# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:05:53 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](NC(=O)c1ccc2n(Cc3ccc(Cl)c(Cl)c3)c(C)nc2c1)c4ccccc4
#
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
 M0T  M0T  1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide  ligand  54  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M0T
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
 M0T  N1    N   NH1   0  -0.660   4.2091  -0.6754   0.4190
 M0T  N3    N   N     0  -0.475  -1.2286  -1.3240  -2.1977
 M0T  C4    C   C     0   0.547   3.4803  -1.1067  -0.6279
 M0T  C5    C   CR6   0  -0.060   2.0146  -1.2645  -0.3919
 M0T  C6    C   CR16  0  -0.311   1.4927  -1.5201   0.8900
 M0T  C7    C   CR16  0  -0.296   0.1388  -1.6968   1.1048
 M0T  C8    C   CR56  0   0.349  -0.6884  -1.6076  -0.0065
 M0T  C20   C   CR6   0   0.171   6.0340   0.7350  -0.4493
 M0T  C21   C   CR16  0  -0.314   7.1421   0.6927  -1.2888
 M0T  C22   C   CR16  0  -0.242   7.5529   1.8242  -1.9813
 M0T  C24   C   CR16  0  -0.241   5.7468   3.0674  -1.0052
 M0T  O1    O   O     0  -0.483   3.9848  -1.3628  -1.7125
 M0T  C2    C   CH2   0  -0.445   6.2210  -0.4341   1.7599
 M0T  N2    N   NR5   0  -0.544  -2.0426  -1.7340  -0.1669
 M0T  C3    C   CH1   0  -0.143   5.6435  -0.4933   0.3437
 M0T  C9    C   CH2   0  -0.376  -3.0133  -1.9717   0.8720
 M0T  C16   C   CR5   0   0.436  -2.3056  -1.5487  -1.4987
 M0T  C18   C   CR56  0   0.161  -0.1922  -1.3553  -1.2950
 M0T  C19   C   CR16  0  -0.360   1.1724  -1.1932  -1.4945
 M0T  C23   C   CR16  0  -0.271   6.8542   3.0162  -1.8426
 M0T  C25   C   CR16  0  -0.313   5.3413   1.9343  -0.3130
 M0T  C10   C   CR6   0   0.091  -3.7793  -0.7347   1.2713
 M0T  C13   C   CR6   0  -0.017  -5.2351   1.5006   2.0837
 M0T  C15   C   CR16  0  -0.259  -5.0617  -0.8793   1.7832
 M0T  CL1   CL  CL    0  -0.095  -6.1247   2.8910   2.5721
 M0T  C11   C   CR16  0  -0.286  -3.2318   0.5386   1.1700
 M0T  C12   C   CR16  0  -0.197  -3.9558   1.6492   1.5714
 M0T  C14   C   CR6   0   0.021  -5.7871   0.2291   2.1911
 M0T  HN1   H   HNH1  0   0.402   3.7344  -0.3209   1.2337
 M0T  H6    H   HCR6  0   0.256   2.1565  -1.6187   1.7389
 M0T  H7    H   HCR6  0   0.277  -0.2409  -1.9073   2.0958
 M0T  H17   H   HCH3  0   0.269  -4.1633  -2.5628  -1.7986
 M0T  H17A  H   HCH3  0   0.265  -4.3114  -0.8188  -1.6223
 M0T  H17B  H   HCH3  0   0.278  -3.6623  -1.4989  -3.1174
 M0T  H21   H   HCR6  0   0.247   7.6877  -0.2371  -1.4049
 M0T  H22   H   HCR6  0   0.254   8.4142   1.7727  -2.6350
 M0T  H24   H   HCR6  0   0.253   5.1964   3.9926  -0.8903
 M0T  H1    H   HCH3  0   0.223   4.9523  -1.9302   2.7153
 M0T  H1A   H   HCH3  0   0.225   6.4483  -2.5710   2.0421
 M0T  H1B   H   HCH3  0   0.237   6.4787  -1.6382   3.5360
 M0T  H2    H   HCH2  0   0.231   5.7874   0.4211   2.2887
 M0T  H2A   H   HCH2  0   0.248   7.2891  -0.2256   1.6749
