# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 22:44:05 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1OCCSc2nc3ccccc3n2CC(O)=O
#
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
 RF4  RF4  '(2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid'  ligand  45  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RF4
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
 RF4  C01  C  CR6   0   0.026   5.0254  -0.1241  -1.3016
 RF4  C02  C  CR16  0  -0.323   6.3423  -0.5762  -1.2887
 RF4  C03  C  CR16  0  -0.240   7.0863  -0.5670  -0.1184
 RF4  C04  C  CR16  0  -0.322   6.5240  -0.0885   1.0555
 RF4  C05  C  CR6   0   0.026   5.2112   0.3748   1.0841
 RF4  C06  C  CR6   0   0.275   4.4802   0.3419  -0.1043
 RF4  O07  O  O2    0  -0.490   3.1955   0.8190  -0.1075
 RF4  C08  C  CH2   0  -0.153   2.2063  -0.1489   0.2003
 RF4  C09  C  CH3   0  -0.717   4.2214  -0.1081  -2.5690
 RF4  C10  C  CH3   0  -0.719   4.6114   0.9197   2.3476
 RF4  C11  C  CH2   0  -0.581   0.8686   0.5631   0.1245
 RF4  S12  S  S2    0   0.041  -0.4129  -0.6218   0.6215
 RF4  C13  C  CR5   0   0.326  -1.8376   0.2965   0.2304
 RF4  N14  N  NR5   0  -0.541  -3.0664  -0.1769   0.5903
 RF4  C15  C  CR56  0   0.347  -3.9835   0.7334   0.1145
 RF4  C16  C  CR56  0   0.142  -3.2163   1.7417  -0.4863
 RF4  N17  N  N     0  -0.467  -1.8768   1.4337  -0.3975
 RF4  C18  C  CR16  0  -0.307  -5.3691   0.7743   0.1647
 RF4  C19  C  CR16  0  -0.276  -5.9784   1.8787  -0.4109
 RF4  C20  C  CR16  0  -0.271  -5.2282   2.8981  -1.0113
 RF4  C21  C  CR16  0  -0.332  -3.8448   2.8452  -1.0574
 RF4  C22  C  CH2   0  -0.479  -3.3523  -1.4214   1.2361
 RF4  C23  C  C     0   0.548  -3.3897  -2.5701   0.2476
 RF4  O24  O  O     0  -0.419  -3.1952  -2.4517  -0.9315
 RF4  O25  O  OH1   0  -0.583  -3.6591  -3.7063   0.8653
 RF4  H1   H  HCR6  0   0.249   6.7864  -0.9373  -2.2085
 RF4  H2   H  HCR6  0   0.252   8.1086  -0.9224  -0.1230
 RF4  H3   H  HCR6  0   0.249   7.1106  -0.0728   1.9663
 RF4  H4   H  HCH2  0   0.241   2.2347  -0.9804  -0.5128
 RF4  H5   H  HCH2  0   0.237   2.3683  -0.5649   1.2010
 RF4  H6   H  HCH3  0   0.247   3.8419   0.8896  -2.7925
 RF4  H7   H  HCH3  0   0.247   4.8277  -0.4310  -3.4138
 RF4  H8   H  HCH3  0   0.244   3.3581  -0.7740  -2.5165
 RF4  H9   H  HCH3  0   0.248   4.2421   1.9369   2.2131
 RF4  H10  H  HCH3  0   0.244   3.7698   0.3201   2.6982
 RF4  H11  H  HCH3  0   0.248   5.3509   0.9358   3.1466
 RF4  H12  H  HCH2  0   0.294   0.8445   1.4180   0.7997
 RF4  H13  H  HCH2  0   0.297   0.6634   0.9013  -0.8899
 RF4  H14  H  HCR6  0   0.273  -5.9536  -0.0112   0.6258
 RF4  H15  H  HCR6  0   0.257  -7.0576   1.9538  -0.3960
 RF4  H16  H  HCR6  0   0.255  -5.7429   3.7432  -1.4490
 RF4  H17  H  HCR6  0   0.257  -3.2676   3.6340  -1.5222
 RF4  H18  H  HCH2  0   0.327  -2.6108  -1.6257   2.0128
 RF4  H19  H  HCH2  0   0.334  -4.3114  -1.3523   1.7532
