# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:57:59 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: ~{N}-[(4-fluorophenyl)methyl]-1,3,6-trimethyl-2-oxidanylidene-benzimidazole-5-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(c(C)cc12)[S](=O)(=O)NCc3ccc(F)cc3
#
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
 JR4  JR4  ~{N}-[(4-fluorophenyl)methyl]-1,3,6-trimethyl-2-oxidanylidene-benzimidazole-5-sulfonamide  ligand  43  25  .  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_JR4
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
 JR4  C01  C  CH3   0  -0.537  -5.0763   1.8798  -1.6915
 JR4  C03  C  CR5   0   0.663  -4.8982   1.1584   0.6962
 JR4  C06  C  CH3   0  -0.537  -4.0996   0.1205   2.8199
 JR4  C07  C  CR56  0   0.349  -2.9798  -0.0097   0.5842
 JR4  C08  C  CR16  0  -0.305  -1.8607  -0.7718   0.8169
 JR4  C09  C  CR6   0  -0.294  -1.0207  -1.0300  -0.2714
 JR4  C10  C  CR6   0   0.150  -1.2766  -0.5386  -1.5613
 JR4  C11  C  CH3   0  -0.773  -0.3675  -0.7567  -2.7383
 JR4  C12  C  CR16  0  -0.367  -2.4241   0.2316  -1.7596
 JR4  C13  C  CR56  0   0.378  -3.2617   0.4834  -0.6924
 JR4  C18  C  CH2   0  -0.368   1.9070   0.1647   0.3001
 JR4  C19  C  CR6   0   0.099   3.3644   0.5334   0.3224
 JR4  C20  C  CR16  0  -0.258   4.2751  -0.2487   1.0295
 JR4  C21  C  CR16  0  -0.397   5.6191   0.0830   1.0695
 JR4  C22  C  CR6   0   0.517   6.0417   1.2101   0.3872
 JR4  C24  C  CR16  0  -0.398   5.1704   2.0049  -0.3282
 JR4  C25  C  CR16  0  -0.288   3.8260   1.6534  -0.3565
 JR4  F23  F  F     0  -0.315   7.3427   1.5402   0.4243
 JR4  N02  N  NR5   0  -0.585  -4.4326   1.1857  -0.6041
 JR4  N05  N  NR5   0  -0.586  -3.9887   0.4187   1.4147
 JR4  N17  N  NC1   0  -0.723   1.7374  -1.1519  -0.3039
 JR4  O15  O  OS    0  -0.649   0.4312  -2.2750   1.4973
 JR4  O16  O  OS    0  -0.657   0.4238  -3.1831  -0.8372
 JR4  S14  S  S     0   1.369   0.4019  -2.0399   0.0621
 JR4  H1   H  HCH3  0   0.272  -6.0617   2.2051  -1.3723
 JR4  H2   H  HCH3  0   0.260  -4.4991   2.7534  -1.9932
 JR4  H3   H  HCH3  0   0.261  -5.1882   1.2159  -2.5470
 JR4  H4   H  HCH3  0   0.271  -4.9274   0.6854   3.2376
 JR4  H5   H  HCH3  0   0.259  -4.2834  -0.9416   2.9799
 JR4  H6   H  HCH3  0   0.259  -3.1870   0.4056   3.3417
 JR4  H7   H  HCR6  0   0.299  -1.6368  -1.1559   1.8018
 JR4  H8   H  HCH3  0   0.262  -0.0521  -1.7917  -2.8468
 JR4  H9   H  HCH3  0   0.270  -0.8725  -0.4716  -3.6588
 JR4  H10  H  HCH3  0   0.251   0.5286  -0.1350  -2.6697
 JR4  H11  H  HCR6  0   0.282  -2.6453   0.6189  -2.7457
 JR4  H12  H  HCH2  0   0.283   1.5247   0.1230   1.3210
 JR4  H13  H  HCH2  0   0.263   1.3314   0.9308  -0.2283
 JR4  H14  H  HCR6  0   0.265   3.9317  -1.1292   1.5584
 JR4  H15  H  HCR6  0   0.281   6.3251  -0.5216   1.6234
