# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 01:01:31 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3S)-3-(2-fluorophenyl)-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)c3ccccc3F
#
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
 KQS  KQS  (3S)-3-(2-fluorophenyl)-N-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]butanamide  ligand  42  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KQS
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
 KQS  F     F  F     0  -0.315   5.2488  -0.2972   2.0248
 KQS  C16   C  CR6   0   0.501   5.3061  -0.7226   0.7481
 KQS  C15   C  CR16  0  -0.402   6.2671  -1.6633   0.4272
 KQS  C14   C  CR16  0  -0.255   6.3414  -2.1238  -0.8786
 KQS  C13   C  CR16  0  -0.255   5.4578  -1.6368  -1.8326
 KQS  C12   C  CR16  0  -0.290   4.5089  -0.6896  -1.4769
 KQS  C11   C  CR6   0  -0.040   4.4092  -0.2020  -0.1741
 KQS  C10   C  CH1   0  -0.325   3.3566   0.8078   0.2195
 KQS  C17   C  CH3   0  -0.663   3.2620   1.9618  -0.7776
 KQS  C9    C  CH2   0  -0.548   2.0060   0.0936   0.3856
 KQS  C8    C  C     0   0.547   0.9419   1.0309   0.9156
 KQS  O1    O  O     0  -0.503   1.0804   1.6173   1.9817
 KQS  N2    N  NH1   0  -0.625  -0.1442   1.1641   0.1372
 KQS  C7    C  CH2   0  -0.337  -1.2752   2.0087   0.4547
 KQS  C3    C  CR6   0   0.059  -2.5730   1.3626   0.0481
 KQS  C2    C  CR16  0  -0.340  -2.9152   0.1114   0.5696
 KQS  C4    C  CR16  0  -0.328  -3.4312   2.0089  -0.8379
 KQS  C5    C  CR16  0  -0.298  -4.6464   1.4489  -1.2287
 KQS  C6    C  CR56  0   0.318  -4.9745   0.2151  -0.7075
 KQS  C1    C  CR56  0   0.344  -4.1152  -0.4441   0.1814
 KQS  N     N  NR15  0  -0.740  -4.7288  -1.6336   0.5071
 KQS  N1    N  NR15  0  -0.736  -6.0657  -0.6079  -0.8787
 KQS  C     C  CR5   0   0.609  -5.9350  -1.7565  -0.1376
 KQS  O     O  O     0  -0.497  -6.7202  -2.6841  -0.0674
 KQS  H15   H  HCR6  0   0.276   6.9445  -2.0269   1.1892
 KQS  H14   H  HCR6  0   0.266   7.0885  -2.8596  -1.1448
 KQS  H13   H  HCR6  0   0.259   5.5072  -1.9926  -2.8530
 KQS  H12   H  HCR6  0   0.257   3.8273  -0.3190  -2.2326
 KQS  H10   H  HCH1  0   0.261   3.6265   1.2306   1.1881
 KQS  H171  H  HCH3  0   0.226   2.8566   1.6454  -1.7397
 KQS  H172  H  HCH3  0   0.242   2.6141   2.7510  -0.3947
 KQS  H173  H  HCH3  0   0.245   4.2423   2.4041  -0.9556
 KQS  H91C  H  HCH2  0   0.255   1.7072  -0.3539  -0.5657
 KQS  H92C  H  HCH2  0   0.280   2.1098  -0.7250   1.1026
 KQS  H2    H  HNH1  0   0.401  -0.1583   0.6897  -0.7513
 KQS  H71C  H  HCH2  0   0.264  -1.2625   2.1950   1.5289
 KQS  H72C  H  HCH2  0   0.258  -1.1764   2.9817  -0.0352
 KQS  HA    H  HCR6  0   0.267  -2.2572  -0.4064   1.2566
 KQS  H4    H  HCR6  0   0.255  -3.1494   2.9752  -1.2371
 KQS  H5    H  HCR6  0   0.270  -5.3003   1.9635  -1.9196
 KQS  H1    H  HNR5  0   0.420  -6.8657  -0.4182  -1.4609
 KQS  H     H  HNR5  0   0.420  -4.3605  -2.3395   1.1241

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
 KQS  F    C16   single    1.347  0.020  1.347
 KQS  C16  C15   aromatic  1.383  0.020  1.383
 KQS  C16  C11   aromatic  1.388  0.020  1.388
 KQS  C15  C14   aromatic  1.387  0.020  1.387
 KQS  C14  C13   aromatic  1.389  0.020  1.389
 KQS  C13  C12   aromatic  1.387  0.020  1.387
 KQS  C12  C11   aromatic  1.395  0.020  1.395
 KQS  C11  C10   single    1.511  0.020  1.511
 KQS  C10  C17   single    1.528  0.020  1.528
 KQS  C10  C9    single    1.537  0.020  1.537
 KQS  C9   C8    single    1.514  0.020  1.514
 KQS  C8   O1    double    1.225  0.020  1.225
 KQS  C8   N2    single    1.343  0.020  1.343
 KQS  N2   C7    single    1.447  0.020  1.447
 KQS  C7   C3    single    1.506  0.020  1.506
