# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:22:28 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 3-[5-(1H-imidazol-1-yl)-7-methyl-1H-benzimidazol-2-yl]-4-[(pyridin-2-ylmethyl)amino]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc2nc([nH]c12)C3=C(NCc4ccccn4)C=CNC3=O)n5ccnc5
#
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
 BMI  BMI  3-[5-(1H-imidazol-1-yl)-7-methyl-1H-benzimidazol-2-yl]-4-[(pyridin-2-ylmethyl)amino]pyridin-2(1H)-one  ligand  49  30  .  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_BMI
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
 BMI  C     C  CR6   0   0.539  3.0821  -3.4611   6.7557
 BMI  O     O  OC    0  -0.530  3.0393  -4.4279   5.9836
 BMI  N     N  NH1   0  -0.724  3.0113   0.2344   7.0268
 BMI  N1    N  NR16  0  -0.670  3.2077  -3.7080   8.1073
 BMI  C1    C  CR6   0   0.501  3.0741  -1.0558   7.3520
 BMI  C2    C  CR16  0  -0.473  3.2066  -1.4361   8.7231
 BMI  C3    C  CR16  0   0.056  3.2675  -2.7463   9.0468
 BMI  C4    C  CH2   0  -0.318  3.0644   1.3132   7.9762
 BMI  C5    C  CR16  0  -0.146  2.9023   5.0316   7.3749
 BMI  C6    C  CR16  0  -0.329  2.9907   3.8193   8.0336
 BMI  C7    C  CR16  0  -0.336  2.7871   5.0383   5.9895
 BMI  C8    C  CR6   0   0.235  2.9634   2.6474   7.2812
 BMI  N2    N  N     0  -0.441  2.8544   2.6532   5.9629
 BMI  C9    C  CR16  0  -0.059  2.7680   3.8214   5.3329
 BMI  C10   C  CR6   0  -0.392  3.0126  -2.0809   6.3742
 BMI  C11   C  CR15  0  -0.119  1.4911   0.7115  -1.2992
 BMI  C12   C  CR6   0   0.360  2.4497  -0.1565   0.8311
 BMI  C13   C  CR16  0  -0.416  2.5442   0.2894   2.1369
 BMI  N3    N  NR5   0  -0.519  2.3280   0.7873  -0.2157
 BMI  C14   C  CR15  0   0.084  3.0205   1.9471  -0.3366
 BMI  N4    N  N     0  -0.449  2.6812   2.6073  -1.4108
 BMI  C15   C  CR15  0  -0.216  1.7240   1.8451  -2.0203
 BMI  C16   C  CR56  0   0.217  2.6819  -0.6797   3.1278
 BMI  N5    N  NR15  0  -0.731  2.8189  -2.6974   3.9833
 BMI  C17   C  CR5   0   0.580  2.8784  -1.7615   4.9700
 BMI  N6    N  N     0  -0.577  2.7965  -0.5373   4.4809
 BMI  C18   C  CR56  0   0.289  2.6925  -2.0415   2.7908
 BMI  C19   C  CR6   0   0.051  2.5834  -2.5031   1.4815
 BMI  C20   C  CR16  0  -0.388  2.4718  -1.5220   0.5079
 BMI  C21   C  CH3   0  -0.736  2.6043  -3.9647   1.1585
 BMI  HN    H  HNH1  0   0.457  2.9080   0.4724   6.0359
 BMI  HN1   H  HNR6  0   0.422  3.2593  -4.6767   8.3891
 BMI  H2    H  HCR6  0   0.295  3.2574  -0.7028   9.5114
 BMI  H3    H  HCR6  0   0.317  3.3675  -3.0842  10.0678
 BMI  H41   H  HCH2  0   0.268  3.9978   1.2908   8.5500
 BMI  H42   H  HCH2  0   0.268  2.2535   1.2375   8.7090
 BMI  H5    H  HCR6  0   0.276  2.9229   5.9591   7.9318
 BMI  H6    H  HCR6  0   0.270  3.0796   3.7765   9.1116
 BMI  H7    H  HCR6  0   0.273  2.7132   5.9624   5.4334
 BMI  H9    H  HCR6  0   0.263  2.6804   3.7796   4.2532
 BMI  H13   H  HCR6  0   0.264  2.4970   1.3416   2.3863
