# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 23:54:39 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-({1-[2-(4-methylphenoxy)ethyl]-1H-benzimidazol-2-yl}sulfanyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(OCCn2c(SCCC(O)=O)nc3ccccc23)cc1
#
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
 YLQ  YLQ  '3-({1-[2-(4-methylphenoxy)ethyl]-1H-benzimidazol-2-yl}sulfanyl)propanoic acid'  ligand  45  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YLQ
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
 YLQ  C01   C  CH3   0  -0.722   7.4121   2.1163   1.4644
 YLQ  C02   C  CR6   0   0.076   6.1497   1.6109   0.8276
 YLQ  C03   C  CR16  0  -0.277   6.0049   1.5974  -0.5617
 YLQ  C04   C  CR16  0  -0.331   4.8464   1.1453  -1.1645
 YLQ  C05   C  CR6   0   0.368   3.7841   0.6865  -0.3843
 YLQ  O06   O  O2    0  -0.477   2.6906   0.2574  -1.0550
 YLQ  C07   C  CH2   0  -0.165   1.6099  -0.2718  -0.3225
 YLQ  C08   C  CH2   0  -0.374   0.5892  -0.7550  -1.3428
 YLQ  N09   N  NR5   0  -0.552  -0.5585  -1.3311  -0.6848
 YLQ  C10   C  CR5   0   0.321  -1.6925  -0.6874  -0.2806
 YLQ  S11   S  S2    0   0.046  -1.9028   1.0041  -0.6324
 YLQ  C12   C  CH2   0  -0.545  -3.5874   1.2529  -0.0008
 YLQ  C13   C  CH2   0  -0.585  -3.9650   2.6956  -0.2872
 YLQ  C14   C  C     0   0.562  -5.3551   3.0135   0.1957
 YLQ  O15   O  O     0  -0.438  -6.0766   2.2409   0.7736
 YLQ  O16   O  OH1   0  -0.591  -5.6956   4.2626  -0.0920
 YLQ  N17   N  N     0  -0.467  -2.5341  -1.4502   0.3536
 YLQ  C18   C  CR56  0   0.141  -1.9283  -2.6860   0.3925
 YLQ  C19   C  CR16  0  -0.332  -2.3709  -3.8832   0.9497
 YLQ  C20   C  CR16  0  -0.271  -1.5447  -4.9903   0.8462
 YLQ  C21   C  CR16  0  -0.277  -0.3029  -4.9173   0.2016
 YLQ  C22   C  CR16  0  -0.308   0.1543  -3.7342  -0.3583
 YLQ  C23   C  CR56  0   0.341  -0.6815  -2.6315  -0.2481
 YLQ  C24   C  CR16  0  -0.366   3.9043   0.6933   0.9996
 YLQ  C25   C  CR16  0  -0.292   5.0815   1.1521   1.5857
 YLQ  H011  H  HCH3  0   0.244   7.5259   3.1927   1.3212
 YLQ  H012  H  HCH3  0   0.242   7.4232   1.9254   2.5369
 YLQ  H013  H  HCH3  0   0.242   8.2949   1.6423   1.0334
 YLQ  H03   H  HCR6  0   0.249   6.8182   1.9459  -1.1880
 YLQ  H25   H  HCR6  0   0.251   5.1556   1.1463   2.6670
 YLQ  H04   H  HCR6  0   0.260   4.7568   1.1406  -2.2439
 YLQ  H24   H  HCR6  0   0.277   3.1037   0.3470   1.6397
 YLQ  H071  H  HCH2  0   0.236   1.9291  -1.1087   0.3094
 YLQ  H072  H  HCH2  0   0.232   1.1609   0.4873   0.3291
 YLQ  H081  H  HCH2  0   0.286   0.2628   0.0662  -1.9830
 YLQ  H082  H  HCH2  0   0.291   1.0306  -1.5082  -1.9958
 YLQ  H121  H  HCH2  0   0.294  -4.2548   0.5581  -0.5068
 YLQ  H122  H  HCH2  0   0.295  -3.5995   1.0394   1.0661
 YLQ  H131  H  HCH2  0   0.300  -3.2691   3.3879   0.1955
 YLQ  H132  H  HCH2  0   0.299  -3.9138   2.9089  -1.3585
 YLQ  H16   H  HOH1  0   0.483  -6.5906   4.4479   0.2304
 YLQ  H19   H  HCR6  0   0.256  -3.3299  -3.9419   1.4486
