# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:22:43 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: ~{N}-[(3-chlorophenyl)methyl]-1-(2-pyrrolidin-1-ylethyl)benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CNC(=O)c2ccc3n(CCN4CCCC4)cnc3c2)c1
#
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
 GKQ  GKQ  ~{N}-[(3-chlorophenyl)methyl]-1-(2-pyrrolidin-1-ylethyl)benzimidazole-5-carboxamide  ligand  50  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GKQ
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
 GKQ  C    C   CR56  0   0.148  -1.8496   2.4997  -0.3054
 GKQ  N    N   N     0  -0.467  -2.9289   3.3249  -0.5171
 GKQ  O    O   O     0  -0.490   2.0539   3.1341   1.1320
 GKQ  C1   C   CR56  0   0.350  -2.2344   1.1570  -0.4643
 GKQ  C2   C   CR15  0   0.110  -3.9108   2.5157  -0.7889
 GKQ  N3   N   NH1   0  -0.648   2.7251   1.2695   0.0477
 GKQ  C13  C   CH2   0  -0.329   4.1364   1.4344   0.3048
 GKQ  C14  C   CR6   0   0.083   4.8099   0.1052   0.5253
 GKQ  C17  C   CR16  0  -0.279   4.2980  -0.8112   1.4412
 GKQ  C18  C   CR16  0  -0.245   4.9375  -2.0224   1.6514
 GKQ  C19  C   CR16  0  -0.229   6.0960  -2.3429   0.9549
 GKQ  C16  C   CR6   0  -0.020   6.5957  -1.4257   0.0466
 GKQ  CL   CL  CL    0  -0.129   8.0375  -1.8040  -0.8408
 GKQ  C15  C   CR16  0  -0.272   5.9655  -0.2103  -0.1782
 GKQ  C11  C   CR6   0  -0.060   0.3756   1.7742   0.1496
 GKQ  C10  C   CR16  0  -0.346  -0.5347   2.8131   0.0177
 GKQ  C20  C   CR16  0  -0.308  -0.0341   0.4354  -0.0058
 GKQ  C9   C   CR16  0  -0.288  -1.3403   0.1038  -0.3082
 GKQ  N1   N   NR5   0  -0.508  -3.5641   1.2016  -0.7810
 GKQ  C4   C   CH2   0  -0.270  -4.9072  -0.5264   0.3404
 GKQ  N2   N   NT    0  -0.431  -5.7859  -1.6485   0.1280
 GKQ  C7   C   CH2   0  -0.275  -6.0234  -2.4292   1.3312
 GKQ  C8   C   CH2   0  -0.466  -7.1860  -3.3452   0.9493
 GKQ  C6   C   CH2   0  -0.464  -7.9254  -2.5771  -0.1669
 GKQ  C5   C   CH2   0  -0.287  -7.1141  -1.2929  -0.3481
 GKQ  H1   H   HCR5  0   0.293  -4.9234   2.8184  -1.0152
 GKQ  H2   H   HCH2  0   0.278  -5.2980   0.4302  -1.5704
 GKQ  H3   H   HCH2  0   0.269  -3.9352  -0.6758  -1.5841
 GKQ  H4   H   HNH1  0   0.407   2.4625   0.5645  -0.6230
 GKQ  H5   H   HCH2  0   0.262   4.6245   1.9657  -0.5171
 GKQ  H6   H   HCH2  0   0.273   4.2469   2.0591   1.1915
 GKQ  H7   H   HCR6  0   0.259   3.3946  -0.5789   1.9911
 GKQ  H8   H   HCR6  0   0.269   4.5347  -2.7288   2.3649
 GKQ  H9   H   HCR6  0   0.281   6.5935  -3.2892   1.1177
 GKQ  H10  H   HCR6  0   0.278   6.3715   0.4873  -0.8999
