# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 00:26:45 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-[(4-fluorophenyl)sulfonyl]-2-methyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccccc2n1[S](=O)(=O)c3ccc(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
 1DD  1DD  1-[(4-fluorophenyl)sulfonyl]-2-methyl-1H-benzimidazole  ligand  31  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1DD
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
 1DD  F20  F  F     0  -0.296   4.5134   1.8286  -1.2859
 1DD  C17  C  CR6   0   0.562   3.5246   1.1551  -0.6987
 1DD  C16  C  CR16  0  -0.395   3.3455  -0.1778  -1.0237
 1DD  C15  C  CR16  0  -0.213   2.3235  -0.8787  -0.4100
 1DD  C18  C  CR16  0  -0.398   2.7242   1.8126   0.2177
 1DD  C19  C  CR16  0  -0.205   1.7021   1.1098   0.8315
 1DD  C14  C  CR6   0  -0.203   1.5067  -0.2277   0.5074
 1DD  S10  S  S     0   1.394   0.1960  -1.1196   1.2695
 1DD  O11  O  OS    0  -0.602   0.4945  -2.5318   1.2442
 1DD  O12  O  OS    0  -0.608  -0.1745  -0.4651   2.5035
 1DD  N9   N  NR5   0  -0.759  -1.1082  -0.8792   0.2114
 1DD  C8   C  CR5   0   0.460  -1.4619  -1.6465  -0.9042
 1DD  C13  C  CH3   0  -0.742  -0.8919  -2.9729  -1.2490
 1DD  N7   N  N     0  -0.447  -2.3789  -1.0667  -1.6043
 1DD  C2   C  CR56  0   0.146  -2.6590   0.1328  -0.9880
 1DD  C3   C  CR56  0   0.359  -1.8749   0.2889   0.1591
 1DD  C4   C  CR16  0  -0.291  -1.9691   1.4175   0.9636
 1DD  C5   C  CR16  0  -0.267  -2.8734   2.3916   0.5685
 1DD  C6   C  CR16  0  -0.264  -3.6637   2.2460  -0.5758
 1DD  C1   C  CR16  0  -0.324  -3.5696   1.1136  -1.3650
 1DD  H1   H  HCR6  0   0.304   3.9970  -0.6643  -1.7364
 1DD  H2   H  HCR6  0   0.302   2.1861  -1.9242  -0.6485
 1DD  H3   H  HCR6  0   0.304   2.8997   2.8524   0.4574
 1DD  H4   H  HCR6  0   0.299   1.0828   1.6120   1.5609
 1DD  H5   H  HCH3  0   0.275  -1.0744  -3.7090  -0.4688
 1DD  H6   H  HCH3  0   0.274  -1.3741  -3.3075  -2.1633
 1DD  H7   H  HCH3  0   0.262   0.1816  -2.9330  -1.4277
 1DD  H8   H  HCR6  0   0.282  -1.3911   1.5480   1.8652
 1DD  H9   H  HCR6  0   0.264  -2.9702   3.2847   1.1711
 1DD  H10  H  HCR6  0   0.261  -4.3594   3.0301  -0.8431
 1DD  H11  H  HCR6  0   0.265  -4.1792   0.9889  -2.2501

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
 1DD  O12  S10  double    1.445  0.020  1.445
 1DD  O11  S10  double    1.444  0.020  1.444
 1DD  S10  C14  single    1.759  0.020  1.759
 1DD  S10  N9   single    1.697  0.020  1.697
 1DD  C19  C14  aromatic  1.390  0.020  1.390
 1DD  C19  C18  aromatic  1.384  0.020  1.384
 1DD  C13  C8   single    1.484  0.020  1.484
 1DD  C14  C15  aromatic  1.390  0.020  1.390
 1DD  C18  C17  aromatic  1.383  0.020  1.383
 1DD  C15  C16  aromatic  1.383  0.020  1.383
 1DD  N9   C8   aromatic  1.399  0.020  1.399
 1DD  N9   C3   aromatic  1.398  0.020  1.398
 1DD  C8   N7   aromatic  1.291  0.020  1.291
 1DD  C17  C16  aromatic  1.384  0.020  1.384
