# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 03:07:02 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (Z)-N~6~-[amino(pyridin-4-yl)methylidene]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C(N)c1ccncc1)C(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
 MIK  MIK  (Z)-N~6~-[amino(pyridin-4-yl)methylidene]-L-lysine  ligand  36  18  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MIK
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
 MIK  N     N  NH2   0  -0.782   2.6053   1.5523   1.5443
 MIK  CA    C  CH1   0  -0.221   2.6303   0.8474   0.2842
 MIK  C     C  C     0   0.516   1.9004   1.5749  -0.8376
 MIK  O     O  O     0  -0.442   1.2197   2.5596  -0.6911
 MIK  CB    C  CH2   0  -0.422   2.0876  -0.5809   0.4379
 MIK  CG    C  CH2   0  -0.439   0.6094  -0.6670   0.7978
 MIK  CD    C  CH2   0  -0.422   0.1323  -2.1078   0.9309
 MIK  CE    C  CH2   0  -0.340  -1.3362  -2.2063   1.3171
 MIK  NZ    N  N     0  -0.426  -1.5484  -1.6551   2.6330
 MIK  CI1   C  C     0   0.403  -2.7300  -1.3690   3.0146
 MIK  CI2   C  CR6   0   0.132  -2.8902  -0.7808   4.3733
 MIK  NI1   N  NH2   0  -0.843  -3.8888  -1.5927   2.3302
 MIK  CI3   C  CR16  0  -0.349  -1.8311  -0.0988   4.9641
 MIK  CI4   C  CR16  0  -0.060  -1.9997   0.4367   6.2291
 MIK  NI2   N  N     0  -0.404  -3.1257   0.3322   6.9289
 MIK  CI5   C  CR16  0  -0.058  -4.1314  -0.3252   6.3676
 MIK  CI6   C  CR16  0  -0.369  -4.0685  -0.8941   5.1030
 MIK  OXT   O  OH1   0  -0.594   2.0961   0.9967  -2.0181
 MIK  H1    H  HNH2  0   0.354   3.0556   2.4535   1.4484
 MIK  H2    H  HNH2  0   0.345   1.6531   1.7497   1.8250
 MIK  HA    H  HCH1  0   0.280   3.6763   0.7602  -0.0281
 MIK  HBC1  H  HCH2  0   0.233   2.2735  -1.1381  -0.4829
 MIK  HBC2  H  HCH2  0   0.238   2.6830  -1.0651   1.2161
 MIK  HGC1  H  HCH2  0   0.224   0.4117  -0.1469   1.7392
 MIK  HGC2  H  HCH2  0   0.217   0.0002  -0.1679   0.0354
 MIK  HDC1  H  HCH2  0   0.219   0.2844  -2.6347  -0.0154
 MIK  HDC2  H  HCH2  0   0.215   0.7360  -2.6307   1.6791
 MIK  HEC1  H  HCH2  0   0.204  -1.9359  -1.6969   0.5460
 MIK  HEC2  H  HCH2  0   0.237  -1.6464  -3.2590   1.2896
 MIK  HI1   H  HNH2  0   0.405  -3.8275  -1.8621   1.3617
 MIK  HI3   H  HCR6  0   0.269  -0.8920   0.0150   4.4412
 MIK  HI4   H  HCR6  0   0.266  -1.1861   0.9784   6.6984
 MIK  HI5   H  HCR6  0   0.267  -5.0417  -0.4107   6.9506
 MIK  HI6   H  HCR6  0   0.270  -4.9285  -1.4292   4.7232
 MIK  HXT   H  HOH1  0   0.479   1.6065   1.4722  -2.7060
 MIK  HN1   H  HNH2  0   0.399  -4.6845  -1.0097   2.5322

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
 MIK  N    CA    single    1.444  0.020  1.444
 MIK  N    H1    single    0.890  0.020  1.040
 MIK  N    H2    single    0.890  0.020  1.040
 MIK  CA   C     single    1.523  0.020  1.523
