# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:43:45 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-(1H-benzimidazol-1-yl)-N-{5-[3-(dimethylamino)propoxy]pyridin-2-yl}pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCOc1ccc(Nc2cc(ncn2)n3cnc4ccccc34)nc1
#
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
 D6I  D6I  6-(1H-benzimidazol-1-yl)-N-{5-[3-(dimethylamino)propoxy]pyridin-2-yl}pyrimidin-4-amine  ligand  52  29  .  2021-08-08  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D6I
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
 D6I  C28   C  CR16  0  -0.267  -8.5077   1.8643  -0.3315
 D6I  C27   C  CR16  0  -0.269  -7.3473   2.6138  -0.1001
 D6I  C29   C  CR16  0  -0.318  -8.4604   0.4849  -0.4119
 D6I  C26   C  CR16  0  -0.282  -6.1086   2.0155   0.0624
 D6I  C9    C  CR16  0  -0.243   3.0934  -2.3590   0.4864
 D6I  C10   C  CR16  0  -0.355   1.7267  -2.5179   0.4426
 D6I  C16   C  CR16  0  -0.486  -2.7460  -1.0264  -0.0940
 D6I  C13   C  CR16  0  -0.194   2.7816  -0.1309  -0.2988
 D6I  C19   C  CR16  0   0.074  -2.0725   1.2648   1.0508
 D6I  C22   C  CR15  0   0.119  -5.6369  -1.5366  -0.1171
 D6I  C24   C  CR56  0   0.117  -7.2233  -0.1336  -0.2537
 D6I  C25   C  CR56  0   0.331  -6.0685   0.6273  -0.0170
 D6I  C8    C  CR6   0   0.313   3.6513  -1.1332   0.1191
 D6I  C17   C  CR6   0   0.562  -3.6848  -0.0867   0.2743
 D6I  C11   C  CR6   0   0.461   0.9418  -1.4476   0.0074
 D6I  C15   C  CR6   0   0.563  -1.4105  -0.7181   0.2050
 D6I  C1    C  CH3   0  -0.525   9.9385   0.6257  -0.7828
 D6I  C3    C  CH3   0  -0.519   9.7108   2.7844   0.1929
 D6I  C5    C  CH2   0  -0.482   7.0707   0.1260   0.1206
 D6I  C4    C  CH2   0  -0.261   7.7590   1.4541  -0.1711
 D6I  C6    C  CH2   0  -0.173   5.5784   0.2405  -0.1078
 D6I  N12   N  N     0  -0.397   1.4645  -0.2993  -0.3658
 D6I  N18   N  N     0  -0.464  -3.3626   1.0715   0.8406
 D6I  N20   N  N     0  -0.442  -1.0811   0.4391   0.7813
 D6I  N23   N  N     0  -0.449  -6.9130  -1.4774  -0.3010
 D6I  N21   N  NR5   0  -0.626  -5.0458  -0.3088   0.0594
 D6I  N14   N  NH1   0  -0.757  -0.4435  -1.6220  -0.0844
 D6I  N2    N  NT    0  -0.408   9.1762   1.4408   0.1391
 D6I  H28   H  HCR6  0   0.258  -9.4535   2.3762  -0.4516
 D6I  H27   H  HCR6  0   0.259  -7.4181   3.6920  -0.0437
 D6I  H29   H  HCR6  0   0.261  -9.3503  -0.1021  -0.5981
 D6I  H26   H  HCR6  0   0.277  -5.2246   2.6042   0.2496
 D6I  H9    H  HCR6  0   0.282   3.7308  -3.1700   0.8155
 D6I  H10   H  HCR6  0   0.283   1.2725  -3.4521   0.7451
 D6I  H16   H  HCR6  0   0.299  -3.0032  -1.9451  -0.6015
 D6I  H13   H  HCR6  0   0.279   3.1454   0.8412  -0.6090
 D6I  H19   H  HCR6  0   0.263  -1.7994   2.2089   1.5095
 D6I  H22   H  HCR5  0   0.304  -5.0614  -2.4493  -0.0739
