# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:23:08 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2S)-2-(1H-indol-3-yl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 2S3  2S3  '(2S)-2-(1H-indol-3-yl)pentanoic acid'  ligand  30  16  .  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_2S3
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
 2S3  OAC   O  OC    -1  -0.613   1.7614   1.8305  -1.7708
 2S3  CAM   C  C      0   0.414   1.8557   1.3710  -0.6155
 2S3  OAB   O  O      0  -0.612   2.4006   1.9267   0.3599
 2S3  CAQ   C  CH1    0  -0.430   1.2027  -0.0065  -0.3486
 2S3  CAK   C  CH2    0  -0.384   2.1197  -0.9347   0.4506
 2S3  CAJ   C  CH2    0  -0.429   3.4218  -1.2733  -0.2656
 2S3  CAI   C  CH3    0  -0.663   4.2897  -2.2403   0.5282
 2S3  CAN   C  CR5    0   0.043  -0.1108   0.1977   0.3462
 2S3  CAP   C  CR5    0   0.003  -1.4053  -0.1974  -0.1251
 2S3  CAG   C  C1     0  -0.378  -1.8589  -0.8402  -1.2835
 2S3  CAE   C  C1     0  -0.271  -3.2115  -1.0742  -1.4369
 2S3  CAD   C  C1     0  -0.288  -4.1313  -0.6793  -0.4501
 2S3  CAF   C  C1     0  -0.307  -3.7154  -0.0448   0.7048
 2S3  CAO   C  CR5    0   0.351  -2.3490   0.1903   0.8551
 2S3  NL    N  NR15   0  -0.689  -1.6570   0.7856   1.8657
 2S3  CAH   C  CR15   0  -0.087  -0.3220   0.7940   1.5589
 2S3  HAQ   H  HCH1   0   0.204   1.0001  -0.4805  -1.3150
 2S3  HAK   H  HCH2   0   0.206   2.3438  -0.4711   1.4155
 2S3  HAKA  H  HCH2   0   0.206   1.5822  -1.8630   0.6733
 2S3  HAJ   H  HCH2   0   0.206   3.1961  -1.7041  -1.2465
 2S3  HAJA  H  HCH2   0   0.214   3.9842  -0.3551  -0.4562
 2S3  HAI   H  HCH3   0   0.215   4.5560  -1.8211   1.5002
 2S3  HAIA  H  HCH3   0   0.214   3.7678  -3.1818   0.7100
 2S3  HAIB  H  HCH3   0   0.224   5.2178  -2.4734   0.0047
 2S3  HAG   H  H      0   0.237  -1.1594  -1.1471  -2.0522
 2S3  HAE   H  H      0   0.242  -3.5741  -1.5652  -2.3308
 2S3  HAD   H  H      0   0.245  -5.1854  -0.8757  -0.5985
 2S3  HAF   H  H      0   0.254  -4.4261   0.2577   1.4639
 2S3  HNL   H  HNR5   0   0.404  -2.0577   1.1790   2.6998
 2S3  HAH   H  HCR5   0   0.270   0.3907   1.2349   2.2369

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
 2S3  OAC  CAM   deloc     1.247  0.020  1.247
 2S3  CAM  OAB   deloc     1.248  0.020  1.248
 2S3  CAM  CAQ   single    1.548  0.020  1.548
 2S3  CAQ  CAK   single    1.530  0.020  1.530
 2S3  CAQ  CAN   single    1.500  0.020  1.500
 2S3  CAQ  HAQ   single    0.970  0.020  1.090
 2S3  CAK  CAJ   single    1.524  0.020  1.524
 2S3  CAK  HAK   single    0.970  0.020  1.090
 2S3  CAK  HAKA  single    0.970  0.020  1.090
