# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 15:22:20 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-(acetylamino)-3-hydroxy-5-nitrobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1c(O)cc(cc1[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
 ST1  ST1  '4-(acetylamino)-3-hydroxy-5-nitrobenzoic acid'  ligand  25  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ST1
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
 ST1  C'    C  C      0   0.559  -0.3114   0.1159  -0.1877
 ST1  O1'   O  O      0  -0.426  -0.3005   0.2136  -1.3893
 ST1  O2'   O  OH1    0  -0.588  -1.3020   0.5353   0.5793
 ST1  C1    C  CR6    0  -0.078   0.8008  -0.4941   0.5918
 ST1  C2    C  CR16   0  -0.395   0.7583  -0.5922   1.9764
 ST1  C3    C  CR6    0   0.373   1.8189  -1.1539   2.6787
 ST1  O3    O  OH1    0  -0.600   1.8444  -1.2302   4.0103
 ST1  C4    C  CR6    0   0.261   2.9317  -1.6498   1.9888
 ST1  N4    N  NH1    0  -0.712   4.0144  -2.1735   2.7052
 ST1  C4'   C  C      0   0.514   3.9444  -3.3863   3.3173
 ST1  O4'   O  O      0  -0.468   2.9254  -4.0488   3.3151
 ST1  CM4   C  CH3    0  -0.786   5.2293  -3.8391   3.9538
 ST1  C5    C  CR6    0   0.250   2.9291  -1.5499   0.6011
 ST1  N5    N  N      1   0.327   4.0406  -2.0968  -0.1684
 ST1  ON1   O  O      0  -0.357   4.4539  -3.1879   0.1345
 ST1  ON2   O  O     -1  -0.364   4.4601  -1.4284  -1.0817
 ST1  C6    C  CR16   0  -0.320   1.9031  -0.9603  -0.1100
 ST1  HO2'  H  HOH1   0   0.494  -2.0025   0.9314   0.0395
 ST1  H2    H  HCR6   0   0.302  -0.0923  -0.2139   2.5288
 ST1  HO3   H  HOH1   0   0.488   1.0398  -0.8580   4.3909
 ST1  HN4   H  HNH1   0   0.420   4.9020  -1.6959   2.6520
 ST1  HM41  H  HCH3   0   0.277   5.7994  -4.4233   3.2291
 ST1  HM42  H  HCH3   0   0.269   5.0181  -4.4795   4.8067
 ST1  HM43  H  HCH3   0   0.259   5.8544  -3.0085   4.2769
 ST1  H6    H  HCR6   0   0.300   1.9414  -0.8908  -1.1876

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
 ST1  C'   O1'   double    1.206  0.020  1.206
 ST1  C'   O2'   single    1.321  0.020  1.321
 ST1  C'   C1    single    1.489  0.020  1.489
 ST1  O2'  HO2'  single    0.850  0.020  0.980
 ST1  C1   C2    aromatic  1.389  0.020  1.389
 ST1  C1   C6    aromatic  1.387  0.020  1.387
 ST1  C2   C3    aromatic  1.391  0.020  1.391
 ST1  C2   H2    single    0.930  0.020  1.080
 ST1  C3   O3    single    1.334  0.020  1.334
 ST1  C3   C4    aromatic  1.400  0.020  1.400
 ST1  O3   HO3   single    0.850  0.020  0.980
 ST1  C4   N4    single    1.400  0.020  1.400
 ST1  C4   C5    aromatic  1.391  0.020  1.391
 ST1  N4   C4'   single    1.360  0.020  1.360
 ST1  N4   HN4   single    0.860  0.020  1.020
 ST1  C4'  O4'   double    1.215  0.020  1.215
 ST1  C4'  CM4   single    1.504  0.020  1.504
 ST1  CM4  HM41  single    0.970  0.020  1.090
 ST1  CM4  HM42  single    0.970  0.020  1.090
 ST1  CM4  HM43  single    0.970  0.020  1.090
 ST1  C5   N5    single    1.458  0.020  1.458
 ST1  C5   C6    aromatic  1.380  0.020  1.380
 ST1  N5   ON1   double    1.205  0.020  1.205
 ST1  N5   ON2   single    1.207  0.020  1.207
 ST1  C6   H6    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
 ST1  C1    C'   O2'   112.72  3.000
 ST1  C1    C'   O1'   123.25  3.000
 ST1  O2'   C'   O1'   124.03  3.000
