# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:24:31 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (2S)-2-aminooctanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCCC(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
 9R1  9R1  '(2S)-2-aminooctanedioic acid'  L-peptide  26  13  .  2019-03-22  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_9R1
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
 9R1  N    N  NH2    0  -0.808  -22.4155  17.3651   7.9466
 9R1  CA   C  CH1    0  -0.154  -21.2216  18.2091   7.9343
 9R1  C    C  C      0   0.385  -20.1790  17.6692   6.9237
 9R1  O    O  O      0  -0.614  -19.7025  18.4983   6.1202
 9R1  CB   C  CH2    0  -0.425  -20.6374  18.2365   9.3453
 9R1  CG   C  CH2    0  -0.426  -19.4089  19.1269   9.5027
 9R1  CD   C  CH2    0  -0.418  -19.0095  19.3689  10.9565
 9R1  CE   C  CH2    0  -0.407  -18.5834  18.1151  11.7122
 9R1  CZ   C  CH2    0  -0.569  -18.2191  18.3817  13.1664
 9R1  CN   C  C      0   0.402  -16.9427  19.2132  13.4174
 9R1  ON1  O  O      0  -0.608  -16.0696  19.2134  12.5258
 9R1  ON2  O  OC    -1  -0.622  -16.8705  19.7882  14.5241
 9R1  O1   O  OC    -1  -0.608  -19.8860  16.4596   7.0061
 9R1  H1   H  HNH2   0   0.329  -23.1094  17.7935   8.5485
 9R1  H2   H  HNH2   0   0.332  -22.8347  17.3534   7.0244
 9R1  H4   H  HCH1   0   0.163  -21.4530  19.2473   7.6501
 9R1  H5   H  HCH2   0   0.200  -21.4143  18.5854  10.0377
 9R1  H6   H  HCH2   0   0.206  -20.4071  17.2088   9.6385
 9R1  H7   H  HCH2   0   0.206  -18.5613  18.6906   8.9644
 9R1  H8   H  HCH2   0   0.208  -19.6033  20.0928   9.0249
 9R1  H9   H  HCH2   0   0.213  -18.1899  20.0914  10.9853
 9R1  H10  H  HCH2   0   0.194  -19.8487  19.8381  11.4835
 9R1  H11  H  HCH2   0   0.206  -19.3938  17.3809  11.6828
 9R1  H12  H  HCH2   0   0.196  -17.7359  17.6527  11.1978
 9R1  H13  H  HCH2   0   0.198  -19.0628  18.8571  13.6765
 9R1  H14  H  HCH2   0   0.222  -18.0783  17.4218  13.6791

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
 9R1  O    C    deloc   1.231  0.020  1.231
 9R1  C    CA   single  1.525  0.021  1.525
 9R1  N    CA   single  1.458  0.019  1.458
 9R1  CA   CB   single  1.521  0.033  1.521
 9R1  CB   CG   single  1.525  0.020  1.525
 9R1  CG   CD   single  1.527  0.020  1.527
 9R1  CD   CE   single  1.525  0.020  1.525
 9R1  CE   CZ   single  1.523  0.020  1.523
 9R1  ON1  CN   deloc   1.248  0.020  1.248
 9R1  CZ   CN   single  1.544  0.020  1.544
 9R1  CN   ON2  deloc   1.249  0.020  1.249
 9R1  C    O1   deloc   1.247  0.020  1.247
 9R1  N    H1   single  0.890  0.020  1.040
 9R1  N    H2   single  0.890  0.020  1.040
 9R1  CA   H4   single  0.970  0.020  1.090
 9R1  CB   H5   single  0.970  0.020  1.090
 9R1  CB   H6   single  0.970  0.020  1.090
 9R1  CG   H7   single  0.970  0.020  1.090
 9R1  CG   H8   single  0.970  0.020  1.090
 9R1  CD   H9   single  0.970  0.020  1.090
 9R1  CD   H10  single  0.970  0.020  1.090
 9R1  CE   H11  single  0.970  0.020  1.090
 9R1  CE   H12  single  0.970  0.020  1.090
 9R1  CZ   H13  single  0.970  0.020  1.090
 9R1  CZ   H14  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
 9R1  H2   N   H1   105.20  3.000
 9R1  H2   N   CA   109.69  3.000
 9R1  H1   N   CA   108.66  3.000
 9R1  H4   CA  CB   107.57  3.000
 9R1  H4   CA  C    107.56  3.000
 9R1  CB   CA  C    110.50  1.500
 9R1  H4   CA  N    112.02  3.000
 9R1  CB   CA  N    110.40  1.500
 9R1  C    CA  N    111.00  2.800
 9R1  O1   C   O    126.63  3.000
 9R1  O1   C   CA   116.94  3.000
 9R1  O    C   CA   120.80  1.700
 9R1  H6   CB  H5   106.18  3.000
 9R1  H6   CB  CG   110.57  3.000
 9R1  H5   CB  CG   108.63  3.000
 9R1  H6   CB  CA   108.15  3.000
 9R1  H5   CB  CA   108.53  3.000
 9R1  CG   CB  CA   114.45  3.000
 9R1  H8   CG  H7   105.93  3.000
 9R1  H8   CG  CD   108.79  3.000
 9R1  H7   CG  CD   109.20  3.000
 9R1  H8   CG  CB   109.08  3.000
 9R1  H7   CG  CB   109.89  3.000
 9R1  CD   CG  CB   113.67  3.000
 9R1  H10  CD  H9   106.17  3.000
 9R1  H10  CD  CE   109.12  3.000
 9R1  H9   CD  CE   108.72  3.000
 9R1  H10  CD  CG   108.98  3.000
 9R1  H9   CD  CG   109.03  3.000
 9R1  CE   CD  CG   114.49  3.000
 9R1  H12  CE  H11  106.12  3.000
 9R1  H12  CE  CZ   109.74  3.000
 9R1  H11  CE  CZ   108.69  3.000
 9R1  H12  CE  CD   109.33  3.000
 9R1  H11  CE  CD   109.36  3.000
 9R1  CZ   CE  CD   113.34  3.000
 9R1  H14  CZ  H13  105.13  3.000
 9R1  H14  CZ  CN   106.81  3.000
 9R1  H13  CZ  CN   109.12  3.000
 9R1  H14  CZ  CE   108.88  3.000
 9R1  H13  CZ  CE   109.68  3.000
 9R1  CN   CZ  CE   116.58  3.000
 9R1  ON2  CN  ON1  126.33  3.000
 9R1  ON2  CN  CZ   116.09  3.000
 9R1  ON1  CN  CZ   117.54  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
 9R1  Var_01  CD   CG  CB  CA   168.24  30.0  3
 9R1  Var_02  CE   CD  CG  CB    63.63  30.0  3
 9R1  Var_03  CZ   CE  CD  CG  -178.78  30.0  3
 9R1  Var_04  CN   CZ  CE  CD   -67.93  30.0  3
 9R1  Var_05  ON1  CN  CZ  CE   -24.47  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
 9R1  chir_01  CA  C  N  CB  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
 9R1  plan-1  CA   0.020
 9R1  plan-1  C    0.020
 9R1  plan-1  O    0.020
 9R1  plan-1  O1   0.020
 9R1  plan-2  CZ   0.020
 9R1  plan-2  CN   0.020
 9R1  plan-2  ON1  0.020
 9R1  plan-2  ON2  0.020

