# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:31:51 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2R,3R,4S,5R)-2-[6-azanyl-8-(quinolin-2-ylmethylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(NCc4ccc5ccccc5n4)nc12
#
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
 3P1  3P1  (2R,3R,4S,5R)-2-[6-azanyl-8-(quinolin-2-ylmethylamino)purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol  ligand  52  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3P1
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
 3P1  N1    N  N     0  -0.467  -3.6318   2.7513  -1.3043
 3P1  C2    C  CR16  0   0.032  -4.1045   1.5381  -1.0514
 3P1  N3    N  N     0  -0.457  -3.5123   0.5555  -0.3880
 3P1  C4    C  CR6   0   0.422  -2.4106   3.0778  -0.8622
 3P1  N5    N  NR5   0  -0.613  -1.4163   0.1451   0.7771
 3P1  C6    C  CR5   0   0.754  -0.2999   0.9464   0.9469
 3P1  N7    N  N     0  -0.536  -0.4338   2.1329   0.4158
 3P1  C8    C  CR56  0   0.033  -1.6859   2.1180  -0.1468
 3P1  C9    C  CR56  0   0.498  -2.3076   0.8980   0.0450
 3P1  C10   C  CH1   0   0.169  -1.5825  -1.2198   1.2065
 3P1  O11   O  O2    0  -0.491  -1.4752  -2.0696   0.0931
 3P1  C12   C  CH1   0   0.015  -2.5125  -3.0373   0.0937
 3P1  C13   C  CH1   0  -0.033  -3.6602  -2.3856   0.8600
 3P1  C14   C  CH1   0  -0.046  -2.9207  -1.5317   1.9013
 3P1  N15   N  NH2   0  -0.822  -1.9150   4.2964  -1.1472
 3P1  N16   N  NH1   0  -0.704   0.7813   0.5286   1.6373
 3P1  C17   C  CH2   0  -0.396   1.9698   1.3451   1.7613
 3P1  C18   C  CR6   0   0.226   2.9878   1.0621   0.6828
 3P1  N19   N  N     0  -0.456   4.1029   0.4917   1.0545
 3P1  C20   C  CR16  0  -0.181   3.6270   1.0975  -1.6266
 3P1  C21   C  CR16  0  -0.324   2.7044   1.3914  -0.6673
 3P1  C22   C  CR66  0   0.083   4.8408   0.4748  -1.2577
 3P1  C23   C  CR66  0   0.198   5.0350   0.1924   0.1160
 3P1  C24   C  CR16  0  -0.295   6.2371  -0.4263   0.5253
 3P1  C25   C  CR16  0  -0.259   7.1964  -0.7495  -0.3971
 3P1  C26   C  CR16  0  -0.254   7.0011  -0.4696  -1.7655
 3P1  C27   C  CR16  0  -0.314   5.8462   0.1323  -2.1879
 3P1  C28   C  CH2   0  -0.156  -2.8864  -3.3901  -1.3241
 3P1  O29   O  OH1   0  -0.670  -1.8073  -4.0481  -1.9419
 3P1  O30   O  OH1   0  -0.663  -4.4780  -3.3695   1.4375
 3P1  O31   O  OH1   0  -0.672  -2.6340  -2.2878   3.0488
 3P1  H2    H  HCR6  0   0.248  -5.0972   1.3270  -1.4337
 3P1  H10   H  HCH1  0   0.257  -0.7873  -1.4228   1.9287
 3P1  H12   H  HCH1  0   0.232  -2.1887  -3.9439   0.6257
 3P1  H13   H  HCH1  0   0.260  -4.2216  -1.7245   0.1954
 3P1  H14   H  HCH1  0   0.250  -3.4692  -0.6182   2.1579
 3P1  HN15  H  HNH2  0   0.395  -2.5489   5.0048  -1.4766
 3P1  HN1A  H  HNH2  0   0.401  -1.1027   4.6207  -0.6511
 3P1  HN16  H  HNH1  0   0.413   0.9148  -0.4598   1.7723
 3P1  H17   H  HCH2  0   0.275   1.6702   2.3926   1.7422
