# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:51:20 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: O-[2-(triaza-1,2-dien-2-ium-1-yl)ethyl]-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(OCCN=[N+]=N)cc1)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
 4LZ  4LZ  O-[2-(triaza-1,2-dien-2-ium-1-yl)ethyl]-L-tyrosine  L-peptide  32  18  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4LZ
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
 4LZ  C    C  C      0   0.411  -10.2325  -857.9851  10.1612
 4LZ  N    N  NH2    0  -0.807  -10.7125  -856.3192   8.3876
 4LZ  O    O  O      0  -0.606  -10.4565  -858.3919  11.3182
 4LZ  N6   N  N      0  -0.117  -13.7402  -848.5540   8.1793
 4LZ  N7   N  N      1   0.538  -13.4595  -847.7345   7.4193
 4LZ  N8   N  N      0  -0.330  -13.1262  -846.8034   6.7955
 4LZ  CA   C  CH1    0  -0.206  -10.7538  -856.5632   9.8197
 4LZ  CB   C  CH2    0  -0.488  -12.1775  -856.3459  10.3496
 4LZ  CG   C  CR6    0   0.115  -12.6943  -854.9631  10.0720
 4LZ  CZ   C  CR6    0   0.366  -13.6007  -852.3563   9.5298
 4LZ  C31  C  CH2    0  -0.191  -14.7755  -850.7566   8.2306
 4LZ  C32  C  CH2    0  -0.369  -15.0358  -849.2714   8.2522
 4LZ  CD1  C  CR16   0  -0.290  -12.3494  -853.8895  10.8956
 4LZ  CD2  C  CR16   0  -0.298  -13.4995  -854.6912   8.9737
 4LZ  CE1  C  CR16   0  -0.327  -12.7904  -852.6043  10.6366
 4LZ  CE2  C  CR16   0  -0.363  -13.9583  -853.4071   8.6947
 4LZ  OXT  O  OC    -1  -0.597   -9.6024  -858.5848   9.2676
 4LZ  HN   H  HNH2   0   0.331  -10.6447  -855.3269   8.2052
 4LZ  HNA  H  HNH2   0   0.333   -9.8760  -856.7511   8.0187
 4LZ  HN8  H  H      0   0.496  -12.6557  -847.0076   5.9044
 4LZ  HA   H  HCH1   0   0.197  -10.0979  -855.8702  10.3765
 4LZ  HB   H  HCH2   0   0.222  -12.8412  -857.0846   9.8914
 4LZ  HBA  H  HCH2   0   0.228  -12.1839  -856.5307  11.4241
 4LZ  H31  H  HCH2   0   0.262  -14.2795  -851.0407   7.2967
 4LZ  H32  H  HCH2   0   0.271  -15.7549  -851.2478   8.2526
 4LZ  H33  H  HCH2   0   0.342  -15.4721  -848.9510   9.1982
 4LZ  H34  H  HCH2   0   0.329  -15.6739  -848.9686   7.4241
 4LZ  HD1  H  HCR6   0   0.244  -11.7231  -854.0631  11.7634
 4LZ  HD2  H  HCR6   0   0.245  -13.7889  -855.4997   8.3135
 4LZ  HE1  H  HCR6   0   0.257  -12.5145  -851.7869  11.2916
 4LZ  HE2  H  HCR6   0   0.276  -14.5911  -853.2570   7.8300
 4LZ  OH   O  O2     0  -0.474  -13.9975  -851.0699   9.3550

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
 4LZ  OXT  C    deloc     1.247  0.020  1.247
 4LZ  C    CA   single    1.525  0.021  1.525
 4LZ  C    O    deloc     1.231  0.020  1.231
 4LZ  N    CA   single    1.458  0.019  1.458
 4LZ  N    HN   single    0.890  0.020  1.040
 4LZ  N    HNA  single    0.890  0.020  1.040
 4LZ  N7   N6   double    1.152  0.020  1.152
 4LZ  N6   C32  single    1.483  0.020  1.483
 4LZ  N8   N7   double    1.169  0.020  1.169
 4LZ  N8   HN8  single    0.890  0.020  1.040
 4LZ  CA   CB   single    1.530  0.020  1.530
 4LZ  CA   HA   single    0.970  0.020  0.970
 4LZ  CG   CB   single    1.502  0.020  1.502
 4LZ  CB   HB   single    0.970  0.020  1.090
 4LZ  CB   HBA  single    0.970  0.020  1.090
 4LZ  CD2  CG   aromatic  1.389  0.020  1.389
 4LZ  CG   CD1  aromatic  1.396  0.020  1.396
 4LZ  C31  OH   single    1.403  0.020  1.403
 4LZ  OH   CZ   single    1.357  0.020  1.357
 4LZ  CE2  CZ   aromatic  1.389  0.020  1.389
 4LZ  CZ   CE1  aromatic  1.394  0.020  1.394
 4LZ  C31  C32  single    1.508  0.020  1.508
 4LZ  C31  H31  single    0.970  0.020  1.090
 4LZ  C31  H32  single    0.970  0.020  1.090
 4LZ  C32  H33  single    0.970  0.020  1.090
 4LZ  C32  H34  single    0.970  0.020  1.090
 4LZ  CE1  CD1  aromatic  1.383  0.020  1.383
 4LZ  CD1  HD1  single    0.930  0.020  1.080
