# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 19:18:14 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}-[4-(5-methylpyrrolo[3,2-d]pyrimidin-4-yl)oxyphenyl]-1~{H}-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc2ncnc(Oc3ccc(Nc4[nH]c5ccccc5n4)cc3)c12
#
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
 6DT  6DT  ~{N}-[4-(5-methylpyrrolo[3,2-d]pyrimidin-4-yl)oxyphenyl]-1~{H}-benzimidazol-2-amine  ligand  43  27  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6DT
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
 6DT  C20  C  CR16  0  -0.286   7.9876   0.4753   0.8030
 6DT  C21  C  CR16  0  -0.271   7.2888   1.4986   1.4508
 6DT  C19  C  CR16  0  -0.311   7.3277  -0.4737   0.0320
 6DT  C22  C  CR16  0  -0.346   5.9084   1.6076   1.3508
 6DT  C11  C  CR16  0  -0.361   0.3651  -1.3593  -1.5089
 6DT  C13  C  CR16  0  -0.321   0.9559   0.4978  -0.0983
 6DT  C10  C  CR16  0  -0.292  -0.9684  -1.0062  -1.4348
 6DT  C14  C  CR16  0  -0.299  -0.3867   0.8450  -0.0242
 6DT  C4   C  CR15  0  -0.412  -6.9968   0.2337   0.9013
 6DT  C3   C  CR15  0  -0.016  -6.8466   1.2066  -0.0535
 6DT  C26  C  CR16  0   0.016  -4.0274  -1.6389   1.7612
 6DT  C18  C  CR56  0   0.322   5.9507  -0.3555  -0.0596
 6DT  C5   C  CR56  0   0.186  -5.7175  -0.3523   1.0619
 6DT  C23  C  CR56  0   0.195   5.2308   0.6652   0.5844
 6DT  C6   C  CR56  0   0.214  -4.8491   0.3138   0.1763
 6DT  C12  C  CR6   0   0.365   1.3465  -0.6154  -0.8439
 6DT  C9   C  CR6   0   0.345  -1.3403   0.1006  -0.6893
 6DT  C7   C  CR6   0   0.520  -3.5179  -0.0985   0.1643
 6DT  C16  C  CR5   0   0.708   3.7905  -0.5112  -0.4509
 6DT  N27  N  N     0  -0.435  -5.2991  -1.3463   1.8676
 6DT  N25  N  N     0  -0.454  -3.1221  -1.0646   0.9534
 6DT  N17  N  NR15  0  -0.746   4.9948  -1.0934  -0.7156
 6DT  N24  N  N     0  -0.536   3.8851   0.5401   0.3206
 6DT  N2   N  NR5   0  -0.506  -5.5625   1.2638  -0.4968
 6DT  N15  N  NH1   0  -0.808   2.6610  -1.0439  -0.9812
 6DT  O8   O  O2    0  -0.511  -2.6599   0.5118  -0.6612
 6DT  H1   H  HCR6  0   0.251   9.0637   0.4199   0.9031
 6DT  H2   H  HCR6  0   0.249   7.8372   2.2213   2.0410
 6DT  H3   H  HCR6  0   0.263   7.8673  -1.2662  -0.4700
 6DT  H4   H  HCR6  0   0.250   5.3714   2.4030   1.8516
 6DT  H5   H  HCR6  0   0.276   0.6495  -2.2266  -2.0928
 6DT  H6   H  HCR6  0   0.294   1.6899   1.0907   0.4238
 6DT  H7   H  HCR6  0   0.275  -1.7096  -1.5913  -1.9637
 6DT  H8   H  HCR6  0   0.272  -0.6801   1.7122   0.5540
 6DT  H9   H  HCR5  0   0.261  -7.9070  -0.0207   1.4192
 6DT  H10  H  HCR5  0   0.297  -7.5838   1.8829  -0.4576
 6DT  H11  H  HCR6  0   0.251  -3.6483  -2.4344   2.3933
 6DT  H12  H  HCH3  0   0.259  -4.6889   1.6459  -2.3678
 6DT  H13  H  HCH3  0   0.262  -5.8920   2.8162  -1.8188
 6DT  H14  H  HCH3  0   0.260  -4.2811   2.8143  -1.0970
 6DT  H15  H  HNR5  0   0.421   5.1542  -1.9103  -1.2838
 6DT  H17  H  HNH1  0   0.419   2.7893  -1.8620  -1.5563
 6DT  C1   C  CH3   0  -0.520  -5.0690   2.1824  -1.5012

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
 6DT  C22  C21  aromatic  1.388  0.020  1.388
 6DT  C22  C23  aromatic  1.391  0.020  1.391
