# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:22:56 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-methyl-5-nitro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ccc(cc2c1)[N+]([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
 70T  70T  2-methyl-5-nitro-1H-indole  ligand  21  13  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_70T
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
 70T  C6   C  CR15   0  -0.442  -2.0045  -1.2897  -0.0299
 70T  C5   C  CR56   0   0.082  -0.7743  -0.5643  -0.0062
 70T  C4   C  CR56   0   0.372  -1.1124   0.8106   0.0437
 70T  C2   C  CR5    0   0.344  -3.0132  -0.3702   0.0057
 70T  C7   C  CR16   0  -0.297  -0.1444   1.8135   0.0760
 70T  C8   C  CR16   0  -0.305   1.1780   1.4329   0.0590
 70T  C9   C  CR6    0   0.238   1.5162   0.0702   0.0111
 70T  C10  C  CR16   0  -0.380   0.5642  -0.9364  -0.0222
 70T  C1   C  CH3    0  -0.738  -4.4846  -0.5659   0.0022
 70T  N3   N  NR15   0  -0.712  -2.4649   0.8902   0.0501
 70T  N11  N  N      1   0.328   2.9139  -0.2975  -0.0053
 70T  O12  O  O     -1  -0.394   3.7429   0.5859   0.0185
 70T  O13  O  O      0  -0.395   3.2015  -1.4742  -0.0426
 70T  H1   H  HCR5   0   0.256  -2.1289  -2.3602  -0.0679
 70T  H2   H  HCR6   0   0.277  -0.4154   2.8601   0.1131
 70T  H3   H  HCR6   0   0.288   1.9482   2.1887   0.0829
 70T  H4   H  HCR6   0   0.285   0.8446  -1.9795  -0.0604
 70T  H5   H  HCH3   0   0.259  -4.9396  -0.1865   0.9189
 70T  H6   H  HCH3   0   0.258  -4.9519  -0.0447  -0.8349
 70T  H7   H  HCH3   0   0.260  -4.7237  -1.6237  -0.0815
 70T  H8   H  HNR5   0   0.415  -2.9965   1.7456   0.0828

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
 70T  C7   C8   aromatic  1.376  0.020  1.376
 70T  C7   C4   aromatic  1.394  0.020  1.394
 70T  C8   C9   aromatic  1.405  0.020  1.405
 70T  C4   N3   aromatic  1.355  0.020  1.355
 70T  C4   C5   aromatic  1.417  0.020  1.417
 70T  N3   C2   aromatic  1.375  0.020  1.375
 70T  C9   N11  single    1.445  0.020  1.445
 70T  C9   C10  aromatic  1.386  0.020  1.386
 70T  O13  N11  double    1.212  0.020  1.212
 70T  N11  O12  single    1.212  0.020  1.212
 70T  C5   C10  aromatic  1.389  0.020  1.389
 70T  C5   C6   aromatic  1.428  0.020  1.428
 70T  C2   C1   single    1.484  0.020  1.484
 70T  C2   C6   aromatic  1.365  0.020  1.365
 70T  C6   H1   single    0.930  0.020  1.080
 70T  C7   H2   single    0.930  0.020  1.080
 70T  C8   H3   single    0.930  0.020  1.080
 70T  C10  H4   single    0.930  0.020  1.080
 70T  C1   H5   single    0.970  0.020  1.090
 70T  C1   H6   single    0.970  0.020  1.090
 70T  C1   H7   single    0.970  0.020  1.090
 70T  N3   H8   single    0.860  0.020  1.020

