# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:21:13 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-[2-(1H-imidazol-4-yl)ethyl]-2,4,6-trimethylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)[n+](CCc2c[nH]cn2)c(C)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
 MIZ  MIZ  1-[2-(1H-imidazol-4-yl)ethyl]-2,4,6-trimethylpyridinium  ligand  34  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MIZ
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
 MIZ  CAA   C  CH3   0  -0.754   0.9847   2.4907   0.6415
 MIZ  CAE   C  CR6   0   0.416   1.6818   1.2082   0.3344
 MIZ  CAD   C  CR16  0  -0.415   3.0272   1.1998   0.0339
 MIZ  CAC   C  CR6   0   0.265   3.6998   0.0141  -0.2282
 MIZ  CAB   C  CH3   0  -0.723   5.1590  -0.0042  -0.5317
 MIZ  CAF   C  CR16  0  -0.412   2.9623  -1.1622  -0.1740
 MIZ  CAG   C  CR6   0   0.418   1.6175  -1.1495   0.1221
 MIZ  CAN   C  CH3   0  -0.758   0.8442  -2.4234   0.1974
 MIZ  NAH   N  NR6   1  -0.517   1.0022   0.0355   0.3689
 MIZ  CAI   C  CH2   0  -0.369  -0.4506   0.0477   0.6146
 MIZ  CAJ   C  CH2   0  -0.541  -1.2445   0.2090  -0.6818
 MIZ  CAK   C  CR5   0   0.147  -2.6998   0.0361  -0.4163
 MIZ  CAO   C  CR15  0  -0.123  -3.7093   0.9458  -0.5641
 MIZ  NAP   N  NR15  0  -0.562  -4.8427   0.2932  -0.1771
 MIZ  CAM   C  CR15  0   0.091  -4.4904  -0.9535   0.1880
 MIZ  NAL   N  N     0  -0.454  -3.2030  -1.1455   0.0563
 MIZ  HAA   H  HCH3  0   0.280   0.1228   2.6657  -0.0001
 MIZ  HAAA  H  HCH3  0   0.291   0.6411   2.5153   1.6768
 MIZ  HAAB  H  HCH3  0   0.292   1.6766   3.3166   0.5028
 MIZ  HAD   H  HCR6  0   0.298   3.5519   2.1444   0.0014
 MIZ  HAB   H  HCH3  0   0.279   5.7139  -0.3023   0.3602
 MIZ  HABA  H  HCH3  0   0.268   5.3898  -0.7271  -1.3128
 MIZ  HABB  H  HCH3  0   0.265   5.5191   0.9757  -0.8370
 MIZ  HAF   H  HCR6  0   0.296   3.4359  -2.1140  -0.3708
 MIZ  HAN   H  HCH3  0   0.292   0.5213  -2.6240   1.2203
 MIZ  HANA  H  HCH3  0   0.280  -0.0433  -2.4166  -0.4348
 MIZ  HANB  H  HCH3  0   0.291   1.4752  -3.2488  -0.1202
 MIZ  HAI   H  HCH2  0   0.316  -0.7225  -0.8787   1.1103
 MIZ  HAIA  H  HCH2  0   0.316  -0.6786   0.8448   1.3159
 MIZ  HAJ   H  HCH2  0   0.272  -1.0578   1.1878  -1.1251
 MIZ  HAJA  H  HCH2  0   0.267  -0.9074  -0.5307  -1.4131
 MIZ  HAO   H  HCR5  0   0.287  -3.7150   1.9667  -0.9070
 MIZ  HNAP  H  HNR5  0   0.422  -5.7753   0.6745  -0.1667
 MIZ  HAM   H  HCR5  0   0.279  -5.2084  -1.6795   0.5371

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
 MIZ  CAA  CAE   single    1.492  0.020  1.492
 MIZ  CAE  CAD   aromatic  1.379  0.020  1.379
 MIZ  CAE  NAH   aromatic  1.356  0.020  1.356
 MIZ  CAD  CAC   aromatic  1.388  0.020  1.388
 MIZ  CAC  CAB   single    1.491  0.020  1.491
 MIZ  CAC  CAF   aromatic  1.389  0.020  1.389
 MIZ  CAF  CAG   aromatic  1.377  0.020  1.377
 MIZ  CAG  CAN   single    1.492  0.020  1.492
 MIZ  CAG  NAH   aromatic  1.358  0.020  1.358
