# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:27:53 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S)-8-[(tert-butoxycarbonyl)amino]-2-(1H-indol-3-yl)octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)NCCCCCC[C@H](C(O)=O)c1c[nH]c2ccccc12
#
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
 2S8  2S8  '(2S)-8-[(tert-butoxycarbonyl)amino]-2-(1H-indol-3-yl)octanoic acid'  ligand  56  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2S8
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
 2S8  OAD   O  OC    -1  -0.612    4.0310  -3.0326  -1.5459
 2S8  CAU   C  C      0   0.410    3.6398  -2.4882  -0.4942
 2S8  OAF   O  O      0  -0.612    3.2392  -3.0698   0.5352
 2S8  CAZ   C  CH1    0  -0.425    3.6933  -0.9447  -0.4430
 2S8  CAW   C  CR5    0   0.032    4.9306  -0.5033   0.2822
 2S8  CAK   C  CR15   0  -0.088    5.5371  -1.1008   1.3522
 2S8  NAS   N  NR15   0  -0.690    6.6275  -0.3722   1.7486
 2S8  CAX   C  CR56   0   0.351    6.7582   0.7185   0.9431
 2S8  CAI   C  CR16   0  -0.308    7.7064   1.7410   0.9458
 2S8  CAG   C  CR16   0  -0.287    7.5798   2.7323  -0.0088
 2S8  CAH   C  CR16   0  -0.271    6.5349   2.7109  -0.9484
 2S8  CAJ   C  CR16   0  -0.377    5.5990   1.6947  -0.9485
 2S8  CAY   C  CR56   0   0.013    5.7008   0.6746   0.0052
 2S8  CAQ   C  CH2    0  -0.386    2.4441  -0.3255   0.1890
 2S8  CAO   C  CH2    0  -0.423    1.1526  -0.6704  -0.5406
 2S8  CAM   C  CH2    0  -0.413   -0.0690   0.0215   0.0516
 2S8  CAL   C  CH2    0  -0.416   -1.3774  -0.4323  -0.5828
 2S8  CAN   C  CH2    0  -0.472   -2.6004   0.2480   0.0177
 2S8  CAP   C  CH2    0  -0.229   -3.8909  -0.2702  -0.5948
 2S8  NAR   N  NH1    0  -0.668   -5.0393   0.3793   0.0001
 2S8  CAV   C  C      0   0.760   -6.2970   0.0021  -0.2897
 2S8  OAE   O  O      0  -0.526   -6.5697  -0.9078  -1.0495
 2S8  OAT   O  O2     0  -0.508   -7.1793   0.7546   0.3727
 2S8  CBA   C  CT     0   0.191   -8.6134   0.5869   0.2261
 2S8  CAC   C  CH3    0  -0.669   -9.0589  -0.7918   0.6993
 2S8  CAB   C  CH3    0  -0.660   -9.1838   1.6550   1.1520
 2S8  CAA   C  CH3    0  -0.671   -9.0525   0.8643  -1.2073
 2S8  HAZ   H  HCH1   0   0.202    3.7642  -0.5777  -1.4735
 2S8  HAK   H  HCR5   0   0.269    5.2672  -2.0075   1.8689
 2S8  HAI   H  HCR6   0   0.255    8.5132   1.7590   1.6677
 2S8  HAG   H  HCR6   0   0.246    8.2992   3.5404  -0.0339
 2S8  HAH   H  HCR6   0   0.242    6.4658   3.5047  -1.6810
 2S8  HAJ   H  HCR6   0   0.238    4.7980   1.6863  -1.6782
 2S8  HAQ   H  HCH2   0   0.205    2.3722  -0.6500   1.2305
 2S8  HAQA  H  HCH2   0   0.207    2.5656   0.7630   0.2146
 2S8  HAO   H  HCH2   0   0.204    1.2451  -0.4061  -1.6001
