# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:01:25 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-[1,3-dimethyl-2-oxo-6-(piperidin-1-yl)-2,3-dihydro-1H-benzimidazol-5-yl]-2-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)Nc2cc3N(C)C(=O)N(C)c3cc2N4CCCCC4
#
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
 9F9  9F9  N-[1,3-dimethyl-2-oxo-6-(piperidin-1-yl)-2,3-dihydro-1H-benzimidazol-5-yl]-2-methoxybenzamide  ligand  55  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9F9
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
 9F9  C01   C  CH3   0  -0.439   5.0650   2.5314  -1.4249
 9F9  O05   O  O2    0  -0.458   4.0006   1.9630  -0.6857
 9F9  C06   C  CR6   0   0.386   4.2342   0.8605   0.0404
 9F9  C07   C  CR16  0  -0.384   5.4778   0.2395   0.1358
 9F9  C09   C  CR16  0  -0.238   5.6224  -0.9187   0.8892
 9F9  C11   C  CR16  0  -0.273   4.5398  -1.4793   1.5470
 9F9  C13   C  CR16  0  -0.261   3.2999  -0.8648   1.4439
 9F9  C15   C  CR6   0  -0.170   3.1330   0.3012   0.7061
 9F9  C16   C  C     0   0.510   1.7939   0.9670   0.6618
 9F9  O17   O  O     0  -0.464   1.6326   2.1379   0.9619
 9F9  N18   N  NH1   0  -0.724   0.8072   0.1256   0.2854
 9F9  C20   C  CR6   0   0.312  -0.5713   0.3254   0.2132
 9F9  C21   C  CR16  0  -0.418  -1.1958   1.5657   0.3729
 9F9  C23   C  CR56  0   0.363  -2.5695   1.5982   0.2393
 9F9  N24   N  NR5   0  -0.586  -3.4580   2.6453   0.3367
 9F9  C25   C  CH3   0  -0.534  -3.1034   4.0178   0.5895
 9F9  C29   C  CR5   0   0.653  -4.7397   2.1953   0.1135
 9F9  O30   O  O     0  -0.505  -5.7593   2.8629   0.1209
 9F9  N31   N  NR5   0  -0.586  -4.6381   0.8442  -0.1174
 9F9  C32   C  CH3   0  -0.536  -5.7477  -0.0300  -0.3935
 9F9  C36   C  CR56  0   0.333  -3.3175   0.4559  -0.0445
 9F9  C37   C  CR16  0  -0.352  -2.7075  -0.7720  -0.1932
 9F9  C39   C  CR6   0   0.211  -1.3218  -0.8356  -0.0635
 9F9  N40   N  NT    0  -0.526  -0.6021  -2.0514  -0.1930
 9F9  C41   C  CH2   0  -0.284  -0.8999  -2.8278  -1.3887
 9F9  C44   C  CH2   0  -0.439   0.1280  -3.9362  -1.5595
 9F9  C47   C  CH2   0  -0.441   0.1882  -4.8227  -0.3212
 9F9  C50   C  CH2   0  -0.441   0.4195  -3.9767   0.9247
 9F9  C53   C  CH2   0  -0.295  -0.6113  -2.8640   1.0220
 9F9  H011  H  HCH3  0   0.232   5.4701   1.8309  -2.1594
 9F9  H012  H  HCH3  0   0.262   4.6500   3.3885  -1.9490
 9F9  H013  H  HCH3  0   0.232   5.8758   2.8742  -0.7772
 9F9  H07   H  HCR6  0   0.287   6.3413   0.6427  -0.3751
 9F9  H09   H  HCR6  0   0.266   6.5979  -1.3826   0.9551
 9F9  H11   H  HCR6  0   0.261   4.6541  -2.3802   2.1339
 9F9  H13   H  HCR6  0   0.265   2.4502  -1.2886   1.9664
 9F9  H18   H  HNH1  0   0.406   1.0559  -0.8188   0.0065
 9F9  H21   H  HCR6  0   0.291  -0.6293   2.4597   0.5801
 9F9  H251  H  HCH3  0   0.254  -2.5820   4.4533  -0.2632
 9F9  H252  H  HCH3  0   0.268  -4.0065   4.5908   0.7767
