# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:13:22 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-{2-[4-(5-chloro-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]ethyl}-4-fluorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)C(=O)NCCN2CCC(CC2)N3C(=O)Nc4cc(Cl)ccc34
#
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
 MJV  MJV  N-{2-[4-(5-chloro-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]ethyl}-4-fluorobenzamide  ligand  51  29  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJV
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
 MJV  C01  C   CR16  0  -0.270    7.1641   0.3197   0.2085
 MJV  C02  C   CR56  0   0.322    5.8517   0.7411   0.1420
 MJV  C04  C   CR5   0   0.667    3.9326   1.9200  -0.0466
 MJV  C07  C   CH1   0  -0.097    2.2669   0.0546   0.2324
 MJV  C08  C   CH2   0  -0.434    1.4696   0.6065   1.4082
 MJV  C09  C   CH2   0  -0.286    0.0841  -0.0227   1.4312
 MJV  C12  C   CH2   0  -0.305   -2.8650   0.3661  -0.8392
 MJV  C14  C   C     0   0.531   -5.1105   0.6239   0.1081
 MJV  C16  C   CR6   0  -0.042   -6.4974   0.0698   0.1714
 MJV  C17  C   CR16  0  -0.251   -7.5375   0.9390   0.4947
 MJV  C18  C   CR16  0  -0.398   -8.8436   0.4870   0.5760
 MJV  C19  C   CR6   0   0.531   -9.0932  -0.8541   0.3504
 MJV  C21  C   CR16  0  -0.397   -8.0854  -1.7497   0.0500
 MJV  C22  C   CR16  0  -0.274   -6.7853  -1.2769  -0.0415
 MJV  C23  C   CH2   0  -0.294    0.1098  -0.3893  -0.9298
 MJV  C24  C   CH2   0  -0.432    1.4929   0.2306  -1.0682
 MJV  C25  C   CR56  0   0.336    4.7779  -0.1467   0.2813
 MJV  C26  C   CR16  0  -0.321    5.0020  -1.4928   0.4946
 MJV  C27  C   CR16  0  -0.232    6.3202  -1.9365   0.5644
 MJV  C28  C   CR6   0  -0.062    7.3695  -1.0390   0.4223
 MJV  F20  F   F     0  -0.309  -10.3537  -1.3001   0.4290
 MJV  N03  N   NR15  0  -0.751    5.3047   1.9834  -0.0537
 MJV  N06  N   NR5   0  -0.606    3.6174   0.5940   0.1629
 MJV  N10  N   NT    0  -0.425   -0.6187   0.2007   0.1802
 MJV  N13  N   NH1   0  -0.646   -4.2523  -0.0170  -0.7012
 MJV  O05  O   O     0  -0.499    3.1629   2.8512  -0.1955
 MJV  O15  O   O     0  -0.491   -4.8019   1.6184   0.7520
 MJV  CL   CL  CL    0  -0.134    9.0005  -1.6274   0.5110
 MJV  H1   H   HCR6  0   0.291    7.9889   1.0103   0.0997
 MJV  H2   H   HCH1  0   0.259    2.3916  -1.0192   0.3963
 MJV  H3   H   HCH2  0   0.244    1.9818   0.3855   2.3467
 MJV  H4   H   HCH2  0   0.238    1.3742   1.6899   1.3245
 MJV  H5   H   HCH2  0   0.193    0.1765  -1.0998   1.6582
 MJV  H6   H   HCH2  0   0.243   -0.4952   0.4198   2.2443
 MJV  H7   H   HCH2  0   0.236   -2.3985   0.0566   1.2192
 MJV  H8   H   HCH2  0   0.198   -2.0780  -1.3509   0.2115
 MJV  H9   H   HCH2  0   0.244   -2.7768   1.4523  -0.8027
 MJV  H10  H   HCH2  0   0.255   -2.5452   0.0488  -1.8306
 MJV  H11  H   HCR6  0   0.271   -7.3293   1.9848   0.6755
 MJV  H12  H   HCR6  0   0.286   -9.6533   1.1646   0.8121
 MJV  H13  H   HCR6  0   0.288   -8.3067  -2.7973  -0.1039
 MJV  H14  H   HCR6  0   0.269   -5.9981  -1.9883  -0.2570
 MJV  H15  H   HCH2  0   0.247   -0.4393  -0.2273  -1.8579
 MJV  H16  H   HCH2  0   0.194    0.2063  -1.4835  -0.8074
 MJV  H17  H   HCH2  0   0.238    1.3931   1.2903  -1.3078
 MJV  H18  H   HCH2  0   0.244    2.0266  -0.2493  -1.8911