 MIZ  NAH  CAI   single    1.474  0.020  1.474
 MIZ  CAI  CAJ   single    1.529  0.020  1.529
 MIZ  CAJ  CAK   single    1.489  0.020  1.489
 MIZ  CAK  CAO   aromatic  1.367  0.020  1.367
 MIZ  CAK  NAL   aromatic  1.369  0.020  1.369
 MIZ  CAO  NAP   aromatic  1.364  0.020  1.364
 MIZ  NAP  CAM   aromatic  1.346  0.020  1.346
 MIZ  CAM  NAL   aromatic  1.308  0.020  1.308
 MIZ  CAA  HAA   single    0.970  0.020  1.090
 MIZ  CAA  HAAA  single    0.970  0.020  1.090
 MIZ  CAA  HAAB  single    0.970  0.020  1.090
 MIZ  CAD  HAD   single    0.930  0.020  1.080
 MIZ  CAB  HAB   single    0.970  0.020  1.090
 MIZ  CAB  HABA  single    0.970  0.020  1.090
 MIZ  CAB  HABB  single    0.970  0.020  1.090
 MIZ  CAF  HAF   single    0.930  0.020  1.080
 MIZ  CAN  HAN   single    0.970  0.020  1.090
 MIZ  CAN  HANA  single    0.970  0.020  1.090
 MIZ  CAN  HANB  single    0.970  0.020  1.090
 MIZ  CAI  HAI   single    0.970  0.020  1.090
 MIZ  CAI  HAIA  single    0.970  0.020  1.090
 MIZ  CAJ  HAJ   single    0.970  0.020  1.090
 MIZ  CAJ  HAJA  single    0.970  0.020  1.090
 MIZ  CAO  HAO   single    0.930  0.020  1.080
 MIZ  NAP  HNAP  single    0.860  0.020  1.020
 MIZ  CAM  HAM   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
 MIZ  HAAB  CAA  HAAA  107.73  3.000
 MIZ  HAAB  CAA  HAA   107.86  3.000
 MIZ  HAAA  CAA  HAA   107.83  3.000
 MIZ  HAAB  CAA  CAE   109.25  3.000
 MIZ  HAAA  CAA  CAE   111.22  3.000
 MIZ  HAA   CAA  CAE   112.76  3.000
 MIZ  NAH   CAE  CAD   119.30  3.000
 MIZ  NAH   CAE  CAA   120.28  3.000
 MIZ  CAD   CAE  CAA   120.41  3.000
 MIZ  HAD   CAD  CAC   120.36  3.000
 MIZ  HAD   CAD  CAE   118.36  3.000
 MIZ  CAC   CAD  CAE   121.28  3.000
 MIZ  CAF   CAC  CAB   121.14  3.000
 MIZ  CAF   CAC  CAD   117.30  3.000
 MIZ  CAB   CAC  CAD   121.55  3.000
 MIZ  HABB  CAB  HABA  109.06  3.000
 MIZ  HABB  CAB  HAB   107.88  3.000
 MIZ  HABA  CAB  HAB   107.27  3.000
 MIZ  HABB  CAB  CAC   111.73  3.000
 MIZ  HABA  CAB  CAC   111.20  3.000
 MIZ  HAB   CAB  CAC   109.55  3.000
 MIZ  HAF   CAF  CAG   118.36  3.000
 MIZ  HAF   CAF  CAC   120.38  3.000
 MIZ  CAG   CAF  CAC   121.26  3.000
 MIZ  NAH   CAG  CAN   120.07  3.000
 MIZ  NAH   CAG  CAF   119.31  3.000
 MIZ  CAN   CAG  CAF   120.60  3.000
 MIZ  HANB  CAN  HANA  107.95  3.000
 MIZ  HANB  CAN  HAN   107.83  3.000
 MIZ  HANA  CAN  HAN   107.69  3.000
 MIZ  HANB  CAN  CAG   109.45  3.000
 MIZ  HANA  CAN  CAG   112.80  3.000
 MIZ  HAN   CAN  CAG   110.95  3.000
 MIZ  CAI   NAH  CAG   118.97  3.000
 MIZ  CAI   NAH  CAE   119.42  3.000
 MIZ  CAG   NAH  CAE   121.54  3.000
 MIZ  HAIA  CAI  HAI   106.20  3.000
 MIZ  HAIA  CAI  CAJ   111.17  3.000
 MIZ  HAI   CAI  CAJ   110.32  3.000
 MIZ  HAIA  CAI  NAH   108.71  3.000
 MIZ  HAI   CAI  NAH   108.43  3.000
 MIZ  CAJ   CAI  NAH   111.81  3.000
 MIZ  HAJA  CAJ  HAJ   106.40  3.000
 MIZ  HAJA  CAJ  CAK   110.00  3.000
 MIZ  HAJ   CAJ  CAK   110.12  3.000