 9F9  H253  H  HCH3  0   0.256  -2.4605   4.0850   1.4663
 9F9  H321  H  HCH3  0   0.268  -6.6632   0.5537  -0.4151
 9F9  H322  H  HCH3  0   0.254  -5.6229  -0.5169  -1.3606
 9F9  H323  H  HCH3  0   0.254  -5.8395  -0.7957   0.3767
 9F9  H37   H  HCR6  0   0.274  -3.2786  -1.6676  -0.4031
 9F9  H411  H  HCH2  0   0.200  -1.9076  -3.2712  -1.3472
 9F9  H412  H  HCH2  0   0.246  -0.8809  -2.1579  -2.2498
 9F9  H531  H  HCH2  0   0.247  -0.3945  -2.2178   1.8755
 9F9  H532  H  HCH2  0   0.212  -1.6097  -3.2960   1.1982
 9F9  H441  H  HCH2  0   0.234  -0.1210  -4.5240  -2.4455
 9F9  H442  H  HCH2  0   0.219   1.1091  -3.4856  -1.7387
 9F9  H471  H  HCH2  0   0.214  -0.7535  -5.3729  -0.2203
 9F9  H472  H  HCH2  0   0.236   0.9765  -5.5711  -0.4261
 9F9  H501  H  HCH2  0   0.237   0.3743  -4.5906   1.8266
 9F9  H502  H  HCH2  0   0.213   1.4211  -3.5347   0.8884

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
 9F9  C01  O05   single    1.415  0.020  1.415
 9F9  O05  C06   single    1.341  0.020  1.341
 9F9  C06  C07   aromatic  1.393  0.020  1.393
 9F9  C06  C15   aromatic  1.403  0.020  1.403
 9F9  C07  C09   aromatic  1.389  0.020  1.389
 9F9  C09  C11   aromatic  1.385  0.020  1.385
 9F9  C11  C13   aromatic  1.388  0.020  1.388
 9F9  C13  C15   aromatic  1.390  0.020  1.390
 9F9  C15  C16   single    1.496  0.020  1.496
 9F9  C16  O17   double    1.219  0.020  1.219
 9F9  C16  N18   single    1.350  0.020  1.350
 9F9  N18  C20   single    1.395  0.020  1.395
 9F9  C20  C21   aromatic  1.398  0.020  1.398
 9F9  C20  C39   aromatic  1.410  0.020  1.410
 9F9  C21  C23   aromatic  1.381  0.020  1.381
 9F9  C23  N24   single    1.377  0.020  1.377
 9F9  C23  C36   aromatic  1.394  0.020  1.394
 9F9  N24  C25   single    1.440  0.020  1.440
 9F9  N24  C29   single    1.377  0.020  1.377
 9F9  C29  O30   double    1.219  0.020  1.219
 9F9  C29  N31   single    1.374  0.020  1.374
 9F9  N31  C32   single    1.439  0.020  1.439
 9F9  N31  C36   single    1.378  0.020  1.378
 9F9  C36  C37   aromatic  1.379  0.020  1.379
 9F9  C37  C39   aromatic  1.393  0.020  1.393
 9F9  C39  N40   single    1.419  0.020  1.419
 9F9  N40  C41   single    1.456  0.020  1.456
 9F9  N40  C53   single    1.462  0.020  1.462
 9F9  C41  C44   single    1.521  0.020  1.521
 9F9  C44  C47   single    1.524  0.020  1.524
 9F9  C47  C50   single    1.524  0.020  1.524
 9F9  C50  C53   single    1.520  0.020  1.520
 9F9  C01  H011  single    0.970  0.020  1.090
 9F9  C01  H012  single    0.970  0.020  1.090
 9F9  C01  H013  single    0.970  0.020  1.090
 9F9  C07  H07   single    0.930  0.020  1.080
 9F9  C09  H09   single    0.930  0.020  1.080
 9F9  C11  H11   single    0.930  0.020  1.080
 9F9  C13  H13   single    0.930  0.020  1.080
 9F9  N18  H18   single    0.860  0.020  1.020
 9F9  C21  H21   single    0.930  0.020  1.080
 9F9  C25  H251  single    0.970  0.020  1.090
