# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:12:42 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-sulfanyl-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(S)[C@@H](N)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
 LEI  LEI  '3-sulfanyl-D-valine      '  D-peptide  19  9  .  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_LEI
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
 LEI  N    N  NH2    0  -0.801   8.3679   2.2773  6.2169
 LEI  CA   C  CH1    0  -0.132   8.2586   0.9299  5.6859
 LEI  CB   C  CT     0  -0.231   8.8769  -0.1663  6.6068
 LEI  C8   C  CH3    0  -0.651   8.2092  -0.1338  7.9842
 LEI  C9   C  CH3    0  -0.616  10.3859  -0.0343  6.7727
 LEI  SG   S  S2     0  -0.256   8.4673  -1.8504  5.9751
 LEI  C    C  C      0   0.404   8.8627   0.9259  4.2539
 LEI  O    O  O      0  -0.597   9.8984   1.6011  4.0858
 LEI  HN   H  HNH2   0   0.338   8.1088   2.3206  7.1933
 LEI  HN2  H  HNH2   0   0.335   9.3251   2.5944  6.1380
 LEI  HA   H  HCH1   0   0.203   7.1947   0.6834  5.6051
 LEI  H8   H  HCH3   0   0.242   8.5365  -0.9744  8.5982
 LEI  H8A  H  HCH3   0   0.236   8.4824   0.7729  8.5252
 LEI  H8B  H  HCH3   0   0.237   7.1213  -0.1708  7.9062
 LEI  H9   H  HCH3   0   0.233  10.9192  -0.1840  5.8359
 LEI  H9A  H  HCH3   0   0.217  10.6399   0.9592  7.1493
 LEI  H9B  H  HCH3   0   0.224  10.7550  -0.7640  7.4939
 LEI  HSG  H  HSH1   0   0.213   8.9783  -1.7338  4.7453
 LEI  OXT  O  OC    -1  -0.600   8.2685   0.2507  3.3907

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
 LEI  N   HN   single  0.890  0.020  1.040
 LEI  N   HN2  single  0.890  0.020  1.040
 LEI  CA  N    single  1.458  0.019  1.458
 LEI  CA  CB   single  1.521  0.033  1.521
 LEI  CA  HA   single  0.970  0.020  0.970
 LEI  CB  C9   single  1.524  0.020  1.524
 LEI  CB  C8   single  1.531  0.020  1.531
 LEI  C8  H8   single  0.970  0.020  1.090
 LEI  C8  H8A  single  0.970  0.020  1.090
 LEI  C8  H8B  single  0.970  0.020  1.090
 LEI  C9  H9   single  0.970  0.020  1.090
 LEI  C9  H9A  single  0.970  0.020  1.090
 LEI  C9  H9B  single  0.970  0.020  1.090
 LEI  SG  CB   single  1.845  0.020  1.845
 LEI  SG  HSG  single  1.200  0.020  1.300
 LEI  C   CA   single  1.525  0.021  1.525
 LEI  C   OXT  deloc   1.247  0.020  1.247
 LEI  O   C    deloc   1.231  0.020  1.231

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
 LEI  HN2  N   HN   107.72  3.000
 LEI  HN2  N   CA   109.49  3.000
 LEI  HN   N   CA   111.93  3.000
 LEI  HA   CA  C    110.00  3.000
 LEI  C    CA  CB   110.50  1.500
 LEI  HA   CA  CB   109.00  3.000
 LEI  C    CA  N    111.00  2.800
 LEI  HA   CA  N    110.00  3.000
 LEI  CB   CA  N    110.40  1.500
 LEI  SG   CB  C9   109.65  3.000
 LEI  SG   CB  C8   103.33  3.000
 LEI  C9   CB  C8   109.40  3.000
 LEI  SG   CB  CA   110.58  3.000
 LEI  C8   CB  CA   110.08  3.000
 LEI  C9   CB  CA   113.33  3.000
 LEI  H8B  C8  H8A  108.26  3.000
 LEI  H8B  C8  H8   108.25  3.000
 LEI  H8A  C8  H8   106.63  3.000
 LEI  H8B  C8  CB   111.70  3.000
 LEI  H8A  C8  CB   110.77  3.000
 LEI  H8   C8  CB   111.04  3.000
 LEI  H9B  C9  H9A  107.58  3.000
 LEI  H9B  C9  H9   108.14  3.000
 LEI  H9A  C9  H9   107.94  3.000
 LEI  H9B  C9  CB   110.44  3.000
 LEI  H9A  C9  CB   110.27  3.000
 LEI  H9   C9  CB   112.31  3.000
 LEI  HSG  SG  CB    98.66  3.000
 LEI  OXT  C   O    126.54  3.000
 LEI  O    C   CA   120.80  1.700
 LEI  OXT  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
 LEI  Var_01  H9  C9  CB  CA  -64.35  30.0  3
 LEI  Var_02  H8  C8  CB  CA  172.66  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
 LEI  chir_01  CA  N  CB  C  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
 LEI  plan-1  CA   0.020
 LEI  plan-1  C    0.020
 LEI  plan-1  O    0.020
 LEI  plan-1  OXT  0.020