 1DD  C17  F20  single    1.333  0.020  1.333
 1DD  C3   C4   aromatic  1.389  0.020  1.389
 1DD  C3   C2   aromatic  1.398  0.020  1.398
 1DD  N7   C2   aromatic  1.377  0.020  1.377
 1DD  C4   C5   aromatic  1.387  0.020  1.387
 1DD  C2   C1   aromatic  1.390  0.020  1.390
 1DD  C5   C6   aromatic  1.398  0.020  1.398
 1DD  C1   C6   aromatic  1.383  0.020  1.383
 1DD  C16  H1   single    0.930  0.020  1.080
 1DD  C15  H2   single    0.930  0.020  1.080
 1DD  C18  H3   single    0.930  0.020  1.080
 1DD  C19  H4   single    0.930  0.020  1.080
 1DD  C13  H5   single    0.970  0.020  1.090
 1DD  C13  H6   single    0.970  0.020  1.090
 1DD  C13  H7   single    0.970  0.020  1.090
 1DD  C4   H8   single    0.930  0.020  1.080
 1DD  C5   H9   single    0.930  0.020  1.080
 1DD  C6   H10  single    0.930  0.020  1.080
 1DD  C1   H11  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
 1DD  C18  C17  C16  122.60  3.000
 1DD  C16  C17  F20  118.65  3.000
 1DD  C18  C17  F20  118.76  3.000
 1DD  H1   C16  C15  120.65  3.000
 1DD  H1   C16  C17  120.68  3.000
 1DD  C15  C16  C17  118.67  3.000
 1DD  H2   C15  C14  121.58  3.000
 1DD  H2   C15  C16  119.09  3.000
 1DD  C14  C15  C16  119.33  3.000
 1DD  H3   C18  C19  120.65  3.000
 1DD  H3   C18  C17  120.67  3.000
 1DD  C19  C18  C17  118.68  3.000
 1DD  H4   C19  C14  121.60  3.000
 1DD  H4   C19  C18  119.12  3.000
 1DD  C14  C19  C18  119.28  3.000
 1DD  S10  C14  C19  119.45  3.000
 1DD  C19  C14  C15  121.45  3.000
 1DD  S10  C14  C15  119.10  3.000
 1DD  N9   S10  O12  105.74  3.000
 1DD  N9   S10  O11  106.65  3.000
 1DD  O12  S10  O11  120.73  3.000
 1DD  N9   S10  C14  103.34  3.000
 1DD  O11  S10  C14  109.53  3.000
 1DD  O12  S10  C14  109.36  3.000
 1DD  C3   N9   C8   106.84  3.000
 1DD  C3   N9   S10  124.28  3.000
 1DD  C8   N9   S10  127.86  3.000
 1DD  N7   C8   C13  123.23  3.000
 1DD  N7   C8   N9   111.44  3.000
 1DD  C13  C8   N9   125.32  3.000
 1DD  H7   C13  H6   108.10  3.000
 1DD  H7   C13  H5   107.93  3.000
 1DD  H6   C13  H5   108.70  3.000
 1DD  H7   C13  C8   112.58  3.000
 1DD  H6   C13  C8   107.48  3.000
 1DD  H5   C13  C8   111.93  3.000
 1DD  C2   N7   C8   107.03  3.000
 1DD  C1   C2   C3   120.73  3.000
 1DD  C1   C2   N7   128.77  3.000
 1DD  C3   C2   N7   110.50  3.000
 1DD  C4   C3   C2   121.85  3.000
 1DD  C2   C3   N9   104.18  3.000
 1DD  C4   C3   N9   133.97  3.000
 1DD  H8   C4   C5   120.17  3.000
 1DD  H8   C4   C3   123.08  3.000
 1DD  C5   C4   C3   116.74  3.000
 1DD  H9   C5   C6   119.43  3.000
 1DD  H9   C5   C4   118.66  3.000
 1DD  C6   C5   C4   121.91  3.000
 1DD  H10  C6   C1   119.74  3.000
 1DD  H10  C6   C5   119.35  3.000
 1DD  C1   C6   C5   120.91  3.000
 1DD  H11  C1   C6   121.51  3.000
 1DD  H11  C1   C2   120.63  3.000
 1DD  C6   C1   C2   117.85  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
 1DD  CONST_01  C14  C19  C18  C17    0.00   0.0  0
