# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:36:21 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: (1~{S},2~{R},3~{S},5~{R})-3-[2-(2-azanyl-3-bromanyl-quinolin-7-yl)ethyl]-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2cc(CC[C@H]3C[C@H]([C@H](O)[C@@H]3O)n4ccc5c(N)ncnc45)ccc2cc1Br
#
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
 K8N  K8N  (1~{S},2~{R},3~{S},5~{R})-3-[2-(2-azanyl-3-bromanyl-quinolin-7-yl)ethyl]-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol  ligand  54  31  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K8N
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
 K8N  N1   N   NH2   0  -0.824  -38.9851  -35.9619   -4.3806
 K8N  C1   C   CR6   0   0.437  -37.7408  -35.7712   -3.9206
 K8N  N2   N   N     0  -0.481  -37.5186  -34.7313   -3.1122
 K8N  C2   C   CR16  0   0.040  -36.2880  -34.5491   -2.6349
 K8N  N3   N   N     0  -0.464  -35.2125  -35.2770   -2.8519
 K8N  C3   C   CR56  0   0.507  -35.4450  -36.3149   -3.6608
 K8N  C4   C   CR56  0  -0.090  -36.6762  -36.6350   -4.2420
 K8N  C5   C   CR15  0  -0.442  -36.4784  -37.8054   -5.0320
 K8N  C6   C   CR15  0  -0.016  -35.1622  -38.1326   -4.8974
 K8N  N4   N   NR5   0  -0.524  -34.5308  -37.2315   -4.0693
 K8N  C7   C   CH1   0  -0.106  -33.1422  -37.2651   -3.6700
 K8N  C8   C   CH2   0  -0.456  -32.1407  -37.2273   -4.8325
 K8N  C9   C   CH1   0  -0.274  -30.9163  -38.0580   -4.3691
 K8N  C10  C   CH2   0  -0.434  -30.6673  -39.2862   -5.2430
 K8N  C11  C   CH2   0  -0.515  -30.2655  -38.9297   -6.6744
 K8N  C12  C   CR6   0   0.140  -29.9751  -40.1568   -7.4903
 K8N  C13  C   CR16  0  -0.312  -28.7087  -40.7784   -7.3889
 K8N  C14  C   CR16  0  -0.298  -28.4264  -41.9143   -8.0978
 K8N  C15  C   CR66  0   0.047  -29.4019  -42.4862   -8.9390
 K8N  C16  C   CR16  0  -0.153  -29.1736  -43.6541   -9.7015
 K8N  C17  C   CR6   0  -0.237  -30.1653  -44.1459  -10.4891
 K8N  BR1  BR  BR    0  -0.025  -29.8761  -45.7177  -11.4895
 K8N  C18  C   CR6   0   0.458  -31.4322  -43.4718  -10.5458
 K8N  N5   N   NH2   0  -0.828  -32.4564  -43.9569  -11.2859
 K8N  N6   N   N     0  -0.500  -31.6452  -42.3843   -9.8431
 K8N  C19  C   CR66  0   0.245  -30.6752  -41.8832   -9.0479
 K8N  C20  C   CR16  0  -0.375  -30.9331  -40.7103   -8.3057
 K8N  C21  C   CH1   0   0.023  -31.2263  -38.4522   -2.9199
 K8N  O1   O   OH1   0  -0.677  -30.7605  -37.4353   -2.0617
 K8N  C22  C   CH1   0   0.015  -32.7543  -38.5181   -2.8934
 K8N  O2   O   OH1   0  -0.660  -33.3227  -38.5005   -1.6118
 K8N  H1   H   HNH2  0   0.398  -39.6909  -35.2686   -4.2013
 K8N  H2   H   HNH2  0   0.406  -39.1809  -36.6512   -5.0844
 K8N  H3   H   HCR6  0   0.243  -36.1629  -33.6879   -1.9862
 K8N  H4   H   HCR5  0   0.256  -37.2020  -38.3389   -5.6273
 K8N  H5   H   HCR5  0   0.286  -34.6183  -38.9527   -5.3378
 K8N  H6   H   HCH1  0   0.276  -32.9967  -36.3997   -3.0224
 K8N  H7   H   HCH2  0   0.263  -31.8769  -36.2026   -5.0902