 9F9  C25  H252  single    0.970  0.020  1.090
 9F9  C25  H253  single    0.970  0.020  1.090
 9F9  C32  H321  single    0.970  0.020  1.090
 9F9  C32  H322  single    0.970  0.020  1.090
 9F9  C32  H323  single    0.970  0.020  1.090
 9F9  C37  H37   single    0.930  0.020  1.080
 9F9  C41  H411  single    0.970  0.020  1.090
 9F9  C41  H412  single    0.970  0.020  1.090
 9F9  C53  H531  single    0.970  0.020  1.090
 9F9  C53  H532  single    0.970  0.020  1.090
 9F9  C44  H441  single    0.970  0.020  1.090
 9F9  C44  H442  single    0.970  0.020  1.090
 9F9  C47  H471  single    0.970  0.020  1.090
 9F9  C47  H472  single    0.970  0.020  1.090
 9F9  C50  H501  single    0.970  0.020  1.090
 9F9  C50  H502  single    0.970  0.020  1.090

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
 9F9  H013  C01  H012  108.76  3.000
 9F9  H013  C01  H011  108.93  3.000
 9F9  H012  C01  H011  108.84  3.000
 9F9  H013  C01  O05   111.98  3.000
 9F9  H012  C01  O05   106.34  3.000
 9F9  H011  C01  O05   111.87  3.000
 9F9  C06   O05  C01   118.83  3.000
 9F9  C15   C06  C07   119.37  3.000
 9F9  C15   C06  O05   116.62  3.000
 9F9  C07   C06  O05   124.00  3.000
 9F9  H07   C07  C09   118.95  3.000
 9F9  H07   C07  C06   120.95  3.000
 9F9  C09   C07  C06   120.11  3.000
 9F9  H09   C09  C11   120.13  3.000
 9F9  H09   C09  C07   118.96  3.000
 9F9  C11   C09  C07   120.90  3.000
 9F9  H11   C11  C13   120.25  3.000
 9F9  H11   C11  C09   120.82  3.000
 9F9  C13   C11  C09   118.93  3.000
 9F9  H13   C13  C15   119.33  3.000
 9F9  H13   C13  C11   119.44  3.000
 9F9  C15   C13  C11   121.21  3.000
 9F9  C16   C15  C13   119.77  3.000
 9F9  C16   C15  C06   120.73  3.000
 9F9  C13   C15  C06   119.47  3.000
 9F9  N18   C16  O17   124.77  3.000
 9F9  N18   C16  C15   112.64  3.000
 9F9  O17   C16  C15   122.58  3.000
 9F9  H18   N18  C20   111.16  3.000
 9F9  H18   N18  C16   118.50  3.000
 9F9  C20   N18  C16   130.34  3.000
 9F9  C39   C20  C21   121.02  3.000
 9F9  C39   C20  N18   114.72  3.000
 9F9  C21   C20  N18   124.25  3.000
 9F9  H21   C21  C23   121.45  3.000
 9F9  H21   C21  C20   121.52  3.000
 9F9  C23   C21  C20   117.02  3.000
 9F9  C36   C23  N24   106.93  3.000
 9F9  C36   C23  C21   122.28  3.000
 9F9  N24   C23  C21   130.78  3.000
 9F9  C29   N24  C25   124.71  3.000
 9F9  C29   N24  C23   109.92  3.000
 9F9  C25   N24  C23   125.34  3.000
 9F9  H253  C25  H252  108.63  3.000
 9F9  H253  C25  H251  108.83  3.000
 9F9  H252  C25  H251  108.77  3.000
 9F9  H253  C25  N24   110.21  3.000
 9F9  H252  C25  N24   109.18  3.000
 9F9  H251  C25  N24   111.18  3.000
 9F9  N31   C29  O30   126.97  3.000
 9F9  N31   C29  N24   106.25  3.000
 9F9  O30   C29  N24   126.78  3.000
 9F9  C36   N31  C32   125.29  3.000
 9F9  C36   N31  C29   109.80  3.000
 9F9  C32   N31  C29   124.91  3.000
 9F9  H323  C32  H322  108.83  3.000