 D6I  H14   H  HNH1  0   0.420  -0.7579  -2.5469  -0.3337
 D6I  H11C  H  HCH3  0   0.233  10.9914   0.6338  -0.4980
 D6I  H12C  H  HCH3  0   0.235   9.6060  -0.4117  -0.7588
 D6I  H13C  H  HCH3  0   0.190   9.8704   0.9755  -1.8253
 D6I  H31C  H  HCH3  0   0.190   9.6490   3.3225  -0.7666
 D6I  H32C  H  HCH3  0   0.232   9.1750   3.3739   0.9385
 D6I  H33C  H  HCH3  0   0.232  10.7615   2.7556   0.4858
 D6I  H51C  H  HCH2  0   0.240   7.4690  -0.6695  -0.5136
 D6I  H52C  H  HCH2  0   0.236   7.2645  -0.1543   1.1589
 D6I  H41C  H  HCH2  0   0.192   7.5764   1.7465  -1.2206
 D6I  H42C  H  HCH2  0   0.230   7.2910   2.2274   0.4450
 D6I  H61C  H  HCH2  0   0.225   5.1536   1.0209   0.5343
 D6I  H62C  H  HCH2  0   0.226   5.3703   0.5199  -1.1471
 D6I  O7    O  O2    0  -0.472   4.9871  -1.0158   0.1937

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
 D6I  C28  C27   aromatic  1.401  0.020  1.401
 D6I  C28  C29   aromatic  1.383  0.020  1.383
 D6I  C27  C26   aromatic  1.385  0.020  1.385
 D6I  C29  C24   aromatic  1.392  0.020  1.392
 D6I  C26  C25   aromatic  1.391  0.020  1.391
 D6I  C9   C10   aromatic  1.377  0.020  1.377
 D6I  C9   C8    aromatic  1.396  0.020  1.396
 D6I  C10  C11   aromatic  1.397  0.020  1.397
 D6I  C16  C17   aromatic  1.378  0.020  1.378
 D6I  C16  C15   aromatic  1.403  0.020  1.403
 D6I  C13  C8    aromatic  1.391  0.020  1.391
 D6I  C13  N12   aromatic  1.329  0.020  1.329
 D6I  C19  N18   aromatic  1.321  0.020  1.321
 D6I  C19  N20   aromatic  1.318  0.020  1.318
 D6I  C22  N23   aromatic  1.291  0.020  1.291
 D6I  C22  N21   aromatic  1.374  0.020  1.374
 D6I  C24  C25   aromatic  1.403  0.020  1.403
 D6I  C24  N23   aromatic  1.380  0.020  1.380
 D6I  C25  N21   aromatic  1.389  0.020  1.389
 D6I  C8   O7    single    1.343  0.020  1.343
 D6I  C17  N18   aromatic  1.329  0.020  1.329
 D6I  C17  N21   single    1.396  0.020  1.396
 D6I  C11  N12   aromatic  1.316  0.020  1.316
 D6I  C11  N14   single    1.399  0.020  1.399
 D6I  C15  N20   aromatic  1.334  0.020  1.334
 D6I  C15  N14   single    1.355  0.020  1.355
 D6I  C1   N2    single    1.448  0.020  1.448
 D6I  C3   N2    single    1.447  0.020  1.447
 D6I  C5   C4    single    1.524  0.020  1.524
 D6I  C5   C6    single    1.514  0.020  1.514
 D6I  C4   N2    single    1.451  0.020  1.451
 D6I  C6   O7    single    1.421  0.020  1.421
 D6I  C28  H28   single    0.930  0.020  1.080
 D6I  C27  H27   single    0.930  0.020  1.080
 D6I  C29  H29   single    0.930  0.020  1.080
 D6I  C26  H26   single    0.930  0.020  1.080
 D6I  C9   H9    single    0.930  0.020  1.080
 D6I  C10  H10   single    0.930  0.020  1.080
 D6I  C16  H16   single    0.930  0.020  1.080
 D6I  C13  H13   single    0.930  0.020  1.080