 K8N  H8   H   HCH2  0   0.243  -32.5881  -37.6628   -5.7297
 K8N  H9   H   HCH1  0   0.253  -30.0088  -37.4480   -4.3836
 K8N  H10  H   HCH2  0   0.231  -31.5580  -39.9237   -5.2659
 K8N  H11  H   HCH2  0   0.243  -29.8723  -39.8866   -4.7914
 K8N  H12  H   HCH2  0   0.246  -29.3791  -38.2891   -6.6468
 K8N  H13  H   HCH2  0   0.250  -31.0570  -38.3500   -7.1548
 K8N  H14  H   HCR6  0   0.250  -27.9540  -40.3407   -6.7466
 K8N  H15  H   HCR6  0   0.259  -27.4512  -42.3802   -8.0243
 K8N  H16  H   HCR6  0   0.288  -28.2090  -44.1440   -9.6467
 K8N  H17  H   HNH2  0   0.394  -33.2499  -43.3468  -11.3949
 K8N  H18  H   HNH2  0   0.400  -32.2784  -44.5614  -12.0693
 K8N  H19  H   HCR6  0   0.245  -31.9101  -40.2496   -8.3966
 K8N  H20  H   HCH1  0   0.223  -30.7781  -39.4209   -2.6568
 K8N  H21  H   HOH1  0   0.443  -31.2151  -37.5324   -1.2168
 K8N  H22  H   HCH1  0   0.225  -33.0699  -39.4091   -3.4549
 K8N  H23  H   HOH1  0   0.461  -33.2787  -39.3881   -1.2428

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
 K8N  BR1  C17  single    1.885  0.020  1.885
 K8N  N5   C18  single    1.354  0.020  1.354
 K8N  C17  C18  aromatic  1.436  0.020  1.436
 K8N  C17  C16  aromatic  1.359  0.020  1.359
 K8N  C18  N6   aromatic  1.312  0.020  1.312
 K8N  C16  C15  aromatic  1.413  0.020  1.413
 K8N  N6   C19  aromatic  1.351  0.020  1.351
 K8N  C15  C19  aromatic  1.413  0.020  1.413
 K8N  C15  C14  aromatic  1.409  0.020  1.409
 K8N  C19  C20  aromatic  1.412  0.020  1.412
 K8N  C14  C13  aromatic  1.368  0.020  1.368
 K8N  C20  C12  aromatic  1.374  0.020  1.374
 K8N  C13  C12  aromatic  1.414  0.020  1.414
 K8N  C12  C11  single    1.502  0.020  1.502
 K8N  C11  C10  single    1.529  0.020  1.529
 K8N  C10  C9   single    1.528  0.020  1.528
 K8N  C8   C9   single    1.550  0.020  1.550
 K8N  C8   C7   single    1.535  0.020  1.535
 K8N  C6   C5   aromatic  1.363  0.020  1.363
 K8N  C6   N4   aromatic  1.377  0.020  1.377
 K8N  C9   C21  single    1.534  0.020  1.534
 K8N  C5   C4   aromatic  1.426  0.020  1.426
 K8N  N4   C7   single    1.445  0.020  1.445
 K8N  N4   C3   aromatic  1.358  0.020  1.358
 K8N  C4   C3   aromatic  1.399  0.020  1.399
 K8N  C4   C1   aromatic  1.408  0.020  1.408
 K8N  N1   C1   single    1.340  0.020  1.340
 K8N  C7   C22  single    1.524  0.020  1.524
 K8N  C3   N3   aromatic  1.336  0.020  1.336
 K8N  C1   N2   aromatic  1.336  0.020  1.336
 K8N  C21  C22  single    1.530  0.020  1.530
 K8N  C21  O1   single    1.410  0.020  1.410
 K8N  C22  O2   single    1.402  0.020  1.402
 K8N  N3   C2   aromatic  1.317  0.020  1.317
 K8N  N2   C2   aromatic  1.332  0.020  1.332
 K8N  N1   H1   single    0.860  0.020  1.020
 K8N  N1   H2   single    0.860  0.020  1.020
 K8N  C2   H3   single    0.930  0.020  1.080
 K8N  C5   H4   single    0.930  0.020  1.080
 K8N  C6   H5   single    0.930  0.020  1.080
