# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 12:15:00 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2S,3R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-3-hydroxybutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS[C@@H]([C@H](O)C(O)=O)C(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
 QVA  QVA  '(2S,3R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-3-hydroxybutanedioic acid'  L-peptide  24  16  .  2022-08-10  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_QVA
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
 QVA  N    N  NH2    0  -0.810  46.7658   4.4812  -1.0721
 QVA  CA   C  CH1    0  -0.170  46.1944   5.7670  -1.4903
 QVA  C    C  C      0   0.399  45.7985   5.6652  -2.9847
 QVA  O    O  O      0  -0.606  46.7269   5.6574  -3.8162
 QVA  CB   C  CH2    0  -0.568  47.2406   6.8422  -1.2436
 QVA  SG   S  S2     0  -0.031  46.7478   8.5289  -1.6997
 QVA  C02  C  C      0   0.441  44.0891   8.4891  -0.7256
 QVA  C04  C  CH1    0  -0.509  45.5408   8.8960  -0.3808
 QVA  C05  C  CH1    0  -0.050  45.6221  10.3763   0.0413
 QVA  C07  C  C      0   0.391  45.2801  11.3666  -1.0962
 QVA  O01  O  OC    -1  -0.617  43.4865   7.8366   0.1524
 QVA  O03  O  O      0  -0.593  43.6381   8.8604  -1.8238
 QVA  O06  O  OH1    0  -0.666  44.7705  10.6060   1.1434
 QVA  O08  O  O      0  -0.609  46.1010  11.3745  -2.0360
 QVA  O09  O  OC    -1  -0.601  44.2702  12.0788  -0.9729
 QVA  H    H  HNH2   0   0.334  46.9228   4.5045  -0.0708
 QVA  H2   H  HNH2   0   0.336  46.0801   3.7485  -1.2138
 QVA  HA   H  HCH1   0   0.189  45.2963   6.0199  -0.9125
 QVA  HB2  H  HCH2   0   0.247  48.1280   6.6236  -1.8402
 QVA  HB3  H  HCH2   0   0.241  47.5478   6.8395  -0.1926
 QVA  H8   H  HCH1   0   0.241  45.8787   8.3068   0.4796
 QVA  H9   H  HCH1   0   0.190  46.6702  10.5645   0.3239
 QVA  H11  H  HOH1   0   0.433  44.9401   9.9173   1.7939
 QVA  OXT  O  OC    -1  -0.611  44.5785   5.5614  -3.2275

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
 QVA  O    C    deloc   1.231  0.020  1.231
 QVA  C    CA   single  1.525  0.021  1.525
 QVA  O08  C07  deloc   1.248  0.020  1.248
 QVA  SG   CB   single  1.815  0.020  1.815
 QVA  SG   C04  single  1.825  0.020  1.825
 QVA  O03  C02  deloc   1.244  0.020  1.244
 QVA  CA   CB   single  1.530  0.020  1.530
 QVA  CA   N    single  1.458  0.019  1.458
 QVA  C07  O09  deloc   1.242  0.020  1.242
 QVA  C07  C05  single  1.546  0.020  1.546
 QVA  O01  C02  deloc   1.249  0.020  1.249
 QVA  C02  C04  single  1.547  0.020  1.547
 QVA  C04  C05  single  1.541  0.020  1.541
 QVA  C05  O06  single  1.412  0.020  1.412
 QVA  N    H    single  0.860  0.020  0.860
 QVA  N    H2   single  0.890  0.020  1.040
 QVA  CA   HA   single  0.970  0.020  0.970
 QVA  CB   HB2  single  0.970  0.020  1.090
 QVA  CB   HB3  single  0.970  0.020  1.090
 QVA  C04  H8   single  0.970  0.020  1.090
 QVA  C05  H9   single  0.970  0.020  1.090
 QVA  O06  H11  single  0.850  0.020  0.980
 QVA  C    OXT  deloc   1.248  0.020  1.248

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
 QVA  H2   N    H    105.04  3.000
 QVA  H2   N    CA   109.27  3.000
 QVA  H    N    CA   114.00  3.000
 QVA  HA   CA   CB   109.00  3.000
 QVA  HA   CA   C    109.00  3.000
 QVA  CB   CA   C    110.10  1.900
 QVA  HA   CA   N    110.00  3.000
 QVA  CB   CA   N    110.50  1.700
 QVA  C    CA   N    111.00  2.800
 QVA  OXT  C    O    126.71  3.000
 QVA  OXT  C    CA   116.29  3.000
 QVA  O    C    CA   120.80  1.700
 QVA  HB3  CB   HB2  107.22  3.000
 QVA  HB3  CB   SG   108.64  3.000
 QVA  HB2  CB   SG   105.63  3.000
 QVA  HB3  CB   CA   110.31  3.000
 QVA  HB2  CB   CA   109.21  3.000
 QVA  SG   CB   CA   115.44  3.000
 QVA  C04  SG   CB   100.65  3.000
 QVA  O03  C02  O01  126.99  3.000
 QVA  O01  C02  C04  115.70  3.000
 QVA  O03  C02  C04  117.29  3.000
 QVA  H8   C04  C05  106.56  3.000
 QVA  H8   C04  C02  108.83  3.000
 QVA  C05  C04  C02  111.30  3.000
 QVA  H8   C04  SG   104.79  3.000
 QVA  C05  C04  SG   110.87  3.000
 QVA  C02  C04  SG   114.00  3.000
 QVA  H9   C05  O06  110.23  3.000
 QVA  H9   C05  C07  106.84  3.000
 QVA  O06  C05  C07  109.68  3.000
 QVA  H9   C05  C04  106.52  3.000
 QVA  O06  C05  C04  109.77  3.000
 QVA  C07  C05  C04  113.70  3.000
 QVA  O09  C07  O08  127.31  3.000
 QVA  O09  C07  C05  118.30  3.000
 QVA  O08  C07  C05  114.36  3.000
 QVA  H11  O06  C05  107.76  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
 QVA  Var_01  HB2  CB  SG  C04  -167.28  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
 QVA  chir_01  CA   C    CB   N    positiv
 QVA  chir_02  C04  SG   C05  C02  negativ
 QVA  chir_03  C05  O06  C04  C07  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
 QVA  plan-1  CA   0.020
 QVA  plan-1  C    0.020
 QVA  plan-1  O    0.020
 QVA  plan-1  OXT  0.020
 QVA  plan-2  C02  0.020
 QVA  plan-2  C04  0.020
 QVA  plan-2  O01  0.020
 QVA  plan-2  O03  0.020
 QVA  plan-3  C05  0.020
 QVA  plan-3  C07  0.020
 QVA  plan-3  O08  0.020
 QVA  plan-3  O09  0.020

