# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:07:35 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@](C)(O)[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
 TS9  TS9  '(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid (non-preferred name)'  L-peptide  23  11  .  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_TS9
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
 TS9  N     N  NH2    0  -0.824  127.3939  84.2847  112.2653
 TS9  CA    C  CH1    0  -0.192  127.8688  85.1314  113.3510
 TS9  C     C  C      0   0.407  128.1434  84.2723  114.6224
 TS9  CB    C  CT     0   0.216  126.8634  86.2826  113.6376
 TS9  OG3   O  OH1    0  -0.684  125.7570  85.6850  114.3018
 TS9  CG2   C  CH3    0  -0.707  127.4801  87.3761  114.5061
 TS9  CG1   C  CH1    0   0.056  126.3559  86.8714  112.3006
 TS9  OD2   O  OH1    0  -0.676  127.4868  87.3179  111.5709
 TS9  CD1   C  CH3    0  -0.709  125.3356  87.9938  112.4509
 TS9  OXT   O  OC    -1  -0.600  128.7230  84.8355  115.5716
 TS9  O     O  O      0  -0.598  127.7999  83.0738  114.5791
 TS9  H     H  HNH2   0   0.328  127.8672  84.5153  111.4038
 TS9  H2    H  HNH2   0   0.337  127.6148  83.3263  112.4986
 TS9  HA    H  HCH1   0   0.204  128.8240  85.6075  113.0951
 TS9  HG3   H  HOH1   0   0.439  125.2332  86.3786  114.7141
 TS9  HG21  H  HCH3   0   0.215  126.7512  88.1591  114.7282
 TS9  HG22  H  HCH3   0   0.248  127.8372  86.9667  115.4459
 TS9  HG23  H  HCH3   0   0.217  128.3235  87.8530  114.0066
 TS9  HG1   H  HCH1   0   0.201  125.8673  86.0460  111.7704
 TS9  HD2   H  HOH1   0   0.445  127.1853  87.6184  110.7083
 TS9  HD11  H  HCH3   0   0.232  124.9692  88.2942  111.4665
 TS9  HD12  H  HCH3   0   0.219  124.4616  87.6784  113.0224
 TS9  HD13  H  HCH3   0   0.225  125.7552  88.8796  112.9291

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
 TS9  N    CA    single  1.458  0.019  1.458
 TS9  CA   C     single  1.525  0.021  1.525
 TS9  CA   CB    single  1.540  0.027  1.540
 TS9  C    OXT   deloc   1.247  0.020  1.247
 TS9  C    O     deloc   1.231  0.020  1.231
 TS9  CB   OG3   single  1.422  0.020  1.422
 TS9  CB   CG2   single  1.527  0.020  1.527
 TS9  CB   CG1   single  1.547  0.020  1.547
 TS9  CG1  OD2   single  1.418  0.020  1.418
 TS9  CG1  CD1   single  1.524  0.020  1.524
 TS9  N    H     single  0.860  0.020  0.860
 TS9  N    H2    single  0.890  0.020  1.040
 TS9  CA   HA    single  0.970  0.020  0.970
 TS9  OG3  HG3   single  0.850  0.020  0.980
 TS9  CG2  HG21  single  0.970  0.020  1.090
 TS9  CG2  HG22  single  0.970  0.020  1.090
 TS9  CG2  HG23  single  0.970  0.020  1.090
 TS9  CG1  HG1   single  0.970  0.020  1.090
 TS9  OD2  HD2   single  0.850  0.020  0.980
 TS9  CD1  HD11  single  0.970  0.020  1.090
 TS9  CD1  HD12  single  0.970  0.020  1.090
 TS9  CD1  HD13  single  0.970  0.020  1.090

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
 TS9  H2    N    H     108.12  3.000
 TS9  H2    N    CA    107.93  3.000
 TS9  H     N    CA    114.00  3.000
 TS9  HA    CA   CB    109.00  3.000
 TS9  HA    CA   C     109.00  3.000
 TS9  CB    CA   C     111.60  2.000
 TS9  HA    CA   N     110.00  3.000
 TS9  CB    CA   N     111.50  1.700
 TS9  C     CA   N     111.00  2.800
 TS9  O     C    OXT   126.05  3.000
 TS9  O     C    CA    120.80  1.700
 TS9  OXT   C    CA    117.00  3.000
 TS9  CG1   CB   CG2   110.59  3.000
 TS9  CG1   CB   OG3   107.97  3.000
 TS9  CG2   CB   OG3   110.46  3.000
 TS9  CG1   CB   CA    109.56  3.000
 TS9  CG2   CB   CA    111.96  3.000
 TS9  OG3   CB   CA    106.14  3.000
 TS9  HG3   OG3  CB    108.71  3.000
 TS9  HG23  CG2  HG22  107.89  3.000
 TS9  HG23  CG2  HG21  107.21  3.000
 TS9  HG22  CG2  HG21  108.28  3.000
 TS9  HG23  CG2  CB    111.43  3.000
 TS9  HG22  CG2  CB    110.81  3.000
 TS9  HG21  CG2  CB    111.07  3.000
 TS9  HG1   CG1  CD1   107.69  3.000
 TS9  HG1   CG1  OD2   110.10  3.000
 TS9  CD1   CG1  OD2   110.66  3.000
 TS9  HG1   CG1  CB    106.13  3.000
 TS9  CD1   CG1  CB    114.51  3.000
 TS9  OD2   CG1  CB    107.64  3.000
 TS9  HD2   OD2  CG1   108.04  3.000
 TS9  HD13  CD1  HD12  108.27  3.000
 TS9  HD13  CD1  HD11  107.50  3.000
 TS9  HD12  CD1  HD11  106.43  3.000
 TS9  HD13  CD1  CG1   112.57  3.000
 TS9  HD12  CD1  CG1   112.03  3.000
 TS9  HD11  CD1  CG1   109.76  3.000

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
 TS9  chir_01  CA   N    C    CB   positiv
 TS9  chir_02  CB   CG1  CG2  CA   positiv
 TS9  chir_03  CG1  OD2  CB   CD1  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
 TS9  plan-1  CA   0.020
 TS9  plan-1  C    0.020
 TS9  plan-1  OXT  0.020
 TS9  plan-1  O    0.020

