# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 19:21:01 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-{5-[2-amino-7-(1-hydroxy-2-methylpropan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(5-chloropyridin-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)n1cc(C(=O)c2cncc(NC(=O)Cc3ccc(Cl)cn3)c2)c4cnc(N)nc14
#
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
 6K4  6K4  N-{5-[2-amino-7-(1-hydroxy-2-methylpropan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(5-chloropyridin-2-yl)acetamide  ligand  56  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6K4
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
 6K4  C4   C   CH2   0  -0.179  -0.0871  -1.4134  -1.6636
 6K4  C7   C   CR15  0  -0.002   1.8052   0.3257  -0.5640
 6K4  C8   C   CR5   0  -0.194   2.8124   1.0251   0.0578
 6K4  C15  C   CR6   0   0.300  -0.6792   3.6152  -0.0244
 6K4  C17  C   C     0   0.563  -2.4616   1.9915   0.4779
 6K4  C20  C   CR6   0   0.283  -4.2284   0.5299  -0.3644
 6K4  C21  C   CR16  0  -0.342  -4.6017  -0.6301   0.3026
 6K4  C22  C   CR16  0  -0.093  -4.7536  -1.8040  -0.4152
 6K4  C28  C   CR56  0  -0.024   3.7854   0.0406   0.4339
 6K4  C2   C   CT    0   0.056   1.1892  -2.0756  -1.1220
 6K4  C3   C   CH3   0  -0.649   1.9211  -2.7956  -2.2530
 6K4  O5   O   OH1   0  -0.657  -0.9215  -2.4250  -2.1639
 6K4  N6   N   NR5   0  -0.553   2.0670  -1.0110  -0.5810
 6K4  O10  O   O     0  -0.408   3.9396   2.9861   0.6322
 6K4  C11  C   CR6   0  -0.107   1.6914   3.2856  -0.0048
 6K4  C12  C   CR16  0  -0.090   1.8280   4.5343  -0.6006
 6K4  N13  N   N     0  -0.384   0.7862   5.2996  -0.8932
 6K4  C14  C   CR16  0  -0.130  -0.4279   4.8514  -0.6251
 6K4  O18  O   O     0  -0.447  -1.7444   1.0698   0.8161
 6K4  C19  C   CH2   0  -0.661  -3.9650   1.8110   0.3737
 6K4  C23  C   CR6   0  -0.122  -4.5226  -1.7631  -1.7791
 6K4  CL   CL  CL    0  -0.108  -4.6666  -3.1870  -2.7446
 6K4  C25  C   CR16  0  -0.064  -4.1681  -0.5606  -2.3742
 6K4  N26  N   N     0  -0.400  -4.0234   0.5546  -1.6772
 6K4  C27  C   CR16  0  -0.272   0.4189   2.8382   0.3271
 6K4  C29  C   CR16  0  -0.081   5.0181  -0.0017   1.0729
 6K4  N30  N   N     0  -0.461   5.6528  -1.1415   1.2681
 6K4  C31  C   CR6   0   0.533   5.0697  -2.2739   0.8300
 6K4  N32  N   NH2   0  -0.823   5.7666  -3.4181   1.0091
 6K4  N33  N   N     0  -0.488   3.8939  -2.3625   0.2120
 6K4  C34  C   CR56  0   0.563   3.2850  -1.2062   0.0291
 6K4  H1   H   HCH2  0   0.221  -0.5851  -0.8577  -0.8563
 6K4  H2   H   HCH2  0   0.224   0.1751  -0.6956  -2.4524
 6K4  H3   H   HCR5  0   0.321   0.9188   0.7225  -1.0256
 6K4  H4   H   HCR6  0   0.283  -4.7655  -0.6201   1.3715
 6K4  H5   H   HCR6  0   0.298  -5.0375  -2.7245   0.0763
 6K4  H6   H   HCH3  0   0.245   0.1756  -3.8261  -0.3624
 6K4  H7   H   HCH3  0   0.255   1.7046  -3.4962   0.4425
 6K4  H8   H   HCH3  0   0.234   0.2837  -2.5053   0.8028
 6K4  H9   H   HCH3  0   0.235   2.1698  -2.1018  -3.0576
 6K4  H10  H   HCH3  0   0.252   2.8393  -3.2593  -1.8983
