# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:26:40 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (3S)-3-aminohexanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(O)=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
 B3E  B3E  '(3S)-3-aminohexanedioic acid'  L-peptide  22  11  .  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_B3E
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
 B3E  N     N  NH2   0  -0.842   1.2475  -2.0336   0.0898
 B3E  CB    C  CH1   0  -0.019   0.9363  -3.4172   0.4265
 B3E  CG    C  CH2   0  -0.435  -0.4579  -3.8759  -0.0144
 B3E  CD    C  CH2   0  -0.597  -1.5680  -3.0858   0.6561
 B3E  CE    C  C     0   0.539  -2.9455  -3.5305   0.2519
 B3E  OF2   O  O     0  -0.414  -3.1957  -4.3998  -0.5429
 B3E  OF1   O  OH1   0  -0.609  -3.8948  -2.8424   0.8851
 B3E  CA    C  CH2   0  -0.592   2.0203  -4.3032  -0.1792
 B3E  C     C  C     0   0.552   2.0539  -5.7047   0.3667
 B3E  O     O  O     0  -0.386   1.5097  -6.0787   1.3714
 B3E  OXT   O  OH1   0  -0.583   2.8099  -6.5077  -0.3855
 B3E  H     H  HNH2  0   0.361   0.6725  -1.3996   0.6277
 B3E  H2    H  HNH2  0   0.343   1.0315  -1.8532  -0.8838
 B3E  HB    H  HCH1  0   0.220   1.0019  -3.5004   1.5154
 B3E  HG2   H  HCH2  0   0.170  -0.5354  -3.7799  -1.1024
 B3E  HG3   H  HCH2  0   0.285  -0.5859  -4.9347   0.2144
 B3E  HD2   H  HCH2  0   0.263  -1.4861  -2.0179   0.4340
 B3E  HD3   H  HCH2  0   0.299  -1.4913  -3.1649   1.7451
 B3E  HOF1  H  HOH1  0   0.484  -4.7599  -3.1665   0.6003
 B3E  HA1   H  HCH2  0   0.283   1.9331  -4.3358  -1.2695
 B3E  HA2   H  HCH2  0   0.201   2.9977  -3.8560   0.0278
 B3E  HXT   H  HOH1  0   0.475   2.8342  -7.3836   0.0238

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
 B3E  N    CB    single  1.458  0.020  1.458
 B3E  N    H     single  0.860  0.020  0.860
 B3E  N    H2    single  0.890  0.020  1.040
 B3E  CB   CG    single  1.533  0.020  1.533
 B3E  CB   CA    single  1.530  0.020  1.530
 B3E  CB   HB    single  0.970  0.020  1.090
 B3E  CG   CD    single  1.519  0.020  1.519
 B3E  CG   HG2   single  0.970  0.020  1.090
 B3E  CG   HG3   single  0.970  0.020  1.090
 B3E  CD   CE    single  1.503  0.020  1.503
 B3E  CD   HD2   single  0.970  0.020  1.090
 B3E  CD   HD3   single  0.970  0.020  1.090
 B3E  CE   OF2   double  1.204  0.020  1.204
 B3E  CE   OF1   single  1.332  0.020  1.332
 B3E  OF1  HOF1  single  0.850  0.020  0.980
 B3E  CA   C     single  1.525  0.021  1.525
 B3E  CA   HA1   single  0.970  0.020  1.090
 B3E  CA   HA2   single  0.970  0.020  1.090
 B3E  C    OXT   single  1.335  0.020  1.335
 B3E  C    O     double  1.231  0.020  1.231
 B3E  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
 B3E  H2    N    H    106.16  3.000
 B3E  H2    N    CB   110.20  3.000
 B3E  H     N    CB   110.55  3.000
 B3E  HB    CB   CA   107.97  3.000
 B3E  HB    CB   CG   108.55  3.000
 B3E  CA    CB   CG   111.01  3.000
 B3E  HB    CB   N    106.81  3.000
 B3E  CA    CB   N    110.50  1.700
 B3E  CG    CB   N    114.32  3.000
 B3E  HG3   CG   HG2  106.57  3.000
 B3E  HG3   CG   CD   109.07  3.000
 B3E  HG2   CG   CD   109.97  3.000
 B3E  HG3   CG   CB   109.69  3.000
 B3E  HG2   CG   CB   108.90  3.000
 B3E  CD    CG   CB   112.47  3.000
 B3E  HD3   CD   HD2  105.51  3.000
 B3E  HD3   CD   CE   108.09  3.000
 B3E  HD2   CD   CE   107.63  3.000
 B3E  HD3   CD   CG   110.51  3.000
 B3E  HD2   CD   CG   111.32  3.000
 B3E  CE    CD   CG   113.41  3.000
 B3E  OF1   CE   OF2  122.58  3.000
 B3E  OF1   CE   CD   111.86  3.000
 B3E  OF2   CE   CD   125.56  3.000
 B3E  HOF1  OF1  CE   108.94  3.000
 B3E  HA2   CA   HA1  105.77  3.000
 B3E  HA2   CA   C    106.98  3.000
 B3E  HA1   CA   C    109.61  3.000
 B3E  HA2   CA   CB   108.79  3.000
 B3E  HA1   CA   CB   110.87  3.000
 B3E  C     CA   CB   110.10  1.900
 B3E  OXT   C    O    122.69  3.000
 B3E  O     C    CA   120.80  1.700
 B3E  OXT   C    CA   111.62  3.000
 B3E  HXT   OXT  C    108.69  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
 B3E  CONST_01  HOF1  OF1  CE  CD   180.00   0.0  0
 B3E  CONST_02  HXT   OXT  C   CA   180.00   0.0  0
 B3E  Var_01    CE    CD   CG  CB  -179.26  30.0  3
 B3E  Var_02    OXT   C    CA  CB   166.53  30.0  3
 B3E  Var_03    OF2   CE   CD  CG    -1.65  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
 B3E  chir_01  CB  N  CG  CA  negativ

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
 B3E  plan-1  CD    0.020
 B3E  plan-1  CE    0.020
 B3E  plan-1  OF2   0.020
 B3E  plan-1  OF1   0.020
 B3E  plan-1  HOF1  0.020
 B3E  plan-2  CA    0.020
 B3E  plan-2  C     0.020
 B3E  plan-2  O     0.020
 B3E  plan-2  OXT   0.020
 B3E  plan-2  HXT   0.020