 K8N  C7   H6   single    0.970  0.020  1.090
 K8N  C8   H7   single    0.970  0.020  1.090
 K8N  C8   H8   single    0.970  0.020  1.090
 K8N  C9   H9   single    0.970  0.020  1.090
 K8N  C10  H10  single    0.970  0.020  1.090
 K8N  C10  H11  single    0.970  0.020  1.090
 K8N  C11  H12  single    0.970  0.020  1.090
 K8N  C11  H13  single    0.970  0.020  1.090
 K8N  C13  H14  single    0.930  0.020  1.080
 K8N  C14  H15  single    0.930  0.020  1.080
 K8N  C16  H16  single    0.930  0.020  1.080
 K8N  N5   H17  single    0.890  0.020  1.040
 K8N  N5   H18  single    0.890  0.020  1.040
 K8N  C20  H19  single    0.930  0.020  1.080
 K8N  C21  H20  single    0.970  0.020  1.090
 K8N  O1   H21  single    0.850  0.020  0.980
 K8N  C22  H22  single    0.970  0.020  1.090
 K8N  O2   H23  single    0.850  0.020  0.980

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
 K8N  H2   N1   H1   117.47  3.000
 K8N  H2   N1   C1   121.27  3.000
 K8N  H1   N1   C1   119.50  3.000
 K8N  C4   C1   N2   119.33  3.000
 K8N  N2   C1   N1   118.23  3.000
 K8N  C4   C1   N1   122.43  3.000
 K8N  C2   N2   C1   118.49  3.000
 K8N  H3   C2   N3   116.29  3.000
 K8N  H3   C2   N2   115.41  3.000
 K8N  N3   C2   N2   128.30  3.000
 K8N  C3   N3   C2   112.77  3.000
 K8N  N4   C3   C4   108.25  3.000
 K8N  C4   C3   N3   125.63  3.000
 K8N  N4   C3   N3   126.12  3.000
 K8N  C5   C4   C3   107.22  3.000
 K8N  C3   C4   C1   115.48  3.000
 K8N  C5   C4   C1   137.30  3.000
 K8N  H4   C5   C6   125.72  3.000
 K8N  H4   C5   C4   128.24  3.000
 K8N  C6   C5   C4   106.04  3.000
 K8N  H5   C6   N4   120.80  3.000
 K8N  H5   C6   C5   129.01  3.000
 K8N  N4   C6   C5   110.19  3.000
 K8N  C7   N4   C6   126.26  3.000
 K8N  C7   N4   C3   125.42  3.000
 K8N  C6   N4   C3   108.30  3.000
 K8N  H6   C7   C22  108.40  3.000
 K8N  H6   C7   C8   110.07  3.000
 K8N  C22  C7   C8   103.89  3.000
 K8N  H6   C7   N4   105.89  3.000
 K8N  C22  C7   N4   113.85  3.000
 K8N  C8   C7   N4   114.65  3.000
 K8N  H8   C8   H7   106.25  3.000
 K8N  H8   C8   C9   110.80  3.000
 K8N  H7   C8   C9   112.56  3.000
 K8N  H8   C8   C7   110.17  3.000
 K8N  H7   C8   C7   111.12  3.000
 K8N  C9   C8   C7   106.01  3.000
 K8N  H9   C9   C21  108.88  3.000
 K8N  H9   C9   C10  107.80  3.000
 K8N  C21  C9   C10  111.52  3.000
 K8N  H9   C9   C8   110.64  3.000
 K8N  C21  C9   C8   105.10  3.000
 K8N  C10  C9   C8   112.86  3.000
 K8N  H11  C10  H10  106.27  3.000
 K8N  H11  C10  C11  108.88  3.000
 K8N  H10  C10  C11  109.26  3.000
 K8N  H11  C10  C9   108.87  3.000
 K8N  H10  C10  C9   110.32  3.000
 K8N  C11  C10  C9   113.01  3.000
 K8N  H13  C11  H12  106.70  3.000
 K8N  H13  C11  C12  109.56  3.000
 K8N  H12  C11  C12  109.60  3.000
 K8N  H13  C11  C10  110.19  3.000
 K8N  H12  C11  C10  109.02  3.000
 K8N  C12  C11  C10  111.65  3.000
 K8N  C20  C12  C13  119.31  3.000
 K8N  C13  C12  C11  119.55  3.000
 K8N  C20  C12  C11  121.10  3.000
