# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 18:11:17 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2E)-1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)\N=C\1NCCN\1Cc2ccc(Cl)nc2
#
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
 IM4  IM4  (2E)-1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine  ligand  27  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IM4
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
 IM4  C5   C   CR16   0  -0.203   1.8403   1.5648   0.4817
 IM4  C6   C   CR16   0  -0.222   3.0166   1.0883  -0.0676
 IM4  C1   C   CR6    0   0.119   3.1787  -0.2875  -0.1139
 IM4  CL7  CL  CL     0  -0.106   4.6355  -0.9373  -0.7914
 IM4  N2   N   N      0  -0.383   2.3010  -1.1539   0.3293
 IM4  C3   C   CR16   0  -0.082   1.1739  -0.6825   0.8492
 IM4  C4   C   CR6    0   0.065   0.8818   0.6722   0.9499
 IM4  C8   C   CH2    0  -0.443  -0.4276   1.1325   1.5294
 IM4  N9   N   NR5    0  -0.392  -1.4490   1.3572   0.5271
 IM4  C13  C   CH2    0  -0.298  -1.4103   2.5114  -0.3575
 IM4  C12  C   CH2    0  -0.259  -2.6268   2.2704  -1.2466
 IM4  N11  N   NR15   0  -0.744  -2.7857   0.8328  -1.1250
 IM4  C10  C   CR5    0   0.695  -2.1631   0.3717  -0.0455
 IM4  N14  N   N      0  -0.423  -2.1203  -0.8321   0.5212
 IM4  N15  N   N      1   0.496  -2.8531  -1.8117   0.0271
 IM4  O16  O   O      0  -0.262  -3.6078  -1.6746  -0.9322
 IM4  O17  O   O     -1  -0.577  -2.7320  -2.8883   0.5870
 IM4  H5   H   HCR6   0   0.294   1.6859   2.6344   0.5542
 IM4  H6   H   HCR6   0   0.297   3.7801   1.7578  -0.4347
 IM4  H3   H   HCR6   0   0.276   0.4634  -1.4202   1.2043
 IM4  H8   H   HCH2   0   0.266  -0.8035   0.4085   2.2494
 IM4  H8A  H   HCH2   0   0.304  -0.2961   2.0688   2.0735
 IM4  H13  H   HCH2   0   0.298  -1.4767   3.4427   0.2017
 IM4  H7   H   HCH2   0   0.310  -0.4870   2.5222  -0.9449
 IM4  H12  H   HCH2   0   0.284  -3.5140   2.7884  -0.8780
 IM4  H9   H   HCH2   0   0.285  -2.4522   2.5622  -2.2786
 IM4  H10  H   HNR5   0   0.406  -3.5130   0.3132  -1.5809

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
 IM4  C5   C4   aromatic  1.391  0.020  1.391
 IM4  C5   H5   single    0.930  0.020  1.080
 IM4  C6   C5   aromatic  1.383  0.020  1.383
 IM4  C6   C1   aromatic  1.386  0.020  1.386
 IM4  C6   H6   single    0.930  0.020  1.080
 IM4  C1   N2   aromatic  1.311  0.020  1.311
 IM4  CL7  C1   single    1.733  0.020  1.733
 IM4  N2   C3   aromatic  1.328  0.020  1.328
 IM4  C3   H3   single    0.930  0.020  1.080
 IM4  C4   C3   aromatic  1.389  0.020  1.389
 IM4  C4   C8   single    1.504  0.020  1.504
 IM4  C8   N9   single    1.449  0.020  1.449
 IM4  C8   H8   single    0.970  0.020  1.090
 IM4  C8   H8A  single    0.970  0.020  1.090
 IM4  N9   C10  single    1.345  0.020  1.345
 IM4  N9   C13  single    1.455  0.020  1.455
 IM4  C13  C12  single    1.526  0.020  1.526
 IM4  N11  C12  single    1.451  0.020  1.451
 IM4  C10  N11  single    1.329  0.020  1.329
 IM4  N14  C10  double    1.331  0.020  1.331
 IM4  N14  N15  single    1.319  0.020  1.319
 IM4  N15  O17  single    1.219  0.020  1.219
 IM4  O16  N15  double    1.228  0.020  1.228
 IM4  C13  H13  single    0.970  0.020  1.090
 IM4  C13  H7   single    0.970  0.020  1.090
 IM4  C12  H12  single    0.970  0.020  1.090
 IM4  C12  H9   single    0.970  0.020  1.090
 IM4  N11  H10  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
 IM4  H5   C5   C4   120.86  3.000
 IM4  H5   C5   C6   119.22  3.000
 IM4  C4   C5   C6   119.91  3.000
 IM4  H6   C6   C1   121.42  3.000
 IM4  H6   C6   C5   121.52  3.000
