# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 17:27:49 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2R)-2-aminoheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCCCC(O)=O)C(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
 P0A  P0A  '(2R)-2-aminoheptanedioic acid'  D-peptide  23  12  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_P0A
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
 P0A  C     C  C      0   0.400  18.3700  5.9360  16.9174
 P0A  N     N  NH2    0  -0.801  19.5606  3.8202  16.5674
 P0A  O     O  O      0  -0.610  17.7084  5.7427  15.8749
 P0A  CA    C  CH1    0  -0.173  18.9585  4.6750  17.5866
 P0A  CB    C  CH2    0  -0.431  17.8776  3.9584  18.4067
 P0A  OAB   O  O      0  -0.625  14.0038  4.7293  23.1959
 P0A  OAD   O  OC    -1  -0.607  14.6442  2.7681  22.3513
 P0A  CAF   C  CH2    0  -0.399  16.3385  3.9470  20.4227
 P0A  CAG   C  CH2    0  -0.414  17.2723  4.7727  19.5453
 P0A  CAH   C  CH2    0  -0.574  15.6892  4.7602  21.5313
 P0A  CAJ   C  C      0   0.406  14.6879  4.0122  22.4351
 P0A  OXT   O  OC    -1  -0.610  18.5725  7.0293  17.4807
 P0A  HN    H  HNH2   0   0.326  19.7498  2.9053  16.9612
 P0A  HNA   H  HNH2   0   0.322  18.8690  3.6754  15.8410
 P0A  HA    H  HCH1   0   0.184  19.7496  4.9874  18.2773
 P0A  HB    H  HCH2   0   0.197  17.0820  3.6266  17.7295
 P0A  HBA   H  HCH2   0   0.201  18.3188  3.0451  18.8248
 P0A  HAF   H  HCH2   0   0.195  15.5634  3.4987  19.7926
 P0A  HAFA  H  HCH2   0   0.196  16.8962  3.1094  20.8515
 P0A  HAG   H  HCH2   0   0.196  18.0750  5.1931  20.1621
 P0A  HAGA  H  HCH2   0   0.205  16.7234  5.6299  19.1440
 P0A  HAH   H  HCH2   0   0.212  16.4703  5.1864  22.1740
 P0A  HAHA  H  HCH2   0   0.205  15.1799  5.6286  21.0990

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
 P0A  O    C     deloc   1.231  0.020  1.231
 P0A  C    CA    single  1.525  0.021  1.525
 P0A  C    OXT   deloc   1.247  0.020  1.247
 P0A  N    CA    single  1.458  0.019  1.458
 P0A  N    HN    single  0.890  0.020  1.040
 P0A  N    HNA   single  0.890  0.020  1.040
 P0A  CA   CB    single  1.521  0.033  1.521
 P0A  CA   HA    single  0.970  0.020  0.970
 P0A  CB   CAG   single  1.525  0.020  1.525
 P0A  CB   HB    single  0.970  0.020  1.090
 P0A  CB   HBA   single  0.970  0.020  1.090
 P0A  OAB  CAJ   deloc   1.249  0.020  1.249
 P0A  CAJ  OAD   deloc   1.248  0.020  1.248
 P0A  CAG  CAF   single  1.524  0.020  1.524
 P0A  CAF  CAH   single  1.520  0.020  1.520
 P0A  CAF  HAF   single  0.970  0.020  1.090
 P0A  CAF  HAFA  single  0.970  0.020  1.090
 P0A  CAG  HAG   single  0.970  0.020  1.090
 P0A  CAG  HAGA  single  0.970  0.020  1.090
 P0A  CAH  CAJ   single  1.542  0.020  1.542
 P0A  CAH  HAH   single  0.970  0.020  1.090
 P0A  CAH  HAHA  single  0.970  0.020  1.090

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
 P0A  OXT   C    CA   120.80  1.700
 P0A  OXT   C    O    126.77  3.000
 P0A  CA    C    O    120.80  1.700
 P0A  HNA   N    HN   106.08  3.000
 P0A  HNA   N    CA   107.61  3.000
 P0A  HN    N    CA   109.52  3.000
 P0A  HA    CA   CB   109.00  3.000
 P0A  HA    CA   N    110.00  3.000
 P0A  CB    CA   N    110.40  1.500
 P0A  HA    CA   C    110.00  3.000
 P0A  CB    CA   C    110.50  1.500
 P0A  N     CA   C    111.00  2.800
 P0A  HBA   CB   HB   105.98  3.000
 P0A  HBA   CB   CAG  108.64  3.000
 P0A  HB    CB   CAG  109.55  3.000
 P0A  HBA   CB   CA   108.01  3.000
 P0A  HB    CB   CA   108.81  3.000
 P0A  CAG   CB   CA   115.42  3.000
 P0A  HAFA  CAF  HAF  105.84  3.000
 P0A  HAFA  CAF  CAH  109.97  3.000
 P0A  HAF   CAF  CAH  109.64  3.000
 P0A  HAFA  CAF  CAG  109.16  3.000
 P0A  HAF   CAF  CAG  108.92  3.000
 P0A  CAH   CAF  CAG  113.05  3.000
 P0A  HAGA  CAG  HAG  105.86  3.000
 P0A  HAGA  CAG  CAF  109.16  3.000
 P0A  HAG   CAG  CAF  109.42  3.000
 P0A  HAGA  CAG  CB   110.09  3.000
 P0A  HAG   CAG  CB   109.52  3.000
 P0A  CAF   CAG  CB   112.56  3.000
 P0A  HAHA  CAH  HAH  104.72  3.000
 P0A  HAHA  CAH  CAJ  108.29  3.000
 P0A  HAH   CAH  CAJ  107.89  3.000
 P0A  HAHA  CAH  CAF  109.56  3.000
 P0A  HAH   CAH  CAF  109.31  3.000
 P0A  CAJ   CAH  CAF  116.43  3.000
 P0A  CAH   CAJ  OAD  117.83  3.000
 P0A  CAH   CAJ  OAB  115.72  3.000
 P0A  OAD   CAJ  OAB  126.44  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
 P0A  Var_01  CAF  CAG  CB   CA   -172.79  30.0  3
 P0A  Var_02  CAH  CAF  CAG  CB   -177.90  30.0  3
 P0A  Var_03  CAJ  CAH  CAF  CAG   177.82  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
 P0A  chir_01  CA  C  N  CB  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
 P0A  plan-1  C    0.020
 P0A  plan-1  O    0.020
 P0A  plan-1  CA   0.020
 P0A  plan-1  OXT  0.020
 P0A  plan-2  OAB  0.020
 P0A  plan-2  OAD  0.020
 P0A  plan-2  CAH  0.020
 P0A  plan-2  CAJ  0.020

