# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:12:38 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 3,4-bis(hydroperoxy)-5-hydroxy-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(O)c(OO)c(OO)c1)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
 TY9  TY9  3,4-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_TY9
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
 TY9  C     C  C      0   0.414  -6.4217   97.7742  66.3208
 TY9  N     N  NH2    0  -0.805  -4.4045   96.3328  66.4344
 TY9  O     O  O      0  -0.596  -6.9011   96.9805  67.1538
 TY9  C1    C  CR6    0   0.148  -3.1843   97.7255  64.1639
 TY9  C2    C  CR16   0  -0.450  -2.6185   96.5387  63.7034
 TY9  C3    C  CR6    0   0.341  -1.2540   96.4821  63.4603
 TY9  O3    O  O2     0  -0.276  -0.5854   95.3891  63.0051
 TY9  C4    C  CR6    0   0.170  -0.4488   97.6048  63.6604
 TY9  O4    O  O2     0  -0.296   0.8834   97.5521  63.3695
 TY9  C5    C  CR6    0   0.321  -1.0193   98.7891  64.1298
 TY9  O5    O  OH1    0  -0.619  -0.1916   99.8300  64.3129
 TY9  C6    C  CR16   0  -0.457  -2.3862   98.8447  64.3727
 TY9  CA    C  CH1    0  -0.210  -4.9133   97.6176  65.9877
 TY9  CB    C  CH2    0  -0.493  -4.6492   97.7929  64.4867
 TY9  O3A   O  OH1    0  -0.419  -1.4094   94.2644  62.9193
 TY9  O4A   O  OH1    0  -0.462   1.6142   97.2358  64.5560
 TY9  OXT   O  OC    -1  -0.605  -7.0136   98.7139  65.7546
 TY9  HN    H  HNH2   0   0.333  -3.4049   96.3841  66.5802
 TY9  HNA   H  HNH2   0   0.334  -4.8259   96.1195  67.3281
 TY9  H2    H  HCR6   0   0.264  -3.2489   95.6759  63.5489
 TY9  H61   H  HOH1   0   0.479  -0.6771  100.5924  64.6500
 TY9  H6    H  HCR6   0   0.264  -2.8324   99.7669  64.7305
 TY9  HA    H  HCH1   0   0.201  -4.4167   98.4623  66.4982
 TY9  HB    H  HCH2   0   0.236  -5.0515   98.7548  64.1694
 TY9  HBA   H  HCH2   0   0.229  -5.1860   97.0145  63.9387
 TY9  HO3A  H  HOH1   0   0.483  -1.6372   94.2392  61.9767
 TY9  HO4A  H  HOH1   0   0.469   1.9172   98.1100  64.8440

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
 TY9  C    OXT   deloc     1.247  0.020  1.247
 TY9  O    C     deloc     1.231  0.020  1.231
 TY9  C1   C6    aromatic  1.390  0.020  1.390
 TY9  C1   CB    single    1.502  0.020  1.502
 TY9  C2   C1    aromatic  1.393  0.020  1.393
 TY9  C3   C2    aromatic  1.387  0.020  1.387
 TY9  C3   C4    aromatic  1.396  0.020  1.396
 TY9  O3   C3    single    1.360  0.020  1.360
 TY9  O3   O3A   single    1.397  0.020  1.397
 TY9  C4   C5    aromatic  1.396  0.020  1.396
 TY9  O4   C4    single    1.365  0.020  1.365
 TY9  O4   O4A   single    1.429  0.020  1.429
 TY9  C5   O5    single    1.342  0.020  1.342
 TY9  C5   C6    aromatic  1.389  0.020  1.389
 TY9  CA   C     single    1.525  0.021  1.525
 TY9  CA   N     single    1.458  0.019  1.458
 TY9  CB   CA    single    1.530  0.020  1.530
 TY9  N    HN    single    0.890  0.020  1.040
 TY9  N    HNA   single    0.890  0.020  1.040
 TY9  C2   H2    single    0.930  0.020  1.080
 TY9  O5   H61   single    0.850  0.020  0.980
 TY9  C6   H6    single    0.930  0.020  1.080
