# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 03:10:38 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S})-3-[2,6-bis(fluoranyl)phenyl]-~{N}-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(=O)NCc1ccc2NC(=O)Nc2c1)c3c(F)cccc3F
#
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
 F6T  F6T  (3~{S})-3-[2,6-bis(fluoranyl)phenyl]-~{N}-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]butanamide  ligand  42  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F6T
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
 F6T  FAT  F  F     0  -0.308  -4.3855   1.2047   2.2097
 F6T  CAS  C  CR6   0   0.522  -4.7772   1.1971   0.9253
 F6T  CAU  C  CR16  0  -0.417  -5.8241   2.0275   0.5718
 F6T  CAV  C  CR16  0  -0.240  -6.2441   2.0372  -0.7484
 F6T  CAW  C  CR16  0  -0.413  -5.6185   1.2310  -1.6870
 F6T  CAX  C  CR6   0   0.534  -4.5775   0.4231  -1.2739
 F6T  FAY  F  F     0  -0.308  -3.9823  -0.3458  -2.2011
 F6T  CAR  C  CR6   0  -0.231  -4.1109   0.3616   0.0351
 F6T  CAB  C  CH1   0  -0.321  -2.9802  -0.5368   0.4827
 F6T  CAA  C  CH3   0  -0.655  -3.3054  -2.0198   0.2931
 F6T  CAC  C  CH2   0  -0.551  -1.6505  -0.1457  -0.1789
 F6T  CAD  C  C     0   0.561  -0.4858  -0.8358   0.5022
 F6T  OAQ  O  O     0  -0.507  -0.3171  -0.7584   1.7131
 F6T  NAE  N  NH1   0  -0.619   0.3261  -1.5290  -0.3111
 F6T  CAF  C  CH2   0  -0.393   1.4986  -2.2531   0.1329
 F6T  CAG  C  CR6   0   0.105   2.7843  -1.4920  -0.0769
 F6T  CAP  C  CR16  0  -0.354   3.0173  -0.3099   0.6319
 F6T  CAO  C  CR56  0   0.348   4.2024   0.3568   0.4041
 F6T  NAM  N  NR15  0  -0.739   4.7214   1.5202   0.9289
 F6T  CAL  C  CR5   0   0.608   5.9567   1.7925   0.3945
 F6T  OAN  O  O     0  -0.498   6.6778   2.7409   0.6451
 F6T  NAK  N  NR15  0  -0.737   6.2028   0.7661  -0.4838
 F6T  CAJ  C  CR56  0   0.318   5.1542  -0.1273  -0.5026
 F6T  CAI  C  CR16  0  -0.300   4.9366  -1.2940  -1.2048
 F6T  CAH  C  CR16  0  -0.330   3.7359  -1.9647  -0.9775
 F6T  H1   H  HCR6  0   0.282  -6.2978   2.6524   1.3168
 F6T  H2   H  HCR6  0   0.278  -7.0625   2.6770  -1.0484
 F6T  H3   H  HCR6  0   0.282  -5.9303   1.2263  -2.7228
 F6T  H4   H  HCH1  0   0.270  -2.8468  -0.3760   1.5521
 F6T  H5   H  HCH3  0   0.231  -3.3484  -2.3073  -0.7567
 F6T  H6   H  HCH3  0   0.239  -2.5462  -2.6389   0.7725
 F6T  H7   H  HCH3  0   0.242  -4.2623  -2.2684   0.7520
 F6T  H8   H  HCH2  0   0.258  -1.6663  -0.3625  -1.2473
 F6T  H9   H  HCH2  0   0.280  -1.4964   0.9318  -0.0734
 F6T  H10  H  HNH1  0   0.402   0.1349  -1.5226  -1.2997
 F6T  H11  H  HCH2  0   0.264   1.3665  -2.4983   1.1864
 F6T  H12  H  HCH2  0   0.271   1.5391  -3.1963  -0.4127
 F6T  H13  H  HCR6  0   0.266   2.2931   0.0697   1.3415