 2S8  HAOA  H  HCH2   0   0.211    1.0000  -1.7537  -0.5075
 2S8  HAM   H  HCH2   0   0.208   -0.1077  -0.1716   1.1295
 2S8  HAMA  H  HCH2   0   0.209    0.0345   1.1066  -0.0572
 2S8  HAL   H  HCH2   0   0.215   -1.3471  -0.2448  -1.6613
 2S8  HALA  H  HCH2   0   0.214   -1.4730  -1.5173  -0.4664
 2S8  HAN   H  HCH2   0   0.228   -2.6185   0.0812   1.0995
 2S8  HANA  H  HCH2   0   0.228   -2.5291   1.3303  -0.1321
 2S8  HAP   H  HCH2   0   0.224   -3.8744  -0.1071  -1.6774
 2S8  HAPA  H  HCH2   0   0.228   -3.9575  -1.3502  -0.4402
 2S8  HNAR  H  HNH1   0   0.396   -4.8906   1.1729   0.6024
 2S8  HAC   H  HCH3   0   0.233   -8.6969  -0.9928   1.7089
 2S8  HACA  H  HCH3   0   0.232  -10.1487  -0.8260   0.7280
 2S8  HACB  H  HCH3   0   0.245   -8.7182  -1.5874   0.0411
 2S8  HAB   H  HCH3   0   0.237   -8.8619   2.6539   0.8540
 2S8  HABA  H  HCH3   0   0.230  -10.2730   1.6296   1.1152
 2S8  HABB  H  HCH3   0   0.237   -8.8812   1.4893   2.1873
 2S8  HAA   H  HCH3   0   0.245   -8.7132   0.0990  -1.9016
 2S8  HAAA  H  HCH3   0   0.232  -10.1421   0.8937  -1.2497
 2S8  HAAB  H  HCH3   0   0.234   -8.6849   1.8337  -1.5484
 2S8  HNAS  H  HNR5   0   0.404    7.2494  -0.6285   2.4962

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
 2S8  CAU  OAD   deloc     1.247  0.020  1.247
 2S8  OAF  CAU   deloc     1.248  0.020  1.248
 2S8  CAZ  CAU   single    1.545  0.020  1.545
 2S8  CAQ  CAZ   single    1.531  0.020  1.531
 2S8  CAZ  CAW   single    1.501  0.020  1.501
 2S8  CAZ  HAZ   single    0.970  0.020  1.090
 2S8  CAK  CAW   aromatic  1.367  0.020  1.367
 2S8  CAW  CAY   aromatic  1.434  0.020  1.434
 2S8  CAK  NAS   aromatic  1.370  0.020  1.370
 2S8  CAK  HAK   single    0.930  0.020  1.080
 2S8  NAS  CAX   aromatic  1.362  0.020  1.362
 2S8  CAX  CAY   aromatic  1.414  0.020  1.414
 2S8  CAX  CAI   aromatic  1.394  0.020  1.394
 2S8  CAI  CAG   aromatic  1.382  0.020  1.382
 2S8  CAI  HAI   single    0.930  0.020  1.080
 2S8  CAG  CAH   aromatic  1.405  0.020  1.405
 2S8  CAG  HAG   single    0.930  0.020  1.080
 2S8  CAJ  CAH   aromatic  1.381  0.020  1.381
 2S8  CAH  HAH   single    0.930  0.020  1.080
 2S8  CAY  CAJ   aromatic  1.400  0.020  1.400
 2S8  CAJ  HAJ   single    0.930  0.020  1.080
 2S8  CAO  CAQ   single    1.523  0.020  1.523
 2S8  CAQ  HAQ   single    0.970  0.020  1.090
 2S8  CAQ  HAQA  single    0.970  0.020  1.090
 2S8  CAM  CAO   single    1.524  0.020  1.524
 2S8  CAO  HAO   single    0.970  0.020  1.090
 2S8  CAO  HAOA  single    0.970  0.020  1.090
 2S8  CAM  CAL   single    1.523  0.020  1.523
 2S8  CAM  HAM   single    0.970  0.020  1.090
