# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:36:41 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 3-aminopentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(CC(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
 B3D  B3D  '3-aminopentanedioic acid '  peptide  19  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_B3D
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
 B3D  OE1  O  OH1   0  -0.593   3.5854  -0.7703  -0.2203
 B3D  CD   C  C     0   0.553   2.5200  -0.0403   0.0901
 B3D  OE2  O  O     0  -0.445   2.5943   1.1104   0.4464
 B3D  CG   C  CH2   0  -0.586   1.2454  -0.8297  -0.0313
 B3D  CB   C  CH1   0  -0.099  -0.0176   0.0282   0.0531
 B3D  N    N  NH2   0  -0.790  -0.1770   0.9946  -1.0203
 B3D  CA   C  CH2   0  -0.558  -1.2420  -0.8835   0.0662
 B3D  C    C  C     0   0.550  -2.5039  -0.0871   0.2605
 B3D  O    O  O     0  -0.452  -2.6555   0.7451   1.1207
 B3D  OXT  O  OH1   0  -0.591  -3.4598  -0.4180  -0.6001
 B3D  HE1  H  HOH1  0   0.480   4.3911  -0.2434  -0.1094
 B3D  HG3  H  HCH2  0   0.276   1.2609  -1.3969  -0.9675
 B3D  HG2  H  HCH2  0   0.288   1.2538  -1.5779   0.7694
 B3D  HB   H  HCH1  0   0.248   0.0022   0.5827   0.9940
 B3D  H    H  HNH2  0   0.353   0.5598   1.6861  -0.9793
 B3D  H2   H  HNH2  0   0.340  -0.0890   0.5340  -1.9192
 B3D  HA1  H  HCH2  0   0.260  -1.2911  -1.4668  -0.8558
 B3D  HA2  H  HCH2  0   0.287  -1.1702  -1.5982   0.8912
 B3D  HXT  H  HOH1  0   0.477  -4.2589   0.0994  -0.4179

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
 B3D  OE1  CD   single  1.328  0.020  1.328
 B3D  OE1  HE1  single  0.850  0.020  0.980
 B3D  CD   OE2  double  1.207  0.020  1.207
 B3D  CD   CG   single  1.504  0.020  1.504
 B3D  CG   CB   single  1.529  0.020  1.529
 B3D  CG   HG3  single  0.970  0.020  1.090
 B3D  CG   HG2  single  0.970  0.020  1.090
 B3D  CB   N    single  1.453  0.020  1.453
 B3D  CB   CA   single  1.530  0.020  1.530
 B3D  CB   HB   single  0.970  0.020  1.090
 B3D  N    H    single  0.860  0.020  0.860
 B3D  N    H2   single  0.890  0.020  1.040
 B3D  CA   C    single  1.525  0.021  1.525
 B3D  CA   HA1  single  0.970  0.020  1.090
 B3D  CA   HA2  single  0.970  0.020  1.090
 B3D  C    OXT  single  1.328  0.020  1.328
 B3D  C    O    double  1.231  0.020  1.231
 B3D  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
 B3D  HE1  OE1  CD   109.96  3.000
 B3D  CG   CD   OE2  125.20  3.000
 B3D  CG   CD   OE1  111.86  3.000
 B3D  OE2  CD   OE1  122.93  3.000
 B3D  HG2  CG   HG3  105.72  3.000
 B3D  HG2  CG   CB   110.43  3.000
 B3D  HG3  CG   CB   110.46  3.000
 B3D  HG2  CG   CD   107.03  3.000
 B3D  HG3  CG   CD   109.20  3.000
 B3D  CB   CG   CD   113.64  3.000
 B3D  HB   CB   CA   108.08  3.000
 B3D  HB   CB   N    107.50  3.000
 B3D  CA   CB   N    110.50  1.700
 B3D  HB   CB   CG   108.50  3.000
 B3D  CA   CB   CG   109.14  3.000
 B3D  N    CB   CG   115.02  3.000
 B3D  H2   N    H    106.46  3.000
 B3D  H2   N    CB   110.07  3.000
 B3D  H    N    CB   110.17  3.000
 B3D  HA2  CA   HA1  106.91  3.000
 B3D  HA2  CA   C    107.66  3.000
 B3D  HA1  CA   C    110.73  3.000
 B3D  HA2  CA   CB   110.12  3.000
 B3D  HA1  CA   CB   110.35  3.000
 B3D  C    CA   CB   110.10  1.900
 B3D  OXT  C    O    122.92  3.000
 B3D  O    C    CA   120.80  1.700
 B3D  OXT  C    CA   112.83  3.000
 B3D  HXT  OXT  C    109.79  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
 B3D  CONST_01  HE1  OE1  CD  OE2     0.00   0.0  0
 B3D  CONST_02  HXT  OXT  C   CA    180.00   0.0  0
 B3D  Var_01    CB   CG   CD  OE1  -168.94  30.0  3
 B3D  Var_02    N    CB   CG  CD     63.83  30.0  3
 B3D  Var_03    C    CA   CB  CG    175.42  30.0  3
 B3D  Var_04    OXT  C    CA  CB    132.52  30.0  3
 B3D  Var_05    H    N    CB  CG    -64.83  30.0  3

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
 B3D  plan-1  OE1  0.020
 B3D  plan-1  CD   0.020
 B3D  plan-1  OE2  0.020
 B3D  plan-1  CG   0.020
 B3D  plan-1  HE1  0.020
 B3D  plan-2  CA   0.020
 B3D  plan-2  C    0.020
 B3D  plan-2  O    0.020
 B3D  plan-2  OXT  0.020
 B3D  plan-2  HXT  0.020