 3P1  H17A  H  HCH2  0   0.278   2.4239   1.1453   2.7311
 3P1  H20   H  HCR6  0   0.271   3.4418   1.3378  -2.6664
 3P1  H21   H  HCR6  0   0.275   1.7703   1.8755  -0.9187
 3P1  H24   H  HCR6  0   0.261   6.3797  -0.6373   1.5775
 3P1  H25   H  HCR6  0   0.264   8.1141  -1.2251  -0.0767
 3P1  H26   H  HCR6  0   0.263   7.7693  -0.7332  -2.4804
 3P1  H27   H  HCR6  0   0.262   5.6900   0.3504  -3.2374
 3P1  H28   H  HCH2  0   0.207  -3.7816  -4.0240  -1.2809
 3P1  H28A  H  HCH2  0   0.197  -3.1667  -2.4690  -1.8535
 3P1  HO29  H  HOH1  0   0.457  -2.0811  -4.3095  -2.8256
 3P1  HO30  H  HOH1  0   0.469  -5.3617  -3.0081   1.5575
 3P1  HO31  H  HOH1  0   0.449  -3.3445  -2.9355   3.1484

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
 3P1  C2   N1    aromatic  1.326  0.020  1.326
 3P1  C4   N1    aromatic  1.339  0.020  1.339
 3P1  N3   C2    aromatic  1.325  0.020  1.325
 3P1  C2   H2    single    0.930  0.020  1.080
 3P1  C9   N3    aromatic  1.325  0.020  1.325
 3P1  C8   C4    aromatic  1.399  0.020  1.399
 3P1  C4   N15   single    1.346  0.020  1.346
 3P1  C10  N5    single    1.440  0.020  1.440
 3P1  N5   C6    aromatic  1.385  0.020  1.385
 3P1  N5   C9    aromatic  1.377  0.020  1.377
 3P1  N16  C6    single    1.349  0.020  1.349
 3P1  C6   N7    aromatic  1.307  0.020  1.307
 3P1  N7   C8    aromatic  1.373  0.020  1.373
 3P1  C9   C8    aromatic  1.383  0.020  1.383
 3P1  C14  C10   single    1.540  0.020  1.540
 3P1  C10  O11   single    1.405  0.020  1.405
 3P1  C10  H10   single    0.970  0.020  1.090
 3P1  C12  O11   single    1.419  0.020  1.419
 3P1  C13  C12   single    1.526  0.020  1.526
 3P1  C28  C12   single    1.508  0.020  1.508
 3P1  C12  H12   single    0.970  0.020  1.090
 3P1  O30  C13   single    1.404  0.020  1.404
 3P1  C13  C14   single    1.536  0.020  1.536
 3P1  C13  H13   single    0.970  0.020  1.090
 3P1  O31  C14   single    1.404  0.020  1.404
 3P1  C14  H14   single    0.970  0.020  1.090
 3P1  N15  HN15  single    0.890  0.020  1.040
 3P1  N15  HN1A  single    0.890  0.020  1.040
 3P1  N16  C17   single    1.447  0.020  1.447
 3P1  N16  HN16  single    0.890  0.020  1.040
 3P1  C18  C17   single    1.510  0.020  1.510
 3P1  C17  H17   single    0.970  0.020  1.090
 3P1  C17  H17A  single    0.970  0.020  1.090
 3P1  C21  C18   aromatic  1.418  0.020  1.418
 3P1  C18  N19   aromatic  1.307  0.020  1.307
 3P1  C23  N19   aromatic  1.356  0.020  1.356
 3P1  C20  C22   aromatic  1.413  0.020  1.413
 3P1  C20  C21   aromatic  1.363  0.020  1.363
 3P1  C20  H20   single    0.930  0.020  1.080
 3P1  C21  H21   single    0.930  0.020  1.080
 3P1  C27  C22   aromatic  1.412  0.020  1.412
 3P1  C22  C23   aromatic  1.416  0.020  1.416
 3P1  C23  C24   aromatic  1.413  0.020  1.413
 3P1  C25  C24   aromatic  1.369  0.020  1.369
