# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 01:29:47 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: ~{N}4,~{N}4-dimethyl-~{N}1-[5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@H]1CC[C@@H](CC1)Nc2ncnc3[nH]cc(C4CCOCC4)c23
#
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
 6QY  6QY  ~{N}4,~{N}4-dimethyl-~{N}1-[5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]cyclohexane-1,4-diamine  ligand  54  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6QY
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
 6QY  C1   C  CH1   0  -0.006  -4.2639   0.5370  -0.2471
 6QY  C2   C  CH2   0  -0.469  -3.7146   0.5554   1.1820
 6QY  C3   C  CH2   0  -0.455  -2.1904   0.5655   1.2191
 6QY  C7   C  CR6   0   0.471   0.6833  -1.5730   0.3153
 6QY  C8   C  CR16  0   0.034   0.9825  -3.8371   0.0841
 6QY  C9   C  CR56  0   0.476   2.8105  -2.6002   0.0976
 6QY  C10  C  CR56  0  -0.124   2.0846  -1.4096   0.2283
 6QY  C11  C  CR5   0   0.063   3.0286  -0.3272   0.2434
 6QY  C12  C  CR15  0  -0.081   4.2572  -0.9147   0.1326
 6QY  C13  C  CH1   0  -0.411   2.7367   1.1405   0.2880
 6QY  C14  C  CH2   0  -0.441   3.9512   1.9938   0.6509
 6QY  C15  C  CH2   0  -0.181   3.5764   3.4674   0.6365
 6QY  C16  C  CH2   0  -0.177   1.9101   3.1461  -0.9762
 6QY  C18  C  CH3   0  -0.532  -6.3622   1.4505   0.5900
 6QY  N    N  NT    0  -0.419  -5.7257   0.4746  -0.2743
 6QY  C    C  CH3   0  -0.529  -6.2480   0.6264  -1.6194
 6QY  C6   C  CH2   0  -0.458  -3.6520  -0.6541  -0.9906
 6QY  C5   C  CH2   0  -0.433  -2.1287  -0.6308  -0.9644
 6QY  C4   C  CH1   0  -0.040  -1.5971  -0.6148   0.4652
 6QY  N1   N  NH1   0  -0.690  -0.1504  -0.5374   0.5084
 6QY  N4   N  NR15  0  -0.669   4.1214  -2.2790   0.0478
 6QY  N3   N  N     0  -0.457   2.2971  -3.8335   0.0253
 6QY  N2   N  N     0  -0.490   0.1606  -2.7981   0.2194
 6QY  C17  C  CH2   0  -0.448   2.1786   1.6511  -1.0484
 6QY  O    O  O2    0  -0.483   3.0638   3.8725  -0.6148
 6QY  H1   H  HCH1  0   0.177  -3.9176   1.4657  -0.7441
 6QY  H2   H  HCH2  0   0.247  -4.0656   1.4350   1.7223
 6QY  H3   H  HCH2  0   0.221  -4.0953  -0.3198   1.7209
 6QY  H4   H  HCH2  0   0.217  -1.8262   1.4986   0.7716
 6QY  H5   H  HCH2  0   0.248  -1.8507   0.5586   2.2574
 6QY  H6   H  HCR6  0   0.242   0.5003  -4.8075   0.0170
 6QY  H7   H  HCR5  0   0.285   5.2365  -0.4654   0.1014
 6QY  H8   H  HCH1  0   0.232   1.9829   1.3265   1.0667
 6QY  H9   H  HCH2  0   0.244   4.3308   1.7265   1.6399
 6QY  H10  H  HCH2  0   0.229   4.7588   1.8197  -0.0670
 6QY  H11  H  HCH2  0   0.197   2.8404   3.6632   1.4311
 6QY  H12  H  HCH2  0   0.238   4.4500   4.0893   0.8390
 6QY  H13  H  HCH2  0   0.239   1.5835   3.5259  -1.9456
 6QY  H14  H  HCH2  0   0.192   1.0982   3.3374  -0.2574
 6QY  H15  H  HCH3  0   0.190  -6.0674   2.4889   0.3699
 6QY  H16  H  HCH3  0   0.235  -7.4440   1.3848   0.4679
 6QY  H17  H  HCH3  0   0.238  -6.1521   1.2568   1.6403
 6QY  H19  H  HCH3  0   0.188  -5.9780   1.5914  -2.0784
 6QY  H20  H  HCH3  0   0.236  -5.8968  -0.1639  -2.2797
 6QY  H21  H  HCH3  0   0.233  -7.3365   0.5650  -1.5998
 6QY  H22  H  HCH2  0   0.217  -4.0183  -1.5761  -0.5262
