# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:01:46 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: S-(2-aminoethyl) 1H-imidazole-4-carbothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCSC(=O)c1c[nH]cn1
#
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
 2JE  2JE  'S-(2-aminoethyl) 1H-imidazole-4-carbothioate'  ligand  20  11  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2JE
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
 2JE  C4   C  CR15  0  -0.034   2.8174   1.0513  -0.0586
 2JE  N3   N  NR15  0  -0.557   3.8379   0.1678  -0.0164
 2JE  C2   C  CR15  0   0.105   3.3118  -1.0798   0.0415
 2JE  N4   N  N     0  -0.436   2.0100  -1.0466   0.0387
 2JE  C5   C  CR5   0   0.076   1.6821   0.2783  -0.0235
 2JE  O6   O  O     0  -0.402   0.0001   1.9235  -0.0917
 2JE  C22  C  C     0   0.153   0.3053   0.7536  -0.0446
 2JE  S1   S  S2    0  -0.001  -0.8818  -0.5577   0.0058
 2JE  C11  C  CH2   0  -0.553  -2.4302   0.3869  -0.0285
 2JE  C12  C  CH2   0  -0.282  -3.5959  -0.5929   0.0127
 2JE  N1   N  NH2   0  -0.796  -4.8443   0.1511  -0.0085
 2JE  H1   H  HCR5  0   0.308   2.9674   2.1160  -0.1084
 2JE  H2   H  HNR5  0   0.435   4.8206   0.3963  -0.0261
 2JE  H3   H  HCR5  0   0.291   3.9280  -1.9640   0.0843
 2JE  H5   H  HCH2  0   0.274  -2.4606   1.0543   0.8339
 2JE  H6   H  HCH2  0   0.276  -2.4752   0.9894  -0.9353
 2JE  H7   H  HCH2  0   0.235  -3.5603  -1.2325  -0.8715
 2JE  H8   H  HCH2  0   0.210  -3.4882  -1.2534   0.8837
 2JE  H9   H  HNH2  0   0.354  -5.6160  -0.4943  -0.1171
 2JE  H4   H  HNH2  0   0.344  -4.9849   0.5973   0.8895

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
 2JE  N3   C2   aromatic  1.355  0.020  1.355
 2JE  N3   C4   aromatic  1.350  0.020  1.350
 2JE  C2   N4   aromatic  1.302  0.020  1.302
 2JE  C4   C5   aromatic  1.374  0.020  1.374
 2JE  N4   C5   aromatic  1.366  0.020  1.366
 2JE  C5   C22  single    1.457  0.020  1.457
 2JE  C22  O6   double    1.210  0.020  1.210
 2JE  C22  S1   single    1.770  0.020  1.770
 2JE  S1   C11  single    1.814  0.020  1.814
 2JE  C11  C12  single    1.523  0.020  1.523
 2JE  C12  N1   single    1.453  0.020  1.453
 2JE  C4   H1   single    0.930  0.020  1.080
 2JE  N3   H2   single    0.860  0.020  1.020
 2JE  C2   H3   single    0.930  0.020  1.080
 2JE  C11  H5   single    0.970  0.020  1.090
 2JE  C11  H6   single    0.970  0.020  1.090
 2JE  C12  H7   single    0.970  0.020  1.090
 2JE  C12  H8   single    0.970  0.020  1.090
 2JE  N1   H9   single    0.890  0.020  1.040
 2JE  N1   H4   single    0.890  0.020  1.040

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
 2JE  H1   C4   C5   132.28  3.000
 2JE  H1   C4   N3   122.91  3.000
 2JE  C5   C4   N3   104.81  3.000
 2JE  H2   N3   C2   125.95  3.000
 2JE  H2   N3   C4   125.98  3.000
 2JE  C2   N3   C4   108.07  3.000
 2JE  H3   C2   N4   126.30  3.000
 2JE  H3   C2   N3   122.32  3.000
 2JE  N4   C2   N3   111.38  3.000
 2JE  C5   N4   C2   105.35  3.000
 2JE  C22  C5   N4   122.95  3.000
 2JE  C22  C5   C4   126.66  3.000
 2JE  N4   C5   C4   110.39  3.000
 2JE  S1   C22  O6   123.26  3.000
 2JE  S1   C22  C5   113.07  3.000
 2JE  O6   C22  C5   123.67  3.000
 2JE  C11  S1   C22  100.73  3.000
 2JE  H6   C11  H5   108.57  3.000
 2JE  H6   C11  C12  110.28  3.000
 2JE  H5   C11  C12  110.54  3.000
 2JE  H6   C11  S1   109.81  3.000
 2JE  H5   C11  S1   109.11  3.000
 2JE  C12  C11  S1   108.52  3.000
 2JE  H8   C12  H7   106.66  3.000
 2JE  H8   C12  N1   113.80  3.000
 2JE  H7   C12  N1   108.42  3.000
 2JE  H8   C12  C11  109.46  3.000
 2JE  H7   C12  C11  109.26  3.000
 2JE  N1   C12  C11  109.13  3.000
 2JE  H4   N1   H9   105.69  3.000
 2JE  H4   N1   C12  109.38  3.000
 2JE  H9   N1   C12  109.28  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
 2JE  CONST_01  N4   C2   N3   C4      0.00   0.0  0
 2JE  CONST_02  C2   N4   C5   C4      0.00   0.0  0
 2JE  CONST_03  C5   N4   C2   N3      0.00   0.0  0
 2JE  CONST_04  N4   C5   C4   N3      0.00   0.0  0
 2JE  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 2JE  CONST_06  C22  C5   C4   N3    180.00   0.0  0
 2JE  CONST_07  C22  C5   N4   C2    180.00   0.0  0
 2JE  CONST_08  H3   C2   N3   C4    180.00   0.0  0
 2JE  CONST_09  H1   C4   N3   C2    180.00   0.0  0
 2JE  CONST_10  H2   N3   C2   N4    180.00   0.0  0
 2JE  Var_01    O6   C22  C5   C4     -0.31  30.0  2
 2JE  Var_02    C12  C11  S1   C22  -179.87  30.0  3
 2JE  Var_03    N1   C12  C11  S1    179.76  30.0  3
 2JE  Var_04    H9   N1   C12  C11   171.83  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
 2JE  plan-1  C4   0.020
 2JE  plan-1  N3   0.020
 2JE  plan-1  C2   0.020
 2JE  plan-1  N4   0.020
 2JE  plan-1  C5   0.020
 2JE  plan-1  C22  0.020
 2JE  plan-1  H1   0.020
 2JE  plan-1  H2   0.020
 2JE  plan-1  H3   0.020
 2JE  plan-2  C5   0.020
 2JE  plan-2  O6   0.020
 2JE  plan-2  C22  0.020
 2JE  plan-2  S1   0.020