 BMI  H14   H  HCR5  0   0.285  3.7718   2.2430   0.3802
 BMI  H15   H  HCR5  0   0.255  1.2494   2.1505  -2.9398
 BMI  HN5   H  HNR5  0   0.422  2.8693  -3.6901   4.1702
 BMI  H20   H  HCR6  0   0.266  2.4127  -1.8186  -0.5323
 BMI  H211  H  HCH3  0   0.252  3.5541  -4.4203   1.4453
 BMI  H212  H  HCH3  0   0.251  1.8168  -4.4994   1.6927
 BMI  H213  H  HCH3  0   0.255  2.4593  -4.1359   0.0934
 BMI  H11   H  HCR5  0   0.296  0.8075  -0.1080  -1.4435

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
 BMI  C    O     double    1.238  0.020  1.238
 BMI  C    N1    aromatic  1.380  0.020  1.380
 BMI  C    C10   aromatic  1.434  0.020  1.434
 BMI  N    C1    single    1.332  0.020  1.332
 BMI  N    C4    single    1.438  0.020  1.438
 BMI  N    HN    single    0.860  0.020  1.020
 BMI  N1   C3    aromatic  1.346  0.020  1.346
 BMI  N1   HN1   single    0.860  0.020  1.020
 BMI  C1   C2    aromatic  1.429  0.020  1.429
 BMI  C1   C10   aromatic  1.418  0.020  1.418
 BMI  C2   C3    aromatic  1.351  0.020  1.351
 BMI  C2   H2    single    0.930  0.020  1.080
 BMI  C3   H3    single    0.930  0.020  1.080
 BMI  C4   C8    single    1.508  0.020  1.508
 BMI  C4   H41   single    0.970  0.020  1.090
 BMI  C4   H42   single    0.970  0.020  1.090
 BMI  C5   C7    aromatic  1.390  0.020  1.390
 BMI  C5   C6    aromatic  1.383  0.020  1.383
 BMI  C5   H5    single    0.930  0.020  1.080
 BMI  C6   C8    aromatic  1.393  0.020  1.393
 BMI  C6   H6    single    0.930  0.020  1.080
 BMI  C7   C9    aromatic  1.383  0.020  1.383
 BMI  C7   H7    single    0.930  0.020  1.080
 BMI  C8   N2    aromatic  1.323  0.020  1.323
 BMI  N2   C9    aromatic  1.330  0.020  1.330
 BMI  C9   H9    single    0.930  0.020  1.080
 BMI  C10  C17   single    1.446  0.020  1.446
 BMI  C11  N3    aromatic  1.371  0.020  1.371
 BMI  C11  C15   aromatic  1.363  0.020  1.363
 BMI  C11  H11   single    0.930  0.020  1.080
 BMI  C12  C13   aromatic  1.383  0.020  1.383
 BMI  C12  N3    single    1.415  0.020  1.415
 BMI  C12  C20   aromatic  1.403  0.020  1.403
 BMI  C13  C16   aromatic  1.393  0.020  1.393
 BMI  C13  H13   single    0.930  0.020  1.080
 BMI  N3   C14   aromatic  1.356  0.020  1.356
 BMI  C14  N4    aromatic  1.306  0.020  1.306
 BMI  C14  H14   single    0.930  0.020  1.080
 BMI  N4   C15   aromatic  1.367  0.020  1.367
 BMI  C15  H15   single    0.930  0.020  1.080
 BMI  C16  N6    aromatic  1.365  0.020  1.365
 BMI  C16  C18   aromatic  1.403  0.020  1.403
 BMI  N5   C17   aromatic  1.361  0.020  1.361
 BMI  N5   C18   aromatic  1.367  0.020  1.367
 BMI  N5   HN5   single    0.860  0.020  1.020
 BMI  C17  N6    aromatic  1.321  0.020  1.321
 BMI  C18  C19   aromatic  1.392  0.020  1.392
 BMI  C19  C20   aromatic  1.387  0.020  1.387
 BMI  C19  C21   single    1.497  0.020  1.497
 BMI  C20  H20   single    0.930  0.020  1.080
 BMI  C21  H211  single    0.970  0.020  1.090
