# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:29:39 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (3S)-3,5-diamino-5-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(N)=O)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
 B3X  B3X  '(3S)-3,5-diamino-5-oxopentanoic acid'  L-peptide  20  10  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3X
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
 B3X  OE1   O  O     0  -0.498  -0.8698  -2.9184   0.1591
 B3X  CD    C  C     0   0.524  -0.8636  -1.7357  -0.1581
 B3X  NE2   N  NH2   0  -0.802  -1.9580  -1.0955  -0.5931
 B3X  CG    C  CH2   0  -0.581   0.3970  -0.8974  -0.1104
 B3X  CB    C  CH1   0  -0.089   1.3241  -1.2828   1.0452
 B3X  N     N  NH2   0  -0.791   0.7233  -1.1125   2.3603
 B3X  CA    C  CH2   0  -0.581   2.6099  -0.4637   1.0052
 B3X  C     C  C     0   0.551   3.5093  -0.7564  -0.1629
 B3X  O     O  O     0  -0.445   3.4442  -1.7353  -0.8652
 B3X  OXT   O  OH1   0  -0.594   4.4357   0.1839  -0.3179
 B3X  HE21  H  HNH2  0   0.406  -1.9355  -0.1259  -0.8570
 B3X  HE22  H  HNH2  0   0.398  -2.8278  -1.5889  -0.7135
 B3X  HG3   H  HCH2  0   0.277   0.9032  -1.0345  -1.0711
 B3X  HG2   H  HCH2  0   0.249   0.1500   0.1668  -0.0443
 B3X  HB    H  HCH1  0   0.240   1.5857  -2.3381   0.9459
 B3X  H     H  HNH2  0   0.350  -0.0411  -1.7653   2.4751
 B3X  H2    H  HNH2  0   0.339   0.3167  -0.1869   2.4361
 B3X  HA1   H  HCH2  0   0.298   3.1889  -0.6761   1.9103
 B3X  HA2   H  HCH2  0   0.269   2.3896   0.6073   1.0392
 B3X  HXT   H  HOH1  0   0.478   5.0306  -0.0525  -1.0456

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
 B3X  OE1  CD    double  1.225  0.020  1.225
 B3X  CD   NE2   single  1.340  0.020  1.340
 B3X  CD   CG    single  1.515  0.020  1.515
 B3X  NE2  HE21  single  0.860  0.020  1.020
 B3X  NE2  HE22  single  0.860  0.020  1.020
 B3X  CG   CB    single  1.531  0.020  1.531
 B3X  CG   HG3   single  0.970  0.020  1.090
 B3X  CG   HG2   single  0.970  0.020  1.090
 B3X  CB   N     single  1.456  0.020  1.456
 B3X  CB   CA    single  1.530  0.020  1.530
 B3X  CB   HB    single  0.970  0.020  1.090
 B3X  N    H     single  0.860  0.020  0.860
 B3X  N    H2    single  0.890  0.020  1.040
 B3X  CA   C     single  1.525  0.021  1.525
 B3X  CA   HA1   single  0.970  0.020  1.090
 B3X  CA   HA2   single  0.970  0.020  1.090
 B3X  C    OXT   single  1.329  0.020  1.329
 B3X  C    O     double  1.231  0.020  1.231
 B3X  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
 B3X  CG    CD   NE2   115.17  3.000
 B3X  CG    CD   OE1   122.05  3.000
 B3X  NE2   CD   OE1   122.77  3.000
 B3X  HE22  NE2  HE21  117.42  3.000
 B3X  HE22  NE2  CD    120.65  3.000
 B3X  HE21  NE2  CD    121.85  3.000
 B3X  HG2   CG   HG3   106.21  3.000
 B3X  HG2   CG   CB    109.62  3.000
 B3X  HG3   CG   CB    110.55  3.000
 B3X  HG2   CG   CD    110.62  3.000
 B3X  HG3   CG   CD    106.74  3.000
 B3X  CB    CG   CD    112.86  3.000
 B3X  HB    CB   CA    108.35  3.000
 B3X  HB    CB   N     107.10  3.000
 B3X  CA    CB   N     110.50  1.700
 B3X  HB    CB   CG    108.65  3.000
 B3X  CA    CB   CG    110.83  3.000
 B3X  N     CB   CG    113.74  3.000
 B3X  H2    N    H     106.11  3.000
 B3X  H2    N    CB    109.86  3.000
 B3X  H     N    CB    109.81  3.000
 B3X  HA2   CA   HA1   105.70  3.000
 B3X  HA2   CA   C     109.59  3.000
 B3X  HA1   CA   C     106.75  3.000
 B3X  HA2   CA   CB    110.81  3.000
 B3X  HA1   CA   CB    108.65  3.000
 B3X  C     CA   CB    110.10  1.900
 B3X  OXT   C    O     122.94  3.000
 B3X  O     C    CA    120.80  1.700
 B3X  OXT   C    CA    111.71  3.000
 B3X  HXT   OXT  C     110.05  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
 B3X  CONST_01  HE21  NE2  CD  OE1  180.00   0.0  0
 B3X  CONST_02  HE22  NE2  CD  OE1    0.00   0.0  0
 B3X  CONST_03  HXT   OXT  C   CA   180.00   0.0  0
 B3X  Var_01    CB    CG   CD  OE1  -34.75  30.0  3
 B3X  Var_02    OXT   C    CA  CB   165.25  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
 B3X  chir_01  CB  CG  N  CA  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
 B3X  plan-1  OE1   0.020
 B3X  plan-1  CD    0.020
 B3X  plan-1  NE2   0.020
 B3X  plan-1  CG    0.020
 B3X  plan-1  HE21  0.020
 B3X  plan-1  HE22  0.020
 B3X  plan-2  CA    0.020
 B3X  plan-2  C     0.020
 B3X  plan-2  O     0.020
 B3X  plan-2  OXT   0.020
 B3X  plan-2  HXT   0.020

