# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:24:44 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-nitro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]ccc2c1
#
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
 2HU  2HU  '5-nitro-1H-indole        '  ligand  18  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HU
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
 2HU  O1   O  O      0  -0.393   3.2979  -0.7088  -0.0158
 2HU  N2   N  N      1   0.328   2.5176   0.2179  -0.0141
 2HU  O3   O  O     -1  -0.394   2.8665   1.3781  -0.0194
 2HU  C4   C  CR6    0   0.239   1.1016  -0.0757  -0.0052
 2HU  C5   C  CR16   0  -0.302   0.6906  -1.4205  -0.0014
 2HU  C6   C  CR16   0  -0.290  -0.6487  -1.7314   0.0078
 2HU  C7   C  CR56   0   0.382  -1.5637  -0.6773   0.0135
 2HU  N8   N  NR15   0  -0.674  -2.9177  -0.6852   0.0229
 2HU  C9   C  CR15   0  -0.016  -3.3849   0.6025   0.0256
 2HU  C10  C  CR15   0  -0.399  -2.3381   1.4740   0.0173
 2HU  C11  C  CR56   0   0.061  -1.1510   0.6784   0.0094
 2HU  C12  C  CR16   0  -0.370   0.2062   0.9798  -0.0002
 2HU  H5   H  HCR6   0   0.289   1.4199  -2.2162  -0.0056
 2HU  H6   H  HCR6   0   0.279  -0.9742  -2.7630   0.0113
 2HU  HN8  H  HNR5   0   0.420  -3.4998  -1.5067   0.0299
 2HU  H9   H  HCR5   0   0.292  -4.4451   0.7960   0.0332
 2HU  H10  H  HCR5   0   0.260  -2.4021   2.5498   0.0169
 2HU  H12  H  HCR6   0   0.287   0.5421   2.0071  -0.0039

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
 2HU  O1   N2   double    1.211  0.020  1.211
 2HU  N2   O3   single    1.212  0.020  1.212
 2HU  N2   C4   single    1.446  0.020  1.446
 2HU  C4   C5   aromatic  1.406  0.020  1.406
 2HU  C4   C12  aromatic  1.384  0.020  1.384
 2HU  C5   C6   aromatic  1.375  0.020  1.375
 2HU  C6   C7   aromatic  1.396  0.020  1.396
 2HU  C7   N8   aromatic  1.354  0.020  1.354
 2HU  C7   C11  aromatic  1.417  0.020  1.417
 2HU  N8   C9   aromatic  1.370  0.020  1.370
 2HU  C9   C10  aromatic  1.362  0.020  1.362
 2HU  C10  C11  aromatic  1.429  0.020  1.429
 2HU  C11  C12  aromatic  1.390  0.020  1.390
 2HU  C5   H5   single    0.930  0.020  1.080
 2HU  C6   H6   single    0.930  0.020  1.080
 2HU  N8   HN8  single    0.860  0.020  1.020
 2HU  C9   H9   single    0.930  0.020  1.080
 2HU  C10  H10  single    0.930  0.020  1.080
 2HU  C12  H12  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
 2HU  C4   N2   O3   118.45  3.000
 2HU  C4   N2   O1   118.39  3.000
 2HU  O3   N2   O1   123.16  3.000
 2HU  C12  C4   C5   122.70  3.000
 2HU  C12  C4   N2   118.60  3.000
 2HU  C5   C4   N2   118.71  3.000
 2HU  H5   C5   C6   119.44  3.000
 2HU  H5   C5   C4   120.50  3.000
 2HU  C6   C5   C4   120.06  3.000
 2HU  H6   C6   C7   121.52  3.000
