# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:55:54 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(O)(CCCCCCC(=O)Nc1ccccc1)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
 6DK  6DK  9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide  ligand  42  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6DK
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
 6DK  N    N  NH1   0  -0.749  -21.1202  4.0327  -1.4034
 6DK  C1   C  CT    0   0.275  -19.7870  6.1714   8.2553
 6DK  O1   O  OH1   0  -0.663  -18.8259  7.1101   7.8971
 6DK  C2   C  CH2   0  -0.467  -19.8278  5.1104   7.1583
 6DK  O2   O  OH1   0  -0.663  -21.0664  6.6991   8.3848
 6DK  C3   C  CH2   0  -0.425  -20.2548  5.6509   5.7975
 6DK  C4   C  CH2   0  -0.417  -20.2364  4.5611   4.7321
 6DK  C5   C  CH2   0  -0.416  -20.6886  5.0664   3.3687
 6DK  C6   C  CH2   0  -0.412  -20.6663  3.9866   2.2941
 6DK  C7   C  CH2   0  -0.595  -21.1276  4.5240   0.9485
 6DK  C8   C  C     0   0.558  -21.1347  3.4894  -0.1567
 6DK  C9   C  CR6   0   0.371  -21.1832  3.4105  -2.6532
 6DK  C10  C  CR16  0  -0.319  -21.3450  2.0373  -2.8471
 6DK  C11  C  CR16  0  -0.244  -21.4028  1.5283  -4.1387
 6DK  C12  C  CR16  0  -0.274  -21.3029  2.3555  -5.2472
 6DK  C13  C  CR16  0  -0.244  -21.1418  3.7216  -5.0520
 6DK  C14  C  CR16  0  -0.350  -21.0828  4.2438  -3.7719
 6DK  F2   F  F     0  -0.305  -20.2430  4.6036  10.0047
 6DK  C    C  CT    0   0.993  -19.3782  5.5390   9.6063
 6DK  F    F  F     0  -0.305  -18.1706  4.9726   9.5518
 6DK  F1   F  F     0  -0.318  -19.3317  6.4690  10.5760
 6DK  O    O  O     0  -0.469  -21.1723  2.2917   0.0598
 6DK  H1   H  HNH1  0   0.414  -21.0649  5.0395  -1.4406
 6DK  H2   H  HOH1  0   0.460  -18.7610  7.8241   8.5436
 6DK  H3   H  HCH2  0   0.251  -20.5118  4.3122   7.4564
 6DK  H4   H  HCH2  0   0.250  -18.8381  4.6555   7.0724
 6DK  H5   H  HOH1  0   0.460  -21.0949  7.4141   9.0327
 6DK  H6   H  HCH2  0   0.225  -19.5935  6.4643   5.4887
 6DK  H7   H  HCH2  0   0.225  -21.2603  6.0732   5.8612
 6DK  H8   H  HCH2  0   0.213  -20.8801  3.7317   5.0444
 6DK  H9   H  HCH2  0   0.213  -19.2257  4.1468   4.6507
 6DK  H10  H  HCH2  0   0.213  -20.0506  5.9019   3.0608
 6DK  H11  H  HCH2  0   0.213  -21.7018  5.4745   3.4516
 6DK  H12  H  HCH2  0   0.225  -21.3041  3.1548   2.6021
 6DK  H13  H  HCH2  0   0.224  -19.6536  3.5836   2.2029
 6DK  H14  H  HCH2  0   0.259  -20.5095  5.3764   0.6522
 6DK  H15  H  HCH2  0   0.277  -22.1481  4.9152   1.0337
 6DK  H16  H  HCR6  0   0.278  -21.4263  1.3650  -2.0096
 6DK  H17  H  HCR6  0   0.257  -21.5283  0.4613  -4.2711
 6DK  H18  H  HCR6  0   0.254  -21.3500  1.9448  -6.2470
 6DK  H19  H  HCR6  0   0.259  -21.0601  4.3896  -5.8995
 6DK  H20  H  HCR6  0   0.268  -20.9592  5.3121  -3.6356

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
 6DK  C12  C13  aromatic  1.389  0.020  1.389
 6DK  C12  C11  aromatic  1.387  0.020  1.387
 6DK  C13  C14  aromatic  1.384  0.020  1.384
 6DK  C11  C10  aromatic  1.389  0.020  1.389
 6DK  C14  C9   aromatic  1.399  0.020  1.399
 6DK  C10  C9   aromatic  1.396  0.020  1.396