 6K4  H11  H   HCH3  0   0.244   1.2904  -3.5804  -2.6659
 6K4  H12  H   HOH1  0   0.455  -1.6613  -2.0075  -2.6123
 6K4  H13  H   HCR6  0   0.273   2.8072   4.9175  -0.8632
 6K4  H14  H   HCR6  0   0.283  -1.2576   5.4986  -0.8950
 6K4  H15  H   HNH1  0   0.423  -2.6966   3.9074  -0.1260
 6K4  H16  H   HCH2  0   0.308  -4.3699   1.7619   1.3864
 6K4  H17  H   HCH2  0   0.293  -4.4458   2.6477  -0.1345
 6K4  H18  H   HCR6  0   0.292  -3.9989  -0.5040  -3.4442
 6K4  H19  H   HCR6  0   0.320   0.2889   1.9070   0.8513
 6K4  H20  H   HCR6  0   0.267   5.5031   0.8986   1.4315
 6K4  H21  H   HNH2  0   0.394   6.5364  -3.4064   1.6553
 6K4  H22  H   HNH2  0   0.394   5.2807  -4.2924   0.9071
 6K4  C9   C   C     0   0.323   2.9020   2.4579   0.2665
 6K4  C1   C   CH3   0  -0.653   0.8200  -3.0327   0.0123
 6K4  N16  N   NH1   0  -0.741  -2.0046   3.2295   0.1560

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
 6K4  C4   O5   single    1.404  0.020  1.404
 6K4  C4   C2   single    1.537  0.020  1.537
 6K4  C1   C2   single    1.529  0.020  1.529
 6K4  C2   C3   single    1.527  0.020  1.527
 6K4  C2   N6   single    1.482  0.020  1.482
 6K4  N6   C7   aromatic  1.362  0.020  1.362
 6K4  N6   C34  aromatic  1.376  0.020  1.376
 6K4  C7   C8   aromatic  1.375  0.020  1.375
 6K4  C22  C21  aromatic  1.384  0.020  1.384
 6K4  C22  C23  aromatic  1.384  0.020  1.384
 6K4  C21  C20  aromatic  1.389  0.020  1.389
 6K4  C34  N33  aromatic  1.320  0.020  1.320
 6K4  C34  C28  aromatic  1.403  0.020  1.403
 6K4  N33  C31  aromatic  1.331  0.020  1.331
 6K4  N13  C14  aromatic  1.322  0.020  1.322
 6K4  N13  C12  aromatic  1.325  0.020  1.325
 6K4  C14  C15  aromatic  1.397  0.020  1.397
 6K4  CL   C23  single    1.726  0.020  1.726
 6K4  O18  C17  double    1.216  0.020  1.216
 6K4  C23  C25  aromatic  1.388  0.020  1.388
 6K4  C12  C11  aromatic  1.390  0.020  1.390
 6K4  C17  C19  single    1.518  0.020  1.518
 6K4  C17  N16  single    1.358  0.020  1.358
 6K4  C20  C19  single    1.502  0.020  1.502
 6K4  C20  N26  aromatic  1.329  0.020  1.329
 6K4  C8   C28  aromatic  1.434  0.020  1.434
 6K4  C8   C9   single    1.451  0.020  1.451
 6K4  C15  N16  single    1.392  0.020  1.392
 6K4  C15  C27  aromatic  1.390  0.020  1.390
 6K4  N32  C31  single    1.352  0.020  1.352
 6K4  C31  N30  aromatic  1.347  0.020  1.347
 6K4  C28  C29  aromatic  1.389  0.020  1.389
 6K4  C11  C27  aromatic  1.389  0.020  1.389
 6K4  C11  C9   single    1.491  0.020  1.491
 6K4  C25  N26  aromatic  1.323  0.020  1.323
 6K4  C9   O10  double    1.220  0.020  1.220
 6K4  N30  C29  aromatic  1.319  0.020  1.319
 6K4  C4   H1   single    0.970  0.020  1.090
 6K4  C4   H2   single    0.970  0.020  1.090
 6K4  C7   H3   single    0.930  0.020  1.080
 6K4  C21  H4   single    0.930  0.020  1.080
 6K4  C22  H5   single    0.930  0.020  1.080
 6K4  C1   H6   single    0.970  0.020  1.090
 6K4  C1   H7   single    0.970  0.020  1.090
 6K4  C1   H8   single    0.970  0.020  1.090
