# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:16:33 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,6-undecakis(fluoranyl)hexanoylamino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F
#
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
 W06  W06  '(2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,6-undecakis(fluoranyl)hexanoylamino]propanoic acid'  ligand  43  33  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W06
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
 W06  FAW  F  F      0  -0.290  -6.0832   0.3355  -0.5635
 W06  CAV  C  CT     0   0.975  -5.0377   0.4191   0.2487
 W06  FAX  F  F      0  -0.288  -5.0253   1.6264   0.7985
 W06  FAY  F  F      0  -0.286  -5.1763  -0.4895   1.2025
 W06  CAU  C  CT     0   0.528  -3.7458   0.1712  -0.5746
 W06  FAZ  F  F      0  -0.314  -3.7774  -1.1045  -0.9920
 W06  FBA  F  F      0  -0.312  -3.7906   0.9780  -1.6443
 W06  CAT  C  CT     0   0.592  -2.4180   0.4377   0.1905
 W06  FBB  F  F      0  -0.312  -2.2753   1.7676   0.3070
 W06  FBC  F  F      0  -0.310  -2.5153  -0.0890   1.4215
 W06  CAS  C  CT     0   0.605  -1.1528  -0.1564  -0.4949
 W06  FBD  F  F      0  -0.316  -1.1427  -1.4828  -0.2659
 W06  FBE  F  F      0  -0.312  -1.2398   0.0430  -1.8198
 W06  CAR  C  CT     0   0.640   0.2026   0.4138  -0.0023
 W06  FBF  F  F      0  -0.313   0.3611   1.6507  -0.4974
 W06  FBG  F  F      0  -0.324   0.1611   0.5049   1.3455
 W06  CAP  C  C      0   0.437   1.3752  -0.4681  -0.4890
 W06  OAQ  O  O      0  -0.463   1.6725  -0.4002  -1.6666
 W06  N    N  NH1    0  -0.616   1.9221  -1.2371   0.4393
 W06  CA   C  CH1    0  -0.209   3.0275  -2.1402   0.2058
 W06  C    C  C      0   0.425   2.8874  -3.3727   1.1302
 W06  O    O  O      0  -0.592   2.0624  -3.2885   2.0599
 W06  OXT  O  OC    -1  -0.600   3.6532  -4.3172   0.8760
 W06  CB   C  CH2    0  -0.534   4.3828  -1.4548   0.4778
 W06  CG   C  CR5    0   0.025   4.5421  -0.1517  -0.2281
 W06  CD2  C  CR5    0   0.017   4.0693   1.1261   0.2163
 W06  CE3  C  C1     0  -0.366   3.4320   1.5720   1.3802
 W06  CZ3  C  C1     0  -0.264   3.1003   2.9072   1.4935
 W06  CH2  C  C1     0  -0.283   3.3924   3.8154   0.4623
 W06  CZ2  C  C1     0  -0.310   4.0247   3.4067  -0.6961
 W06  CE2  C  CR5    0   0.357   4.3548   2.0566  -0.8073
 W06  NE1  N  NR15   0  -0.689   4.9737   1.3742  -1.8125
 W06  CD1  C  CR15   0  -0.076   5.0856   0.0572  -1.4629
 W06  H1   H  HNH1   0   0.396   1.5299  -1.2949   1.3693
 W06  H2   H  HCH1   0   0.253   3.0005  -2.4576  -0.8385
 W06  H4   H  HCH2   0   0.234   4.4918  -1.3051   1.5570
