# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 07:19:49 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3R)-3-[1-(1H-benzimidazol-2-yl)-5-hydroxy-3-methyl-1H-pyrazol-4-yl]-2-benzofuran-1(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nn(c(O)c1[C@@H]2OC(=O)c3ccccc23)c4[nH]c5ccccc5n4
#
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
 A9Y  A9Y  (3R)-3-[1-(1H-benzimidazol-2-yl)-5-hydroxy-3-methyl-1H-pyrazol-4-yl]-2-benzofuran-1(3H)-one  ligand  40  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9Y
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
 A9Y  CAH  C  CR16  0  -0.286   4.4517  -2.0215   0.6294
 A9Y  CAD  C  CR16  0  -0.259   4.4789  -1.8877   2.0085
 A9Y  CAE  C  CR16  0  -0.234   3.9167  -0.7679   2.6263
 A9Y  CAI  C  CR16  0  -0.317   3.3154   0.2426   1.8862
 A9Y  CAT  C  CR56  0   0.142   3.2966   0.1018   0.5110
 A9Y  CAR  C  CR56  0  -0.122   3.8505  -1.0048  -0.0966
 A9Y  CAP  C  CR5   0   0.549   3.6593  -0.8691  -1.5454
 A9Y  OAB  O  O     0  -0.422   3.9864  -1.6066  -2.4358
 A9Y  OAO  O  O     0  -0.456   3.0154   0.2859  -1.7754
 A9Y  CAY  C  CR15  0  -0.108   2.7335   1.0002  -0.5513
 A9Y  CAV  C  CR5   0  -0.235   1.2853   1.2801  -0.4235
 A9Y  CAS  C  CR5   0   0.634   0.2829   0.3586  -0.2381
 A9Y  OAC  O  OH1   0  -0.606   0.3415  -0.9477  -0.1231
 A9Y  CAQ  C  CR5   0   0.299   0.6150   2.5305  -0.4855
 A9Y  CAA  C  CH3   0  -0.748   1.2393   3.8651  -0.6839
 A9Y  NAM  N  N     0  -0.333  -0.6814   2.3995  -0.3413
 A9Y  NAZ  N  NR5   0  -0.478  -0.8795   1.0670  -0.1933
 A9Y  CAU  C  CR5   0   0.798  -2.1260   0.5225  -0.0339
 A9Y  NAL  N  NR15  0  -0.722  -3.2522   1.2534   0.0082
 A9Y  CAW  C  CR56  0   0.319  -4.2855   0.3560   0.1724
 A9Y  CAJ  C  CR16  0  -0.301  -5.6574   0.5248   0.2792
 A9Y  CAF  C  CR16  0  -0.278  -6.4139  -0.6259   0.4363
 A9Y  CAG  C  CR16  0  -0.267  -5.8181  -1.8928   0.4850
 A9Y  CAK  C  CR16  0  -0.326  -4.4465  -2.0528   0.3776
 A9Y  CAX  C  CR56  0   0.218  -3.6733  -0.9072   0.2194
 A9Y  NAN  N  N     0  -0.605  -2.3086  -0.7634   0.0869
 A9Y  H1   H  HCR6  0   0.272   4.8804  -2.8863   0.1404
 A9Y  H2   H  HCR6  0   0.271   4.9369  -2.6568   2.6156
 A9Y  H3   H  HCR6  0   0.273   3.9491  -0.6886   3.7050
 A9Y  H4   H  HCR6  0   0.266   2.8747   1.1021   2.3745
 A9Y  H5   H  HCR5  0   0.301   3.2893   1.9419  -0.5900
