# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:53:53 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  54  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.719   0.4898   1.4769   1.6464
 B5K  C    C   CR16   0  -0.221   3.6600   1.4447  -0.9416
 B5K  O    O   O      0  -0.481   1.0535  -3.0595  -1.9362
 B5K  C1   C   CR6    0  -0.071   3.5800   2.5119  -0.0363
 B5K  C10  C   CH2    0  -0.363  -2.2627  -1.2018  -1.6080
 B5K  C11  C   CR6    0   0.133  -2.9372  -0.0276  -0.9376
 B5K  C12  C   CR16   0  -0.461  -2.3633   1.2364  -0.9213
 B5K  C13  C   CR6    0   0.440  -3.0204   2.2732  -0.2928
 B5K  C14  C   CR6    0   0.249  -4.2481   2.0884   0.3108
 B5K  C15  C   CR6    0   0.421  -4.8145   0.8277   0.2773
 B5K  C16  C   CR16   0  -0.459  -4.1747  -0.2260  -0.3365
 B5K  C17  C   CT     0   0.100   2.9434  -3.7516   0.1853
 B5K  C18  C   CH3    0  -0.643   2.4007  -5.1637  -0.0362
 B5K  C19  C   CH3    0  -0.681   3.5698  -3.6600   1.5753
 B5K  C2   C   CR16   0  -0.267   2.5571   2.6329   0.8786
 B5K  C20  C   CH3    0  -0.645   3.9968  -3.4064  -0.8679
 B5K  C22  C   C1     0   0.263  -0.2329  -0.6260  -2.7944
 B5K  C3   C   CR56   0   0.344   1.5840   1.6354   0.8598
 B5K  C4   C   CR56   0   0.071   1.6154   0.5500  -0.0465
 B5K  C5   C   CR16   0  -0.396   2.6861   0.4673  -0.9457
 B5K  C6   C   CR5    0   0.130  -0.1823   0.3429   1.2986
 B5K  C7   C   CR5    0   0.013   0.4716  -0.2615   0.2486
 B5K  C8   C   CH1    0  -0.359  -0.0415  -1.4498  -0.5066
 B5K  C9   C   C      0   0.574   1.0276  -2.5030  -0.8498
 B5K  F    F   F      0  -0.301  -4.8681   3.1000   0.9205
 B5K  F1   F   F      0  -0.305  -5.9983   0.6476   0.8699
 B5K  F2   F   F      0  -0.305  -2.4731   3.4913  -0.2553
 B5K  N1   N   NT     0  -0.407  -0.8242  -1.0938  -1.6803
 B5K  N2   N   NH1    0  -0.649   1.8547  -2.7662   0.1675
 B5K  O1   O   O      0  -0.568  -1.8802  -1.1782   1.8806
 B5K  O2   O   OC    -1  -0.584  -1.8218   0.8202   2.8817
 B5K  O3   O   O      0  -0.487  -0.8171  -0.2916  -3.8104
 B5K  CL   CL  CL     0  -0.140   4.8272   3.7222  -0.0698
 B5K  H1   H   HNR5   0   0.400   0.1833   2.0880   2.3863
 B5K  H2   H   HCR6   0   0.272   4.4891   1.3870  -1.6332
 B5K  H3   H   HCH2   0   0.276  -2.5191  -2.1150  -1.0696
 B5K  H4   H   HCH2   0   0.284  -2.6558  -1.3165  -2.6192
 B5K  H5   H   HCR6   0   0.283  -1.3964   1.4322  -1.3643
 B5K  H6   H   HCR6   0   0.283  -4.6368  -1.2052  -0.3241
 B5K  H7   H   HCH3   0   0.239   1.9655  -5.2771  -1.0273
 B5K  H8   H   HCH3   0   0.227   3.2094  -5.8894   0.0600
 B5K  H9   H   HCH3   0   0.228   1.6389  -5.4082   0.7055
 B5K  H10  H   HCH3   0   0.239   2.8356  -3.8766   2.3537
 B5K  H11  H   HCH3   0   0.243   4.3825  -4.3794   1.6717
 B5K  H12  H   HCH3   0   0.237   3.9806  -2.6651   1.7601
 B5K  H13  H   HCR6   0   0.282   2.5130   3.4566   1.5785
 B5K  H14  H   HCH3   0   0.227   4.3881  -2.4004  -0.7065
 B5K  H15  H   HCH3   0   0.228   4.8309  -4.1073  -0.8052
 B5K  H16  H   HCH3   0   0.239   3.5909  -3.4606  -1.8765