 GKQ  H11  H   HCR6  0   0.261  -0.2288   3.8428   0.1489
 GKQ  H12  H   HCR6  0   0.259   0.6752  -0.3684   0.1430
 GKQ  H13  H   HCR6  0   0.275  -1.6410  -0.9308  -0.4093
 GKQ  H14  H   HCH2  0   0.246  -4.0292  -0.8722   0.8928
 GKQ  H15  H   HCH2  0   0.206  -5.3797   0.2609   0.9531
 GKQ  H17  H   HCH2  0   0.235  -5.1229  -2.9721   1.6260
 GKQ  H18  H   HCH2  0   0.194  -6.3100  -1.7866   2.1804
 GKQ  H19  H   HCH2  0   0.235  -6.8185  -4.3029   0.5802
 GKQ  H20  H   HCH2  0   0.235  -7.8250  -3.5547   1.8066
 GKQ  H21  H   HCH2  0   0.236  -7.9440  -3.1573  -1.0898
 GKQ  H22  H   HCH2  0   0.235  -8.9598  -2.3555   0.0935
 GKQ  H23  H   HCH2  0   0.196  -7.5452  -0.4766   0.2557
 GKQ  H24  H   HCH2  0   0.236  -7.0930  -0.9530  -1.3850
 GKQ  C3   C   CH2   0  -0.336  -4.4500   0.0759  -0.9845
 GKQ  C12  C   C     0   0.538   1.7852   2.1262   0.4920

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
 GKQ  C6   C8   single    1.544  0.020  1.544
 GKQ  C6   C5   single    1.530  0.020  1.530
 GKQ  C8   C7   single    1.529  0.020  1.529
 GKQ  C5   N2   single    1.455  0.020  1.455
 GKQ  C7   N2   single    1.454  0.020  1.454
 GKQ  N2   C4   single    1.441  0.020  1.441
 GKQ  C4   C3   single    1.525  0.020  1.525
 GKQ  C3   N1   single    1.447  0.020  1.447
 GKQ  C9   C1   aromatic  1.390  0.020  1.390
 GKQ  C9   C20  aromatic  1.381  0.020  1.381
 GKQ  N1   C1   aromatic  1.368  0.020  1.368
 GKQ  N1   C2   aromatic  1.359  0.020  1.359
 GKQ  C1   C    aromatic  1.406  0.020  1.406
 GKQ  C20  C11  aromatic  1.409  0.020  1.409
 GKQ  C2   N    aromatic  1.301  0.020  1.301
 GKQ  O    C12  double    1.224  0.020  1.224
 GKQ  C    N    aromatic  1.375  0.020  1.375
 GKQ  C    C10  aromatic  1.390  0.020  1.390
 GKQ  C11  C10  aromatic  1.388  0.020  1.388
 GKQ  C11  C12  single    1.493  0.020  1.493
 GKQ  C12  N3   single    1.347  0.020  1.347
 GKQ  N3   C13  single    1.444  0.020  1.444
 GKQ  C13  C14  single    1.506  0.020  1.506
 GKQ  C14  C15  aromatic  1.389  0.020  1.389
 GKQ  C14  C17  aromatic  1.393  0.020  1.393
 GKQ  C15  C16  aromatic  1.387  0.020  1.387
 GKQ  C17  C18  aromatic  1.386  0.020  1.386
 GKQ  C16  CL   single    1.735  0.020  1.735
 GKQ  C16  C19  aromatic  1.384  0.020  1.384
 GKQ  C18  C19  aromatic  1.389  0.020  1.389
 GKQ  C2   H1   single    0.930  0.020  1.080
 GKQ  C3   H2   single    0.970  0.020  1.090
 GKQ  C3   H3   single    0.970  0.020  1.090
 GKQ  N3   H4   single    0.860  0.020  1.020
 GKQ  C13  H5   single    0.970  0.020  1.090
 GKQ  C13  H6   single    0.970  0.020  1.090
 GKQ  C17  H7   single    0.930  0.020  1.080
