# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 01:07:23 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 4-hydroxy-3-methoxy-5-nitrobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(c1O)[N+]([O-])=O)C(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
 1DF  1DF  '4-hydroxy-3-methoxy-5-nitrobenzoic acid'  ligand  21  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1DF
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
 1DF  C1   C  CR6    0  -0.095   1.2683   0.6086  -0.0193
 1DF  CO1  C  CR16   0  -0.389   0.0396   1.2199   0.0029
 1DF  CO2  C  CR16   0  -0.417   1.3333  -0.7924   0.0006
 1DF  CM1  C  CR6    0   0.204  -1.1252   0.4460   0.0479
 1DF  CM2  C  CR6    0   0.344   0.1947  -1.5665   0.0401
 1DF  OM   O  O2     0  -0.464   0.1651  -2.9097   0.0568
 1DF  CZ   C  CR6    0   0.265  -1.0800  -0.9554   0.0673
 1DF  CC   C  C      0   0.419   2.5477   1.4357  -0.0653
 1DF  CV   C  CH3    0  -0.440   1.3982  -3.5980  -0.0129
 1DF  O1   O  OC    -1  -0.588   2.4063   2.6714  -0.1095
 1DF  O2   O  O      0  -0.588   3.6170   0.7987  -0.0554
 1DF  O3   O  OH1    0  -0.592  -2.1235  -1.7703   0.1076
 1DF  N    N  N      1   0.361  -2.3901   1.1255   0.0726
 1DF  O11  O  O      0  -0.432  -3.4142   0.4540   0.1134
 1DF  O22  O  O     -1  -0.366  -2.4124   2.3299   0.0530
 1DF  H1   H  HCR6   0   0.281  -0.0222   2.2977  -0.0135
 1DF  H2   H  HCR6   0   0.287   2.3114  -1.2541  -0.0170
 1DF  H3   H  HCH3   0   0.232   1.9453  -3.3589  -0.9284
 1DF  H4   H  HCH3   0   0.232   2.0379  -3.3782   0.8458
 1DF  H5   H  HCH3   0   0.263   1.1592  -4.6583  -0.0110
 1DF  H7   H  HOH1   0   0.483  -2.9348  -1.2292   0.1228

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
 1DF  CV   OM   single    1.414  0.020  1.414
 1DF  OM   CM2  single    1.344  0.020  1.344
 1DF  CM2  CZ   aromatic  1.414  0.020  1.414
 1DF  CM2  CO2  aromatic  1.377  0.020  1.377
 1DF  O3   CZ   single    1.325  0.020  1.325
 1DF  CZ   CM1  aromatic  1.402  0.020  1.402
 1DF  CO2  C1   aromatic  1.403  0.020  1.403
 1DF  O2   CC   deloc     1.245  0.020  1.245
 1DF  CM1  N    single    1.436  0.020  1.436
 1DF  CM1  CO1  aromatic  1.399  0.020  1.399
 1DF  O11  N    double    1.225  0.020  1.225
 1DF  C1   CO1  aromatic  1.373  0.020  1.373
 1DF  C1   CC   single    1.524  0.020  1.524
 1DF  N    O22  single    1.205  0.020  1.205
 1DF  CC   O1   deloc     1.245  0.020  1.245
 1DF  CO1  H1   single    0.930  0.020  1.080
 1DF  CO2  H2   single    0.930  0.020  1.080
 1DF  CV   H3   single    0.970  0.020  1.090
 1DF  CV   H4   single    0.970  0.020  1.090
 1DF  CV   H5   single    0.970  0.020  1.090
 1DF  O3   H7   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
 1DF  CC   C1   CO2  120.24  3.000
 1DF  CC   C1   CO1  120.68  3.000