 B5K  H17  H   H      0   0.195   0.8582  -0.5525  -2.7090
 B5K  H18  H   HCR6   0   0.248   2.7768  -0.3521  -1.6472
 B5K  H19  H   HCH1   0   0.327  -0.7327  -1.9541   0.1734
 B5K  H20  H   HNH1   0   0.404   1.7306  -2.2176   1.0057
 B5K  C21  C   C      0   0.412  -1.4146  -0.0423   2.0842

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  deloc     1.244  0.020  1.244
 B5K  C2   C3   aromatic  1.394  0.020  1.394
 B5K  C2   C1   aromatic  1.378  0.020  1.378
 B5K  CL   C1   single    1.738  0.020  1.738
 B5K  N    C3   aromatic  1.357  0.020  1.357
 B5K  N    C6   aromatic  1.363  0.020  1.363
 B5K  C3   C4   aromatic  1.414  0.020  1.414
 B5K  C1   C    aromatic  1.402  0.020  1.402
 B5K  C21  C6   single    1.511  0.020  1.511
 B5K  C21  O2   deloc     1.243  0.020  1.243
 B5K  C6   C7   aromatic  1.377  0.020  1.377
 B5K  C17  N2   single    1.468  0.020  1.468
 B5K  C17  C20  single    1.529  0.020  1.529
 B5K  C17  C19  single    1.527  0.020  1.527
 B5K  N2   C9   single    1.337  0.020  1.337
 B5K  C4   C7   aromatic  1.433  0.020  1.433
 B5K  C4   C5   aromatic  1.401  0.020  1.401
 B5K  C    C5   aromatic  1.380  0.020  1.380
 B5K  C7   C8   single    1.499  0.020  1.499
 B5K  C9   C8   single    1.540  0.020  1.540
 B5K  C9   O    double    1.221  0.020  1.221
 B5K  C8   N1   single    1.455  0.020  1.455
 B5K  F1   C15  single    1.336  0.020  1.336
 B5K  F    C14  single    1.334  0.020  1.334
 B5K  C15  C14  aromatic  1.382  0.020  1.382
 B5K  C15  C16  aromatic  1.377  0.020  1.377
 B5K  N1   C22  single    1.345  0.020  1.345
 B5K  N1   C10  single    1.444  0.020  1.444
 B5K  C22  O3   double    1.219  0.020  1.219
 B5K  C14  C13  aromatic  1.380  0.020  1.380
 B5K  C16  C11  aromatic  1.390  0.020  1.390
 B5K  C13  F2   single    1.336  0.020  1.336
 B5K  C13  C12  aromatic  1.379  0.020  1.379
 B5K  C11  C12  aromatic  1.388  0.020  1.388
 B5K  C11  C10  single    1.511  0.020  1.511
 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

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   122.82  3.000
 B5K  H1   N    C3   126.89  3.000
 B5K  C6   N    C3   110.29  3.000
 B5K  H2   C    C5   120.10  3.000
 B5K  H2   C    C1   119.83  3.000
 B5K  C5   C    C1   120.06  3.000
 B5K  CL   C1   C2   118.97  3.000
 B5K  CL   C1   C    118.47  3.000
 B5K  C2   C1   C    122.56  3.000
 B5K  H4   C10  H3   106.54  3.000
 B5K  H4   C10  N1   108.69  3.000
 B5K  H3   C10  N1   108.75  3.000
 B5K  H4   C10  C11  109.39  3.000
 B5K  H3   C10  C11  109.07  3.000
 B5K  N1   C10  C11  114.13  3.000
 B5K  C16  C11  C12  119.53  3.000
 B5K  C12  C11  C10  121.88  3.000
 B5K  C16  C11  C10  118.58  3.000
 B5K  H5   C12  C13  118.47  3.000
 B5K  H5   C12  C11  121.98  3.000
 B5K  C13  C12  C11  119.53  3.000
 B5K  F2   C13  C14  118.30  3.000
 B5K  F2   C13  C12  120.20  3.000
 B5K  C14  C13  C12  121.49  3.000
 B5K  F    C14  C15  120.82  3.000
 B5K  C15  C14  C13  118.41  3.000
 B5K  F    C14  C13  120.77  3.000
 B5K  F1   C15  C16  120.41  3.000
 B5K  C16  C15  C14  121.22  3.000
 B5K  F1   C15  C14  118.37  3.000
