# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:54:56 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-azido-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(c1)N=[N+]=[N-])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
 AZY  AZY  '3-azido-L-tyrosine       '  L-peptide  25  16  .  2012-08-28  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_AZY
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
 AZY  OXT  O  OC    -1  -0.612   4.9709  28.3528  17.6495
 AZY  C    C  C      0   0.400   5.4010  28.4073  16.4804
 AZY  O    O  O      0  -0.599   4.7420  28.6333  15.4466
 AZY  CA   C  CH1    0  -0.194   6.9298  28.2359  16.3127
 AZY  N    N  NH2    0  -0.794   7.2610  27.7799  14.9764
 AZY  CB   C  CH2    0  -0.522   7.5965  29.5725  16.7192
 AZY  CG   C  C      0   0.118   9.0919  29.5287  16.6128
 AZY  CD2  C  C1     0  -0.366   9.8557  28.9599  17.6260
 AZY  CD1  C  C1     0  -0.319   9.7565  29.9889  15.4804
 AZY  CE1  C  C1     0  -0.367  11.1362  29.8869  15.3696
 AZY  CZ   C  C      0   0.323  11.8907  29.3182  16.3852
 AZY  OH   O  OH1    0  -0.635  13.2315  29.1955  16.3356
 AZY  CE2  C  C      0   0.215  11.2375  28.8469  17.5328
 AZY  N1   N  N      0  -0.403  11.8736  28.2571  18.6335
 AZY  N2   N  N      1   0.366  13.0740  28.0466  18.6767
 AZY  N3   N  N     -1  -0.205  14.1462  27.7830  18.8791
 AZY  HA   H  HCH1   0   0.206   7.2696  27.4770  17.0263
 AZY  HN1  H  HNH2   0   0.324   6.8083  28.3891  14.3063
 AZY  HN2  H  HNH2   0   0.334   8.2583  27.8543  14.8146
 AZY  HB1  H  HCH2   0   0.232   7.2063  30.3694  16.0783
 AZY  HB2  H  HCH2   0   0.234   7.3023  29.8116  17.7435
 AZY  HD2  H  H      0   0.257   9.3738  28.5889  18.5233
 AZY  HD1  H  H      0   0.253   9.1951  30.4438  14.6734
 AZY  HE1  H  H      0   0.272  11.6358  30.2578  14.4814
 AZY  HOH  H  HOH1   0   0.482  13.5769  29.5539  15.5097

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
 AZY  OXT  C    deloc     1.247  0.020  1.247
 AZY  C    O    deloc     1.231  0.020  1.231
 AZY  C    CA   single    1.525  0.021  1.525
 AZY  CA   N    single    1.458  0.019  1.458
 AZY  CA   CB   single    1.530  0.020  1.530
 AZY  CA   HA   single    0.970  0.020  0.970
 AZY  N    HN1  single    0.890  0.020  1.040
 AZY  N    HN2  single    0.890  0.020  1.040
 AZY  CB   CG   single    1.500  0.020  1.500
 AZY  CB   HB1  single    0.970  0.020  1.090
 AZY  CB   HB2  single    0.970  0.020  1.090
 AZY  CG   CD1  aromatic  1.391  0.020  1.391
 AZY  CG   CD2  aromatic  1.390  0.020  1.390
 AZY  CD2  CE2  aromatic  1.390  0.020  1.390
 AZY  CD2  HD2  single    0.930  0.020  1.080
 AZY  CD1  CE1  aromatic  1.388  0.020  1.388
 AZY  CD1  HD1  single    0.930  0.020  1.080
 AZY  CE1  CZ   aromatic  1.387  0.020  1.387
 AZY  CE1  HE1  single    0.930  0.020  1.080
 AZY  CZ   OH   single    1.347  0.020  1.347
 AZY  CZ   CE2  aromatic  1.402  0.020  1.402
 AZY  OH   HOH  single    0.850  0.020  0.980
 AZY  CE2  N1   single    1.401  0.020  1.401
 AZY  N1   N2   double    1.220  0.020  1.220
 AZY  N2   N3   double    1.122  0.020  1.122

