# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:11:00 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 2,4-bis(hydroperoxy)-5-hydroxy-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(O)c(OO)cc1OO)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
 TY8  TY8  2,4-bis(hydroperoxy)-5-hydroxy-L-phenylalanine  L-peptide  27  17  .  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_TY8
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
 TY8  C     C  C      0   0.417  -6.5394   97.8900  66.4591
 TY8  N     N  NH2    0  -0.806  -4.5721   96.3787  66.4456
 TY8  C1    C  CR6    0   0.048  -3.4206   97.7308  64.1380
 TY8  C2    C  CR6    0   0.296  -2.9489   96.6431  63.4100
 TY8  O2    O  O2     0  -0.305  -3.8423   95.7164  62.9320
 TY8  C3    C  CR16   0  -0.399  -1.5952   96.5145  63.1099
 TY8  C4    C  CR6    0   0.283  -0.6993   97.4790  63.5171
 TY8  O4    O  O2     0  -0.304   0.6173   97.3712  63.1590
 TY8  C5    C  CR6    0   0.315  -1.1472   98.5978  64.2326
 TY8  O5    O  OH1    0  -0.622  -0.2287   99.5113  64.5891
 TY8  C6    C  CR16   0  -0.428  -2.4965   98.7047  64.5239
 TY8  CA    C  CH1    0  -0.215  -5.0545   97.6911  66.0529
 TY8  CB    C  CH2    0  -0.483  -4.8583   97.8958  64.5444
 TY8  O2A   O  OH1    0  -0.453  -3.6004   94.4573  63.5422
 TY8  O4A   O  OH1    0  -0.457   1.3888   97.0480  64.3098
 TY8  O     O  O      0  -0.604  -7.1321   98.8475  65.9246
 TY8  OXT   O  OC    -1  -0.596  -7.0004   97.1053  67.3110
 TY8  HN    H  HNH2   0   0.332  -3.5676   96.3978  66.5638
 TY8  HNA   H  HNH2   0   0.334  -4.9736   96.1534  67.3456
 TY8  H3    H  HCR6   0   0.280  -1.2328   95.6652  62.5425
 TY8  H4    H  HOH1   0   0.480  -0.6381  100.2342  65.0792
 TY8  H6    H  HCR6   0   0.273  -2.8495   99.5696  65.0776
 TY8  HA    H  HCH1   0   0.201  -4.5049   98.5025  66.5623
 TY8  HB    H  HCH2   0   0.238  -5.1885   98.9018  64.2834
 TY8  HBA   H  HCH2   0   0.233  -5.4954   97.1981  64.0016
 TY8  HO2A  H  HOH1   0   0.473  -3.1870   93.9590  62.8219
 TY8  HO4A  H  HOH1   0   0.471   1.7509   97.9106  64.5637

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
 TY8  C1   C6    aromatic  1.397  0.020  1.397
 TY8  C1   CB    single    1.503  0.020  1.503
 TY8  C2   C1    aromatic  1.391  0.020  1.391
 TY8  O2   C2    single    1.373  0.020  1.373
 TY8  C3   C2    aromatic  1.393  0.020  1.393
 TY8  C3   C4    aromatic  1.378  0.020  1.378
 TY8  C4   C5    aromatic  1.402  0.020  1.402
 TY8  O4   C4    single    1.369  0.020  1.369
 TY8  O4   O4A   single    1.423  0.020  1.423
 TY8  C5   O5    single    1.344  0.020  1.344
 TY8  C5   C6    aromatic  1.385  0.020  1.385
 TY8  CA   C     single    1.525  0.021  1.525
 TY8  CA   N     single    1.458  0.019  1.458
 TY8  CB   CA    single    1.530  0.020  1.530
 TY8  O2A  O2    single    1.420  0.020  1.420
 TY8  C    O     deloc     1.231  0.020  1.231
 TY8  C    OXT   deloc     1.247  0.020  1.247
 TY8  N    HN    single    0.890  0.020  1.040
 TY8  N    HNA   single    0.890  0.020  1.040
 TY8  C3   H3    single    0.930  0.020  1.080
 TY8  O5   H4    single    0.850  0.020  0.980