 YLQ  H20   H  HCR6  0   0.254  -1.8632  -5.9334   1.2708
 YLQ  H21   H  HCR6  0   0.257   0.3144  -5.8037   0.1389
 YLQ  H22   H  HCR6  0   0.271   1.1154  -3.6860  -0.8545

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
 YLQ  C01  C02   single    1.502  0.020  1.502
 YLQ  C02  C03   aromatic  1.397  0.020  1.397
 YLQ  C02  C25   aromatic  1.388  0.020  1.388
 YLQ  C03  C04   aromatic  1.382  0.020  1.382
 YLQ  C04  C05   aromatic  1.396  0.020  1.396
 YLQ  C05  O06   single    1.353  0.020  1.353
 YLQ  C05  C24   aromatic  1.389  0.020  1.389
 YLQ  O06  C07   single    1.409  0.020  1.409
 YLQ  C07  C08   single    1.522  0.020  1.522
 YLQ  C08  N09   single    1.443  0.020  1.443
 YLQ  N09  C10   aromatic  1.365  0.020  1.365
 YLQ  N09  C23   aromatic  1.377  0.020  1.377
 YLQ  C10  S11   single    1.740  0.020  1.740
 YLQ  C10  N17   aromatic  1.301  0.020  1.301
 YLQ  S11  C12   single    1.816  0.020  1.816
 YLQ  C12  C13   single    1.518  0.020  1.518
 YLQ  C13  C14   single    1.506  0.020  1.506
 YLQ  C14  O15   double    1.205  0.020  1.205
 YLQ  C14  O16   single    1.326  0.020  1.326
 YLQ  N17  C18   aromatic  1.377  0.020  1.377
 YLQ  C18  C19   aromatic  1.393  0.020  1.393
 YLQ  C18  C23   aromatic  1.403  0.020  1.403
 YLQ  C19  C20   aromatic  1.385  0.020  1.385
 YLQ  C20  C21   aromatic  1.401  0.020  1.401
 YLQ  C21  C22   aromatic  1.386  0.020  1.386
 YLQ  C22  C23   aromatic  1.388  0.020  1.388
 YLQ  C24  C25   aromatic  1.393  0.020  1.393
 YLQ  C01  H011  single    0.970  0.020  1.090
 YLQ  C01  H012  single    0.970  0.020  1.090
 YLQ  C01  H013  single    0.970  0.020  1.090
 YLQ  C03  H03   single    0.930  0.020  1.080
 YLQ  C25  H25   single    0.930  0.020  1.080
 YLQ  C04  H04   single    0.930  0.020  1.080
 YLQ  C24  H24   single    0.930  0.020  1.080
 YLQ  C07  H071  single    0.970  0.020  1.090
 YLQ  C07  H072  single    0.970  0.020  1.090
 YLQ  C08  H081  single    0.970  0.020  1.090
 YLQ  C08  H082  single    0.970  0.020  1.090
 YLQ  C12  H121  single    0.970  0.020  1.090
 YLQ  C12  H122  single    0.970  0.020  1.090
 YLQ  C13  H131  single    0.970  0.020  1.090
 YLQ  C13  H132  single    0.970  0.020  1.090
 YLQ  O16  H16   single    0.850  0.020  0.980
 YLQ  C19  H19   single    0.930  0.020  1.080
 YLQ  C20  H20   single    0.930  0.020  1.080
 YLQ  C21  H21   single    0.930  0.020  1.080
 YLQ  C22  H22   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
 YLQ  H013  C01  H012  107.73  3.000
 YLQ  H013  C01  H011  107.00  3.000
 YLQ  H012  C01  H011  107.51  3.000
 YLQ  H013  C01  C02   111.50  3.000
 YLQ  H012  C01  C02   111.53  3.000
 YLQ  H011  C01  C02   111.33  3.000
 YLQ  C25   C02  C03   117.41  3.000
 YLQ  C25   C02  C01   121.78  3.000
 YLQ  C03   C02  C01   120.81  3.000
 YLQ  H03   C03  C04   118.82  3.000
 YLQ  H03   C03  C02   119.59  3.000
 YLQ  C04   C03  C02   121.59  3.000
 YLQ  H04   C04  C05   119.52  3.000
 YLQ  H04   C04  C03   120.36  3.000
 YLQ  C05   C04  C03   120.12  3.000