 IM4  C1   C6   C5   117.05  3.000
 IM4  N2   C1   CL7  116.57  3.000
 IM4  CL7  C1   C6   118.92  3.000
 IM4  N2   C1   C6   124.51  3.000
 IM4  C3   N2   C1   117.79  3.000
 IM4  H3   C3   C4   120.13  3.000
 IM4  C4   C3   N2   123.57  3.000
 IM4  H3   C3   N2   116.30  3.000
 IM4  C8   C4   C3   120.62  3.000
 IM4  C8   C4   C5   122.22  3.000
 IM4  C3   C4   C5   117.16  3.000
 IM4  H8A  C8   H8   106.43  3.000
 IM4  H8A  C8   N9   107.27  3.000
 IM4  H8   C8   N9   108.51  3.000
 IM4  H8A  C8   C4   110.48  3.000
 IM4  H8   C8   C4   110.61  3.000
 IM4  N9   C8   C4   113.25  3.000
 IM4  C10  N9   C13  109.67  3.000
 IM4  C13  N9   C8   121.67  3.000
 IM4  C10  N9   C8   123.73  3.000
 IM4  H7   C13  H13  108.59  3.000
 IM4  H7   C13  C12  111.19  3.000
 IM4  H13  C13  C12  112.70  3.000
 IM4  H7   C13  N9   110.90  3.000
 IM4  H13  C13  N9   111.40  3.000
 IM4  C12  C13  N9   101.99  3.000
 IM4  H9   C12  H12  108.90  3.000
 IM4  H9   C12  N11  111.29  3.000
 IM4  H12  C12  N11  110.66  3.000
 IM4  H9   C12  C13  112.52  3.000
 IM4  H12  C12  C13  112.10  3.000
 IM4  N11  C12  C13  101.24  3.000
 IM4  H10  N11  C10  121.94  3.000
 IM4  H10  N11  C12  123.66  3.000
 IM4  C10  N11  C12  111.13  3.000
 IM4  N14  C10  N11  132.44  3.000
 IM4  N14  C10  N9   117.66  3.000
 IM4  N11  C10  N9   109.90  3.000
 IM4  N15  N14  C10  119.61  3.000
 IM4  O17  N15  O16  121.21  3.000
 IM4  O16  N15  N14  123.43  3.000
 IM4  O17  N15  N14  115.36  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
 IM4  CONST_01  N2   C3   C4   C5     0.00   0.0  0
 IM4  CONST_02  N2   C1   C6   C5     0.00   0.0  0
 IM4  CONST_03  C3   C4   C5   C6     0.00   0.0  0
 IM4  CONST_04  C3   N2   C1   C6     0.00   0.0  0
 IM4  CONST_05  C4   C5   C6   C1     0.00   0.0  0
 IM4  CONST_06  C4   C3   N2   C1     0.00   0.0  0
 IM4  CONST_07  C12  N11  C10  N9     0.00   0.0  0
 IM4  CONST_09  N11  C10  N9   C13    0.00   0.0  0
 IM4  CONST_12  CL7  C1   C6   C5   180.00   0.0  0
 IM4  CONST_13  C8   C4   C5   C6   180.00   0.0  0
 IM4  CONST_14  C3   N2   C1   CL7  180.00   0.0  0
 IM4  CONST_15  C8   C4   C3   N2   180.00   0.0  0
 IM4  CONST_16  N11  C10  N9   C8   180.00   0.0  0
 IM4  CONST_17  C12  C13  N9   C8   180.00   0.0  0
 IM4  CONST_18  N14  C10  N9   C13  180.00   0.0  0
 IM4  CONST_19  N14  C10  N11  C12  180.00   0.0  0
 IM4  CONST_20  H3   C3   C4   C5   180.00   0.0  0
 IM4  CONST_21  H5   C5   C6   C1   180.00   0.0  0
 IM4  CONST_22  H6   C6   C1   N2   180.00   0.0  0
 IM4  CONST_23  H10  N11  C10  N9   180.00   0.0  0
 IM4  CONST_24  N14  C10  N9   C8     0.00   0.0  0
 IM4  CONST_25  N15  N14  C10  N9   180.00   0.0  0
 IM4  CONST_26  N15  N14  C10  N11    0.00   0.0  0
 IM4  Var_01    N9   C8   C4   C5    85.79  30.0  2
 IM4  Var_02    C10  N9   C8   C4    79.05  30.0  3
 IM4  Var_03    H12  C12  C13  N9    94.52  30.0  1
 IM4  Var_04    O17  N15  N14  C10  178.43  30.0  3

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
 IM4  plan-1  C5   0.020
 IM4  plan-1  C6   0.020
 IM4  plan-1  C1   0.020
 IM4  plan-1  CL7  0.020
 IM4  plan-1  N2   0.020
 IM4  plan-1  C3   0.020
 IM4  plan-1  C4   0.020
 IM4  plan-1  C8   0.020
 IM4  plan-1  H5   0.020
 IM4  plan-1  H6   0.020
 IM4  plan-1  H3   0.020
 IM4  plan-2  C8   0.020
 IM4  plan-2  N9   0.020
 IM4  plan-2  C13  0.020
 IM4  plan-2  C12  0.020
 IM4  plan-2  N11  0.020
 IM4  plan-2  C10  0.020
 IM4  plan-2  N14  0.020
 IM4  plan-2  N15  0.020
 IM4  plan-2  H10  0.020
 IM4  plan-3  N14  0.020
 IM4  plan-3  N15  0.020
 IM4  plan-3  O16  0.020
 IM4  plan-3  O17  0.020