 4LZ  CE2  CD2  aromatic  1.392  0.020  1.392
 4LZ  CD2  HD2  single    0.930  0.020  1.080
 4LZ  CE1  HE1  single    0.930  0.020  1.080
 4LZ  CE2  HE2  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
 4LZ  OXT  C    CA   116.90  3.000
 4LZ  CA   C    O    120.80  1.700
 4LZ  OXT  C    O    126.79  3.000
 4LZ  HNA  N    HN   107.33  3.000
 4LZ  HNA  N    CA   108.14  3.000
 4LZ  HN   N    CA   110.14  3.000
 4LZ  C32  N6   N7   126.12  3.000
 4LZ  N8   N7   N6   170.96  3.000
 4LZ  HN8  N8   N7   115.76  3.000
 4LZ  HA   CA   CB   109.00  3.000
 4LZ  HA   CA   N    110.00  3.000
 4LZ  CB   CA   N    110.50  1.700
 4LZ  HA   CA   C    109.00  3.000
 4LZ  CB   CA   C    110.10  1.900
 4LZ  N    CA   C    111.00  2.800
 4LZ  HBA  CB   HB   107.15  3.000
 4LZ  HBA  CB   CG   109.64  3.000
 4LZ  HB   CB   CG   109.61  3.000
 4LZ  HBA  CB   CA   108.77  3.000
 4LZ  HB   CB   CA   108.83  3.000
 4LZ  CG   CB   CA   112.69  3.000
 4LZ  CD2  CG   CD1  117.33  3.000
 4LZ  CD1  CG   CB   120.92  3.000
 4LZ  CD2  CG   CB   121.73  3.000
 4LZ  CE2  CZ   CE1  119.50  3.000
 4LZ  CE1  CZ   OH   116.15  3.000
 4LZ  CE2  CZ   OH   124.34  3.000
 4LZ  H32  C31  H31  107.80  3.000
 4LZ  H32  C31  C32  106.67  3.000
 4LZ  H31  C31  C32  110.25  3.000
 4LZ  H32  C31  OH   112.30  3.000
 4LZ  H31  C31  OH   111.99  3.000
 4LZ  C32  C31  OH   107.72  3.000
 4LZ  H34  C32  H33  110.12  3.000
 4LZ  H34  C32  C31  111.37  3.000
 4LZ  H33  C32  C31  111.79  3.000
 4LZ  H34  C32  N6   109.89  3.000
 4LZ  H33  C32  N6   104.49  3.000
 4LZ  C31  C32  N6   108.96  3.000
 4LZ  HD1  CD1  CE1  118.87  3.000
 4LZ  HD1  CD1  CG   119.45  3.000
 4LZ  CE1  CD1  CG   121.68  3.000
 4LZ  HD2  CD2  CE2  118.58  3.000
 4LZ  HD2  CD2  CG   119.40  3.000
 4LZ  CE2  CD2  CG   122.03  3.000
 4LZ  HE1  CE1  CD1  120.44  3.000
 4LZ  HE1  CE1  CZ   119.60  3.000
 4LZ  CD1  CE1  CZ   119.96  3.000
 4LZ  HE2  CE2  CD2  118.75  3.000
 4LZ  HE2  CE2  CZ   121.74  3.000
 4LZ  CD2  CE2  CZ   119.51  3.000
 4LZ  C31  OH   CZ   118.49  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
 4LZ  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 4LZ  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 4LZ  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 4LZ  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 4LZ  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 4LZ  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 4LZ  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 4LZ  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 4LZ  CONST_09  CD2  CE2  CZ   OH    180.00   0.0  0
 4LZ  CONST_10  CD1  CE1  CZ   OH    180.00   0.0  0
 4LZ  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 4LZ  CONST_12  HE1  CE1  CD1  CG    180.00   0.0  0
 4LZ  CONST_13  HD2  CD2  CE2  CZ    180.00   0.0  0
 4LZ  CONST_14  HD1  CD1  CE1  CZ    180.00   0.0  0
 4LZ  Var_01    CD2  CG   CB   CA     96.57  30.0  2
 4LZ  Var_02    CE2  CZ   OH   C31    -2.74  30.0  2
 4LZ  Var_03    C32  C31  OH   CZ   -178.11  30.0  1
 4LZ  Var_04    OH   C31  C32  N6     61.06  30.0  2
 4LZ  Var_05    C31  C32  N6   N7    126.77  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
 4LZ  chir_01  CA  C  N  CB  negativ

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
 4LZ  plan-1  CB   0.020
 4LZ  plan-1  CG   0.020
 4LZ  plan-1  CZ   0.020
 4LZ  plan-1  CD1  0.020
 4LZ  plan-1  CD2  0.020
 4LZ  plan-1  CE1  0.020
 4LZ  plan-1  CE2  0.020
 4LZ  plan-1  HD1  0.020
 4LZ  plan-1  HD2  0.020
 4LZ  plan-1  HE1  0.020
 4LZ  plan-1  HE2  0.020
 4LZ  plan-1  OH   0.020
 4LZ  plan-2  C    0.020
 4LZ  plan-2  O    0.020
 4LZ  plan-2  CA   0.020
 4LZ  plan-2  OXT  0.020
 4LZ  plan-3  N6   0.020
 4LZ  plan-3  N7   0.020
 4LZ  plan-3  N8   0.020
 4LZ  plan-3  C32  0.020
 4LZ  plan-3  HN8  0.020

