# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:47:11 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 3-[(1~{R})-2-(~{tert}-butylamino)-1-[methanoyl-[[3,4,5-tris(fluoranyl)phenyl]methyl]amino]-2-oxidanylidene-ethyl]-6-chloranyl-1~{H}-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)[C@H](N(Cc1cc(F)c(F)c(F)c1)C=O)c2c([nH]c3cc(Cl)ccc23)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
 B5K  B5K  '3-[(1~{R})-2-(~{tert}-butylamino)-1-[methanoyl-[[3,4,5-tris(fluoranyl)phenyl]methyl]amino]-2-oxidanylidene-ethyl]-6-chloranyl-1~{H}-indole-2-carboxylic acid'  ligand  55  34  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B5K
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
 B5K  N    N   NR15  0  -0.735   1.4287   2.3017   1.1490
 B5K  C    C   CR16  0  -0.216   4.4057   0.9474  -1.3002
 B5K  O    O   O     0  -0.480   1.1441  -2.3168  -1.9456
 B5K  C1   C   CR6   0  -0.061   4.6829   2.0737  -0.5057
 B5K  C10  C   CH2   0  -0.419  -1.9359  -1.0587  -2.0017
 B5K  C11  C   CR6   0   0.148  -3.0168  -0.5591  -1.0809
 B5K  C12  C   CR16  0  -0.444  -3.4085   0.7751  -1.1384
 B5K  C13  C   CR6   0   0.429  -4.3747   1.2319  -0.2724
 B5K  C14  C   CR6   0   0.257  -4.9665   0.3896   0.6536
 B5K  C15  C   CR6   0   0.429  -4.5738  -0.9323   0.6945
 B5K  C16  C   CR16  0  -0.472  -3.6065  -1.4162  -0.1639
 B5K  C17  C   CT    0   0.094   2.3078  -3.5799   0.4347
 B5K  C18  C   CH3   0  -0.640   1.7139  -4.8424  -0.1899
 B5K  C19  C   CH3   0  -0.681   2.5032  -3.8057   1.9324
 B5K  C2   C   CR16  0  -0.262   3.7592   2.6193   0.3526
 B5K  C20  C   CH3   0  -0.644   3.6545  -3.2385  -0.2038
 B5K  C22  C   C1    0   0.264  -0.1497   0.3773  -2.8085
 B5K  C3   C   CR56  0   0.355   2.5151   1.9880   0.4045
 B5K  C4   C   CR56  0   0.071   2.1974   0.8505  -0.3673
 B5K  C5   C   CR16  0  -0.362   3.1738   0.3400  -1.2380
 B5K  C6   C   CR5   0   0.181   0.4296   1.4020   0.9009
 B5K  C7   C   CR5   0   0.033   0.8537   0.4865  -0.0392
 B5K  C8   C   CH1   0  -0.339   0.0467  -0.6527  -0.5954
 B5K  C9   C   C     0   0.576   0.9218  -1.9045  -0.8188
 B5K  F    F   F     0  -0.299  -5.8952   0.8501   1.4914
 B5K  F1   F   F     0  -0.303  -5.1451  -1.7395   1.5911
 B5K  F2   F   F     0  -0.303  -4.7688   2.5070  -0.3046
 B5K  N1   N   NT    0  -0.395  -0.6910  -0.3388  -1.8046
 B5K  N2   N   NH1   0  -0.634   1.3784  -2.4468   0.3125
 B5K  O1   O   O     0  -0.407  -1.6883   0.6151   1.6193
 B5K  O2   O   OH1   0  -0.600  -0.9580   2.6169   2.2968
 B5K  O3   O   O     0  -0.485  -0.6740   0.5775  -3.8890
 B5K  CL   CL  CL    0  -0.123   6.2532   2.7972  -0.6245
 B5K  H1   H   HNR5  0   0.425   1.3795   3.0583   1.8131
 B5K  H2   H   HCR6  0   0.280   5.1652   0.5597  -1.9645
 B5K  H3   H   HCH2  0   0.277  -1.7751  -2.1280  -1.8443
 B5K  H4   H   HCH2  0   0.293  -2.2372  -0.9349  -3.0406
