# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:58:25 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2S)-2-[(N-acetyl-L-alpha-aspartyl)amino]nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@H](NC(=O)[C@H](CC(O)=O)NC(C)=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
 SDR  SDR  '(2S)-2-[(N-acetyl-L-alpha-aspartyl)amino]nonanoic acid'  peptide  47  23  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SDR
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
 SDR  CAR   C  C      0   0.519   2.5432  -1.9638  -1.5398
 SDR  OAC   O  O      0  -0.507   1.3530  -2.2050  -1.3803
 SDR  CAB   C  CH3    0  -0.777   3.3866  -2.7101  -2.5425
 SDR  NAP   N  NH1    0  -0.620   3.1890  -1.0461  -0.8048
 SDR  CAW   C  CH1    0  -0.195   2.5161  -0.2501   0.1889
 SDR  CAU   C  C      0   0.569   1.4988   0.6846  -0.4600
 SDR  OAF   O  O      0  -0.513   1.6969   1.1872  -1.5579
 SDR  CAO   C  CH2    0  -0.609   3.5376   0.5788   0.9591
 SDR  CAS   C  C      0   0.413   4.4880  -0.2614   1.8386
 SDR  OAD   O  O      0  -0.604   4.0144  -1.2896   2.3586
 SDR  OAG   O  OC    -1  -0.614   5.6425   0.1848   1.9825
 SDR  C     C  C      0   0.414   0.0378   3.3626   0.6090
 SDR  N     N  NH1    0  -0.609   0.4131   0.9231   0.2857
 SDR  CA    C  CH1    0  -0.211  -0.4895   2.0202   0.0334
 SDR  CB    C  CH2    0  -0.442  -1.8854   1.6894   0.5571
 SDR  CAA   C  CH3    0  -0.661  -8.1669  -2.5569  -0.1697
 SDR  CAI   C  CH2    0  -0.419  -6.6827  -2.4343  -0.4869
 SDR  CAJ   C  CH2    0  -0.405  -6.0610  -1.1582   0.0674
 SDR  CAK   C  CH2    0  -0.411  -4.5779  -1.0180  -0.2530
 SDR  CAM   C  CH2    0  -0.403  -2.4941   0.4351  -0.0587
 SDR  HAB   H  HCH3   0   0.268   3.5979  -3.7096  -2.1595
 SDR  HABA  H  HCH3   0   0.260   2.8369  -2.8267  -3.4748
 SDR  HABB  H  HCH3   0   0.248   4.3368  -2.2237  -2.7545
 SDR  HNAP  H  HNH1   0   0.397   4.1498  -0.8343  -1.0190
 SDR  HAW   H  HCH1   0   0.254   2.0082  -0.9123   0.8952
 SDR  HAO   H  HCH2   0   0.265   2.9956   1.2746   1.6081
 SDR  HAOA  H  HCH2   0   0.227   4.1068   1.2033   0.2645
 SDR  HN    H  HNH1   0   0.381   0.3991   0.5340   1.2159
 SDR  HA    H  HCH1   0   0.236  -0.5612   2.1367  -1.0516
 SDR  HB    H  HCH2   0   0.213  -1.8579   1.5853   1.6487
 SDR  HBA   H  HCH2   0   0.227  -2.5282   2.5468   0.3506
 SDR  HAA   H  HCH3   0   0.215  -8.3399  -2.5685   0.9081
 SDR  HAAA  H  HCH3   0   0.215  -8.7297  -1.7176  -0.5832
 SDR  HAAB  H  HCH3   0   0.225  -8.5910  -3.4736  -0.5815
 SDR  HAI   H  HCH2   0   0.210  -6.1498  -3.3010  -0.0833
 SDR  HAIA  H  HCH2   0   0.209  -6.5357  -2.4668  -1.5710
 SDR  HAJ   H  HCH2   0   0.205  -6.5996  -0.2910  -0.3310
 SDR  HAJA  H  HCH2   0   0.205  -6.2032  -1.1293   1.1536
 SDR  HAK   H  HCH2   0   0.206  -4.0383  -1.8898   0.1334
 SDR  HAKA  H  HCH2   0   0.205  -4.4399  -1.0334  -1.3399
 SDR  HAL   H  HCH2   0   0.205  -4.5289   1.1210  -0.0342
 SDR  HALA  H  HCH2   0   0.206  -4.0606   0.2462   1.4075
 SDR  HAM   H  HCH2   0   0.205  -2.4041   0.4883  -1.1496
 SDR  HAMA  H  HCH2   0   0.212  -1.9251  -0.4478   0.2480
 SDR  O     O  O      0  -0.587   1.1237   3.3478   1.2134
 SDR  OXT   O  OC    -1  -0.617  -0.6941   4.3513   0.3997
 SDR  CAL   C  CH2    0  -0.412  -3.9597   0.2529   0.3164

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