 MJV  H19  H   HCR6  0   0.283    4.1923  -2.2008   0.6047
 MJV  H20  H   HCR6  0   0.279    6.5212  -2.9858   0.7284
 MJV  H21  H   HNR5  0   0.421    5.8130   2.8413  -0.1980
 MJV  H23  H   HNH1  0   0.410   -4.5811  -0.7845  -1.2622
 MJV  C11  C   CH2   0  -0.265   -1.9933  -0.2520   0.2526

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
 MJV  F20  C19  single    1.339  0.020  1.339
 MJV  C19  C18  aromatic  1.383  0.020  1.383
 MJV  C19  C21  aromatic  1.381  0.020  1.381
 MJV  C18  C17  aromatic  1.384  0.020  1.384
 MJV  C21  C22  aromatic  1.386  0.020  1.386
 MJV  C17  C16  aromatic  1.393  0.020  1.393
 MJV  C22  C16  aromatic  1.394  0.020  1.394
 MJV  C16  C14  single    1.495  0.020  1.495
 MJV  C14  O15  double    1.224  0.020  1.224
 MJV  C14  N13  single    1.342  0.020  1.342
 MJV  N13  C12  single    1.446  0.020  1.446
 MJV  C12  C11  single    1.528  0.020  1.528
 MJV  C09  N10  single    1.452  0.020  1.452
 MJV  C09  C08  single    1.522  0.020  1.522
 MJV  C11  N10  single    1.449  0.020  1.449
 MJV  N10  C23  single    1.453  0.020  1.453
 MJV  C27  C26  aromatic  1.393  0.020  1.393
 MJV  C27  C28  aromatic  1.388  0.020  1.388
 MJV  C08  C07  single    1.524  0.020  1.524
 MJV  CL   C28  single    1.736  0.020  1.736
 MJV  C26  C25  aromatic  1.381  0.020  1.381
 MJV  C28  C01  aromatic  1.391  0.020  1.391
 MJV  C23  C24  single    1.522  0.020  1.522
 MJV  C25  N06  single    1.382  0.020  1.382
 MJV  C25  C02  aromatic  1.400  0.020  1.400
 MJV  C07  C24  single    1.524  0.020  1.524
 MJV  C07  N06  single    1.456  0.020  1.456
 MJV  C01  C02  aromatic  1.380  0.020  1.380
 MJV  N06  C04  single    1.379  0.020  1.379
 MJV  C02  N03  single    1.371  0.020  1.371
 MJV  C04  N03  single    1.374  0.020  1.374
 MJV  C04  O05  double    1.217  0.020  1.217
 MJV  C01  H1   single    0.930  0.020  1.080
 MJV  C07  H2   single    0.970  0.020  1.090
 MJV  C08  H3   single    0.970  0.020  1.090
 MJV  C08  H4   single    0.970  0.020  1.090
 MJV  C09  H5   single    0.970  0.020  1.090
 MJV  C09  H6   single    0.970  0.020  1.090
 MJV  C11  H7   single    0.970  0.020  1.090
 MJV  C11  H8   single    0.970  0.020  1.090
 MJV  C12  H9   single    0.970  0.020  1.090
 MJV  C12  H10  single    0.970  0.020  1.090
 MJV  C17  H11  single    0.930  0.020  1.080
 MJV  C18  H12  single    0.930  0.020  1.080
 MJV  C21  H13  single    0.930  0.020  1.080
 MJV  C22  H14  single    0.930  0.020  1.080
 MJV  C23  H15  single    0.970  0.020  1.090
 MJV  C23  H16  single    0.970  0.020  1.090
 MJV  C24  H17  single    0.970  0.020  1.090
 MJV  C24  H18  single    0.970  0.020  1.090
 MJV  C26  H19  single    0.930  0.020  1.080
 MJV  C27  H20  single    0.930  0.020  1.080
 MJV  N03  H21  single    0.860  0.020  1.020
 MJV  N13  H23  single    0.860  0.020  1.020

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
 MJV  H1   C01  C28  121.79  3.000
 MJV  H1   C01  C02  121.71  3.000
 MJV  C28  C01  C02  116.50  3.000
 MJV  N03  C02  C25  106.42  3.000
 MJV  N03  C02  C01  131.51  3.000
 MJV  C25  C02  C01  122.07  3.000
 MJV  O05  C04  N06  127.56  3.000
 MJV  O05  C04  N03  126.56  3.000
 MJV  N06  C04  N03  105.87  3.000
 MJV  H2   C07  N06  105.38  3.000