 F6T  H14  H  HNR5  0   0.419   4.2771   2.1094   1.6145
 F6T  H15  H  HNR5  0   0.419   7.0484   0.6973  -1.0269
 F6T  H16  H  HCR6  0   0.269   5.6653  -1.6781  -1.9058
 F6T  H17  H  HCR6  0   0.254   3.5404  -2.8833  -1.5171

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
 F6T  CAU  CAV  aromatic  1.385  0.020  1.385
 F6T  CAU  CAS  aromatic  1.382  0.020  1.382
 F6T  CAV  CAW  aromatic  1.387  0.020  1.387
 F6T  FAT  CAS  single    1.343  0.020  1.343
 F6T  CAS  CAR  aromatic  1.391  0.020  1.391
 F6T  CAW  CAX  aromatic  1.381  0.020  1.381
 F6T  CAR  CAX  aromatic  1.391  0.020  1.391
 F6T  CAR  CAB  single    1.512  0.020  1.512
 F6T  CAX  FAY  single    1.344  0.020  1.344
 F6T  CAC  CAB  single    1.536  0.020  1.536
 F6T  CAC  CAD  single    1.515  0.020  1.515
 F6T  CAB  CAA  single    1.530  0.020  1.530
 F6T  NAE  CAD  single    1.342  0.020  1.342
 F6T  NAE  CAF  single    1.448  0.020  1.448
 F6T  CAD  OAQ  double    1.225  0.020  1.225
 F6T  CAF  CAG  single    1.509  0.020  1.509
 F6T  CAH  CAG  aromatic  1.393  0.020  1.393
 F6T  CAH  CAI  aromatic  1.394  0.020  1.394
 F6T  CAG  CAP  aromatic  1.398  0.020  1.398
 F6T  CAI  CAJ  aromatic  1.379  0.020  1.379
 F6T  CAP  CAO  aromatic  1.379  0.020  1.379
 F6T  CAJ  CAO  aromatic  1.401  0.020  1.401
 F6T  CAJ  NAK  single    1.378  0.020  1.378
 F6T  CAO  NAM  single    1.378  0.020  1.378
 F6T  NAK  CAL  single    1.373  0.020  1.373
 F6T  NAM  CAL  single    1.373  0.020  1.373
 F6T  CAL  OAN  double    1.218  0.020  1.218
 F6T  CAU  H1   single    0.930  0.020  1.080
 F6T  CAV  H2   single    0.930  0.020  1.080
 F6T  CAW  H3   single    0.930  0.020  1.080
 F6T  CAB  H4   single    0.970  0.020  1.090
 F6T  CAA  H5   single    0.970  0.020  1.090
 F6T  CAA  H6   single    0.970  0.020  1.090
 F6T  CAA  H7   single    0.970  0.020  1.090
 F6T  CAC  H8   single    0.970  0.020  1.090
 F6T  CAC  H9   single    0.970  0.020  1.090
 F6T  NAE  H10  single    0.860  0.020  1.020
 F6T  CAF  H11  single    0.970  0.020  1.090
 F6T  CAF  H12  single    0.970  0.020  1.090
 F6T  CAP  H13  single    0.930  0.020  1.080
 F6T  NAM  H14  single    0.860  0.020  1.020
 F6T  NAK  H15  single    0.860  0.020  1.020
 F6T  CAI  H16  single    0.930  0.020  1.080
 F6T  CAH  H17  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
 F6T  CAR  CAS  CAU  124.06  3.000
 F6T  CAR  CAS  FAT  118.41  3.000
 F6T  CAU  CAS  FAT  117.53  3.000
 F6T  H1   CAU  CAV  121.31  3.000
 F6T  H1   CAU  CAS  120.17  3.000
 F6T  CAV  CAU  CAS  118.53  3.000
 F6T  H2   CAV  CAW  119.85  3.000
 F6T  H2   CAV  CAU  119.87  3.000
 F6T  CAW  CAV  CAU  120.29  3.000
 F6T  H3   CAW  CAX  120.08  3.000
 F6T  H3   CAW  CAV  121.38  3.000