 2S3  CAJ  CAI   single    1.523  0.020  1.523
 2S3  CAJ  HAJ   single    0.970  0.020  1.090
 2S3  CAJ  HAJA  single    0.970  0.020  1.090
 2S3  CAI  HAI   single    0.970  0.020  1.090
 2S3  CAI  HAIA  single    0.970  0.020  1.090
 2S3  CAI  HAIB  single    0.970  0.020  1.090
 2S3  CAN  CAP   aromatic  1.433  0.020  1.433
 2S3  CAN  CAH   aromatic  1.368  0.020  1.368
 2S3  CAP  CAG   aromatic  1.400  0.020  1.400
 2S3  CAP  CAO   aromatic  1.415  0.020  1.415
 2S3  CAG  CAE   aromatic  1.381  0.020  1.381
 2S3  CAG  HAG   single    0.930  0.020  1.080
 2S3  CAE  CAD   aromatic  1.406  0.020  1.406
 2S3  CAE  HAE   single    0.930  0.020  1.080
 2S3  CAD  CAF   aromatic  1.382  0.020  1.382
 2S3  CAD  HAD   single    0.930  0.020  1.080
 2S3  CAF  CAO   aromatic  1.395  0.020  1.395
 2S3  CAF  HAF   single    0.930  0.020  1.080
 2S3  CAO  NL    aromatic  1.362  0.020  1.362
 2S3  NL   CAH   aromatic  1.370  0.020  1.370
 2S3  NL   HNL   single    0.860  0.020  1.020
 2S3  CAH  HAH   single    0.930  0.020  1.080

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
 2S3  CAQ   CAM  OAB   116.47  3.000
 2S3  CAQ   CAM  OAC   117.12  3.000
 2S3  OAB   CAM  OAC   126.38  3.000
 2S3  HAQ   CAQ  CAN   107.80  3.000
 2S3  HAQ   CAQ  CAK   108.01  3.000
 2S3  CAN   CAQ  CAK   111.44  3.000
 2S3  HAQ   CAQ  CAM   108.12  3.000
 2S3  CAN   CAQ  CAM   109.17  3.000
 2S3  CAK   CAQ  CAM   112.15  3.000
 2S3  HAKA  CAK  HAK   106.29  3.000
 2S3  HAKA  CAK  CAJ   109.05  3.000
 2S3  HAK   CAK  CAJ   109.50  3.000
 2S3  HAKA  CAK  CAQ   109.03  3.000
 2S3  HAK   CAK  CAQ   109.05  3.000
 2S3  CAJ   CAK  CAQ   113.67  3.000
 2S3  HAJA  CAJ  HAJ   106.27  3.000
 2S3  HAJA  CAJ  CAI   109.33  3.000
 2S3  HAJ   CAJ  CAI   109.56  3.000
 2S3  HAJA  CAJ  CAK   109.55  3.000
 2S3  HAJ   CAJ  CAK   109.41  3.000
 2S3  CAI   CAJ  CAK   112.53  3.000
 2S3  HAIB  CAI  HAIA  107.60  3.000
 2S3  HAIB  CAI  HAI   107.57  3.000
 2S3  HAIA  CAI  HAI   107.44  3.000
 2S3  HAIB  CAI  CAJ   111.75  3.000
 2S3  HAIA  CAI  CAJ   111.22  3.000
 2S3  HAI   CAI  CAJ   111.06  3.000
 2S3  CAH   CAN  CAP   105.80  3.000
 2S3  CAH   CAN  CAQ   127.25  3.000
 2S3  CAP   CAN  CAQ   126.95  3.000
 2S3  CAO   CAP  CAG   118.87  3.000
 2S3  CAO   CAP  CAN   107.41  3.000
 2S3  CAG   CAP  CAN   133.72  3.000
 2S3  HAG   CAG  CAE   120.36  3.000
 2S3  HAG   CAG  CAP   120.51  3.000
 2S3  CAE   CAG  CAP   119.13  3.000
 2S3  HAE   CAE  CAD   119.20  3.000
 2S3  HAE   CAE  CAG   119.78  3.000
 2S3  CAD   CAE  CAG   121.02  3.000
 2S3  HAD   CAD  CAF   119.40  3.000
 2S3  HAD   CAD  CAE   119.34  3.000
 2S3  CAF   CAD  CAE   121.25  3.000
