# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:12:12 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-chloranyl-6-methoxy-1-(4-methylphenyl)sulfonyl-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc(Cl)n(c2c1)[S](=O)(=O)c3ccc(C)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
 V1K  V1K  2-chloranyl-6-methoxy-1-(4-methylphenyl)sulfonyl-benzimidazole  ligand  35  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V1K
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
 V1K  C02  C   CH3   0  -0.719  -19.5421  -19.8609   4.9940
 V1K  C03  C   CR6   0   0.117  -18.7180  -20.2127   3.7941
 V1K  C04  C   CR16  0  -0.284  -18.1103  -19.2183   3.0303
 V1K  C05  C   CR16  0  -0.208  -17.3698  -19.5301   1.9023
 V1K  C06  C   CR6   0  -0.229  -17.2391  -20.8627   1.5382
 V1K  C09  C   CR56  0   0.403  -17.4916  -23.1483  -1.5545
 V1K  C10  C   CR16  0  -0.400  -16.7632  -24.3130  -1.3913
 V1K  C11  C   CR6   0   0.401  -17.1324  -25.4043  -2.1758
 V1K  C13  C   CH3   0  -0.437  -16.6651  -27.6567  -2.7762
 V1K  C14  C   CR16  0  -0.387  -18.1973  -25.3235  -3.0872
 V1K  C15  C   CR16  0  -0.308  -18.9120  -24.1482  -3.2326
 V1K  C16  C   CR56  0   0.130  -18.5550  -23.0523  -2.4625
 V1K  C18  C   CR5   0   0.407  -18.4143  -21.1339  -1.5909
 V1K  C22  C   CR16  0  -0.191  -17.8209  -21.8801   2.2870
 V1K  C23  C   CR16  0  -0.283  -18.5599  -21.5446   3.4057
 V1K  N08  N   NR5   0  -0.751  -17.4163  -21.8759  -0.9803
 V1K  N17  N   N     0  -0.407  -19.1022  -21.7845  -2.4495
 V1K  S07  S   S     0   1.389  -16.2596  -21.2983   0.1483
 V1K  CL1  CL  CL    0  -0.036  -18.6854  -19.5087  -1.1989
 V1K  H1   H   HCH3  0   0.261  -20.5902  -19.7419   4.7120
 V1K  H2   H   HCH3  0   0.253  -19.4970  -20.6415   5.7522
 V1K  H3   H   HCH3  0   0.253  -19.2172  -18.9235   5.4427
 V1K  H4   H   HCR6  0   0.269  -18.2140  -18.1804   3.3206
 V1K  H5   H   HCR6  0   0.291  -16.9065  -18.7415   1.3260
 V1K  H6   H   HCR6  0   0.292  -15.9373  -24.4043  -0.7043
 V1K  H7   H   HCH3  0   0.260  -15.9437  -28.4127  -2.4764
 V1K  H8   H   HCH3  0   0.229  -17.6722  -28.0449  -2.6048
 V1K  H9   H   HCH3  0   0.229  -16.5406  -27.4569  -3.8438
 V1K  H10  H   HCR6  0   0.284  -18.4752  -26.1754  -3.6917
 V1K  H11  H   HCR6  0   0.271  -19.7306  -24.0835  -3.9369
 V1K  H12  H   HCR6  0   0.293  -17.7075  -22.9199   2.0081
 V1K  H13  H   HCR6  0   0.270  -19.0150  -22.3325   3.9923
 V1K  O12  O   O2    0  -0.468  -16.3952  -26.5144  -1.9895
 V1K  O20  O   OS    0  -0.592  -15.6614  -20.1232  -0.4361
 V1K  O21  O   OS    0  -0.603  -15.4543  -22.4558   0.4618

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
 V1K  C15  C14  aromatic  1.383  0.020  1.383
 V1K  C15  C16  aromatic  1.386  0.020  1.386
 V1K  C14  C11  aromatic  1.404  0.020  1.404
 V1K  N17  C16  aromatic  1.381  0.020  1.381
 V1K  N17  C18  aromatic  1.278  0.020  1.278
 V1K  C16  C09  aromatic  1.402  0.020  1.402
 V1K  C18  CL1  single    1.694  0.020  1.694
 V1K  C18  N08  aromatic  1.385  0.020  1.385
 V1K  C13  O12  single    1.413  0.020  1.413
 V1K  C11  O12  single    1.346  0.020  1.346
 V1K  C11  C10  aromatic  1.394  0.020  1.394
 V1K  C09  C10  aromatic  1.383  0.020  1.383
 V1K  C09  N08  aromatic  1.398  0.020  1.398