 6QY  H23  H  HCH2  0   0.241  -3.9730  -0.6796  -2.0323
 6QY  H24  H  HCH2  0   0.242  -1.7346  -1.4988  -1.4975
 6QY  H25  H  HCH2  0   0.213  -1.7599   0.2588  -1.4876
 6QY  H26  H  HCH1  0   0.237  -1.9019  -1.5404   0.9610
 6QY  H27  H  HNH1  0   0.394   0.2549   0.3781   0.6016
 6QY  H28  H  HNR5  0   0.409   4.8787  -2.9360  -0.0451
 6QY  H29  H  HCH2  0   0.236   2.9044   1.4397  -1.8394
 6QY  H30  H  HCH2  0   0.229   1.2551   1.1332  -1.3237

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
 6QY  C18  N    single    1.451  0.020  1.451
 6QY  C    N    single    1.451  0.020  1.451
 6QY  N    C1   single    1.463  0.020  1.463
 6QY  C2   C1   single    1.531  0.020  1.531
 6QY  C2   C3   single    1.525  0.020  1.525
 6QY  C1   C6   single    1.532  0.020  1.532
 6QY  C3   C4   single    1.521  0.020  1.521
 6QY  C6   C5   single    1.524  0.020  1.524
 6QY  C5   C4   single    1.525  0.020  1.525
 6QY  C4   N1   single    1.449  0.020  1.449
 6QY  N2   C8   aromatic  1.332  0.020  1.332
 6QY  N2   C7   aromatic  1.335  0.020  1.335
 6QY  N1   C7   single    1.343  0.020  1.343
 6QY  C8   N3   aromatic  1.316  0.020  1.316
 6QY  C7   C10  aromatic  1.413  0.020  1.413
 6QY  N3   C9   aromatic  1.338  0.020  1.338
 6QY  C10  C9   aromatic  1.401  0.020  1.401
 6QY  C10  C11  aromatic  1.436  0.020  1.436
 6QY  C17  C16  single    1.521  0.020  1.521
 6QY  C17  C13  single    1.536  0.020  1.536
 6QY  C16  O    single    1.410  0.020  1.410
 6QY  C9   N4   aromatic  1.351  0.020  1.351
 6QY  C11  C13  single    1.497  0.020  1.497
 6QY  C11  C12  aromatic  1.366  0.020  1.366
 6QY  C13  C14  single    1.528  0.020  1.528
 6QY  N4   C12  aromatic  1.374  0.020  1.374
 6QY  O    C15  single    1.412  0.020  1.412
 6QY  C14  C15  single    1.521  0.020  1.521
 6QY  C1   H1   single    0.970  0.020  1.090
 6QY  C2   H2   single    0.970  0.020  1.090
 6QY  C2   H3   single    0.970  0.020  1.090
 6QY  C3   H4   single    0.970  0.020  1.090
 6QY  C3   H5   single    0.970  0.020  1.090
 6QY  C8   H6   single    0.930  0.020  1.080
 6QY  C12  H7   single    0.930  0.020  1.080
 6QY  C13  H8   single    0.970  0.020  1.090
 6QY  C14  H9   single    0.970  0.020  1.090
 6QY  C14  H10  single    0.970  0.020  1.090
 6QY  C15  H11  single    0.970  0.020  1.090
 6QY  C15  H12  single    0.970  0.020  1.090
 6QY  C16  H13  single    0.970  0.020  1.090
 6QY  C16  H14  single    0.970  0.020  1.090
 6QY  C18  H15  single    0.970  0.020  1.090
 6QY  C18  H16  single    0.970  0.020  1.090
 6QY  C18  H17  single    0.970  0.020  1.090
 6QY  C    H19  single    0.970  0.020  1.090
 6QY  C    H20  single    0.970  0.020  1.090
 6QY  C    H21  single    0.970  0.020  1.090
 6QY  C6   H22  single    0.970  0.020  1.090
 6QY  C6   H23  single    0.970  0.020  1.090
 6QY  C5   H24  single    0.970  0.020  1.090
 6QY  C5   H25  single    0.970  0.020  1.090
 6QY  C4   H26  single    0.970  0.020  1.090
 6QY  N1   H27  single    0.860  0.020  1.020
 6QY  N4   H28  single    0.860  0.020  1.020
 6QY  C17  H29  single    0.970  0.020  1.090
 6QY  C17  H30  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
 6QY  H1   C1   C6   108.00  3.000
