# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:20:43 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  17  10  .  2022-03-15  2022-07-24
;
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  OC    -1  -0.628   3.6132  -0.7539  -0.1332
 B3D  CD   C  C      0   0.412   2.5824  -0.0908   0.1059
 B3D  OE2  O  O      0  -0.609   2.5485   1.1094   0.4521
 B3D  CG   C  CH2    0  -0.579   1.2473  -0.8479  -0.0140
 B3D  CB   C  CH1    0  -0.078  -0.0203   0.0030   0.0202
 B3D  N    N  NH2    0  -0.798  -0.0984   0.9848  -1.0597
 B3D  CA   C  CH2    0  -0.542  -1.2662  -0.8755  -0.0186
 B3D  C    C  C      0   0.407  -2.5724  -0.0868   0.1428
 B3D  O    O  O      0  -0.627  -2.6557   0.6584   1.1424
 B3D  OXT  O  OC    -1  -0.627  -3.4626  -0.2633  -0.7150
 B3D  HG3  H  HCH2   0   0.205   1.2604  -1.4444  -0.9351
 B3D  HG2  H  HCH2   0   0.218   1.2157  -1.5827   0.8009
 B3D  HB   H  HCH1   0   0.193  -0.0354   0.5610   0.9600
 B3D  H    H  HNH2   0   0.334   0.7483   1.5402  -1.0305
 B3D  H2   H  HNH2   0   0.318  -0.0713   0.4926  -1.9470
 B3D  HA1  H  HCH2   0   0.187  -1.2763  -1.4473  -0.9535
 B3D  HA2  H  HCH2   0   0.213  -1.2004  -1.6120   0.7907

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   deloc   1.249  0.020  1.249
 B3D  CD   OE2  deloc   1.250  0.020  1.250
 B3D  CD   CG   single  1.539  0.020  1.539
 B3D  CG   CB   single  1.527  0.020  1.527
 B3D  CG   HG3  single  0.970  0.020  1.090
 B3D  CG   HG2  single  0.970  0.020  1.090
 B3D  CB   N    single  1.462  0.020  1.462
 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  deloc   1.249  0.020  1.249
 B3D  C    O    deloc   1.231  0.020  1.231

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  CG   CD  OE2  118.05  3.000
 B3D  CG   CD  OE1  116.10  3.000
 B3D  OE2  CD  OE1  125.84  3.000
 B3D  HG2  CG  HG3  105.04  3.000
 B3D  HG2  CG  CB   109.42  3.000
 B3D  HG3  CG  CB   109.36  3.000
 B3D  HG2  CG  CD   107.24  3.000
 B3D  HG3  CG  CD   108.80  3.000
 B3D  CB   CG  CD   116.37  3.000
 B3D  HB   CB  CA   107.73  3.000
 B3D  HB   CB  N    106.96  3.000
 B3D  CA   CB  N    110.50  1.700
 B3D  HB   CB  CG   108.37  3.000
 B3D  CA   CB  CG   110.89  3.000
 B3D  N    CB  CG   113.71  3.000
 B3D  H2   N   H    105.59  3.000
 B3D  H2   N   CB   108.58  3.000
 B3D  H    N   CB   107.60  3.000
 B3D  HA2  CA  HA1  106.25  3.000
 B3D  HA2  CA  C    108.59  3.000
 B3D  HA1  CA  C    110.49  3.000
 B3D  HA2  CA  CB   108.62  3.000
 B3D  HA1  CA  CB   109.26  3.000
 B3D  C    CA  CB   110.10  1.900
 B3D  OXT  C   O    125.89  3.000
 B3D  O    C   CA   120.80  1.700
 B3D  OXT  C   CA   117.51  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  Var_01  CB   CG  CD  OE1  -169.06  30.0  3
 B3D  Var_02  N    CB  CG  CD     60.41  30.0  3
 B3D  Var_03  C    CA  CB  CG    174.71  30.0  3
 B3D  Var_04  OXT  C   CA  CB    127.71  30.0  3
 B3D  Var_05  H    N   CB  CG    -54.30  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-2  CA   0.020
 B3D  plan-2  C    0.020
 B3D  plan-2  O    0.020
 B3D  plan-2  OXT  0.020