 MIK  CA   CB    single    1.536  0.020  1.536
 MIK  CA   HA    single    0.970  0.020  1.090
 MIK  C    O     double    1.206  0.020  1.206
 MIK  C    OXT   single    1.329  0.020  1.329
 MIK  CB   CG    single    1.524  0.020  1.524
 MIK  CB   HBC1  single    0.970  0.020  1.090
 MIK  CB   HBC2  single    0.970  0.020  1.090
 MIK  CG   CD    single    1.524  0.020  1.524
 MIK  CG   HGC1  single    0.970  0.020  1.090
 MIK  CG   HGC2  single    0.970  0.020  1.090
 MIK  CD   CE    single    1.522  0.020  1.522
 MIK  CD   HDC1  single    0.970  0.020  1.090
 MIK  CD   HDC2  single    0.970  0.020  1.090
 MIK  CE   NZ    single    1.442  0.020  1.442
 MIK  CE   HEC1  single    0.970  0.020  1.090
 MIK  CE   HEC2  single    0.970  0.020  1.090
 MIK  NZ   CI1   double    1.274  0.020  1.274
 MIK  CI1  CI2   single    1.489  0.020  1.489
 MIK  CI1  NI1   single    1.364  0.020  1.364
 MIK  CI2  CI3   aromatic  1.391  0.020  1.391
 MIK  CI2  CI6   aromatic  1.391  0.020  1.391
 MIK  NI1  HI1   single    0.890  0.020  1.040
 MIK  CI3  CI4   aromatic  1.384  0.020  1.384
 MIK  CI3  HI3   single    0.930  0.020  1.080
 MIK  CI4  NI2   aromatic  1.330  0.020  1.330
 MIK  CI4  HI4   single    0.930  0.020  1.080
 MIK  NI2  CI5   aromatic  1.326  0.020  1.326
 MIK  CI5  CI6   aromatic  1.388  0.020  1.388
 MIK  CI5  HI5   single    0.930  0.020  1.080
 MIK  CI6  HI6   single    0.930  0.020  1.080
 MIK  OXT  HXT   single    0.850  0.020  0.980
 MIK  HN1  NI1   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
 MIK  H2    N    H1    105.74  3.000
 MIK  H2    N    CA    110.70  3.000
 MIK  H1    N    CA    110.14  3.000
 MIK  HA    CA   CB    106.98  3.000
 MIK  HA    CA   C     106.60  3.000
 MIK  CB    CA   C     110.40  3.000
 MIK  HA    CA   N     107.71  3.000
 MIK  CB    CA   N     111.14  3.000
 MIK  C     CA   N     113.65  3.000
 MIK  OXT   C    O     123.11  3.000
 MIK  OXT   C    CA    112.07  3.000
 MIK  O     C    CA    124.82  3.000
 MIK  HBC2  CB   HBC1  106.35  3.000
 MIK  HBC2  CB   CG    109.59  3.000
 MIK  HBC1  CB   CG    109.60  3.000
 MIK  HBC2  CB   CA    106.90  3.000
 MIK  HBC1  CB   CA    109.27  3.000
 MIK  CG    CB   CA    114.77  3.000
 MIK  HGC2  CG   HGC1  106.37  3.000
 MIK  HGC2  CG   CD    108.50  3.000
 MIK  HGC1  CG   CD    108.54  3.000
 MIK  HGC2  CG   CB    110.44  3.000
 MIK  HGC1  CG   CB    110.60  3.000
 MIK  CD    CG   CB    112.20  3.000
 MIK  HDC2  CD   HDC1  106.53  3.000
 MIK  HDC2  CD   CE    109.14  3.000
 MIK  HDC1  CD   CE    108.82  3.000
 MIK  HDC2  CD   CG    109.81  3.000
 MIK  HDC1  CD   CG    109.66  3.000
 MIK  CE    CD   CG    112.68  3.000
 MIK  HEC2  CE   HEC1  105.79  3.000
 MIK  HEC2  CE   NZ    110.35  3.000
 MIK  HEC1  CE   NZ    112.44  3.000