 3P1  C24  H24   single    0.930  0.020  1.080
 3P1  C26  C25   aromatic  1.410  0.020  1.410
 3P1  C25  H25   single    0.930  0.020  1.080
 3P1  C27  C26   aromatic  1.369  0.020  1.369
 3P1  C26  H26   single    0.930  0.020  1.080
 3P1  C27  H27   single    0.930  0.020  1.080
 3P1  C28  O29   single    1.407  0.020  1.407
 3P1  C28  H28   single    0.970  0.020  1.090
 3P1  C28  H28A  single    0.970  0.020  1.090
 3P1  O29  HO29  single    0.850  0.020  0.980
 3P1  O30  HO30  single    0.850  0.020  0.980
 3P1  O31  HO31  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
 3P1  C4    N1   C2    119.02  3.000
 3P1  H2    C2   N3    116.18  3.000
 3P1  H2    C2   N1    115.91  3.000
 3P1  N3    C2   N1    127.90  3.000
 3P1  C9    N3   C2    112.22  3.000
 3P1  N15   C4   C8    122.58  3.000
 3P1  N15   C4   N1    119.12  3.000
 3P1  C8    C4   N1    118.28  3.000
 3P1  C10   N5   C9    126.99  3.000
 3P1  C9    N5   C6    105.70  3.000
 3P1  C10   N5   C6    127.22  3.000
 3P1  N16   C6   N7    124.83  3.000
 3P1  N7    C6   N5    113.14  3.000
 3P1  N16   C6   N5    121.99  3.000
 3P1  C8    N7   C6    104.48  3.000
 3P1  C9    C8   N7    111.27  3.000
 3P1  C9    C8   C4    116.31  3.000
 3P1  N7    C8   C4    132.41  3.000
 3P1  C8    C9   N5    105.38  3.000
 3P1  C8    C9   N3    126.26  3.000
 3P1  N5    C9   N3    128.36  3.000
 3P1  H10   C10  C14   107.25  3.000
 3P1  H10   C10  O11   110.83  3.000
 3P1  C14   C10  O11   107.55  3.000
 3P1  H10   C10  N5    106.80  3.000
 3P1  O11   C10  N5    109.16  3.000
 3P1  C14   C10  N5    115.26  3.000
 3P1  C12   O11  C10   110.88  3.000
 3P1  H12   C12  C28   109.57  3.000
 3P1  H12   C12  C13   109.30  3.000
 3P1  C28   C12  C13   112.67  3.000
 3P1  H12   C12  O11   110.32  3.000
 3P1  C28   C12  O11   109.91  3.000
 3P1  C13   C12  O11   105.00  3.000
 3P1  H13   C13  O30   112.02  3.000
 3P1  H13   C13  C14   108.86  3.000
 3P1  O30   C13  C14   113.03  3.000
 3P1  H13   C13  C12   109.83  3.000
 3P1  C14   C13  C12   102.46  3.000
 3P1  O30   C13  C12   110.20  3.000
 3P1  H14   C14  O31   111.08  3.000
 3P1  H14   C14  C13   112.40  3.000
 3P1  O31   C14  C13   110.67  3.000
 3P1  H14   C14  C10   111.82  3.000
 3P1  O31   C14  C10   107.49  3.000
 3P1  C13   C14  C10   103.01  3.000
 3P1  HN1A  N15  HN15  116.32  3.000
 3P1  HN1A  N15  C4    119.01  3.000
 3P1  HN15  N15  C4    118.35  3.000
 3P1  HN16  N16  C17   115.69  3.000
 3P1  HN16  N16  C6    118.63  3.000
 3P1  C17   N16  C6    121.82  3.000
 3P1  H17A  C17  H17   107.85  3.000
 3P1  H17A  C17  C18   108.70  3.000
 3P1  H17   C17  C18   110.67  3.000
 3P1  H17A  C17  N16   108.37  3.000
 3P1  H17   C17  N16   108.37  3.000
 3P1  C18   C17  N16   112.75  3.000
 3P1  C21   C18  N19   122.87  3.000
 3P1  N19   C18  C17   117.01  3.000
