# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:34:07 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-azanylpropyl-[3-(pyrimidin-2-ylamino)propyl]amino]methyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN(CCCNc1ncccn1)C[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 KY8  KY8  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-azanylpropyl-[3-(pyrimidin-2-ylamino)propyl]amino]methyl]oxolane-3,4-diol  ligand  63  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KY8
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
 KY8  C02  C  CH1   0  -0.035   1.3422   0.1136   3.3245
 KY8  C03  C  CH1   0  -0.044   2.6569   0.3231   2.5702
 KY8  C05  C  CH1   0   0.215   2.3893  -0.4882   1.3066
 KY8  C07  C  CR56  0   0.491   4.0727  -0.9066  -0.4973
 KY8  C13  C  CR56  0  -0.012   4.5909  -0.1090  -1.5047
 KY8  C15  C  CR15  0   0.119   3.2235   1.1080  -0.4549
 KY8  C17  C  CH1   0  -0.005   0.3303   0.1439   2.1815
 KY8  C18  C  CH2   0  -0.294  -0.2679   1.5246   1.9615
 KY8  C20  C  CH2   0  -0.276  -1.2963   2.8695   0.2378
 KY8  C09  C  CR16  0   0.046   5.2720  -2.6361  -1.1200
 KY8  C11  C  CR6   0   0.459   5.5365  -0.7125  -2.3543
 KY8  C21  C  CH2   0  -0.451  -0.1092   3.2149  -0.6484
 KY8  C22  C  CH2   0  -0.268  -0.2754   4.5650  -1.3283
 KY8  C24  C  CH2   0  -0.285  -2.4962   1.0076   1.1871
 KY8  C25  C  CH2   0  -0.481  -3.1783   0.3721  -0.0162
 KY8  C26  C  CH2   0  -0.234  -4.5677  -0.1375   0.3323
 KY8  C28  C  CR6   0   0.595  -6.3713  -1.3600  -0.8197
 KY8  C30  C  CR16  0  -0.021  -7.9851  -2.4361  -1.9869
 KY8  C31  C  CR16  0  -0.394  -8.7110  -2.6592  -0.8242
 KY8  C32  C  CR16  0  -0.010  -8.1459  -2.1577   0.3353
 KY8  N06  N  NR5   0  -0.542   3.1943  -0.1062   0.1767
 KY8  N08  N  N     0  -0.457   4.3792  -2.1792  -0.2591
 KY8  N10  N  N     0  -0.474   5.8547  -1.9923  -2.1277
 KY8  N14  N  N     0  -0.448   4.0432   1.1480  -1.4615
 KY8  N19  N  NT    0  -0.419  -1.1919   1.5528   0.8472
 KY8  N23  N  NH2   0  -0.798   0.8654   4.8557  -2.1852
 KY8  N27  N  NH1   0  -0.660  -5.1863  -0.7282  -0.8310
 KY8  N29  N  N     0  -0.461  -6.8308  -1.7976  -2.0037
 KY8  N33  N  N     0  -0.466  -6.9909  -1.5102   0.3562
 KY8  O01  O  OH1   0  -0.669   1.3096  -1.1547   3.9281
 KY8  O04  O  OH1   0  -0.654   3.7965  -0.1597   3.2156
 KY8  O16  O  O2    0  -0.485   1.0392  -0.2793   1.0092
 KY8  H1   H  HCH1  0   0.249   1.1574   0.9129   4.0539
 KY8  H2   H  HCH1  0   0.246   2.7570   1.3869   2.3164
 KY8  H3   H  HCH1  0   0.255   2.6122  -1.5462   1.4881
 KY8  H4   H  HNH2  0   0.412   5.8796   0.8885  -3.5759
 KY8  H5   H  HNH2  0   0.404   6.7617  -0.5415  -3.9702
 KY8  H6   H  HCR5  0   0.283   2.6075   1.9327  -0.1299
 KY8  H7   H  HCH1  0   0.251  -0.4649  -0.5819   2.3806
 KY8  H8   H  HCH2  0   0.219  -0.7398   1.8517   2.9025
 KY8  H9   H  HCH2  0   0.234   0.5422   2.2331   1.7699
 KY8  H10  H  HCH2  0   0.198  -1.4398   3.6560   0.9980
 KY8  H11  H  HCH2  0   0.232  -2.1962   2.8838  -0.3819