 M0T  H3    H   HCH1  0   0.256   6.0650  -1.3685  -0.1589
 M0T  H9    H   HCH2  0   0.297  -3.7031  -2.7530   0.5505
 M0T  H9A   H   HCH2  0   0.307  -2.4854  -2.3756   1.7372
 M0T  H19   H   HCR6  0   0.258   1.5668  -1.0077  -2.4850
 M0T  H23   H   HCR6  0   0.254   7.1676   3.8981  -2.3864
 M0T  H25   H   HCR6  0   0.243   4.4739   1.9889   0.3341
 M0T  H15   H   HCR6  0   0.287  -5.5072  -1.8628   1.8658
 M0T  H11   H   HCR6  0   0.273  -2.2350   0.6876   0.7752
 M0T  H12   H   HCR6  0   0.292  -3.5249   2.6371   1.4843
 M0T  C17   C   CH3   0  -0.762  -3.6859  -1.6112  -2.0368
 M0T  C1    C   CH3   0  -0.665   6.0091  -1.7142   2.5553
 M0T  CL2   CL  CL    0  -0.093  -7.3754   0.0128   2.8193

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
 M0T  N1   C4    single    1.347  0.020  1.347
 M0T  N1   C3    single    1.448  0.020  1.448
 M0T  N3   C16   aromatic  1.304  0.020  1.304
 M0T  N3   C18   aromatic  1.375  0.020  1.375
 M0T  C4   C5    single    1.493  0.020  1.493
 M0T  C4   O1    double    1.223  0.020  1.223
 M0T  C5   C6    aromatic  1.407  0.020  1.407
 M0T  C5   C19   aromatic  1.389  0.020  1.389
 M0T  C6   C7    aromatic  1.382  0.020  1.382
 M0T  C7   C8    aromatic  1.388  0.020  1.388
 M0T  C8   N2    aromatic  1.370  0.020  1.370
 M0T  C8   C18   aromatic  1.404  0.020  1.404
 M0T  C17  C16   single    1.483  0.020  1.483
 M0T  C20  C21   aromatic  1.391  0.020  1.391
 M0T  C20  C3    single    1.513  0.020  1.513
 M0T  C20  C25   aromatic  1.392  0.020  1.392
 M0T  C21  C22   aromatic  1.389  0.020  1.389
 M0T  C22  C23   aromatic  1.389  0.020  1.389
 M0T  C24  C23   aromatic  1.389  0.020  1.389
 M0T  C24  C25   aromatic  1.388  0.020  1.388
 M0T  C1   C2    single    1.522  0.020  1.522
 M0T  C2   C3    single    1.531  0.020  1.531
 M0T  N2   C9    single    1.442  0.020  1.442
 M0T  N2   C16   aromatic  1.370  0.020  1.370
 M0T  C9   C10   single    1.509  0.020  1.509
 M0T  C18  C19   aromatic  1.389  0.020  1.389
 M0T  C10  C15   aromatic  1.388  0.020  1.388
 M0T  C10  C11   aromatic  1.390  0.020  1.390
 M0T  C13  CL1   single    1.721  0.020  1.721
 M0T  C13  C12   aromatic  1.386  0.020  1.386
 M0T  C13  C14   aromatic  1.390  0.020  1.390
 M0T  C15  C14   aromatic  1.386  0.020  1.386
 M0T  CL2  C14   single    1.722  0.020  1.722
 M0T  C11  C12   aromatic  1.385  0.020  1.385
 M0T  N1   HN1   single    0.860  0.020  1.020
 M0T  C6   H6    single    0.930  0.020  1.080
 M0T  C7   H7    single    0.930  0.020  1.080
 M0T  C17  H17   single    0.970  0.020  1.090
 M0T  C17  H17A  single    0.970  0.020  1.090
 M0T  C17  H17B  single    0.970  0.020  1.090
 M0T  C21  H21   single    0.930  0.020  1.080
 M0T  C22  H22   single    0.930  0.020  1.080
 M0T  C24  H24   single    0.930  0.020  1.080
 M0T  C1   H1    single    0.970  0.020  1.090
 M0T  C1   H1A   single    0.970  0.020  1.090
 M0T  C1   H1B   single    0.970  0.020  1.090