 F6T  CAX  CAW  CAV  118.54  3.000
 F6T  CAR  CAX  FAY  118.39  3.000
 F6T  FAY  CAX  CAW  117.54  3.000
 F6T  CAR  CAX  CAW  124.07  3.000
 F6T  CAB  CAR  CAX  123.76  3.000
 F6T  CAB  CAR  CAS  121.72  3.000
 F6T  CAX  CAR  CAS  114.52  3.000
 F6T  H4   CAB  CAC  106.21  3.000
 F6T  H4   CAB  CAA  106.90  3.000
 F6T  CAC  CAB  CAA  112.17  3.000
 F6T  H4   CAB  CAR  107.12  3.000
 F6T  CAA  CAB  CAR  112.36  3.000
 F6T  CAC  CAB  CAR  111.63  3.000
 F6T  H7   CAA  H6   107.25  3.000
 F6T  H7   CAA  H5   108.11  3.000
 F6T  H6   CAA  H5   107.53  3.000
 F6T  H7   CAA  CAB  110.82  3.000
 F6T  H6   CAA  CAB  110.35  3.000
 F6T  H5   CAA  CAB  112.56  3.000
 F6T  H9   CAC  H8   107.01  3.000
 F6T  H9   CAC  CAD  107.28  3.000
 F6T  H8   CAC  CAD  111.17  3.000
 F6T  H9   CAC  CAB  109.35  3.000
 F6T  H8   CAC  CAB  111.03  3.000
 F6T  CAD  CAC  CAB  110.85  3.000
 F6T  NAE  CAD  OAQ  123.25  3.000
 F6T  OAQ  CAD  CAC  121.42  3.000
 F6T  NAE  CAD  CAC  115.33  3.000
 F6T  H10  NAE  CAF  117.26  3.000
 F6T  H10  NAE  CAD  118.48  3.000
 F6T  CAF  NAE  CAD  124.22  3.000
 F6T  H12  CAF  H11  107.07  3.000
 F6T  H12  CAF  CAG  109.58  3.000
 F6T  H11  CAF  CAG  110.56  3.000
 F6T  H12  CAF  NAE  108.02  3.000
 F6T  H11  CAF  NAE  108.12  3.000
 F6T  CAG  CAF  NAE  113.28  3.000
 F6T  CAH  CAG  CAP  120.06  3.000
 F6T  CAP  CAG  CAF  119.87  3.000
 F6T  CAH  CAG  CAF  120.06  3.000
 F6T  H13  CAP  CAO  120.92  3.000
 F6T  H13  CAP  CAG  121.16  3.000
 F6T  CAO  CAP  CAG  117.93  3.000
 F6T  CAJ  CAO  NAM  106.41  3.000
 F6T  NAM  CAO  CAP  132.00  3.000
 F6T  CAJ  CAO  CAP  121.59  3.000
 F6T  H14  NAM  CAL  123.07  3.000
 F6T  H14  NAM  CAO  125.95  3.000
 F6T  CAL  NAM  CAO  110.98  3.000
 F6T  NAK  CAL  OAN  127.43  3.000
 F6T  OAN  CAL  NAM  127.39  3.000
 F6T  NAK  CAL  NAM  105.19  3.000
 F6T  H15  NAK  CAJ  125.96  3.000
 F6T  H15  NAK  CAL  123.12  3.000
 F6T  CAJ  NAK  CAL  110.91  3.000
 F6T  CAI  CAJ  NAK  132.50  3.000
 F6T  NAK  CAJ  CAO  106.51  3.000
 F6T  CAI  CAJ  CAO  120.99  3.000
 F6T  H16  CAI  CAH  121.01  3.000
 F6T  H16  CAI  CAJ  121.61  3.000
 F6T  CAH  CAI  CAJ  117.38  3.000
 F6T  H17  CAH  CAI  118.83  3.000
 F6T  H17  CAH  CAG  119.12  3.000
 F6T  CAI  CAH  CAG  122.05  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
 F6T  CONST_01  CAW  CAV  CAU  CAS     0.00   0.0  0
 F6T  CONST_02  CAW  CAX  CAR  CAS     0.00   0.0  0
 F6T  CONST_03  CAX  CAW  CAV  CAU     0.00   0.0  0
 F6T  CONST_04  CAX  CAR  CAS  CAU     0.00   0.0  0
 F6T  CONST_05  CAR  CAS  CAU  CAV     0.00   0.0  0
 F6T  CONST_06  CAR  CAX  CAW  CAV     0.00   0.0  0
 F6T  CONST_07  CAJ  CAI  CAH  CAG     0.00   0.0  0
 F6T  CONST_08  CAJ  CAO  CAP  CAG     0.00   0.0  0