 6K4  C3   H9   single    0.970  0.020  1.090
 6K4  C3   H10  single    0.970  0.020  1.090
 6K4  C3   H11  single    0.970  0.020  1.090
 6K4  O5   H12  single    0.850  0.020  0.980
 6K4  C12  H13  single    0.930  0.020  1.080
 6K4  C14  H14  single    0.930  0.020  1.080
 6K4  N16  H15  single    0.860  0.020  1.020
 6K4  C19  H16  single    0.970  0.020  1.090
 6K4  C19  H17  single    0.970  0.020  1.090
 6K4  C25  H18  single    0.930  0.020  1.080
 6K4  C27  H19  single    0.930  0.020  1.080
 6K4  C29  H20  single    0.930  0.020  1.080
 6K4  N32  H21  single    0.890  0.020  1.040
 6K4  N32  H22  single    0.890  0.020  1.040

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
 6K4  H2   C4   H1   107.77  3.000
 6K4  H2   C4   O5   110.91  3.000
 6K4  H1   C4   O5   110.90  3.000
 6K4  H2   C4   C2   109.66  3.000
 6K4  H1   C4   C2   109.59  3.000
 6K4  O5   C4   C2   107.99  3.000
 6K4  H3   C7   N6   121.01  3.000
 6K4  H3   C7   C8   127.61  3.000
 6K4  N6   C7   C8   111.35  3.000
 6K4  C9   C8   C28  126.75  3.000
 6K4  C9   C8   C7   127.79  3.000
 6K4  C28  C8   C7   105.45  3.000
 6K4  C27  C15  N16  124.36  3.000
 6K4  C27  C15  C14  117.46  3.000
 6K4  N16  C15  C14  118.17  3.000
 6K4  C19  C17  O18  120.88  3.000
 6K4  C19  C17  N16  115.17  3.000
 6K4  O18  C17  N16  123.95  3.000
 6K4  N26  C20  C19  116.26  3.000
 6K4  N26  C20  C21  122.09  3.000
 6K4  C19  C20  C21  121.57  3.000
 6K4  H4   C21  C22  120.25  3.000
 6K4  H4   C21  C20  120.50  3.000
 6K4  C22  C21  C20  119.25  3.000
 6K4  H5   C22  C23  121.12  3.000
 6K4  H5   C22  C21  121.00  3.000
 6K4  C23  C22  C21  117.88  3.000
 6K4  C34  C28  C29  114.97  3.000
 6K4  C29  C28  C8   138.03  3.000
 6K4  C34  C28  C8   106.99  3.000
 6K4  N6   C2   C3   108.97  3.000
 6K4  N6   C2   C1   108.77  3.000
 6K4  C3   C2   C1   111.71  3.000
 6K4  N6   C2   C4   108.12  3.000
 6K4  C3   C2   C4   109.89  3.000
 6K4  C1   C2   C4   109.31  3.000
 6K4  H11  C3   H10  107.79  3.000
 6K4  H11  C3   H9   108.11  3.000
 6K4  H10  C3   H9   108.60  3.000
 6K4  H11  C3   C2   110.07  3.000
 6K4  H10  C3   C2   111.34  3.000
 6K4  H9   C3   C2   110.82  3.000
 6K4  H12  O5   C4   108.12  3.000
 6K4  C34  N6   C2   125.74  3.000
 6K4  C34  N6   C7   107.68  3.000
 6K4  C2   N6   C7   126.55  3.000
 6K4  C27  C11  C12  118.79  3.000
 6K4  C27  C11  C9   121.43  3.000
 6K4  C12  C11  C9   119.78  3.000
 6K4  H13  C12  N13  116.91  3.000
 6K4  H13  C12  C11  120.67  3.000
 6K4  N13  C12  C11  122.41  3.000
 6K4  C14  N13  C12  118.78  3.000
 6K4  H14  C14  N13  116.69  3.000
 6K4  H14  C14  C15  119.78  3.000
 6K4  N13  C14  C15  123.54  3.000
 6K4  H17  C19  H16  107.65  3.000
 6K4  H17  C19  C20  110.38  3.000
 6K4  H16  C19  C20  110.64  3.000
 6K4  H17  C19  C17  112.17  3.000
 6K4  H16  C19  C17  107.99  3.000
 6K4  C20  C19  C17  108.00  3.000
 6K4  C25  C23  CL   119.74  3.000
 6K4  C25  C23  C22  119.40  3.000
 6K4  CL   C23  C22  120.86  3.000
 6K4  H18  C25  N26  117.29  3.000