 6DK  C9   N    single    1.398  0.020  1.398
 6DK  N    C8   single    1.360  0.020  1.360
 6DK  C8   O    double    1.218  0.020  1.218
 6DK  C8   C7   single    1.514  0.020  1.514
 6DK  C7   C6   single    1.521  0.020  1.521
 6DK  C6   C5   single    1.524  0.020  1.524
 6DK  C5   C4   single    1.523  0.020  1.523
 6DK  C4   C3   single    1.524  0.020  1.524
 6DK  C3   C2   single    1.525  0.020  1.525
 6DK  C2   C1   single    1.527  0.020  1.527
 6DK  O1   C1   single    1.390  0.020  1.390
 6DK  C1   O2   single    1.390  0.020  1.390
 6DK  C1   C    single    1.547  0.020  1.547
 6DK  F    C    single    1.335  0.020  1.335
 6DK  C    F2   single    1.335  0.020  1.335
 6DK  C    F1   single    1.344  0.020  1.344
 6DK  N    H1   single    0.860  0.020  1.020
 6DK  O1   H2   single    0.850  0.020  0.980
 6DK  C2   H3   single    0.970  0.020  1.090
 6DK  C2   H4   single    0.970  0.020  1.090
 6DK  O2   H5   single    0.850  0.020  0.980
 6DK  C3   H6   single    0.970  0.020  1.090
 6DK  C3   H7   single    0.970  0.020  1.090
 6DK  C4   H8   single    0.970  0.020  1.090
 6DK  C4   H9   single    0.970  0.020  1.090
 6DK  C5   H10  single    0.970  0.020  1.090
 6DK  C5   H11  single    0.970  0.020  1.090
 6DK  C6   H12  single    0.970  0.020  1.090
 6DK  C6   H13  single    0.970  0.020  1.090
 6DK  C7   H14  single    0.970  0.020  1.090
 6DK  C7   H15  single    0.970  0.020  1.090
 6DK  C10  H16  single    0.930  0.020  1.080
 6DK  C11  H17  single    0.930  0.020  1.080
 6DK  C12  H18  single    0.930  0.020  1.080
 6DK  C13  H19  single    0.930  0.020  1.080
 6DK  C14  H20  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
 6DK  H1   N    C9   114.44  3.000
 6DK  H1   N    C8   115.66  3.000
 6DK  C9   N    C8   129.90  3.000
 6DK  C    C1   O2   108.49  3.000
 6DK  C    C1   C2   110.52  3.000
 6DK  O2   C1   C2   107.83  3.000
 6DK  C    C1   O1   108.56  3.000
 6DK  O2   C1   O1   113.82  3.000
 6DK  C2   C1   O1   107.62  3.000
 6DK  H2   O1   C1   111.92  3.000
 6DK  H4   C2   H3   106.52  3.000
 6DK  H4   C2   C3   109.32  3.000
 6DK  H3   C2   C3   109.09  3.000
 6DK  H4   C2   C1   108.76  3.000
 6DK  H3   C2   C1   109.18  3.000
 6DK  C3   C2   C1   113.72  3.000
 6DK  H5   O2   C1   111.77  3.000
 6DK  H7   C3   H6   106.60  3.000
 6DK  H7   C3   C4   109.16  3.000
 6DK  H6   C3   C4   109.11  3.000
 6DK  H7   C3   C2   110.04  3.000
 6DK  H6   C3   C2   110.27  3.000
 6DK  C4   C3   C2   111.52  3.000
 6DK  H9   C4   H8   106.09  3.000
 6DK  H9   C4   C5   109.45  3.000
 6DK  H8   C4   C5   109.39  3.000
 6DK  H9   C4   C3   109.48  3.000
 6DK  H8   C4   C3   109.57  3.000
 6DK  C5   C4   C3   112.64  3.000
 6DK  H11  C5   H10  106.01  3.000
 6DK  H11  C5   C6   109.32  3.000
 6DK  H10  C5   C6   109.50  3.000
 6DK  H11  C5   C4   109.31  3.000
 6DK  H10  C5   C4   109.38  3.000
 6DK  C6   C5   C4   113.08  3.000
 6DK  H13  C6   H12  106.47  3.000
 6DK  H13  C6   C7   109.72  3.000
 6DK  H12  C6   C7   109.97  3.000
 6DK  H13  C6   C5   109.48  3.000
 6DK  H12  C6   C5   109.40  3.000
 6DK  C7   C6   C5   111.67  3.000