 6QY  H1   C1   N    109.84  3.000
 6QY  C6   C1   N    110.92  3.000
 6QY  H1   C1   C2   107.23  3.000
 6QY  C6   C1   C2   108.61  3.000
 6QY  N    C1   C2   112.10  3.000
 6QY  H3   C2   H2   106.79  3.000
 6QY  H3   C2   C3   109.91  3.000
 6QY  H2   C2   C3   107.72  3.000
 6QY  H3   C2   C1   108.95  3.000
 6QY  H2   C2   C1   110.90  3.000
 6QY  C3   C2   C1   112.42  3.000
 6QY  H5   C3   H4   106.85  3.000
 6QY  H5   C3   C4   110.17  3.000
 6QY  H4   C3   C4   109.17  3.000
 6QY  H5   C3   C2   109.50  3.000
 6QY  H4   C3   C2   109.12  3.000
 6QY  C4   C3   C2   111.89  3.000
 6QY  N2   C7   N1   118.33  3.000
 6QY  N1   C7   C10  122.35  3.000
 6QY  N2   C7   C10  119.32  3.000
 6QY  H6   C8   N2   115.44  3.000
 6QY  H6   C8   N3   116.32  3.000
 6QY  N2   C8   N3   128.24  3.000
 6QY  N3   C9   N4   126.13  3.000
 6QY  N4   C9   C10  107.72  3.000
 6QY  N3   C9   C10  126.14  3.000
 6QY  C11  C10  C9   107.51  3.000
 6QY  C11  C10  C7   137.56  3.000
 6QY  C9   C10  C7   114.92  3.000
 6QY  C13  C11  C12  126.82  3.000
 6QY  C12  C11  C10  105.43  3.000
 6QY  C13  C11  C10  127.66  3.000
 6QY  H7   C12  N4   120.14  3.000
 6QY  H7   C12  C11  129.80  3.000
 6QY  N4   C12  C11  110.07  3.000
 6QY  H8   C13  C17  108.11  3.000
 6QY  H8   C13  C14  106.39  3.000
 6QY  C17  C13  C14  108.05  3.000
 6QY  H8   C13  C11  108.69  3.000
 6QY  C14  C13  C11  113.55  3.000
 6QY  C17  C13  C11  111.77  3.000
 6QY  H10  C14  H9   107.37  3.000
 6QY  H10  C14  C15  109.26  3.000
 6QY  H9   C14  C15  109.34  3.000
 6QY  H10  C14  C13  109.99  3.000
 6QY  H9   C14  C13  110.76  3.000
 6QY  C15  C14  C13  110.06  3.000
 6QY  H12  C15  H11  107.46  3.000
 6QY  H12  C15  O    106.96  3.000
 6QY  H11  C15  O    110.25  3.000
 6QY  H12  C15  C14  110.68  3.000
 6QY  H11  C15  C14  109.30  3.000
 6QY  O    C15  C14  112.08  3.000
 6QY  H14  C16  H13  107.38  3.000
 6QY  H14  C16  O    110.27  3.000
 6QY  H13  C16  O    107.05  3.000
 6QY  H14  C16  C17  109.39  3.000
 6QY  H13  C16  C17  110.66  3.000
 6QY  O    C16  C17  111.97  3.000
 6QY  H17  C18  H16  106.78  3.000
 6QY  H17  C18  H15  107.99  3.000
 6QY  H16  C18  H15  107.45  3.000
 6QY  H17  C18  N    111.75  3.000
 6QY  H16  C18  N    109.14  3.000
 6QY  H15  C18  N    113.43  3.000
 6QY  C    N    C18  108.91  3.000
 6QY  C    N    C1   111.86  3.000
 6QY  C18  N    C1   113.49  3.000
 6QY  H21  C    H20  106.99  3.000
 6QY  H21  C    H19  107.54  3.000
 6QY  H20  C    H19  107.71  3.000
 6QY  H21  C    N    109.68  3.000
 6QY  H20  C    N    111.74  3.000
 6QY  H19  C    N    112.93  3.000
 6QY  H23  C6   H22  106.67  3.000
 6QY  H23  C6   C5   108.13  3.000
 6QY  H22  C6   C5   109.87  3.000
 6QY  H23  C6   C1   111.37  3.000
 6QY  H22  C6   C1   108.37  3.000
 6QY  C5   C6   C1   112.28  3.000
 6QY  H25  C5   H24  106.89  3.000
 6QY  H25  C5   C4   108.76  3.000
 6QY  H24  C5   C4   109.88  3.000
 6QY  H25  C5   C6   109.91  3.000
 6QY  H24  C5   C6   109.89  3.000
 6QY  C4   C5   C6   111.39  3.000
 6QY  H26  C4   N1   108.06  3.000
 6QY  H26  C4   C5   108.60  3.000
 6QY  N1   C4   C5   112.11  3.000
 6QY  H26  C4   C3   108.87  3.000
 6QY  N1   C4   C3   109.46  3.000