 1DF  CO2  C1   CO1  119.08  3.000
 1DF  H1   CO1  CM1  120.33  3.000
 1DF  H1   CO1  C1   119.70  3.000
 1DF  CM1  CO1  C1   119.96  3.000
 1DF  H2   CO2  CM2  120.53  3.000
 1DF  H2   CO2  C1   117.90  3.000
 1DF  CM2  CO2  C1   121.57  3.000
 1DF  N    CM1  CZ   120.07  3.000
 1DF  N    CM1  CO1  118.17  3.000
 1DF  CZ   CM1  CO1  121.76  3.000
 1DF  CZ   CM2  OM   114.33  3.000
 1DF  CZ   CM2  CO2  120.19  3.000
 1DF  OM   CM2  CO2  125.48  3.000
 1DF  CV   OM   CM2  117.83  3.000
 1DF  O3   CZ   CM2  116.42  3.000
 1DF  O3   CZ   CM1  126.15  3.000
 1DF  CM2  CZ   CM1  117.44  3.000
 1DF  O2   CC   O1   127.30  3.000
 1DF  O1   CC   C1   116.39  3.000
 1DF  O2   CC   C1   116.30  3.000
 1DF  H5   CV   H4   108.88  3.000
 1DF  H5   CV   H3   108.96  3.000
 1DF  H4   CV   H3   108.72  3.000
 1DF  H5   CV   OM   106.44  3.000
 1DF  H4   CV   OM   111.95  3.000
 1DF  H3   CV   OM   111.80  3.000
 1DF  H7   O3   CZ   108.33  3.000
 1DF  O22  N    O11  122.20  3.000
 1DF  O22  N    CM1  119.28  3.000
 1DF  O11  N    CM1  118.52  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
 1DF  CONST_01  CZ   CM2  CO2  C1     0.00   0.0  0
 1DF  CONST_02  CZ   CM1  CO1  C1     0.00   0.0  0
 1DF  CONST_03  CM2  CZ   CM1  CO1    0.00   0.0  0
 1DF  CONST_04  CM2  CO2  C1   CO1    0.00   0.0  0
 1DF  CONST_05  CM1  CZ   CM2  CO2    0.00   0.0  0
 1DF  CONST_06  CM1  CO1  C1   CO2    0.00   0.0  0
 1DF  CONST_07  OM   CM2  CO2  C1   180.00   0.0  0
 1DF  CONST_08  N    CM1  CO1  C1   180.00   0.0  0
 1DF  CONST_09  O3   CZ   CM1  CO1  180.00   0.0  0
 1DF  CONST_10  O3   CZ   CM2  CO2  180.00   0.0  0
 1DF  CONST_11  OM   CM2  CZ   CM1  180.00   0.0  0
 1DF  CONST_12  CC   C1   CO1  CM1  180.00   0.0  0
 1DF  CONST_13  N    CM1  CZ   CM2  180.00   0.0  0
 1DF  CONST_14  CC   C1   CO2  CM2  180.00   0.0  0
 1DF  CONST_15  H2   CO2  C1   CO1  180.00   0.0  0
 1DF  CONST_16  H1   CO1  C1   CO2  180.00   0.0  0
 1DF  CONST_17  O11  N    CM1  CO1  180.00   0.0  0
 1DF  CONST_18  O22  N    CM1  CO1    0.00   0.0  0
 1DF  CONST_19  O11  N    CM1  CZ     0.00   0.0  0
 1DF  CONST_20  O22  N    CM1  CZ   180.00   0.0  0
 1DF  Var_01    O2   CC   C1   CO1  178.58  30.0  2
 1DF  Var_02    H3   CV   OM   CM2  -59.76  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
 1DF  plan-1  C1   0.020
 1DF  plan-1  CO1  0.020
 1DF  plan-1  CO2  0.020
 1DF  plan-1  CM1  0.020
 1DF  plan-1  CM2  0.020
 1DF  plan-1  OM   0.020
 1DF  plan-1  CZ   0.020
 1DF  plan-1  CC   0.020
 1DF  plan-1  O3   0.020
 1DF  plan-1  N    0.020
 1DF  plan-1  H1   0.020
 1DF  plan-1  H2   0.020
 1DF  plan-2  CM1  0.020
 1DF  plan-2  N    0.020
 1DF  plan-2  O11  0.020
 1DF  plan-2  O22  0.020
 1DF  plan-3  C1   0.020
 1DF  plan-3  CC   0.020
 1DF  plan-3  O1   0.020
 1DF  plan-3  O2   0.020