 6DT  C21  C20  aromatic  1.398  0.020  1.398
 6DT  C23  N24  aromatic  1.377  0.020  1.377
 6DT  C23  C18  aromatic  1.405  0.020  1.405
 6DT  N24  C16  aromatic  1.307  0.020  1.307
 6DT  C20  C19  aromatic  1.389  0.020  1.389
 6DT  C18  C19  aromatic  1.385  0.020  1.385
 6DT  C18  N17  aromatic  1.374  0.020  1.374
 6DT  C16  N15  single    1.357  0.020  1.357
 6DT  C16  N17  aromatic  1.364  0.020  1.364
 6DT  N15  C12  single    1.389  0.020  1.389
 6DT  C12  C11  aromatic  1.400  0.020  1.400
 6DT  C12  C13  aromatic  1.396  0.020  1.396
 6DT  C11  C10  aromatic  1.381  0.020  1.381
 6DT  C13  C14  aromatic  1.389  0.020  1.389
 6DT  C10  C9   aromatic  1.385  0.020  1.385
 6DT  C14  C9   aromatic  1.381  0.020  1.381
 6DT  C9   O8   single    1.382  0.020  1.382
 6DT  O8   C7   single    1.338  0.020  1.338
 6DT  C1   N2   single    1.448  0.020  1.448
 6DT  C7   N25  aromatic  1.309  0.020  1.309
 6DT  C7   C6   aromatic  1.394  0.020  1.394
 6DT  N25  C26  aromatic  1.342  0.020  1.342
 6DT  N2   C6   aromatic  1.365  0.020  1.365
 6DT  N2   C3   aromatic  1.360  0.020  1.360
 6DT  C6   C5   aromatic  1.408  0.020  1.408
 6DT  C26  N27  aromatic  1.309  0.020  1.309
 6DT  C3   C4   aromatic  1.371  0.020  1.371
 6DT  C5   N27  aromatic  1.346  0.020  1.346
 6DT  C5   C4   aromatic  1.416  0.020  1.416
 6DT  C20  H1   single    0.930  0.020  1.080
 6DT  C21  H2   single    0.930  0.020  1.080
 6DT  C19  H3   single    0.930  0.020  1.080
 6DT  C22  H4   single    0.930  0.020  1.080
 6DT  C11  H5   single    0.930  0.020  1.080
 6DT  C13  H6   single    0.930  0.020  1.080
 6DT  C10  H7   single    0.930  0.020  1.080
 6DT  C14  H8   single    0.930  0.020  1.080
 6DT  C4   H9   single    0.930  0.020  1.080
 6DT  C3   H10  single    0.930  0.020  1.080
 6DT  C26  H11  single    0.930  0.020  1.080
 6DT  C1   H12  single    0.970  0.020  1.090
 6DT  C1   H13  single    0.970  0.020  1.090
 6DT  C1   H14  single    0.970  0.020  1.090
 6DT  N17  H15  single    0.860  0.020  1.020
 6DT  N15  H17  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
 6DT  H1   C20  C19  119.25  3.000
 6DT  H1   C20  C21  119.44  3.000
 6DT  C19  C20  C21  121.30  3.000
 6DT  H2   C21  C22  119.39  3.000
 6DT  H2   C21  C20  119.21  3.000
 6DT  C22  C21  C20  121.40  3.000
 6DT  H3   C19  C18  121.84  3.000
 6DT  H3   C19  C20  121.38  3.000
 6DT  C18  C19  C20  116.78  3.000
 6DT  H4   C22  C23  120.74  3.000
 6DT  H4   C22  C21  121.17  3.000
 6DT  C23  C22  C21  118.09  3.000
 6DT  H5   C11  C12  119.83  3.000
 6DT  H5   C11  C10  119.14  3.000
 6DT  C12  C11  C10  121.03  3.000
 6DT  H6   C13  C12  120.44  3.000
 6DT  H6   C13  C14  119.65  3.000
 6DT  C12  C13  C14  119.91  3.000
 6DT  H7   C10  C9   120.73  3.000
 6DT  H7   C10  C11  119.78  3.000
 6DT  C9   C10  C11  119.49  3.000
 6DT  H8   C14  C9   120.13  3.000
 6DT  H8   C14  C13  119.39  3.000
 6DT  C9   C14  C13  120.48  3.000
 6DT  H9   C4   C5   127.65  3.000
 6DT  H9   C4   C3   126.48  3.000
 6DT  C5   C4   C3   105.88  3.000
 6DT  H10  C3   N2   119.79  3.000
 6DT  H10  C3   C4   129.10  3.000
 6DT  N2   C3   C4   111.12  3.000
 6DT  H11  C26  N25  115.39  3.000