 M0T  C2   H2    single    0.970  0.020  1.090
 M0T  C2   H2A   single    0.970  0.020  1.090
 M0T  C3   H3    single    0.970  0.020  1.090
 M0T  C9   H9    single    0.970  0.020  1.090
 M0T  C9   H9A   single    0.970  0.020  1.090
 M0T  C19  H19   single    0.930  0.020  1.080
 M0T  C23  H23   single    0.930  0.020  1.080
 M0T  C25  H25   single    0.930  0.020  1.080
 M0T  C15  H15   single    0.930  0.020  1.080
 M0T  C11  H11   single    0.930  0.020  1.080
 M0T  C12  H12   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
 M0T  HN1   N1   C3    117.69  3.000
 M0T  HN1   N1   C4    119.10  3.000
 M0T  C3    N1   C4    122.42  3.000
 M0T  C18   N3   C16   105.48  3.000
 M0T  O1    C4   C5    121.53  3.000
 M0T  O1    C4   N1    122.22  3.000
 M0T  C5    C4   N1    116.25  3.000
 M0T  C19   C5   C6    120.49  3.000
 M0T  C19   C5   C4    117.66  3.000
 M0T  C6    C5   C4    121.82  3.000
 M0T  H6    C6   C7    117.86  3.000
 M0T  H6    C6   C5    120.24  3.000
 M0T  C7    C6   C5    121.87  3.000
 M0T  H7    C7   C8    122.45  3.000
 M0T  H7    C7   C6    120.73  3.000
 M0T  C8    C7   C6    116.81  3.000
 M0T  C18   C8   N2    104.99  3.000
 M0T  C18   C8   C7    122.40  3.000
 M0T  N2    C8   C7    132.61  3.000
 M0T  C25   C20  C3    121.31  3.000
 M0T  C25   C20  C21   118.81  3.000
 M0T  C3    C20  C21   119.82  3.000
 M0T  H21   C21  C22   119.76  3.000
 M0T  H21   C21  C20   119.44  3.000
 M0T  C22   C21  C20   120.79  3.000
 M0T  H22   C22  C23   120.10  3.000
 M0T  H22   C22  C21   119.85  3.000
 M0T  C23   C22  C21   120.05  3.000
 M0T  H24   C24  C25   119.74  3.000
 M0T  H24   C24  C23   120.05  3.000
 M0T  C25   C24  C23   120.22  3.000
 M0T  H2A   C2   H2    106.02  3.000
 M0T  H2A   C2   C3    107.73  3.000
 M0T  H2    C2   C3    109.12  3.000
 M0T  H2A   C2   C1    109.73  3.000
 M0T  H2    C2   C1    110.45  3.000
 M0T  C3    C2   C1    113.48  3.000
 M0T  C16   N2   C9    126.41  3.000
 M0T  C16   N2   C8    106.93  3.000
 M0T  C9    N2   C8    126.63  3.000
 M0T  H3    C3   C2    108.10  3.000
 M0T  H3    C3   C20   108.02  3.000
 M0T  C2    C3   C20   110.86  3.000
 M0T  H3    C3   N1    107.76  3.000
 M0T  C2    C3   N1    109.30  3.000
 M0T  C20   C3   N1    112.64  3.000
 M0T  H9A   C9   H9    105.94  3.000
 M0T  H9A   C9   C10   109.84  3.000
 M0T  H9    C9   C10   110.13  3.000
 M0T  H9A   C9   N2    107.86  3.000
 M0T  H9    C9   N2    109.36  3.000
 M0T  C10   C9   N2    113.42  3.000
 M0T  N2    C16  C17   121.72  3.000
 M0T  N2    C16  N3    112.70  3.000
 M0T  C17   C16  N3    125.58  3.000
 M0T  C19   C18  C8    120.02  3.000
 M0T  C19   C18  N3    130.08  3.000
 M0T  C8    C18  N3    109.90  3.000
 M0T  H19   C19  C18   120.64  3.000
 M0T  H19   C19  C5    120.95  3.000
 M0T  C18   C19  C5    118.40  3.000
 M0T  H23   C23  C24   120.24  3.000
 M0T  H23   C23  C22   120.23  3.000
 M0T  C24   C23  C22   119.53  3.000
