# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:53:30 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-amino-2,3,5-trideoxy-D-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)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
 B3T  B3T  '3-amino-2,3,5-trideoxy-D-threo-pentonic acid'  L-peptide  19  9  .  2022-03-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3T
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
 B3T  CG    C  CH1    0   0.043  -1.8586   0.3699  -0.3878
 B3T  OD1   O  OH1    0  -0.677  -2.1719   1.2933   0.6442
 B3T  CD2   C  CH3    0  -0.685  -2.9802  -0.6397  -0.5776
 B3T  CB    C  CH1    0  -0.091  -0.5039  -0.3091  -0.1531
 B3T  N     N  NH2    0  -0.810  -0.5340  -1.0519   1.1052
 B3T  CA    C  CH2    0  -0.587   0.6555   0.6772  -0.2469
 B3T  C     C  C      0   0.412   2.0572   0.0441  -0.1588
 B3T  O     O  O      0  -0.610   2.1610  -1.1743  -0.4148
 B3T  HG    H  HCH1   0   0.212  -1.7760   0.9737  -1.2979
 B3T  HOD1  H  HOH1   0   0.437  -2.3604   0.7870   1.4414
 B3T  H1D2  H  HCH3   0   0.227  -3.9369  -0.1391  -0.7326
 B3T  H2D2  H  HCH3   0   0.221  -2.7906  -1.2724  -1.4459
 B3T  H3D2  H  HCH3   0   0.221  -3.0662  -1.2919   0.2932
 B3T  HB    H  HCH1   0   0.208  -0.3845  -1.0468  -0.9523
 B3T  HN    H  HNH2   0   0.344   0.2854  -1.6461   1.1254
 B3T  HA    H  HCH2   0   0.222   0.6031   1.2187  -1.2011
 B3T  HAA   H  HCH2   0   0.211   0.5545   1.4426   0.5288
 B3T  HNA   H  HNH2   0   0.328  -0.4065  -0.4065   1.8778
 B3T  OXT   O  OC    -1  -0.624   2.9946   0.8141   0.1349

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
 B3T  CG    CD2   single  1.521  0.020  1.521
 B3T  OD1   CG    single  1.420  0.020  1.420
 B3T  CD2   H1D2  single  0.970  0.020  1.090
 B3T  CD2   H2D2  single  0.970  0.020  1.090
 B3T  CD2   H3D2  single  0.970  0.020  1.090
 B3T  CB    CG    single  1.533  0.020  1.533
 B3T  CB    N     single  1.462  0.020  1.462
 B3T  N     HNA   single  0.890  0.020  1.040
 B3T  CA    CB    single  1.521  0.033  1.521
 B3T  CA    HA    single  0.970  0.020  0.970
 B3T  CA    HAA   single  0.970  0.020  1.090
 B3T  C     CA    single  1.525  0.021  1.525
 B3T  C     OXT   deloc   1.248  0.020  1.248
 B3T  O     C     deloc   1.231  0.020  1.231
 B3T  HG    CG    single  0.970  0.020  1.090
 B3T  HOD1  OD1   single  0.850  0.020  0.980
 B3T  HB    CB    single  0.970  0.020  1.090
 B3T  HN    N     single  0.890  0.020  1.040

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
 B3T  HG    CG   CB    107.74  3.000
 B3T  HG    CG   CD2   108.53  3.000
 B3T  CB    CG   CD2   112.12  3.000
 B3T  HG    CG   OD1   105.19  3.000
 B3T  CB    CG   OD1   111.82  3.000
 B3T  CD2   CG   OD1   111.09  3.000
 B3T  HOD1  OD1  CG    107.63  3.000
 B3T  H3D2  CD2  H2D2  107.59  3.000
 B3T  H3D2  CD2  H1D2  108.58  3.000
 B3T  H2D2  CD2  H1D2  107.78  3.000
 B3T  H3D2  CD2  CG    110.81  3.000
 B3T  H2D2  CD2  CG    110.87  3.000
 B3T  H1D2  CD2  CG    111.09  3.000
 B3T  HB    CB   CA    107.94  3.000
 B3T  HB    CB   N     106.77  3.000
 B3T  CA    CB   N     110.40  1.500
 B3T  HB    CB   CG    106.45  3.000
 B3T  CA    CB   CG    112.08  3.000
 B3T  N     CB   CG    109.80  3.000
 B3T  HNA   N    HN    104.86  3.000
 B3T  HN    N    CB    107.39  3.000
 B3T  HNA   N    CB    109.25  3.000
 B3T  HAA   CA   HA    105.46  3.000
 B3T  HAA   CA   C     109.32  3.000
 B3T  HA    CA   C     110.00  3.000
 B3T  C     CA   CB    110.50  1.500
 B3T  HAA   CA   CB    109.78  3.000
 B3T  HA    CA   CB    109.00  3.000
 B3T  OXT   C    O     125.98  3.000
 B3T  O     C    CA    120.80  1.700
 B3T  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
 B3T  Var_01  OXT  C  CA  CB  -161.00  30.0  2

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
 B3T  chir_01  CG  CD2  OD1  CB  negativ
 B3T  chir_02  CB  N    CA   CG  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
 B3T  plan-1  CA   0.020
 B3T  plan-1  C    0.020
 B3T  plan-1  O    0.020
 B3T  plan-1  OXT  0.020