 2S8  CAM  HAMA  single    0.970  0.020  1.090
 2S8  CAN  CAL   single    1.523  0.020  1.523
 2S8  CAL  HAL   single    0.970  0.020  1.090
 2S8  CAL  HALA  single    0.970  0.020  1.090
 2S8  CAP  CAN   single    1.520  0.020  1.520
 2S8  CAN  HAN   single    0.970  0.020  1.090
 2S8  CAN  HANA  single    0.970  0.020  1.090
 2S8  CAP  NAR   single    1.447  0.020  1.447
 2S8  CAP  HAP   single    0.970  0.020  1.090
 2S8  CAP  HAPA  single    0.970  0.020  1.090
 2S8  NAR  CAV   single    1.345  0.020  1.345
 2S8  NAR  HNAR  single    0.860  0.020  1.020
 2S8  OAE  CAV   double    1.216  0.020  1.216
 2S8  CAV  OAT   single    1.335  0.020  1.335
 2S8  OAT  CBA   single    1.451  0.020  1.451
 2S8  CAB  CBA   single    1.524  0.020  1.524
 2S8  CBA  CAC   single    1.524  0.020  1.524
 2S8  CBA  CAA   single    1.525  0.020  1.525
 2S8  CAC  HAC   single    0.970  0.020  1.090
 2S8  CAC  HACA  single    0.970  0.020  1.090
 2S8  CAC  HACB  single    0.970  0.020  1.090
 2S8  CAB  HAB   single    0.970  0.020  1.090
 2S8  CAB  HABA  single    0.970  0.020  1.090
 2S8  CAB  HABB  single    0.970  0.020  1.090
 2S8  CAA  HAA   single    0.970  0.020  1.090
 2S8  CAA  HAAA  single    0.970  0.020  1.090
 2S8  CAA  HAAB  single    0.970  0.020  1.090
 2S8  NAS  HNAS  single    0.860  0.020  1.020

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
 2S8  CAZ   CAU  OAF   116.69  3.000
 2S8  CAZ   CAU  OAD   116.94  3.000
 2S8  OAF   CAU  OAD   126.34  3.000
 2S8  HAZ   CAZ  CAQ   107.79  3.000
 2S8  HAZ   CAZ  CAW   107.61  3.000
 2S8  CAQ   CAZ  CAW   110.76  3.000
 2S8  HAZ   CAZ  CAU   107.79  3.000
 2S8  CAW   CAZ  CAU   109.78  3.000
 2S8  CAQ   CAZ  CAU   112.92  3.000
 2S8  CAY   CAW  CAK   105.77  3.000
 2S8  CAY   CAW  CAZ   126.23  3.000
 2S8  CAK   CAW  CAZ   127.98  3.000
 2S8  HAK   CAK  NAS   120.53  3.000
 2S8  HAK   CAK  CAW   129.16  3.000
 2S8  NAS   CAK  CAW   110.31  3.000
 2S8  HNAS  NAS  CAX   125.75  3.000
 2S8  HNAS  NAS  CAK   124.87  3.000
 2S8  CAX   NAS  CAK   109.34  3.000
 2S8  CAY   CAX  CAI   122.17  3.000
 2S8  CAI   CAX  NAS   130.63  3.000
 2S8  CAY   CAX  NAS   107.19  3.000
 2S8  HAI   CAI  CAG   121.12  3.000
 2S8  HAI   CAI  CAX   121.34  3.000
 2S8  CAG   CAI  CAX   117.54  3.000
 2S8  HAG   CAG  CAH   119.35  3.000
 2S8  HAG   CAG  CAI   119.39  3.000
 2S8  CAH   CAG  CAI   121.27  3.000
 2S8  HAH   CAH  CAJ   119.75  3.000
 2S8  HAH   CAH  CAG   119.26  3.000
 2S8  CAJ   CAH  CAG   120.99  3.000
 2S8  HAJ   CAJ  CAY   120.45  3.000
 2S8  HAJ   CAJ  CAH   120.43  3.000
 2S8  CAY   CAJ  CAH   119.12  3.000
 2S8  CAJ   CAY  CAX   118.92  3.000
 2S8  CAJ   CAY  CAW   133.69  3.000
