# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 15:44:47 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: 1-methyl-5-nitro-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cncc1[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
 EIV  EIV  "1-methyl-5-nitro-1H-imidazole"
  ligand  14  9  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EIV
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
 EIV  C06  C  CR5    0   0.406  20.9370  4.2338  36.5787
 EIV  C07  C  CH3    0  -0.540  18.9657  4.3874  34.9041
 EIV  C08  C  CR15   0   0.151  20.0892  2.4048  35.8221
 EIV  C09  C  CR15   0  -0.134  21.6054  3.1505  37.0987
 EIV  N03  N  NR5    0  -0.446  19.9550  3.7361  35.7558
 EIV  N04  N  N      0  -0.430  21.0629  2.0178  36.6199
 EIV  N05  N  N      1   0.335  21.1944  5.5918  36.8644
 EIV  O01  O  O      0  -0.393  20.4413  6.4452  36.4462
 EIV  O02  O  O     -1  -0.390  22.1749  5.8245  37.5379
 EIV  H1   H  HCH3   0   0.288  19.0076  5.4598  35.0218
 EIV  H2   H  HCH3   0   0.275  19.1629  4.1340  33.8656
 EIV  H3   H  HCH3   0   0.275  17.9740  4.0386  35.1802
 EIV  H4   H  HCR5   0   0.304  19.4446  1.7470  35.2580
 EIV  H5   H  HCR5   0   0.297  22.4311  3.1541  37.7927

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
 EIV  C07  N03  single    1.459  0.020  1.459
 EIV  N03  C08  aromatic  1.340  0.020  1.340
 EIV  N03  C06  aromatic  1.374  0.020  1.374
 EIV  C08  N04  aromatic  1.317  0.020  1.317
 EIV  O01  N05  double    1.213  0.020  1.213
 EIV  C06  N05  single    1.411  0.020  1.411
 EIV  C06  C09  aromatic  1.375  0.020  1.375
 EIV  N04  C09  aromatic  1.344  0.020  1.344
 EIV  N05  O02  single    1.212  0.020  1.212
 EIV  C07  H1   single    0.970  0.020  1.090
 EIV  C07  H2   single    0.970  0.020  1.090
 EIV  C07  H3   single    0.970  0.020  1.090
 EIV  C08  H4   single    0.930  0.020  1.080
 EIV  C09  H5   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
 EIV  N05  C06  N03  126.86  3.000
 EIV  N05  C06  C09  126.35  3.000
 EIV  N03  C06  C09  106.77  3.000
 EIV  H3   C07  H2   109.48  3.000
 EIV  H3   C07  H1   109.06  3.000
 EIV  H2   C07  H1   109.19  3.000
 EIV  H3   C07  N03  109.10  3.000
 EIV  H2   C07  N03  109.31  3.000
 EIV  H1   C07  N03  110.70  3.000
 EIV  H4   C08  N04  125.36  3.000
 EIV  H4   C08  N03  121.31  3.000
 EIV  N04  C08  N03  113.34  3.000
 EIV  H5   C09  N04  122.74  3.000
 EIV  H5   C09  C06  127.80  3.000
 EIV  N04  C09  C06  109.45  3.000
 EIV  C08  N03  C07  122.72  3.000
 EIV  C08  N03  C06  104.99  3.000
 EIV  C07  N03  C06  132.25  3.000
 EIV  C09  N04  C08  105.46  3.000
 EIV  O02  N05  O01  123.98  3.000
 EIV  O02  N05  C06  116.41  3.000
 EIV  O01  N05  C06  119.61  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
 EIV  CONST_01  N04  C08  N03  C06     0.00   0.0  0
 EIV  CONST_02  C08  N04  C09  C06     0.00   0.0  0
 EIV  CONST_03  C09  C06  N03  C08     0.00   0.0  0
 EIV  CONST_04  N03  C08  N04  C09     0.00   0.0  0
 EIV  CONST_05  N04  C09  C06  N03     0.00   0.0  0
 EIV  CONST_06  N04  C08  N03  C07   180.00   0.0  0
 EIV  CONST_07  C09  C06  N03  C07   180.00   0.0  0
 EIV  CONST_08  N05  C06  N03  C08   180.00   0.0  0
 EIV  CONST_09  N05  C06  C09  N04   180.00   0.0  0
 EIV  CONST_10  H4   C08  N03  C06   180.00   0.0  0
 EIV  CONST_11  H5   C09  N04  C08   180.00   0.0  0
 EIV  CONST_12  H4   C08  N04  C09   180.00   0.0  0
 EIV  CONST_13  H5   C09  C06  N03   180.00   0.0  0
 EIV  CONST_14  O01  N05  C06  C09   180.00   0.0  0
 EIV  CONST_15  O02  N05  C06  C09     0.00   0.0  0
 EIV  CONST_16  O01  N05  C06  N03     0.00   0.0  0
 EIV  CONST_17  O02  N05  C06  N03   180.00   0.0  0
 EIV  Var_01    H1   C07  N03  C06    -4.47  30.0  2
 EIV  Var_02    H2   C07  N03  C06   115.84  30.0  2
 EIV  Var_03    H3   C07  N03  C06  -124.48  30.0  2
 EIV  Var_04    H1   C07  N03  C08   178.38  30.0  2
 EIV  Var_05    H2   C07  N03  C08   -61.31  30.0  2
 EIV  Var_06    H3   C07  N03  C08    58.37  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
 EIV  plan-1  C06  0.020
 EIV  plan-1  C07  0.020
 EIV  plan-1  C08  0.020
 EIV  plan-1  C09  0.020
 EIV  plan-1  N03  0.020
 EIV  plan-1  N04  0.020
 EIV  plan-1  N05  0.020
 EIV  plan-1  H4   0.020
 EIV  plan-1  H5   0.020
 EIV  plan-2  C06  0.020
 EIV  plan-2  N05  0.020
 EIV  plan-2  O01  0.020
 EIV  plan-2  O02  0.020