 A9Y  H7   H  HCH3  0   0.259   1.7589   3.9138  -1.6417
 A9Y  H8   H  HCH3  0   0.264   0.4867   4.6502  -0.6631
 A9Y  H9   H  HCH3  0   0.257   1.9742   4.0756   0.0940
 A9Y  H10  H  HNR5  0   0.434  -3.3135   2.2578  -0.0638
 A9Y  H11  H  HCR6  0   0.273  -6.1161   1.5039   0.2418
 A9Y  H12  H  HCR6  0   0.260  -7.4891  -0.5433   0.5223
 A9Y  H13  H  HCR6  0   0.258  -6.4464  -2.7648   0.6096
 A9Y  H14  H  HCR6  0   0.262  -3.9894  -3.0329   0.4148
 A9Y  H6   H  HOH1  0   0.494  -0.5743  -1.3057  -0.0104

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
 A9Y  OAB  CAP  double    1.202  0.020  1.202
 A9Y  CAG  CAF  aromatic  1.401  0.020  1.401
 A9Y  CAG  CAK  aromatic  1.385  0.020  1.385
 A9Y  CAF  CAJ  aromatic  1.386  0.020  1.386
 A9Y  CAK  CAX  aromatic  1.391  0.020  1.391
 A9Y  CAP  CAR  single    1.468  0.020  1.468
 A9Y  CAP  OAO  single    1.342  0.020  1.342
 A9Y  CAH  CAR  aromatic  1.386  0.020  1.386
 A9Y  CAH  CAD  aromatic  1.386  0.020  1.386
 A9Y  CAJ  CAW  aromatic  1.386  0.020  1.386
 A9Y  CAX  CAW  aromatic  1.405  0.020  1.405
 A9Y  CAX  NAN  aromatic  1.379  0.020  1.379
 A9Y  CAR  CAT  aromatic  1.379  0.020  1.379
 A9Y  CAW  NAL  aromatic  1.378  0.020  1.378
 A9Y  NAN  CAU  aromatic  1.304  0.020  1.304
 A9Y  OAC  CAS  single    1.313  0.020  1.313
 A9Y  CAD  CAE  aromatic  1.397  0.020  1.397
 A9Y  OAO  CAY  single    1.445  0.020  1.445
 A9Y  NAL  CAU  aromatic  1.343  0.020  1.343
 A9Y  CAU  NAZ  single    1.370  0.020  1.370
 A9Y  CAS  NAZ  aromatic  1.362  0.020  1.362
 A9Y  CAS  CAV  aromatic  1.374  0.020  1.374
 A9Y  NAZ  NAM  aromatic  1.355  0.020  1.355
 A9Y  CAT  CAY  single    1.501  0.020  1.501
 A9Y  CAT  CAI  aromatic  1.382  0.020  1.382
 A9Y  CAV  CAY  single    1.481  0.020  1.481
 A9Y  CAV  CAQ  aromatic  1.420  0.020  1.420
 A9Y  CAE  CAI  aromatic  1.389  0.020  1.389
 A9Y  NAM  CAQ  aromatic  1.311  0.020  1.311
 A9Y  CAQ  CAA  single    1.487  0.020  1.487
 A9Y  CAH  H1   single    0.930  0.020  1.080
 A9Y  CAD  H2   single    0.930  0.020  1.080
 A9Y  CAE  H3   single    0.930  0.020  1.080
 A9Y  CAI  H4   single    0.930  0.020  1.080
 A9Y  CAY  H5   single    0.970  0.020  1.090
 A9Y  CAA  H7   single    0.970  0.020  1.090
 A9Y  CAA  H8   single    0.970  0.020  1.090
 A9Y  CAA  H9   single    0.970  0.020  1.090