 2S8  CAX   CAY  CAW   107.39  3.000
 2S8  HAQA  CAQ  HAQ   106.26  3.000
 2S8  HAQA  CAQ  CAO   109.28  3.000
 2S8  HAQ   CAQ  CAO   109.48  3.000
 2S8  HAQA  CAQ  CAZ   108.72  3.000
 2S8  HAQ   CAQ  CAZ   109.08  3.000
 2S8  CAO   CAQ  CAZ   113.74  3.000
 2S8  HAOA  CAO  HAO   106.24  3.000
 2S8  HAOA  CAO  CAM   109.02  3.000
 2S8  HAO   CAO  CAM   109.50  3.000
 2S8  HAOA  CAO  CAQ   109.14  3.000
 2S8  HAO   CAO  CAQ   109.70  3.000
 2S8  CAM   CAO  CAQ   113.01  3.000
 2S8  HAMA  CAM  HAM   106.00  3.000
 2S8  HAMA  CAM  CAL   109.57  3.000
 2S8  HAM   CAM  CAL   109.08  3.000
 2S8  HAMA  CAM  CAO   109.60  3.000
 2S8  HAM   CAM  CAO   109.30  3.000
 2S8  CAL   CAM  CAO   113.05  3.000
 2S8  HALA  CAL  HAL   106.06  3.000
 2S8  HALA  CAL  CAN   109.30  3.000
 2S8  HAL   CAL  CAN   109.52  3.000
 2S8  HALA  CAL  CAM   109.02  3.000
 2S8  HAL   CAL  CAM   109.59  3.000
 2S8  CAN   CAL  CAM   113.11  3.000
 2S8  HANA  CAN  HAN   106.67  3.000
 2S8  HANA  CAN  CAP   109.71  3.000
 2S8  HAN   CAN  CAP   109.41  3.000
 2S8  HANA  CAN  CAL   109.59  3.000
 2S8  HAN   CAN  CAL   109.57  3.000
 2S8  CAP   CAN  CAL   111.76  3.000
 2S8  HAPA  CAP  HAP   106.74  3.000
 2S8  HAPA  CAP  NAR   109.69  3.000
 2S8  HAP   CAP  NAR   110.58  3.000
 2S8  HAPA  CAP  CAN   109.37  3.000
 2S8  HAP   CAP  CAN   109.57  3.000
 2S8  NAR   CAP  CAN   110.80  3.000
 2S8  HNAR  NAR  CAV   119.20  3.000
 2S8  HNAR  NAR  CAP   118.83  3.000
 2S8  CAV   NAR  CAP   121.85  3.000
 2S8  OAT   CAV  OAE   125.67  3.000
 2S8  OAT   CAV  NAR   110.67  3.000
 2S8  OAE   CAV  NAR   123.65  3.000
 2S8  CBA   OAT  CAV   122.53  3.000
 2S8  CAA   CBA  CAB   109.63  3.000
 2S8  CAA   CBA  CAC   111.86  3.000
 2S8  CAB   CBA  CAC   109.62  3.000
 2S8  CAA   CBA  OAT   111.01  3.000
 2S8  CAC   CBA  OAT   111.22  3.000
 2S8  CAB   CBA  OAT   103.15  3.000
 2S8  HACB  CAC  HACA  107.82  3.000
 2S8  HACB  CAC  HAC   108.75  3.000
 2S8  HACA  CAC  HAC   107.54  3.000
 2S8  HACB  CAC  CBA   112.48  3.000
 2S8  HACA  CAC  CBA   109.18  3.000
 2S8  HAC   CAC  CBA   110.91  3.000
 2S8  HABB  CAB  HABA  107.79  3.000
 2S8  HABB  CAB  HAB   108.44  3.000
 2S8  HABA  CAB  HAB   107.87  3.000
 2S8  HABB  CAB  CBA   111.48  3.000
 2S8  HABA  CAB  CBA   109.70  3.000
 2S8  HAB   CAB  CBA   111.42  3.000
 2S8  HAAB  CAA  HAAA  107.48  3.000
 2S8  HAAB  CAA  HAA   108.69  3.000
 2S8  HAAA  CAA  HAA   107.81  3.000
 2S8  HAAB  CAA  CBA   111.00  3.000
 2S8  HAAA  CAA  CBA   109.22  3.000
 2S8  HAA   CAA  CBA   112.48  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
 2S8  CONST_01  CAX   NAS  CAK  CAW     0.00   0.0  0
 2S8  CONST_02  NAS   CAX  CAY  CAW     0.00   0.0  0
