# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:54:52 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: 3-amino-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[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
 2RA  2RA  '3-amino-D-alanine        '  D-peptide  14  7  .  2016-04-22  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_2RA
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
 2RA  C    C  C      0   0.395  -3.8941  64.1940  15.2983
 2RA  N    N  NH2    0  -0.796  -5.7014  65.5284  16.3407
 2RA  O    O  O      0  -0.602  -4.7986  63.6249  14.6560
 2RA  CA   C  CH1    0  -0.204  -4.2741  65.4837  16.0627
 2RA  CB   C  CH2    0  -0.287  -3.7416  66.6849  15.2694
 2RA  NG   N  NH2    0  -0.804  -4.0226  67.9469  15.9439
 2RA  OXT  O  OC    -1  -0.615  -2.6925  63.8608  15.3563
 2RA  H    H  HNH2   0   0.327  -5.9581  66.4277  16.7288
 2RA  H2   H  HNH2   0   0.323  -6.2122  65.4219  15.4732
 2RA  HA   H  HCH1   0   0.196  -3.7492  65.4802  17.0249
 2RA  HB1  H  HCH2   0   0.210  -2.6583  66.5852  15.1794
 2RA  HB2  H  HCH2   0   0.181  -4.1481  66.6421  14.2467
 2RA  HG1  H  HNH2   0   0.344  -3.5022  68.6890  15.4941
 2RA  HG2  H  HNH2   0   0.333  -4.9958  68.1937  15.8146

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
 2RA  C   O    deloc   1.231  0.020  1.231
 2RA  C   CA   single  1.525  0.021  1.525
 2RA  C   OXT  deloc   1.248  0.020  1.248
 2RA  N   CA   single  1.458  0.019  1.458
 2RA  CA  CB   single  1.521  0.033  1.521
 2RA  CB  NG   single  1.458  0.020  1.458
 2RA  N   H    single  0.860  0.020  0.860
 2RA  N   H2   single  0.890  0.020  1.040
 2RA  CA  HA   single  0.970  0.020  0.970
 2RA  CB  HB1  single  0.970  0.020  1.090
 2RA  CB  HB2  single  0.970  0.020  1.090
 2RA  NG  HG1  single  0.890  0.020  1.040
 2RA  NG  HG2  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
 2RA  OXT  C   CA   115.86  3.000
 2RA  OXT  C   O    126.90  3.000
 2RA  CA   C   O    120.80  1.700
 2RA  H2   N   H    107.10  3.000
 2RA  H2   N   CA   109.15  3.000
 2RA  H    N   CA   114.00  3.000
 2RA  HA   CA  CB   109.00  3.000
 2RA  HA   CA  N    110.00  3.000
 2RA  CB   CA  N    110.40  1.500
 2RA  HA   CA  C    109.00  3.000
 2RA  CB   CA  C    110.50  1.500
 2RA  N    CA  C    111.00  2.800
 2RA  HB2  CB  HB1  106.63  3.000
 2RA  HB2  CB  NG   113.08  3.000
 2RA  HB1  CB  NG   107.96  3.000
 2RA  HB2  CB  CA   108.75  3.000
 2RA  HB1  CB  CA   108.39  3.000
 2RA  NG   CB  CA   111.80  3.000
 2RA  HG2  NG  HG1  105.00  3.000
 2RA  HG2  NG  CB   109.70  3.000
 2RA  HG1  NG  CB   109.27  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
 2RA  Var_01  HG1  NG  CB  CA  168.74  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
 2RA  chir_01  CA  C  N  CB  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
 2RA  plan-1  C    0.020
 2RA  plan-1  O    0.020
 2RA  plan-1  CA   0.020
 2RA  plan-1  OXT  0.020