 9F9  H323  C32  H321  108.70  3.000
 9F9  H322  C32  H321  108.61  3.000
 9F9  H323  C32  N31   110.86  3.000
 9F9  H322  C32  N31   110.69  3.000
 9F9  H321  C32  N31   109.11  3.000
 9F9  C37   C36  N31   131.98  3.000
 9F9  C37   C36  C23   120.93  3.000
 9F9  N31   C36  C23   107.09  3.000
 9F9  H37   C37  C39   120.32  3.000
 9F9  H37   C37  C36   121.61  3.000
 9F9  C39   C37  C36   118.07  3.000
 9F9  N40   C39  C37   122.35  3.000
 9F9  N40   C39  C20   116.98  3.000
 9F9  C37   C39  C20   120.67  3.000
 9F9  C53   N40  C41   112.63  3.000
 9F9  C53   N40  C39   113.41  3.000
 9F9  C41   N40  C39   115.34  3.000
 9F9  H412  C41  H411  107.03  3.000
 9F9  H412  C41  C44   110.30  3.000
 9F9  H411  C41  C44   109.21  3.000
 9F9  H412  C41  N40   108.48  3.000
 9F9  H411  C41  N40   111.75  3.000
 9F9  C44   C41  N40   110.02  3.000
 9F9  H442  C44  H441  107.05  3.000
 9F9  H442  C44  C47   109.70  3.000
 9F9  H441  C44  C47   110.80  3.000
 9F9  H442  C44  C41   108.92  3.000
 9F9  H441  C44  C41   109.22  3.000
 9F9  C47   C44  C41   111.05  3.000
 9F9  H472  C47  H471  106.57  3.000
 9F9  H472  C47  C50   110.46  3.000
 9F9  H471  C47  C50   109.52  3.000
 9F9  H472  C47  C44   110.43  3.000
 9F9  H471  C47  C44   109.46  3.000
 9F9  C50   C47  C44   110.33  3.000
 9F9  H502  C50  H501  106.98  3.000
 9F9  H502  C50  C53   109.08  3.000
 9F9  H501  C50  C53   109.31  3.000
 9F9  H502  C50  C47   109.62  3.000
 9F9  H501  C50  C47   110.91  3.000
 9F9  C53   C50  C47   110.85  3.000
 9F9  H532  C53  H531  106.67  3.000
 9F9  H532  C53  C50   109.74  3.000
 9F9  H531  C53  C50   110.39  3.000
 9F9  H532  C53  N40   110.89  3.000
 9F9  H531  C53  N40   108.63  3.000
 9F9  C50   C53  N40   110.45  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
 9F9  CONST_01  C11   C09  C07  C06     0.00   0.0  0
 9F9  CONST_02  C11   C13  C15  C06     0.00   0.0  0
 9F9  CONST_03  C13   C15  C06  C07     0.00   0.0  0
 9F9  CONST_04  C13   C11  C09  C07     0.00   0.0  0
 9F9  CONST_05  C15   C06  C07  C09     0.00   0.0  0
 9F9  CONST_06  C15   C13  C11  C09     0.00   0.0  0
 9F9  CONST_07  C36   C23  C21  C20     0.00   0.0  0
 9F9  CONST_08  C36   C37  C39  C20     0.00   0.0  0
 9F9  CONST_09  C37   C39  C20  C21     0.00   0.0  0
 9F9  CONST_10  C37   C36  C23  C21     0.00   0.0  0
 9F9  CONST_11  C39   C20  C21  C23     0.00   0.0  0
 9F9  CONST_12  C39   C37  C36  C23     0.00   0.0  0
 9F9  CONST_13  N40   C39  C20  C21   180.00   0.0  0
 9F9  CONST_14  N40   C39  C37  C36   180.00   0.0  0
 9F9  CONST_15  N31   C29  N24  C23     0.00   0.0  0
 9F9  CONST_16  C29   N31  C36  C23     0.00   0.0  0
 9F9  CONST_17  N31   C36  C23  N24     0.00   0.0  0
 9F9  CONST_18  C36   N31  C29  N24     0.00   0.0  0
 9F9  CONST_19  C36   C23  N24  C29     0.00   0.0  0
 9F9  CONST_20  C09   C07  C06  O05   180.00   0.0  0