 6QY  C5   C4   C3   109.68  3.000
 6QY  H27  N1   C4   116.98  3.000
 6QY  H27  N1   C7   117.71  3.000
 6QY  C4   N1   C7   125.03  3.000
 6QY  H28  N4   C12  125.40  3.000
 6QY  H28  N4   C9   125.33  3.000
 6QY  C12  N4   C9   109.26  3.000
 6QY  C9   N3   C8   112.55  3.000
 6QY  C8   N2   C7   118.78  3.000
 6QY  H30  C17  H29  106.65  3.000
 6QY  H30  C17  C16  109.17  3.000
 6QY  H29  C17  C16  109.96  3.000
 6QY  H30  C17  C13  111.62  3.000
 6QY  H29  C17  C13  108.89  3.000
 6QY  C16  C17  C13  110.47  3.000
 6QY  C16  O    C15  112.11  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
 6QY  CONST_01  N3   C8   N2   C7     0.00   0.0  0
 6QY  CONST_02  N3   C9   C10  C7     0.00   0.0  0
 6QY  CONST_03  N4   C9   C10  C7   180.00   0.0  0
 6QY  CONST_04  C12  C11  C10  C7   180.00   0.0  0
 6QY  CONST_05  C10  C7   N2   C8     0.00   0.0  0
 6QY  CONST_06  C10  C9   N3   C8     0.00   0.0  0
 6QY  CONST_07  N4   C9   N3   C8   180.00   0.0  0
 6QY  CONST_08  N2   C8   N3   C9     0.00   0.0  0
 6QY  CONST_09  N2   C7   C10  C9     0.00   0.0  0
 6QY  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 6QY  CONST_11  C11  C12  N4   C9     0.00   0.0  0
 6QY  CONST_12  C12  N4   C9   C10    0.00   0.0  0
 6QY  CONST_13  N4   C12  C11  C10    0.00   0.0  0
 6QY  CONST_14  N2   C7   C10  C11  180.00   0.0  0
 6QY  CONST_15  N3   C9   C10  C11  180.00   0.0  0
 6QY  CONST_16  N4   C9   C10  C11    0.00   0.0  0
 6QY  CONST_17  N3   C9   N4   C12  180.00   0.0  0
 6QY  CONST_18  C13  C11  C10  C7     0.00   0.0  0
 6QY  CONST_19  C13  C11  C10  C9   180.00   0.0  0
 6QY  CONST_20  N4   C12  C11  C13  180.00   0.0  0
 6QY  CONST_21  N1   C7   N2   C8   180.00   0.0  0
 6QY  CONST_22  N1   C7   C10  C9   180.00   0.0  0
 6QY  CONST_23  N1   C7   C10  C11    0.00   0.0  0
 6QY  CONST_24  C4   N1   C7   C10  180.00   0.0  0
 6QY  CONST_25  N2   C7   N1   C4     0.00   0.0  0
 6QY  CONST_26  H6   C8   N2   C7   180.00   0.0  0
 6QY  CONST_27  H7   C12  N4   C9   180.00   0.0  0
 6QY  CONST_28  H28  N4   C9   C10  180.00   0.0  0
 6QY  CONST_29  H27  N1   C7   C10    0.00   0.0  0
 6QY  Var_01    C4   C3   C2   C1   -56.44  30.0  1
 6QY  Var_02    C4   C5   C6   C1    57.56  30.0  1
 6QY  Var_03    O    C16  C17  C13   56.47  30.0  1
 6QY  Var_04    O    C15  C14  C13  -57.49  30.0  1
 6QY  Var_05    C17  C16  O    C15  -58.81  30.0  1
 6QY  Var_06    H15  C18  N    C1    56.68  30.0  3
 6QY  Var_07    H19  C    N    C1   -60.63  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
 6QY  chir_01  C1   N    C2   C6   negativ
 6QY  chir_02  C13  C17  C11  C14  negativ
 6QY  chir_03  C4   N1   C3   C5   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
 6QY  plan-1  C7   0.020
 6QY  plan-1  C4   0.020
 6QY  plan-1  N1   0.020
 6QY  plan-1  H27  0.020
 6QY  plan-2  C7   0.020
 6QY  plan-2  C8   0.020
 6QY  plan-2  C9   0.020
 6QY  plan-2  C10  0.020
 6QY  plan-2  C11  0.020
 6QY  plan-2  C12  0.020
 6QY  plan-2  C13  0.020
 6QY  plan-2  N1   0.020
 6QY  plan-2  N4   0.020
 6QY  plan-2  N3   0.020
 6QY  plan-2  N2   0.020
 6QY  plan-2  H6   0.020
 6QY  plan-2  H7   0.020
 6QY  plan-2  H28  0.020