 MJV  H2   C07  C24  107.42  3.000
 MJV  N06  C07  C24  112.81  3.000
 MJV  H2   C07  C08  107.44  3.000
 MJV  N06  C07  C08  112.83  3.000
 MJV  C24  C07  C08  110.55  3.000
 MJV  H4   C08  H3   107.94  3.000
 MJV  H4   C08  C09  109.40  3.000
 MJV  H3   C08  C09  109.29  3.000
 MJV  H4   C08  C07  110.26  3.000
 MJV  H3   C08  C07  110.15  3.000
 MJV  C09  C08  C07  109.77  3.000
 MJV  H6   C09  H5   106.65  3.000
 MJV  H6   C09  N10  108.81  3.000
 MJV  H5   C09  N10  111.56  3.000
 MJV  H6   C09  C08  109.07  3.000
 MJV  H5   C09  C08  109.27  3.000
 MJV  N10  C09  C08  111.34  3.000
 MJV  H10  C12  H9   107.28  3.000
 MJV  H10  C12  N13  106.94  3.000
 MJV  H9   C12  N13  109.78  3.000
 MJV  H10  C12  C11  111.42  3.000
 MJV  H9   C12  C11  109.45  3.000
 MJV  N13  C12  C11  111.84  3.000
 MJV  O15  C14  N13  122.94  3.000
 MJV  N13  C14  C16  116.21  3.000
 MJV  O15  C14  C16  120.84  3.000
 MJV  C22  C16  C17  118.95  3.000
 MJV  C22  C16  C14  122.92  3.000
 MJV  C17  C16  C14  118.11  3.000
 MJV  H11  C17  C18  119.18  3.000
 MJV  H11  C17  C16  119.88  3.000
 MJV  C18  C17  C16  120.94  3.000
 MJV  H12  C18  C19  120.53  3.000
 MJV  H12  C18  C17  120.95  3.000
 MJV  C19  C18  C17  118.52  3.000
 MJV  F20  C19  C21  118.91  3.000
 MJV  C21  C19  C18  122.18  3.000
 MJV  F20  C19  C18  118.90  3.000
 MJV  H13  C21  C22  120.84  3.000
 MJV  H13  C21  C19  120.64  3.000
 MJV  C22  C21  C19  118.52  3.000
 MJV  H14  C22  C21  118.09  3.000
 MJV  H14  C22  C16  121.02  3.000
 MJV  C21  C22  C16  120.88  3.000
 MJV  H16  C23  H15  106.58  3.000
 MJV  H16  C23  N10  111.17  3.000
 MJV  H15  C23  N10  109.72  3.000
 MJV  H16  C23  C24  109.51  3.000
 MJV  H15  C23  C24  108.65  3.000
 MJV  N10  C23  C24  111.08  3.000
 MJV  H18  C24  H17  107.82  3.000
 MJV  H18  C24  C23  109.49  3.000
 MJV  H17  C24  C23  109.42  3.000
 MJV  H18  C24  C07  110.13  3.000
 MJV  H17  C24  C07  110.25  3.000
 MJV  C23  C24  C07  109.69  3.000
 MJV  N06  C25  C26  132.22  3.000
 MJV  N06  C25  C02  107.19  3.000
 MJV  C26  C25  C02  120.59  3.000
 MJV  H19  C26  C27  119.68  3.000
 MJV  H19  C26  C25  122.16  3.000
 MJV  C27  C26  C25  118.15  3.000
 MJV  H20  C27  C28  120.18  3.000
 MJV  H20  C27  C26  119.53  3.000
 MJV  C28  C27  C26  120.29  3.000
 MJV  CL   C28  C27  119.06  3.000
 MJV  CL   C28  C01  118.54  3.000
 MJV  C27  C28  C01  122.40  3.000
 MJV  H21  N03  C04  122.96  3.000
 MJV  H21  N03  C02  126.19  3.000
 MJV  C04  N03  C02  110.85  3.000
 MJV  C25  N06  C07  125.19  3.000
 MJV  C07  N06  C04  125.14  3.000
 MJV  C25  N06  C04  109.67  3.000
 MJV  C23  N10  C11  112.77  3.000
 MJV  C23  N10  C09  110.67  3.000
 MJV  C11  N10  C09  111.59  3.000
 MJV  H23  N13  C14  119.44  3.000
 MJV  H23  N13  C12  117.56  3.000
 MJV  C14  N13  C12  122.98  3.000
 MJV  H8   C11  H7   106.62  3.000
 MJV  H8   C11  N10  112.47  3.000
 MJV  H7   C11  N10  107.93  3.000
 MJV  H8   C11  C12  109.43  3.000
 MJV  H7   C11  C12  107.84  3.000
 MJV  N10  C11  C12  112.28  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
 MJV  CONST_01  C26  C27  C28  C01     0.00   0.0  0
 MJV  CONST_02  C26  C25  C02  C01     0.00   0.0  0
 MJV  CONST_03  C27  C26  C25  C02     0.00   0.0  0
 MJV  CONST_04  C27  C28  C01  C02     0.00   0.0  0