 6DT  H11  C26  N27  117.14  3.000
 6DT  N25  C26  N27  127.47  3.000
 6DT  N17  C18  C23  104.62  3.000
 6DT  N17  C18  C19  132.63  3.000
 6DT  C23  C18  C19  122.75  3.000
 6DT  N27  C5   C6   122.28  3.000
 6DT  N27  C5   C4   130.85  3.000
 6DT  C6   C5   C4   106.86  3.000
 6DT  N24  C23  C18  110.30  3.000
 6DT  C18  C23  C22  119.68  3.000
 6DT  N24  C23  C22  130.03  3.000
 6DT  N2   C6   C7   134.48  3.000
 6DT  N2   C6   C5   108.48  3.000
 6DT  C7   C6   C5   117.04  3.000
 6DT  N15  C12  C13  124.31  3.000
 6DT  C13  C12  C11  118.79  3.000
 6DT  N15  C12  C11  116.91  3.000
 6DT  O8   C9   C14  119.29  3.000
 6DT  O8   C9   C10  120.32  3.000
 6DT  C14  C9   C10  120.31  3.000
 6DT  O8   C7   N25  120.99  3.000
 6DT  N25  C7   C6   120.14  3.000
 6DT  O8   C7   C6   118.88  3.000
 6DT  N15  C16  N24  127.35  3.000
 6DT  N15  C16  N17  119.45  3.000
 6DT  N24  C16  N17  113.20  3.000
 6DT  C5   N27  C26  114.72  3.000
 6DT  C7   N25  C26  118.34  3.000
 6DT  H15  N17  C16  126.53  3.000
 6DT  H15  N17  C18  126.47  3.000
 6DT  C16  N17  C18  107.00  3.000
 6DT  C16  N24  C23  104.88  3.000
 6DT  C1   N2   C6   127.25  3.000
 6DT  C6   N2   C3   107.66  3.000
 6DT  C1   N2   C3   125.09  3.000
 6DT  H17  N15  C16  115.83  3.000
 6DT  H17  N15  C12  115.27  3.000
 6DT  C16  N15  C12  128.90  3.000
 6DT  C7   O8   C9   119.27  3.000
 6DT  H14  C1   H13  108.57  3.000
 6DT  H14  C1   H12  109.23  3.000
 6DT  H13  C1   H12  108.64  3.000
 6DT  H14  C1   N2   110.96  3.000
 6DT  H13  C1   N2   108.35  3.000
 6DT  H12  C1   N2   111.02  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
 6DT  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 6DT  CONST_02  C23  C18  C19  C20     0.00   0.0  0
 6DT  CONST_03  N17  C18  C19  C20   180.00   0.0  0
 6DT  CONST_04  N24  C23  C22  C21   180.00   0.0  0
 6DT  CONST_05  C18  C23  C22  C21     0.00   0.0  0
 6DT  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 6DT  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 6DT  CONST_08  C22  C23  C18  C19     0.00   0.0  0
 6DT  CONST_09  N24  C23  C18  C19   180.00   0.0  0
 6DT  CONST_10  C16  N17  C18  C19   180.00   0.0  0
 6DT  CONST_11  C16  N24  C23  C22   180.00   0.0  0
 6DT  CONST_12  N17  C18  C23  C22   180.00   0.0  0
 6DT  CONST_13  C14  C13  C12  C11     0.00   0.0  0
 6DT  CONST_14  C14  C9   C10  C11     0.00   0.0  0
 6DT  CONST_15  C10  C11  C12  C13     0.00   0.0  0
 6DT  CONST_16  C10  C9   C14  C13     0.00   0.0  0
 6DT  CONST_17  C6   N2   C3   C4      0.00   0.0  0
 6DT  CONST_18  C7   C6   C5   C4    180.00   0.0  0
 6DT  CONST_19  N2   C6   C5   C4      0.00   0.0  0
 6DT  CONST_20  C26  N27  C5   C4    180.00   0.0  0
 6DT  CONST_21  C7   C6   N2   C3    180.00   0.0  0
 6DT  CONST_22  C5   C6   N2   C3      0.00   0.0  0
 6DT  CONST_23  C6   C5   C4   C3      0.00   0.0  0
 6DT  CONST_24  N27  C5   C4   C3    180.00   0.0  0
 6DT  CONST_25  C6   C7   N25  C26     0.00   0.0  0
 6DT  CONST_26  C6   C5   N27  C26     0.00   0.0  0
 6DT  CONST_27  C16  N24  C23  C18     0.00   0.0  0
 6DT  CONST_28  N24  C16  N17  C18     0.00   0.0  0
 6DT  CONST_29  N25  C7   C6   C5      0.00   0.0  0