 TY9  CA   HA    single    0.970  0.020  0.970
 TY9  CB   HB    single    0.970  0.020  1.090
 TY9  CB   HBA   single    0.970  0.020  1.090
 TY9  O3A  HO3A  single    0.850  0.020  0.980
 TY9  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
 TY9  OXT   C    CA  116.09  3.000
 TY9  CA    C    O   120.80  1.700
 TY9  OXT   C    O   126.94  3.000
 TY9  HNA   N    HN  107.17  3.000
 TY9  HNA   N    CA  108.21  3.000
 TY9  HN    N    CA  110.23  3.000
 TY9  CB    C1   C6  119.45  3.000
 TY9  CB    C1   C2  120.36  3.000
 TY9  C6    C1   C2  120.15  3.000
 TY9  H2    C2   C3  121.11  3.000
 TY9  H2    C2   C1  119.40  3.000
 TY9  C3    C2   C1  119.48  3.000
 TY9  C4    C3   O3  114.26  3.000
 TY9  O3    C3   C2  125.11  3.000
 TY9  C4    C3   C2  120.63  3.000
 TY9  O3A   O3   C3  112.20  3.000
 TY9  C5    C4   O4  120.23  3.000
 TY9  O4    C4   C3  120.10  3.000
 TY9  C5    C4   C3  119.66  3.000
 TY9  O4A   O4   C4  109.32  3.000
 TY9  C6    C5   O5  123.48  3.000
 TY9  C6    C5   C4  119.66  3.000
 TY9  O5    C5   C4  116.86  3.000
 TY9  H61   O5   C5  110.50  3.000
 TY9  H6    C6   C5  119.75  3.000
 TY9  H6    C6   C1  119.83  3.000
 TY9  C5    C6   C1  120.41  3.000
 TY9  HA    CA   CB  109.00  3.000
 TY9  HA    CA   N   110.00  3.000
 TY9  CB    CA   N   110.50  1.700
 TY9  HA    CA   C   109.00  3.000
 TY9  CB    CA   C   110.10  1.900
 TY9  N     CA   C   111.00  2.800
 TY9  HBA   CB   HB  107.54  3.000
 TY9  HBA   CB   CA  108.94  3.000
 TY9  HB    CB   CA  108.80  3.000
 TY9  HBA   CB   C1  109.84  3.000
 TY9  HB    CB   C1  109.70  3.000
 TY9  CA    CB   C1  111.91  3.000
 TY9  HO3A  O3A  O3  102.65  3.000
 TY9  HO4A  O4A  O4  101.94  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
 TY9  CONST_01  C4  C5  C6  C1    0.00   0.0  0
 TY9  CONST_02  C4  C3  C2  C1    0.00   0.0  0
 TY9  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 TY9  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 TY9  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 TY9  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 TY9  CONST_07  O5  C5  C6  C1  180.00   0.0  0
 TY9  CONST_08  O3  C3  C2  C1  180.00   0.0  0
 TY9  CONST_09  O4  C4  C3  C2  180.00   0.0  0
 TY9  CONST_10  CB  C1  C2  C3  180.00   0.0  0
 TY9  CONST_11  O5  C5  C4  C3  180.00   0.0  0
 TY9  CONST_12  C5  C4  C3  O3  180.00   0.0  0
 TY9  CONST_13  C6  C5  C4  O4  180.00   0.0  0
 TY9  CONST_14  CB  C1  C6  C5  180.00   0.0  0
 TY9  CONST_15  H6  C6  C1  C2  180.00   0.0  0
 TY9  CONST_16  H2  C2  C3  C4  180.00   0.0  0
 TY9  Var_01    CA  CB  C1  C2   97.70  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
 TY9  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
 TY9  plan-1  C1   0.020
 TY9  plan-1  C2   0.020
 TY9  plan-1  C3   0.020
 TY9  plan-1  O3   0.020
 TY9  plan-1  C4   0.020
 TY9  plan-1  O4   0.020
 TY9  plan-1  C5   0.020
 TY9  plan-1  O5   0.020
 TY9  plan-1  C6   0.020
 TY9  plan-1  CB   0.020
 TY9  plan-1  H2   0.020
 TY9  plan-1  H6   0.020
 TY9  plan-2  C    0.020
 TY9  plan-2  O    0.020
 TY9  plan-2  CA   0.020
 TY9  plan-2  OXT  0.020