 KY8  H12  H  HCR6  0   0.252   5.5722  -3.6707  -0.9924
 KY8  H13  H  HCH2  0   0.213   0.8108   3.2389  -0.0541
 KY8  H14  H  HCH2  0   0.222   0.0178   2.4329  -1.4009
 KY8  H15  H  HCH2  0   0.213  -1.1744   4.5440  -1.9512
 KY8  H16  H  HCH2  0   0.189  -0.4519   5.3320  -0.5596
 KY8  H17  H  HCH2  0   0.207  -3.1503   1.7755   1.6322
 KY8  H18  H  HCH2  0   0.237  -2.3756   0.2411   1.9558
 KY8  H19  H  HCH2  0   0.234  -3.2557   1.0964  -0.8332
 KY8  H20  H  HCH2  0   0.236  -2.5597  -0.4532  -0.3787
 KY8  H21  H  HCH2  0   0.230  -4.5005  -0.8800   1.1315
 KY8  H22  H  HCH2  0   0.223  -5.1780   0.6854   0.7211
 KY8  H23  H  HCR6  0   0.268  -8.3545  -2.7884  -2.9444
 KY8  H24  H  HCR6  0   0.268  -9.6532  -3.1858  -0.8256
 KY8  H25  H  HCR6  0   0.267  -8.6448  -2.2799   1.2911
 KY8  H27  H  HNH2  0   0.345   0.7389   5.7622  -2.6170
 KY8  H28  H  HNH2  0   0.336   1.6967   4.9435  -1.6131
 KY8  H30  H  HNH1  0   0.392  -4.7722  -0.5668  -1.7344
 KY8  H31  H  HOH1  0   0.449   2.1365  -1.2751   4.4094
 KY8  H32  H  HOH1  0   0.470   4.1104   0.5083   3.8335
 KY8  N12  N  NH2   0  -0.816   6.1227  -0.0620  -3.3598

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
 KY8  C09  N10  aromatic  1.330  0.020  1.330
 KY8  C09  N08  aromatic  1.322  0.020  1.322
 KY8  N10  C11  aromatic  1.338  0.020  1.338
 KY8  N08  C07  aromatic  1.331  0.020  1.331
 KY8  C11  N12  single    1.333  0.020  1.333
 KY8  C11  C13  aromatic  1.407  0.020  1.407
 KY8  C07  C13  aromatic  1.386  0.020  1.386
 KY8  C07  N06  aromatic  1.366  0.020  1.366
 KY8  O01  C02  single    1.405  0.020  1.405
 KY8  C13  N14  aromatic  1.372  0.020  1.372
 KY8  O04  C03  single    1.396  0.020  1.396
 KY8  C05  N06  single    1.439  0.020  1.439
 KY8  C05  C03  single    1.525  0.020  1.525
 KY8  C05  O16  single    1.398  0.020  1.398
 KY8  N06  C15  aromatic  1.369  0.020  1.369
 KY8  C03  C02  single    1.530  0.020  1.530
 KY8  O16  C17  single    1.434  0.020  1.434
 KY8  C02  C17  single    1.527  0.020  1.527
 KY8  C22  N23  single    1.456  0.020  1.456
 KY8  C22  C21  single    1.521  0.020  1.521
 KY8  C17  C18  single    1.521  0.020  1.521
 KY8  N14  C15  aromatic  1.299  0.020  1.299
 KY8  C21  C20  single    1.521  0.020  1.521
 KY8  C20  N19  single    1.455  0.020  1.455
 KY8  C18  N19  single    1.448  0.020  1.448
 KY8  N19  C24  single    1.454  0.020  1.454
 KY8  C24  C25  single    1.522  0.020  1.522
 KY8  C25  C26  single    1.520  0.020  1.520
 KY8  C26  N27  single    1.444  0.020  1.444
 KY8  N27  C28  single    1.343  0.020  1.343
 KY8  N33  C28  aromatic  1.338  0.020  1.338
 KY8  N33  C32  aromatic  1.324  0.020  1.324
 KY8  C28  N29  aromatic  1.343  0.020  1.343
 KY8  C32  C31  aromatic  1.384  0.020  1.384
 KY8  N29  C30  aromatic  1.319  0.020  1.319
 KY8  C31  C30  aromatic  1.389  0.020  1.389
 KY8  C02  H1   single    0.970  0.020  1.090
 KY8  C03  H2   single    0.970  0.020  1.090
 KY8  C05  H3   single    0.970  0.020  1.090
 KY8  N12  H4   single    0.860  0.020  1.020