 B5K  H5   H   HCR6  0   0.287  -2.9631   1.4600  -1.8490
 B5K  H6   H   HCR6  0   0.292  -3.3121  -2.4563  -0.1004
 B5K  H7   H   HCH3  0   0.241   1.5748  -4.7401  -1.2641
 B5K  H8   H   HCH3  0   0.228   2.3852  -5.6851  -0.0172
 B5K  H9   H   HCH3  0   0.229   0.7509  -5.0821   0.2629
 B5K  H10  H   HCH3  0   0.241   1.5633  -4.0691   2.4217
 B5K  H11  H   HCH3  0   0.244   3.2070  -4.6208   2.0984
 B5K  H12  H   HCH3  0   0.239   2.9054  -2.9152   2.4197
 B5K  H13  H   HCR6  0   0.292   3.9783   3.4906   0.9545
 B5K  H14  H   HCH3  0   0.230   4.0893  -2.3509   0.2590
 B5K  H15  H   HCH3  0   0.231   4.3499  -4.0674  -0.0653
 B5K  H16  H   HCH3  0   0.239   3.5638  -3.0558  -1.2733
 B5K  H17  H   H     0   0.218   0.8273   0.8075  -2.5561
 B5K  H18  H   HCR6  0   0.268   2.9813  -0.5172  -1.8676
 B5K  H19  H   HCH1  0   0.315  -0.7031  -0.9042   0.1567
 B5K  H20  H   HNH1  0   0.403   1.1111  -1.9963   1.1748
 B5K  H21  H   HOH1  0   0.496  -1.7850   2.6314   2.8022
 B5K  C21  C   C     0   0.503  -0.8481   1.4790   1.6242

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
 B5K  C18  C17  single    1.529  0.020  1.529
 B5K  O1   C21  double    1.205  0.020  1.205
 B5K  C2   C3   aromatic  1.396  0.020  1.396
 B5K  C2   C1   aromatic  1.374  0.020  1.374
 B5K  CL   C1   single    1.733  0.020  1.733
 B5K  N    C3   aromatic  1.354  0.020  1.354
 B5K  N    C6   aromatic  1.367  0.020  1.367
 B5K  C3   C4   aromatic  1.411  0.020  1.411
 B5K  C1   C    aromatic  1.406  0.020  1.406
 B5K  C21  C6   single    1.470  0.020  1.470
 B5K  C21  O2   single    1.326  0.020  1.326
 B5K  C6   C7   aromatic  1.379  0.020  1.379
 B5K  C17  N2   single    1.471  0.020  1.471
 B5K  C17  C20  single    1.529  0.020  1.529
 B5K  C17  C19  single    1.527  0.020  1.527
 B5K  N2   C9   single    1.335  0.020  1.335
 B5K  C4   C7   aromatic  1.430  0.020  1.430
 B5K  C4   C5   aromatic  1.404  0.020  1.404
 B5K  C    C5   aromatic  1.375  0.020  1.375
 B5K  C7   C8   single    1.503  0.020  1.503
 B5K  C9   C8   single    1.544  0.020  1.544
 B5K  C9   O    double    1.220  0.020  1.220
 B5K  C8   N1   single    1.451  0.020  1.451
 B5K  F1   C15  single    1.335  0.020  1.335
 B5K  F    C14  single    1.333  0.020  1.333
 B5K  C15  C14  aromatic  1.380  0.020  1.380
 B5K  C15  C16  aromatic  1.381  0.020  1.381
 B5K  N1   C22  single    1.347  0.020  1.347
 B5K  N1   C10  single    1.451  0.020  1.451
 B5K  C22  O3   double    1.218  0.020  1.218
 B5K  C14  C13  aromatic  1.385  0.020  1.385
 B5K  C16  C11  aromatic  1.387  0.020  1.387
 B5K  C13  F2   single    1.335  0.020  1.335
 B5K  C13  C12  aromatic  1.376  0.020  1.376
 B5K  C11  C12  aromatic  1.392  0.020  1.392
 B5K  C11  C10  single    1.505  0.020  1.505
 B5K  N    H1   single    0.860  0.020  1.020
 B5K  C    H2   single    0.930  0.020  1.080
 B5K  C10  H3   single    0.970  0.020  1.090