 RF4  H20  H  HOH1  0   0.491  -3.6792  -4.4417   0.2339

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
 RF4  C09  C01  single    1.501  0.020  1.501
 RF4  C02  C01  aromatic  1.392  0.020  1.392
 RF4  C02  C03  aromatic  1.387  0.020  1.387
 RF4  C01  C06  aromatic  1.396  0.020  1.396
 RF4  C03  C04  aromatic  1.387  0.020  1.387
 RF4  C04  C05  aromatic  1.392  0.020  1.392
 RF4  C06  C05  aromatic  1.396  0.020  1.396
 RF4  C06  O07  single    1.370  0.020  1.370
 RF4  C05  C10  single    1.501  0.020  1.501
 RF4  O07  C08  single    1.418  0.020  1.418
 RF4  C08  C11  single    1.517  0.020  1.517
 RF4  C11  S12  single    1.815  0.020  1.815
 RF4  C22  N14  single    1.431  0.020  1.431
 RF4  C22  C23  single    1.516  0.020  1.516
 RF4  O24  C23  double    1.201  0.020  1.201
 RF4  N14  C15  aromatic  1.377  0.020  1.377
 RF4  N14  C13  aromatic  1.365  0.020  1.365
 RF4  C18  C15  aromatic  1.387  0.020  1.387
 RF4  C18  C19  aromatic  1.386  0.020  1.386
 RF4  C23  O25  single    1.321  0.020  1.321
 RF4  S12  C13  single    1.740  0.020  1.740
 RF4  C15  C16  aromatic  1.402  0.020  1.402
 RF4  C13  N17  aromatic  1.300  0.020  1.300
 RF4  C19  C20  aromatic  1.401  0.020  1.401
 RF4  C16  N17  aromatic  1.377  0.020  1.377
 RF4  C16  C21  aromatic  1.392  0.020  1.392
 RF4  C20  C21  aromatic  1.385  0.020  1.385
 RF4  C02  H1   single    0.930  0.020  1.080
 RF4  C03  H2   single    0.930  0.020  1.080
 RF4  C04  H3   single    0.930  0.020  1.080
 RF4  C08  H4   single    0.970  0.020  1.090
 RF4  C08  H5   single    0.970  0.020  1.090
 RF4  C09  H6   single    0.970  0.020  1.090
 RF4  C09  H7   single    0.970  0.020  1.090
 RF4  C09  H8   single    0.970  0.020  1.090
 RF4  C10  H9   single    0.970  0.020  1.090
 RF4  C10  H10  single    0.970  0.020  1.090
 RF4  C10  H11  single    0.970  0.020  1.090
 RF4  C11  H12  single    0.970  0.020  1.090
 RF4  C11  H13  single    0.970  0.020  1.090
 RF4  C18  H14  single    0.930  0.020  1.080
 RF4  C19  H15  single    0.930  0.020  1.080
 RF4  C20  H16  single    0.930  0.020  1.080
 RF4  C21  H17  single    0.930  0.020  1.080
 RF4  C22  H18  single    0.970  0.020  1.090
 RF4  C22  H19  single    0.970  0.020  1.090
 RF4  O25  H20  single    0.850  0.020  0.980

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
 RF4  C09  C01  C06  120.77  3.000
 RF4  C06  C01  C02  118.03  3.000
 RF4  C09  C01  C02  121.19  3.000
 RF4  H1   C02  C03  119.92  3.000
 RF4  H1   C02  C01  119.21  3.000
 RF4  C03  C02  C01  120.87  3.000
 RF4  H2   C03  C04  119.99  3.000
 RF4  H2   C03  C02  120.06  3.000
 RF4  C04  C03  C02  119.94  3.000
 RF4  H3   C04  C05  119.23  3.000
 RF4  H3   C04  C03  119.81  3.000
 RF4  C05  C04  C03  120.96  3.000
 RF4  C10  C05  C06  121.07  3.000
 RF4  C10  C05  C04  120.98  3.000
 RF4  C06  C05  C04  117.94  3.000
 RF4  O07  C06  C05  119.00  3.000
