# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:56:40 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: 3-amino-L-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
 DPP  DPP  '3-amino-L-alanine        '  L-peptide  14  7  .  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_DPP
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
 DPP  N    N  NH2    0  -0.798  5.0744  19.8143  15.3916
 DPP  CA   C  CH1    0  -0.227  3.9272  20.3163  16.1316
 DPP  C    C  C      0   0.412  2.6301  20.1932  15.2934
 DPP  O    O  O      0  -0.606  2.6231  19.3190  14.4046
 DPP  CB   C  CH2    0  -0.265  4.2027  21.7413  16.5906
 DPP  NG   N  NH2    0  -0.802  5.3866  21.7893  17.4458
 DPP  OXT  O  OC    -1  -0.608  1.6833  20.9427  15.6062
 DPP  H    H  HNH2   0   0.324  5.8610  19.7281  16.0211
 DPP  H2   H  HNH2   0   0.327  4.8623  18.8894  15.0445
 DPP  HA   H  HCH1   0   0.183  3.7334  19.7245  17.0491
 DPP  HB2  H  HCH2   0   0.198  4.3944  22.3649  15.7122
 DPP  HB3  H  HCH2   0   0.188  3.3035  22.1361  17.0739
 DPP  HG1  H  HNH2   0   0.342  5.5900  22.7521  17.6825
 DPP  HG2  H  HNH2   0   0.332  5.1723  21.3353  18.3263

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
 DPP  N   CA   single  1.458  0.019  1.458
 DPP  N   H    single  0.860  0.020  0.860
 DPP  N   H2   single  0.890  0.020  1.040
 DPP  CA  C    single  1.525  0.021  1.525
 DPP  CA  CB   single  1.521  0.033  1.521
 DPP  CA  HA   single  0.970  0.020  0.970
 DPP  C   O    deloc   1.231  0.020  1.231
 DPP  C   OXT  deloc   1.247  0.020  1.247
 DPP  CB  NG   single  1.461  0.020  1.461
 DPP  CB  HB2  single  0.970  0.020  1.090
 DPP  CB  HB3  single  0.970  0.020  1.090
 DPP  NG  HG1  single  0.890  0.020  1.040
 DPP  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
 DPP  H2   N   H    107.40  3.000
 DPP  H2   N   CA   108.97  3.000
 DPP  H    N   CA   114.00  3.000
 DPP  HA   CA  CB   109.00  3.000
 DPP  HA   CA  C    109.00  3.000
 DPP  CB   CA  C    110.50  1.500
 DPP  HA   CA  N    110.00  3.000
 DPP  CB   CA  N    110.40  1.500
 DPP  C    CA  N    111.00  2.800
 DPP  OXT  C   O    126.57  3.000
 DPP  OXT  C   CA   116.87  3.000
 DPP  O    C   CA   120.80  1.700
 DPP  HB3  CB  HB2  107.03  3.000
 DPP  HB3  CB  NG   113.29  3.000
 DPP  HB2  CB  NG   108.01  3.000
 DPP  HB3  CB  CA   108.79  3.000
 DPP  HB2  CB  CA   108.86  3.000
 DPP  NG   CB  CA   110.72  3.000
 DPP  HG2  NG  HG1  105.39  3.000
 DPP  HG2  NG  CB   108.81  3.000
 DPP  HG1  NG  CB   109.33  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
 DPP  Var_01  HG1  NG  CB  CA  175.86  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
 DPP  chir_01  CA  N  C  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
 DPP  plan-1  CA   0.020
 DPP  plan-1  C    0.020
 DPP  plan-1  O    0.020
 DPP  plan-1  OXT  0.020