 W06  H5   H  HCH2   0   0.251   5.1684  -2.1518   0.1821
 W06  H6   H  H      0   0.234   3.2071   0.8811   2.1837
 W06  H7   H  H      0   0.239   2.6076   3.2647   2.3886
 W06  H8   H  H      0   0.243   3.1190   4.8565   0.5788
 W06  H9   H  H      0   0.253   4.2510   4.1101  -1.4879
 W06  H10  H  HNR5   0   0.404   5.3172   1.7739  -2.6689
 W06  H11  H  HCR5   0   0.275   5.5463  -0.6493  -2.1361

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
 W06  FAY  CAV  single    1.325  0.020  1.325
 W06  FAW  CAV  single    1.327  0.020  1.327
 W06  CAV  FAX  single    1.327  0.020  1.327
 W06  CAV  CAU  single    1.552  0.020  1.552
 W06  FAZ  CAU  single    1.343  0.020  1.343
 W06  CAU  FBA  single    1.341  0.020  1.341
 W06  CAU  CAT  single    1.555  0.020  1.555
 W06  FBB  CAT  single    1.343  0.020  1.343
 W06  CAT  FBC  single    1.342  0.020  1.342
 W06  CAT  CAS  single    1.557  0.020  1.557
 W06  FBG  CAR  single    1.351  0.020  1.351
 W06  FBE  CAS  single    1.343  0.020  1.343
 W06  CAS  CAR  single    1.551  0.020  1.551
 W06  CAS  FBD  single    1.346  0.020  1.346
 W06  OAQ  CAP  double    1.216  0.020  1.216
 W06  CAR  CAP  single    1.546  0.020  1.546
 W06  CAR  FBF  single    1.342  0.020  1.342
 W06  CAP  N    single    1.324  0.020  1.324
 W06  N    CA   single    1.446  0.020  1.446
 W06  CA   C    single    1.547  0.020  1.547
 W06  CA   CB   single    1.543  0.020  1.543
 W06  O    C    deloc     1.246  0.020  1.246
 W06  C    OXT  deloc     1.242  0.020  1.242
 W06  CB   CG   single    1.491  0.020  1.491
 W06  CG   CD1  aromatic  1.365  0.020  1.365
 W06  CG   CD2  aromatic  1.433  0.020  1.433
 W06  CD1  NE1  aromatic  1.367  0.020  1.367
 W06  CE3  CD2  aromatic  1.400  0.020  1.400
 W06  CE3  CZ3  aromatic  1.380  0.020  1.380
 W06  CD2  CE2  aromatic  1.412  0.020  1.412
 W06  NE1  CE2  aromatic  1.363  0.020  1.363
 W06  CZ3  CH2  aromatic  1.405  0.020  1.405
 W06  CE2  CZ2  aromatic  1.394  0.020  1.394
 W06  CH2  CZ2  aromatic  1.382  0.020  1.382
 W06  N    H1   single    0.860  0.020  1.020
 W06  CA   H2   single    0.970  0.020  1.090
 W06  CB   H4   single    0.970  0.020  1.090
 W06  CB   H5   single    0.970  0.020  1.090
 W06  CE3  H6   single    0.930  0.020  1.080
 W06  CZ3  H7   single    0.930  0.020  1.080
 W06  CH2  H8   single    0.930  0.020  1.080
 W06  CZ2  H9   single    0.930  0.020  1.080
 W06  NE1  H10  single    0.860  0.020  1.020
 W06  CD1  H11  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
 W06  CAU  CAV  FAY  111.08  3.000
 W06  CAU  CAV  FAX  110.94  3.000
 W06  FAY  CAV  FAX  109.08  3.000
 W06  CAU  CAV  FAW  108.73  3.000