 MJV  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 MJV  CONST_06  C19  C21  C22  C16     0.00   0.0  0
 MJV  CONST_07  C21  C19  C18  C17     0.00   0.0  0
 MJV  CONST_08  C21  C22  C16  C17     0.00   0.0  0
 MJV  CONST_09  C22  C21  C19  C18     0.00   0.0  0
 MJV  CONST_10  C22  C16  C17  C18     0.00   0.0  0
 MJV  CONST_11  C28  C27  C26  C25     0.00   0.0  0
 MJV  CONST_12  C28  C01  C02  C25     0.00   0.0  0
 MJV  CONST_13  C07  N06  C25  C02   180.00   0.0  0
 MJV  CONST_14  C04  N06  C25  C02     0.00   0.0  0
 MJV  CONST_15  N06  C04  N03  C02     0.00   0.0  0
 MJV  CONST_16  C25  C02  N03  C04     0.00   0.0  0
 MJV  CONST_17  N03  C04  N06  C07   180.00   0.0  0
 MJV  CONST_18  N03  C04  N06  C25     0.00   0.0  0
 MJV  CONST_19  N06  C25  C02  N03     0.00   0.0  0
 MJV  CONST_20  CL   C28  C01  C02   180.00   0.0  0
 MJV  CONST_21  C18  C17  C16  C14   180.00   0.0  0
 MJV  CONST_22  C21  C22  C16  C14   180.00   0.0  0
 MJV  CONST_23  F20  C19  C18  C17   180.00   0.0  0
 MJV  CONST_24  F20  C19  C21  C22   180.00   0.0  0
 MJV  CONST_25  CL   C28  C27  C26   180.00   0.0  0
 MJV  CONST_26  O05  C04  N03  C02   180.00   0.0  0
 MJV  CONST_27  O05  C04  N06  C07     0.00   0.0  0
 MJV  CONST_28  O05  C04  N06  C25   180.00   0.0  0
 MJV  CONST_29  H20  C27  C28  C01   180.00   0.0  0
 MJV  CONST_30  H19  C26  C25  C02   180.00   0.0  0
 MJV  CONST_31  H12  C18  C17  C16   180.00   0.0  0
 MJV  CONST_32  H13  C21  C22  C16   180.00   0.0  0
 MJV  CONST_33  H14  C22  C16  C17   180.00   0.0  0
 MJV  CONST_34  H11  C17  C18  C19   180.00   0.0  0
 MJV  CONST_35  H1   C01  C02  C25   180.00   0.0  0
 MJV  CONST_36  H21  N03  C02  C25   180.00   0.0  0
 MJV  CONST_37  C16  C14  N13  C12   180.00   0.0  0
 MJV  CONST_38  H23  N13  C14  C16     0.00   0.0  0
 MJV  CONST_39  O15  C14  N13  C12     0.00   0.0  0
 MJV  Var_01    N10  C09  C08  C07   -56.89  30.0  1
 MJV  Var_02    N10  C23  C24  C07    57.52  30.0  1
 MJV  Var_03    C23  N10  C09  C08    60.53  30.0  1
 MJV  Var_04    C24  C23  N10  C09   -60.80  30.0  1
 MJV  Var_05    C12  C11  N10  C09   161.20  30.0  2
 MJV  Var_06    O15  C14  C16  C17    25.76  30.0  2
 MJV  Var_07    N13  C12  C11  N10  -175.91  30.0  1
 MJV  Var_08    C14  N13  C12  C11    84.44  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
 MJV  chir_01  C07  C08  C24  N06  negativ

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
 MJV  plan-1  C14  0.020
 MJV  plan-1  C16  0.020
 MJV  plan-1  C17  0.020
 MJV  plan-1  C18  0.020
 MJV  plan-1  C19  0.020
 MJV  plan-1  C21  0.020
 MJV  plan-1  C22  0.020
 MJV  plan-1  F20  0.020
 MJV  plan-1  H11  0.020
 MJV  plan-1  H12  0.020
 MJV  plan-1  H13  0.020
 MJV  plan-1  H14  0.020
 MJV  plan-2  C01  0.020
 MJV  plan-2  C02  0.020
 MJV  plan-2  C04  0.020
 MJV  plan-2  C07  0.020
 MJV  plan-2  C25  0.020
 MJV  plan-2  C26  0.020
 MJV  plan-2  C27  0.020
 MJV  plan-2  C28  0.020
 MJV  plan-2  N03  0.020
 MJV  plan-2  N06  0.020
 MJV  plan-2  O05  0.020
 MJV  plan-2  CL   0.020
 MJV  plan-2  H1   0.020
 MJV  plan-2  H19  0.020
 MJV  plan-2  H20  0.020
 MJV  plan-2  H21  0.020
 MJV  plan-3  C12  0.020
 MJV  plan-3  C14  0.020
 MJV  plan-3  C16  0.020
 MJV  plan-3  N13  0.020
 MJV  plan-3  O15  0.020
 MJV  plan-3  H23  0.020

