# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:38:14 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (4-hydroxy-3-nitrophenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1ccc(O)c(c1)[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
 NPA  NPA  '(4-hydroxy-3-nitrophenyl)acetic acid'  ligand  20  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPA
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
 NPA  C1   C  CR6    0   0.159   0.3326  -0.6281   0.9983
 NPA  C2   C  CR16   0  -0.369  -0.5433  -0.5866  -0.0608
 NPA  C3   C  CR6    0   0.178  -0.1078  -0.2655  -1.3543
 NPA  C4   C  CR6    0   0.345   1.2435   0.0221  -1.6146
 NPA  C5   C  CR16   0  -0.342   2.1259  -0.0313  -0.5301
 NPA  C6   C  CR16   0  -0.254   1.6806  -0.3398   0.7335
 NPA  C7   C  CH2    0  -0.690  -0.1267  -0.9431   2.3842
 NPA  C8   C  C      0   0.426  -0.1176   0.2715   3.3480
 NPA  N1   N  N      1   0.361  -1.0776  -0.2392  -2.4071
 NPA  O1   O  O     -1  -0.436  -0.7009   0.0435  -3.5392
 NPA  O2   O  O      0  -0.372  -2.2305  -0.4919  -2.1593
 NPA  O3   O  OH1    0  -0.607   1.7507   0.3342  -2.8015
 NPA  O4   O  O      0  -0.595   0.4989   1.2886   2.9839
 NPA  O5   O  OC    -1  -0.617  -0.7208   0.1006   4.4241
 NPA  H2   H  HCR6   0   0.287  -1.5899  -0.8018   0.1054
 NPA  H5   H  HCR6   0   0.280   3.1727   0.1787  -0.7084
 NPA  H6   H  HCR6   0   0.265   2.4002  -0.3749   1.5409
 NPA  H71  H  HCH2   0   0.255   0.5202  -1.7110   2.8229
 NPA  H72  H  HCH2   0   0.247  -1.1286  -1.3778   2.3612
 NPA  HO3  H  HOH1   0   0.480   1.0316   0.3291  -3.4597

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
 NPA  C1  C2   aromatic  1.375  0.020  1.375
 NPA  C1  C6   aromatic  1.404  0.020  1.404
 NPA  C1  C7   single    1.494  0.020  1.494
 NPA  C2  C3   aromatic  1.402  0.020  1.402
 NPA  C2  H2   single    0.930  0.020  1.080
 NPA  C3  C4   aromatic  1.406  0.020  1.406
 NPA  C3  N1   single    1.432  0.020  1.432
 NPA  C4  C5   aromatic  1.399  0.020  1.399
 NPA  C4  O3   single    1.328  0.020  1.328
 NPA  C5  C6   aromatic  1.375  0.020  1.375
 NPA  C5  H5   single    0.930  0.020  1.080
 NPA  C6  H6   single    0.930  0.020  1.080
 NPA  C7  C8   single    1.551  0.020  1.551
 NPA  C7  H71  single    0.970  0.020  1.090
 NPA  C7  H72  single    0.970  0.020  1.090
 NPA  C8  O4   deloc     1.244  0.020  1.244
 NPA  C8  O5   deloc     1.245  0.020  1.245
 NPA  N1  O1   single    1.226  0.020  1.226
 NPA  N1  O2   double    1.206  0.020  1.206
 NPA  O3  HO3  single    0.850  0.020  0.980

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
 NPA  C7   C1  C6   120.91  3.000
 NPA  C7   C1  C2   121.68  3.000
 NPA  C6   C1  C2   117.40  3.000
 NPA  H2   C2  C3   119.20  3.000
 NPA  H2   C2  C1   119.48  3.000
 NPA  C3   C2  C1   121.31  3.000
 NPA  N1   C3  C4   120.74  3.000
 NPA  N1   C3  C2   118.18  3.000
 NPA  C4   C3  C2   121.08  3.000
 NPA  O3   C4  C5   117.45  3.000
 NPA  O3   C4  C3   125.50  3.000
 NPA  C5   C4  C3   117.05  3.000
 NPA  H5   C5  C6   120.54  3.000
 NPA  H5   C5  C4   118.35  3.000
 NPA  C6   C5  C4   121.11  3.000
 NPA  H6   C6  C5   118.53  3.000
 NPA  H6   C6  C1   119.42  3.000
 NPA  C5   C6  C1   122.04  3.000
 NPA  H72  C7  H71  105.72  3.000
 NPA  H72  C7  C8   109.28  3.000
 NPA  H71  C7  C8   107.25  3.000
 NPA  H72  C7  C1   110.27  3.000
 NPA  H71  C7  C1   109.74  3.000
 NPA  C8   C7  C1   114.19  3.000
 NPA  O5   C8  O4   127.24  3.000
 NPA  O5   C8  C7   115.26  3.000
 NPA  O4   C8  C7   117.49  3.000
 NPA  O2   N1  O1   122.12  3.000
 NPA  O2   N1  C3   119.51  3.000
 NPA  O1   N1  C3   118.37  3.000
 NPA  HO3  O3  C4   108.69  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
 NPA  CONST_01  C4  C3  C2  C1     0.00   0.0  0
 NPA  CONST_02  C4  C5  C6  C1     0.00   0.0  0
 NPA  CONST_03  C5  C6  C1  C2     0.00   0.0  0
 NPA  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 NPA  CONST_05  C6  C1  C2  C3     0.00   0.0  0
 NPA  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 NPA  CONST_07  N1  C3  C2  C1   180.00   0.0  0
 NPA  CONST_08  O3  C4  C3  C2   180.00   0.0  0
 NPA  CONST_09  C7  C1  C2  C3   180.00   0.0  0
 NPA  CONST_10  N1  C3  C4  C5   180.00   0.0  0
 NPA  CONST_11  C7  C1  C6  C5   180.00   0.0  0
 NPA  CONST_12  O3  C4  C5  C6   180.00   0.0  0
 NPA  CONST_13  H5  C5  C6  C1   180.00   0.0  0
 NPA  CONST_14  H6  C6  C1  C2   180.00   0.0  0
 NPA  CONST_15  H2  C2  C3  C4   180.00   0.0  0
 NPA  CONST_16  O1  N1  C3  C2   180.00   0.0  0
 NPA  CONST_17  O2  N1  C3  C2     0.00   0.0  0
 NPA  CONST_18  O1  N1  C3  C4     0.00   0.0  0
 NPA  CONST_19  O2  N1  C3  C4   180.00   0.0  0
 NPA  Var_01    C8  C7  C1  C2  -108.29  30.0  2
 NPA  Var_02    O4  C8  C7  C1   -13.89  30.0  3

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
 NPA  plan-1  C1  0.020
 NPA  plan-1  C2  0.020
 NPA  plan-1  C3  0.020
 NPA  plan-1  C4  0.020
 NPA  plan-1  C5  0.020
 NPA  plan-1  C6  0.020
 NPA  plan-1  C7  0.020
 NPA  plan-1  N1  0.020
 NPA  plan-1  O3  0.020
 NPA  plan-1  H2  0.020
 NPA  plan-1  H5  0.020
 NPA  plan-1  H6  0.020
 NPA  plan-2  C3  0.020
 NPA  plan-2  N1  0.020
 NPA  plan-2  O1  0.020
 NPA  plan-2  O2  0.020
 NPA  plan-3  C7  0.020
 NPA  plan-3  C8  0.020
 NPA  plan-3  O4  0.020
 NPA  plan-3  O5  0.020