 GKQ  C18  H8   single    0.930  0.020  1.080
 GKQ  C19  H9   single    0.930  0.020  1.080
 GKQ  C15  H10  single    0.930  0.020  1.080
 GKQ  C10  H11  single    0.930  0.020  1.080
 GKQ  C20  H12  single    0.930  0.020  1.080
 GKQ  C9   H13  single    0.930  0.020  1.080
 GKQ  C4   H14  single    0.970  0.020  1.090
 GKQ  C4   H15  single    0.970  0.020  1.090
 GKQ  C7   H17  single    0.970  0.020  1.090
 GKQ  C7   H18  single    0.970  0.020  1.090
 GKQ  C8   H19  single    0.970  0.020  1.090
 GKQ  C8   H20  single    0.970  0.020  1.090
 GKQ  C6   H21  single    0.970  0.020  1.090
 GKQ  C6   H22  single    0.970  0.020  1.090
 GKQ  C5   H23  single    0.970  0.020  1.090
 GKQ  C5   H24  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
 GKQ  C10  C    C1   120.05  3.000
 GKQ  C10  C    N    130.02  3.000
 GKQ  C1   C    N    109.93  3.000
 GKQ  C2   N    C    104.55  3.000
 GKQ  N1   C1   C9   132.53  3.000
 GKQ  N1   C1   C    105.14  3.000
 GKQ  C9   C1   C    122.33  3.000
 GKQ  H1   C2   N1   120.73  3.000
 GKQ  H1   C2   N    125.21  3.000
 GKQ  N1   C2   N    114.06  3.000
 GKQ  H4   N3   C13  116.94  3.000
 GKQ  H4   N3   C12  118.85  3.000
 GKQ  C13  N3   C12  123.40  3.000
 GKQ  H6   C13  H5   106.72  3.000
 GKQ  H6   C13  C14  109.95  3.000
 GKQ  H5   C13  C14  109.82  3.000
 GKQ  H6   C13  N3   108.02  3.000
 GKQ  H5   C13  N3   110.97  3.000
 GKQ  C14  C13  N3   111.24  3.000
 GKQ  C15  C14  C17  119.29  3.000
 GKQ  C17  C14  C13  120.82  3.000
 GKQ  C15  C14  C13  119.89  3.000
 GKQ  H7   C17  C18  119.70  3.000
 GKQ  H7   C17  C14  119.96  3.000
 GKQ  C18  C17  C14  120.34  3.000
 GKQ  H8   C18  C19  119.37  3.000
 GKQ  H8   C18  C17  119.93  3.000
 GKQ  C19  C18  C17  120.69  3.000
 GKQ  H9   C19  C16  120.83  3.000
 GKQ  H9   C19  C18  120.67  3.000
 GKQ  C16  C19  C18  118.50  3.000
 GKQ  C15  C16  CL   119.06  3.000
 GKQ  CL   C16  C19  119.42  3.000
 GKQ  C15  C16  C19  121.52  3.000
 GKQ  H10  C15  C16  120.14  3.000
 GKQ  H10  C15  C14  120.21  3.000
 GKQ  C16  C15  C14  119.66  3.000
 GKQ  C20  C11  C10  120.68  3.000
 GKQ  C10  C11  C12  117.69  3.000
 GKQ  C20  C11  C12  121.61  3.000
 GKQ  H11  C10  C11  121.03  3.000
 GKQ  H11  C10  C    120.68  3.000
 GKQ  C11  C10  C    118.29  3.000
 GKQ  H12  C20  C9   118.14  3.000
 GKQ  H12  C20  C11  120.00  3.000
 GKQ  C9   C20  C11  121.83  3.000
 GKQ  H13  C9   C20  120.85  3.000
 GKQ  H13  C9   C1   122.35  3.000
 GKQ  C20  C9   C1   116.80  3.000
 GKQ  C3   N1   C2   126.53  3.000
 GKQ  C2   N1   C1   106.32  3.000
 GKQ  C3   N1   C1   127.05  3.000