 3P1  C21   C18  C17   120.12  3.000
 3P1  C23   N19  C18   119.09  3.000
 3P1  H20   C20  C22   119.68  3.000
 3P1  H20   C20  C21   120.80  3.000
 3P1  C22   C20  C21   119.52  3.000
 3P1  H21   C21  C20   121.16  3.000
 3P1  H21   C21  C18   119.84  3.000
 3P1  C20   C21  C18   118.99  3.000
 3P1  C27   C22  C23   119.55  3.000
 3P1  C23   C22  C20   117.32  3.000
 3P1  C27   C22  C20   123.13  3.000
 3P1  C24   C23  C22   119.02  3.000
 3P1  C24   C23  N19   118.76  3.000
 3P1  C22   C23  N19   122.22  3.000
 3P1  H24   C24  C25   121.09  3.000
 3P1  H24   C24  C23   118.63  3.000
 3P1  C25   C24  C23   120.29  3.000
 3P1  H25   C25  C26   119.47  3.000
 3P1  H25   C25  C24   119.89  3.000
 3P1  C26   C25  C24   120.64  3.000
 3P1  H26   C26  C27   120.14  3.000
 3P1  H26   C26  C25   119.63  3.000
 3P1  C27   C26  C25   120.22  3.000
 3P1  H27   C27  C26   120.60  3.000
 3P1  H27   C27  C22   119.12  3.000
 3P1  C26   C27  C22   120.27  3.000
 3P1  H28A  C28  H28   107.16  3.000
 3P1  H28A  C28  O29   112.09  3.000
 3P1  H28   C28  O29   111.89  3.000
 3P1  H28A  C28  C12   108.67  3.000
 3P1  H28   C28  C12   107.48  3.000
 3P1  O29   C28  C12   109.39  3.000
 3P1  HO29  O29  C28   108.21  3.000
 3P1  HO30  O30  C13   108.85  3.000
 3P1  HO31  O31  C14   107.16  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
 3P1  CONST_01  C9    N3   C2   N1     0.00   0.0  0
 3P1  CONST_02  N7    C8   C4   N1   180.00   0.0  0
 3P1  CONST_03  C9    C8   C4   N1     0.00   0.0  0
 3P1  CONST_04  C8    C4   N1   C2     0.00   0.0  0
 3P1  CONST_05  N5    C9   N3   C2   180.00   0.0  0
 3P1  CONST_06  C8    C9   N3   C2     0.00   0.0  0
 3P1  CONST_07  C4    N1   C2   N3     0.00   0.0  0
 3P1  CONST_08  C6    N5   C9   N3   180.00   0.0  0
 3P1  CONST_09  C4    C8   C9   N3     0.00   0.0  0
 3P1  CONST_10  N7    C8   C9   N3   180.00   0.0  0
 3P1  CONST_11  C6    N7   C8   C4   180.00   0.0  0
 3P1  CONST_12  N5    C9   C8   C4   180.00   0.0  0
 3P1  CONST_13  C8    N7   C6   N5     0.00   0.0  0
 3P1  CONST_14  N7    C8   C9   N5     0.00   0.0  0
 3P1  CONST_15  C8    C9   N5   C6     0.00   0.0  0
 3P1  CONST_16  C9    C8   N7   C6     0.00   0.0  0
 3P1  CONST_17  C9    N5   C6   N7     0.00   0.0  0
 3P1  CONST_18  C22   C20  C21  C18    0.00   0.0  0
 3P1  CONST_19  C22   C23  N19  C18    0.00   0.0  0
 3P1  CONST_20  C24   C23  N19  C18  180.00   0.0  0
 3P1  CONST_21  C20   C21  C18  N19    0.00   0.0  0
 3P1  CONST_22  C20   C22  C23  N19    0.00   0.0  0
 3P1  CONST_23  C27   C22  C23  N19  180.00   0.0  0
 3P1  CONST_24  C25   C24  C23  N19  180.00   0.0  0
 3P1  CONST_25  C26   C27  C22  C20  180.00   0.0  0
 3P1  CONST_26  C24   C23  C22  C20  180.00   0.0  0
 3P1  CONST_27  C23   N19  C18  C21    0.00   0.0  0
 3P1  CONST_28  C27   C22  C20  C21  180.00   0.0  0