 A9Y  NAL  H10  single    0.860  0.020  1.020
 A9Y  CAJ  H11  single    0.930  0.020  1.080
 A9Y  CAF  H12  single    0.930  0.020  1.080
 A9Y  CAG  H13  single    0.930  0.020  1.080
 A9Y  CAK  H14  single    0.930  0.020  1.080
 A9Y  OAC  H6   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
 A9Y  H1   CAH  CAR  121.42  3.000
 A9Y  H1   CAH  CAD  121.27  3.000
 A9Y  CAR  CAH  CAD  117.31  3.000
 A9Y  H2   CAD  CAE  119.49  3.000
 A9Y  H2   CAD  CAH  119.88  3.000
 A9Y  CAE  CAD  CAH  120.63  3.000
 A9Y  H3   CAE  CAI  119.38  3.000
 A9Y  H3   CAE  CAD  119.18  3.000
 A9Y  CAI  CAE  CAD  121.44  3.000
 A9Y  H4   CAI  CAT  121.62  3.000
 A9Y  H4   CAI  CAE  120.89  3.000
 A9Y  CAT  CAI  CAE  117.49  3.000
 A9Y  CAY  CAT  CAR  108.62  3.000
 A9Y  CAY  CAT  CAI  130.40  3.000
 A9Y  CAR  CAT  CAI  120.98  3.000
 A9Y  CAP  CAR  CAT  107.97  3.000
 A9Y  CAT  CAR  CAH  122.14  3.000
 A9Y  CAP  CAR  CAH  129.89  3.000
 A9Y  OAO  CAP  OAB  122.13  3.000
 A9Y  OAO  CAP  CAR  108.14  3.000
 A9Y  OAB  CAP  CAR  129.74  3.000
 A9Y  CAY  OAO  CAP  111.95  3.000
 A9Y  H5   CAY  CAV  109.71  3.000
 A9Y  H5   CAY  OAO  107.24  3.000
 A9Y  CAV  CAY  OAO  110.94  3.000
 A9Y  H5   CAY  CAT  110.46  3.000
 A9Y  CAV  CAY  CAT  114.78  3.000
 A9Y  OAO  CAY  CAT  103.32  3.000
 A9Y  CAQ  CAV  CAS  104.60  3.000
 A9Y  CAQ  CAV  CAY  128.64  3.000
 A9Y  CAS  CAV  CAY  126.76  3.000
 A9Y  NAZ  CAS  OAC  123.56  3.000
 A9Y  NAZ  CAS  CAV  106.15  3.000
 A9Y  OAC  CAS  CAV  130.28  3.000
 A9Y  H6   OAC  CAS  109.18  3.000
 A9Y  NAM  CAQ  CAA  121.31  3.000
 A9Y  CAA  CAQ  CAV  126.73  3.000
 A9Y  NAM  CAQ  CAV  111.96  3.000
 A9Y  H9   CAA  H8   108.26  3.000
 A9Y  H9   CAA  H7   107.26  3.000
 A9Y  H8   CAA  H7   108.31  3.000
 A9Y  H9   CAA  CAQ  111.17  3.000
 A9Y  H8   CAA  CAQ  110.78  3.000
 A9Y  H7   CAA  CAQ  110.93  3.000
 A9Y  NAZ  NAM  CAQ  104.76  3.000
 A9Y  CAU  NAZ  NAM  122.46  3.000
 A9Y  NAM  NAZ  CAS  112.52  3.000
 A9Y  CAU  NAZ  CAS  125.02  3.000
 A9Y  NAN  CAU  NAL  114.59  3.000
 A9Y  NAL  CAU  NAZ  123.39  3.000
 A9Y  NAN  CAU  NAZ  122.01  3.000
 A9Y  H10  NAL  CAW  127.67  3.000
 A9Y  H10  NAL  CAU  126.18  3.000
 A9Y  CAW  NAL  CAU  106.14  3.000
 A9Y  CAX  CAW  CAJ  122.57  3.000
 A9Y  CAX  CAW  NAL  105.23  3.000
 A9Y  CAJ  CAW  NAL  132.20  3.000
