# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 02:38:01 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S,4Z,6E)-2-amino-7-hydroperoxy-4-[(E)-2-hydroxyethenyl]hepta-4,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(/C=C/O)=C/C=C/OO)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
 TYO  TYO  '(2S,4Z,6E)-2-amino-7-hydroperoxy-4-[(E)-2-hydroxyethenyl]hepta-4,6-dienoic acid'  L-peptide  27  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 PERFECT (side chain)
;

data_comp_TYO
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
 TYO  N     N  NH2    0  -0.796  30.1361  -5.7390  22.4121
 TYO  CA    C  CH1    0  -0.186  28.8492  -6.1405  21.8588
 TYO  CB    C  CH2    0  -0.496  27.8898  -4.9456  21.6786
 TYO  CG    C  C      0   0.081  26.5460  -5.2858  21.0865
 TYO  CD1   C  C1     0  -0.422  25.7718  -6.3095  21.8139
 TYO  CE1   C  C1     0   0.058  24.6949  -6.0390  22.5490
 TYO  OE1   O  OH1    0  -0.617  23.9789  -6.9085  23.2886
 TYO  CD2   C  C1     0  -0.313  26.1569  -4.6968  19.9446
 TYO  CE2   C  C1     0  -0.348  24.9661  -4.9239  19.1276
 TYO  CZ    C  C1     0   0.062  23.7023  -4.9998  19.5393
 TYO  OH    O  O2     0  -0.276  22.6989  -5.0894  18.6159
 TYO  OH1   O  OH1    0  -0.438  21.6051  -5.7753  19.1785
 TYO  C     C  C      0   0.412  29.0537  -6.8341  20.4959
 TYO  O     O  O      0  -0.607  29.8479  -6.2741  19.7119
 TYO  OXT   O  OC    -1  -0.602  28.3899  -7.8664  20.2758
 TYO  HN1   H  HNH2   0   0.324  30.6242  -5.1998  21.7066
 TYO  HN2   H  HNH2   0   0.330  29.9902  -5.1130  23.1957
 TYO  HA    H  HCH1   0   0.200  28.3931  -6.8507  22.5542
 TYO  HB1   H  HCH2   0   0.227  27.7353  -4.4911  22.6650
 TYO  HB2   H  HCH2   0   0.220  28.3899  -4.1975  21.0567
 TYO  HD1   H  H      0   0.255  26.1788  -7.3183  21.8040
 TYO  HE1   H  H      0   0.257  24.2959  -5.0331  22.6320
 TYO  HOE1  H  HOH1   0   0.464  24.3483  -7.7965  23.2079
 TYO  HD21  H  H      0   0.234  26.8642  -4.0039  19.4949
 TYO  HE2   H  H      0   0.254  25.1460  -4.9649  18.0561
 TYO  HZ    H  H      0   0.248  23.3824  -4.9123  20.5698
 TYO  HOH1  H  HOH1   0   0.474  21.7683  -6.6924  18.9090

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
 TYO  N    CA    single  1.458  0.019  1.458
 TYO  N    HN1   single  0.890  0.020  1.040
 TYO  N    HN2   single  0.890  0.020  1.040
 TYO  CA   C     single  1.525  0.021  1.525
 TYO  CA   CB    single  1.530  0.020  1.530
 TYO  CA   HA    single  0.970  0.020  0.970
 TYO  CB   CG    single  1.507  0.020  1.507
 TYO  CB   HB1   single  0.970  0.020  1.090
 TYO  CB   HB2   single  0.970  0.020  1.090
 TYO  CG   CD2   double  1.342  0.020  1.342
 TYO  CG   CD1   single  1.475  0.020  1.475
 TYO  CD1  CE1   double  1.332  0.020  1.332
 TYO  CD1  HD1   single  0.930  0.020  1.080
 TYO  CE1  OE1   single  1.348  0.020  1.348
 TYO  CE1  HE1   single  0.930  0.020  1.080
 TYO  OE1  HOE1  single  0.850  0.020  0.980
 TYO  CD2  CE2   single  1.462  0.020  1.462
 TYO  CD2  HD21  single  0.930  0.020  1.080
 TYO  CE2  CZ    double  1.331  0.020  1.331
 TYO  CE2  HE2   single  0.930  0.020  1.080
 TYO  CZ   OH    single  1.367  0.020  1.367
 TYO  CZ   HZ    single  0.930  0.020  1.080
 TYO  OH   OH1   single  1.408  0.020  1.408
 TYO  OH1  HOH1  single  0.850  0.020  0.980
 TYO  C    O     deloc   1.231  0.020  1.231
 TYO  C    OXT   deloc   1.247  0.020  1.247