 B5K  C10  H4   single    0.970  0.020  1.090
 B5K  C12  H5   single    0.930  0.020  1.080
 B5K  C16  H6   single    0.930  0.020  1.080
 B5K  C18  H7   single    0.970  0.020  1.090
 B5K  C18  H8   single    0.970  0.020  1.090
 B5K  C18  H9   single    0.970  0.020  1.090
 B5K  C19  H10  single    0.970  0.020  1.090
 B5K  C19  H11  single    0.970  0.020  1.090
 B5K  C19  H12  single    0.970  0.020  1.090
 B5K  C2   H13  single    0.930  0.020  1.080
 B5K  C20  H14  single    0.970  0.020  1.090
 B5K  C20  H15  single    0.970  0.020  1.090
 B5K  C20  H16  single    0.970  0.020  1.090
 B5K  C22  H17  single    0.930  0.020  1.080
 B5K  C5   H18  single    0.930  0.020  1.080
 B5K  C8   H19  single    0.970  0.020  1.090
 B5K  N2   H20  single    0.860  0.020  1.020
 B5K  O2   H21  single    0.850  0.020  0.980

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
 B5K  H1   N    C6   125.30  3.000
 B5K  H1   N    C3   125.13  3.000
 B5K  C6   N    C3   109.52  3.000
 B5K  H2   C    C5   119.93  3.000
 B5K  H2   C    C1   119.74  3.000
 B5K  C5   C    C1   120.33  3.000
 B5K  CL   C1   C2   119.09  3.000
 B5K  CL   C1   C    118.32  3.000
 B5K  C2   C1   C    122.59  3.000
 B5K  H4   C10  H3   106.82  3.000
 B5K  H4   C10  N1   108.09  3.000
 B5K  H3   C10  N1   109.85  3.000
 B5K  H4   C10  C11  110.32  3.000
 B5K  H3   C10  C11  110.02  3.000
 B5K  N1   C10  C11  111.61  3.000
 B5K  C16  C11  C12  120.01  3.000
 B5K  C12  C11  C10  119.67  3.000
 B5K  C16  C11  C10  120.31  3.000
 B5K  H5   C12  C13  119.47  3.000
 B5K  H5   C12  C11  121.18  3.000
 B5K  C13  C12  C11  119.34  3.000
 B5K  F2   C13  C14  118.10  3.000
 B5K  F2   C13  C12  120.62  3.000
 B5K  C14  C13  C12  121.28  3.000
 B5K  F    C14  C15  120.72  3.000
 B5K  C15  C14  C13  118.75  3.000
 B5K  F    C14  C13  120.53  3.000
 B5K  F1   C15  C16  120.36  3.000
 B5K  C16  C15  C14  121.12  3.000
 B5K  F1   C15  C14  118.52  3.000
 B5K  H6   C16  C15  119.38  3.000
 B5K  H6   C16  C11  121.12  3.000
 B5K  C15  C16  C11  119.49  3.000
 B5K  N2   C17  C20  110.48  3.000
 B5K  C20  C17  C19  109.26  3.000
 B5K  N2   C17  C19  106.04  3.000
 B5K  C19  C17  C18  109.17  3.000
 B5K  C20  C17  C18  110.85  3.000
 B5K  N2   C17  C18  110.91  3.000
 B5K  H9   C18  H8   107.92  3.000
 B5K  H9   C18  H7   108.52  3.000
 B5K  H8   C18  H7   107.92  3.000
 B5K  H9   C18  C17  110.78  3.000
 B5K  H8   C18  C17  109.52  3.000
 B5K  H7   C18  C17  112.05  3.000
 B5K  H12  C19  H11  107.71  3.000
 B5K  H12  C19  H10  108.29  3.000
 B5K  H11  C19  H10  107.89  3.000
 B5K  H12  C19  C17  111.36  3.000
 B5K  H11  C19  C17  110.04  3.000
 B5K  H10  C19  C17  111.41  3.000
 B5K  H13  C2   C3   121.61  3.000
 B5K  H13  C2   C1   122.10  3.000
 B5K  C3   C2   C1   116.28  3.000
 B5K  H16  C20  H15  107.78  3.000
 B5K  H16  C20  H14  108.26  3.000
 B5K  H15  C20  H14  108.07  3.000