 W06  FAX  CAV  FAW  108.57  3.000
 W06  FAY  CAV  FAW  108.37  3.000
 W06  CAT  CAU  FBA  108.54  3.000
 W06  CAT  CAU  FAZ  109.62  3.000
 W06  FBA  CAU  FAZ  108.85  3.000
 W06  CAT  CAU  CAV  114.98  3.000
 W06  FBA  CAU  CAV  107.42  3.000
 W06  FAZ  CAU  CAV  107.28  3.000
 W06  CAS  CAT  FBC  108.24  3.000
 W06  CAS  CAT  FBB  109.26  3.000
 W06  FBC  CAT  FBB  108.46  3.000
 W06  CAS  CAT  CAU  114.32  3.000
 W06  FBC  CAT  CAU  108.78  3.000
 W06  FBB  CAT  CAU  107.64  3.000
 W06  CAR  CAS  FBE  108.39  3.000
 W06  CAR  CAS  FBD  107.56  3.000
 W06  FBE  CAS  FBD  108.34  3.000
 W06  FBD  CAS  CAT  107.89  3.000
 W06  CAR  CAS  CAT  115.48  3.000
 W06  FBE  CAS  CAT  108.97  3.000
 W06  CAP  CAR  FBG  112.07  3.000
 W06  CAP  CAR  FBF  108.67  3.000
 W06  FBG  CAR  FBF  108.03  3.000
 W06  FBF  CAR  CAS  108.96  3.000
 W06  CAP  CAR  CAS  110.68  3.000
 W06  FBG  CAR  CAS  108.34  3.000
 W06  N    CAP  OAQ  127.61  3.000
 W06  N    CAP  CAR  115.09  3.000
 W06  OAQ  CAP  CAR  117.28  3.000
 W06  H1   N    CA   114.17  3.000
 W06  H1   N    CAP  121.20  3.000
 W06  CA   N    CAP  124.42  3.000
 W06  H2   CA   CB   108.63  3.000
 W06  H2   CA   C    109.74  3.000
 W06  CB   CA   C    109.15  3.000
 W06  H2   CA   N    108.49  3.000
 W06  CB   CA   N    111.44  3.000
 W06  C    CA   N    109.38  3.000
 W06  OXT  C    O    127.76  3.000
 W06  OXT  C    CA   115.32  3.000
 W06  O    C    CA   116.87  3.000
 W06  H5   CB   H4   106.43  3.000
 W06  H5   CB   CG   110.68  3.000
 W06  H4   CB   CG   109.67  3.000
 W06  H5   CB   CA   107.51  3.000
 W06  H4   CB   CA   108.78  3.000
 W06  CG   CB   CA   113.50  3.000
 W06  CD1  CG   CD2  105.98  3.000
 W06  CD2  CG   CB   126.68  3.000
 W06  CD1  CG   CB   127.21  3.000
 W06  CE2  CD2  CE3  118.99  3.000
 W06  CE2  CD2  CG   107.21  3.000
 W06  CE3  CD2  CG   133.79  3.000
 W06  H6   CE3  CZ3  120.40  3.000
 W06  H6   CE3  CD2  120.54  3.000
 W06  CZ3  CE3  CD2  119.06  3.000
 W06  H7   CZ3  CH2  119.22  3.000
 W06  H7   CZ3  CE3  119.78  3.000
 W06  CH2  CZ3  CE3  121.00  3.000
 W06  H8   CH2  CZ2  119.36  3.000
 W06  H8   CH2  CZ3  119.35  3.000
 W06  CZ2  CH2  CZ3  121.29  3.000
 W06  H9   CZ2  CE2  121.41  3.000
 W06  H9   CZ2  CH2  121.10  3.000
 W06  CE2  CZ2  CH2  117.50  3.000
 W06  NE1  CE2  CZ2  130.61  3.000
 W06  CZ2  CE2  CD2  122.16  3.000
 W06  NE1  CE2  CD2  107.24  3.000
 W06  H10  NE1  CD1  124.93  3.000
 W06  H10  NE1  CE2  125.74  3.000
 W06  CD1  NE1  CE2  109.31  3.000
 W06  H11  CD1  NE1  120.41  3.000
 W06  H11  CD1  CG   129.34  3.000
 W06  NE1  CD1  CG   110.25  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