 SDR  O    C     deloc   1.231  0.020  1.231
 SDR  OXT  C     deloc   1.248  0.020  1.248
 SDR  C    CA    single  1.525  0.021  1.525
 SDR  CA   N     single  1.458  0.019  1.458
 SDR  N    CAU   single  1.339  0.020  1.339
 SDR  N    HN    single  0.890  0.020  1.040
 SDR  CB   CA    single  1.521  0.033  1.521
 SDR  CA   HA    single  0.970  0.020  0.970
 SDR  CAM  CB    single  1.524  0.020  1.524
 SDR  CB   HB    single  0.970  0.020  1.090
 SDR  CB   HBA   single  0.970  0.020  1.090
 SDR  CAI  CAA   single  1.523  0.020  1.523
 SDR  CAA  HAA   single  0.970  0.020  1.090
 SDR  CAA  HAAA  single  0.970  0.020  1.090
 SDR  CAA  HAAB  single  0.970  0.020  1.090
 SDR  CAR  CAB   single  1.508  0.020  1.508
 SDR  CAB  HAB   single  0.970  0.020  1.090
 SDR  CAB  HABA  single  0.970  0.020  1.090
 SDR  CAB  HABB  single  0.970  0.020  1.090
 SDR  CAR  OAC   double  1.225  0.020  1.225
 SDR  CAS  OAD   deloc   1.246  0.020  1.246
 SDR  OAF  CAU   double  1.224  0.020  1.224
 SDR  CAS  OAG   deloc   1.246  0.020  1.246
 SDR  CAI  CAJ   single  1.524  0.020  1.524
 SDR  CAI  HAI   single  0.970  0.020  1.090
 SDR  CAI  HAIA  single  0.970  0.020  1.090
 SDR  CAK  CAJ   single  1.524  0.020  1.524
 SDR  CAJ  HAJ   single  0.970  0.020  1.090
 SDR  CAJ  HAJA  single  0.970  0.020  1.090
 SDR  CAK  CAL   single  1.524  0.020  1.524
 SDR  CAK  HAK   single  0.970  0.020  1.090
 SDR  CAK  HAKA  single  0.970  0.020  1.090
 SDR  CAL  CAM   single  1.524  0.020  1.524
 SDR  CAL  HAL   single  0.970  0.020  1.090
 SDR  CAL  HALA  single  0.970  0.020  1.090
 SDR  CAM  HAM   single  0.970  0.020  1.090
 SDR  CAM  HAMA  single  0.970  0.020  1.090
 SDR  CAO  CAW   single  1.524  0.020  1.524
 SDR  CAO  CAS   single  1.544  0.020  1.544
 SDR  CAO  HAO   single  0.970  0.020  1.090
 SDR  CAO  HAOA  single  0.970  0.020  1.090
 SDR  CAW  NAP   single  1.440  0.020  1.440
 SDR  NAP  CAR   single  1.341  0.020  1.341
 SDR  NAP  HNAP  single  0.860  0.020  1.020
 SDR  CAU  CAW   single  1.526  0.020  1.526
 SDR  CAW  HAW   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
 SDR  NAP   CAR  CAB   115.70  3.000
 SDR  NAP   CAR  OAC   122.09  3.000
 SDR  CAB   CAR  OAC   122.18  3.000
 SDR  HABB  CAB  HABA  108.78  3.000
 SDR  HABB  CAB  HAB   107.98  3.000
 SDR  HABA  CAB  HAB   107.48  3.000
 SDR  HABB  CAB  CAR   113.37  3.000
 SDR  HABA  CAB  CAR   109.89  3.000
 SDR  HAB   CAB  CAR   109.16  3.000
 SDR  HNAP  NAP  CAW   118.45  3.000
 SDR  HNAP  NAP  CAR   119.13  3.000
 SDR  CAW   NAP  CAR   122.09  3.000
 SDR  HAW   CAW  CAO   108.32  3.000
 SDR  HAW   CAW  CAU   109.62  3.000
 SDR  CAO   CAW  CAU   109.17  3.000
 SDR  HAW   CAW  NAP   109.15  3.000
 SDR  CAU   CAW  NAP   110.89  3.000
 SDR  CAO   CAW  NAP   109.64  3.000
 SDR  N     CAU  OAF   123.91  3.000
 SDR  OAF   CAU  CAW   121.68  3.000
 SDR  N     CAU  CAW   114.39  3.000
 SDR  HAOA  CAO  HAO   105.74  3.000
 SDR  HAOA  CAO  CAS   110.62  3.000
 SDR  HAO   CAO  CAS   108.24  3.000
 SDR  HAOA  CAO  CAW   109.77  3.000
 SDR  HAO   CAO  CAW   108.26  3.000
 SDR  CAS   CAO  CAW   113.86  3.000
 SDR  OAG   CAS  OAD   126.84  3.000
 SDR  OAG   CAS  CAO   116.19  3.000
 SDR  OAD   CAS  CAO   116.94  3.000
 SDR  OXT   C    CA    120.80  1.700
 SDR  CA    C    O     120.80  1.700
 SDR  OXT   C    O     127.13  3.000
