# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:08:19 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 5-nitro-1H-benzotriazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]nnc2c1
#
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
 3NY  3NY  '5-nitro-1H-benzotriazole '  ligand  16  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3NY
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
 3NY  N1   N  NR15   0  -0.530  -2.8528   0.6337   0.0212
 3NY  N2   N  N      0  -0.032  -3.2479  -0.6347   0.0074
 3NY  N3   N  N      0  -0.313  -2.2314  -1.4019  -0.0075
 3NY  C4   C  CR16   0  -0.309   0.2363  -0.9721  -0.0164
 3NY  C5   C  CR6    0   0.249   1.1304   0.0750  -0.0096
 3NY  C6   C  CR16   0  -0.284   0.7345   1.4293   0.0083
 3NY  C7   C  CR16   0  -0.275  -0.5937   1.7733   0.0208
 3NY  O11  O  O      0  -0.377   2.8832  -1.3937  -0.0251
 3NY  O21  O  O     -1  -0.376   3.3329   0.6908  -0.0311
 3NY  C3A  C  CR56   0   0.149  -1.1100  -0.6210  -0.0043
 3NY  C7A  C  CR56   0   0.403  -1.5098   0.7182   0.0142
 3NY  NO1  N  N      1   0.331   2.5520  -0.2316  -0.0228
 3NY  H4   H  HCR6   0   0.314   0.5454  -2.0071  -0.0314
 3NY  H6   H  HCR6   0   0.306   1.4799   2.2099   0.0130
 3NY  H7   H  HCR6   0   0.300  -0.9040   2.8081   0.0355
 3NY  HN1  H  HNR5   0   0.443  -3.5414   1.3721   0.0335

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
 3NY  N1   N2   aromatic  1.329  0.020  1.329
 3NY  N1   C7A  aromatic  1.346  0.020  1.346
 3NY  N1   HN1  single    0.860  0.020  1.020
 3NY  N2   N3   aromatic  1.274  0.020  1.274
 3NY  N3   C3A  aromatic  1.367  0.020  1.367
 3NY  C4   C5   aromatic  1.377  0.020  1.377
 3NY  C4   H4   single    0.930  0.020  1.080
 3NY  C5   NO1  single    1.454  0.020  1.454
 3NY  C6   C5   aromatic  1.411  0.020  1.411
 3NY  C6   H6   single    0.930  0.020  1.080
 3NY  C7   C6   aromatic  1.372  0.020  1.372
 3NY  C7   H7   single    0.930  0.020  1.080
 3NY  C3A  C4   aromatic  1.391  0.020  1.391
 3NY  C7A  C7   aromatic  1.397  0.020  1.397
 3NY  C7A  C3A  aromatic  1.398  0.020  1.398
 3NY  NO1  O11  double    1.208  0.020  1.208
 3NY  NO1  O21  single    1.208  0.020  1.208

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
 3NY  HN1  N1   C7A  129.40  3.000
 3NY  HN1  N1   N2   119.70  3.000
 3NY  C7A  N1   N2   110.90  3.000
 3NY  N3   N2   N1   109.75  3.000
 3NY  C3A  N3   N2   108.10  3.000
 3NY  H4   C4   C3A  121.25  3.000
 3NY  C3A  C4   C5   115.87  3.000
 3NY  H4   C4   C5   122.88  3.000
 3NY  NO1  C5   C6   118.47  3.000
 3NY  C6   C5   C4   123.21  3.000
 3NY  NO1  C5   C4   118.32  3.000
 3NY  H6   C6   C7   119.15  3.000
 3NY  C7   C6   C5   120.82  3.000
 3NY  H6   C6   C5   120.03  3.000
 3NY  H7   C7   C7A  122.34  3.000
 3NY  C7A  C7   C6   116.44  3.000
 3NY  H7   C7   C6   121.22  3.000
 3NY  C7A  C3A  C4   121.24  3.000
 3NY  C7A  C3A  N3   108.23  3.000
 3NY  C4   C3A  N3   130.53  3.000
 3NY  C3A  C7A  C7   122.41  3.000
 3NY  C3A  C7A  N1   103.02  3.000
 3NY  C7   C7A  N1   134.56  3.000
 3NY  O21  NO1  O11  123.84  3.000
 3NY  O21  NO1  C5   118.09  3.000
 3NY  O11  NO1  C5   118.08  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
 3NY  CONST_01  C3A  N3   N2   N1     0.00  0.0  0
 3NY  CONST_02  C6   C7   C7A  N1   180.00  0.0  0
 3NY  CONST_03  N3   C3A  C7A  N1     0.00  0.0  0
 3NY  CONST_04  C4   C3A  C7A  N1   180.00  0.0  0
 3NY  CONST_05  C7   C7A  N1   N2   180.00  0.0  0
 3NY  CONST_06  C3A  C7A  N1   N2     0.00  0.0  0
 3NY  CONST_07  C4   C3A  N3   N2   180.00  0.0  0
 3NY  CONST_08  C7A  C3A  N3   N2     0.00  0.0  0
 3NY  CONST_09  C7A  N1   N2   N3     0.00  0.0  0
 3NY  CONST_10  C5   C4   C3A  N3   180.00  0.0  0
 3NY  CONST_11  C7   C7A  C3A  N3   180.00  0.0  0
 3NY  CONST_12  C7   C6   C5   C4     0.00  0.0  0
 3NY  CONST_13  C7   C7A  C3A  C4     0.00  0.0  0
 3NY  CONST_14  C7A  C3A  C4   C5     0.00  0.0  0
 3NY  CONST_15  C7A  C7   C6   C5     0.00  0.0  0
 3NY  CONST_16  C3A  C4   C5   C6     0.00  0.0  0
 3NY  CONST_17  C3A  C7A  C7   C6     0.00  0.0  0
 3NY  CONST_18  NO1  C5   C6   C7   180.00  0.0  0
 3NY  CONST_19  NO1  C5   C4   C3A  180.00  0.0  0
 3NY  CONST_20  H7   C7   C7A  N1     0.00  0.0  0
 3NY  CONST_21  HN1  N1   N2   N3   180.00  0.0  0
 3NY  CONST_22  H4   C4   C3A  N3     0.00  0.0  0
 3NY  CONST_23  H6   C6   C5   C4   180.00  0.0  0
 3NY  CONST_24  O11  NO1  C5   C4     0.00  0.0  0
 3NY  CONST_25  O21  NO1  C5   C4   180.00  0.0  0
 3NY  CONST_26  O11  NO1  C5   C6   180.00  0.0  0
 3NY  CONST_27  O21  NO1  C5   C6     0.00  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
 3NY  plan-1  N1   0.020
 3NY  plan-1  N2   0.020
 3NY  plan-1  N3   0.020
 3NY  plan-1  C4   0.020
 3NY  plan-1  C5   0.020
 3NY  plan-1  C6   0.020
 3NY  plan-1  C7   0.020
 3NY  plan-1  C3A  0.020
 3NY  plan-1  C7A  0.020
 3NY  plan-1  NO1  0.020
 3NY  plan-1  H4   0.020
 3NY  plan-1  H6   0.020
 3NY  plan-1  H7   0.020
 3NY  plan-1  HN1  0.020
 3NY  plan-2  C5   0.020
 3NY  plan-2  O11  0.020
 3NY  plan-2  O21  0.020
 3NY  plan-2  NO1  0.020