 6K4  H18  C25  C23  120.54  3.000
 6K4  N26  C25  C23  122.17  3.000
 6K4  C25  N26  C20  119.20  3.000
 6K4  H19  C27  C11  120.37  3.000
 6K4  H19  C27  C15  120.74  3.000
 6K4  C11  C27  C15  118.89  3.000
 6K4  H20  C29  N30  116.97  3.000
 6K4  H20  C29  C28  121.61  3.000
 6K4  N30  C29  C28  121.42  3.000
 6K4  C31  N30  C29  118.04  3.000
 6K4  N33  C31  N32  117.42  3.000
 6K4  N32  C31  N30  116.45  3.000
 6K4  N33  C31  N30  126.10  3.000
 6K4  H22  N32  H21  116.45  3.000
 6K4  H22  N32  C31  118.26  3.000
 6K4  H21  N32  C31  118.05  3.000
 6K4  C34  N33  C31  114.43  3.000
 6K4  N33  C34  N6   126.45  3.000
 6K4  N33  C34  C28  125.04  3.000
 6K4  N6   C34  C28  108.52  3.000
 6K4  C11  C9   O10  120.30  3.000
 6K4  O10  C9   C8   121.54  3.000
 6K4  C11  C9   C8   118.16  3.000
 6K4  H8   C1   H7   108.61  3.000
 6K4  H8   C1   H6   108.10  3.000
 6K4  H7   C1   H6   107.88  3.000
 6K4  H8   C1   C2   110.70  3.000
 6K4  H7   C1   C2   111.33  3.000
 6K4  H6   C1   C2   110.10  3.000
 6K4  H15  N16  C17  116.61  3.000
 6K4  H15  N16  C15  115.51  3.000
 6K4  C17  N16  C15  127.12  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
 6K4  CONST_01  N33  C34  N6   C7    180.00   0.0  0
 6K4  CONST_02  C28  C34  N6   C7      0.00   0.0  0
 6K4  CONST_03  C34  C28  C8   C7      0.00   0.0  0
 6K4  CONST_04  C29  C28  C8   C7    180.00   0.0  0
 6K4  CONST_05  C34  N6   C7   C8      0.00   0.0  0
 6K4  CONST_06  N6   C34  C28  C8      0.00   0.0  0
 6K4  CONST_07  N33  C34  C28  C8    180.00   0.0  0
 6K4  CONST_08  N30  C29  C28  C8    180.00   0.0  0
 6K4  CONST_09  C12  N13  C14  C15     0.00   0.0  0
 6K4  CONST_10  C12  C11  C27  C15     0.00   0.0  0
 6K4  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 6K4  CONST_12  C23  C25  N26  C20     0.00   0.0  0
 6K4  CONST_13  C25  C23  C22  C21     0.00   0.0  0
 6K4  CONST_14  C25  N26  C20  C21     0.00   0.0  0
 6K4  CONST_15  N26  C20  C21  C22     0.00   0.0  0
 6K4  CONST_16  N26  C25  C23  C22     0.00   0.0  0
 6K4  CONST_17  C31  N33  C34  C28     0.00   0.0  0
 6K4  CONST_18  N6   C7   C8   C28     0.00   0.0  0
 6K4  CONST_19  C31  N30  C29  C28     0.00   0.0  0
 6K4  CONST_20  C31  N33  C34  N6    180.00   0.0  0
 6K4  CONST_21  C29  C28  C34  N6    180.00   0.0  0
 6K4  CONST_22  C14  N13  C12  C11     0.00   0.0  0
 6K4  CONST_23  C14  C15  C27  C11     0.00   0.0  0
 6K4  CONST_24  C27  C15  C14  N13     0.00   0.0  0
 6K4  CONST_25  C27  C11  C12  N13     0.00   0.0  0
 6K4  CONST_26  N33  C34  C28  C29     0.00   0.0  0
 6K4  CONST_27  N33  C31  N30  C29     0.00   0.0  0
 6K4  CONST_28  C34  N33  C31  N30     0.00   0.0  0
 6K4  CONST_29  C34  C28  C29  N30     0.00   0.0  0
 6K4  CONST_30  C2   N6   C7   C8    180.00   0.0  0
 6K4  CONST_31  C9   C11  C27  C15   180.00   0.0  0
 6K4  CONST_32  CL   C23  C22  C21   180.00   0.0  0
 6K4  CONST_33  C19  C20  C21  C22   180.00   0.0  0
 6K4  CONST_34  C2   N6   C34  C28   180.00   0.0  0
 6K4  CONST_35  N33  C34  N6   C2      0.00   0.0  0