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
 AZY  CA   C    O    120.80  1.700
 AZY  CA   C    OXT  115.95  3.000
 AZY  O    C    OXT  127.09  3.000
 AZY  HA   CA   CB   109.00  3.000
 AZY  HA   CA   N    110.00  3.000
 AZY  CB   CA   N    110.50  1.700
 AZY  HA   CA   C    109.00  3.000
 AZY  CB   CA   C    110.10  1.900
 AZY  N    CA   C    111.00  2.800
 AZY  HN2  N    HN1  106.87  3.000
 AZY  HN2  N    CA   110.42  3.000
 AZY  HN1  N    CA   108.57  3.000
 AZY  HB2  CB   HB1  107.08  3.000
 AZY  HB2  CB   CG   109.96  3.000
 AZY  HB1  CB   CG   109.58  3.000
 AZY  HB2  CB   CA   108.62  3.000
 AZY  HB1  CB   CA   108.75  3.000
 AZY  CG   CB   CA   112.68  3.000
 AZY  CD1  CG   CD2  117.77  3.000
 AZY  CD2  CG   CB   120.53  3.000
 AZY  CD1  CG   CB   121.62  3.000
 AZY  HD2  CD2  CE2  118.02  3.000
 AZY  HD2  CD2  CG   119.93  3.000
 AZY  CE2  CD2  CG   122.05  3.000
 AZY  HD1  CD1  CE1  119.12  3.000
 AZY  HD1  CD1  CG   119.85  3.000
 AZY  CE1  CD1  CG   121.03  3.000
 AZY  HE1  CE1  CZ   119.30  3.000
 AZY  HE1  CE1  CD1  119.88  3.000
 AZY  CZ   CE1  CD1  120.82  3.000
 AZY  CE2  CZ   OH   117.59  3.000
 AZY  CE2  CZ   CE1  118.93  3.000
 AZY  OH   CZ   CE1  123.48  3.000
 AZY  HOH  OH   CZ   110.74  3.000
 AZY  N1   CE2  CZ   124.96  3.000
 AZY  N1   CE2  CD2  115.65  3.000
 AZY  CZ   CE2  CD2  119.39  3.000
 AZY  N2   N1   CE2  123.18  3.000
 AZY  N3   N2   N1   170.80  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
 AZY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 AZY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 AZY  CONST_03  CE1  CD1  CG   CD2    0.00   0.0  0
 AZY  CONST_04  CE1  CZ   CE2  CD2    0.00   0.0  0
 AZY  CONST_05  CE2  CD2  CG   CD1    0.00   0.0  0
 AZY  CONST_06  CE2  CZ   CE1  CD1    0.00   0.0  0
 AZY  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 AZY  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 AZY  CONST_09  N1   CE2  CD2  CG   180.00   0.0  0
 AZY  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 AZY  CONST_11  OH   CZ   CE1  CD1  180.00   0.0  0
 AZY  CONST_12  N1   CE2  CZ   CE1  180.00   0.0  0
 AZY  CONST_13  HE1  CE1  CD1  CG   180.00   0.0  0
 AZY  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 AZY  CONST_15  HD2  CD2  CG   CD1  180.00   0.0  0
 AZY  CONST_16  N2   N1   CE2  CD2  180.00   0.0  0
 AZY  CONST_17  N2   N1   CE2  CZ     0.00   0.0  0
 AZY  Var_01    CD1  CG   CB   CA    95.51  30.0  2

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
 AZY  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
 AZY  plan-1  CB   0.020
 AZY  plan-1  CG   0.020
 AZY  plan-1  CD2  0.020
 AZY  plan-1  CD1  0.020
 AZY  plan-1  CE1  0.020
 AZY  plan-1  CZ   0.020
 AZY  plan-1  OH   0.020
 AZY  plan-1  CE2  0.020
 AZY  plan-1  N1   0.020
 AZY  plan-1  N2   0.020
 AZY  plan-1  N3   0.020
 AZY  plan-1  HD2  0.020
 AZY  plan-1  HD1  0.020
 AZY  plan-1  HE1  0.020
 AZY  plan-2  OXT  0.020
 AZY  plan-2  C    0.020
 AZY  plan-2  O    0.020
 AZY  plan-2  CA   0.020