 KY8  N12  H5   single    0.860  0.020  1.020
 KY8  C15  H6   single    0.930  0.020  1.080
 KY8  C17  H7   single    0.970  0.020  1.090
 KY8  C18  H8   single    0.970  0.020  1.090
 KY8  C18  H9   single    0.970  0.020  1.090
 KY8  C20  H10  single    0.970  0.020  1.090
 KY8  C20  H11  single    0.970  0.020  1.090
 KY8  C09  H12  single    0.930  0.020  1.080
 KY8  C21  H13  single    0.970  0.020  1.090
 KY8  C21  H14  single    0.970  0.020  1.090
 KY8  C22  H15  single    0.970  0.020  1.090
 KY8  C22  H16  single    0.970  0.020  1.090
 KY8  C24  H17  single    0.970  0.020  1.090
 KY8  C24  H18  single    0.970  0.020  1.090
 KY8  C25  H19  single    0.970  0.020  1.090
 KY8  C25  H20  single    0.970  0.020  1.090
 KY8  C26  H21  single    0.970  0.020  1.090
 KY8  C26  H22  single    0.970  0.020  1.090
 KY8  C30  H23  single    0.930  0.020  1.080
 KY8  C31  H24  single    0.930  0.020  1.080
 KY8  C32  H25  single    0.930  0.020  1.080
 KY8  N23  H27  single    0.890  0.020  1.040
 KY8  N23  H28  single    0.890  0.020  1.040
 KY8  N27  H30  single    0.860  0.020  1.020
 KY8  O01  H31  single    0.850  0.020  0.980
 KY8  O04  H32  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
 KY8  H1   C02  O01  111.58  3.000
 KY8  H1   C02  C17  111.80  3.000
 KY8  O01  C02  C17  108.91  3.000
 KY8  H1   C02  C03  111.87  3.000
 KY8  C17  C02  C03  101.40  3.000
 KY8  O01  C02  C03  110.82  3.000
 KY8  H2   C03  O04  111.55  3.000
 KY8  H2   C03  C05  109.87  3.000
 KY8  O04  C03  C05  110.02  3.000
 KY8  H2   C03  C02  108.96  3.000
 KY8  C05  C03  C02  100.65  3.000
 KY8  O04  C03  C02  115.23  3.000
 KY8  H3   C05  O16  112.07  3.000
 KY8  H3   C05  N06  105.81  3.000
 KY8  O16  C05  N06  109.48  3.000
 KY8  H3   C05  C03  109.91  3.000
 KY8  O16  C05  C03  105.43  3.000
 KY8  N06  C05  C03  114.27  3.000
 KY8  N08  C07  N06  128.33  3.000
 KY8  N06  C07  C13  105.18  3.000
 KY8  N08  C07  C13  126.48  3.000
 KY8  N14  C13  C11  132.87  3.000
 KY8  N14  C13  C07  110.81  3.000
 KY8  C11  C13  C07  116.32  3.000
 KY8  H6   C15  N14  124.75  3.000
 KY8  H6   C15  N06  121.77  3.000
 KY8  N14  C15  N06  113.47  3.000
 KY8  H7   C17  O16  108.18  3.000
 KY8  H7   C17  C18  110.03  3.000
 KY8  O16  C17  C18  110.13  3.000
 KY8  H7   C17  C02  109.39  3.000
 KY8  C18  C17  C02  112.77  3.000
 KY8  O16  C17  C02  106.17  3.000
 KY8  H9   C18  H8   105.93  3.000
 KY8  H9   C18  N19  108.99  3.000
 KY8  H8   C18  N19  112.21  3.000
 KY8  H9   C18  C17  108.80  3.000
 KY8  H8   C18  C17  108.32  3.000
 KY8  N19  C18  C17  112.34  3.000
 KY8  H11  C20  H10  105.92  3.000
 KY8  H11  C20  N19  107.97  3.000
 KY8  H10  C20  N19  111.47  3.000
 KY8  H11  C20  C21  108.02  3.000
 KY8  H10  C20  C21  109.94  3.000
 KY8  N19  C20  C21  113.18  3.000
 KY8  H12  C09  N10  115.44  3.000
 KY8  H12  C09  N08  116.10  3.000
 KY8  N10  C09  N08  128.46  3.000
 KY8  N10  C11  C13  117.89  3.000
 KY8  C13  C11  N12  122.79  3.000
 KY8  N10  C11  N12  119.32  3.000
