# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:17:40 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-sulfanyl-L-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
 LE1  LE1  '3-sulfanyl-L-valine      '  L-peptide  19  9  .  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_LE1
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
 LE1  O    O  O      0  -0.628  13.0615  -5.9231   8.9828
 LE1  C    C  C      0   0.417  11.8454  -6.1468   9.1243
 LE1  CA   C  CH1    0  -0.232  10.8751  -4.9713   8.8055
 LE1  N    N  NH2    0  -0.799   9.6951  -5.5107   8.1554
 LE1  CB   C  CT     0  -0.139  10.5913  -4.1138  10.0743
 LE1  C9   C  CH3    0  -0.633  11.8712  -3.5834  10.7085
 LE1  C8   C  CH3    0  -0.668   9.7577  -4.8475  11.1128
 LE1  SG   S  S2     0  -0.363   9.6191  -2.6675   9.4346
 LE1  OXT  O  OC    -1  -0.546  11.3170  -7.2154   9.4925
 LE1  HA   H  HCH1   0   0.260  11.3895  -4.3087   8.0993
 LE1  HN   H  HNH2   0   0.348   9.3682  -6.2998   8.6983
 LE1  HNA  H  HNH2   0   0.342   8.9449  -4.8298   8.1358
 LE1  H9   H  HCH3   0   0.216  12.5076  -3.0889   9.9747
 LE1  H9A  H  HCH3   0   0.281  11.6392  -2.8623  11.4937
 LE1  H9B  H  HCH3   0   0.207  12.4447  -4.3921  11.1627
 LE1  H8   H  HCH3   0   0.219   8.8093  -5.1966  10.7056
 LE1  H8A  H  HCH3   0   0.232  10.3036  -5.7104  11.4953
 LE1  H8B  H  HCH3   0   0.263   9.5373  -4.1912  11.9563
 LE1  HSG  H  HSH1   0   0.222   9.2957  -2.1347  10.6199

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
 LE1  O   C    deloc   1.231  0.020  1.231
 LE1  C   OXT  deloc   1.248  0.020  1.248
 LE1  CA  C    single  1.525  0.021  1.525
 LE1  CA  CB   single  1.540  0.027  1.540
 LE1  CA  HA   single  0.970  0.020  0.970
 LE1  N   CA   single  1.458  0.019  1.458
 LE1  N   HN   single  0.890  0.020  1.040
 LE1  N   HNA  single  0.890  0.020  1.040
 LE1  CB  C9   single  1.524  0.020  1.524
 LE1  CB  C8   single  1.520  0.020  1.520
 LE1  C9  H9   single  0.970  0.020  1.090
 LE1  C9  H9A  single  0.970  0.020  1.090
 LE1  C9  H9B  single  0.970  0.020  1.090
 LE1  C8  H8   single  0.970  0.020  1.090
 LE1  C8  H8A  single  0.970  0.020  1.090
 LE1  C8  H8B  single  0.970  0.020  1.090
 LE1  SG  CB   single  1.856  0.020  1.856
 LE1  SG  HSG  single  1.200  0.020  1.300

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
 LE1  OXT  C   CA   116.30  3.000
 LE1  CA   C   O    120.80  1.700
 LE1  OXT  C   O    126.97  3.000
 LE1  HA   CA  CB   109.00  3.000
 LE1  HA   CA  N    110.00  3.000
 LE1  CB   CA  N    111.50  1.700
 LE1  N    CA  C    111.00  2.800
 LE1  HA   CA  C    109.00  3.000
 LE1  CB   CA  C    111.40  1.900
 LE1  HNA  N   HN   107.17  3.000
 LE1  HNA  N   CA   111.15  3.000
 LE1  HN   N   CA   108.19  3.000
 LE1  SG   CB  C8   108.92  3.000
 LE1  SG   CB  C9   108.19  3.000
 LE1  C8   CB  C9   110.13  3.000
 LE1  SG   CB  CA   104.10  3.000
 LE1  C8   CB  CA   112.99  3.000
 LE1  C9   CB  CA   112.19  3.000
 LE1  H9B  C9  H9A  107.59  3.000
 LE1  H9B  C9  H9   108.05  3.000
 LE1  H9A  C9  H9   107.98  3.000
 LE1  H9B  C9  CB   110.92  3.000
 LE1  H9A  C9  CB   110.55  3.000
 LE1  H9   C9  CB   111.60  3.000
 LE1  H8B  C8  H8A  107.81  3.000
 LE1  H8B  C8  H8   107.81  3.000
 LE1  H8A  C8  H8   108.26  3.000
 LE1  H8B  C8  CB   110.39  3.000
 LE1  H8A  C8  CB   110.30  3.000
 LE1  H8   C8  CB   112.12  3.000
 LE1  HSG  SG  CB    97.55  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
 LE1  Var_01  H9  C9  CB  CA   50.81  30.0  3
 LE1  Var_02  H8  C8  CB  CA  -56.60  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
 LE1  chir_01  CA  C  CB  N  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
 LE1  plan-1  O    0.020
 LE1  plan-1  C    0.020
 LE1  plan-1  CA   0.020
 LE1  plan-1  OXT  0.020