 MIK  HEC2  CE   CD    109.17  3.000
 MIK  HEC1  CE   CD    108.53  3.000
 MIK  NZ    CE   CD    110.41  3.000
 MIK  CI1   NZ   CE    119.70  3.000
 MIK  NI1   CI1  CI2   115.53  3.000
 MIK  NI1   CI1  NZ    126.91  3.000
 MIK  CI2   CI1  NZ    117.50  3.000
 MIK  CI6   CI2  CI3   117.52  3.000
 MIK  CI6   CI2  CI1   122.53  3.000
 MIK  CI3   CI2  CI1   119.94  3.000
 MIK  HN1   NI1  HI1   113.32  3.000
 MIK  HN1   NI1  CI1   118.41  3.000
 MIK  HI1   NI1  CI1   118.33  3.000
 MIK  HI3   CI3  CI4   120.48  3.000
 MIK  HI3   CI3  CI2   120.50  3.000
 MIK  CI4   CI3  CI2   119.02  3.000
 MIK  HI4   CI4  NI2   116.54  3.000
 MIK  HI4   CI4  CI3   119.83  3.000
 MIK  NI2   CI4  CI3   123.62  3.000
 MIK  CI5   NI2  CI4   117.28  3.000
 MIK  HI5   CI5  CI6   119.71  3.000
 MIK  HI5   CI5  NI2   116.62  3.000
 MIK  CI6   CI5  NI2   123.67  3.000
 MIK  HI6   CI6  CI5   119.12  3.000
 MIK  HI6   CI6  CI2   121.99  3.000
 MIK  CI5   CI6  CI2   118.88  3.000
 MIK  HXT   OXT  C     110.04  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
 MIK  CONST_01  NI2  CI4  CI3  CI2    0.00   0.0  0
 MIK  CONST_02  NI2  CI5  CI6  CI2    0.00   0.0  0
 MIK  CONST_03  CI5  CI6  CI2  CI3    0.00   0.0  0
 MIK  CONST_04  CI5  NI2  CI4  CI3    0.00   0.0  0
 MIK  CONST_05  CI6  CI2  CI3  CI4    0.00   0.0  0
 MIK  CONST_06  CI6  CI5  NI2  CI4    0.00   0.0  0
 MIK  CONST_07  CI4  CI3  CI2  CI1  180.00   0.0  0
 MIK  CONST_08  CI5  CI6  CI2  CI1  180.00   0.0  0
 MIK  CONST_09  HI4  CI4  CI3  CI2  180.00   0.0  0
 MIK  CONST_10  HI5  CI5  CI6  CI2  180.00   0.0  0
 MIK  CONST_11  HI6  CI6  CI2  CI3  180.00   0.0  0
 MIK  CONST_12  HI3  CI3  CI4  NI2  180.00   0.0  0
 MIK  CONST_13  CI2  CI1  NZ   CE   180.00   0.0  0
 MIK  CONST_14  HI1  NI1  CI1  CI2  180.00   0.0  0
 MIK  CONST_16  NI1  CI1  NZ   CE     0.00   0.0  0
 MIK  CONST_17  HXT  OXT  C    CA   180.00   0.0  0
 MIK  Var_01    CI3  CI2  CI1  NZ    24.57  30.0  2
 MIK  Var_02    CD   CG   CB   CA   179.81  30.0  3
 MIK  Var_03    CE   CD   CG   CB   178.87  30.0  3
 MIK  Var_04    NZ   CE   CD   CG   -64.66  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 MIK  chir_01  CA  N  C  CB  positiv

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
 MIK  plan-1  CI1  0.020
 MIK  plan-1  CI2  0.020
 MIK  plan-1  CI3  0.020
 MIK  plan-1  CI4  0.020
 MIK  plan-1  NI2  0.020
 MIK  plan-1  CI5  0.020
 MIK  plan-1  CI6  0.020
 MIK  plan-1  HI3  0.020
 MIK  plan-1  HI4  0.020
 MIK  plan-1  HI5  0.020
 MIK  plan-1  HI6  0.020
 MIK  plan-2  CE   0.020
 MIK  plan-2  NZ   0.020
 MIK  plan-2  CI1  0.020
 MIK  plan-2  CI2  0.020
 MIK  plan-2  NI1  0.020
 MIK  plan-2  HI1  0.020
 MIK  plan-2  HN1  0.020
 MIK  plan-3  CA   0.020
 MIK  plan-3  C    0.020
 MIK  plan-3  O    0.020
 MIK  plan-3  OXT  0.020
 MIK  plan-3  HXT  0.020

