# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 18:12:55 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: 1-methyl-1H-imidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc[nH+]c1
#
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
 1MZ  1MZ  1-methyl-1H-imidazol-3-ium  ligand  13  6  .  2022-07-22  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_1MZ
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
 1MZ  N1    N  NR5   0  -0.391   0.6770   0.0144  -0.0095
 1MZ  C2    C  CR15  0   0.260  -0.1110  -1.0422  -0.1148
 1MZ  N3    N  NR15  1  -0.555  -1.3651  -0.6239  -0.0861
 1MZ  C4    C  CR15  0  -0.062  -1.3923   0.7364   0.0409
 1MZ  C5    C  CR15  0  -0.073  -0.1008   1.1411   0.0899
 1MZ  CM1   C  CH3   0  -0.518   2.1298  -0.0100   0.0003
 1MZ  H2    H  HCR5  0   0.361   0.2099  -2.0652  -0.2086
 1MZ  HN3   H  HNR5  0   0.461  -2.1713  -1.2282  -0.1568
 1MZ  H4    H  HCR5  0   0.330  -2.3095   1.2956   0.0845
 1MZ  H5    H  HCR5  0   0.333   0.3237   2.1252   0.1855
 1MZ  HM11  H  HCH3  0   0.286   2.5079   0.5954  -0.8184
 1MZ  HM12  H  HCH3  0   0.286   2.4946   0.3804   0.9460
 1MZ  HM13  H  HCH3  0   0.281   2.4690  -1.0333  -0.1231

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
 1MZ  N1   C2    aromatic  1.322  0.020  1.322
 1MZ  N1   C5    aromatic  1.373  0.020  1.373
 1MZ  N1   CM1   single    1.453  0.020  1.453
 1MZ  C2   N3    aromatic  1.322  0.020  1.322
 1MZ  C2   H2    single    0.930  0.020  1.080
 1MZ  N3   C4    aromatic  1.366  0.020  1.366
 1MZ  N3   HN3   single    0.860  0.020  1.020
 1MZ  C4   C5    aromatic  1.354  0.020  1.354
 1MZ  C4   H4    single    0.930  0.020  1.080
 1MZ  C5   H5    single    0.930  0.020  1.080
 1MZ  CM1  HM11  single    0.970  0.020  1.090
 1MZ  CM1  HM12  single    0.970  0.020  1.090
 1MZ  CM1  HM13  single    0.970  0.020  1.090

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
 1MZ  CM1   N1   C5    125.44  3.000
 1MZ  CM1   N1   C2    125.66  3.000
 1MZ  C5    N1   C2    108.91  3.000
 1MZ  H2    C2   N3    125.82  3.000
 1MZ  H2    C2   N1    126.08  3.000
 1MZ  N3    C2   N1    108.10  3.000
 1MZ  HN3   N3   C4    125.89  3.000
 1MZ  HN3   N3   C2    124.49  3.000
 1MZ  C4    N3   C2    109.62  3.000
 1MZ  H4    C4   C5    131.04  3.000
 1MZ  H4    C4   N3    122.59  3.000
 1MZ  C5    C4   N3    106.37  3.000
 1MZ  H5    C5   C4    130.75  3.000
 1MZ  H5    C5   N1    122.25  3.000
 1MZ  C4    C5   N1    107.00  3.000
 1MZ  HM13  CM1  HM12  109.45  3.000
 1MZ  HM13  CM1  HM11  109.33  3.000
 1MZ  HM12  CM1  HM11  109.82  3.000
 1MZ  HM13  CM1  N1    109.13  3.000
 1MZ  HM12  CM1  N1    109.61  3.000
 1MZ  HM11  CM1  N1    109.49  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
 1MZ  CONST_01  C4    N3   C2  N1    0.00   0.0  0
 1MZ  CONST_02  N3    C4   C5  N1    0.00   0.0  0
 1MZ  CONST_03  C4    C5   N1  C2    0.00   0.0  0
 1MZ  CONST_04  C5    C4   N3  C2    0.00   0.0  0
 1MZ  CONST_05  C5    N1   C2  N3    0.00   0.0  0
 1MZ  CONST_06  CM1   N1   C2  N3  180.00   0.0  0
 1MZ  CONST_07  CM1   N1   C5  C4  180.00   0.0  0
 1MZ  CONST_08  HN3   N3   C2  N1  180.00   0.0  0
 1MZ  CONST_09  H4    C4   C5  N1  180.00   0.0  0
 1MZ  CONST_10  H5    C5   N1  C2  180.00   0.0  0
 1MZ  CONST_11  H2    C2   N3  C4  180.00   0.0  0
 1MZ  Var_01    HM11  CM1  N1  C2  121.33  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
 1MZ  plan-1  N1   0.020
 1MZ  plan-1  C2   0.020
 1MZ  plan-1  N3   0.020
 1MZ  plan-1  C4   0.020
 1MZ  plan-1  C5   0.020
 1MZ  plan-1  CM1  0.020
 1MZ  plan-1  H2   0.020
 1MZ  plan-1  HN3  0.020
 1MZ  plan-1  H4   0.020
 1MZ  plan-1  H5   0.020