 F6T  CONST_09  CAI  CAH  CAG  CAP     0.00   0.0  0
 F6T  CONST_10  CAI  CAJ  CAO  CAP     0.00   0.0  0
 F6T  CONST_11  CAH  CAG  CAP  CAO     0.00   0.0  0
 F6T  CONST_12  CAH  CAI  CAJ  CAO     0.00   0.0  0
 F6T  CONST_13  CAL  NAK  CAJ  CAO     0.00   0.0  0
 F6T  CONST_14  NAK  CAL  NAM  CAO     0.00   0.0  0
 F6T  CONST_15  NAK  CAJ  CAO  NAM     0.00   0.0  0
 F6T  CONST_16  CAJ  NAK  CAL  NAM     0.00   0.0  0
 F6T  CONST_17  CAJ  CAO  NAM  CAL     0.00   0.0  0
 F6T  CONST_18  CAV  CAU  CAS  FAT   180.00   0.0  0
 F6T  CONST_19  CAX  CAR  CAS  FAT   180.00   0.0  0
 F6T  CONST_20  FAY  CAX  CAR  CAS   180.00   0.0  0
 F6T  CONST_21  CAB  CAR  CAS  CAU   180.00   0.0  0
 F6T  CONST_22  FAY  CAX  CAW  CAV   180.00   0.0  0
 F6T  CONST_23  CAB  CAR  CAX  CAW   180.00   0.0  0
 F6T  CONST_24  CAI  CAH  CAG  CAF   180.00   0.0  0
 F6T  CONST_25  CAO  CAP  CAG  CAF   180.00   0.0  0
 F6T  CONST_26  OAN  CAL  NAM  CAO   180.00   0.0  0
 F6T  CONST_27  CAJ  NAK  CAL  OAN   180.00   0.0  0
 F6T  CONST_28  H2   CAV  CAU  CAS   180.00   0.0  0
 F6T  CONST_29  H3   CAW  CAV  CAU   180.00   0.0  0
 F6T  CONST_30  H1   CAU  CAV  CAW   180.00   0.0  0
 F6T  CONST_31  H16  CAI  CAH  CAG   180.00   0.0  0
 F6T  CONST_32  H17  CAH  CAG  CAP   180.00   0.0  0
 F6T  CONST_33  H13  CAP  CAO  NAM     0.00   0.0  0
 F6T  CONST_34  H15  NAK  CAJ  CAO   180.00   0.0  0
 F6T  CONST_35  H14  NAM  CAL  NAK   180.00   0.0  0
 F6T  CONST_36  CAF  NAE  CAD  CAC   180.00   0.0  0
 F6T  CONST_37  CAF  NAE  CAD  OAQ     0.00   0.0  0
 F6T  CONST_38  H10  NAE  CAD  CAC     0.00   0.0  0
 F6T  Var_01    CAH  CAG  CAF  NAE  -114.27  30.0  2
 F6T  Var_02    CAG  CAF  NAE  CAD   -98.86  30.0  3
 F6T  Var_03    NAE  CAD  CAC  CAB   126.38  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
 F6T  chir_01  CAB  CAR  CAC  CAA  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
 F6T  plan-1  FAT  0.020
 F6T  plan-1  CAS  0.020
 F6T  plan-1  CAU  0.020
 F6T  plan-1  CAV  0.020
 F6T  plan-1  CAW  0.020
 F6T  plan-1  CAX  0.020
 F6T  plan-1  FAY  0.020
 F6T  plan-1  CAR  0.020
 F6T  plan-1  CAB  0.020
 F6T  plan-1  H1   0.020
 F6T  plan-1  H2   0.020
 F6T  plan-1  H3   0.020
 F6T  plan-2  CAF  0.020
 F6T  plan-2  CAG  0.020
 F6T  plan-2  CAP  0.020
 F6T  plan-2  CAO  0.020
 F6T  plan-2  NAM  0.020
 F6T  plan-2  CAL  0.020
 F6T  plan-2  OAN  0.020
 F6T  plan-2  NAK  0.020
 F6T  plan-2  CAJ  0.020
 F6T  plan-2  CAI  0.020
 F6T  plan-2  CAH  0.020
 F6T  plan-2  H13  0.020
 F6T  plan-2  H14  0.020
 F6T  plan-2  H15  0.020
 F6T  plan-2  H16  0.020
 F6T  plan-2  H17  0.020
 F6T  plan-3  CAC  0.020
 F6T  plan-3  CAD  0.020
 F6T  plan-3  OAQ  0.020
 F6T  plan-3  NAE  0.020
 F6T  plan-3  CAF  0.020
 F6T  plan-3  H10  0.020

