# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:17:10 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 6-nitro-1H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2cn[nH]c2c1
#
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
 6NI  6NI  '6-nitro-1H-indazole      '  ligand  17  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6NI
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
 6NI  C6    C  CR6    0   0.244   1.0899  -0.0639   0.0143
 6NI  C7    C  CR16   0  -0.314   0.1858   0.9749   0.0141
 6NI  C8    C  CR56   0   0.443  -1.1563   0.6032   0.0078
 6NI  C9    C  CR56   0  -0.078  -1.5707  -0.7413   0.0021
 6NI  C4    C  CR16   0  -0.307  -0.6140  -1.7642   0.0027
 6NI  C5    C  CR16   0  -0.290   0.7156  -1.4225   0.0087
 6NI  N1    N  NR15   0  -0.539  -2.2887   1.3421   0.0056
 6NI  N2    N  N      0  -0.208  -3.3809   0.5846  -0.0011
 6NI  C3    C  CR15   0  -0.112  -2.9871  -0.6653  -0.0035
 6NI  N10   N  N      1   0.330   2.5082   0.2655   0.0211
 6NI  O11   O  O     -1  -0.377   3.3035  -0.6445   0.0213
 6NI  O12   O  O      0  -0.379   2.8237   1.4325   0.0258
 6NI  H71   H  HCR6   0   0.311   0.4892   2.0118   0.0186
 6NI  H41   H  HCR6   0   0.275  -0.9094  -2.8046  -0.0011
 6NI  H51   H  HCR6   0   0.295   1.4688  -2.1954   0.0092
 6NI  HN11  H  HNR5   0   0.427  -2.3748   2.3460   0.0076
 6NI  H31   H  HCR5   0   0.280  -3.7044  -1.4707  -0.0089

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
 6NI  C6   C7    aromatic  1.377  0.020  1.377
 6NI  C6   C5    aromatic  1.409  0.020  1.409
 6NI  C6   N10   single    1.456  0.020  1.456
 6NI  C7   C8    aromatic  1.393  0.020  1.393
 6NI  C7   H71   single    0.930  0.020  1.080
 6NI  C8   C9    aromatic  1.407  0.020  1.407
 6NI  C8   N1    aromatic  1.352  0.020  1.352
 6NI  C9   C4    aromatic  1.401  0.020  1.401
 6NI  C9   C3    aromatic  1.418  0.020  1.418
 6NI  C4   C5    aromatic  1.373  0.020  1.373
 6NI  C4   H41   single    0.930  0.020  1.080
 6NI  C5   H51   single    0.930  0.020  1.080
 6NI  N1   N2    aromatic  1.329  0.020  1.329
 6NI  N1   HN11  single    0.860  0.020  1.020
 6NI  N2   C3    aromatic  1.310  0.020  1.310
 6NI  C3   H31   single    0.930  0.020  1.080
 6NI  N10  O11   single    1.209  0.020  1.209
 6NI  N10  O12   double    1.209  0.020  1.209

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
 6NI  N10   C6   C5   118.48  3.000
 6NI  N10   C6   C7   117.96  3.000
 6NI  C5    C6   C7   123.56  3.000
 6NI  H71   C7   C8   121.79  3.000
 6NI  H71   C7   C6   122.66  3.000
 6NI  C8    C7   C6   115.55  3.000
 6NI  N1    C8   C9   105.99  3.000
 6NI  N1    C8   C7   131.40  3.000
 6NI  C9    C8   C7   122.61  3.000
 6NI  C3    C9   C4   136.16  3.000
 6NI  C3    C9   C8   104.06  3.000
 6NI  C4    C9   C8   119.78  3.000
 6NI  H41   C4   C5   120.26  3.000
 6NI  H41   C4   C9   121.06  3.000
 6NI  C5    C4   C9   118.67  3.000
 6NI  H51   C5   C4   119.85  3.000
 6NI  H51   C5   C6   120.34  3.000
 6NI  C4    C5   C6   119.82  3.000
 6NI  HN11  N1   N2   119.84  3.000
 6NI  HN11  N1   C8   128.02  3.000
 6NI  N2    N1   C8   112.13  3.000
 6NI  C3    N2   N1   107.25  3.000
 6NI  H31   C3   N2   120.82  3.000
 6NI  H31   C3   C9   128.62  3.000
 6NI  N2    C3   C9   110.56  3.000
 6NI  O12   N10  O11  123.71  3.000
 6NI  O12   N10  C6   118.20  3.000
 6NI  O11   N10  C6   118.08  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
 6NI  CONST_01  C9    C8   C7  C6    0.00  0.0  0
 6NI  CONST_02  N1    C8   C7  C6  180.00  0.0  0
 6NI  CONST_03  C9    C4   C5  C6    0.00  0.0  0
 6NI  CONST_04  C4    C5   C6  C7    0.00  0.0  0
 6NI  CONST_05  C4    C9   C8  C7    0.00  0.0  0
 6NI  CONST_06  C3    C9   C8  C7  180.00  0.0  0
 6NI  CONST_07  N2    N1   C8  C7  180.00  0.0  0
 6NI  CONST_08  C5    C6   C7  C8    0.00  0.0  0
 6NI  CONST_09  C5    C4   C9  C8    0.00  0.0  0
 6NI  CONST_10  N2    C3   C9  C8    0.00  0.0  0
 6NI  CONST_11  C3    N2   N1  C8    0.00  0.0  0
 6NI  CONST_12  N2    N1   C8  C9    0.00  0.0  0
 6NI  CONST_13  N1    N2   C3  C9    0.00  0.0  0
 6NI  CONST_14  N1    C8   C9  C4  180.00  0.0  0
 6NI  CONST_15  N2    C3   C9  C4  180.00  0.0  0
 6NI  CONST_16  C3    C9   C4  C5  180.00  0.0  0
 6NI  CONST_17  C3    C9   C8  N1    0.00  0.0  0
 6NI  CONST_18  N10   C6   C7  C8  180.00  0.0  0
 6NI  CONST_19  N10   C6   C5  C4  180.00  0.0  0
 6NI  CONST_20  H41   C4   C5  C6  180.00  0.0  0
 6NI  CONST_21  H51   C5   C6  C7  180.00  0.0  0
 6NI  CONST_22  HN11  N1   C8  C7    0.00  0.0  0
 6NI  CONST_23  H31   C3   C9  C8  180.00  0.0  0
 6NI  CONST_24  H71   C7   C8  C9  180.00  0.0  0
 6NI  CONST_25  O11   N10  C6  C7  180.00  0.0  0
 6NI  CONST_26  O12   N10  C6  C7    0.00  0.0  0
 6NI  CONST_27  O11   N10  C6  C5    0.00  0.0  0
 6NI  CONST_28  O12   N10  C6  C5  180.00  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
 6NI  plan-1  C6    0.020
 6NI  plan-1  C7    0.020
 6NI  plan-1  C8    0.020
 6NI  plan-1  C9    0.020
 6NI  plan-1  C4    0.020
 6NI  plan-1  C5    0.020
 6NI  plan-1  N1    0.020
 6NI  plan-1  N2    0.020
 6NI  plan-1  C3    0.020
 6NI  plan-1  N10   0.020
 6NI  plan-1  H71   0.020
 6NI  plan-1  H41   0.020
 6NI  plan-1  H51   0.020
 6NI  plan-1  HN11  0.020
 6NI  plan-1  H31   0.020
 6NI  plan-2  C6    0.020
 6NI  plan-2  N10   0.020
 6NI  plan-2  O11   0.020
 6NI  plan-2  O12   0.020

