# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:45:09 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: (3R)-3-amino-4-hydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)CC(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
 B3S  B3S  '(3R)-3-amino-4-hydroxybutanoic acid'  D-peptide  16  8  .  2022-03-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B3S
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
 B3S  N    N  NH2    0  -0.812  -0.6817  -1.3769   2.3203
 B3S  OD   O  OH1    0  -0.688   0.9636  -3.4880   2.0649
 B3S  CG   C  CH2    0  -0.131   1.1632  -2.4087   1.1825
 B3S  CB   C  CH1    0  -0.127   0.6582  -1.1050   1.7962
 B3S  CA   C  CH2    0  -0.589   0.7227   0.0488   0.8037
 B3S  C    C  C      0   0.408   2.1367   0.4732   0.3639
 B3S  O    O  O      0  -0.611   3.0637   0.2924   1.1798
 B3S  OXT  O  OC    -1  -0.622   2.2367   1.0019  -0.7618
 B3S  H    H  HNH2   0   0.344  -1.3655  -1.3201   1.5736
 B3S  H2   H  HNH2   0   0.356  -0.9443  -0.6735   2.9982
 B3S  HD   H  HOH1   0   0.432   0.1234  -3.2673   2.4997
 B3S  HG3  H  HCH2   0   0.166   0.6417  -2.5766   0.2257
 B3S  HG2  H  HCH2   0   0.213   2.2285  -2.3298   0.9581
 B3S  HB   H  HCH1   0   0.220   1.2927  -0.8663   2.6535
 B3S  HA1  H  HCH2   0   0.206   0.1133  -0.1890  -0.0750
 B3S  HA2  H  HCH2   0   0.236   0.2495   0.9248   1.2646

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
 B3S  N   CB   single  1.464  0.020  1.464
 B3S  N   H    single  0.860  0.020  0.860
 B3S  N   H2   single  0.890  0.020  1.040
 B3S  OD  CG   single  1.408  0.020  1.408
 B3S  OD  HD   single  0.850  0.020  0.980
 B3S  CG  CB   single  1.527  0.020  1.527
 B3S  CG  HG3  single  0.970  0.020  1.090
 B3S  CG  HG2  single  0.970  0.020  1.090
 B3S  CB  CA   single  1.521  0.033  1.521
 B3S  CB  HB   single  0.970  0.020  1.090
 B3S  CA  C    single  1.525  0.021  1.525
 B3S  CA  HA1  single  0.970  0.020  1.090
 B3S  CA  HA2  single  0.970  0.020  1.090
 B3S  C   OXT  deloc   1.248  0.020  1.248
 B3S  C   O    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
 B3S  H2   N   H    106.23  3.000
 B3S  H2   N   CB   110.38  3.000
 B3S  H    N   CB   110.06  3.000
 B3S  HD   OD  CG   103.24  3.000
 B3S  HG2  CG  HG3  107.11  3.000
 B3S  HG2  CG  CB   110.10  3.000
 B3S  HG3  CG  CB   108.81  3.000
 B3S  HG2  CG  OD   108.82  3.000
 B3S  HG3  CG  OD   111.10  3.000
 B3S  CB   CG  OD   110.83  3.000
 B3S  HB   CB  CA   108.73  3.000
 B3S  HB   CB  CG   108.04  3.000
 B3S  CA   CB  CG   111.77  3.000
 B3S  HB   CB  N    106.92  3.000
 B3S  CA   CB  N    110.40  1.500
 B3S  CG   CB  N    106.73  3.000
 B3S  HA2  CA  HA1  105.69  3.000
 B3S  HA2  CA  C    107.21  3.000
 B3S  HA1  CA  C    109.96  3.000
 B3S  HA2  CA  CB   108.23  3.000
 B3S  HA1  CA  CB   109.55  3.000
 B3S  C    CA  CB   110.50  1.500
 B3S  OXT  C   O    126.27  3.000
 B3S  O    C   CA   120.80  1.700
 B3S  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
 B3S  Var_01  OXT  C  CA  CB  153.02  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
 B3S  chir_01  CB  N  CG  CA  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
 B3S  plan-1  CA   0.020
 B3S  plan-1  C    0.020
 B3S  plan-1  O    0.020
 B3S  plan-1  OXT  0.020