 W06  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 W06  CONST_02  CZ3  CE3  CD2  CG   180.00   0.0  0
 W06  CONST_03  NE1  CE2  CD2  CG     0.00   0.0  0
 W06  CONST_04  CZ2  CE2  CD2  CG   180.00   0.0  0
 W06  CONST_05  NE1  CD1  CG   CD2    0.00   0.0  0
 W06  CONST_06  CH2  CZ3  CE3  CD2    0.00   0.0  0
 W06  CONST_07  CD1  NE1  CE2  CD2    0.00   0.0  0
 W06  CONST_08  CH2  CZ2  CE2  CD2    0.00   0.0  0
 W06  CONST_09  CD1  CG   CD2  CE3  180.00   0.0  0
 W06  CONST_10  NE1  CE2  CD2  CE3  180.00   0.0  0
 W06  CONST_11  CZ2  CE2  CD2  CE3    0.00   0.0  0
 W06  CONST_12  CZ2  CH2  CZ3  CE3    0.00   0.0  0
 W06  CONST_13  CE2  CD2  CE3  CZ3    0.00   0.0  0
 W06  CONST_14  CE2  CZ2  CH2  CZ3    0.00   0.0  0
 W06  CONST_15  NE1  CE2  CZ2  CH2  180.00   0.0  0
 W06  CONST_16  CD1  NE1  CE2  CZ2  180.00   0.0  0
 W06  CONST_17  CD1  CG   CD2  CE2    0.00   0.0  0
 W06  CONST_18  NE1  CD1  CG   CB   180.00   0.0  0
 W06  CONST_19  CE3  CD2  CG   CB     0.00   0.0  0
 W06  CONST_20  CE2  CD2  CG   CB   180.00   0.0  0
 W06  CONST_21  H10  NE1  CD1  CG   180.00   0.0  0
 W06  CONST_22  H6   CE3  CD2  CG     0.00   0.0  0
 W06  CONST_23  H11  CD1  CG   CD2  180.00   0.0  0
 W06  CONST_24  H7   CZ3  CE3  CD2  180.00   0.0  0
 W06  CONST_25  H9   CZ2  CE2  CD2  180.00   0.0  0
 W06  CONST_26  H8   CH2  CZ3  CE3  180.00   0.0  0
 W06  CONST_27  CA   N    CAP  CAR  180.00   0.0  0
 W06  CONST_28  CA   N    CAP  OAQ    0.00   0.0  0
 W06  CONST_29  H1   N    CAP  CAR    0.00   0.0  0
 W06  Var_01    CD1  CG   CB   CA   -91.34  30.0  2
 W06  Var_02    FAZ  CAU  CAV  FAW  -66.25  30.0  3
 W06  Var_03    FBB  CAT  CAU  CAV  -73.61  30.0  3
 W06  Var_04    FBE  CAS  CAT  CAU   41.12  30.0  3
 W06  Var_05    FBG  CAR  CAS  CAT   43.15  30.0  3
 W06  Var_06    OAQ  CAP  CAR  CAS   73.57  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
 W06  chir_01  CA  N  C  CB  positiv

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
 W06  plan-1  CB   0.020
 W06  plan-1  CG   0.020
 W06  plan-1  CD2  0.020
 W06  plan-1  CE3  0.020
 W06  plan-1  CZ3  0.020
 W06  plan-1  CH2  0.020
 W06  plan-1  CZ2  0.020
 W06  plan-1  CE2  0.020
 W06  plan-1  NE1  0.020
 W06  plan-1  CD1  0.020
 W06  plan-1  H6   0.020
 W06  plan-1  H7   0.020
 W06  plan-1  H8   0.020
 W06  plan-1  H9   0.020
 W06  plan-1  H10  0.020
 W06  plan-1  H11  0.020
 W06  plan-2  CAR  0.020
 W06  plan-2  CAP  0.020
 W06  plan-2  OAQ  0.020
 W06  plan-2  N    0.020
 W06  plan-2  CA   0.020
 W06  plan-2  H1   0.020
 W06  plan-3  CA   0.020
 W06  plan-3  C    0.020
 W06  plan-3  O    0.020
 W06  plan-3  OXT  0.020

