09  C08  C10  114.51  3.000
 JBK  H4   O09  C08  110.66  3.000
 JBK  H6   N11  H5   117.92  3.000
 JBK  H6   N11  C10  119.04  3.000
 JBK  H5   N11  C10  120.44  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
 JBK  CONST_01  C06  C07  C08  C10    0.00  0.0  0
 JBK  CONST_02  C06  C05  C04  C10    0.00  0.0  0
 JBK  CONST_03  C07  C08  C10  C04    0.00  0.0  0
 JBK  CONST_04  C07  C06  C05  C04    0.00  0.0  0
 JBK  CONST_05  C08  C07  C06  C05    0.00  0.0  0
 JBK  CONST_06  C08  C10  C04  C05    0.00  0.0  0
 JBK  CONST_07  C08  C10  C04  N02  180.00  0.0  0
 JBK  CONST_08  C06  C05  C04  N02  180.00  0.0  0
 JBK  CONST_09  O09  C08  C10  C04  180.00  0.0  0
 JBK  CONST_10  N11  C10  C04  C05  180.00  0.0  0
 JBK  CONST_11  O09  C08  C07  C06  180.00  0.0  0
 JBK  CONST_12  N11  C10  C08  C07  180.00  0.0  0
 JBK  CONST_13  H3   C07  C08  C10  180.00  0.0  0
 JBK  CONST_14  H1   C05  C04  C10  180.00  0.0  0
 JBK  CONST_15  H2   C06  C05  C04  180.00  0.0  0
 JBK  CONST_16  O01  N02  C04  C10  180.00  0.0  0
 JBK  CONST_17  O03  N02  C04  C10    0.00  0.0  0
 JBK  CONST_18  C05  C04  N02  O01    0.00  0.0  0
 JBK  CONST_19  C05  C04  N02  O03  180.00  0.0  0
 JBK  CONST_20  H5   N11  C10  C04    0.00  0.0  0
 JBK  CONST_21  H6   N11  C10  C04  180.00  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
 JBK  plan-1  C10  0.020
 JBK  plan-1  N02  0.020
 JBK  plan-1  C04  0.020
 JBK  plan-1  C05  0.020
 JBK  plan-1  C06  0.020
 JBK  plan-1  C07  0.020
 JBK  plan-1  C08  0.020
 JBK  plan-1  O09  0.020
 JBK  plan-1  N11  0.020
 JBK  plan-1  H1   0.020
 JBK  plan-1  H2   0.020
 JBK  plan-1  H3   0.020
 JBK  plan-2  O01  0.020
 JBK  plan-2  N02  0.020
 JBK  plan-2  O03  0.020
 JBK  plan-2  C04  0.020
 JBK  plan-3  C10  0.020
 JBK  plan-3  N11  0.020
 JBK  plan-3  H5   0.020
 JBK  plan-3  H6   0.020