 BMI  C21  H212  single    0.970  0.020  1.090
 BMI  C21  H213  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
 BMI  C10   C    N1    115.94  3.000
 BMI  C10   C    O     125.75  3.000
 BMI  N1    C    O     118.32  3.000
 BMI  HN    N    C4    117.91  3.000
 BMI  HN    N    C1    117.77  3.000
 BMI  C4    N    C1    124.31  3.000
 BMI  HN1   N1   C3    119.22  3.000
 BMI  HN1   N1   C     116.72  3.000
 BMI  C3    N1   C     124.06  3.000
 BMI  C10   C1   C2    118.25  3.000
 BMI  C10   C1   N     121.99  3.000
 BMI  C2    C1   N     119.76  3.000
 BMI  H2    C2   C3    118.85  3.000
 BMI  H2    C2   C1    121.67  3.000
 BMI  C3    C2   C1    119.48  3.000
 BMI  H3    C3   C2    122.28  3.000
 BMI  H3    C3   N1    116.14  3.000
 BMI  C2    C3   N1    121.58  3.000
 BMI  H42   C4   H41   106.19  3.000
 BMI  H42   C4   C8    108.66  3.000
 BMI  H41   C4   C8    108.46  3.000
 BMI  H42   C4   N     111.24  3.000
 BMI  H41   C4   N     111.21  3.000
 BMI  C8    C4   N     110.92  3.000
 BMI  H5    C5   C7    120.69  3.000
 BMI  H5    C5   C6    120.34  3.000
 BMI  C7    C5   C6    118.97  3.000
 BMI  H6    C6   C8    120.42  3.000
 BMI  H6    C6   C5    120.96  3.000
 BMI  C8    C6   C5    118.62  3.000
 BMI  H7    C7   C9    120.47  3.000
 BMI  H7    C7   C5    121.49  3.000
 BMI  C9    C7   C5    118.04  3.000
 BMI  N2    C8   C6    122.43  3.000
 BMI  N2    C8   C4    117.96  3.000
 BMI  C6    C8   C4    119.61  3.000
 BMI  C9    N2   C8    118.76  3.000
 BMI  H9    C9   N2    116.30  3.000
 BMI  H9    C9   C7    120.53  3.000
 BMI  N2    C9   C7    123.17  3.000
 BMI  C17   C10  C1    120.92  3.000
 BMI  C17   C10  C     118.39  3.000
 BMI  C1    C10  C     120.69  3.000
 BMI  H11   C11  C15   132.08  3.000
 BMI  H11   C11  N3    122.37  3.000
 BMI  C15   C11  N3    105.53  3.000
 BMI  C20   C12  N3    118.69  3.000
 BMI  C20   C12  C13   122.01  3.000
 BMI  N3    C12  C13   119.30  3.000
 BMI  H13   C13  C16   121.11  3.000
 BMI  H13   C13  C12   121.87  3.000
 BMI  C16   C13  C12   117.01  3.000
 BMI  C14   N3   C12   126.34  3.000
 BMI  C14   N3   C11   106.77  3.000
 BMI  C12   N3   C11   126.89  3.000
 BMI  H14   C14  N4    126.05  3.000
 BMI  H14   C14  N3    122.04  3.000
 BMI  N4    C14  N3    111.90  3.000
 BMI  C15   N4   C14   105.48  3.000
 BMI  H15   C15  N4    122.01  3.000
 BMI  H15   C15  C11   127.66  3.000
 BMI  N4    C15  C11   110.33  3.000
 BMI  C18   C16  N6    109.79  3.000
 BMI  C18   C16  C13   120.35  3.000
 BMI  N6    C16  C13   129.85  3.000
 BMI  HN5   N5   C18   129.55  3.000
 BMI  HN5   N5   C17   122.60  3.000
 BMI  C18   N5   C17   107.85  3.000
 BMI  N6    C17  N5    111.47  3.000
 BMI  N6    C17  C10   124.75  3.000
 BMI  N5    C17  C10   123.77  3.000
 BMI  C17   N6   C16   106.00  3.000
 BMI  C19   C18  N5    131.95  3.000
 BMI  C19   C18  C16   123.16  3.000
 BMI  N5    C18  C16   104.88  3.000
 BMI  C21   C19  C20   122.71  3.000
 BMI  C21   C19  C18   121.70  3.000