 6DT  CONST_30  N25  C26  N27  C5      0.00   0.0  0
 6DT  CONST_31  N2   C3   C4   C5      0.00   0.0  0
 6DT  CONST_32  N17  C16  N24  C23     0.00   0.0  0
 6DT  CONST_33  C16  N17  C18  C23     0.00   0.0  0
 6DT  CONST_34  C9   C10  C11  C12     0.00   0.0  0
 6DT  CONST_35  C9   C14  C13  C12     0.00   0.0  0
 6DT  CONST_36  N27  C26  N25  C7      0.00   0.0  0
 6DT  CONST_37  N27  C5   C6   C7      0.00   0.0  0
 6DT  CONST_38  N2   C6   C5   N27   180.00   0.0  0
 6DT  CONST_39  N2   C6   C7   N25   180.00   0.0  0
 6DT  CONST_40  N24  C23  C18  N17     0.00   0.0  0
 6DT  CONST_41  O8   C9   C10  C11   180.00   0.0  0
 6DT  CONST_42  O8   C9   C14  C13   180.00   0.0  0
 6DT  CONST_43  N15  C12  C11  C10   180.00   0.0  0
 6DT  CONST_44  N15  C12  C13  C14   180.00   0.0  0
 6DT  CONST_45  C1   N2   C3   C4    180.00   0.0  0
 6DT  CONST_46  O8   C7   N25  C26   180.00   0.0  0
 6DT  CONST_47  N15  C16  N17  C18   180.00   0.0  0
 6DT  CONST_48  O8   C7   C6   C5    180.00   0.0  0
 6DT  CONST_49  C1   N2   C6   C5    180.00   0.0  0
 6DT  CONST_50  N15  C16  N24  C23   180.00   0.0  0
 6DT  CONST_51  C1   N2   C6   C7      0.00   0.0  0
 6DT  CONST_52  O8   C7   C6   N2      0.00   0.0  0
 6DT  CONST_53  H4   C22  C21  C20   180.00   0.0  0
 6DT  CONST_54  H3   C19  C20  C21   180.00   0.0  0
 6DT  CONST_55  H2   C21  C20  C19   180.00   0.0  0
 6DT  CONST_56  H15  N17  C18  C19     0.00   0.0  0
 6DT  CONST_57  H1   C20  C21  C22   180.00   0.0  0
 6DT  CONST_58  H6   C13  C12  C11   180.00   0.0  0
 6DT  CONST_59  H5   C11  C12  C13   180.00   0.0  0
 6DT  CONST_60  H8   C14  C9   C10   180.00   0.0  0
 6DT  CONST_61  H7   C10  C9   C14   180.00   0.0  0
 6DT  CONST_62  H11  C26  N27  C5    180.00   0.0  0
 6DT  CONST_63  H10  C3   C4   C5    180.00   0.0  0
 6DT  CONST_64  H9   C4   C5   C6    180.00   0.0  0
 6DT  Var_01    C16  N15  C12  C11   179.92  30.0  2
 6DT  Var_02    N24  C16  N15  C12     0.12  30.0  2
 6DT  Var_03    N25  C7   O8   C9      0.82  30.0  2
 6DT  Var_04    H12  C1   N2   C3   -118.36  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
 6DT  plan-1  C11  0.020
 6DT  plan-1  C13  0.020
 6DT  plan-1  C10  0.020
 6DT  plan-1  C14  0.020
 6DT  plan-1  C12  0.020
 6DT  plan-1  C9   0.020
 6DT  plan-1  N15  0.020
 6DT  plan-1  O8   0.020
 6DT  plan-1  H5   0.020
 6DT  plan-1  H6   0.020
 6DT  plan-1  H7   0.020
 6DT  plan-1  H8   0.020
 6DT  plan-2  C20  0.020
 6DT  plan-2  C21  0.020
 6DT  plan-2  C19  0.020
 6DT  plan-2  C22  0.020
 6DT  plan-2  C18  0.020
 6DT  plan-2  C23  0.020
 6DT  plan-2  C16  0.020
 6DT  plan-2  N17  0.020
 6DT  plan-2  N24  0.020
 6DT  plan-2  N15  0.020
 6DT  plan-2  H1   0.020
 6DT  plan-2  H2   0.020
 6DT  plan-2  H3   0.020
 6DT  plan-2  H4   0.020
 6DT  plan-2  H15  0.020
 6DT  plan-3  C4   0.020
 6DT  plan-3  C3   0.020
 6DT  plan-3  C26  0.020
 6DT  plan-3  C5   0.020
 6DT  plan-3  C6   0.020
 6DT  plan-3  C7   0.020
 6DT  plan-3  N27  0.020
 6DT  plan-3  N25  0.020
 6DT  plan-3  N2   0.020
 6DT  plan-3  O8   0.020
 6DT  plan-3  H9   0.020
 6DT  plan-3  H10  0.020
 6DT  plan-3  H11  0.020
 6DT  plan-3  C1   0.020

