# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:01:11 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 5-nitro-1H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]ncc2c1
#
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
 5NI  5NI  '5-nitro-1H-indazole      '  ligand  17  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_5NI
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
 5NI  C6    C  CR16   0  -0.288   0.7437  -1.4173   0.0092
 5NI  C7    C  CR16   0  -0.276  -0.5866  -1.7463   0.0316
 5NI  C8    C  CR56   0   0.449  -1.5067  -0.6898   0.0261
 5NI  C9    C  CR56   0  -0.088  -1.0983   0.6576  -0.0012
 5NI  C4    C  CR16   0  -0.342   0.2547   0.9828  -0.0240
 5NI  C5    C  CR6    0   0.245   1.1500  -0.0658  -0.0180
 5NI  N1    N  NR15   0  -0.539  -2.8511  -0.6640   0.0438
 5NI  N2    N  N      0  -0.214  -3.3394   0.5820   0.0301
 5NI  C3    C  CR15   0  -0.099  -2.3162   1.3925   0.0029
 5NI  N10   N  N      1   0.330   2.5675   0.2325  -0.0406
 5NI  O11   O  O     -1  -0.386   3.3475  -0.6928  -0.0325
 5NI  O12   O  O      0  -0.387   2.9092   1.3933  -0.0667
 5NI  H61   H  HCR6   0   0.299   1.4817  -2.2053   0.0110
 5NI  H71   H  HCR6   0   0.290  -0.9035  -2.7796   0.0525
 5NI  H41   H  HCR6   0   0.298   0.5783   2.0137  -0.0456
 5NI  HN11  H  HNR5   0   0.426  -3.4849  -1.4467   0.0659
 5NI  H31   H  HCR5   0   0.281  -2.4555   2.4624  -0.0113

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
 5NI  C6   C7    aromatic  1.371  0.020  1.371
 5NI  C6   C5    aromatic  1.412  0.020  1.412
 5NI  C6   H61   single    0.930  0.020  1.080
 5NI  C7   C8    aromatic  1.401  0.020  1.401
 5NI  C7   H71   single    0.930  0.020  1.080
 5NI  C8   C9    aromatic  1.408  0.020  1.408
 5NI  C8   N1    aromatic  1.345  0.020  1.345
 5NI  C9   C4    aromatic  1.392  0.020  1.392
 5NI  C9   C3    aromatic  1.422  0.020  1.422
 5NI  C4   C5    aromatic  1.379  0.020  1.379
 5NI  C4   H41   single    0.930  0.020  1.080
 5NI  C5   N10   single    1.449  0.020  1.449
 5NI  N1   N2    aromatic  1.338  0.020  1.338
 5NI  N1   HN11  single    0.860  0.020  1.020
 5NI  N2   C3    aromatic  1.306  0.020  1.306
 5NI  C3   H31   single    0.930  0.020  1.080
 5NI  N10  O11   single    1.210  0.020  1.210
 5NI  N10  O12   double    1.210  0.020  1.210

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
 5NI  H61   C6   C5   120.14  3.000
 5NI  H61   C6   C7   119.23  3.000
 5NI  C5    C6   C7   120.63  3.000
 5NI  H71   C7   C8   121.90  3.000
 5NI  H71   C7   C6   120.95  3.000
 5NI  C8    C7   C6   117.15  3.000
 5NI  N1    C8   C9   105.77  3.000
 5NI  N1    C8   C7   132.14  3.000
 5NI  C9    C8   C7   122.09  3.000
 5NI  C3    C9   C4   135.38  3.000
 5NI  C3    C9   C8   104.24  3.000
 5NI  C4    C9   C8   120.38  3.000
 5NI  H41   C4   C5   122.08  3.000
 5NI  H41   C4   C9   120.95  3.000
 5NI  C5    C4   C9   116.97  3.000
 5NI  N10   C5   C4   118.60  3.000
 5NI  N10   C5   C6   118.62  3.000
 5NI  C4    C5   C6   122.78  3.000
 5NI  HN11  N1   N2   119.60  3.000
 5NI  HN11  N1   C8   127.90  3.000
 5NI  N2    N1   C8   112.49  3.000
 5NI  C3    N2   N1   106.99  3.000
 5NI  H31   C3   N2   120.97  3.000
 5NI  H31   C3   C9   128.52  3.000
 5NI  N2    C3   C9   110.51  3.000
 5NI  O12   N10  O11  123.47  3.000
 5NI  O12   N10  C5   118.29  3.000
 5NI  O11   N10  C5   118.24  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
 5NI  CONST_01  C9    C8   C7  C6    0.00  0.0  0
 5NI  CONST_02  N1    C8   C7  C6  180.00  0.0  0
 5NI  CONST_03  C9    C4   C5  C6    0.00  0.0  0
 5NI  CONST_04  C4    C5   C6  C7    0.00  0.0  0
 5NI  CONST_05  C4    C9   C8  C7    0.00  0.0  0
 5NI  CONST_06  C3    C9   C8  C7  180.00  0.0  0
 5NI  CONST_07  N2    N1   C8  C7  180.00  0.0  0
 5NI  CONST_08  C5    C6   C7  C8    0.00  0.0  0
 5NI  CONST_09  C5    C4   C9  C8    0.00  0.0  0
 5NI  CONST_10  N2    C3   C9  C8    0.00  0.0  0
 5NI  CONST_11  C3    N2   N1  C8    0.00  0.0  0
 5NI  CONST_12  N2    N1   C8  C9    0.00  0.0  0
 5NI  CONST_13  N1    N2   C3  C9    0.00  0.0  0
 5NI  CONST_14  N1    C8   C9  C4  180.00  0.0  0
 5NI  CONST_15  N2    C3   C9  C4  180.00  0.0  0
 5NI  CONST_16  C3    C9   C4  C5  180.00  0.0  0
 5NI  CONST_17  C3    C9   C8  N1    0.00  0.0  0
 5NI  CONST_18  N10   C5   C6  C7  180.00  0.0  0
 5NI  CONST_19  N10   C5   C4  C9  180.00  0.0  0
 5NI  CONST_20  H41   C4   C5  C6  180.00  0.0  0
 5NI  CONST_21  HN11  N1   C8  C7    0.00  0.0  0
 5NI  CONST_22  H61   C6   C7  C8  180.00  0.0  0
 5NI  CONST_23  H31   C3   C9  C8  180.00  0.0  0
 5NI  CONST_24  H71   C7   C8  C9  180.00  0.0  0
 5NI  CONST_25  O11   N10  C5  C6    0.00  0.0  0
 5NI  CONST_26  O12   N10  C5  C6  180.00  0.0  0
 5NI  CONST_27  O11   N10  C5  C4  180.00  0.0  0
 5NI  CONST_28  O12   N10  C5  C4    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
 5NI  plan-1  C6    0.020
 5NI  plan-1  C7    0.020
 5NI  plan-1  C8    0.020
 5NI  plan-1  C9    0.020
 5NI  plan-1  C4    0.020
 5NI  plan-1  C5    0.020
 5NI  plan-1  N1    0.020
 5NI  plan-1  N2    0.020
 5NI  plan-1  C3    0.020
 5NI  plan-1  N10   0.020
 5NI  plan-1  H61   0.020
 5NI  plan-1  H71   0.020
 5NI  plan-1  H41   0.020
 5NI  plan-1  HN11  0.020
 5NI  plan-1  H31   0.020
 5NI  plan-2  C5    0.020
 5NI  plan-2  N10   0.020
 5NI  plan-2  O11   0.020
 5NI  plan-2  O12   0.020