 B5K  H16  C20  C17  111.98  3.000
 B5K  H15  C20  C17  109.80  3.000
 B5K  H14  C20  C17  110.82  3.000
 B5K  H17  C22  O3   121.55  3.000
 B5K  H17  C22  N1   113.27  3.000
 B5K  O3   C22  N1   125.16  3.000
 B5K  C4   C3   C2   123.02  3.000
 B5K  C4   C3   N    107.88  3.000
 B5K  C2   C3   N    129.11  3.000
 B5K  C7   C4   C5   134.66  3.000
 B5K  C5   C4   C3   118.40  3.000
 B5K  C7   C4   C3   106.93  3.000
 B5K  H18  C5   C4   121.71  3.000
 B5K  H18  C5   C    118.92  3.000
 B5K  C4   C5   C    119.37  3.000
 B5K  C7   C6   C21  129.60  3.000
 B5K  C7   C6   N    109.62  3.000
 B5K  C21  C6   N    120.75  3.000
 B5K  C8   C7   C6   126.18  3.000
 B5K  C8   C7   C4   127.77  3.000
 B5K  C6   C7   C4   106.04  3.000
 B5K  H19  C8   N1   105.96  3.000
 B5K  H19  C8   C9   107.59  3.000
 B5K  N1   C8   C9   110.07  3.000
 B5K  H19  C8   C7   106.77  3.000
 B5K  N1   C8   C7   114.68  3.000
 B5K  C9   C8   C7   111.34  3.000
 B5K  N2   C9   C8   113.62  3.000
 B5K  C8   C9   O    120.72  3.000
 B5K  N2   C9   O    125.66  3.000
 B5K  C8   N1   C22  122.14  3.000
 B5K  C22  N1   C10  120.48  3.000
 B5K  C8   N1   C10  116.23  3.000
 B5K  H20  N2   C9   116.89  3.000
 B5K  H20  N2   C17  116.13  3.000
 B5K  C9   N2   C17  126.84  3.000
 B5K  H21  O2   C21  110.36  3.000
 B5K  O2   C21  O1   124.00  3.000
 B5K  O2   C21  C6   111.50  3.000
 B5K  O1   C21  C6   124.50  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
 B5K  CONST_01  C1   C2   C3   N     180.00   0.0  0
 B5K  CONST_02  C7   C4   C3   N       0.00   0.0  0
 B5K  CONST_03  C5   C4   C3   N     180.00   0.0  0
 B5K  CONST_04  C4   C7   C6   N       0.00   0.0  0
 B5K  CONST_05  C3   C2   C1   C       0.00   0.0  0
 B5K  CONST_06  C3   C4   C5   C       0.00   0.0  0
 B5K  CONST_07  C7   C4   C5   C     180.00   0.0  0
 B5K  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 B5K  CONST_09  C4   C5   C    C1      0.00   0.0  0
 B5K  CONST_10  C14  C15  C16  C11     0.00   0.0  0
 B5K  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 B5K  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 B5K  CONST_13  C15  C16  C11  C12     0.00   0.0  0
 B5K  CONST_14  C16  C15  C14  C13     0.00   0.0  0
 B5K  CONST_15  C16  C11  C12  C13     0.00   0.0  0
 B5K  CONST_16  C6   N    C3   C2    180.00   0.0  0
 B5K  CONST_17  C7   C4   C3   C2    180.00   0.0  0
 B5K  CONST_18  C5   C4   C3   C2      0.00   0.0  0
 B5K  CONST_19  C5   C    C1   C2      0.00   0.0  0
 B5K  CONST_20  C7   C6   N    C3      0.00   0.0  0
 B5K  CONST_21  C6   C7   C4   C3      0.00   0.0  0
 B5K  CONST_22  C6   N    C3   C4      0.00   0.0  0
 B5K  CONST_23  C6   C7   C4   C5    180.00   0.0  0
 B5K  CONST_24  C8   C7   C6   N     180.00   0.0  0
 B5K  CONST_25  C15  C16  C11  C10   180.00   0.0  0
 B5K  CONST_26  C13  C12  C11  C10   180.00   0.0  0
 B5K  CONST_27  F1   C15  C16  C11   180.00   0.0  0
