# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:58:15 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 3-nitropyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1[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
 JBE  JBE  '3-nitropyridin-2-amine   '  ligand  15  10  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JBE
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
 JBE  O01  O  O      0  -0.420   2.3396   0.5604   0.0126
 JBE  N02  N  N      1   0.346   1.6540  -0.4451  -0.0305
 JBE  O03  O  O     -1  -0.396   2.1325  -1.5577  -0.0763
 JBE  C04  C  CR6    0   0.113   0.2310  -0.3097  -0.0257
 JBE  C05  C  CR16   0  -0.178  -0.5361  -1.4725  -0.0675
 JBE  C06  C  CR16   0  -0.353  -1.9068  -1.3874  -0.0624
 JBE  C07  C  CR16   0  -0.032  -2.4641  -0.1105  -0.0146
 JBE  N08  N  N      0  -0.452  -1.7654   1.0008   0.0246
 JBE  C09  C  CR6    0   0.480  -0.4211   0.9544   0.0208
 JBE  N10  N  NH2    0  -0.803   0.1856   2.1396   0.0618
 JBE  H1   H  HCR6   0   0.307  -0.0505  -2.4370  -0.1040
 JBE  H2   H  HCR6   0   0.279  -2.5313  -2.2672  -0.0942
 JBE  H3   H  HCR6   0   0.281  -3.5421   0.0086  -0.0081
 JBE  H4   H  HNH2   0   0.421   1.1840   2.2340   0.0619
 JBE  H5   H  HNH2   0   0.406  -0.3892   2.9648   0.0918

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
 JBE  O01  N02  double    1.218  0.020  1.218
 JBE  N02  O03  single    1.212  0.020  1.212
 JBE  N02  C04  single    1.429  0.020  1.429
 JBE  C04  C05  aromatic  1.394  0.020  1.394
 JBE  C04  C09  aromatic  1.423  0.020  1.423
 JBE  C05  C06  aromatic  1.373  0.020  1.373
 JBE  N10  C09  single    1.332  0.020  1.332
 JBE  C09  N08  aromatic  1.345  0.020  1.345
 JBE  C06  C07  aromatic  1.394  0.020  1.394
 JBE  N08  C07  aromatic  1.313  0.020  1.313
 JBE  C05  H1   single    0.930  0.020  1.080
 JBE  C06  H2   single    0.930  0.020  1.080
 JBE  C07  H3   single    0.930  0.020  1.080
 JBE  N10  H4   single    0.860  0.020  1.020
 JBE  N10  H5   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
 JBE  C04  N02  O03  118.69  3.000
 JBE  C04  N02  O01  118.83  3.000
 JBE  O03  N02  O01  122.48  3.000
 JBE  C09  C04  C05  119.33  3.000
 JBE  C09  C04  N02  122.71  3.000
 JBE  C05  C04  N02  117.96  3.000
 JBE  H1   C05  C06  120.26  3.000
 JBE  H1   C05  C04  119.90  3.000
 JBE  C06  C05  C04  119.84  3.000
 JBE  H2   C06  C07  121.08  3.000
 JBE  H2   C06  C05  121.79  3.000
 JBE  C07  C06  C05  117.12  3.000
 JBE  H3   C07  N08  115.83  3.000
 JBE  H3   C07  C06  119.88  3.000
 JBE  N08  C07  C06  124.30  3.000
 JBE  C09  N08  C07  120.16  3.000
 JBE  N10  C09  N08  115.11  3.000
 JBE  N08  C09  C04  119.26  3.000
 JBE  N10  C09  C04  125.63  3.000
 JBE  H5   N10  H4   119.44  3.000
 JBE  H5   N10  C09  118.07  3.000
 JBE  H4   N10  C09  122.49  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
 JBE  CONST_01  C07  C06  C05  C04    0.00  0.0  0
 JBE  CONST_02  C07  N08  C09  C04    0.00  0.0  0
 JBE  CONST_03  N08  C09  C04  C05    0.00  0.0  0
 JBE  CONST_04  N08  C07  C06  C05    0.00  0.0  0
 JBE  CONST_05  C09  C04  C05  C06    0.00  0.0  0
 JBE  CONST_06  C09  N08  C07  C06    0.00  0.0  0
 JBE  CONST_07  C06  C05  C04  N02  180.00  0.0  0
 JBE  CONST_08  N08  C09  C04  N02  180.00  0.0  0
 JBE  CONST_09  N10  C09  C04  C05  180.00  0.0  0
 JBE  CONST_10  N10  C09  N08  C07  180.00  0.0  0
 JBE  CONST_11  H2   C06  C05  C04  180.00  0.0  0
 JBE  CONST_12  H3   C07  C06  C05  180.00  0.0  0
 JBE  CONST_13  H1   C05  C06  C07  180.00  0.0  0
 JBE  CONST_14  C05  C04  N02  O01  180.00  0.0  0
 JBE  CONST_15  C09  C04  N02  O01    0.00  0.0  0
 JBE  CONST_16  C05  C04  N02  O03    0.00  0.0  0
 JBE  CONST_17  C09  C04  N02  O03  180.00  0.0  0
 JBE  CONST_18  H4   N10  C09  C04    0.00  0.0  0
 JBE  CONST_19  H5   N10  C09  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
 JBE  plan-1  N02  0.020
 JBE  plan-1  C04  0.020
 JBE  plan-1  C05  0.020
 JBE  plan-1  C06  0.020
 JBE  plan-1  C07  0.020
 JBE  plan-1  N08  0.020
 JBE  plan-1  C09  0.020
 JBE  plan-1  N10  0.020
 JBE  plan-1  H1   0.020
 JBE  plan-1  H2   0.020
 JBE  plan-1  H3   0.020
 JBE  plan-2  O01  0.020
 JBE  plan-2  N02  0.020
 JBE  plan-2  O03  0.020
 JBE  plan-2  C04  0.020
 JBE  plan-3  C09  0.020
 JBE  plan-3  N10  0.020
 JBE  plan-3  H4   0.020
 JBE  plan-3  H5   0.020