 D6I  C19  H19   single    0.930  0.020  1.080
 D6I  C22  H22   single    0.930  0.020  1.080
 D6I  N14  H14   single    0.860  0.020  1.020
 D6I  C1   H11C  single    0.970  0.020  1.090
 D6I  C1   H12C  single    0.970  0.020  1.090
 D6I  C1   H13C  single    0.970  0.020  1.090
 D6I  C3   H31C  single    0.970  0.020  1.090
 D6I  C3   H32C  single    0.970  0.020  1.090
 D6I  C3   H33C  single    0.970  0.020  1.090
 D6I  C5   H51C  single    0.970  0.020  1.090
 D6I  C5   H52C  single    0.970  0.020  1.090
 D6I  C4   H41C  single    0.970  0.020  1.090
 D6I  C4   H42C  single    0.970  0.020  1.090
 D6I  C6   H61C  single    0.970  0.020  1.090
 D6I  C6   H62C  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
 D6I  H28   C28  C29   119.70  3.000
 D6I  H28   C28  C27   119.30  3.000
 D6I  C29   C28  C27   121.00  3.000
 D6I  H27   C27  C26   118.87  3.000
 D6I  H27   C27  C28   119.18  3.000
 D6I  C26   C27  C28   121.95  3.000
 D6I  H29   C29  C24   120.62  3.000
 D6I  H29   C29  C28   121.53  3.000
 D6I  C24   C29  C28   117.85  3.000
 D6I  H26   C26  C25   122.08  3.000
 D6I  H26   C26  C27   121.17  3.000
 D6I  C25   C26  C27   116.75  3.000
 D6I  H9    C9   C8    120.16  3.000
 D6I  H9    C9   C10   120.50  3.000
 D6I  C8    C9   C10   119.33  3.000
 D6I  H10   C10  C11   120.86  3.000
 D6I  H10   C10  C9    120.50  3.000
 D6I  C11   C10  C9    118.64  3.000
 D6I  H16   C16  C15   120.90  3.000
 D6I  H16   C16  C17   122.89  3.000
 D6I  C15   C16  C17   116.21  3.000
 D6I  H13   C13  N12   115.59  3.000
 D6I  H13   C13  C8    121.50  3.000
 D6I  N12   C13  C8    122.90  3.000
 D6I  H19   C19  N20   116.26  3.000
 D6I  H19   C19  N18   116.13  3.000
 D6I  N20   C19  N18   127.61  3.000
 D6I  H22   C22  N21   121.39  3.000
 D6I  H22   C22  N23   124.85  3.000
 D6I  N21   C22  N23   113.74  3.000
 D6I  N23   C24  C25   110.41  3.000
 D6I  N23   C24  C29   128.95  3.000
 D6I  C25   C24  C29   120.64  3.000
 D6I  N21   C25  C24   104.47  3.000
 D6I  N21   C25  C26   133.70  3.000
 D6I  C24   C25  C26   121.81  3.000
 D6I  O7    C8   C13   125.13  3.000
 D6I  O7    C8   C9    117.36  3.000
 D6I  C13   C8   C9    117.50  3.000
 D6I  N21   C17  N18   116.15  3.000
 D6I  N21   C17  C16   120.97  3.000
 D6I  N18   C17  C16   122.88  3.000
 D6I  N14   C11  N12   118.91  3.000
 D6I  N14   C11  C10   118.77  3.000
 D6I  N12   C11  C10   122.27  3.000
 D6I  N14   C15  N20   119.65  3.000
 D6I  N14   C15  C16   119.16  3.000
 D6I  N20   C15  C16   121.18  3.000
 D6I  H13C  C1   H12C  107.72  3.000
 D6I  H13C  C1   H11C  107.73  3.000
 D6I  H12C  C1   H11C  107.21  3.000
 D6I  H13C  C1   N2    113.03  3.000
 D6I  H12C  C1   N2    111.18  3.000
 D6I  H11C  C1   N2    109.75  3.000
 D6I  H33C  C3   H32C  107.68  3.000