 KQS  C3   C2    aromatic  1.398  0.020  1.398
 KQS  C3   C4    aromatic  1.392  0.020  1.392
 KQS  C2   C1    aromatic  1.378  0.020  1.378
 KQS  C4   C5    aromatic  1.394  0.020  1.394
 KQS  C5   C6    aromatic  1.379  0.020  1.379
 KQS  C6   C1    aromatic  1.401  0.020  1.401
 KQS  C6   N1    single    1.377  0.020  1.377
 KQS  C1   N     single    1.378  0.020  1.378
 KQS  N    C     single    1.373  0.020  1.373
 KQS  N1   C     single    1.373  0.020  1.373
 KQS  C    O     double    1.217  0.020  1.217
 KQS  C15  H15   single    0.930  0.020  1.080
 KQS  C14  H14   single    0.930  0.020  1.080
 KQS  C13  H13   single    0.930  0.020  1.080
 KQS  C12  H12   single    0.930  0.020  1.080
 KQS  C10  H10   single    0.970  0.020  1.090
 KQS  C17  H171  single    0.970  0.020  1.090
 KQS  C17  H172  single    0.970  0.020  1.090
 KQS  C17  H173  single    0.970  0.020  1.090
 KQS  C9   H91C  single    0.970  0.020  1.090
 KQS  C9   H92C  single    0.970  0.020  1.090
 KQS  N2   H2    single    0.860  0.020  1.020
 KQS  C7   H71C  single    0.970  0.020  1.090
 KQS  C7   H72C  single    0.970  0.020  1.090
 KQS  C2   HA    single    0.930  0.020  1.080
 KQS  C4   H4    single    0.930  0.020  1.080
 KQS  C5   H5    single    0.930  0.020  1.080
 KQS  N1   H1    single    0.860  0.020  1.020
 KQS  N    H     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
 KQS  C11   C16  C15   123.38  3.000
 KQS  C11   C16  F     118.94  3.000
 KQS  C15   C16  F     117.68  3.000
 KQS  H15   C15  C14   121.19  3.000
 KQS  H15   C15  C16   120.01  3.000
 KQS  C14   C15  C16   118.81  3.000
 KQS  H14   C14  C13   120.59  3.000
 KQS  H14   C14  C15   119.65  3.000
 KQS  C13   C14  C15   119.77  3.000
 KQS  H13   C13  C12   119.85  3.000
 KQS  H13   C13  C14   120.25  3.000
 KQS  C12   C13  C14   119.90  3.000
 KQS  H12   C12  C11   119.16  3.000
 KQS  H12   C12  C13   119.02  3.000
 KQS  C11   C12  C13   121.82  3.000
 KQS  C10   C11  C12   121.80  3.000
 KQS  C10   C11  C16   121.86  3.000
 KQS  C12   C11  C16   116.32  3.000
 KQS  H10   C10  C9    107.55  3.000
 KQS  H10   C10  C17   107.59  3.000
 KQS  C9    C10  C17   111.53  3.000
 KQS  H10   C10  C11   108.55  3.000
 KQS  C9    C10  C11   109.26  3.000
 KQS  C17   C10  C11   112.20  3.000
 KQS  H173  C17  H172  107.34  3.000
 KQS  H173  C17  H171  107.94  3.000
 KQS  H172  C17  H171  107.38  3.000
 KQS  H173  C17  C10   110.93  3.000
 KQS  H172  C17  C10   110.74  3.000
 KQS  H171  C17  C10   112.30  3.000
 KQS  H92C  C9   H91C  106.87  3.000
 KQS  H92C  C9   C8    107.50  3.000
 KQS  H91C  C9   C8    111.48  3.000
 KQS  H92C  C9   C10   109.60  3.000
 KQS  H91C  C9   C10   109.66  3.000
 KQS  C8    C9   C10   111.58  3.000
 KQS  N2    C8   O1    123.27  3.000
 KQS  N2    C8   C9    115.27  3.000
 KQS  O1    C8   C9    121.45  3.000
 KQS  H2    N2   C7    117.23  3.000
 KQS  H2    N2   C8    118.42  3.000
 KQS  C7    N2   C8    124.26  3.000
 KQS  H72C  C7   H71C  106.76  3.000
 KQS  H72C  C7   C3    109.79  3.000
 KQS  H71C  C7   C3    110.46  3.000
 KQS  H72C  C7   N2    110.51  3.000
 KQS  H71C  C7   N2    107.86  3.000
 KQS  C3    C7   N2    111.35  3.000
 KQS  C4    C3   C2    120.12  3.000
 KQS  C4    C3   C7    120.26  3.000
 KQS  C2    C3   C7    119.62  3.000
 KQS  HA    C2   C1    120.99  3.000
 KQS  HA    C2   C3    121.05  3.000
 KQS  C1    C2   C3    117.96  3.000
 KQS  H4    C4   C5    118.81  3.000
 KQS  H4    C4   C3    119.24  3.000
 KQS  C5    C4   C3    121.95  3.000
 KQS  H5    C5   C6    121.55  3.000
 KQS  H5    C5   C4    121.00  3.000
 KQS  C6    C5   C4    117.44  3.000
 KQS  N1    C6   C1    106.48  3.000
 KQS  N1    C6   C5    132.53  3.000