 2S8  CONST_03  CAI   CAX  CAY  CAW   180.00   0.0  0
 2S8  CONST_04  CAH   CAJ  CAY  CAW   180.00   0.0  0
 2S8  CONST_05  CAX   CAY  CAW  CAK     0.00   0.0  0
 2S8  CONST_06  CAJ   CAY  CAW  CAK   180.00   0.0  0
 2S8  CONST_07  CAY   CAX  NAS  CAK     0.00   0.0  0
 2S8  CONST_08  CAI   CAX  NAS  CAK   180.00   0.0  0
 2S8  CONST_09  CAY   CAW  CAK  NAS     0.00   0.0  0
 2S8  CONST_10  CAJ   CAY  CAX  NAS   180.00   0.0  0
 2S8  CONST_11  CAG   CAI  CAX  NAS   180.00   0.0  0
 2S8  CONST_12  CAH   CAJ  CAY  CAX     0.00   0.0  0
 2S8  CONST_13  CAH   CAG  CAI  CAX     0.00   0.0  0
 2S8  CONST_14  CAJ   CAY  CAX  CAI     0.00   0.0  0
 2S8  CONST_15  CAJ   CAH  CAG  CAI     0.00   0.0  0
 2S8  CONST_16  CAY   CAX  CAI  CAG     0.00   0.0  0
 2S8  CONST_17  CAY   CAJ  CAH  CAG     0.00   0.0  0
 2S8  CONST_18  NAS   CAK  CAW  CAZ   180.00   0.0  0
 2S8  CONST_19  CAX   CAY  CAW  CAZ   180.00   0.0  0
 2S8  CONST_20  CAJ   CAY  CAW  CAZ     0.00   0.0  0
 2S8  CONST_21  HNAS  NAS  CAK  CAW   180.00   0.0  0
 2S8  CONST_22  HAJ   CAJ  CAY  CAW     0.00   0.0  0
 2S8  CONST_23  HAI   CAI  CAX  NAS     0.00   0.0  0
 2S8  CONST_24  HAK   CAK  NAS  CAX   180.00   0.0  0
 2S8  CONST_25  HAG   CAG  CAI  CAX   180.00   0.0  0
 2S8  CONST_26  HAH   CAH  CAG  CAI   180.00   0.0  0
 2S8  Var_01    CAM   CAO  CAQ  CAZ  -176.53  30.0  1
 2S8  Var_02    CAL   CAM  CAO  CAQ  -174.04  30.0  1
 2S8  Var_03    CAN   CAL  CAM  CAO   179.42  30.0  3
 2S8  Var_04    CAP   CAN  CAL  CAM  -177.54  30.0  1
 2S8  Var_05    NAR   CAP  CAN  CAL   179.39  30.0  1
 2S8  Var_06    CAV   NAR  CAP  CAN  -173.83  30.0  3
 2S8  Var_07    OAE   CAV  NAR  CAP     0.82  30.0  2
 2S8  Var_08    CAB   CBA  OAT  CAV  -179.60  30.0  3
 2S8  Var_09    HAB   CAB  CBA  OAT    60.03  30.0  3
 2S8  Var_10    HAC   CAC  CBA  OAT    52.58  30.0  3
 2S8  Var_11    HAA   CAA  CBA  OAT    69.68  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
 2S8  chir_01  CAZ  CAU  CAQ  CAW  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
 2S8  plan-1  CAZ   0.020
 2S8  plan-1  CAW   0.020
 2S8  plan-1  CAK   0.020
 2S8  plan-1  NAS   0.020
 2S8  plan-1  CAX   0.020
 2S8  plan-1  CAI   0.020
 2S8  plan-1  CAG   0.020
 2S8  plan-1  CAH   0.020
 2S8  plan-1  CAJ   0.020
 2S8  plan-1  CAY   0.020
 2S8  plan-1  HAK   0.020
 2S8  plan-1  HAI   0.020
 2S8  plan-1  HAG   0.020
 2S8  plan-1  HAH   0.020
 2S8  plan-1  HAJ   0.020
 2S8  plan-1  HNAS  0.020
 2S8  plan-2  OAD   0.020
 2S8  plan-2  CAU   0.020
 2S8  plan-2  OAF   0.020
 2S8  plan-2  CAZ   0.020
 2S8  plan-3  NAR   0.020
 2S8  plan-3  CAV   0.020
 2S8  plan-3  OAE   0.020
 2S8  plan-3  OAT   0.020