 V1K  N08  S07  single    1.716  0.020  1.716
 V1K  O20  S07  double    1.442  0.020  1.442
 V1K  O21  S07  double    1.445  0.020  1.445
 V1K  S07  C06  single    1.755  0.020  1.755
 V1K  C06  C05  aromatic  1.388  0.020  1.388
 V1K  C06  C22  aromatic  1.391  0.020  1.391
 V1K  C05  C04  aromatic  1.385  0.020  1.385
 V1K  C22  C23  aromatic  1.382  0.020  1.382
 V1K  C04  C03  aromatic  1.393  0.020  1.393
 V1K  C23  C03  aromatic  1.396  0.020  1.396
 V1K  C03  C02  single    1.498  0.020  1.498
 V1K  C02  H1   single    0.970  0.020  1.090
 V1K  C02  H2   single    0.970  0.020  1.090
 V1K  C02  H3   single    0.970  0.020  1.090
 V1K  C04  H4   single    0.930  0.020  1.080
 V1K  C05  H5   single    0.930  0.020  1.080
 V1K  C10  H6   single    0.930  0.020  1.080
 V1K  C13  H7   single    0.970  0.020  1.090
 V1K  C13  H8   single    0.970  0.020  1.090
 V1K  C13  H9   single    0.970  0.020  1.090
 V1K  C14  H10  single    0.930  0.020  1.080
 V1K  C15  H11  single    0.930  0.020  1.080
 V1K  C22  H12  single    0.930  0.020  1.080
 V1K  C23  H13  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
 V1K  H3   C02  H2   108.53  3.000
 V1K  H3   C02  H1   107.39  3.000
 V1K  H2   C02  H1   107.32  3.000
 V1K  H3   C02  C03  111.61  3.000
 V1K  H2   C02  C03  111.51  3.000
 V1K  H1   C02  C03  110.30  3.000
 V1K  C23  C03  C04  118.61  3.000
 V1K  C23  C03  C02  120.61  3.000
 V1K  C04  C03  C02  120.77  3.000
 V1K  H4   C04  C05  119.04  3.000
 V1K  H4   C04  C03  119.69  3.000
 V1K  C05  C04  C03  121.26  3.000
 V1K  H5   C05  C06  121.36  3.000
 V1K  H5   C05  C04  119.93  3.000
 V1K  C06  C05  C04  118.71  3.000
 V1K  S07  C06  C22  118.57  3.000
 V1K  C22  C06  C05  121.46  3.000
 V1K  S07  C06  C05  119.91  3.000
 V1K  N08  C09  C16  104.16  3.000
 V1K  N08  C09  C10  133.59  3.000
 V1K  C16  C09  C10  122.25  3.000
 V1K  H6   C10  C11  119.69  3.000
 V1K  H6   C10  C09  123.36  3.000
 V1K  C11  C10  C09  116.96  3.000
 V1K  O12  C11  C14  123.57  3.000
 V1K  O12  C11  C10  115.02  3.000
 V1K  C14  C11  C10  121.41  3.000
 V1K  H9   C13  H8   108.85  3.000
 V1K  H9   C13  H7   108.71  3.000
 V1K  H8   C13  H7   108.74  3.000
 V1K  H9   C13  O12  111.98  3.000
 V1K  H8   C13  O12  112.08  3.000
 V1K  H7   C13  O12  106.37  3.000
 V1K  H10  C14  C15  118.56  3.000
 V1K  H10  C14  C11  120.84  3.000
 V1K  C15  C14  C11  120.60  3.000
 V1K  H11  C15  C16  120.62  3.000
 V1K  H11  C15  C14  120.68  3.000
 V1K  C16  C15  C14  118.70  3.000
 V1K  N17  C16  C15  128.98  3.000
 V1K  N17  C16  C09  110.94  3.000
 V1K  C15  C16  C09  120.08  3.000
 V1K  CL1  C18  N17  123.90  3.000
 V1K  CL1  C18  N08  121.81  3.000
 V1K  N17  C18  N08  114.28  3.000
 V1K  H12  C22  C23  119.85  3.000
 V1K  H12  C22  C06  121.34  3.000
 V1K  C23  C22  C06  118.81  3.000
 V1K  H13  C23  C22  119.12  3.000
 V1K  H13  C23  C03  119.73  3.000
 V1K  C22  C23  C03  121.15  3.000
 V1K  S07  N08  C18  126.52  3.000
 V1K  S07  N08  C09  127.79  3.000
 V1K  C18  N08  C09  105.52  3.000
 V1K  C18  N17  C16  105.09  3.000
 V1K  O21  S07  O20  120.63  3.000
 V1K  O21  S07  N08  104.40  3.000
 V1K  O20  S07  N08  106.69  3.000
 V1K  O21  S07  C06  109.76  3.000
 V1K  O20  S07  C06  110.50  3.000
 V1K  N08  S07  C06  103.19  3.000
