# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:20:43 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-nitro-2-oxidanyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1C#N)[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
 6VP  6VP  5-nitro-2-oxidanyl-benzenecarbonitrile  ligand  16  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6VP
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
 6VP  NAA  N  NS     0  -0.238  -3.0844  -2.2381   0.0882
 6VP  CAE  C  CSP    0   0.086  -2.2463  -1.4481   0.0834
 6VP  CAJ  C  CR6    0  -0.089  -1.2078  -0.4745   0.0781
 6VP  CAH  C  CR16   0  -0.254   0.1196  -0.8732   0.0123
 6VP  CAI  C  CR6    0   0.411  -1.5471   0.8878   0.1380
 6VP  OAB  O  OH1    0  -0.579  -2.8334   1.1887   0.1983
 6VP  CAF  C  CR16   0  -0.368  -0.5279   1.8406   0.1302
 6VP  CAG  C  CR16   0  -0.237   0.7899   1.4474   0.0659
 6VP  CAK  C  CR6    0   0.249   1.1079   0.0931   0.0073
 6VP  NAL  N  N      1   0.328   2.4947  -0.3144  -0.0613
 6VP  OAD  O  O      0  -0.379   2.7378  -1.4975  -0.1171
 6VP  OAC  O  O     -1  -0.377   3.3399   0.5498  -0.0595
 6VP  H1   H  HCR6   0   0.321   0.3565  -1.9262  -0.0353
 6VP  H2   H  HOH1   0   0.500  -2.9746   2.1439   0.2328
 6VP  H3   H  HCR6   0   0.310  -0.7708   2.8944   0.1755
 6VP  H4   H  HCR6   0   0.317   1.5641   2.2004   0.0614

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
 6VP  NAA  CAE  triple    1.152  0.020  1.152
 6VP  CAE  CAJ  single    1.424  0.020  1.424
 6VP  OAB  CAI  single    1.322  0.020  1.322
 6VP  CAJ  CAI  aromatic  1.405  0.020  1.405
 6VP  CAJ  CAH  aromatic  1.388  0.020  1.388
 6VP  CAI  CAF  aromatic  1.395  0.020  1.395
 6VP  CAF  CAG  aromatic  1.377  0.020  1.377
 6VP  CAH  CAK  aromatic  1.382  0.020  1.382
 6VP  CAG  CAK  aromatic  1.392  0.020  1.392
 6VP  CAK  NAL  single    1.447  0.020  1.447
 6VP  NAL  OAD  double    1.209  0.020  1.209
 6VP  NAL  OAC  single    1.209  0.020  1.209
 6VP  CAH  H1   single    0.930  0.020  1.080
 6VP  OAB  H2   single    0.850  0.020  0.980
 6VP  CAF  H3   single    0.930  0.020  1.080
 6VP  CAG  H4   single    0.930  0.020  1.080

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
 6VP  CAJ  CAE  NAA  180.00  3.000
 6VP  CAI  CAJ  CAH  120.77  3.000
 6VP  CAH  CAJ  CAE  120.10  3.000
 6VP  CAI  CAJ  CAE  119.13  3.000
 6VP  H1   CAH  CAK  121.63  3.000
 6VP  H1   CAH  CAJ  119.47  3.000
 6VP  CAK  CAH  CAJ  118.90  3.000
 6VP  CAF  CAI  OAB  123.74  3.000
 6VP  CAF  CAI  CAJ  119.04  3.000
 6VP  OAB  CAI  CAJ  117.22  3.000
 6VP  H2   OAB  CAI  111.63  3.000
 6VP  H3   CAF  CAG  119.66  3.000
 6VP  H3   CAF  CAI  120.04  3.000
 6VP  CAG  CAF  CAI  120.30  3.000
 6VP  H4   CAG  CAK  120.95  3.000
 6VP  H4   CAG  CAF  119.16  3.000
 6VP  CAK  CAG  CAF  119.89  3.000
 6VP  NAL  CAK  CAG  119.65  3.000
 6VP  NAL  CAK  CAH  119.24  3.000
 6VP  CAG  CAK  CAH  121.10  3.000
 6VP  OAC  NAL  OAD  124.00  3.000
 6VP  OAC  NAL  CAK  117.94  3.000
 6VP  OAD  NAL  CAK  118.06  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
 6VP  CONST_01  CAG  CAF  CAI  CAJ    0.00  0.0  0
 6VP  CONST_02  CAG  CAK  CAH  CAJ    0.00  0.0  0
 6VP  CONST_03  CAF  CAI  CAJ  CAH    0.00  0.0  0
 6VP  CONST_04  CAF  CAG  CAK  CAH    0.00  0.0  0
 6VP  CONST_05  CAK  CAH  CAJ  CAI    0.00  0.0  0
 6VP  CONST_06  CAK  CAG  CAF  CAI    0.00  0.0  0
 6VP  CONST_07  CAF  CAI  CAJ  CAE  180.00  0.0  0
 6VP  CONST_08  CAK  CAH  CAJ  CAE  180.00  0.0  0
 6VP  CONST_09  NAL  CAK  CAH  CAJ  180.00  0.0  0
 6VP  CONST_10  OAB  CAI  CAJ  CAH  180.00  0.0  0
 6VP  CONST_11  CAG  CAF  CAI  OAB  180.00  0.0  0
 6VP  CONST_12  NAL  CAK  CAG  CAF  180.00  0.0  0
 6VP  CONST_13  H3   CAF  CAI  CAJ  180.00  0.0  0
 6VP  CONST_14  H4   CAG  CAK  CAH  180.00  0.0  0
 6VP  CONST_15  H1   CAH  CAJ  CAI  180.00  0.0  0
 6VP  CONST_16  OAD  NAL  CAK  CAH    0.00  0.0  0
 6VP  CONST_17  OAC  NAL  CAK  CAH  180.00  0.0  0
 6VP  CONST_18  OAD  NAL  CAK  CAG  180.00  0.0  0
 6VP  CONST_19  OAC  NAL  CAK  CAG    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
 6VP  plan-1  NAA  0.020
 6VP  plan-1  CAE  0.020
 6VP  plan-1  CAJ  0.020
 6VP  plan-1  CAH  0.020
 6VP  plan-1  CAI  0.020
 6VP  plan-1  OAB  0.020
 6VP  plan-1  CAF  0.020
 6VP  plan-1  CAG  0.020
 6VP  plan-1  CAK  0.020
 6VP  plan-1  NAL  0.020
 6VP  plan-1  H1   0.020
 6VP  plan-1  H3   0.020
 6VP  plan-1  H4   0.020
 6VP  plan-2  CAK  0.020
 6VP  plan-2  NAL  0.020
 6VP  plan-2  OAD  0.020
 6VP  plan-2  OAC  0.020

