# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 23:53:42 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-[(3Z)-4-hydroxy-3-imino-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=N)C(=CC1=O)O)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
 TYY  TYY  3-[(3Z)-4-hydroxy-3-imino-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine  L-peptide  24  15  .  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_TYY
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
 TYY  N    N  NH2    0  -0.792  66.3004  76.6424  -2.9824
 TYY  CA   C  CH1    0  -0.198  65.7406  75.4216  -2.4439
 TYY  C    C  C      0   0.402  64.4135  75.7111  -1.6969
 TYY  O    O  O      0  -0.599  64.3172  76.8268  -1.1493
 TYY  CB   C  CH2    0  -0.513  66.6645  74.6741  -1.4434
 TYY  CG   C  CR6    0   0.001  67.9774  74.3012  -2.0412
 TYY  CD1  C  CR6    0   0.389  68.0498  73.0932  -2.9056
 TYY  CD2  C  CR16   0  -0.337  69.0811  75.0408  -1.8779
 TYY  CE1  C  CR16   0  -0.483  69.3291  72.7639  -3.5174
 TYY  CE2  C  CR6    0   0.151  70.3763  74.7276  -2.4827
 TYY  CZ   C  CR6    0   0.391  70.4348  73.5092  -3.3392
 TYY  OZ   O  O      0  -0.406  67.0644  72.3987  -3.0938
 TYY  N5   N  N      0  -0.549  71.3407  75.5153  -2.2234
 TYY  OH   O  OH1    0  -0.594  71.5668  73.1383  -3.9288
 TYY  OXT  O  OC    -1  -0.606  63.5811  74.7848  -1.6706
 TYY  H    H  HNH2   0   0.336  67.2541  76.5006  -3.2924
 TYY  H2   H  HNH2   0   0.327  66.3247  77.3382  -2.2471
 TYY  HA   H  HCH1   0   0.213  65.5287  74.7394  -3.2716
 TYY  HB2  H  HCH2   0   0.244  66.8352  75.3226  -0.5803
 TYY  HB3  H  HCH2   0   0.243  66.1474  73.7818  -1.0868
 TYY  HD2  H  HCR6   0   0.276  69.0701  75.9260  -1.2527
 TYY  HE1  H  HCR6   0   0.279  69.3671  71.8768  -4.1383
 TYY  HN5  H  H      0   0.348  72.2302  75.2729  -2.6513
 TYY  HH   H  HOH1   0   0.480  72.3011  73.7450  -3.7815

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
 TYY  N    CA   single  1.458  0.019  1.458
 TYY  N    H    single  0.860  0.020  0.860
 TYY  N    H2   single  0.890  0.020  1.040
 TYY  CA   C    single  1.525  0.021  1.525
 TYY  CA   CB   single  1.530  0.020  1.530
 TYY  CA   HA   single  0.970  0.020  0.970
 TYY  C    O    deloc   1.231  0.020  1.231
 TYY  C    OXT  deloc   1.246  0.020  1.246
 TYY  CB   CG   single  1.490  0.020  1.490
 TYY  CB   HB2  single  0.970  0.020  1.090
 TYY  CB   HB3  single  0.970  0.020  1.090
 TYY  CG   CD1  single  1.487  0.020  1.487
 TYY  CG   CD2  double  1.339  0.020  1.339
 TYY  CD1  CE1  single  1.456  0.020  1.456
 TYY  CD1  OZ   double  1.220  0.020  1.220
 TYY  CD2  CE2  single  1.463  0.020  1.463
 TYY  CD2  HD2  single  0.930  0.020  1.080
 TYY  CE1  CZ   double  1.345  0.020  1.345
 TYY  CE1  HE1  single  0.930  0.020  1.080
 TYY  CE2  CZ   single  1.490  0.020  1.490
 TYY  CE2  N5   double  1.272  0.020  1.272
 TYY  CZ   OH   single  1.329  0.020  1.329
 TYY  N5   HN5  single  0.890  0.020  1.040
 TYY  OH   HH   single  0.850  0.020  0.980

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
 TYY  H2   N    H    107.21  3.000
 TYY  H2   N    CA   108.60  3.000
 TYY  H    N    CA   114.00  3.000
 TYY  HA   CA   CB   109.00  3.000
 TYY  HA   CA   C    109.00  3.000
 TYY  CB   CA   C    110.10  1.900
 TYY  HA   CA   N    110.00  3.000
 TYY  CB   CA   N    110.50  1.700
 TYY  C    CA   N    111.00  2.800
 TYY  OXT  C    O    127.20  3.000
 TYY  OXT  C    CA   116.32  3.000
 TYY  O    C    CA   120.80  1.700
 TYY  HB3  CB   HB2  107.52  3.000
 TYY  HB3  CB   CG   110.12  3.000
 TYY  HB2  CB   CG   109.13  3.000
 TYY  HB3  CB   CA   108.79  3.000
 TYY  HB2  CB   CA   108.42  3.000
 TYY  CG   CB   CA   112.71  3.000
 TYY  CD2  CG   CD1  118.66  3.000
 TYY  CD2  CG   CB   122.63  3.000
 TYY  CD1  CG   CB   118.65  3.000
 TYY  OZ   CD1  CE1  121.07  3.000
 TYY  OZ   CD1  CG   120.84  3.000
 TYY  CE1  CD1  CG   118.09  3.000
 TYY  HD2  CD2  CE2  114.98  3.000
 TYY  HD2  CD2  CG   120.89  3.000
 TYY  CE2  CD2  CG   124.13  3.000
 TYY  HE1  CE1  CZ   120.05  3.000
 TYY  HE1  CE1  CD1  117.18  3.000
 TYY  CZ   CE1  CD1  122.77  3.000
 TYY  N5   CE2  CZ   126.42  3.000
 TYY  N5   CE2  CD2  117.02  3.000
 TYY  CZ   CE2  CD2  116.57  3.000
 TYY  OH   CZ   CE2  121.09  3.000
 TYY  OH   CZ   CE1  119.12  3.000
 TYY  CE2  CZ   CE1  119.79  3.000
 TYY  HN5  N5   CE2  115.47  3.000
 TYY  HH   OH   CZ   113.91  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
 TYY  Var_01  CD1  CG  CB  CA  -80.07  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
 TYY  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
 TYY  plan-1  CB   0.020
 TYY  plan-1  CG   0.020
 TYY  plan-1  CD1  0.020
 TYY  plan-1  CD2  0.020
 TYY  plan-1  CE1  0.020
 TYY  plan-1  CE2  0.020
 TYY  plan-1  CZ   0.020
 TYY  plan-1  OZ   0.020
 TYY  plan-1  N5   0.020
 TYY  plan-1  OH   0.020
 TYY  plan-1  HD2  0.020
 TYY  plan-1  HE1  0.020
 TYY  plan-1  HN5  0.020
 TYY  plan-2  CA   0.020
 TYY  plan-2  C    0.020
 TYY  plan-2  O    0.020
 TYY  plan-2  OXT  0.020

