# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 23:31:26 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-[(5S)-4,5-dihydroxycyclohexa-1,3-dien-1-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC=C(O)[C@@H](O)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
 TXY  TXY  3-[(5S)-4,5-dihydroxycyclohexa-1,3-dien-1-yl]-L-alanine  L-peptide  26  14  .  2016-04-26  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_TXY
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
 TXY  N    N  NH2    0  -0.782  -4.3279  -4.6270  -17.9222
 TXY  CA   C  CH1    0  -0.203  -5.5923  -3.9245  -17.7744
 TXY  C    C  C      0   0.380  -5.6635  -2.9025  -16.6104
 TXY  O    O  O      0  -0.603  -4.8849  -3.0794  -15.6518
 TXY  CB   C  CH2    0  -0.514  -6.7313  -4.9427  -17.5838
 TXY  CG   C  C      0   0.117  -6.9823  -5.8255  -18.7635
 TXY  CD1  C  C1     0  -0.304  -6.7353  -7.1411  -18.7785
 TXY  CD2  C  CH2    0  -0.538  -7.6667  -5.2269  -19.9626
 TXY  CE1  C  C1     0  -0.399  -7.0724  -7.9778  -19.9235
 TXY  CE2  C  CH1    0   0.010  -7.3134  -5.9273  -21.2698
 TXY  CZ   C  C      0   0.308  -7.3996  -7.4238  -21.1000
 TXY  OE2  O  OH1    0  -0.663  -8.1539  -5.5286  -22.3243
 TXY  OZ   O  OH1    0  -0.615  -7.7060  -8.0927  -22.2244
 TXY  OXT  O  OC    -1  -0.616  -6.5287  -2.0086  -16.7180
 TXY  H1   H  HNH2   0   0.332  -3.6055  -3.9502  -18.1387
 TXY  H2   H  HNH2   0   0.320  -4.0692  -4.9874  -17.0099
 TXY  H4   H  HCH1   0   0.209  -5.7795  -3.3799  -18.7066
 TXY  H6   H  HCH2   0   0.230  -7.6484  -4.3886  -17.3568
 TXY  H7   H  HCH2   0   0.227  -6.5101  -5.5556  -16.7034
 TXY  H8   H  H      0   0.229  -6.2992  -7.6229  -17.9102
 TXY  H9   H  HCH2   0   0.247  -7.4350  -4.1625  -20.0585
 TXY  H10  H  HCH2   0   0.240  -8.7542  -5.2935  -19.8126
 TXY  H11  H  H      0   0.249  -7.0329  -9.0564  -19.8139
 TXY  H12  H  HCH1   0   0.219  -6.2590  -5.6984  -21.5068
 TXY  H13  H  HOH1   0   0.452  -8.0334  -4.5828  -22.4543
 TXY  H14  H  HOH1   0   0.468  -7.6862  -9.0425  -22.0535

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
 TXY  OZ   CZ   single  1.344  0.020  1.344
 TXY  OE2  CE2  single  1.406  0.020  1.406
 TXY  CE2  CZ   single  1.509  0.020  1.509
 TXY  CE2  CD2  single  1.525  0.020  1.525
 TXY  CZ   CE1  double  1.341  0.020  1.341
 TXY  CE1  CD1  single  1.458  0.020  1.458
 TXY  CD2  CG   single  1.505  0.020  1.505
 TXY  CG   CD1  double  1.339  0.020  1.339
 TXY  CG   CB   single  1.495  0.020  1.495
 TXY  N    CA   single  1.458  0.019  1.458
 TXY  CA   CB   single  1.530  0.020  1.530
 TXY  CA   C    single  1.525  0.021  1.525
 TXY  OXT  C    deloc   1.249  0.020  1.249
 TXY  C    O    deloc   1.231  0.020  1.231
