# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:40:10 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 5-nitro-1H-indole-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1[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
 B25  B25  5-nitro-1H-indole-2-carboximidamide  ligand  23  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B25
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
 B25  C1    C  CR56   0   0.380  -0.3978   0.9157   0.1005
 B25  N1    N  N      1   0.329   3.5780  -0.3517  -0.1057
 B25  O1    O  O      0  -0.391   3.8165  -1.5348  -0.2067
 B25  C2    C  CR16   0  -0.292   0.6124   1.8779   0.1485
 B25  N2    N  NH2    0  -0.828  -4.5183   0.7480  -0.2256
 B25  O2    O  O     -1  -0.390   4.4395   0.4983  -0.0613
 B25  C3    C  CR16   0  -0.300   1.9138   1.4433   0.0791
 B25  N3    N  N      0  -0.639  -4.2511  -1.4959   0.4869
 B25  C4    C  CR6    0   0.243   2.1952   0.0690  -0.0344
 B25  N4    N  NR15   0  -0.734  -1.7429   1.0543   0.1452
 B25  C5    C  CR16   0  -0.371   1.2058  -0.8954  -0.0792
 B25  C6    C  CR56   0   0.071  -0.1170  -0.4679  -0.0072
 B25  C7    C  CR15   0  -0.390  -1.3696  -1.1461  -0.0098
 B25  C8    C  CR5    0   0.338  -2.3355  -0.1861   0.0872
 B25  C9    C  C      0   0.301  -3.7977  -0.3638   0.1126
 B25  H2    H  HCR6   0   0.281   0.3863   2.9320   0.2344
 B25  H1N2  H  HNH2   0   0.398  -5.5151   0.6304  -0.3244
 B25  H2N2  H  HNH2   0   0.397  -4.1297   1.3771  -0.9107
 B25  H3    H  HCR6   0   0.292   2.7158   2.1649   0.1111
 B25  H1N3  H  H      0   0.331  -5.2649  -1.5257   0.4189
 B25  HN4   H  HNR5   0   0.420  -2.2287   1.9233   0.3038
 B25  H5    H  HCR6   0   0.290   1.4393  -1.9470  -0.1664
 B25  H7    H  HCR5   0   0.263  -1.5398  -2.2069  -0.0919

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
 B25  N3  C9    double    1.276  0.020  1.276
 B25  N4  C8    aromatic  1.376  0.020  1.376
 B25  N4  C1    aromatic  1.353  0.020  1.353
 B25  C9  C8    single    1.473  0.020  1.473
 B25  C9  N2    single    1.367  0.020  1.367
 B25  C2  C1    aromatic  1.396  0.020  1.396
 B25  C2  C3    aromatic  1.374  0.020  1.374
 B25  C8  C7    aromatic  1.365  0.020  1.365
 B25  C1  C6    aromatic  1.416  0.020  1.416
 B25  C3  C4    aromatic  1.407  0.020  1.407
 B25  C7  C6    aromatic  1.424  0.020  1.424
 B25  C6  C5    aromatic  1.392  0.020  1.392
 B25  C4  C5    aromatic  1.382  0.020  1.382
 B25  C4  N1    single    1.447  0.020  1.447
 B25  N1  O2    single    1.211  0.020  1.211
 B25  N1  O1    double    1.211  0.020  1.211
 B25  C2  H2    single    0.930  0.020  1.080
 B25  N2  H1N2  single    0.890  0.020  1.040
 B25  N2  H2N2  single    0.890  0.020  1.040
 B25  C3  H3    single    0.930  0.020  1.080
 B25  N3  H1N3  single    0.890  0.020  1.040
 B25  N4  HN4   single    0.860  0.020  1.020
 B25  C5  H5    single    0.930  0.020  1.080
 B25  C7  H7    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
 B25  C6    C1  N4    107.45  3.000
 B25  C6    C1  C2    122.18  3.000
 B25  N4    C1  C2    130.37  3.000
 B25  C4    N1  O2    118.28  3.000
 B25  O2    N1  O1    123.27  3.000
 B25  C4    N1  O1    118.44  3.000
 B25  H2    C2  C3    120.69  3.000
 B25  H2    C2  C1    121.55  3.000
 B25  C3    C2  C1    117.76  3.000
 B25  H2N2  N2  H1N2  112.78  3.000
 B25  H2N2  N2  C9    118.19  3.000