 3P1  CONST_29  C23   C22  C20  C21    0.00   0.0  0
 3P1  CONST_30  C25   C26  C27  C22    0.00   0.0  0
 3P1  CONST_31  C25   C24  C23  C22    0.00   0.0  0
 3P1  CONST_32  C26   C27  C22  C23    0.00   0.0  0
 3P1  CONST_33  C26   C25  C24  C23    0.00   0.0  0
 3P1  CONST_34  C27   C22  C23  C24    0.00   0.0  0
 3P1  CONST_35  C27   C26  C25  C24    0.00   0.0  0
 3P1  CONST_36  C10   N5   C9   N3     0.00   0.0  0
 3P1  CONST_37  C10   N5   C6   N7   180.00   0.0  0
 3P1  CONST_38  C10   N5   C9   C8   180.00   0.0  0
 3P1  CONST_39  N15   C4   N1   C2   180.00   0.0  0
 3P1  CONST_40  N15   C4   C8   N7     0.00   0.0  0
 3P1  CONST_41  N16   C6   N7   C8   180.00   0.0  0
 3P1  CONST_42  N16   C6   N5   C9   180.00   0.0  0
 3P1  CONST_43  N15   C4   C8   C9   180.00   0.0  0
 3P1  CONST_44  N16   C6   N5   C10    0.00   0.0  0
 3P1  CONST_45  C20   C21  C18  C17  180.00   0.0  0
 3P1  CONST_46  C23   N19  C18  C17  180.00   0.0  0
 3P1  CONST_47  H2    C2   N1   C4   180.00   0.0  0
 3P1  CONST_48  H20   C20  C21  C18  180.00   0.0  0
 3P1  CONST_49  H21   C21  C18  N19  180.00   0.0  0
 3P1  CONST_50  H24   C24  C23  N19    0.00   0.0  0
 3P1  CONST_51  H27   C27  C22  C20    0.00   0.0  0
 3P1  CONST_52  H26   C26  C27  C22  180.00   0.0  0
 3P1  CONST_53  H25   C25  C24  C23  180.00   0.0  0
 3P1  CONST_54  C17   N16  C6   N5   180.00   0.0  0
 3P1  CONST_55  C17   N16  C6   N7     0.00   0.0  0
 3P1  CONST_57  HN1A  N15  C4   N1   180.00   0.0  0
 3P1  Var_01    C18   C17  N16  C6   -92.12  30.0  3
 3P1  Var_02    C21   C18  C17  N16   67.23  30.0  2

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
 3P1  chir_01  C10  N5   C14  O11  negativ
 3P1  chir_02  C12  O11  C13  C28  negativ
 3P1  chir_03  C13  O30  C12  C14  positiv
 3P1  chir_04  C14  O31  C13  C10  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
 3P1  plan-1  N1    0.020
 3P1  plan-1  C2    0.020
 3P1  plan-1  N3    0.020
 3P1  plan-1  C4    0.020
 3P1  plan-1  N5    0.020
 3P1  plan-1  C6    0.020
 3P1  plan-1  N7    0.020
 3P1  plan-1  C8    0.020
 3P1  plan-1  C9    0.020
 3P1  plan-1  C10   0.020
 3P1  plan-1  N15   0.020
 3P1  plan-1  N16   0.020
 3P1  plan-1  H2    0.020
 3P1  plan-2  C17   0.020
 3P1  plan-2  C18   0.020
 3P1  plan-2  N19   0.020
 3P1  plan-2  C20   0.020
 3P1  plan-2  C21   0.020
 3P1  plan-2  C22   0.020
 3P1  plan-2  C23   0.020
 3P1  plan-2  C24   0.020
 3P1  plan-2  C25   0.020
 3P1  plan-2  C26   0.020
 3P1  plan-2  C27   0.020
 3P1  plan-2  H20   0.020
 3P1  plan-2  H21   0.020
 3P1  plan-2  H24   0.020
 3P1  plan-2  H25   0.020
 3P1  plan-2  H26   0.020
 3P1  plan-2  H27   0.020
 3P1  plan-3  C4    0.020
 3P1  plan-3  N15   0.020
 3P1  plan-3  HN15  0.020
 3P1  plan-3  HN1A  0.020
 3P1  plan-4  C6    0.020
 3P1  plan-4  N16   0.020
 3P1  plan-4  C17   0.020
 3P1  plan-4  HN16  0.020