 9F9  CONST_21  C13   C15  C06  O05   180.00   0.0  0
 9F9  CONST_22  C16   C15  C06  C07   180.00   0.0  0
 9F9  CONST_23  C16   C15  C13  C11   180.00   0.0  0
 9F9  CONST_24  C23   C21  C20  N18   180.00   0.0  0
 9F9  CONST_25  C37   C39  C20  N18   180.00   0.0  0
 9F9  CONST_26  N40   C39  C20  N18     0.00   0.0  0
 9F9  CONST_27  O30   C29  N24  C23   180.00   0.0  0
 9F9  CONST_28  C32   N31  C36  C23   180.00   0.0  0
 9F9  CONST_29  C32   N31  C29  N24   180.00   0.0  0
 9F9  CONST_30  C36   C23  N24  C25   180.00   0.0  0
 9F9  CONST_31  N31   C29  N24  C25   180.00   0.0  0
 9F9  CONST_32  C36   N31  C29  O30   180.00   0.0  0
 9F9  CONST_33  H09   C09  C07  C06   180.00   0.0  0
 9F9  CONST_34  H13   C13  C15  C06   180.00   0.0  0
 9F9  CONST_35  H11   C11  C09  C07   180.00   0.0  0
 9F9  CONST_36  H07   C07  C09  C11   180.00   0.0  0
 9F9  CONST_37  H37   C37  C39  C20   180.00   0.0  0
 9F9  CONST_38  H21   C21  C23  N24     0.00   0.0  0
 9F9  CONST_39  C20   N18  C16  C15   180.00   0.0  0
 9F9  CONST_40  C21   C20  N18  C16     0.00   0.0  0
 9F9  CONST_41  C39   C20  N18  C16   180.00   0.0  0
 9F9  CONST_42  O30   C29  N24  C25     0.00   0.0  0
 9F9  CONST_43  C32   N31  C29  O30     0.00   0.0  0
 9F9  CONST_44  H18   N18  C20  C21   180.00   0.0  0
 9F9  CONST_45  C20   N18  C16  O17     0.00   0.0  0
 9F9  Var_01    C41   N40  C39  C20  -129.73  30.0  2
 9F9  Var_02    C44   C41  N40  C39   168.07  30.0  1
 9F9  Var_03    C50   C53  N40  C39  -167.17  30.0  1
 9F9  Var_04    C47   C44  C41  N40    56.18  30.0  1
 9F9  Var_05    C47   C50  C53  N40   -55.62  30.0  1
 9F9  Var_06    C50   C47  C44  C41   -53.66  30.0  1
 9F9  Var_07    C53   C50  C47  C44    53.26  30.0  1
 9F9  Var_08    C07   C06  O05  C01     1.12  30.0  2
 9F9  Var_09    O17   C16  C15  C06   -52.86  30.0  2
 9F9  Var_10    H251  C25  N24  C23    69.28  30.0  3
 9F9  Var_11    H321  C32  N31  C29     1.49  30.0  3
 9F9  Var_12    H011  C01  O05  C06    59.93  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
 9F9  plan-1  O05  0.020
 9F9  plan-1  C06  0.020
 9F9  plan-1  C07  0.020
 9F9  plan-1  C09  0.020
 9F9  plan-1  C11  0.020
 9F9  plan-1  C13  0.020
 9F9  plan-1  C15  0.020
 9F9  plan-1  C16  0.020
 9F9  plan-1  H07  0.020
 9F9  plan-1  H09  0.020
 9F9  plan-1  H11  0.020
 9F9  plan-1  H13  0.020
 9F9  plan-2  N18  0.020
 9F9  plan-2  C20  0.020
 9F9  plan-2  C21  0.020
 9F9  plan-2  C23  0.020
 9F9  plan-2  N24  0.020
 9F9  plan-2  C25  0.020
 9F9  plan-2  C29  0.020
 9F9  plan-2  O30  0.020
 9F9  plan-2  N31  0.020
 9F9  plan-2  C32  0.020
 9F9  plan-2  C36  0.020
 9F9  plan-2  C37  0.020
 9F9  plan-2  C39  0.020
 9F9  plan-2  N40  0.020
 9F9  plan-2  H21  0.020
 9F9  plan-2  H37  0.020
 9F9  plan-3  C15  0.020
 9F9  plan-3  C16  0.020
 9F9  plan-3  O17  0.020
 9F9  plan-3  N18  0.020
 9F9  plan-3  C20  0.020
 9F9  plan-3  H18  0.020