 JR4  H16  H  HCR6  0   0.282   5.5286   2.8792  -0.8556
 JR4  H17  H  HCR6  0   0.267   3.1334   2.2664  -0.9199
 JR4  H18  H  HNC1  0   0.416   1.9998  -1.2113  -1.2809
 JR4  O04  O  O     0  -0.491  -5.9102   1.6846   1.1162

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
 JR4  C21  C20  aromatic  1.385  0.020  1.385
 JR4  C21  C22  aromatic  1.384  0.020  1.384
 JR4  F23  C22  single    1.343  0.020  1.343
 JR4  C20  C19  aromatic  1.393  0.020  1.393
 JR4  C22  C24  aromatic  1.379  0.020  1.379
 JR4  C19  C25  aromatic  1.389  0.020  1.389
 JR4  C19  C18  single    1.504  0.020  1.504
 JR4  C24  C25  aromatic  1.390  0.020  1.390
 JR4  C18  N17  single    1.458  0.020  1.458
 JR4  C06  N05  single    1.441  0.020  1.441
 JR4  N17  S14  single    1.645  0.020  1.645
 JR4  N05  C03  single    1.375  0.020  1.375
 JR4  N05  C07  single    1.375  0.020  1.375
 JR4  O04  C03  double    1.216  0.020  1.216
 JR4  O16  S14  double    1.455  0.020  1.455
 JR4  C03  N02  single    1.381  0.020  1.381
 JR4  C08  C07  aromatic  1.374  0.020  1.374
 JR4  C08  C09  aromatic  1.399  0.020  1.399
 JR4  C07  C13  aromatic  1.397  0.020  1.397
 JR4  S14  C09  single    1.776  0.020  1.776
 JR4  S14  O15  double    1.455  0.020  1.455
 JR4  C09  C10  aromatic  1.404  0.020  1.404
 JR4  N02  C13  single    1.368  0.020  1.368
 JR4  N02  C01  single    1.442  0.020  1.442
 JR4  C13  C12  aromatic  1.380  0.020  1.380
 JR4  C10  C12  aromatic  1.396  0.020  1.396
 JR4  C10  C11  single    1.503  0.020  1.503
 JR4  C01  H1   single    0.970  0.020  1.090
 JR4  C01  H2   single    0.970  0.020  1.090
 JR4  C01  H3   single    0.970  0.020  1.090
 JR4  C06  H4   single    0.970  0.020  1.090
 JR4  C06  H5   single    0.970  0.020  1.090
 JR4  C06  H6   single    0.970  0.020  1.090
 JR4  C08  H7   single    0.930  0.020  1.080
 JR4  C11  H8   single    0.970  0.020  1.090
 JR4  C11  H9   single    0.970  0.020  1.090
 JR4  C11  H10  single    0.970  0.020  1.090
 JR4  C12  H11  single    0.930  0.020  1.080
 JR4  C18  H12  single    0.970  0.020  1.090
 JR4  C18  H13  single    0.970  0.020  1.090
 JR4  C20  H14  single    0.930  0.020  1.080
 JR4  C21  H15  single    0.930  0.020  1.080
 JR4  C24  H16  single    0.930  0.020  1.080
 JR4  C25  H17  single    0.930  0.020  1.080
 JR4  N17  H18  single    0.890  0.020  1.040

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
 JR4  H3   C01  H2   109.02  3.000
 JR4  H3   C01  H1   108.69  3.000
 JR4  H2   C01  H1   108.78  3.000
 JR4  H3   C01  N02  110.18  3.000
 JR4  H2   C01  N02  110.99  3.000
 JR4  H1   C01  N02  109.13  3.000
 JR4  O04  C03  N05  127.08  3.000
 JR4  O04  C03  N02  126.68  3.000
 JR4  N05  C03  N02  106.24  3.000
 JR4  H6   C06  H5   109.03  3.000
 JR4  H6   C06  H4   108.56  3.000