 2S3  HAF   CAF  CAO   121.36  3.000
 2S3  HAF   CAF  CAD   121.10  3.000
 2S3  CAO   CAF  CAD   117.54  3.000
 2S3  NL    CAO  CAF   130.66  3.000
 2S3  NL    CAO  CAP   107.15  3.000
 2S3  CAF   CAO  CAP   122.19  3.000
 2S3  HNL   NL   CAH   124.88  3.000
 2S3  HNL   NL   CAO   125.74  3.000
 2S3  CAH   NL   CAO   109.37  3.000
 2S3  HAH   CAH  NL    120.39  3.000
 2S3  HAH   CAH  CAN   129.34  3.000
 2S3  NL    CAH  CAN   110.27  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
 2S3  CONST_01  CAE  CAG  CAP  CAN   180.00   0.0  0
 2S3  CONST_02  CAF  CAO  CAP  CAN   180.00   0.0  0
 2S3  CONST_03  NL   CAO  CAP  CAN     0.00   0.0  0
 2S3  CONST_04  CAO  NL   CAH  CAN     0.00   0.0  0
 2S3  CONST_05  NL   CAH  CAN  CAP     0.00   0.0  0
 2S3  CONST_06  CAD  CAE  CAG  CAP     0.00   0.0  0
 2S3  CONST_07  CAD  CAF  CAO  CAP     0.00   0.0  0
 2S3  CONST_08  CAH  NL   CAO  CAP     0.00   0.0  0
 2S3  CONST_09  CAH  CAN  CAP  CAG   180.00   0.0  0
 2S3  CONST_10  CAF  CAO  CAP  CAG     0.00   0.0  0
 2S3  CONST_11  NL   CAO  CAP  CAG   180.00   0.0  0
 2S3  CONST_12  CAF  CAD  CAE  CAG     0.00   0.0  0
 2S3  CONST_13  CAO  CAP  CAG  CAE     0.00   0.0  0
 2S3  CONST_14  CAO  CAF  CAD  CAE     0.00   0.0  0
 2S3  CONST_15  NL   CAO  CAF  CAD   180.00   0.0  0
 2S3  CONST_16  CAH  NL   CAO  CAF   180.00   0.0  0
 2S3  CONST_17  CAH  CAN  CAP  CAO     0.00   0.0  0
 2S3  CONST_18  CAG  CAP  CAN  CAQ     0.00   0.0  0
 2S3  CONST_19  CAO  CAP  CAN  CAQ   180.00   0.0  0
 2S3  CONST_20  NL   CAH  CAN  CAQ   180.00   0.0  0
 2S3  CONST_21  HAG  CAG  CAP  CAN     0.00   0.0  0
 2S3  CONST_22  HNL  NL   CAH  CAN   180.00   0.0  0
 2S3  CONST_23  HAH  CAH  CAN  CAP   180.00   0.0  0
 2S3  CONST_24  HAE  CAE  CAG  CAP   180.00   0.0  0
 2S3  CONST_25  HAF  CAF  CAO  CAP   180.00   0.0  0
 2S3  CONST_26  HAD  CAD  CAE  CAG   180.00   0.0  0
 2S3  Var_01    CAI  CAJ  CAK  CAQ  -177.77  30.0  3
 2S3  Var_02    HAI  CAI  CAJ  CAK   -59.84  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
 2S3  chir_01  CAQ  CAM  CAK  CAN  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
 2S3  plan-1  CAQ  0.020
 2S3  plan-1  CAN  0.020
 2S3  plan-1  CAP  0.020
 2S3  plan-1  CAG  0.020
 2S3  plan-1  CAE  0.020
 2S3  plan-1  CAD  0.020
 2S3  plan-1  CAF  0.020
 2S3  plan-1  CAO  0.020
 2S3  plan-1  NL   0.020
 2S3  plan-1  CAH  0.020
 2S3  plan-1  HAG  0.020
 2S3  plan-1  HAE  0.020
 2S3  plan-1  HAD  0.020
 2S3  plan-1  HAF  0.020
 2S3  plan-1  HNL  0.020
 2S3  plan-1  HAH  0.020
 2S3  plan-2  OAC  0.020
 2S3  plan-2  CAM  0.020
 2S3  plan-2  OAB  0.020
 2S3  plan-2  CAQ  0.020