 RF4  O07  C06  C01  118.71  3.000
 RF4  C05  C06  C01  122.26  3.000
 RF4  C08  O07  C06  114.57  3.000
 RF4  H5   C08  H4   107.60  3.000
 RF4  H5   C08  C11  110.74  3.000
 RF4  H4   C08  C11  110.27  3.000
 RF4  H5   C08  O07  110.75  3.000
 RF4  H4   C08  O07  111.02  3.000
 RF4  C11  C08  O07  106.49  3.000
 RF4  H8   C09  H7   107.27  3.000
 RF4  H8   C09  H6   107.02  3.000
 RF4  H7   C09  H6   107.82  3.000
 RF4  H8   C09  C01  112.12  3.000
 RF4  H7   C09  C01  110.71  3.000
 RF4  H6   C09  C01  111.67  3.000
 RF4  H11  C10  H10  107.23  3.000
 RF4  H11  C10  H9   107.86  3.000
 RF4  H10  C10  H9   106.92  3.000
 RF4  H11  C10  C05  110.59  3.000
 RF4  H10  C10  C05  112.28  3.000
 RF4  H9   C10  C05  111.72  3.000
 RF4  H13  C11  H12  109.24  3.000
 RF4  H13  C11  S12  108.96  3.000
 RF4  H12  C11  S12  109.08  3.000
 RF4  H13  C11  C08  111.00  3.000
 RF4  H12  C11  C08  110.90  3.000
 RF4  S12  C11  C08  107.61  3.000
 RF4  C13  S12  C11   99.91  3.000
 RF4  N17  C13  N14  113.81  3.000
 RF4  N17  C13  S12  126.53  3.000
 RF4  N14  C13  S12  119.66  3.000
 RF4  C22  N14  C15  126.71  3.000
 RF4  C15  N14  C13  106.21  3.000
 RF4  C22  N14  C13  126.90  3.000
 RF4  C18  C15  C16  122.74  3.000
 RF4  C16  C15  N14  105.01  3.000
 RF4  C18  C15  N14  132.24  3.000
 RF4  C21  C16  N17  129.99  3.000
 RF4  C21  C16  C15  119.91  3.000
 RF4  N17  C16  C15  110.10  3.000
 RF4  C16  N17  C13  104.84  3.000
 RF4  H14  C18  C19  121.18  3.000
 RF4  H14  C18  C15  122.25  3.000
 RF4  C19  C18  C15  116.58  3.000
 RF4  H15  C19  C20  119.31  3.000
 RF4  H15  C19  C18  119.20  3.000
 RF4  C20  C19  C18  121.49  3.000
 RF4  H16  C20  C21  119.44  3.000
 RF4  H16  C20  C19  119.15  3.000
 RF4  C21  C20  C19  121.42  3.000
 RF4  H17  C21  C20  121.27  3.000
 RF4  H17  C21  C16  120.86  3.000
 RF4  C20  C21  C16  117.87  3.000
 RF4  H19  C22  H18  105.73  3.000
 RF4  H19  C22  C23  109.58  3.000
 RF4  H18  C22  C23  109.78  3.000
 RF4  H19  C22  N14  109.52  3.000
 RF4  H18  C22  N14  110.34  3.000
 RF4  C23  C22  N14  111.70  3.000
 RF4  O25  C23  O24  125.23  3.000
 RF4  O25  C23  C22  110.60  3.000
 RF4  O24  C23  C22  124.16  3.000
 RF4  H20  O25  C23  110.62  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
 RF4  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 RF4  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 RF4  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 RF4  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 RF4  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 RF4  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 RF4  CONST_07  C18  C15  N14  C13   180.00   0.0  0
 RF4  CONST_08  C16  C15  N14  C13     0.00   0.0  0
 RF4  CONST_09  C15  C16  N17  C13     0.00   0.0  0
 RF4  CONST_10  C21  C16  N17  C13   180.00   0.0  0
 RF4  CONST_11  C19  C18  C15  N14   180.00   0.0  0