 V1K  C13  O12  C11  119.02  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
 V1K  CONST_01  C06  C05  C04  C03     0.00   0.0  0
 V1K  CONST_02  C06  C22  C23  C03     0.00   0.0  0
 V1K  CONST_03  C22  C06  C05  C04     0.00   0.0  0
 V1K  CONST_04  C22  C23  C03  C04     0.00   0.0  0
 V1K  CONST_05  C23  C22  C06  C05     0.00   0.0  0
 V1K  CONST_06  C23  C03  C04  C05     0.00   0.0  0
 V1K  CONST_07  C14  C15  C16  C09     0.00   0.0  0
 V1K  CONST_08  C18  N17  C16  C09     0.00   0.0  0
 V1K  CONST_09  C14  C11  C10  C09     0.00   0.0  0
 V1K  CONST_10  N17  C18  N08  C09     0.00   0.0  0
 V1K  CONST_11  C15  C14  C11  C10     0.00   0.0  0
 V1K  CONST_12  C15  C16  C09  C10     0.00   0.0  0
 V1K  CONST_13  N17  C16  C09  C10   180.00   0.0  0
 V1K  CONST_14  C18  N08  C09  C10   180.00   0.0  0
 V1K  CONST_15  C16  C15  C14  C11     0.00   0.0  0
 V1K  CONST_16  C16  C09  C10  C11     0.00   0.0  0
 V1K  CONST_17  N08  C09  C10  C11   180.00   0.0  0
 V1K  CONST_18  N17  C16  C15  C14   180.00   0.0  0
 V1K  CONST_19  C18  N17  C16  C15   180.00   0.0  0
 V1K  CONST_20  N08  C09  C16  C15   180.00   0.0  0
 V1K  CONST_21  N08  C18  N17  C16     0.00   0.0  0
 V1K  CONST_22  C18  N08  C09  C16     0.00   0.0  0
 V1K  CONST_23  N17  C16  C09  N08     0.00   0.0  0
 V1K  CONST_24  C05  C04  C03  C02   180.00   0.0  0
 V1K  CONST_25  C22  C23  C03  C02   180.00   0.0  0
 V1K  CONST_26  S07  C06  C05  C04   180.00   0.0  0
 V1K  CONST_27  O12  C11  C10  C09   180.00   0.0  0
 V1K  CONST_28  CL1  C18  N08  C09   180.00   0.0  0
 V1K  CONST_29  S07  N08  C09  C10     0.00   0.0  0
 V1K  CONST_30  O12  C11  C14  C15   180.00   0.0  0
 V1K  CONST_31  CL1  C18  N17  C16   180.00   0.0  0
 V1K  CONST_32  S07  N08  C09  C16   180.00   0.0  0
 V1K  CONST_33  S07  C06  C22  C23   180.00   0.0  0
 V1K  CONST_34  S07  N08  C18  N17   180.00   0.0  0
 V1K  CONST_35  H5   C05  C04  C03   180.00   0.0  0
 V1K  CONST_36  H12  C22  C23  C03   180.00   0.0  0
 V1K  CONST_37  H13  C23  C03  C04   180.00   0.0  0
 V1K  CONST_38  H4   C04  C05  C06   180.00   0.0  0
 V1K  CONST_39  H11  C15  C16  C09   180.00   0.0  0
 V1K  CONST_40  H10  C14  C11  C10   180.00   0.0  0
 V1K  CONST_41  H6   C10  C11  C14   180.00   0.0  0
 V1K  Var_01    N08  S07  C06  C05  -112.17  30.0  2
 V1K  Var_02    C18  N08  S07  C06    65.72  30.0  2
 V1K  Var_03    C14  C11  O12  C13     2.15  30.0  1
 V1K  Var_04    H1   C02  C03  C04    91.55  30.0  2
 V1K  Var_05    H7   C13  O12  C11   178.65  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
 V1K  plan-1  C02  0.020
 V1K  plan-1  C03  0.020
 V1K  plan-1  C04  0.020
 V1K  plan-1  C05  0.020
 V1K  plan-1  C06  0.020
 V1K  plan-1  C22  0.020
 V1K  plan-1  C23  0.020
 V1K  plan-1  S07  0.020
 V1K  plan-1  H4   0.020
 V1K  plan-1  H5   0.020
 V1K  plan-1  H12  0.020
 V1K  plan-1  H13  0.020
 V1K  plan-2  C09  0.020
 V1K  plan-2  C10  0.020
 V1K  plan-2  C11  0.020
 V1K  plan-2  C14  0.020
 V1K  plan-2  C15  0.020
 V1K  plan-2  C16  0.020
 V1K  plan-2  C18  0.020
 V1K  plan-2  N08  0.020
 V1K  plan-2  N17  0.020
 V1K  plan-2  S07  0.020
 V1K  plan-2  CL1  0.020
 V1K  plan-2  H6   0.020
 V1K  plan-2  H10  0.020
 V1K  plan-2  H11  0.020
 V1K  plan-2  O12  0.020

