# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:39:34 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (2S)-2-aminononanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@H](N)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
 AN8  AN8  '(2S)-2-aminononanoic acid'  L-peptide  30  12  .  2012-08-28  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_AN8
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
 AN8  C     C  C      0   0.384  16.9595  44.0055  40.7660
 AN8  N     N  NH2    0  -0.807  16.9203  45.2714  42.8993
 AN8  O     O  O      0  -0.616  16.6107  42.8761  40.3617
 AN8  CA    C  CH1    0  -0.150  16.0886  44.6324  41.8821
 AN8  CB    C  CH2    0  -0.426  15.1512  45.6905  41.2966
 AN8  CAA   C  CH3    0  -0.664  11.5995  49.1610  40.4567
 AN8  CAI   C  CH2    0  -0.423  12.9336  49.6546  39.9139
 AN8  CAJ   C  CH2    0  -0.429  14.0455  48.6079  39.9018
 AN8  CAK   C  CH2    0  -0.448  13.7300  47.3692  39.0507
 AN8  CAL   C  CH2    0  -0.431  13.1196  46.1816  39.8096
 AN8  CAM   C  CH2    0  -0.428  14.1430  45.1537  40.2892
 AN8  OXT   O  OC    -1  -0.606  17.9168  44.6837  40.3449
 AN8  HN    H  HNH2   0   0.328  16.3258  45.5711  43.6634
 AN8  HNA   H  HNH2   0   0.331  17.5512  44.5899  43.3033
 AN8  HA    H  HCH1   0   0.164  15.4626  43.8299  42.3025
 AN8  HB    H  HCH2   0   0.202  14.6044  46.1650  42.1213
 AN8  HBA   H  HCH2   0   0.209  15.7626  46.4770  40.8444
 AN8  HAA   H  HCH3   0   0.226  10.8616  49.9643  40.4707
 AN8  HAAA  H  HCH3   0   0.221  11.1888  48.3534  39.8491
 AN8  HAAB  H  HCH3   0   0.213  11.6997  48.7865  41.4774
 AN8  HAI   H  HCH2   0   0.208  12.7897  50.0266  38.8944
 AN8  HAIA  H  HCH2   0   0.215  13.2645  50.5145  40.5033
 AN8  HAJ   H  HCH2   0   0.218  14.9539  49.0870  39.5265
 AN8  HAJA  H  HCH2   0   0.217  14.2714  48.3077  40.9288
 AN8  HAK   H  HCH2   0   0.220  13.0573  47.6705  38.2411
 AN8  HAKA  H  HCH2   0   0.222  14.6412  47.0254  38.5516
 AN8  HAL   H  HCH2   0   0.215  12.5400  46.5388  40.6661
 AN8  HALA  H  HCH2   0   0.218  12.4056  45.6674  39.1605
 AN8  HAM   H  HCH2   0   0.210  14.6678  44.7516  39.4176
 AN8  HAMA  H  HCH2   0   0.207  13.6087  44.3084  40.7356

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
 AN8  O    C     deloc   1.231  0.020  1.231
 AN8  OXT  C     deloc   1.247  0.020  1.247
 AN8  C    CA    single  1.525  0.021  1.525
 AN8  CA   N     single  1.458  0.019  1.458
 AN8  N    HN    single  0.890  0.020  1.040
 AN8  N    HNA   single  0.890  0.020  1.040
 AN8  CB   CA    single  1.521  0.033  1.521
 AN8  CA   HA    single  0.970  0.020  0.970
 AN8  CAM  CB    single  1.523  0.020  1.523
 AN8  CB   HB    single  0.970  0.020  1.090
 AN8  CB   HBA   single  0.970  0.020  1.090
 AN8  CAI  CAA   single  1.523  0.020  1.523
 AN8  CAA  HAA   single  0.970  0.020  1.090
 AN8  CAA  HAAA  single  0.970  0.020  1.090
 AN8  CAA  HAAB  single  0.970  0.020  1.090
 AN8  CAI  CAJ   single  1.527  0.020  1.527
 AN8  CAI  HAI   single  0.970  0.020  1.090
 AN8  CAI  HAIA  single  0.970  0.020  1.090