 D6I  H33C  C3   H31C  107.50  3.000
 D6I  H32C  C3   H31C  107.68  3.000
 D6I  H33C  C3   N2    109.95  3.000
 D6I  H32C  C3   N2    110.22  3.000
 D6I  H31C  C3   N2    113.60  3.000
 D6I  H52C  C5   H51C  107.46  3.000
 D6I  H52C  C5   C6    109.73  3.000
 D6I  H51C  C5   C6    109.08  3.000
 D6I  H52C  C5   C4    108.98  3.000
 D6I  H51C  C5   C4    111.02  3.000
 D6I  C6    C5   C4    110.51  3.000
 D6I  H42C  C4   H41C  106.09  3.000
 D6I  H42C  C4   N2    107.70  3.000
 D6I  H41C  C4   N2    111.53  3.000
 D6I  H42C  C4   C5    108.36  3.000
 D6I  H41C  C4   C5    109.75  3.000
 D6I  N2    C4   C5    113.10  3.000
 D6I  H62C  C6   H61C  107.48  3.000
 D6I  H62C  C6   O7    110.33  3.000
 D6I  H61C  C6   O7    110.12  3.000
 D6I  H62C  C6   C5    110.45  3.000
 D6I  H61C  C6   C5    110.33  3.000
 D6I  O7    C6   C5    108.14  3.000
 D6I  C11   N12  C13   119.33  3.000
 D6I  C17   N18  C19   115.60  3.000
 D6I  C15   N20  C19   116.49  3.000
 D6I  C24   N23  C22   105.20  3.000
 D6I  C17   N21  C25   128.27  3.000
 D6I  C17   N21  C22   125.55  3.000
 D6I  C25   N21  C22   106.17  3.000
 D6I  H14   N14  C15   116.25  3.000
 D6I  H14   N14  C11   116.06  3.000
 D6I  C15   N14  C11   127.55  3.000
 D6I  C4    N2   C3    111.12  3.000
 D6I  C4    N2   C1    112.55  3.000
 D6I  C3    N2   C1    110.60  3.000
 D6I  C6    O7   C8    118.65  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
 D6I  CONST_01  C25   C26  C27  C28     0.00   0.0  0
 D6I  CONST_02  C25   C24  C29  C28     0.00   0.0  0
 D6I  CONST_03  N23   C24  C29  C28   180.00   0.0  0
 D6I  CONST_04  C24   C29  C28  C27     0.00   0.0  0
 D6I  CONST_05  C24   C25  C26  C27     0.00   0.0  0
 D6I  CONST_06  N21   C25  C26  C27   180.00   0.0  0
 D6I  CONST_07  C26   C27  C28  C29     0.00   0.0  0
 D6I  CONST_08  C26   C25  C24  C29     0.00   0.0  0
 D6I  CONST_09  N21   C25  C24  C29   180.00   0.0  0
 D6I  CONST_10  C22   N23  C24  C29   180.00   0.0  0
 D6I  CONST_11  N23   C24  C25  C26   180.00   0.0  0
 D6I  CONST_12  C22   N21  C25  C26   180.00   0.0  0
 D6I  CONST_13  C17   N21  C25  C26     0.00   0.0  0
 D6I  CONST_14  N12   C11  C10  C9      0.00   0.0  0
 D6I  CONST_15  N12   C13  C8   C9      0.00   0.0  0
 D6I  CONST_16  C13   C8   C9   C10     0.00   0.0  0
 D6I  CONST_17  C13   N12  C11  C10     0.00   0.0  0
 D6I  CONST_18  C19   N18  C17  C16     0.00   0.0  0
 D6I  CONST_21  C19   N20  C15  C16     0.00   0.0  0
 D6I  CONST_22  N21   C17  N18  C19   180.00   0.0  0
 D6I  CONST_23  C25   C24  N23  C22     0.00   0.0  0
 D6I  CONST_24  C24   C25  N21  C22     0.00   0.0  0
 D6I  CONST_26  C17   N21  C25  C24   180.00   0.0  0
 D6I  CONST_27  N21   C22  N23  C24     0.00   0.0  0