 ST1  HO2'  O2'  C'    110.38  3.000
 ST1  C6    C1   C2    120.33  3.000
 ST1  C6    C1   C'    117.79  3.000
 ST1  C2    C1   C'    121.87  3.000
 ST1  H2    C2   C3    118.87  3.000
 ST1  H2    C2   C1    120.55  3.000
 ST1  C3    C2   C1    120.57  3.000
 ST1  C4    C3   O3    117.15  3.000
 ST1  C4    C3   C2    120.03  3.000
 ST1  O3    C3   C2    122.81  3.000
 ST1  HO3   O3   C3    110.84  3.000
 ST1  C5    C4   N4    122.60  3.000
 ST1  C5    C4   C3    117.68  3.000
 ST1  N4    C4   C3    119.68  3.000
 ST1  HN4   N4   C4'   119.39  3.000
 ST1  HN4   N4   C4    118.43  3.000
 ST1  C4'   N4   C4    121.60  3.000
 ST1  CM4   C4'  O4'   123.57  3.000
 ST1  CM4   C4'  N4    114.52  3.000
 ST1  O4'   C4'  N4    121.89  3.000
 ST1  HM43  CM4  HM42  109.15  3.000
 ST1  HM43  CM4  HM41  107.79  3.000
 ST1  HM42  CM4  HM41  107.87  3.000
 ST1  HM43  CM4  C4'   112.74  3.000
 ST1  HM42  CM4  C4'   110.09  3.000
 ST1  HM41  CM4  C4'   109.06  3.000
 ST1  C6    C5   N5    117.05  3.000
 ST1  C6    C5   C4    123.08  3.000
 ST1  N5    C5   C4    119.86  3.000
 ST1  ON2   N5   ON1   124.90  3.000
 ST1  ON2   N5   C5    117.16  3.000
 ST1  ON1   N5   C5    117.92  3.000
 ST1  H6    C6   C5    120.99  3.000
 ST1  H6    C6   C1    120.73  3.000
 ST1  C5    C6   C1    118.26  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
 ST1  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 ST1  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 ST1  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 ST1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 ST1  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 ST1  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 ST1  CONST_07  C3    C2   C1   C'    180.00   0.0  0
 ST1  CONST_08  C5    C6   C1   C'    180.00   0.0  0
 ST1  CONST_09  O3    C3   C2   C1    180.00   0.0  0
 ST1  CONST_10  N5    C5   C6   C1    180.00   0.0  0
 ST1  CONST_11  N4    C4   C3   C2    180.00   0.0  0
 ST1  CONST_12  N5    C5   C4   C3    180.00   0.0  0
 ST1  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 ST1  CONST_14  C6    C5   C4   N4    180.00   0.0  0
 ST1  CONST_15  H6    C6   C1   C2    180.00   0.0  0
 ST1  CONST_16  H2    C2   C3   C4    180.00   0.0  0
 ST1  CONST_24  O4'   C4'  N4   C4      0.00   0.0  0
 ST1  CONST_25  CM4   C4'  N4   C4    180.00   0.0  0
 ST1  CONST_26  HO2'  O2'  C'   C1    180.00   0.0  0
 ST1  Var_01    C2    C1   C'   O1'  -180.00  30.0  2
 ST1  Var_02    HM41  CM4  C4'  N4    -91.07  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
 ST1  plan-1  C'    0.020
 ST1  plan-1  C1    0.020
 ST1  plan-1  C2    0.020
 ST1  plan-1  C3    0.020
 ST1  plan-1  O3    0.020
 ST1  plan-1  C4    0.020
 ST1  plan-1  N4    0.020
 ST1  plan-1  C5    0.020
 ST1  plan-1  N5    0.020
 ST1  plan-1  C6    0.020
 ST1  plan-1  H2    0.020
 ST1  plan-1  H6    0.020
 ST1  plan-2  C4    0.020
 ST1  plan-2  N4    0.020
 ST1  plan-2  C4'   0.020
 ST1  plan-2  O4'   0.020
 ST1  plan-2  CM4   0.020
 ST1  plan-2  HN4   0.020
 ST1  plan-3  C5    0.020
 ST1  plan-3  N5    0.020
 ST1  plan-3  ON1   0.020
 ST1  plan-3  ON2   0.020
 ST1  plan-4  C'    0.020
 ST1  plan-4  O1'   0.020
 ST1  plan-4  O2'   0.020
 ST1  plan-4  C1    0.020
 ST1  plan-4  HO2'  0.020