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
 TYO  HN2   N    HN1  106.20  3.000
 TYO  HN2   N    CA   109.67  3.000
 TYO  HN1   N    CA   107.92  3.000
 TYO  HA    CA   C    109.00  3.000
 TYO  HA    CA   CB   109.00  3.000
 TYO  C     CA   CB   110.10  1.900
 TYO  HA    CA   N    110.00  3.000
 TYO  CB    CA   N    110.50  1.700
 TYO  C     CA   N    111.00  2.800
 TYO  HB2   CB   HB1  106.99  3.000
 TYO  HB2   CB   CG   109.79  3.000
 TYO  HB1   CB   CG   108.73  3.000
 TYO  HB2   CB   CA   108.17  3.000
 TYO  HB1   CB   CA   107.66  3.000
 TYO  CG    CB   CA   115.18  3.000
 TYO  CD2   CG   CD1  124.87  3.000
 TYO  CD1   CG   CB   115.52  3.000
 TYO  CD2   CG   CB   119.57  3.000
 TYO  HD1   CD1  CE1  119.73  3.000
 TYO  HD1   CD1  CG   116.27  3.000
 TYO  CE1   CD1  CG   123.75  3.000
 TYO  HE1   CE1  OE1  111.15  3.000
 TYO  HE1   CE1  CD1  121.86  3.000
 TYO  OE1   CE1  CD1  126.99  3.000
 TYO  HOE1  OE1  CE1  110.14  3.000
 TYO  HD21  CD2  CE2  113.43  3.000
 TYO  HD21  CD2  CG   116.28  3.000
 TYO  CE2   CD2  CG   130.04  3.000
 TYO  HE2   CE2  CZ   117.37  3.000
 TYO  HE2   CE2  CD2  114.95  3.000
 TYO  CZ    CE2  CD2  127.54  3.000
 TYO  HZ    CZ   OH   115.56  3.000
 TYO  HZ    CZ   CE2  124.77  3.000
 TYO  OH    CZ   CE2  119.46  3.000
 TYO  OH1   OH   CZ   109.41  3.000
 TYO  HOH1  OH1  OH   102.64  3.000
 TYO  OXT   C    O    126.80  3.000
 TYO  OXT   C    CA   117.23  3.000
 TYO  O     C    CA   120.80  1.700

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
 TYO  Var_01  CE2  CD2  CG   CB    174.96   0.0  2
 TYO  Var_02  OE1  CE1  CD1  CG   -176.60   0.0  2
 TYO  Var_03  OH   CZ   CE2  CD2   173.71   0.0  2
 TYO  Var_04  CD2  CG   CB   CA   -121.34  30.0  3
 TYO  Var_05  CE1  CD1  CG   CB    106.96  30.0  2
 TYO  Var_06  CZ   CE2  CD2  CG     48.17  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
 TYO  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
 TYO  plan-1  CA    0.020
 TYO  plan-1  C     0.020
 TYO  plan-1  O     0.020
 TYO  plan-1  OXT   0.020
 TYO  plan-2  CB    0.020
 TYO  plan-2  CG    0.020
 TYO  plan-2  CD1   0.020
 TYO  plan-2  CD2   0.020
 TYO  plan-2  CE2   0.020
 TYO  plan-2  HD21  0.020
 TYO  plan-3  CG    0.020
 TYO  plan-3  CD1   0.020
 TYO  plan-3  CE1   0.020
 TYO  plan-3  OE1   0.020
 TYO  plan-3  HD1   0.020
 TYO  plan-3  HE1   0.020
 TYO  plan-4  CD2   0.020
 TYO  plan-4  CE2   0.020
 TYO  plan-4  CZ    0.020
 TYO  plan-4  OH    0.020
 TYO  plan-4  HE2   0.020
 TYO  plan-4  HZ    0.020