 TXY  N    H1   single  0.890  0.020  1.040
 TXY  N    H2   single  0.890  0.020  1.040
 TXY  CA   H4   single  0.970  0.020  1.090
 TXY  CB   H6   single  0.970  0.020  1.090
 TXY  CB   H7   single  0.970  0.020  1.090
 TXY  CD1  H8   single  0.930  0.020  1.080
 TXY  CD2  H9   single  0.970  0.020  1.090
 TXY  CD2  H10  single  0.970  0.020  1.090
 TXY  CE1  H11  single  0.930  0.020  1.080
 TXY  CE2  H12  single  0.970  0.020  1.090
 TXY  OE2  H13  single  0.850  0.020  0.980
 TXY  OZ   H14  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
 TXY  H2   N    H1   104.33  3.000
 TXY  H2   N    CA   107.57  3.000
 TXY  H1   N    CA   108.60  3.000
 TXY  H4   CA   CB   107.92  3.000
 TXY  H4   CA   C    107.65  3.000
 TXY  CB   CA   C    110.10  1.900
 TXY  H4   CA   N    107.59  3.000
 TXY  C    CA   N    111.00  2.800
 TXY  CB   CA   N    110.50  1.700
 TXY  OXT  C    O    126.87  3.000
 TXY  O    C    CA   120.80  1.700
 TXY  OXT  C    CA   116.04  3.000
 TXY  H7   CB   H6   106.60  3.000
 TXY  H7   CB   CG   109.75  3.000
 TXY  H6   CB   CG   108.76  3.000
 TXY  H7   CB   CA   108.67  3.000
 TXY  H6   CB   CA   108.09  3.000
 TXY  CG   CB   CA   114.65  3.000
 TXY  CD2  CG   CD1  117.77  3.000
 TXY  CD1  CG   CB   123.93  3.000
 TXY  CD2  CG   CB   118.06  3.000
 TXY  H8   CD1  CE1  117.83  3.000
 TXY  H8   CD1  CG   120.12  3.000
 TXY  CE1  CD1  CG   122.02  3.000
 TXY  H10  CD2  H9   106.29  3.000
 TXY  H10  CD2  CE2  108.56  3.000
 TXY  H9   CD2  CE2  108.84  3.000
 TXY  H10  CD2  CG   108.48  3.000
 TXY  H9   CD2  CG   111.14  3.000
 TXY  CE2  CD2  CG   113.27  3.000
 TXY  H11  CE1  CZ   120.55  3.000
 TXY  H11  CE1  CD1  118.88  3.000
 TXY  CZ   CE1  CD1  120.56  3.000
 TXY  H12  CE2  OE2  110.54  3.000
 TXY  H12  CE2  CZ   106.52  3.000
 TXY  OE2  CE2  CZ   109.36  3.000
 TXY  H12  CE2  CD2  108.06  3.000
 TXY  CZ   CE2  CD2  110.24  3.000
 TXY  OE2  CE2  CD2  111.97  3.000
 TXY  OZ   CZ   CE2  114.37  3.000
 TXY  CE2  CZ   CE1  119.65  3.000
 TXY  OZ   CZ   CE1  125.74  3.000
 TXY  H13  OE2  CE2  107.76  3.000
 TXY  H14  OZ   CZ   109.69  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
 TXY  Var_01  CZ   CE1  CD1  CG    13.18  30.0  1
 TXY  Var_02  CE2  CZ   CE1  CD1    4.81  30.0  1
 TXY  Var_03  CE2  CD2  CG   CD1  -32.18  30.0  1
 TXY  Var_04  CE1  CD1  CG   CD2    1.83  30.0  1
 TXY  Var_05  CD2  CG   CB   CA   -73.97  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
 TXY  chir_01  CA   N    CB   C   negativ
 TXY  chir_02  CE2  OE2  CD2  CZ  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
 TXY  plan-1  CA   0.020
 TXY  plan-1  C    0.020
 TXY  plan-1  O    0.020
 TXY  plan-1  OXT  0.020

