# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:53:48 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  17  8  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.805  -0.6753  -1.3085   2.3334
 B3S  OD   O  OH1   0  -0.678   0.9093  -3.4957   2.1266
 B3S  CG   C  CH2   0  -0.129   1.1082  -2.4535   1.2055
 B3S  CB   C  CH1   0  -0.136   0.6673  -1.1164   1.8003
 B3S  CA   C  CH2   0  -0.603   0.7540   0.0163   0.7792
 B3S  C    C  C     0   0.550   2.1539   0.3977   0.3818
 B3S  O    O  O     0  -0.445   3.1458   0.1595   1.0263
 B3S  OXT  O  OH1   0  -0.593   2.1797   1.0733  -0.7619
 B3S  H    H  HNH2  0   0.351  -1.3645  -1.2692   1.5911
 B3S  H2   H  HNH2  0   0.363  -0.9109  -0.5747   2.9884
 B3S  HD   H  HOH1  0   0.436   0.0708  -3.2705   2.5588
 B3S  HG3  H  HCH2  0   0.178   0.5460  -2.6274   0.2737
 B3S  HG2  H  HCH2  0   0.220   2.1665  -2.4272   0.9391
 B3S  HB   H  HCH1  0   0.244   1.3172  -0.8846   2.6480
 B3S  HA1  H  HCH2  0   0.269   0.1689  -0.2283  -0.1120
 B3S  HA2  H  HCH2  0   0.299   0.2936   0.9168   1.2011
 B3S  HXT  H  HOH1  0   0.479   3.0886   1.3388  -0.9691

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  1.457  0.020  1.457
 B3S  N    H    single  0.860  0.020  0.860
 B3S  N    H2   single  0.890  0.020  1.040
 B3S  OD   CG   single  1.405  0.020  1.405
 B3S  OD   HD   single  0.850  0.020  0.980
 B3S  CG   CB   single  1.528  0.020  1.528
 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  single  1.329  0.020  1.329
 B3S  C    O    double  1.231  0.020  1.231
 B3S  OXT  HXT  single  0.850  0.020  0.980

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    106.72  3.000
 B3S  H2   N    CB   110.85  3.000
 B3S  H    N    CB   110.70  3.000
 B3S  HD   OD   CG   104.03  3.000
 B3S  HG2  CG   HG3  106.98  3.000
 B3S  HG2  CG   CB   110.71  3.000
 B3S  HG3  CG   CB   108.66  3.000
 B3S  HG2  CG   OD   108.37  3.000
 B3S  HG3  CG   OD   111.41  3.000
 B3S  CB   CG   OD   110.66  3.000
 B3S  HB   CB   CA   109.11  3.000
 B3S  HB   CB   CG   108.41  3.000
 B3S  CA   CB   CG   111.85  3.000
 B3S  HB   CB   N    106.99  3.000
 B3S  CA   CB   N    110.40  1.500
 B3S  CG   CB   N    107.03  3.000
 B3S  HA2  CA   HA1  105.83  3.000
 B3S  HA2  CA   C    106.52  3.000
 B3S  HA1  CA   C    109.83  3.000
 B3S  HA2  CA   CB   109.15  3.000
 B3S  HA1  CA   CB   110.40  3.000
 B3S  C    CA   CB   110.50  1.500
 B3S  OXT  C    O    122.97  3.000
 B3S  O    C    CA   120.80  1.700
 B3S  OXT  C    CA   120.80  1.700
 B3S  HXT  OXT  C    109.96  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
 B3S  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 B3S  Var_01    OXT  C    CA  CB  161.14  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
 B3S  plan-1  HXT  0.020