 KY8  H14  C21  H13  106.95  3.000
 KY8  H14  C21  C22  109.88  3.000
 KY8  H13  C21  C22  108.35  3.000
 KY8  H14  C21  C20  109.24  3.000
 KY8  H13  C21  C20  110.14  3.000
 KY8  C22  C21  C20  112.14  3.000
 KY8  H16  C22  H15  106.23  3.000
 KY8  H16  C22  N23  113.44  3.000
 KY8  H15  C22  N23  108.22  3.000
 KY8  H16  C22  C21  108.91  3.000
 KY8  H15  C22  C21  109.10  3.000
 KY8  N23  C22  C21  110.78  3.000
 KY8  H18  C24  H17  105.67  3.000
 KY8  H18  C24  N19  109.19  3.000
 KY8  H17  C24  N19  111.43  3.000
 KY8  H18  C24  C25  108.23  3.000
 KY8  H17  C24  C25  110.13  3.000
 KY8  N19  C24  C25  111.94  3.000
 KY8  H20  C25  H19  106.98  3.000
 KY8  H20  C25  C26  109.88  3.000
 KY8  H19  C25  C26  109.17  3.000
 KY8  H20  C25  C24  108.89  3.000
 KY8  H19  C25  C24  110.21  3.000
 KY8  C26  C25  C24  111.60  3.000
 KY8  H22  C26  H21  106.56  3.000
 KY8  H22  C26  N27  110.75  3.000
 KY8  H21  C26  N27  109.72  3.000
 KY8  H22  C26  C25  109.79  3.000
 KY8  H21  C26  C25  109.83  3.000
 KY8  N27  C26  C25  110.12  3.000
 KY8  N33  C28  N29  125.44  3.000
 KY8  N29  C28  N27  116.60  3.000
 KY8  N33  C28  N27  117.96  3.000
 KY8  H23  C30  N29  116.34  3.000
 KY8  H23  C30  C31  120.58  3.000
 KY8  N29  C30  C31  123.08  3.000
 KY8  H24  C31  C32  122.30  3.000
 KY8  H24  C31  C30  122.24  3.000
 KY8  C32  C31  C30  115.46  3.000
 KY8  H25  C32  N33  116.24  3.000
 KY8  H25  C32  C31  120.63  3.000
 KY8  N33  C32  C31  123.13  3.000
 KY8  C15  N06  C07  106.16  3.000
 KY8  C15  N06  C05  127.57  3.000
 KY8  C07  N06  C05  126.26  3.000
 KY8  C09  N08  C07  111.70  3.000
 KY8  C11  N10  C09  119.15  3.000
 KY8  C15  N14  C13  104.37  3.000
 KY8  C24  N19  C20  111.90  3.000
 KY8  C24  N19  C18  112.66  3.000
 KY8  C20  N19  C18  112.70  3.000
 KY8  H28  N23  H27  105.42  3.000
 KY8  H28  N23  C22  109.14  3.000
 KY8  H27  N23  C22  109.39  3.000
 KY8  H30  N27  C28  116.48  3.000
 KY8  H30  N27  C26  118.75  3.000
 KY8  C28  N27  C26  124.32  3.000
 KY8  C30  N29  C28  116.47  3.000
 KY8  C32  N33  C28  116.42  3.000
 KY8  H31  O01  C02  107.89  3.000
 KY8  H32  O04  C03  108.85  3.000
 KY8  C17  O16  C05  110.34  3.000
 KY8  H5   N12  H4   118.32  3.000
 KY8  H5   N12  C11  120.31  3.000
 KY8  H4   N12  C11  121.16  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
 KY8  CONST_01  N10  C09  N08  C07     0.00   0.0  0
 KY8  CONST_02  N10  C11  C13  C07     0.00   0.0  0
 KY8  CONST_03  C15  N14  C13  C07     0.00   0.0  0
 KY8  CONST_04  N14  C15  N06  C07     0.00   0.0  0
 KY8  CONST_05  C09  N10  C11  C13     0.00   0.0  0
 KY8  CONST_06  C09  N08  C07  C13     0.00   0.0  0
 KY8  CONST_07  C15  N06  C07  C13     0.00   0.0  0
 KY8  CONST_08  N06  C15  N14  C13     0.00   0.0  0
 KY8  CONST_09  N08  C07  N06  C15   180.00   0.0  0
 KY8  CONST_10  C11  C13  N14  C15   180.00   0.0  0
 KY8  CONST_11  N06  C07  N08  C09   180.00   0.0  0
 KY8  CONST_12  N08  C09  N10  C11     0.00   0.0  0
 KY8  CONST_13  N08  C07  C13  C11     0.00   0.0  0