 MIZ  HAJA  CAJ  CAI   109.62  3.000
 MIZ  HAJ   CAJ  CAI   110.52  3.000
 MIZ  CAK   CAJ  CAI   110.12  3.000
 MIZ  NAL   CAK  CAO   109.90  3.000
 MIZ  NAL   CAK  CAJ   121.41  3.000
 MIZ  CAO   CAK  CAJ   128.69  3.000
 MIZ  HAO   CAO  NAP   122.65  3.000
 MIZ  HAO   CAO  CAK   132.01  3.000
 MIZ  NAP   CAO  CAK   105.34  3.000
 MIZ  HNAP  NAP  CAM   126.16  3.000
 MIZ  HNAP  NAP  CAO   126.23  3.000
 MIZ  CAM   NAP  CAO   107.62  3.000
 MIZ  HAM   CAM  NAL   126.06  3.000
 MIZ  HAM   CAM  NAP   122.46  3.000
 MIZ  NAL   CAM  NAP   111.48  3.000
 MIZ  CAM   NAL  CAK   105.66  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
 MIZ  CONST_01  CAF   CAC  CAD  CAE    0.00   0.0  0
 MIZ  CONST_02  CAF   CAG  NAH  CAE    0.00   0.0  0
 MIZ  CONST_03  CAG   NAH  CAE  CAD    0.00   0.0  0
 MIZ  CONST_04  CAG   CAF  CAC  CAD    0.00   0.0  0
 MIZ  CONST_05  NAH   CAE  CAD  CAC    0.00   0.0  0
 MIZ  CONST_06  NAH   CAG  CAF  CAC    0.00   0.0  0
 MIZ  CONST_07  CAM   NAP  CAO  CAK    0.00   0.0  0
 MIZ  CONST_08  NAP   CAM  NAL  CAK    0.00   0.0  0
 MIZ  CONST_09  CAM   NAL  CAK  CAO    0.00   0.0  0
 MIZ  CONST_10  NAL   CAM  NAP  CAO    0.00   0.0  0
 MIZ  CONST_11  NAL   CAK  CAO  NAP    0.00   0.0  0
 MIZ  CONST_12  CAC   CAD  CAE  CAA  180.00   0.0  0
 MIZ  CONST_13  CAG   NAH  CAE  CAA  180.00   0.0  0
 MIZ  CONST_14  CAB   CAC  CAD  CAE  180.00   0.0  0
 MIZ  CONST_15  CAN   CAG  NAH  CAE  180.00   0.0  0
 MIZ  CONST_16  CAI   NAH  CAE  CAD  180.00   0.0  0
 MIZ  CONST_17  CAN   CAG  CAF  CAC  180.00   0.0  0
 MIZ  CONST_18  CAG   CAF  CAC  CAB  180.00   0.0  0
 MIZ  CONST_19  CAI   NAH  CAG  CAF  180.00   0.0  0
 MIZ  CONST_20  NAP   CAO  CAK  CAJ  180.00   0.0  0
 MIZ  CONST_21  CAM   NAL  CAK  CAJ  180.00   0.0  0
 MIZ  CONST_22  HAF   CAF  CAC  CAD  180.00   0.0  0
 MIZ  CONST_23  HAD   CAD  CAC  CAF  180.00   0.0  0
 MIZ  CONST_24  HNAP  NAP  CAO  CAK  180.00   0.0  0
 MIZ  CONST_25  HAM   CAM  NAL  CAK  180.00   0.0  0
 MIZ  CONST_26  HAO   CAO  NAP  CAM  180.00   0.0  0
 MIZ  Var_01    CAJ   CAI  NAH  CAE   87.51  30.0  2
 MIZ  Var_02    CAK   CAJ  CAI  NAH  172.53  30.0  3
 MIZ  Var_03    CAO   CAK  CAJ  CAI  116.80  30.0  2
 MIZ  Var_04    HAA   CAA  CAE  CAD  124.41  30.0  2
 MIZ  Var_05    HAB   CAB  CAC  CAD  100.78  30.0  2
 MIZ  Var_06    HAN   CAN  CAG  CAF  112.44  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
 MIZ  plan-1  CAJ   0.020
 MIZ  plan-1  CAK   0.020
 MIZ  plan-1  CAO   0.020
 MIZ  plan-1  NAP   0.020
 MIZ  plan-1  CAM   0.020
 MIZ  plan-1  NAL   0.020
 MIZ  plan-1  HAO   0.020
 MIZ  plan-1  HNAP  0.020
 MIZ  plan-1  HAM   0.020
 MIZ  plan-2  CAA   0.020
 MIZ  plan-2  CAE   0.020
 MIZ  plan-2  CAD   0.020
 MIZ  plan-2  CAC   0.020
 MIZ  plan-2  CAB   0.020
 MIZ  plan-2  CAF   0.020
 MIZ  plan-2  CAG   0.020
 MIZ  plan-2  CAN   0.020
 MIZ  plan-2  NAH   0.020
 MIZ  plan-2  CAI   0.020
 MIZ  plan-2  HAD   0.020
 MIZ  plan-2  HAF   0.020