 A9Y  H11  CAJ  CAF  121.59  3.000
 A9Y  H11  CAJ  CAW  121.81  3.000
 A9Y  CAF  CAJ  CAW  116.59  3.000
 A9Y  H12  CAF  CAG  119.28  3.000
 A9Y  H12  CAF  CAJ  119.21  3.000
 A9Y  CAG  CAF  CAJ  121.52  3.000
 A9Y  H13  CAG  CAK  119.40  3.000
 A9Y  H13  CAG  CAF  119.07  3.000
 A9Y  CAK  CAG  CAF  121.53  3.000
 A9Y  H14  CAK  CAX  120.99  3.000
 A9Y  H14  CAK  CAG  121.35  3.000
 A9Y  CAX  CAK  CAG  117.65  3.000
 A9Y  NAN  CAX  CAK  130.32  3.000
 A9Y  NAN  CAX  CAW  109.54  3.000
 A9Y  CAK  CAX  CAW  120.14  3.000
 A9Y  CAX  NAN  CAU  104.50  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
 A9Y  CONST_01  CAI  CAT  CAR  CAH    0.00   0.0  0
 A9Y  CONST_02  CAI  CAE  CAD  CAH    0.00   0.0  0
 A9Y  CONST_03  CAT  CAR  CAH  CAD    0.00   0.0  0
 A9Y  CONST_04  CAT  CAI  CAE  CAD    0.00   0.0  0
 A9Y  CONST_05  CAR  CAH  CAD  CAE    0.00   0.0  0
 A9Y  CONST_06  CAR  CAT  CAI  CAE    0.00   0.0  0
 A9Y  CONST_07  CAU  NAZ  CAS  CAV  180.00   0.0  0
 A9Y  CONST_08  NAM  NAZ  CAS  CAV    0.00   0.0  0
 A9Y  CONST_09  NAZ  NAM  CAQ  CAV    0.00   0.0  0
 A9Y  CONST_10  NAN  CAU  NAZ  CAS    0.00   0.0  0
 A9Y  CONST_11  NAL  CAU  NAZ  CAS  180.00   0.0  0
 A9Y  CONST_12  CAQ  NAM  NAZ  CAS    0.00   0.0  0
 A9Y  CONST_13  NAM  CAQ  CAV  CAS    0.00   0.0  0
 A9Y  CONST_14  NAZ  CAS  CAV  CAQ    0.00   0.0  0
 A9Y  CONST_15  CAU  NAZ  NAM  CAQ  180.00   0.0  0
 A9Y  CONST_16  NAN  CAU  NAZ  NAM  180.00   0.0  0
 A9Y  CONST_17  NAL  CAU  NAZ  NAM    0.00   0.0  0
 A9Y  CONST_18  CAX  NAN  CAU  NAZ  180.00   0.0  0
 A9Y  CONST_19  CAW  NAL  CAU  NAZ  180.00   0.0  0
 A9Y  CONST_20  CAK  CAX  NAN  CAU  180.00   0.0  0
 A9Y  CONST_21  CAW  CAX  NAN  CAU    0.00   0.0  0
 A9Y  CONST_22  CAJ  CAW  NAL  CAU  180.00   0.0  0
 A9Y  CONST_23  CAX  CAW  NAL  CAU    0.00   0.0  0
 A9Y  CONST_24  CAF  CAJ  CAW  NAL  180.00   0.0  0
 A9Y  CONST_25  CAK  CAX  CAW  NAL  180.00   0.0  0
 A9Y  CONST_26  NAN  CAX  CAW  NAL    0.00   0.0  0
 A9Y  CONST_27  CAX  NAN  CAU  NAL    0.00   0.0  0
 A9Y  CONST_28  CAG  CAF  CAJ  CAW    0.00   0.0  0
 A9Y  CONST_29  CAG  CAK  CAX  CAW    0.00   0.0  0
 A9Y  CONST_30  NAN  CAU  NAL  CAW    0.00   0.0  0
 A9Y  CONST_31  CAK  CAG  CAF  CAJ    0.00   0.0  0
 A9Y  CONST_32  CAK  CAX  CAW  CAJ    0.00   0.0  0
 A9Y  CONST_33  NAN  CAX  CAW  CAJ  180.00   0.0  0