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
 70T  H1   C6   C2   125.75  3.000
 70T  H1   C6   C5   127.16  3.000
 70T  C2   C6   C5   107.09  3.000
 70T  C10  C5   C4   119.36  3.000
 70T  C10  C5   C6   133.91  3.000
 70T  C4   C5   C6   106.73  3.000
 70T  N3   C4   C7   130.60  3.000
 70T  N3   C4   C5   107.18  3.000
 70T  C7   C4   C5   122.22  3.000
 70T  N3   C2   C1   121.07  3.000
 70T  C1   C2   C6   130.05  3.000
 70T  N3   C2   C6   108.88  3.000
 70T  H2   C7   C8   120.58  3.000
 70T  H2   C7   C4   121.52  3.000
 70T  C8   C7   C4   117.90  3.000
 70T  H3   C8   C9   120.54  3.000
 70T  H3   C8   C7   119.46  3.000
 70T  C9   C8   C7   120.00  3.000
 70T  N11  C9   C10  118.64  3.000
 70T  C10  C9   C8   122.68  3.000
 70T  N11  C9   C8   118.68  3.000
 70T  H4   C10  C9   121.57  3.000
 70T  H4   C10  C5   120.59  3.000
 70T  C9   C10  C5   117.84  3.000
 70T  H7   C1   H6   108.14  3.000
 70T  H7   C1   H5   108.13  3.000
 70T  H6   C1   H5   107.44  3.000
 70T  H7   C1   C2   110.26  3.000
 70T  H6   C1   C2   111.30  3.000
 70T  H5   C1   C2   111.43  3.000
 70T  H8   N3   C2   124.67  3.000
 70T  H8   N3   C4   125.21  3.000
 70T  C2   N3   C4   110.12  3.000
 70T  O13  N11  O12  123.10  3.000
 70T  O12  N11  C9   118.42  3.000
 70T  O13  N11  C9   118.48  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
 70T  CONST_01  C7   C4   C5   C6   180.00   0.0  0
 70T  CONST_02  N3   C4   C5   C6     0.00   0.0  0
 70T  CONST_03  C9   C10  C5   C6   180.00   0.0  0
 70T  CONST_04  C4   N3   C2   C6     0.00   0.0  0
 70T  CONST_05  C8   C7   C4   C5     0.00   0.0  0
 70T  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 70T  CONST_07  C8   C9   C10  C5     0.00   0.0  0
 70T  CONST_08  N3   C2   C6   C5     0.00   0.0  0
 70T  CONST_09  C9   C8   C7   C4     0.00   0.0  0
 70T  CONST_10  C9   C10  C5   C4     0.00   0.0  0
 70T  CONST_11  C2   C6   C5   C4     0.00   0.0  0
 70T  CONST_12  C7   C4   N3   C2   180.00   0.0  0
 70T  CONST_13  C10  C5   C6   C2   180.00   0.0  0
 70T  CONST_14  C10  C9   C8   C7     0.00   0.0  0
 70T  CONST_15  C10  C5   C4   C7     0.00   0.0  0
 70T  CONST_16  N3   C4   C7   C8   180.00   0.0  0
 70T  CONST_17  N3   C4   C5   C10  180.00   0.0  0
 70T  CONST_18  N11  C9   C10  C5   180.00   0.0  0
 70T  CONST_19  C1   C2   C6   C5   180.00   0.0  0
 70T  CONST_20  C1   C2   N3   C4   180.00   0.0  0
 70T  CONST_21  N11  C9   C8   C7   180.00   0.0  0
 70T  CONST_22  H4   C10  C5   C6     0.00   0.0  0
 70T  CONST_23  H8   N3   C2   C6   180.00   0.0  0
 70T  CONST_24  H2   C7   C4   C5   180.00   0.0  0
 70T  CONST_25  H3   C8   C7   C4   180.00   0.0  0
 70T  CONST_26  H1   C6   C5   C4   180.00   0.0  0
 70T  CONST_27  O13  N11  C9   C8   180.00   0.0  0
 70T  CONST_28  O12  N11  C9   C8     0.00   0.0  0
 70T  CONST_29  O13  N11  C9   C10    0.00   0.0  0
 70T  CONST_30  O12  N11  C9   C10  180.00   0.0  0
 70T  Var_01    H5   C1   C2   C6   117.48  30.0  2

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
 70T  plan-1  C6   0.020
 70T  plan-1  C5   0.020
 70T  plan-1  C4   0.020
 70T  plan-1  C2   0.020
 70T  plan-1  C7   0.020
 70T  plan-1  C8   0.020
 70T  plan-1  C9   0.020
 70T  plan-1  C10  0.020
 70T  plan-1  C1   0.020
 70T  plan-1  N3   0.020
 70T  plan-1  N11  0.020
 70T  plan-1  H1   0.020
 70T  plan-1  H2   0.020
 70T  plan-1  H3   0.020
 70T  plan-1  H4   0.020
 70T  plan-1  H8   0.020
 70T  plan-2  C9   0.020
 70T  plan-2  N11  0.020
 70T  plan-2  O12  0.020
 70T  plan-2  O13  0.020