 BMI  C20   C19  C18   115.59  3.000
 BMI  H20   C20  C19   119.00  3.000
 BMI  H20   C20  C12   119.12  3.000
 BMI  C19   C20  C12   121.87  3.000
 BMI  H213  C21  H212  107.80  3.000
 BMI  H213  C21  H211  107.90  3.000
 BMI  H212  C21  H211  107.13  3.000
 BMI  H213  C21  C19   111.28  3.000
 BMI  H212  C21  C19   111.26  3.000
 BMI  H211  C21  C19   111.28  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
 BMI  CONST_01  C2    C3   N1   C       0.00   0.0  0
 BMI  CONST_02  C2    C1   C10  C       0.00   0.0  0
 BMI  CONST_03  N5    C17  C10  C       0.00   0.0  0
 BMI  CONST_04  N6    C17  C10  C     180.00   0.0  0
 BMI  CONST_05  C1    C10  C    N1      0.00   0.0  0
 BMI  CONST_06  C17   C10  C    N1    180.00   0.0  0
 BMI  CONST_07  C1    C2   C3   N1      0.00   0.0  0
 BMI  CONST_08  N5    C17  C10  C1    180.00   0.0  0
 BMI  CONST_09  N6    C17  C10  C1      0.00   0.0  0
 BMI  CONST_10  C17   C10  C1   C2    180.00   0.0  0
 BMI  CONST_11  C10   C    N1   C3      0.00   0.0  0
 BMI  CONST_12  C10   C1   C2   C3      0.00   0.0  0
 BMI  CONST_13  N2    C9   C7   C5      0.00   0.0  0
 BMI  CONST_14  N2    C8   C6   C5      0.00   0.0  0
 BMI  CONST_15  C9    C7   C5   C6      0.00   0.0  0
 BMI  CONST_16  C9    N2   C8   C6      0.00   0.0  0
 BMI  CONST_17  C8    C6   C5   C7      0.00   0.0  0
 BMI  CONST_18  C8    N2   C9   C7      0.00   0.0  0
 BMI  CONST_19  C18   N5   C17  C10   180.00   0.0  0
 BMI  CONST_20  C16   N6   C17  C10   180.00   0.0  0
 BMI  CONST_23  N4    C14  N3   C11     0.00   0.0  0
 BMI  CONST_24  C14   N4   C15  C11     0.00   0.0  0
 BMI  CONST_25  N6    C16  C13  C12   180.00   0.0  0
 BMI  CONST_26  C18   C16  C13  C12     0.00   0.0  0
 BMI  CONST_27  C15   C11  N3   C12   180.00   0.0  0
 BMI  CONST_28  N4    C14  N3   C12   180.00   0.0  0
 BMI  CONST_29  C18   C19  C20  C12     0.00   0.0  0
 BMI  CONST_31  C19   C20  C12  C13     0.00   0.0  0
 BMI  CONST_32  C17   N6   C16  C13   180.00   0.0  0
 BMI  CONST_33  N5    C18  C16  C13   180.00   0.0  0
 BMI  CONST_34  C19   C18  C16  C13     0.00   0.0  0
 BMI  CONST_35  N4    C15  C11  N3      0.00   0.0  0
 BMI  CONST_36  C16   C13  C12  N3    180.00   0.0  0
 BMI  CONST_37  C19   C20  C12  N3    180.00   0.0  0
 BMI  CONST_38  C15   N4   C14  N3      0.00   0.0  0
 BMI  CONST_39  C15   C11  N3   C14     0.00   0.0  0
 BMI  CONST_41  C20   C12  C13  C16     0.00   0.0  0
 BMI  CONST_42  N5    C17  N6   C16     0.00   0.0  0
 BMI  CONST_43  C17   N5   C18  C16     0.00   0.0  0
 BMI  CONST_44  C20   C19  C18  C16     0.00   0.0  0
 BMI  CONST_45  N6    C16  C18  N5      0.00   0.0  0
 BMI  CONST_46  C20   C19  C18  N5    180.00   0.0  0
 BMI  CONST_47  C19   C18  N5   C17   180.00   0.0  0
 BMI  CONST_48  C18   C16  N6   C17     0.00   0.0  0
 BMI  CONST_49  C19   C18  C16  N6    180.00   0.0  0
 BMI  CONST_50  C18   N5   C17  N6      0.00   0.0  0