 B5K  CONST_28  F2   C13  C12  C11   180.00   0.0  0
 B5K  CONST_29  F    C14  C13  C12   180.00   0.0  0
 B5K  CONST_30  F1   C15  C14  C13   180.00   0.0  0
 B5K  CONST_31  F2   C13  C14  C15   180.00   0.0  0
 B5K  CONST_32  F    C14  C15  C16   180.00   0.0  0
 B5K  CONST_33  C3   N    C6   C21   180.00   0.0  0
 B5K  CONST_34  C4   C7   C6   C21   180.00   0.0  0
 B5K  CONST_35  CL   C1   C2   C3    180.00   0.0  0
 B5K  CONST_36  C8   C7   C4   C3    180.00   0.0  0
 B5K  CONST_37  C8   C7   C4   C5      0.00   0.0  0
 B5K  CONST_38  CL   C1   C    C5    180.00   0.0  0
 B5K  CONST_39  H13  C2   C3   N       0.00   0.0  0
 B5K  CONST_40  H18  C5   C    C1    180.00   0.0  0
 B5K  CONST_41  H6   C16  C11  C12   180.00   0.0  0
 B5K  CONST_42  H5   C12  C13  C14   180.00   0.0  0
 B5K  CONST_43  H1   N    C3   C2      0.00   0.0  0
 B5K  CONST_44  H2   C    C1   C2    180.00   0.0  0
 B5K  CONST_45  H21  O2   C21  C6    180.00   0.0  0
 B5K  CONST_46  C17  N2   C9   O       0.00   0.0  0
 B5K  CONST_47  O3   C22  N1   C10     0.00   0.0  0
 B5K  CONST_48  C8   C9   N2   C17   180.00   0.0  0
 B5K  CONST_49  O3   C22  N1   C8    180.00   0.0  0
 B5K  CONST_50  H20  N2   C9   O     180.00   0.0  0
 B5K  Var_01    O1   C21  C6   N    -167.83  30.0  3
 B5K  Var_02    N1   C10  C11  C12    59.43  30.0  2
 B5K  Var_03    C8   N1   C10  C11    73.59  30.0  1
 B5K  Var_04    C9   N2   C17  C18   -61.42  30.0  3
 B5K  Var_05    H14  C20  C17  C18  -178.64  30.0  3
 B5K  Var_06    H10  C19  C17  C18   -57.66  30.0  3
 B5K  Var_07    H7   C18  C17  C19  -178.77  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
 B5K  chir_01  C8  C7  C9  N1  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
 B5K  plan-1  C10  0.020
 B5K  plan-1  C11  0.020
 B5K  plan-1  C12  0.020
 B5K  plan-1  C13  0.020
 B5K  plan-1  C14  0.020
 B5K  plan-1  C15  0.020
 B5K  plan-1  C16  0.020
 B5K  plan-1  F    0.020
 B5K  plan-1  F1   0.020
 B5K  plan-1  F2   0.020
 B5K  plan-1  H5   0.020
 B5K  plan-1  H6   0.020
 B5K  plan-2  N    0.020
 B5K  plan-2  C    0.020
 B5K  plan-2  C1   0.020
 B5K  plan-2  C2   0.020
 B5K  plan-2  C3   0.020
 B5K  plan-2  C4   0.020
 B5K  plan-2  C5   0.020
 B5K  plan-2  C6   0.020
 B5K  plan-2  C7   0.020
 B5K  plan-2  C8   0.020
 B5K  plan-2  CL   0.020
 B5K  plan-2  H1   0.020
 B5K  plan-2  H2   0.020
 B5K  plan-2  H13  0.020
 B5K  plan-2  H18  0.020
 B5K  plan-2  C21  0.020
 B5K  plan-3  C10  0.020
 B5K  plan-3  C22  0.020
 B5K  plan-3  C8   0.020
 B5K  plan-3  N1   0.020
 B5K  plan-3  O3   0.020
 B5K  plan-3  H17  0.020
 B5K  plan-4  O    0.020
 B5K  plan-4  C17  0.020
 B5K  plan-4  C8   0.020
 B5K  plan-4  C9   0.020
 B5K  plan-4  N2   0.020
 B5K  plan-4  H20  0.020
 B5K  plan-5  C6   0.020
 B5K  plan-5  O1   0.020
 B5K  plan-5  O2   0.020
 B5K  plan-5  H21  0.020
 B5K  plan-5  C21  0.020