 YLQ  C24   C05  O06   124.44  3.000
 YLQ  C24   C05  C04   119.30  3.000
 YLQ  O06   C05  C04   116.26  3.000
 YLQ  C07   O06  C05   118.78  3.000
 YLQ  H072  C07  H071  107.77  3.000
 YLQ  H072  C07  C08   110.09  3.000
 YLQ  H071  C07  C08   109.84  3.000
 YLQ  H072  C07  O06   111.28  3.000
 YLQ  H071  C07  O06   111.30  3.000
 YLQ  C08   C07  O06   106.57  3.000
 YLQ  H082  C08  H081  106.85  3.000
 YLQ  H082  C08  N09   108.62  3.000
 YLQ  H081  C08  N09   109.27  3.000
 YLQ  H082  C08  C07   110.45  3.000
 YLQ  H081  C08  C07   110.79  3.000
 YLQ  N09   C08  C07   110.76  3.000
 YLQ  C23   N09  C10   106.09  3.000
 YLQ  C23   N09  C08   126.34  3.000
 YLQ  C10   N09  C08   127.40  3.000
 YLQ  N17   C10  S11   126.18  3.000
 YLQ  N17   C10  N09   113.90  3.000
 YLQ  S11   C10  N09   119.92  3.000
 YLQ  C12   S11  C10   100.08  3.000
 YLQ  H122  C12  H121  108.90  3.000
 YLQ  H122  C12  C13   111.63  3.000
 YLQ  H121  C12  C13   111.49  3.000
 YLQ  H122  C12  S11   108.93  3.000
 YLQ  H121  C12  S11   108.64  3.000
 YLQ  C13   C12  S11   107.17  3.000
 YLQ  H132  C13  H131  106.20  3.000
 YLQ  H132  C13  C14   108.44  3.000
 YLQ  H131  C13  C14   108.19  3.000
 YLQ  H132  C13  C12   111.01  3.000
 YLQ  H131  C13  C12   111.09  3.000
 YLQ  C14   C13  C12   111.70  3.000
 YLQ  O16   C14  O15   123.66  3.000
 YLQ  O16   C14  C13   111.49  3.000
 YLQ  O15   C14  C13   124.85  3.000
 YLQ  H16   O16  C14   110.19  3.000
 YLQ  C18   N17  C10   104.80  3.000
 YLQ  C23   C18  C19   119.90  3.000
 YLQ  C23   C18  N17   110.08  3.000
 YLQ  C19   C18  N17   130.02  3.000
 YLQ  H19   C19  C20   121.29  3.000
 YLQ  H19   C19  C18   120.83  3.000
 YLQ  C20   C19  C18   117.88  3.000
 YLQ  H20   C20  C21   119.12  3.000
 YLQ  H20   C20  C19   119.45  3.000
 YLQ  C21   C20  C19   121.43  3.000
 YLQ  H21   C21  C22   119.18  3.000
 YLQ  H21   C21  C20   119.32  3.000
 YLQ  C22   C21  C20   121.50  3.000
 YLQ  H22   C22  C23   122.38  3.000
 YLQ  H22   C22  C21   121.05  3.000
 YLQ  C23   C22  C21   116.57  3.000
 YLQ  C22   C23  C18   122.72  3.000
 YLQ  C22   C23  N09   132.15  3.000
 YLQ  C18   C23  N09   105.12  3.000
 YLQ  H24   C24  C25   118.81  3.000
 YLQ  H24   C24  C05   121.59  3.000
 YLQ  C25   C24  C05   119.61  3.000
 YLQ  H25   C25  C24   118.42  3.000
 YLQ  H25   C25  C02   119.61  3.000
 YLQ  C24   C25  C02   121.97  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
 YLQ  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 YLQ  CONST_02  C05   C24  C25  C02     0.00   0.0  0
 YLQ  CONST_03  C24   C25  C02  C03     0.00   0.0  0
 YLQ  CONST_04  C24   C05  C04  C03     0.00   0.0  0
 YLQ  CONST_05  C25   C02  C03  C04     0.00   0.0  0
 YLQ  CONST_06  C25   C24  C05  C04     0.00   0.0  0
 YLQ  CONST_07  C18   N17  C10  N09     0.00   0.0  0
 YLQ  CONST_08  N17   C18  C23  N09     0.00   0.0  0
 YLQ  CONST_09  C19   C18  C23  N09   180.00   0.0  0
 YLQ  CONST_10  C21   C22  C23  N09   180.00   0.0  0
 YLQ  CONST_11  C18   C23  N09  C10     0.00   0.0  0