 6DK  H15  C7   H14  105.60  3.000
 6DK  H15  C7   C8   107.23  3.000
 6DK  H14  C7   C8   109.72  3.000
 6DK  H15  C7   C6   109.87  3.000
 6DK  H14  C7   C6   110.10  3.000
 6DK  C8   C7   C6   113.95  3.000
 6DK  O    C8   C7   122.85  3.000
 6DK  C7   C8   N    113.34  3.000
 6DK  O    C8   N    123.80  3.000
 6DK  C14  C9   C10  118.90  3.000
 6DK  C10  C9   N    124.56  3.000
 6DK  C14  C9   N    116.54  3.000
 6DK  H16  C10  C11  119.41  3.000
 6DK  H16  C10  C9   120.97  3.000
 6DK  C11  C10  C9   119.61  3.000
 6DK  H17  C11  C12  119.91  3.000
 6DK  H17  C11  C10  118.65  3.000
 6DK  C12  C11  C10  121.44  3.000
 6DK  H18  C12  C13  120.54  3.000
 6DK  H18  C12  C11  120.60  3.000
 6DK  C13  C12  C11  118.86  3.000
 6DK  H19  C13  C14  119.23  3.000
 6DK  H19  C13  C12  120.38  3.000
 6DK  C14  C13  C12  120.40  3.000
 6DK  H20  C14  C13  119.54  3.000
 6DK  H20  C14  C9   119.66  3.000
 6DK  C13  C14  C9   120.80  3.000
 6DK  F1   C    F    106.96  3.000
 6DK  F1   C    F2   106.97  3.000
 6DK  F    C    F2   107.51  3.000
 6DK  F1   C    C1   110.88  3.000
 6DK  F2   C    C1   112.09  3.000
 6DK  F    C    C1   112.14  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
 6DK  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 6DK  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 6DK  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 6DK  CONST_04  C13  C14  C9   C10     0.00   0.0  0
 6DK  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 6DK  CONST_06  C14  C9   C10  C11     0.00   0.0  0
 6DK  CONST_07  C13  C14  C9   N     180.00   0.0  0
 6DK  CONST_08  C11  C10  C9   N     180.00   0.0  0
 6DK  CONST_09  H19  C13  C14  C9    180.00   0.0  0
 6DK  CONST_10  H17  C11  C10  C9    180.00   0.0  0
 6DK  CONST_11  H18  C12  C11  C10   180.00   0.0  0
 6DK  CONST_12  H20  C14  C9   C10   180.00   0.0  0
 6DK  CONST_13  H16  C10  C11  C12   180.00   0.0  0
 6DK  CONST_14  C14  C9   N    C8    180.00   0.0  0
 6DK  CONST_15  C10  C9   N    C8      0.00   0.0  0
 6DK  CONST_16  H1   N    C9   C10   180.00   0.0  0
 6DK  CONST_17  C9   N    C8   C7    180.00   0.0  0
 6DK  CONST_18  O    C8   N    C9      0.00   0.0  0
 6DK  Var_01    C6   C7   C8   N    -159.96  30.0  3
 6DK  Var_02    C4   C3   C2   C1    178.22  30.0  2
 6DK  Var_03    C3   C2   C1   O1    -62.91  30.0  1
 6DK  Var_04    F    C    C1   O1    -57.69  30.0  3
 6DK  Var_05    C5   C4   C3   C2    178.72  30.0  1
 6DK  Var_06    C6   C5   C4   C3    179.67  30.0  1
 6DK  Var_07    C7   C6   C5   C4    179.81  30.0  1
 6DK  Var_08    C8   C7   C6   C5   -179.59  30.0  1

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
 6DK  plan-1  N    0.020
 6DK  plan-1  C9   0.020
 6DK  plan-1  C10  0.020
 6DK  plan-1  C11  0.020
 6DK  plan-1  C12  0.020
 6DK  plan-1  C13  0.020
 6DK  plan-1  C14  0.020
 6DK  plan-1  H16  0.020
 6DK  plan-1  H17  0.020
 6DK  plan-1  H18  0.020
 6DK  plan-1  H19  0.020
 6DK  plan-1  H20  0.020
 6DK  plan-2  N    0.020
 6DK  plan-2  C7   0.020
 6DK  plan-2  C8   0.020
 6DK  plan-2  C9   0.020
 6DK  plan-2  O    0.020
 6DK  plan-2  H1   0.020