 GKQ  H15  C4   H14  106.79  3.000
 GKQ  H15  C4   N2   112.10  3.000
 GKQ  H14  C4   N2   108.53  3.000
 GKQ  H15  C4   C3   109.19  3.000
 GKQ  H14  C4   C3   108.84  3.000
 GKQ  N2   C4   C3   111.23  3.000
 GKQ  C5   N2   C7   104.65  3.000
 GKQ  C7   N2   C4   113.32  3.000
 GKQ  C5   N2   C4   114.49  3.000
 GKQ  H18  C7   H17  107.22  3.000
 GKQ  H18  C7   C8   110.12  3.000
 GKQ  H17  C7   C8   113.37  3.000
 GKQ  H18  C7   N2   111.52  3.000
 GKQ  H17  C7   N2   110.83  3.000
 GKQ  C8   C7   N2   103.84  3.000
 GKQ  H20  C8   H19  107.17  3.000
 GKQ  H20  C8   C6   112.56  3.000
 GKQ  H19  C8   C6   110.72  3.000
 GKQ  H20  C8   C7   111.39  3.000
 GKQ  H19  C8   C7   110.77  3.000
 GKQ  C6   C8   C7   104.29  3.000
 GKQ  H22  C6   H21  107.12  3.000
 GKQ  H22  C6   C5   111.17  3.000
 GKQ  H21  C6   C5   110.82  3.000
 GKQ  H22  C6   C8   112.53  3.000
 GKQ  H21  C6   C8   110.82  3.000
 GKQ  C5   C6   C8   104.44  3.000
 GKQ  H24  C5   H23  107.28  3.000
 GKQ  H24  C5   C6   112.60  3.000
 GKQ  H23  C5   C6   110.44  3.000
 GKQ  H24  C5   N2   111.67  3.000
 GKQ  H23  C5   N2   111.01  3.000
 GKQ  C6   C5   N2   103.90  3.000
 GKQ  H3   C3   H2   107.20  3.000
 GKQ  H3   C3   C4   110.30  3.000
 GKQ  H2   C3   C4   111.23  3.000
 GKQ  H3   C3   N1   108.93  3.000
 GKQ  H2   C3   N1   107.40  3.000
 GKQ  C4   C3   N1   111.63  3.000
 GKQ  C11  C12  N3   115.67  3.000
 GKQ  N3   C12  O    122.89  3.000
 GKQ  C11  C12  O    121.44  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
 GKQ  CONST_01  C20  C9   C1   C       0.00   0.0  0
 GKQ  CONST_02  C2   N1   C1   C       0.00   0.0  0
 GKQ  CONST_03  N1   C2   N    C       0.00   0.0  0
 GKQ  CONST_04  C20  C11  C10  C       0.00   0.0  0
 GKQ  CONST_05  C1   N1   C2   N       0.00   0.0  0
 GKQ  CONST_06  C9   C1   C    N     180.00   0.0  0
 GKQ  CONST_07  N1   C1   C    N       0.00   0.0  0
 GKQ  CONST_08  C11  C10  C    N     180.00   0.0  0
 GKQ  CONST_09  C11  C20  C9   C1      0.00   0.0  0
 GKQ  CONST_10  C2   N    C    C1      0.00   0.0  0
 GKQ  CONST_11  C11  C10  C    C1      0.00   0.0  0
 GKQ  CONST_12  C9   C1   N1   C2    180.00   0.0  0
 GKQ  CONST_13  C10  C    N    C2    180.00   0.0  0
 GKQ  CONST_14  C19  C16  C15  C14     0.00   0.0  0
 GKQ  CONST_15  C19  C18  C17  C14     0.00   0.0  0
 GKQ  CONST_16  C16  C15  C14  C17     0.00   0.0  0
 GKQ  CONST_17  C16  C19  C18  C17     0.00   0.0  0
 GKQ  CONST_18  C15  C14  C17  C18     0.00   0.0  0
 GKQ  CONST_19  C15  C16  C19  C18     0.00   0.0  0
 GKQ  CONST_20  C9   C1   C    C10     0.00   0.0  0