 TY8  C6   H6    single    0.930  0.020  1.080
 TY8  CA   HA    single    0.970  0.020  0.970
 TY8  CB   HB    single    0.970  0.020  1.090
 TY8  CB   HBA   single    0.970  0.020  1.090
 TY8  O2A  HO2A  single    0.850  0.020  0.980
 TY8  O4A  HO4A  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
 TY8  OXT   C    O   126.92  3.000
 TY8  OXT   C    CA  116.87  3.000
 TY8  O     C    CA  120.80  1.700
 TY8  HNA   N    HN  107.13  3.000
 TY8  HNA   N    CA  108.07  3.000
 TY8  HN    N    CA  110.14  3.000
 TY8  CB    C1   C6  118.78  3.000
 TY8  CB    C1   C2  123.48  3.000
 TY8  C6    C1   C2  117.73  3.000
 TY8  C3    C2   O2  119.68  3.000
 TY8  C3    C2   C1  120.97  3.000
 TY8  O2    C2   C1  119.29  3.000
 TY8  O2A   O2   C2  109.76  3.000
 TY8  H3    C3   C4  119.07  3.000
 TY8  H3    C3   C2  120.68  3.000
 TY8  C4    C3   C2  120.25  3.000
 TY8  C5    C4   O4  120.25  3.000
 TY8  O4    C4   C3  119.54  3.000
 TY8  C5    C4   C3  120.12  3.000
 TY8  O4A   O4   C4  109.14  3.000
 TY8  C6    C5   O5  123.91  3.000
 TY8  C6    C5   C4  118.72  3.000
 TY8  O5    C5   C4  117.37  3.000
 TY8  H4    O5   C5  110.74  3.000
 TY8  H6    C6   C5  119.05  3.000
 TY8  H6    C6   C1  118.75  3.000
 TY8  C5    C6   C1  122.19  3.000
 TY8  HA    CA   CB  109.00  3.000
 TY8  HA    CA   N   110.00  3.000
 TY8  CB    CA   N   110.50  1.700
 TY8  HA    CA   C   109.00  3.000
 TY8  CB    CA   C   110.10  1.900
 TY8  N     CA   C   111.00  2.800
 TY8  HBA   CB   HB  107.13  3.000
 TY8  HBA   CB   CA  109.24  3.000
 TY8  HB    CB   CA  108.64  3.000
 TY8  HBA   CB   C1  110.74  3.000
 TY8  HB    CB   C1  109.04  3.000
 TY8  CA    CB   C1  111.92  3.000
 TY8  HO2A  O2A  O2  102.09  3.000
 TY8  HO4A  O4A  O4  102.26  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
 TY8  CONST_01  C4  C5  C6  C1    0.00   0.0  0
 TY8  CONST_02  C4  C3  C2  C1    0.00   0.0  0
 TY8  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 TY8  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 TY8  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 TY8  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 TY8  CONST_07  O5  C5  C6  C1  180.00   0.0  0
 TY8  CONST_08  O4  C4  C3  C2  180.00   0.0  0
 TY8  CONST_09  C6  C1  C2  O2  180.00   0.0  0
 TY8  CONST_10  C4  C3  C2  O2  180.00   0.0  0
 TY8  CONST_11  CB  C1  C2  C3  180.00   0.0  0
 TY8  CONST_12  O5  C5  C4  C3  180.00   0.0  0
 TY8  CONST_13  C6  C5  C4  O4  180.00   0.0  0
 TY8  CONST_14  CB  C1  C6  C5  180.00   0.0  0
 TY8  CONST_15  H3  C3  C2  C1  180.00   0.0  0
 TY8  CONST_16  H6  C6  C1  C2  180.00   0.0  0
 TY8  Var_01    CA  CB  C1  C2  108.64  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
 TY8  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
 TY8  plan-1  C1   0.020
 TY8  plan-1  C2   0.020
 TY8  plan-1  O2   0.020
 TY8  plan-1  C3   0.020
 TY8  plan-1  C4   0.020
 TY8  plan-1  O4   0.020
 TY8  plan-1  C5   0.020
 TY8  plan-1  O5   0.020
 TY8  plan-1  C6   0.020
 TY8  plan-1  CB   0.020
 TY8  plan-1  H3   0.020
 TY8  plan-1  H6   0.020
 TY8  plan-2  C    0.020
 TY8  plan-2  CA   0.020
 TY8  plan-2  O    0.020
 TY8  plan-2  OXT  0.020