 K8N  H14  C13  C14  119.92  3.000
 K8N  H14  C13  C12  119.26  3.000
 K8N  C14  C13  C12  120.82  3.000
 K8N  H15  C14  C15  119.28  3.000
 K8N  H15  C14  C13  120.50  3.000
 K8N  C15  C14  C13  120.22  3.000
 K8N  C19  C15  C16  117.17  3.000
 K8N  C19  C15  C14  119.77  3.000
 K8N  C16  C15  C14  123.06  3.000
 K8N  H16  C16  C17  121.04  3.000
 K8N  H16  C16  C15  119.36  3.000
 K8N  C17  C16  C15  119.60  3.000
 K8N  C18  C17  BR1  120.38  3.000
 K8N  C18  C17  C16  119.79  3.000
 K8N  BR1  C17  C16  119.83  3.000
 K8N  N6   C18  N5   117.84  3.000
 K8N  N6   C18  C17  120.74  3.000
 K8N  N5   C18  C17  121.39  3.000
 K8N  H18  N5   H17  114.80  3.000
 K8N  H18  N5   C18  120.51  3.000
 K8N  H17  N5   C18  116.00  3.000
 K8N  C19  N6   C18  120.41  3.000
 K8N  C20  C19  N6   119.11  3.000
 K8N  C20  C19  C15  118.60  3.000
 K8N  N6   C19  C15  122.29  3.000
 K8N  H19  C20  C19  118.27  3.000
 K8N  H19  C20  C12  120.45  3.000
 K8N  C19  C20  C12  121.28  3.000
 K8N  H20  C21  C22  111.42  3.000
 K8N  H20  C21  O1   110.81  3.000
 K8N  C22  C21  O1   110.52  3.000
 K8N  H20  C21  C9   111.73  3.000
 K8N  O1   C21  C9   108.85  3.000
 K8N  C22  C21  C9   103.26  3.000
 K8N  H21  O1   C21  107.75  3.000
 K8N  H22  C22  O2   111.14  3.000
 K8N  H22  C22  C21  108.23  3.000
 K8N  O2   C22  C21  114.85  3.000
 K8N  H22  C22  C7   109.44  3.000
 K8N  O2   C22  C7   110.62  3.000
 K8N  C21  C22  C7   102.12  3.000
 K8N  H23  O2   C22  108.69  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
 K8N  CONST_01  C6   C5   C4   C1   180.00   0.0  0
 K8N  CONST_02  N4   C3   C4   C1   180.00   0.0  0
 K8N  CONST_03  N3   C3   C4   C1     0.00   0.0  0
 K8N  CONST_04  N3   C2   N2   C1     0.00   0.0  0
 K8N  CONST_05  C5   C4   C1   N2   180.00   0.0  0
 K8N  CONST_06  C3   C4   C1   N2     0.00   0.0  0
 K8N  CONST_07  C3   N3   C2   N2     0.00   0.0  0
 K8N  CONST_08  N4   C3   N3   C2   180.00   0.0  0
 K8N  CONST_09  C4   C3   N3   C2     0.00   0.0  0
 K8N  CONST_10  C4   C1   N2   C2     0.00   0.0  0
 K8N  CONST_11  C6   N4   C3   N3   180.00   0.0  0
 K8N  CONST_12  C5   C4   C3   N3   180.00   0.0  0
 K8N  CONST_13  C5   C6   N4   C3     0.00   0.0  0
 K8N  CONST_14  C6   C5   C4   C3     0.00   0.0  0
 K8N  CONST_15  N4   C6   C5   C4     0.00   0.0  0
 K8N  CONST_16  C6   N4   C3   C4     0.00   0.0  0
 K8N  CONST_17  N4   C3   C4   C5     0.00   0.0  0
 K8N  CONST_18  N6   C19  C20  C12  180.00   0.0  0
 K8N  CONST_19  C15  C19  C20  C12    0.00   0.0  0
 K8N  CONST_20  C15  C14  C13  C12    0.00   0.0  0
 K8N  CONST_21  C16  C15  C14  C13  180.00   0.0  0
 K8N  CONST_22  C19  C15  C14  C13    0.00   0.0  0
 K8N  CONST_23  C19  C20  C12  C13    0.00   0.0  0
 K8N  CONST_24  C17  C16  C15  C14  180.00   0.0  0
 K8N  CONST_25  N6   C19  C15  C14  180.00   0.0  0
 K8N  CONST_26  C20  C19  C15  C14    0.00   0.0  0
 K8N  CONST_27  C20  C12  C13  C14    0.00   0.0  0