 B5K  H6   C16  C15  119.25  3.000
 B5K  H6   C16  C11  120.93  3.000
 B5K  C15  C16  C11  119.81  3.000
 B5K  N2   C17  C20  110.55  3.000
 B5K  C20  C17  C19  109.31  3.000
 B5K  N2   C17  C19  105.95  3.000
 B5K  C19  C17  C18  109.44  3.000
 B5K  C20  C17  C18  110.69  3.000
 B5K  N2   C17  C18  110.78  3.000
 B5K  H9   C18  H8   107.98  3.000
 B5K  H9   C18  H7   108.45  3.000
 B5K  H8   C18  H7   107.90  3.000
 B5K  H9   C18  C17  110.88  3.000
 B5K  H8   C18  C17  109.79  3.000
 B5K  H7   C18  C17  111.72  3.000
 B5K  H12  C19  H11  107.82  3.000
 B5K  H12  C19  H10  108.25  3.000
 B5K  H11  C19  H10  107.91  3.000
 B5K  H12  C19  C17  111.27  3.000
 B5K  H11  C19  C17  110.29  3.000
 B5K  H10  C19  C17  111.17  3.000
 B5K  H13  C2   C3   121.68  3.000
 B5K  H13  C2   C1   121.79  3.000
 B5K  C3   C2   C1   116.53  3.000
 B5K  H16  C20  H15  107.83  3.000
 B5K  H16  C20  H14  108.45  3.000
 B5K  H15  C20  H14  108.04  3.000
 B5K  H16  C20  C17  111.71  3.000
 B5K  H15  C20  C17  110.00  3.000
 B5K  H14  C20  C17  110.69  3.000
 B5K  H17  C22  O3   121.55  3.000
 B5K  H17  C22  N1   113.33  3.000
 B5K  O3   C22  N1   125.11  3.000
 B5K  C4   C3   C2   122.85  3.000
 B5K  C4   C3   N    107.44  3.000
 B5K  C2   C3   N    129.71  3.000
 B5K  C7   C4   C5   135.14  3.000
 B5K  C5   C4   C3   118.27  3.000
 B5K  C7   C4   C3   106.55  3.000
 B5K  H18  C5   C4   121.66  3.000
 B5K  H18  C5   C    118.62  3.000
 B5K  C4   C5   C    119.72  3.000
 B5K  C7   C6   C21  132.21  3.000
 B5K  C7   C6   N    109.01  3.000
 B5K  C21  C6   N    118.77  3.000
 B5K  C8   C7   C6   124.74  3.000
 B5K  C8   C7   C4   128.21  3.000
 B5K  C6   C7   C4   106.71  3.000
 B5K  H19  C8   N1   105.94  3.000
 B5K  H19  C8   C9   105.20  3.000
 B5K  N1   C8   C9   111.17  3.000
 B5K  H19  C8   C7   105.60  3.000
 B5K  N1   C8   C7   113.38  3.000
 B5K  C9   C8   C7   114.65  3.000
 B5K  N2   C9   C8   113.24  3.000
 B5K  C8   C9   O    121.67  3.000
 B5K  N2   C9   O    125.03  3.000
 B5K  C8   N1   C22  121.12  3.000
 B5K  C22  N1   C10  120.34  3.000
 B5K  C8   N1   C10  118.50  3.000
 B5K  H20  N2   C9   116.66  3.000
 B5K  H20  N2   C17  116.47  3.000
 B5K  C9   N2   C17  126.86  3.000
 B5K  O2   C21  O1   128.01  3.000
 B5K  O2   C21  C6   115.06  3.000
 B5K  O1   C21  C6   116.91  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  C17  N2   C9   O       0.00   0.0  0
 B5K  CONST_46  O3   C22  N1   C10     0.00   0.0  0
 B5K  CONST_47  C8   C9   N2   C17   180.00   0.0  0
 B5K  CONST_48  O3   C22  N1   C8    180.00   0.0  0
 B5K  CONST_49  H20  N2   C9   O     180.00   0.0  0
 B5K  Var_01    O1   C21  C6   N    -169.14  30.0  3
 B5K  Var_02    N1   C10  C11  C12    26.25  30.0  2
 B5K  Var_03    C8   N1   C10  C11    81.20  30.0  1
 B5K  Var_04    C9   N2   C17  C18   -61.16  30.0  3
 B5K  Var_05    H14  C20  C17  C18  -179.70  30.0  3
 B5K  Var_06    H10  C19  C17  C18   -60.06  30.0  3
 B5K  Var_07    H7   C18  C17  C19  -178.66  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  C21  0.020