 SDR  HN    N    CA    116.49  3.000
 SDR  HN    N    CAU   117.15  3.000
 SDR  CA    N    CAU   123.06  3.000
 SDR  HA    CA   CB    109.00  3.000
 SDR  HA    CA   N     110.00  3.000
 SDR  CB    CA   N     110.40  1.500
 SDR  HA    CA   C     110.00  3.000
 SDR  CB    CA   C     110.50  1.500
 SDR  N     CA   C     111.00  2.800
 SDR  HBA   CB   HB    106.12  3.000
 SDR  HBA   CB   CAM   109.56  3.000
 SDR  HB    CB   CAM   109.51  3.000
 SDR  HBA   CB   CA    107.66  3.000
 SDR  HB    CB   CA    109.82  3.000
 SDR  CAM   CB   CA    113.87  3.000
 SDR  HAAB  CAA  HAAA  107.62  3.000
 SDR  HAAB  CAA  HAA   107.59  3.000
 SDR  HAAA  CAA  HAA   107.48  3.000
 SDR  HAAB  CAA  CAI   111.59  3.000
 SDR  HAAA  CAA  CAI   111.20  3.000
 SDR  HAA   CAA  CAI   111.16  3.000
 SDR  HAIA  CAI  HAI   106.04  3.000
 SDR  HAIA  CAI  CAJ   109.30  3.000
 SDR  HAI   CAI  CAJ   109.29  3.000
 SDR  HAIA  CAI  CAA   109.56  3.000
 SDR  HAI   CAI  CAA   109.51  3.000
 SDR  CAJ   CAI  CAA   112.91  3.000
 SDR  HAJA  CAJ  HAJ   106.01  3.000
 SDR  HAJA  CAJ  CAK   109.41  3.000
 SDR  HAJ   CAJ  CAK   109.21  3.000
 SDR  HAJA  CAJ  CAI   109.25  3.000
 SDR  HAJ   CAJ  CAI   109.26  3.000
 SDR  CAK   CAJ  CAI   113.43  3.000
 SDR  HAKA  CAK  HAK   106.05  3.000
 SDR  HAKA  CAK  CAL   109.35  3.000
 SDR  HAK   CAK  CAL   109.39  3.000
 SDR  HAKA  CAK  CAJ   109.26  3.000
 SDR  HAK   CAK  CAJ   109.39  3.000
 SDR  CAL   CAK  CAJ   113.15  3.000
 SDR  HAMA  CAM  HAM   105.99  3.000
 SDR  HAMA  CAM  CAL   109.55  3.000
 SDR  HAM   CAM  CAL   109.26  3.000
 SDR  HAMA  CAM  CB    110.07  3.000
 SDR  HAM   CAM  CB    109.23  3.000
 SDR  CAL   CAM  CB    112.52  3.000
 SDR  HALA  CAL  HAL   106.00  3.000
 SDR  HALA  CAL  CAM   109.53  3.000
 SDR  HAL   CAL  CAM   109.04  3.000
 SDR  HALA  CAL  CAK   109.25  3.000
 SDR  HAL   CAL  CAK   109.30  3.000
 SDR  CAM   CAL  CAK   113.45  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
 SDR  CONST_01  CAW   NAP  CAR  OAC     0.00   0.0  0
 SDR  CONST_02  CAW   NAP  CAR  CAB   180.00   0.0  0
 SDR  CONST_04  CA    N    CAU  OAF     0.00   0.0  0
 SDR  CONST_05  HNAP  NAP  CAR  OAC   180.00   0.0  0
 SDR  CONST_06  HN    N    CAU  CAW     0.00   0.0  0
 SDR  Var_01    OAD   CAS  CAO  CAW   -34.01  30.0  3
 SDR  Var_02    CAL   CAM  CB   CA   -171.06  30.0  1
 SDR  Var_03    CAK   CAL  CAM  CB   -178.22  30.0  2
 SDR  Var_04    CAK   CAJ  CAI  CAA  -179.53  30.0  3
 SDR  Var_05    CAL   CAK  CAJ  CAI  -179.41  30.0  1
 SDR  Var_06    CAM   CAL  CAK  CAJ  -177.11  30.0  3
 SDR  Var_07    HAB   CAB  CAR  OAC   -74.57  30.0  3
 SDR  Var_08    HAA   CAA  CAI  CAJ   -60.26  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
 SDR  chir_01  CAW  CAO  NAP  CAU  positiv
 SDR  chir_02  CA   N    CB   C    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
 SDR  plan-1  CAR   0.020
 SDR  plan-1  OAC   0.020
 SDR  plan-1  CAB   0.020
 SDR  plan-1  NAP   0.020
 SDR  plan-1  CAW   0.020
 SDR  plan-1  HNAP  0.020
 SDR  plan-2  CAW   0.020
 SDR  plan-2  CAU   0.020
 SDR  plan-2  OAF   0.020
 SDR  plan-2  N     0.020
 SDR  plan-2  CA    0.020
 SDR  plan-2  HN    0.020
 SDR  plan-3  CAO   0.020
 SDR  plan-3  CAS   0.020
 SDR  plan-3  OAD   0.020
 SDR  plan-3  OAG   0.020
 SDR  plan-4  C     0.020
 SDR  plan-4  CA    0.020
 SDR  plan-4  O     0.020
 SDR  plan-4  OXT   0.020

