# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:59:20 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (2R,3S)-2,3-diaminobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[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
 Q3S  Q3S  '(2R,3S)-2,3-diaminobutanoic acid'  L-peptide  17  8  .  2022-09-22  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_Q3S
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
 Q3S  N     N  NH2    0  -0.809  -0.1456   1.9275  -0.3881
 Q3S  CA    C  CH1    0  -0.164  -0.0875   0.4772  -0.5097
 Q3S  C     C  C      0   0.401   1.3102  -0.0182  -0.0852
 Q3S  O     O  O      0  -0.613   1.7437   0.4360   0.9952
 Q3S  C02   C  CH1    0  -0.109  -1.1767  -0.2370   0.3131
 Q3S  N2    N  NH2    0  -0.790  -2.4796   0.3014  -0.0755
 Q3S  OXT   O  OC    -1  -0.614   1.8856  -0.8377  -0.8270
 Q3S  H1    H  HNH2   0   0.329  -1.1217   2.2027  -0.3715
 Q3S  H     H  HNH2   0   0.321   0.2309   2.1698   0.5214
 Q3S  HA    H  HCH1   0   0.182  -0.2462   0.2083  -1.5625
 Q3S  H021  H  HCH1   0   0.206  -1.0192   0.0395   1.3618
 Q3S  H2    H  HNH2   0   0.332  -2.7151  -0.0426  -1.0008
 Q3S  H4    H  HNH2   0   0.344  -3.1932  -0.0697   0.5404
 Q3S  C01   C  CH3    0  -0.668  -1.1073  -1.7578   0.1944
 Q3S  H011  H  HCH3   0   0.220  -1.9238  -2.2185   0.7540
 Q3S  H013  H  HCH3   0   0.210  -1.2025  -2.0707  -0.8488
 Q3S  H012  H  HCH3   0   0.223  -0.1736  -2.1686   0.5790

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
 Q3S  O    C     deloc   1.231  0.020  1.231
 Q3S  N2   C02   single  1.462  0.020  1.462
 Q3S  C    CA    single  1.525  0.021  1.525
 Q3S  C02  CA    single  1.540  0.020  1.540
 Q3S  C02  C01   single  1.527  0.020  1.527
 Q3S  CA   N     single  1.458  0.019  1.458
 Q3S  C    OXT   deloc   1.246  0.020  1.246
 Q3S  N    H1    single  0.890  0.020  1.040
 Q3S  N    H     single  0.860  0.020  0.860
 Q3S  CA   HA    single  0.970  0.020  0.970
 Q3S  C01  H011  single  0.970  0.020  1.090
 Q3S  C01  H013  single  0.970  0.020  1.090
 Q3S  C01  H012  single  0.970  0.020  1.090
 Q3S  C02  H021  single  0.970  0.020  1.090
 Q3S  N2   H2    single  0.890  0.020  1.040
 Q3S  N2   H4    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
 Q3S  H     N    H1    106.13  3.000
 Q3S  H     N    CA    114.00  3.000
 Q3S  H1    N    CA    108.05  3.000
 Q3S  HA    CA   C02   107.24  3.000
 Q3S  HA    CA   C     110.00  3.000
 Q3S  C02   CA   C     110.17  3.000
 Q3S  HA    CA   N     110.00  3.000
 Q3S  C02   CA   N     112.88  3.000
 Q3S  C     CA   N     111.00  2.800
 Q3S  OXT   C    O     126.41  3.000
 Q3S  OXT   C    CA    120.80  1.700
 Q3S  O     C    CA    120.80  1.700
 Q3S  H021  C02  N2    106.82  3.000
 Q3S  H021  C02  C01   108.60  3.000
 Q3S  N2    C02  C01   112.74  3.000
 Q3S  H021  C02  CA    107.01  3.000
 Q3S  C01   C02  CA    112.84  3.000
 Q3S  N2    C02  CA    108.50  3.000
 Q3S  H4    N2   H2    105.47  3.000
 Q3S  H4    N2   C02   109.34  3.000
 Q3S  H2    N2   C02   108.92  3.000
 Q3S  H012  C01  H013  107.66  3.000
 Q3S  H012  C01  H011  107.50  3.000
 Q3S  H013  C01  H011  107.65  3.000
 Q3S  H012  C01  C02   112.76  3.000
 Q3S  H013  C01  C02   110.81  3.000
 Q3S  H011  C01  C02   110.27  3.000

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
 Q3S  chir_01  CA   C   C02  N    negativ
 Q3S  chir_02  C02  N2  CA   C01  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
 Q3S  plan-1  CA   0.020
 Q3S  plan-1  C    0.020
 Q3S  plan-1  O    0.020
 Q3S  plan-1  OXT  0.020