 A9Y  CONST_34  CAX  CAK  CAG  CAF    0.00   0.0  0
 A9Y  CONST_35  CAX  CAW  CAJ  CAF    0.00   0.0  0
 A9Y  CONST_36  NAN  CAX  CAK  CAG  180.00   0.0  0
 A9Y  CONST_37  NAZ  CAS  CAV  CAY  180.00   0.0  0
 A9Y  CONST_38  NAM  CAQ  CAV  CAY  180.00   0.0  0
 A9Y  CONST_39  OAC  CAS  CAV  CAY    0.00   0.0  0
 A9Y  CONST_40  CAA  CAQ  CAV  CAY    0.00   0.0  0
 A9Y  CONST_41  CAA  CAQ  CAV  CAS  180.00   0.0  0
 A9Y  CONST_42  CAU  NAZ  CAS  OAC    0.00   0.0  0
 A9Y  CONST_43  NAM  NAZ  CAS  OAC  180.00   0.0  0
 A9Y  CONST_44  CAQ  CAV  CAS  OAC  180.00   0.0  0
 A9Y  CONST_45  NAZ  NAM  CAQ  CAA  180.00   0.0  0
 A9Y  CONST_46  H3   CAE  CAD  CAH  180.00   0.0  0
 A9Y  CONST_47  H4   CAI  CAE  CAD  180.00   0.0  0
 A9Y  CONST_48  H1   CAH  CAD  CAE  180.00   0.0  0
 A9Y  CONST_49  H2   CAD  CAE  CAI  180.00   0.0  0
 A9Y  CONST_50  H10  NAL  CAU  NAZ    0.00   0.0  0
 A9Y  CONST_51  H11  CAJ  CAW  NAL    0.00   0.0  0
 A9Y  CONST_52  H12  CAF  CAJ  CAW  180.00   0.0  0
 A9Y  CONST_53  H14  CAK  CAX  CAW  180.00   0.0  0
 A9Y  CONST_54  H13  CAG  CAF  CAJ  180.00   0.0  0
 A9Y  Var_01    OAO  CAP  CAR  CAH  179.62  30.0  1
 A9Y  Var_02    H7   CAA  CAQ  CAV   61.18  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A9Y  chir_01  CAY  OAO  CAT  CAV  positiv

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
 A9Y  plan-1  CAY  0.020
 A9Y  plan-1  CAV  0.020
 A9Y  plan-1  CAS  0.020
 A9Y  plan-1  OAC  0.020
 A9Y  plan-1  CAQ  0.020
 A9Y  plan-1  CAA  0.020
 A9Y  plan-1  NAM  0.020
 A9Y  plan-1  NAZ  0.020
 A9Y  plan-1  CAU  0.020
 A9Y  plan-2  CAH  0.020
 A9Y  plan-2  CAD  0.020
 A9Y  plan-2  CAE  0.020
 A9Y  plan-2  CAI  0.020
 A9Y  plan-2  CAT  0.020
 A9Y  plan-2  CAR  0.020
 A9Y  plan-2  CAP  0.020
 A9Y  plan-2  CAY  0.020
 A9Y  plan-2  H1   0.020
 A9Y  plan-2  H2   0.020
 A9Y  plan-2  H3   0.020
 A9Y  plan-2  H4   0.020
 A9Y  plan-3  NAZ  0.020
 A9Y  plan-3  CAU  0.020
 A9Y  plan-3  NAL  0.020
 A9Y  plan-3  CAW  0.020
 A9Y  plan-3  CAJ  0.020
 A9Y  plan-3  CAF  0.020
 A9Y  plan-3  CAG  0.020
 A9Y  plan-3  CAK  0.020
 A9Y  plan-3  CAX  0.020
 A9Y  plan-3  NAN  0.020
 A9Y  plan-3  H10  0.020
 A9Y  plan-3  H11  0.020
 A9Y  plan-3  H12  0.020
 A9Y  plan-3  H13  0.020
 A9Y  plan-3  H14  0.020
 A9Y  plan-4  CAR  0.020
 A9Y  plan-4  CAP  0.020
 A9Y  plan-4  OAB  0.020
 A9Y  plan-4  OAO  0.020