 B25  H1N2  N2  C9    116.76  3.000
 B25  H3    C3  C4    120.44  3.000
 B25  H3    C3  C2    119.40  3.000
 B25  C4    C3  C2    120.16  3.000
 B25  H1N3  N3  C9    111.15  3.000
 B25  C5    C4  C3    122.73  3.000
 B25  C5    C4  N1    118.65  3.000
 B25  C3    C4  N1    118.62  3.000
 B25  HN4   N4  C8    125.18  3.000
 B25  HN4   N4  C1    124.93  3.000
 B25  C8    N4  C1    109.54  3.000
 B25  H5    C5  C6    120.56  3.000
 B25  H5    C5  C4    121.79  3.000
 B25  C6    C5  C4    117.66  3.000
 B25  C7    C6  C5    133.57  3.000
 B25  C5    C6  C1    119.51  3.000
 B25  C7    C6  C1    106.91  3.000
 B25  H7    C7  C8    125.87  3.000
 B25  H7    C7  C6    127.43  3.000
 B25  C8    C7  C6    106.69  3.000
 B25  C9    C8  C7    128.22  3.000
 B25  C7    C8  N4    109.40  3.000
 B25  C9    C8  N4    122.38  3.000
 B25  C8    C9  N3    117.70  3.000
 B25  C8    C9  N2    114.88  3.000
 B25  N3    C9  N2    127.36  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
 B25  CONST_01  C7    C8  N4  C1    0.00   0.0  0
 B25  CONST_02  C4    C3  C2  C1    0.00   0.0  0
 B25  CONST_03  C8    C7  C6  C1    0.00   0.0  0
 B25  CONST_04  C4    C5  C6  C1    0.00   0.0  0
 B25  CONST_05  C8    N4  C1  C2  180.00   0.0  0
 B25  CONST_06  C7    C6  C1  C2  180.00   0.0  0
 B25  CONST_07  C5    C6  C1  C2    0.00   0.0  0
 B25  CONST_08  C5    C4  C3  C2    0.00   0.0  0
 B25  CONST_09  N4    C1  C2  C3  180.00   0.0  0
 B25  CONST_10  C6    C1  C2  C3    0.00   0.0  0
 B25  CONST_11  C6    C5  C4  C3    0.00   0.0  0
 B25  CONST_12  C7    C6  C5  C4  180.00   0.0  0
 B25  CONST_13  C6    C7  C8  N4    0.00   0.0  0
 B25  CONST_14  C7    C6  C1  N4    0.00   0.0  0
 B25  CONST_15  C5    C6  C1  N4  180.00   0.0  0
 B25  CONST_16  C8    C7  C6  C5  180.00   0.0  0
 B25  CONST_17  C8    N4  C1  C6    0.00   0.0  0
 B25  CONST_18  C9    C8  N4  C1  180.00   0.0  0
 B25  CONST_19  C2    C3  C4  N1  180.00   0.0  0
 B25  CONST_20  C6    C5  C4  N1  180.00   0.0  0
 B25  CONST_21  C9    C8  C7  C6  180.00   0.0  0
 B25  CONST_22  H3    C3  C2  C1  180.00   0.0  0
 B25  CONST_23  H7    C7  C6  C1  180.00   0.0  0
 B25  CONST_24  H5    C5  C6  C1  180.00   0.0  0
 B25  CONST_25  HN4   N4  C1  C2    0.00   0.0  0
 B25  CONST_26  H2    C2  C3  C4  180.00   0.0  0
 B25  CONST_27  C3    C4  N1  O1  180.00   0.0  0
 B25  CONST_28  C5    C4  N1  O1    0.00   0.0  0
 B25  CONST_29  C3    C4  N1  O2    0.00   0.0  0
 B25  CONST_30  C5    C4  N1  O2  180.00   0.0  0
 B25  CONST_31  H1N3  N3  C9  C8  180.00   0.0  0
 B25  CONST_32  H1N2  N2  C9  C8  180.00   0.0  0
 B25  Var_01    N4    C8  C9  N2   19.79  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
 B25  plan-1  C1    0.020
 B25  plan-1  N1    0.020
 B25  plan-1  C2    0.020
 B25  plan-1  C3    0.020
 B25  plan-1  C4    0.020
 B25  plan-1  N4    0.020
 B25  plan-1  C5    0.020
 B25  plan-1  C6    0.020
 B25  plan-1  C7    0.020
 B25  plan-1  C8    0.020
 B25  plan-1  C9    0.020
 B25  plan-1  H2    0.020
 B25  plan-1  H3    0.020
 B25  plan-1  HN4   0.020
 B25  plan-1  H5    0.020
 B25  plan-1  H7    0.020
 B25  plan-2  N1    0.020
 B25  plan-2  O1    0.020
 B25  plan-2  O2    0.020
 B25  plan-2  C4    0.020
 B25  plan-3  N2    0.020
 B25  plan-3  N3    0.020
 B25  plan-3  C8    0.020
 B25  plan-3  C9    0.020
 B25  plan-3  H1N2  0.020
 B25  plan-3  H2N2  0.020
 B25  plan-3  H1N3  0.020