 2HU  H6   C6   C5   120.59  3.000
 2HU  C7   C6   C5   117.89  3.000
 2HU  C11  C7   N8   107.27  3.000
 2HU  C11  C7   C6   122.11  3.000
 2HU  N8   C7   C6   130.62  3.000
 2HU  HN8  N8   C9   124.73  3.000
 2HU  HN8  N8   C7   125.66  3.000
 2HU  C9   N8   C7   109.61  3.000
 2HU  H9   C9   C10  129.88  3.000
 2HU  H9   C9   N8   120.29  3.000
 2HU  C10  C9   N8   109.83  3.000
 2HU  H10  C10  C11  127.23  3.000
 2HU  H10  C10  C9   126.37  3.000
 2HU  C11  C10  C9   106.39  3.000
 2HU  C12  C11  C10  133.65  3.000
 2HU  C12  C11  C7   119.45  3.000
 2HU  C10  C11  C7   106.90  3.000
 2HU  H12  C12  C11  120.63  3.000
 2HU  H12  C12  C4   121.58  3.000
 2HU  C11  C12  C4   117.79  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
 2HU  CONST_01  C7   C6   C5   C4    0.00  0.0  0
 2HU  CONST_02  C7   C11  C12  C4    0.00  0.0  0
 2HU  CONST_03  C10  C11  C12  C4  180.00  0.0  0
 2HU  CONST_04  C11  C12  C4   C5    0.00  0.0  0
 2HU  CONST_05  N8   C7   C6   C5  180.00  0.0  0
 2HU  CONST_06  C11  C7   C6   C5    0.00  0.0  0
 2HU  CONST_07  C12  C4   C5   C6    0.00  0.0  0
 2HU  CONST_08  C9   N8   C7   C6  180.00  0.0  0
 2HU  CONST_09  C10  C11  C7   C6  180.00  0.0  0
 2HU  CONST_10  C12  C11  C7   C6    0.00  0.0  0
 2HU  CONST_11  C10  C9   N8   C7    0.00  0.0  0
 2HU  CONST_12  C9   C10  C11  C7    0.00  0.0  0
 2HU  CONST_13  C10  C11  C7   N8    0.00  0.0  0
 2HU  CONST_14  C12  C11  C7   N8  180.00  0.0  0
 2HU  CONST_15  C11  C10  C9   N8    0.00  0.0  0
 2HU  CONST_16  C11  C7   N8   C9    0.00  0.0  0
 2HU  CONST_17  C12  C11  C10  C9  180.00  0.0  0
 2HU  CONST_18  C6   C5   C4   N2  180.00  0.0  0
 2HU  CONST_19  C11  C12  C4   N2  180.00  0.0  0
 2HU  CONST_20  H6   C6   C5   C4  180.00  0.0  0
 2HU  CONST_21  H12  C12  C4   C5  180.00  0.0  0
 2HU  CONST_22  HN8  N8   C7   C6    0.00  0.0  0
 2HU  CONST_23  H5   C5   C6   C7  180.00  0.0  0
 2HU  CONST_24  H9   C9   N8   C7  180.00  0.0  0
 2HU  CONST_25  H10  C10  C11  C7  180.00  0.0  0
 2HU  CONST_26  C5   C4   N2   O1    0.00  0.0  0
 2HU  CONST_27  C12  C4   N2   O1  180.00  0.0  0
 2HU  CONST_28  C5   C4   N2   O3  180.00  0.0  0
 2HU  CONST_29  C12  C4   N2   O3    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
 2HU  plan-1  N2   0.020
 2HU  plan-1  C4   0.020
 2HU  plan-1  C5   0.020
 2HU  plan-1  C6   0.020
 2HU  plan-1  C7   0.020
 2HU  plan-1  N8   0.020
 2HU  plan-1  C9   0.020
 2HU  plan-1  C10  0.020
 2HU  plan-1  C11  0.020
 2HU  plan-1  C12  0.020
 2HU  plan-1  H5   0.020
 2HU  plan-1  H6   0.020
 2HU  plan-1  HN8  0.020
 2HU  plan-1  H9   0.020
 2HU  plan-1  H10  0.020
 2HU  plan-1  H12  0.020
 2HU  plan-2  O1   0.020
 2HU  plan-2  N2   0.020
 2HU  plan-2  O3   0.020
 2HU  plan-2  C4   0.020