 D6I  CONST_28  N23   C22  N21  C25     0.00   0.0  0
 D6I  CONST_30  C11   C10  C9   C8      0.00   0.0  0
 D6I  CONST_31  C11   N12  C13  C8      0.00   0.0  0
 D6I  CONST_32  N20   C15  C16  C17     0.00   0.0  0
 D6I  CONST_33  N20   C19  N18  C17     0.00   0.0  0
 D6I  CONST_34  N23   C22  N21  C17   180.00   0.0  0
 D6I  CONST_35  N18   C17  C16  C15     0.00   0.0  0
 D6I  CONST_36  N21   C17  C16  C15   180.00   0.0  0
 D6I  CONST_37  N18   C19  N20  C15     0.00   0.0  0
 D6I  CONST_38  N21   C25  C24  N23     0.00   0.0  0
 D6I  CONST_39  N14   C11  C10  C9    180.00   0.0  0
 D6I  CONST_40  O7    C8   C9   C10   180.00   0.0  0
 D6I  CONST_41  N14   C11  N12  C13   180.00   0.0  0
 D6I  CONST_42  N14   C15  N20  C19   180.00   0.0  0
 D6I  CONST_43  N14   C15  C16  C17   180.00   0.0  0
 D6I  CONST_44  O7    C8   C13  N12   180.00   0.0  0
 D6I  CONST_45  H26   C26  C27  C28   180.00   0.0  0
 D6I  CONST_46  H29   C29  C28  C27   180.00   0.0  0
 D6I  CONST_47  H27   C27  C28  C29   180.00   0.0  0
 D6I  CONST_48  H28   C28  C27  C26   180.00   0.0  0
 D6I  CONST_49  H13   C13  C8   C9    180.00   0.0  0
 D6I  CONST_50  H9    C9   C8   C13   180.00   0.0  0
 D6I  CONST_51  H22   C22  N23  C24   180.00   0.0  0
 D6I  CONST_52  H10   C10  C9   C8    180.00   0.0  0
 D6I  CONST_53  H19   C19  N18  C17   180.00   0.0  0
 D6I  CONST_54  H16   C16  C17  N18   180.00   0.0  0
 D6I  Var_01    C15   N14  C11  C10   142.64  30.0  2
 D6I  Var_02    C11   N14  C15  C16   172.81  30.0  2
 D6I  Var_03    C5    C6   O7   C8    177.06  30.0  1
 D6I  Var_04    C5    C4   N2   C1     70.66  30.0  2
 D6I  Var_05    O7    C6   C5   C4   -179.29  30.0  3
 D6I  Var_06    N2    C4   C5   C6    175.05  30.0  3
 D6I  Var_07    H31C  C3   N2   C1     62.89  30.0  3
 D6I  Var_08    H11C  C1   N2   C3     56.04  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
 D6I  plan-1  C9   0.020
 D6I  plan-1  C10  0.020
 D6I  plan-1  C13  0.020
 D6I  plan-1  C8   0.020
 D6I  plan-1  C11  0.020
 D6I  plan-1  N12  0.020
 D6I  plan-1  N14  0.020
 D6I  plan-1  H9   0.020
 D6I  plan-1  H10  0.020
 D6I  plan-1  H13  0.020
 D6I  plan-1  O7   0.020
 D6I  plan-2  C16  0.020
 D6I  plan-2  C19  0.020
 D6I  plan-2  C17  0.020
 D6I  plan-2  C15  0.020
 D6I  plan-2  N18  0.020
 D6I  plan-2  N20  0.020
 D6I  plan-2  N21  0.020
 D6I  plan-2  N14  0.020
 D6I  plan-2  H16  0.020
 D6I  plan-2  H19  0.020
 D6I  plan-3  C28  0.020
 D6I  plan-3  C27  0.020
 D6I  plan-3  C29  0.020
 D6I  plan-3  C26  0.020
 D6I  plan-3  C22  0.020
 D6I  plan-3  C24  0.020
 D6I  plan-3  C25  0.020
 D6I  plan-3  C17  0.020
 D6I  plan-3  N23  0.020
 D6I  plan-3  N21  0.020
 D6I  plan-3  H28  0.020
 D6I  plan-3  H27  0.020
 D6I  plan-3  H29  0.020
 D6I  plan-3  H26  0.020
 D6I  plan-3  H22  0.020