 6K4  CONST_36  C9   C8   C7   N6    180.00   0.0  0
 6K4  CONST_37  C34  C28  C8   C9    180.00   0.0  0
 6K4  CONST_38  C29  C28  C8   C9      0.00   0.0  0
 6K4  CONST_39  N13  C12  C11  C9    180.00   0.0  0
 6K4  CONST_40  N16  C15  C27  C11   180.00   0.0  0
 6K4  CONST_41  N16  C15  C14  N13   180.00   0.0  0
 6K4  CONST_42  C25  N26  C20  C19   180.00   0.0  0
 6K4  CONST_43  N26  C25  C23  CL    180.00   0.0  0
 6K4  CONST_44  N32  C31  N30  C29   180.00   0.0  0
 6K4  CONST_45  C34  N33  C31  N32   180.00   0.0  0
 6K4  CONST_46  H20  C29  C28  C8      0.00   0.0  0
 6K4  CONST_47  H5   C22  C21  C20   180.00   0.0  0
 6K4  CONST_48  H18  C25  N26  C20   180.00   0.0  0
 6K4  CONST_49  H3   C7   C8   C28   180.00   0.0  0
 6K4  CONST_50  H14  C14  N13  C12   180.00   0.0  0
 6K4  CONST_51  H19  C27  C11  C12   180.00   0.0  0
 6K4  CONST_52  H13  C12  N13  C14   180.00   0.0  0
 6K4  CONST_53  H4   C21  C22  C23   180.00   0.0  0
 6K4  CONST_54  C14  C15  N16  C17   180.00   0.0  0
 6K4  CONST_55  C27  C15  N16  C17     0.00   0.0  0
 6K4  CONST_56  H15  N16  C15  C14     0.00   0.0  0
 6K4  CONST_58  H22  N32  C31  N30   180.00   0.0  0
 6K4  CONST_59  O18  C17  N16  C15     0.00   0.0  0
 6K4  CONST_60  C19  C17  N16  C15   180.00   0.0  0
 6K4  Var_01    C11  C9   C8   C7     11.11  30.0  2
 6K4  Var_02    C12  C11  C9   C8   -141.29  30.0  1
 6K4  Var_03    C7   N6   C2   C4     -0.23  30.0  2
 6K4  Var_04    C21  C20  C19  C17   102.16  30.0  1
 6K4  Var_05    O18  C17  C19  C20   -46.18  30.0  1
 6K4  Var_06    N6   C2   C4   O5   -179.47  30.0  3
 6K4  Var_07    H6   C1   C2   N6   -179.89  30.0  3
 6K4  Var_08    H9   C3   C2   N6    -60.29  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
 6K4  plan-1  C20  0.020
 6K4  plan-1  C21  0.020
 6K4  plan-1  C22  0.020
 6K4  plan-1  C19  0.020
 6K4  plan-1  C23  0.020
 6K4  plan-1  CL   0.020
 6K4  plan-1  C25  0.020
 6K4  plan-1  N26  0.020
 6K4  plan-1  H4   0.020
 6K4  plan-1  H5   0.020
 6K4  plan-1  H18  0.020
 6K4  plan-2  C8   0.020
 6K4  plan-2  O10  0.020
 6K4  plan-2  C11  0.020
 6K4  plan-2  C9   0.020
 6K4  plan-3  C15  0.020
 6K4  plan-3  C11  0.020
 6K4  plan-3  C12  0.020
 6K4  plan-3  N13  0.020
 6K4  plan-3  C14  0.020
 6K4  plan-3  C27  0.020
 6K4  plan-3  H13  0.020
 6K4  plan-3  H14  0.020
 6K4  plan-3  H19  0.020
 6K4  plan-3  C9   0.020
 6K4  plan-3  N16  0.020
 6K4  plan-4  C7   0.020
 6K4  plan-4  C8   0.020
 6K4  plan-4  C28  0.020
 6K4  plan-4  C2   0.020
 6K4  plan-4  N6   0.020
 6K4  plan-4  C29  0.020
 6K4  plan-4  N30  0.020
 6K4  plan-4  C31  0.020
 6K4  plan-4  N32  0.020
 6K4  plan-4  N33  0.020
 6K4  plan-4  C34  0.020
 6K4  plan-4  H3   0.020
 6K4  plan-4  H20  0.020
 6K4  plan-4  C9   0.020
 6K4  plan-5  C15  0.020
 6K4  plan-5  C17  0.020
 6K4  plan-5  O18  0.020
 6K4  plan-5  C19  0.020
 6K4  plan-5  H15  0.020
 6K4  plan-5  N16  0.020
 6K4  plan-6  C31  0.020
 6K4  plan-6  N32  0.020
 6K4  plan-6  H21  0.020
 6K4  plan-6  H22  0.020