 JR4  H5   C06  H4   108.79  3.000
 JR4  H6   C06  N05  110.40  3.000
 JR4  H5   C06  N05  110.97  3.000
 JR4  H4   C06  N05  109.04  3.000
 JR4  N05  C07  C13  107.08  3.000
 JR4  C13  C07  C08  120.99  3.000
 JR4  N05  C07  C08  131.93  3.000
 JR4  H7   C08  C09  121.28  3.000
 JR4  H7   C08  C07  121.35  3.000
 JR4  C09  C08  C07  117.37  3.000
 JR4  S14  C09  C10  121.16  3.000
 JR4  C10  C09  C08  122.74  3.000
 JR4  S14  C09  C08  116.09  3.000
 JR4  C12  C10  C11  117.77  3.000
 JR4  C11  C10  C09  123.95  3.000
 JR4  C12  C10  C09  118.25  3.000
 JR4  H10  C11  H9   106.54  3.000
 JR4  H10  C11  H8   108.06  3.000
 JR4  H9   C11  H8   107.43  3.000
 JR4  H10  C11  C10  111.36  3.000
 JR4  H9   C11  C10  110.11  3.000
 JR4  H8   C11  C10  113.06  3.000
 JR4  H11  C12  C13  121.01  3.000
 JR4  H11  C12  C10  119.66  3.000
 JR4  C13  C12  C10  119.33  3.000
 JR4  N02  C13  C12  131.54  3.000
 JR4  C12  C13  C07  121.32  3.000
 JR4  N02  C13  C07  107.15  3.000
 JR4  H13  C18  H12  107.11  3.000
 JR4  H13  C18  N17  111.77  3.000
 JR4  H12  C18  N17  108.20  3.000
 JR4  H13  C18  C19  110.20  3.000
 JR4  H12  C18  C19  109.58  3.000
 JR4  N17  C18  C19  109.90  3.000
 JR4  C25  C19  C20  118.93  3.000
 JR4  C25  C19  C18  120.85  3.000
 JR4  C20  C19  C18  120.23  3.000
 JR4  H14  C20  C21  119.23  3.000
 JR4  H14  C20  C19  119.80  3.000
 JR4  C21  C20  C19  120.97  3.000
 JR4  H15  C21  C22  120.55  3.000
 JR4  H15  C21  C20  120.94  3.000
 JR4  C22  C21  C20  118.50  3.000
 JR4  F23  C22  C24  119.00  3.000
 JR4  C24  C22  C21  122.15  3.000
 JR4  F23  C22  C21  118.85  3.000
 JR4  H16  C24  C25  120.98  3.000
 JR4  H16  C24  C22  120.61  3.000
 JR4  C25  C24  C22  118.41  3.000
 JR4  H17  C25  C24  119.08  3.000
 JR4  H17  C25  C19  119.89  3.000
 JR4  C24  C25  C19  121.03  3.000
 JR4  C13  N02  C03  109.82  3.000
 JR4  C13  N02  C01  125.49  3.000
 JR4  C03  N02  C01  124.68  3.000
 JR4  C07  N05  C06  125.52  3.000
 JR4  C07  N05  C03  109.71  3.000
 JR4  C06  N05  C03  124.76  3.000
 JR4  H18  N17  S14  113.14  3.000
 JR4  H18  N17  C18  114.97  3.000
 JR4  S14  N17  C18  119.32  3.000
 JR4  O16  S14  O15  118.86  3.000
 JR4  O15  S14  N17  106.88  3.000
 JR4  O16  S14  N17  105.93  3.000
 JR4  O15  S14  C09  107.05  3.000
 JR4  O16  S14  C09  110.05  3.000
 JR4  N17  S14  C09  107.55  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
 JR4  CONST_01  C10  C09  C08  C07     0.00   0.0  0
 JR4  CONST_02  C10  C12  C13  C07     0.00   0.0  0
 JR4  CONST_03  C12  C13  C07  C08     0.00   0.0  0
 JR4  CONST_04  C12  C10  C09  C08     0.00   0.0  0
 JR4  CONST_05  C13  C07  C08  C09     0.00   0.0  0
 JR4  CONST_06  C13  C12  C10  C09     0.00   0.0  0
 JR4  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 JR4  CONST_08  C22  C24  C25  C19     0.00   0.0  0
