# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:16:21 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  22  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  -0.078   1.2805   0.6061   0.0105
 1DF  CO1  C  CR16   0  -0.355   0.0546   1.2267   0.0346
 1DF  CO2  C  CR16   0  -0.392   1.3606  -0.7961   0.0335
 1DF  CM1  C  CR6    0   0.211  -1.1024   0.4475   0.0821
 1DF  CM2  C  CR6    0   0.352   0.2252  -1.5682   0.0789
 1DF  OM   O  O2     0  -0.457   0.1933  -2.9051   0.1015
 1DF  CZ   C  CR6    0   0.292  -1.0527  -0.9532   0.1057
 1DF  CC   C  C      0   0.553   2.5486   1.3706  -0.0416
 1DF  CV   C  CH3    0  -0.446   1.4244  -3.6009   0.0224
 1DF  O1   O  OH1    0  -0.593   2.3625   2.6811  -0.0697
 1DF  O2   O  O      0  -0.436   3.6383   0.8505  -0.0574
 1DF  O3   O  OH1    0  -0.576  -2.0875  -1.7665   0.1492
 1DF  N    N  N      1   0.365  -2.3713   1.1273   0.1040
 1DF  O11  O  O      0  -0.422  -3.3889   0.4509   0.1516
 1DF  O22  O  O     -1  -0.356  -2.3913   2.3298   0.0754
 1DF  H1   H  HCR6   0   0.306  -0.0298   2.3024   0.0174
 1DF  H2   H  HCR6   0   0.306   2.3372  -1.2602   0.0138
 1DF  H3   H  HCH3   0   0.237   1.9660  -3.3582  -0.8950
 1DF  H4   H  HCH3   0   0.237   2.0663  -3.3874   0.8805
 1DF  H5   H  HCH3   0   0.269   1.1782  -4.6591   0.0197
 1DF  H6   H  HOH1   0   0.491   3.2160   3.1379  -0.1081
 1DF  H7   H  HOH1   0   0.489  -2.9057  -1.2341   0.1645

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    1.416  0.020  1.416
 1DF  OM   CM2  single    1.337  0.020  1.337
 1DF  CM2  CZ   aromatic  1.418  0.020  1.418
 1DF  CM2  CO2  aromatic  1.374  0.020  1.374
 1DF  O3   CZ   single    1.317  0.020  1.317
 1DF  CZ   CM1  aromatic  1.402  0.020  1.402
 1DF  CO2  C1   aromatic  1.405  0.020  1.405
 1DF  O2   CC   double    1.208  0.020  1.208
 1DF  CM1  N    single    1.440  0.020  1.440
 1DF  CM1  CO1  aromatic  1.396  0.020  1.396
 1DF  O11  N    double    1.223  0.020  1.223
 1DF  C1   CO1  aromatic  1.374  0.020  1.374
 1DF  C1   CC   single    1.482  0.020  1.482
 1DF  N    O22  single    1.203  0.020  1.203
 1DF  CC   O1   single    1.324  0.020  1.324
 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  O1   H6   single    0.850  0.020  0.980
 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  117.83  3.000
 1DF  CC   C1   CO1  122.07  3.000
 1DF  CO2  C1   CO1  120.10  3.000
 1DF  H1   CO1  CM1  119.49  3.000
 1DF  H1   CO1  C1   121.31  3.000
 1DF  CM1  CO1  C1   119.20  3.000
 1DF  H2   CO2  CM2  120.38  3.000
 1DF  H2   CO2  C1   118.66  3.000
 1DF  CM2  CO2  C1   120.96  3.000
 1DF  N    CM1  CZ   120.19  3.000
 1DF  N    CM1  CO1  117.87  3.000
 1DF  CZ   CM1  CO1  121.94  3.000
 1DF  CZ   CM2  OM   114.30  3.000
 1DF  CZ   CM2  CO2  120.10  3.000
 1DF  OM   CM2  CO2  125.60  3.000
 1DF  CV   OM   CM2  117.99  3.000
 1DF  O3   CZ   CM2  116.15  3.000
 1DF  O3   CZ   CM1  126.14  3.000
 1DF  CM2  CZ   CM1  117.70  3.000
 1DF  O2   CC   O1   123.56  3.000
 1DF  O1   CC   C1   113.03  3.000
 1DF  O2   CC   C1   123.41  3.000
 1DF  H5   CV   H4   108.99  3.000
 1DF  H5   CV   H3   109.06  3.000
 1DF  H4   CV   H3   108.95  3.000
 1DF  H5   CV   OM   106.36  3.000
 1DF  H4   CV   OM   111.76  3.000
 1DF  H3   CV   OM   111.63  3.000
 1DF  H6   O1   CC   110.11  3.000
 1DF  H7   O3   CZ   108.80  3.000
 1DF  O22  N    O11  122.68  3.000
 1DF  O22  N    CM1  119.10  3.000
 1DF  O11  N    CM1  118.22  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  CONST_21  H6   O1   CC   C1   180.00   0.0  0
 1DF  Var_01    O2   CC   C1   CO1  179.65  30.0  2
 1DF  Var_02    H3   CV   OM   CM2  -59.13  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
 1DF  plan-3  H6   0.020