 AN8  CAK  CAJ   single  1.536  0.020  1.536
 AN8  CAJ  HAJ   single  0.970  0.020  1.090
 AN8  CAJ  HAJA  single  0.970  0.020  1.090
 AN8  CAK  CAL   single  1.536  0.020  1.536
 AN8  CAK  HAK   single  0.970  0.020  1.090
 AN8  CAK  HAKA  single  0.970  0.020  1.090
 AN8  CAL  CAM   single  1.528  0.020  1.528
 AN8  CAL  HAL   single  0.970  0.020  1.090
 AN8  CAL  HALA  single  0.970  0.020  1.090
 AN8  CAM  HAM   single  0.970  0.020  1.090
 AN8  CAM  HAMA  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
 AN8  OXT   C    CA    117.07  3.000
 AN8  CA    C    O     120.80  1.700
 AN8  OXT   C    O     126.66  3.000
 AN8  HNA   N    HN    105.28  3.000
 AN8  HNA   N    CA    109.76  3.000
 AN8  HN    N    CA    108.69  3.000
 AN8  HA    CA   CB    109.00  3.000
 AN8  HA    CA   N     110.00  3.000
 AN8  CB    CA   N     110.40  1.500
 AN8  HA    CA   C     109.00  3.000
 AN8  CB    CA   C     110.50  1.500
 AN8  N     CA   C     111.00  2.800
 AN8  HBA   CB   HB    106.15  3.000
 AN8  HBA   CB   CAM   110.48  3.000
 AN8  HB    CB   CAM   108.64  3.000
 AN8  HBA   CB   CA    108.24  3.000
 AN8  HB    CB   CA    108.47  3.000
 AN8  CAM   CB   CA    114.52  3.000
 AN8  HAAB  CAA  HAAA  107.53  3.000
 AN8  HAAB  CAA  HAA   107.62  3.000
 AN8  HAAA  CAA  HAA   107.32  3.000
 AN8  HAAB  CAA  CAI   111.35  3.000
 AN8  HAAA  CAA  CAI   111.80  3.000
 AN8  HAA   CAA  CAI   111.01  3.000
 AN8  HAIA  CAI  HAI   105.93  3.000
 AN8  HAIA  CAI  CAJ   108.84  3.000
 AN8  HAI   CAI  CAJ   108.74  3.000
 AN8  HAIA  CAI  CAA   109.14  3.000
 AN8  HAI   CAI  CAA   109.08  3.000
 AN8  CAJ   CAI  CAA   114.75  3.000
 AN8  HAJA  CAJ  HAJ   105.73  3.000
 AN8  HAJA  CAJ  CAK   109.97  3.000
 AN8  HAJ   CAJ  CAK   109.50  3.000
 AN8  HAJA  CAJ  CAI   109.33  3.000
 AN8  HAJ   CAJ  CAI   107.90  3.000
 AN8  CAK   CAJ  CAI   114.06  3.000
 AN8  HAKA  CAK  HAK   105.12  3.000
 AN8  HAKA  CAK  CAL   108.26  3.000
 AN8  HAK   CAK  CAL   109.51  3.000
 AN8  HAKA  CAK  CAJ   109.58  3.000
 AN8  HAK   CAK  CAJ   108.31  3.000
 AN8  CAL   CAK  CAJ   115.56  3.000
 AN8  HALA  CAL  HAL   105.81  3.000
 AN8  HALA  CAL  CAM   107.90  3.000
 AN8  HAL   CAL  CAM   109.19  3.000
 AN8  HALA  CAL  CAK   109.26  3.000
 AN8  HAL   CAL  CAK   110.17  3.000
 AN8  CAM   CAL  CAK   114.15  3.000
 AN8  HAMA  CAM  HAM   105.97  3.000
 AN8  HAMA  CAM  CAL   108.69  3.000
 AN8  HAM   CAM  CAL   108.57  3.000
 AN8  HAMA  CAM  CB    108.99  3.000
 AN8  HAM   CAM  CB    109.82  3.000
 AN8  CAL   CAM  CB    114.46  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
 AN8  Var_01  CAL  CAM  CB   CA   174.25  30.0  1
 AN8  Var_02  CAK  CAL  CAM  CB    62.92  30.0  1
 AN8  Var_03  CAK  CAJ  CAI  CAA   60.00  30.0  3
 AN8  Var_04  CAL  CAK  CAJ  CAI  -94.23  30.0  1
 AN8  Var_05  CAM  CAL  CAK  CAJ  -93.80  30.0  3
 AN8  Var_06  HAA  CAA  CAI  CAJ  177.99  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
 AN8  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
 AN8  plan-1  C    0.020
 AN8  plan-1  O    0.020
 AN8  plan-1  CA   0.020
 AN8  plan-1  OXT  0.020