 KQS  C1    C6   C5    120.99  3.000
 KQS  N     C1   C6    106.44  3.000
 KQS  N     C1   C2    132.02  3.000
 KQS  C6    C1   C2    121.54  3.000
 KQS  H     N    C     123.10  3.000
 KQS  H     N    C1    125.95  3.000
 KQS  C     N    C1    110.95  3.000
 KQS  H1    N1   C     123.02  3.000
 KQS  H1    N1   C6    126.05  3.000
 KQS  C     N1   C6    110.93  3.000
 KQS  O     C    N1    127.38  3.000
 KQS  O     C    N     127.42  3.000
 KQS  N1    C    N     105.20  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
 KQS  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 KQS  CONST_02  C13  C12  C11  C16     0.00   0.0  0
 KQS  CONST_03  C12  C11  C16  C15     0.00   0.0  0
 KQS  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 KQS  CONST_05  C11  C16  C15  C14     0.00   0.0  0
 KQS  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 KQS  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 KQS  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 KQS  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 KQS  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 KQS  CONST_11  C1   C2   C3   C4      0.00   0.0  0
 KQS  CONST_12  C1   C6   C5   C4      0.00   0.0  0
 KQS  CONST_13  C    N    C1   C6      0.00   0.0  0
 KQS  CONST_14  N    C    N1   C6      0.00   0.0  0
 KQS  CONST_15  C    N1   C6   C1      0.00   0.0  0
 KQS  CONST_16  N1   C    N    C1      0.00   0.0  0
 KQS  CONST_17  N1   C6   C1   N       0.00   0.0  0
 KQS  CONST_18  C14  C15  C16  F     180.00   0.0  0
 KQS  CONST_19  C12  C11  C16  F     180.00   0.0  0
 KQS  CONST_20  C10  C11  C16  C15   180.00   0.0  0
 KQS  CONST_21  C10  C11  C12  C13   180.00   0.0  0
 KQS  CONST_22  C1   C2   C3   C7    180.00   0.0  0
 KQS  CONST_23  C5   C4   C3   C7    180.00   0.0  0
 KQS  CONST_24  O    C    N1   C6    180.00   0.0  0
 KQS  CONST_25  O    C    N    C1    180.00   0.0  0
 KQS  CONST_26  H14  C14  C15  C16   180.00   0.0  0
 KQS  CONST_27  H12  C12  C11  C16   180.00   0.0  0
 KQS  CONST_28  H13  C13  C14  C15   180.00   0.0  0
 KQS  CONST_29  H15  C15  C14  C13   180.00   0.0  0
 KQS  CONST_30  H5   C5   C4   C3    180.00   0.0  0
 KQS  CONST_31  H4   C4   C3   C2    180.00   0.0  0
 KQS  CONST_32  HA   C2   C3   C4    180.00   0.0  0
 KQS  CONST_33  H    N    C1   C6    180.00   0.0  0
 KQS  CONST_34  H1   N1   C6   C1    180.00   0.0  0
 KQS  CONST_35  C7   N2   C8   C9    180.00   0.0  0
 KQS  CONST_36  C7   N2   C8   O1      0.00   0.0  0
 KQS  CONST_37  H2   N2   C8   C9      0.00   0.0  0
 KQS  Var_01    C2   C3   C7   N2     57.99  30.0  2
 KQS  Var_02    C3   C7   N2   C8   -141.95  30.0  3
 KQS  Var_03    O1   C8   C9   C10   -58.05  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
 KQS  chir_01  C10  C11  C17  C9  negativ

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
 KQS  plan-1  F    0.020
 KQS  plan-1  C16  0.020
 KQS  plan-1  C15  0.020
 KQS  plan-1  C14  0.020
 KQS  plan-1  C13  0.020
 KQS  plan-1  C12  0.020
 KQS  plan-1  C11  0.020
 KQS  plan-1  C10  0.020
 KQS  plan-1  H15  0.020
 KQS  plan-1  H14  0.020
 KQS  plan-1  H13  0.020
 KQS  plan-1  H12  0.020
 KQS  plan-2  C7   0.020
 KQS  plan-2  C3   0.020
 KQS  plan-2  C2   0.020
 KQS  plan-2  C4   0.020
 KQS  plan-2  C5   0.020
 KQS  plan-2  C6   0.020
 KQS  plan-2  C1   0.020
 KQS  plan-2  N    0.020
 KQS  plan-2  N1   0.020
 KQS  plan-2  C    0.020
 KQS  plan-2  O    0.020
 KQS  plan-2  HA   0.020
 KQS  plan-2  H4   0.020
 KQS  plan-2  H5   0.020
 KQS  plan-2  H1   0.020
 KQS  plan-2  H    0.020
 KQS  plan-3  C9   0.020
 KQS  plan-3  C8   0.020
 KQS  plan-3  O1   0.020
 KQS  plan-3  N2   0.020
 KQS  plan-3  C7   0.020
 KQS  plan-3  H2   0.020