 M0T  H25   C25  C24   119.37  3.000
 M0T  H25   C25  C20   120.02  3.000
 M0T  C24   C25  C20   120.60  3.000
 M0T  C11   C10  C15   119.09  3.000
 M0T  C11   C10  C9    122.13  3.000
 M0T  C15   C10  C9    118.76  3.000
 M0T  C14   C13  C12   119.54  3.000
 M0T  C14   C13  CL1   120.77  3.000
 M0T  C12   C13  CL1   119.68  3.000
 M0T  H15   C15  C14   119.25  3.000
 M0T  H15   C15  C10   120.18  3.000
 M0T  C14   C15  C10   120.58  3.000
 M0T  H11   C11  C12   118.46  3.000
 M0T  H11   C11  C10   121.03  3.000
 M0T  C12   C11  C10   120.51  3.000
 M0T  H12   C12  C11   120.06  3.000
 M0T  H12   C12  C13   119.70  3.000
 M0T  C11   C12  C13   120.23  3.000
 M0T  CL2   C14  C15   119.32  3.000
 M0T  CL2   C14  C13   120.62  3.000
 M0T  C15   C14  C13   120.06  3.000
 M0T  H17B  C17  H17A  108.37  3.000
 M0T  H17B  C17  H17   108.47  3.000
 M0T  H17A  C17  H17   107.44  3.000
 M0T  H17B  C17  C16   109.65  3.000
 M0T  H17A  C17  C16   111.41  3.000
 M0T  H17   C17  C16   111.40  3.000
 M0T  H1B   C1   H1A   107.73  3.000
 M0T  H1B   C1   H1    107.42  3.000
 M0T  H1A   C1   H1    107.68  3.000
 M0T  H1B   C1   C2    110.58  3.000
 M0T  H1A   C1   C2    111.02  3.000
 M0T  H1    C1   C2    112.22  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
 M0T  CONST_01  C8   N2   C16  N3     0.00   0.0  0
 M0T  CONST_02  C7   C8   C18  N3   180.00   0.0  0
 M0T  CONST_03  N2   C8   C18  N3     0.00   0.0  0
 M0T  CONST_04  C5   C19  C18  N3   180.00   0.0  0
 M0T  CONST_05  C8   C7   C6   C5     0.00   0.0  0
 M0T  CONST_06  C8   C18  C19  C5     0.00   0.0  0
 M0T  CONST_07  C18  C19  C5   C6     0.00   0.0  0
 M0T  CONST_08  N2   C8   C7   C6   180.00   0.0  0
 M0T  CONST_09  C18  C8   C7   C6     0.00   0.0  0
 M0T  CONST_10  C19  C5   C6   C7     0.00   0.0  0
 M0T  CONST_11  C16  N2   C8   C7   180.00   0.0  0
 M0T  CONST_12  C19  C18  C8   C7     0.00   0.0  0
 M0T  CONST_13  C16  N3   C18  C8     0.00   0.0  0
 M0T  CONST_14  C23  C22  C21  C20    0.00   0.0  0
 M0T  CONST_15  C23  C24  C25  C20    0.00   0.0  0
 M0T  CONST_16  C24  C25  C20  C21    0.00   0.0  0
 M0T  CONST_17  C24  C23  C22  C21    0.00   0.0  0
 M0T  CONST_18  C25  C20  C21  C22    0.00   0.0  0
 M0T  CONST_19  C25  C24  C23  C22    0.00   0.0  0
 M0T  CONST_20  C19  C18  C8   N2   180.00   0.0  0
 M0T  CONST_21  C18  N3   C16  N2     0.00   0.0  0
 M0T  CONST_22  C19  C18  N3   C16  180.00   0.0  0
 M0T  CONST_23  C18  C8   N2   C16    0.00   0.0  0
 M0T  CONST_24  C13  C14  C15  C10    0.00   0.0  0
 M0T  CONST_25  C13  C12  C11  C10    0.00   0.0  0
 M0T  CONST_26  C12  C11  C10  C15    0.00   0.0  0
 M0T  CONST_27  C12  C13  C14  C15    0.00   0.0  0
 M0T  CONST_28  C14  C15  C10  C11    0.00   0.0  0
 M0T  CONST_29  C14  C13  C12  C11    0.00   0.0  0
 M0T  CONST_30  C9   N2   C16  N3   180.00   0.0  0
 M0T  CONST_31  C7   C6   C5   C4   180.00   0.0  0