 BMI  CONST_51  N     C1   C10  C     180.00   0.0  0
 BMI  CONST_52  C3    N1   C    O     180.00   0.0  0
 BMI  CONST_53  C1    C10  C    O     180.00   0.0  0
 BMI  CONST_54  C17   C10  C    O       0.00   0.0  0
 BMI  CONST_55  C3    C2   C1   N     180.00   0.0  0
 BMI  CONST_56  C17   C10  C1   N       0.00   0.0  0
 BMI  CONST_57  C5    C6   C8   C4    180.00   0.0  0
 BMI  CONST_58  C9    N2   C8   C4    180.00   0.0  0
 BMI  CONST_59  C21   C19  C20  C12   180.00   0.0  0
 BMI  CONST_60  C21   C19  C18  C16   180.00   0.0  0
 BMI  CONST_61  C21   C19  C18  N5      0.00   0.0  0
 BMI  CONST_62  H3    C3   N1   C     180.00   0.0  0
 BMI  CONST_63  H2    C2   C3   N1    180.00   0.0  0
 BMI  CONST_64  HN1   N1   C3   C2    180.00   0.0  0
 BMI  CONST_65  H9    C9   C7   C5    180.00   0.0  0
 BMI  CONST_66  H7    C7   C5   C6    180.00   0.0  0
 BMI  CONST_67  H6    C6   C5   C7    180.00   0.0  0
 BMI  CONST_68  H5    C5   C6   C8    180.00   0.0  0
 BMI  CONST_69  HN5   N5   C17  C10     0.00   0.0  0
 BMI  CONST_70  H14   C14  N3   C11   180.00   0.0  0
 BMI  CONST_71  H11   C11  N3   C12     0.00   0.0  0
 BMI  CONST_72  H20   C20  C12  C13   180.00   0.0  0
 BMI  CONST_73  H15   C15  C11  N3    180.00   0.0  0
 BMI  CONST_74  H13   C13  C12  N3      0.00   0.0  0
 BMI  CONST_75  C4    N    C1   C2      0.00   0.0  0
 BMI  CONST_76  C10   C1   N    C4    180.00   0.0  0
 BMI  CONST_77  HN    N    C1   C2    180.00   0.0  0
 BMI  Var_01    C6    C8   C4   N     179.74  30.0  2
 BMI  Var_02    C8    C4   N    C1   -179.80  30.0  3
 BMI  Var_03    H211  C21  C19  C18   -62.38  30.0  2

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
 BMI  plan-1  C11  0.020
 BMI  plan-1  C12  0.020
 BMI  plan-1  N3   0.020
 BMI  plan-1  C14  0.020
 BMI  plan-1  N4   0.020
 BMI  plan-1  C15  0.020
 BMI  plan-1  H14  0.020
 BMI  plan-1  H15  0.020
 BMI  plan-1  H11  0.020
 BMI  plan-2  C    0.020
 BMI  plan-2  O    0.020
 BMI  plan-2  N    0.020
 BMI  plan-2  N1   0.020
 BMI  plan-2  C1   0.020
 BMI  plan-2  C2   0.020
 BMI  plan-2  C3   0.020
 BMI  plan-2  C10  0.020
 BMI  plan-2  C17  0.020
 BMI  plan-2  HN1  0.020
 BMI  plan-2  H2   0.020
 BMI  plan-2  H3   0.020
 BMI  plan-3  C4   0.020
 BMI  plan-3  C5   0.020
 BMI  plan-3  C6   0.020
 BMI  plan-3  C7   0.020
 BMI  plan-3  C8   0.020
 BMI  plan-3  N2   0.020
 BMI  plan-3  C9   0.020
 BMI  plan-3  H5   0.020
 BMI  plan-3  H6   0.020
 BMI  plan-3  H7   0.020
 BMI  plan-3  H9   0.020
 BMI  plan-4  C10  0.020
 BMI  plan-4  C12  0.020
 BMI  plan-4  C13  0.020
 BMI  plan-4  N3   0.020
 BMI  plan-4  C16  0.020
 BMI  plan-4  N5   0.020
 BMI  plan-4  C17  0.020
 BMI  plan-4  N6   0.020
 BMI  plan-4  C18  0.020
 BMI  plan-4  C19  0.020
 BMI  plan-4  C20  0.020
 BMI  plan-4  C21  0.020
 BMI  plan-4  H13  0.020
 BMI  plan-4  HN5  0.020
 BMI  plan-4  H20  0.020
 BMI  plan-5  N    0.020
 BMI  plan-5  C1   0.020
 BMI  plan-5  C4   0.020
 BMI  plan-5  HN   0.020