 JR4  CONST_09  C24  C22  C21  C20     0.00   0.0  0
 JR4  CONST_10  C24  C25  C19  C20     0.00   0.0  0
 JR4  CONST_11  C25  C19  C20  C21     0.00   0.0  0
 JR4  CONST_12  C25  C24  C22  C21     0.00   0.0  0
 JR4  CONST_13  C13  C07  N05  C03     0.00   0.0  0
 JR4  CONST_14  C07  C13  N02  C03     0.00   0.0  0
 JR4  CONST_15  N02  C03  N05  C07     0.00   0.0  0
 JR4  CONST_16  N05  C03  N02  C13     0.00   0.0  0
 JR4  CONST_17  N05  C07  C13  N02     0.00   0.0  0
 JR4  CONST_18  S14  C09  C08  C07   180.00   0.0  0
 JR4  CONST_19  C11  C10  C09  C08   180.00   0.0  0
 JR4  CONST_20  C13  C12  C10  C11   180.00   0.0  0
 JR4  CONST_21  S14  C09  C10  C12   180.00   0.0  0
 JR4  CONST_22  C21  C20  C19  C18   180.00   0.0  0
 JR4  CONST_23  C24  C25  C19  C18   180.00   0.0  0
 JR4  CONST_24  F23  C22  C21  C20   180.00   0.0  0
 JR4  CONST_25  F23  C22  C24  C25   180.00   0.0  0
 JR4  CONST_26  N05  C03  N02  C01   180.00   0.0  0
 JR4  CONST_27  C07  C13  N02  C01   180.00   0.0  0
 JR4  CONST_28  N02  C03  N05  C06   180.00   0.0  0
 JR4  CONST_29  C13  C07  N05  C06   180.00   0.0  0
 JR4  CONST_30  O04  C03  N05  C07   180.00   0.0  0
 JR4  CONST_31  O04  C03  N02  C13   180.00   0.0  0
 JR4  CONST_32  H11  C12  C13  C07   180.00   0.0  0
 JR4  CONST_33  H7   C08  C09  C10   180.00   0.0  0
 JR4  CONST_34  H15  C21  C20  C19   180.00   0.0  0
 JR4  CONST_35  H16  C24  C25  C19   180.00   0.0  0
 JR4  CONST_36  H17  C25  C19  C20   180.00   0.0  0
 JR4  CONST_37  H14  C20  C21  C22   180.00   0.0  0
 JR4  CONST_38  O04  C03  N02  C01     0.00   0.0  0
 JR4  CONST_39  O04  C03  N05  C06     0.00   0.0  0
 JR4  Var_01    N17  S14  C09  C08  -120.02  30.0  2
 JR4  Var_02    N17  C18  C19  C20   -61.16  30.0  2
 JR4  Var_03    H4   C06  N05  C03    -7.96  30.0  3
 JR4  Var_04    H1   C01  N02  C03   -10.79  30.0  3
 JR4  Var_05    H8   C11  C10  C09    47.77  30.0  2
 JR4  Var_06    C18  N17  S14  C09    53.88  30.0  2
 JR4  Var_07    S14  N17  C18  C19   156.07  30.0  3

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
 JR4  plan-1  C18  0.020
 JR4  plan-1  C19  0.020
 JR4  plan-1  C20  0.020
 JR4  plan-1  C21  0.020
 JR4  plan-1  C22  0.020
 JR4  plan-1  C24  0.020
 JR4  plan-1  C25  0.020
 JR4  plan-1  F23  0.020
 JR4  plan-1  H14  0.020
 JR4  plan-1  H15  0.020
 JR4  plan-1  H16  0.020
 JR4  plan-1  H17  0.020
 JR4  plan-2  C01  0.020
 JR4  plan-2  C03  0.020
 JR4  plan-2  C06  0.020
 JR4  plan-2  C07  0.020
 JR4  plan-2  C08  0.020
 JR4  plan-2  C09  0.020
 JR4  plan-2  C10  0.020
 JR4  plan-2  C11  0.020
 JR4  plan-2  C12  0.020
 JR4  plan-2  C13  0.020
 JR4  plan-2  N02  0.020
 JR4  plan-2  N05  0.020
 JR4  plan-2  S14  0.020
 JR4  plan-2  H7   0.020
 JR4  plan-2  H11  0.020
 JR4  plan-2  O04  0.020