 RF4  CONST_12  N17  C16  C15  N14     0.00   0.0  0
 RF4  CONST_13  C21  C16  C15  N14   180.00   0.0  0
 RF4  CONST_14  C16  N17  C13  N14     0.00   0.0  0
 RF4  CONST_15  N17  C13  N14  C15     0.00   0.0  0
 RF4  CONST_16  C20  C19  C18  C15     0.00   0.0  0
 RF4  CONST_17  C20  C21  C16  C15     0.00   0.0  0
 RF4  CONST_18  C19  C18  C15  C16     0.00   0.0  0
 RF4  CONST_19  C19  C20  C21  C16     0.00   0.0  0
 RF4  CONST_20  C18  C15  C16  N17   180.00   0.0  0
 RF4  CONST_21  C20  C21  C16  N17   180.00   0.0  0
 RF4  CONST_22  C21  C16  C15  C18     0.00   0.0  0
 RF4  CONST_23  C21  C20  C19  C18     0.00   0.0  0
 RF4  CONST_24  C10  C05  C06  C01   180.00   0.0  0
 RF4  CONST_25  O07  C06  C01  C02   180.00   0.0  0
 RF4  CONST_26  C09  C01  C02  C03   180.00   0.0  0
 RF4  CONST_27  C10  C05  C04  C03   180.00   0.0  0
 RF4  CONST_28  O07  C06  C05  C04   180.00   0.0  0
 RF4  CONST_29  C09  C01  C06  C05   180.00   0.0  0
 RF4  CONST_30  C15  N14  C13  S12   180.00   0.0  0
 RF4  CONST_31  C16  N17  C13  S12   180.00   0.0  0
 RF4  CONST_32  C22  N14  C15  C16   180.00   0.0  0
 RF4  CONST_33  C22  N14  C13  N17   180.00   0.0  0
 RF4  CONST_34  C22  N14  C15  C18     0.00   0.0  0
 RF4  CONST_35  H2   C03  C02  C01   180.00   0.0  0
 RF4  CONST_36  H3   C04  C03  C02   180.00   0.0  0
 RF4  CONST_37  H1   C02  C03  C04   180.00   0.0  0
 RF4  CONST_38  H14  C18  C15  N14     0.00   0.0  0
 RF4  CONST_39  H15  C19  C18  C15   180.00   0.0  0
 RF4  CONST_40  H17  C21  C16  C15   180.00   0.0  0
 RF4  CONST_41  H16  C20  C21  C16   180.00   0.0  0
 RF4  CONST_42  H20  O25  C23  C22   180.00   0.0  0
 RF4  Var_01    N14  C13  S12  C11  -172.72  30.0  2
 RF4  Var_02    C23  C22  N14  C13   -81.57  30.0  2
 RF4  Var_03    H6   C09  C01  C02  -123.33  30.0  2
 RF4  Var_04    H9   C10  C05  C04   123.24  30.0  2
 RF4  Var_05    C11  C08  O07  C06  -179.14  30.0  3
 RF4  Var_06    O24  C23  C22  N14     0.43  30.0  3
 RF4  Var_07    H12  C11  S12  C13    67.97  30.0  2
 RF4  Var_08    S12  C11  C08  O07  -176.30  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
 RF4  plan-1  C01  0.020
 RF4  plan-1  C02  0.020
 RF4  plan-1  C03  0.020
 RF4  plan-1  C04  0.020
 RF4  plan-1  C05  0.020
 RF4  plan-1  C06  0.020
 RF4  plan-1  O07  0.020
 RF4  plan-1  C09  0.020
 RF4  plan-1  C10  0.020
 RF4  plan-1  H1   0.020
 RF4  plan-1  H2   0.020
 RF4  plan-1  H3   0.020
 RF4  plan-2  S12  0.020
 RF4  plan-2  C13  0.020
 RF4  plan-2  N14  0.020
 RF4  plan-2  C15  0.020
 RF4  plan-2  C16  0.020
 RF4  plan-2  N17  0.020
 RF4  plan-2  C18  0.020
 RF4  plan-2  C19  0.020
 RF4  plan-2  C20  0.020
 RF4  plan-2  C21  0.020
 RF4  plan-2  C22  0.020
 RF4  plan-2  H14  0.020
 RF4  plan-2  H15  0.020
 RF4  plan-2  H16  0.020
 RF4  plan-2  H17  0.020
 RF4  plan-3  C22  0.020
 RF4  plan-3  C23  0.020
 RF4  plan-3  O24  0.020
 RF4  plan-3  O25  0.020
 RF4  plan-3  H20  0.020