 1DD  CONST_02  C14  C15  C16  C17    0.00   0.0  0
 1DD  CONST_03  C19  C14  C15  C16    0.00   0.0  0
 1DD  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 1DD  CONST_05  C18  C19  C14  C15    0.00   0.0  0
 1DD  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 1DD  CONST_07  C2   N7   C8   N9     0.00   0.0  0
 1DD  CONST_08  C5   C4   C3   N9   180.00   0.0  0
 1DD  CONST_09  N7   C2   C3   N9     0.00   0.0  0
 1DD  CONST_10  C1   C2   C3   N9   180.00   0.0  0
 1DD  CONST_11  C4   C3   N9   C8   180.00   0.0  0
 1DD  CONST_12  C2   C3   N9   C8     0.00   0.0  0
 1DD  CONST_13  C3   C2   N7   C8     0.00   0.0  0
 1DD  CONST_14  C1   C2   N7   C8   180.00   0.0  0
 1DD  CONST_15  C3   N9   C8   N7     0.00   0.0  0
 1DD  CONST_16  C4   C3   C2   N7   180.00   0.0  0
 1DD  CONST_17  C6   C1   C2   N7   180.00   0.0  0
 1DD  CONST_18  C5   C4   C3   C2     0.00   0.0  0
 1DD  CONST_19  C5   C6   C1   C2     0.00   0.0  0
 1DD  CONST_20  C6   C5   C4   C3     0.00   0.0  0
 1DD  CONST_21  C6   C1   C2   C3     0.00   0.0  0
 1DD  CONST_22  C1   C2   C3   C4     0.00   0.0  0
 1DD  CONST_23  C1   C6   C5   C4     0.00   0.0  0
 1DD  CONST_24  C19  C18  C17  F20  180.00   0.0  0
 1DD  CONST_25  C15  C16  C17  F20  180.00   0.0  0
 1DD  CONST_26  S10  C14  C15  C16  180.00   0.0  0
 1DD  CONST_27  S10  C14  C19  C18  180.00   0.0  0
 1DD  CONST_28  N7   C8   N9   S10  180.00   0.0  0
 1DD  CONST_29  C4   C3   N9   S10    0.00   0.0  0
 1DD  CONST_30  C2   C3   N9   S10  180.00   0.0  0
 1DD  CONST_31  C3   N9   C8   C13  180.00   0.0  0
 1DD  CONST_32  C2   N7   C8   C13  180.00   0.0  0
 1DD  CONST_33  H4   C19  C18  C17  180.00   0.0  0
 1DD  CONST_34  H2   C15  C16  C17  180.00   0.0  0
 1DD  CONST_35  H3   C18  C17  C16  180.00   0.0  0
 1DD  CONST_36  H1   C16  C17  C18  180.00   0.0  0
 1DD  CONST_37  H8   C4   C3   N9     0.00   0.0  0
 1DD  CONST_38  H11  C1   C2   N7     0.00   0.0  0
 1DD  CONST_39  H10  C6   C1   C2   180.00   0.0  0
 1DD  CONST_40  H9   C5   C4   C3   180.00   0.0  0
 1DD  Var_01    N9   S10  C14  C15  -89.61  30.0  2
 1DD  Var_02    C8   N9   S10  C14   88.46  30.0  2
 1DD  Var_03    H5   C13  C8   N9    60.37  30.0  2

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
 1DD  plan-1  F20  0.020
 1DD  plan-1  C17  0.020
 1DD  plan-1  C16  0.020
 1DD  plan-1  C15  0.020
 1DD  plan-1  C18  0.020
 1DD  plan-1  C19  0.020
 1DD  plan-1  C14  0.020
 1DD  plan-1  S10  0.020
 1DD  plan-1  H1   0.020
 1DD  plan-1  H2   0.020
 1DD  plan-1  H3   0.020
 1DD  plan-1  H4   0.020
 1DD  plan-2  S10  0.020
 1DD  plan-2  N9   0.020
 1DD  plan-2  C8   0.020
 1DD  plan-2  C13  0.020
 1DD  plan-2  N7   0.020
 1DD  plan-2  C2   0.020
 1DD  plan-2  C3   0.020
 1DD  plan-2  C4   0.020
 1DD  plan-2  C5   0.020
 1DD  plan-2  C6   0.020
 1DD  plan-2  C1   0.020
 1DD  plan-2  H8   0.020
 1DD  plan-2  H9   0.020
 1DD  plan-2  H10  0.020
 1DD  plan-2  H11  0.020