 YLQ  CONST_12  C22   C23  N09  C10   180.00   0.0  0
 YLQ  CONST_13  C19   C18  N17  C10   180.00   0.0  0
 YLQ  CONST_14  C23   C18  N17  C10     0.00   0.0  0
 YLQ  CONST_15  C23   N09  C10  N17     0.00   0.0  0
 YLQ  CONST_16  C20   C19  C18  N17   180.00   0.0  0
 YLQ  CONST_17  C22   C23  C18  N17   180.00   0.0  0
 YLQ  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 YLQ  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 YLQ  CONST_20  C22   C23  C18  C19     0.00   0.0  0
 YLQ  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 YLQ  CONST_22  C23   C18  C19  C20     0.00   0.0  0
 YLQ  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 YLQ  CONST_24  C04   C03  C02  C01   180.00   0.0  0
 YLQ  CONST_25  C24   C25  C02  C01   180.00   0.0  0
 YLQ  CONST_26  O06   C05  C04  C03   180.00   0.0  0
 YLQ  CONST_27  C25   C24  C05  O06   180.00   0.0  0
 YLQ  CONST_28  N17   C10  N09  C08   180.00   0.0  0
 YLQ  CONST_29  C18   C23  N09  C08   180.00   0.0  0
 YLQ  CONST_30  C22   C23  N09  C08     0.00   0.0  0
 YLQ  CONST_31  C23   N09  C10  S11   180.00   0.0  0
 YLQ  CONST_32  C18   N17  C10  S11   180.00   0.0  0
 YLQ  CONST_33  H04   C04  C03  C02   180.00   0.0  0
 YLQ  CONST_34  H24   C24  C25  C02   180.00   0.0  0
 YLQ  CONST_35  H25   C25  C02  C03   180.00   0.0  0
 YLQ  CONST_36  H03   C03  C04  C05   180.00   0.0  0
 YLQ  CONST_37  H22   C22  C23  N09     0.00   0.0  0
 YLQ  CONST_38  H19   C19  C18  N17     0.00   0.0  0
 YLQ  CONST_39  H20   C20  C19  C18   180.00   0.0  0
 YLQ  CONST_40  H21   C21  C20  C19   180.00   0.0  0
 YLQ  CONST_41  H16   O16  C14  C13   180.00   0.0  0
 YLQ  Var_01    C24   C05  O06  C07    -2.67  30.0  3
 YLQ  Var_02    C10   N09  C08  C07    89.51  30.0  2
 YLQ  Var_03    N17   C10  S11  C12    -4.34  30.0  2
 YLQ  Var_04    H011  C01  C02  C03    68.25  30.0  2
 YLQ  Var_05    C08   C07  O06  C05  -175.96  30.0  3
 YLQ  Var_06    N09   C08  C07  O06   179.42  30.0  3
 YLQ  Var_07    C13   C12  S11  C10  -177.58  30.0  3
 YLQ  Var_08    C14   C13  C12  S11   179.87  30.0  3
 YLQ  Var_09    O15   C14  C13  C12     1.98  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
 YLQ  plan-1  C01  0.020
 YLQ  plan-1  C02  0.020
 YLQ  plan-1  C03  0.020
 YLQ  plan-1  C04  0.020
 YLQ  plan-1  C05  0.020
 YLQ  plan-1  O06  0.020
 YLQ  plan-1  C24  0.020
 YLQ  plan-1  C25  0.020
 YLQ  plan-1  H03  0.020
 YLQ  plan-1  H25  0.020
 YLQ  plan-1  H04  0.020
 YLQ  plan-1  H24  0.020
 YLQ  plan-2  C08  0.020
 YLQ  plan-2  N09  0.020
 YLQ  plan-2  C10  0.020
 YLQ  plan-2  S11  0.020
 YLQ  plan-2  N17  0.020
 YLQ  plan-2  C18  0.020
 YLQ  plan-2  C19  0.020
 YLQ  plan-2  C20  0.020
 YLQ  plan-2  C21  0.020
 YLQ  plan-2  C22  0.020
 YLQ  plan-2  C23  0.020
 YLQ  plan-2  H19  0.020
 YLQ  plan-2  H20  0.020
 YLQ  plan-2  H21  0.020
 YLQ  plan-2  H22  0.020
 YLQ  plan-3  C13  0.020
 YLQ  plan-3  C14  0.020
 YLQ  plan-3  O15  0.020
 YLQ  plan-3  O16  0.020
 YLQ  plan-3  H16  0.020