 KY8  CONST_14  N06  C07  C13  C11   180.00   0.0  0
 KY8  CONST_15  C31  C32  N33  C28     0.00   0.0  0
 KY8  CONST_16  C31  C30  N29  C28     0.00   0.0  0
 KY8  CONST_17  N33  C28  N29  C30     0.00   0.0  0
 KY8  CONST_18  N33  C32  C31  C30     0.00   0.0  0
 KY8  CONST_19  N29  C28  N33  C32     0.00   0.0  0
 KY8  CONST_20  N29  C30  C31  C32     0.00   0.0  0
 KY8  CONST_21  N14  C13  C07  N06     0.00   0.0  0
 KY8  CONST_22  N14  C13  C07  N08   180.00   0.0  0
 KY8  CONST_23  N14  C13  C11  N10   180.00   0.0  0
 KY8  CONST_24  N08  C07  N06  C05     0.00   0.0  0
 KY8  CONST_25  C13  C07  N06  C05   180.00   0.0  0
 KY8  CONST_26  N14  C15  N06  C05   180.00   0.0  0
 KY8  CONST_27  N12  C11  C13  C07   180.00   0.0  0
 KY8  CONST_28  C09  N10  C11  N12   180.00   0.0  0
 KY8  CONST_29  N14  C13  C11  N12     0.00   0.0  0
 KY8  CONST_30  N27  C28  N29  C30   180.00   0.0  0
 KY8  CONST_31  N27  C28  N33  C32   180.00   0.0  0
 KY8  CONST_32  H6   C15  N06  C05     0.00   0.0  0
 KY8  CONST_33  H12  C09  N08  C07   180.00   0.0  0
 KY8  CONST_34  H25  C32  N33  C28   180.00   0.0  0
 KY8  CONST_35  H23  C30  N29  C28   180.00   0.0  0
 KY8  CONST_36  H24  C31  C30  N29   180.00   0.0  0
 KY8  CONST_37  N33  C28  N27  C26     0.00   0.0  0
 KY8  CONST_38  N29  C28  N27  C26   180.00   0.0  0
 KY8  CONST_39  H4   N12  C11  C13     0.00   0.0  0
 KY8  CONST_40  H5   N12  C11  C13   180.00   0.0  0
 KY8  CONST_41  H30  N27  C28  N29     0.00   0.0  0
 KY8  Var_01    C20  N19  C18  C17  -153.55  30.0  3
 KY8  Var_02    C28  N27  C26  C25   174.56  30.0  3
 KY8  Var_03    C21  C20  N19  C18    76.56  30.0  2
 KY8  Var_04    C25  C24  N19  C18  -150.13  30.0  3
 KY8  Var_05    N23  C22  C21  C20  -179.06  30.0  1
 KY8  Var_06    N19  C20  C21  C22   177.11  30.0  3
 KY8  Var_07    N27  C26  C25  C24   179.78  30.0  3
 KY8  Var_08    N19  C24  C25  C26  -177.35  30.0  1
 KY8  Var_09    H27  N23  C22  C21  -179.28  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
 KY8  chir_01  C02  O01  C03  C17  negativ
 KY8  chir_02  C03  O04  C05  C02  negativ
 KY8  chir_03  C05  O16  N06  C03  negativ
 KY8  chir_04  C17  O16  C18  C02  positiv

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
 KY8  plan-1  C28  0.020
 KY8  plan-1  C30  0.020
 KY8  plan-1  C31  0.020
 KY8  plan-1  C32  0.020
 KY8  plan-1  N27  0.020
 KY8  plan-1  N29  0.020
 KY8  plan-1  N33  0.020
 KY8  plan-1  H23  0.020
 KY8  plan-1  H24  0.020
 KY8  plan-1  H25  0.020
 KY8  plan-2  C05  0.020
 KY8  plan-2  C07  0.020
 KY8  plan-2  C13  0.020
 KY8  plan-2  C15  0.020
 KY8  plan-2  C09  0.020
 KY8  plan-2  C11  0.020
 KY8  plan-2  N06  0.020
 KY8  plan-2  N08  0.020
 KY8  plan-2  N10  0.020
 KY8  plan-2  N14  0.020
 KY8  plan-2  H6   0.020
 KY8  plan-2  H12  0.020
 KY8  plan-2  N12  0.020
 KY8  plan-3  C26  0.020
 KY8  plan-3  C28  0.020
 KY8  plan-3  N27  0.020
 KY8  plan-3  H30  0.020
 KY8  plan-4  C11  0.020
 KY8  plan-4  H4   0.020
 KY8  plan-4  H5   0.020
 KY8  plan-4  N12  0.020