 M0T  CONST_32  C18  C19  C5   C4   180.00   0.0  0
 M0T  CONST_33  C9   N2   C8   C7     0.00   0.0  0
 M0T  CONST_34  C17  C16  N2   C8   180.00   0.0  0
 M0T  CONST_35  C18  N3   C16  C17  180.00   0.0  0
 M0T  CONST_36  C3   C20  C21  C22  180.00   0.0  0
 M0T  CONST_37  C3   C20  C25  C24  180.00   0.0  0
 M0T  CONST_38  C18  C8   N2   C9   180.00   0.0  0
 M0T  CONST_39  C14  C15  C10  C9   180.00   0.0  0
 M0T  CONST_40  C12  C11  C10  C9   180.00   0.0  0
 M0T  CONST_41  CL2  C14  C15  C10  180.00   0.0  0
 M0T  CONST_42  CL1  C13  C14  C15  180.00   0.0  0
 M0T  CONST_43  C11  C12  C13  CL1  180.00   0.0  0
 M0T  CONST_44  C12  C13  C14  CL2  180.00   0.0  0
 M0T  CONST_45  H19  C19  C18  N3     0.00   0.0  0
 M0T  CONST_46  H7   C7   C6   C5   180.00   0.0  0
 M0T  CONST_47  H6   C6   C7   C8   180.00   0.0  0
 M0T  CONST_48  H22  C22  C21  C20  180.00   0.0  0
 M0T  CONST_49  H24  C24  C25  C20  180.00   0.0  0
 M0T  CONST_50  H25  C25  C20  C21  180.00   0.0  0
 M0T  CONST_51  H23  C23  C22  C21  180.00   0.0  0
 M0T  CONST_52  H21  C21  C22  C23  180.00   0.0  0
 M0T  CONST_53  H12  C12  C11  C10  180.00   0.0  0
 M0T  CONST_54  H11  C11  C12  C13  180.00   0.0  0
 M0T  CONST_55  H15  C15  C14  C13  180.00   0.0  0
 M0T  CONST_56  C3   N1   C4   C5   180.00   0.0  0
 M0T  CONST_57  HN1  N1   C4   C5     0.00   0.0  0
 M0T  CONST_58  C3   N1   C4   O1     0.00   0.0  0
 M0T  Var_01    C10  C9   N2   C8   102.41  30.0  2
 M0T  Var_02    C15  C10  C9   N2   152.52  30.0  2
 M0T  Var_03    C6   C5   C4   N1   -26.43  30.0  2
 M0T  Var_04    H17  C17  C16  N3   123.39  30.0  2
 M0T  Var_05    H1   C1   C2   C3   -62.79  30.0  3

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
 M0T  chir_01  C3  N1  C20  C2  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
 M0T  plan-1  C20  0.020
 M0T  plan-1  C21  0.020
 M0T  plan-1  C22  0.020
 M0T  plan-1  C24  0.020
 M0T  plan-1  C3   0.020
 M0T  plan-1  C23  0.020
 M0T  plan-1  C25  0.020
 M0T  plan-1  H21  0.020
 M0T  plan-1  H22  0.020
 M0T  plan-1  H24  0.020
 M0T  plan-1  H23  0.020
 M0T  plan-1  H25  0.020
 M0T  plan-2  C9   0.020
 M0T  plan-2  C10  0.020
 M0T  plan-2  C13  0.020
 M0T  plan-2  C15  0.020
 M0T  plan-2  CL1  0.020
 M0T  plan-2  C11  0.020
 M0T  plan-2  C12  0.020
 M0T  plan-2  C14  0.020
 M0T  plan-2  H15  0.020
 M0T  plan-2  H11  0.020
 M0T  plan-2  H12  0.020
 M0T  plan-2  CL2  0.020
 M0T  plan-3  N3   0.020
 M0T  plan-3  C4   0.020
 M0T  plan-3  C5   0.020
 M0T  plan-3  C6   0.020
 M0T  plan-3  C7   0.020
 M0T  plan-3  C8   0.020
 M0T  plan-3  N2   0.020
 M0T  plan-3  C9   0.020
 M0T  plan-3  C16  0.020
 M0T  plan-3  C18  0.020
 M0T  plan-3  C19  0.020
 M0T  plan-3  H6   0.020
 M0T  plan-3  H7   0.020
 M0T  plan-3  H19  0.020
 M0T  plan-3  C17  0.020
 M0T  plan-4  N1   0.020
 M0T  plan-4  C4   0.020
 M0T  plan-4  C5   0.020
 M0T  plan-4  O1   0.020
 M0T  plan-4  C3   0.020
 M0T  plan-4  HN1  0.020

