# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:20:38 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  20  11  .  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_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  -0.814   1.0906  -1.9726  -0.1630
 B3E  CB   C  CH1    0  -0.055   0.8936  -3.3258   0.3628
 B3E  CG   C  CH2    0  -0.391  -0.4769  -3.8461  -0.0619
 B3E  CD   C  CH2    0  -0.598  -1.6443  -3.0875   0.5510
 B3E  CE   C  C      0   0.414  -3.0485  -3.6212   0.2116
 B3E  OF2  O  O      0  -0.609  -3.1350  -4.5817  -0.5782
 B3E  OF1  O  OC    -1  -0.635  -4.0033  -3.0327   0.7635
 B3E  CA   C  CH2    0  -0.570   2.0121  -4.2185  -0.1609
 B3E  C    C  C      0   0.403   2.0872  -5.6292   0.4491
 B3E  O    O  O      0  -0.615   1.6953  -5.7707   1.6259
 B3E  OXT  O  OC    -1  -0.626   2.5778  -6.5226  -0.2727
 B3E  H    H  HNH2   0   0.334   1.9892  -1.6221   0.1480
 B3E  H2   H  HNH2   0   0.338   0.4089  -1.3459   0.2467
 B3E  HB   H  HCH1   0   0.174   0.9358  -3.3491   1.4616
 B3E  HG2  H  HCH2   0   0.190  -0.5386  -3.8155  -1.1543
 B3E  HG3  H  HCH2   0   0.207  -0.5516  -4.8976   0.2224
 B3E  HD2  H  HCH2   0   0.215  -1.6173  -2.0319   0.2561
 B3E  HD3  H  HCH2   0   0.215  -1.5393  -3.0775   1.6426
 B3E  HA1  H  HCH2   0   0.201   1.9450  -4.2866  -1.2511
 B3E  HA2  H  HCH2   0   0.224   2.9758  -3.7330   0.0474

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  1.465  0.020  1.465
 B3E  N   H    single  0.860  0.020  0.860
 B3E  N   H2   single  0.890  0.020  1.040
 B3E  CB  CG   single  1.526  0.020  1.526
 B3E  CB  CA   single  1.530  0.020  1.530
 B3E  CB  HB   single  0.970  0.020  1.090
 B3E  CG  CD   single  1.521  0.020  1.521
 B3E  CG  HG2  single  0.970  0.020  1.090
 B3E  CG  HG3  single  0.970  0.020  1.090
 B3E  CD  CE   single  1.540  0.020  1.540
 B3E  CD  HD2  single  0.970  0.020  1.090
 B3E  CD  HD3  single  0.970  0.020  1.090
 B3E  CE  OF2  deloc   1.247  0.020  1.247
 B3E  CE  OF1  deloc   1.250  0.020  1.250
 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  deloc   1.249  0.020  1.249
 B3E  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
 B3E  H2   N   H    104.99  3.000
 B3E  H2   N   CB   109.63  3.000
 B3E  H    N   CB   109.18  3.000
 B3E  HB   CB  CA   107.63  3.000
 B3E  HB   CB  CG   107.77  3.000
 B3E  CA   CB  CG   111.33  3.000
 B3E  HB   CB  N    111.90  3.000
 B3E  CA   CB  N    110.50  1.700
 B3E  CG   CB  N    109.62  3.000
 B3E  HG3  CG  HG2  106.43  3.000
 B3E  HG3  CG  CD   108.84  3.000
 B3E  HG2  CG  CD   110.17  3.000
 B3E  HG3  CG  CB   108.50  3.000
 B3E  HG2  CG  CB   108.59  3.000
 B3E  CD   CG  CB   114.02  3.000
 B3E  HD3  CD  HD2  104.87  3.000
 B3E  HD3  CD  CE   108.04  3.000
 B3E  HD2  CD  CE   107.27  3.000
 B3E  HD3  CD  CG   109.40  3.000
 B3E  HD2  CD  CG   110.67  3.000
 B3E  CE   CD  CG   115.98  3.000
 B3E  OF1  CE  OF2  126.12  3.000
 B3E  OF1  CE  CD   115.85  3.000
 B3E  OF2  CE  CD   118.03  3.000
 B3E  HA2  CA  HA1  105.67  3.000
 B3E  HA2  CA  C    106.68  3.000
 B3E  HA1  CA  C    109.93  3.000
 B3E  HA2  CA  CB   108.65  3.000
 B3E  HA1  CA  CB   109.50  3.000
 B3E  C    CA  CB   110.10  1.900
 B3E  OXT  C   O    125.95  3.000
 B3E  O    C   CA   120.80  1.700
 B3E  OXT  C   CA   116.48  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  Var_01  CE   CD  CG  CB  -176.91  30.0  3
 B3E  Var_02  OXT  C   CA  CB   152.05  30.0  3
 B3E  Var_03  OF2  CE  CD  CG    -3.28  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-2  CA   0.020
 B3E  plan-2  C    0.020
 B3E  plan-2  O    0.020
 B3E  plan-2  OXT  0.020