 GKQ  CONST_21  N1   C1   C    C10   180.00   0.0  0
 GKQ  CONST_22  C9   C20  C11  C10     0.00   0.0  0
 GKQ  CONST_23  N1   C1   C9   C20   180.00   0.0  0
 GKQ  CONST_24  C3   N1   C1   C     180.00   0.0  0
 GKQ  CONST_25  C12  C11  C10  C     180.00   0.0  0
 GKQ  CONST_26  C3   N1   C2   N     180.00   0.0  0
 GKQ  CONST_27  C9   C1   N1   C3      0.00   0.0  0
 GKQ  CONST_28  C9   C20  C11  C12   180.00   0.0  0
 GKQ  CONST_29  C16  C15  C14  C13   180.00   0.0  0
 GKQ  CONST_30  C18  C17  C14  C13   180.00   0.0  0
 GKQ  CONST_31  CL   C16  C15  C14   180.00   0.0  0
 GKQ  CONST_32  CL   C16  C19  C18   180.00   0.0  0
 GKQ  CONST_33  H13  C9   C1   C     180.00   0.0  0
 GKQ  CONST_34  H1   C2   N    C     180.00   0.0  0
 GKQ  CONST_35  H11  C10  C    N       0.00   0.0  0
 GKQ  CONST_36  H12  C20  C9   C1    180.00   0.0  0
 GKQ  CONST_37  H8   C18  C17  C14   180.00   0.0  0
 GKQ  CONST_38  H10  C15  C14  C17   180.00   0.0  0
 GKQ  CONST_39  H9   C19  C18  C17   180.00   0.0  0
 GKQ  CONST_40  H7   C17  C18  C19   180.00   0.0  0
 GKQ  CONST_41  C11  C12  N3   C13   180.00   0.0  0
 GKQ  CONST_42  H4   N3   C12  C11     0.00   0.0  0
 GKQ  CONST_43  C13  N3   C12  O       0.00   0.0  0
 GKQ  Var_01    C8   C6   C5   N2     24.51  30.0  1
 GKQ  Var_02    C6   C8   C7   N2    -25.89  30.0  1
 GKQ  Var_03    C5   C6   C8   C7      0.82  30.0  1
 GKQ  Var_04    C6   C5   N2   C7    -42.16  30.0  1
 GKQ  Var_05    C5   N2   C7   C8     42.73  30.0  1
 GKQ  Var_06    C20  C11  C12  O    -150.26  30.0  2
 GKQ  Var_07    C4   C3   N1   C1     78.76  30.0  3
 GKQ  Var_08    C15  C14  C13  N3    129.72  30.0  2
 GKQ  Var_09    N2   C4   C3   N1   -179.85  30.0  1
 GKQ  Var_10    C14  C13  N3   C12   143.49  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
 GKQ  plan-1  C13  0.020
 GKQ  plan-1  C14  0.020
 GKQ  plan-1  C17  0.020
 GKQ  plan-1  C18  0.020
 GKQ  plan-1  C19  0.020
 GKQ  plan-1  C16  0.020
 GKQ  plan-1  CL   0.020
 GKQ  plan-1  C15  0.020
 GKQ  plan-1  H7   0.020
 GKQ  plan-1  H8   0.020
 GKQ  plan-1  H9   0.020
 GKQ  plan-1  H10  0.020
 GKQ  plan-2  C    0.020
 GKQ  plan-2  N    0.020
 GKQ  plan-2  C1   0.020
 GKQ  plan-2  C2   0.020
 GKQ  plan-2  C11  0.020
 GKQ  plan-2  C10  0.020
 GKQ  plan-2  C20  0.020
 GKQ  plan-2  C9   0.020
 GKQ  plan-2  N1   0.020
 GKQ  plan-2  H1   0.020
 GKQ  plan-2  H11  0.020
 GKQ  plan-2  H12  0.020
 GKQ  plan-2  H13  0.020
 GKQ  plan-2  C3   0.020
 GKQ  plan-2  C12  0.020
 GKQ  plan-3  O    0.020
 GKQ  plan-3  N3   0.020
 GKQ  plan-3  C13  0.020
 GKQ  plan-3  C11  0.020
 GKQ  plan-3  H4   0.020
 GKQ  plan-3  C12  0.020