 K8N  CONST_28  C18  C17  C16  C15    0.00   0.0  0
 K8N  CONST_29  C18  N6   C19  C15    0.00   0.0  0
 K8N  CONST_30  N6   C18  C17  C16    0.00   0.0  0
 K8N  CONST_31  N6   C19  C15  C16    0.00   0.0  0
 K8N  CONST_32  C20  C19  C15  C16  180.00   0.0  0
 K8N  CONST_33  C19  N6   C18  C17    0.00   0.0  0
 K8N  CONST_34  C19  C15  C16  C17    0.00   0.0  0
 K8N  CONST_35  C20  C19  N6   C18  180.00   0.0  0
 K8N  CONST_36  C7   N4   C3   N3     0.00   0.0  0
 K8N  CONST_37  C7   N4   C3   C4   180.00   0.0  0
 K8N  CONST_38  C7   N4   C6   C5   180.00   0.0  0
 K8N  CONST_39  C5   C4   C1   N1     0.00   0.0  0
 K8N  CONST_40  C3   C4   C1   N1   180.00   0.0  0
 K8N  CONST_41  C2   N2   C1   N1   180.00   0.0  0
 K8N  CONST_42  C19  C20  C12  C11  180.00   0.0  0
 K8N  CONST_43  C14  C13  C12  C11  180.00   0.0  0
 K8N  CONST_44  BR1  C17  C16  C15  180.00   0.0  0
 K8N  CONST_45  N5   C18  C17  C16  180.00   0.0  0
 K8N  CONST_46  N6   C18  C17  BR1  180.00   0.0  0
 K8N  CONST_47  C19  N6   C18  N5   180.00   0.0  0
 K8N  CONST_48  H4   C5   C4   C1     0.00   0.0  0
 K8N  CONST_49  H3   C2   N2   C1   180.00   0.0  0
 K8N  CONST_50  H5   C6   N4   C3   180.00   0.0  0
 K8N  CONST_51  H15  C14  C13  C12  180.00   0.0  0
 K8N  CONST_52  H19  C20  C12  C13  180.00   0.0  0
 K8N  CONST_53  H16  C16  C15  C14    0.00   0.0  0
 K8N  CONST_54  H14  C13  C14  C15  180.00   0.0  0
 K8N  CONST_55  H1   N1   C1   N2     0.00   0.0  0
 K8N  CONST_56  H2   N1   C1   N2   180.00   0.0  0
 K8N  CONST_57  H17  N5   C18  C17  180.00   0.0  0
 K8N  Var_01    C12  C11  C10  C9   177.72  30.0  1
 K8N  Var_02    C20  C12  C11  C10   96.33  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
 K8N  chir_01  C7   C8   N4   C22  negativ
 K8N  chir_02  C9   C21  C8   C10  positiv
 K8N  chir_03  C21  O1   C22  C9   negativ
 K8N  chir_04  C22  O2   C7   C21  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
 K8N  plan-1  N1   0.020
 K8N  plan-1  C1   0.020
 K8N  plan-1  N2   0.020
 K8N  plan-1  C2   0.020
 K8N  plan-1  N3   0.020
 K8N  plan-1  C3   0.020
 K8N  plan-1  C4   0.020
 K8N  plan-1  C5   0.020
 K8N  plan-1  C6   0.020
 K8N  plan-1  N4   0.020
 K8N  plan-1  C7   0.020
 K8N  plan-1  H3   0.020
 K8N  plan-1  H4   0.020
 K8N  plan-1  H5   0.020
 K8N  plan-2  C11  0.020
 K8N  plan-2  C12  0.020
 K8N  plan-2  C13  0.020
 K8N  plan-2  C14  0.020
 K8N  plan-2  C15  0.020
 K8N  plan-2  C16  0.020
 K8N  plan-2  C17  0.020
 K8N  plan-2  BR1  0.020
 K8N  plan-2  C18  0.020
 K8N  plan-2  N5   0.020
 K8N  plan-2  N6   0.020
 K8N  plan-2  C19  0.020
 K8N  plan-2  C20  0.020
 K8N  plan-2  H14  0.020
 K8N  plan-2  H15  0.020
 K8N  plan-2  H16  0.020
 K8N  plan-2  H19  0.020
 K8N  plan-3  N1   0.020
 K8N  plan-3  C1   0.020
 K8N  plan-3  H1   0.020
 K8N  plan-3  H2   0.020
 K8N  plan-4  C18  0.020
 K8N  plan-4  N5   0.020
 K8N  plan-4  H17  0.020
 K8N  plan-4  H18  0.020

