# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 17:46:19 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 8ZB  8ZB  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol  ligand  37  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8ZB
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
 8ZB  C24  C  CH3   0  -0.664   5.1925  -2.5529  -0.2781
 8ZB  C28  C  CH2   0  -0.425   4.2996  -1.4389  -0.8059
 8ZB  C31  C  CH2   0  -0.442   3.5818  -0.6961   0.3151
 8ZB  C36  C  CH1   0   0.048   2.7894   0.5043  -0.1530
 8ZB  C38  C  CH1   0   0.173   0.5864   0.8076  -0.8601
 8ZB  C39  C  CH1   0  -0.041   0.8918   1.8987   0.1643
 8ZB  C40  C  CH1   0  -0.032   2.0351   1.2449   0.9486
 8ZB  C49  C  CR15  0   0.102  -0.2652  -1.3786   0.1379
 8ZB  C50  C  CR56  0  -0.003  -2.3447  -1.0161   0.1798
 8ZB  C51  C  CR56  0   0.486  -1.7693   0.1277  -0.3506
 8ZB  C53  C  CR16  0   0.039  -3.7137   1.1159  -0.5901
 8ZB  C55  C  CR6   0   0.457  -3.7469  -1.0076   0.2989
 8ZB  N47  N  NR5   0  -0.534  -0.4289  -0.1196  -0.3697
 8ZB  N48  N  N     0  -0.452  -1.3857  -1.9471   0.4793
 8ZB  N52  N  N     0  -0.458  -2.4065   1.2266  -0.7513
 8ZB  N54  N  N     0  -0.474  -4.4025   0.0883  -0.0999
 8ZB  N57  N  NH2   0  -0.816  -4.4370  -2.0439   0.7778
 8ZB  O37  O  O2    0  -0.499   1.7713   0.1096  -1.0795
 8ZB  O41  O  OH1   0  -0.666   1.3400   3.0280  -0.5339
 8ZB  O42  O  OH1   0  -0.658   2.8834   2.1608   1.5821
 8ZB  H2   H  HCH3  0   0.218   5.9693  -2.1588   0.3798
 8ZB  H1   H  HCH3  0   0.219   4.6172  -3.2838   0.2933
 8ZB  H29  H  HCH3  0   0.230   5.6860  -3.0854  -1.0914
 8ZB  H28  H  HCH2  0   0.218   4.8996  -0.7292  -1.3835
 8ZB  H33  H  HCH2  0   0.224   3.5669  -1.8583  -1.4995
 8ZB  H35  H  HCH2  0   0.221   2.9314  -1.3849   0.8652
 8ZB  H31  H  HCH2  0   0.238   4.3185  -0.3301   1.0372
 8ZB  H61  H  HCH1  0   0.234   3.4688   1.2047  -0.6570
 8ZB  H62  H  HCH1  0   0.280   0.2058   1.2315  -1.7939
 8ZB  H44  H  HCH1  0   0.258   0.0215   2.1268   0.7919
 8ZB  H43  H  HCH1  0   0.241   1.6145   0.5246   1.6631
 8ZB  H58  H  HCR5  0   0.294   0.7072  -1.8363   0.2295
 8ZB  H56  H  HCR6  0   0.252  -4.3073   1.9714  -0.8947
 8ZB  H60  H  HNH2  0   0.411  -3.9674  -2.8507   1.1487
 8ZB  H59  H  HNH2  0   0.403  -5.4328  -1.9764   0.8982
 8ZB  H46  H  HOH1  0   0.451   1.9781   3.4866   0.0269
 8ZB  H45  H  HOH1  0   0.468   2.4961   2.4136   2.4264

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
 8ZB  N57  C55  single    1.334  0.020  1.334
 8ZB  C55  C50  aromatic  1.407  0.020  1.407
 8ZB  C55  N54  aromatic  1.338  0.020  1.338
 8ZB  N48  C50  aromatic  1.370  0.020  1.370
 8ZB  N48  C49  aromatic  1.302  0.020  1.302
 8ZB  C50  C51  aromatic  1.386  0.020  1.386
 8ZB  N54  C53  aromatic  1.331  0.020  1.331
 8ZB  C49  N47  aromatic  1.367  0.020  1.367
 8ZB  C51  N47  aromatic  1.363  0.020  1.363
 8ZB  C51  N52  aromatic  1.332  0.020  1.332
 8ZB  C53  N52  aromatic  1.322  0.020  1.322
 8ZB  N47  C38  single    1.460  0.020  1.460
 8ZB  C38  C39  single    1.527  0.020  1.527
 8ZB  C38  O37  single    1.393  0.020  1.393
 8ZB  C39  O41  single    1.401  0.020  1.401
 8ZB  C39  C40  single    1.533  0.020  1.533
 8ZB  O37  C36  single    1.432  0.020  1.432
 8ZB  C31  C36  single    1.513  0.020  1.513
 8ZB  C31  C28  single    1.524  0.020  1.524
 8ZB  C24  C28  single    1.522  0.020  1.522
 8ZB  C36  C40  single    1.527  0.020  1.527
 8ZB  C40  O42  single    1.400  0.020  1.400
 8ZB  C24  H2   single    0.970  0.020  1.090
 8ZB  C24  H1   single    0.970  0.020  1.090
 8ZB  C24  H29  single    0.970  0.020  1.090
 8ZB  C28  H28  single    0.970  0.020  1.090
 8ZB  C28  H33  single    0.970  0.020  1.090
 8ZB  C31  H35  single    0.970  0.020  1.090
 8ZB  C31  H31  single    0.970  0.020  1.090
 8ZB  C36  H61  single    0.970  0.020  1.090
 8ZB  C38  H62  single    0.970  0.020  1.090
 8ZB  C39  H44  single    0.970  0.020  1.090
 8ZB  C40  H43  single    0.970  0.020  1.090
 8ZB  C49  H58  single    0.930  0.020  1.080
 8ZB  C53  H56  single    0.930  0.020  1.080
 8ZB  N57  H60  single    0.860  0.020  1.020
 8ZB  N57  H59  single    0.860  0.020  1.020
 8ZB  O41  H46  single    0.850  0.020  0.980
 8ZB  O42  H45  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
 8ZB  H29  C24  H1   107.58  3.000
 8ZB  H29  C24  H2   107.69  3.000
 8ZB  H1   C24  H2   107.53  3.000
 8ZB  H29  C24  C28  111.37  3.000
 8ZB  H1   C24  C28  111.24  3.000
 8ZB  H2   C24  C28  111.24  3.000
 8ZB  H33  C28  H28  106.36  3.000
 8ZB  H33  C28  C31  109.76  3.000
 8ZB  H28  C28  C31  109.29  3.000
 8ZB  H33  C28  C24  109.43  3.000
 8ZB  H28  C28  C24  109.63  3.000
 8ZB  C31  C28  C24  112.20  3.000
 8ZB  H31  C31  H35  106.18  3.000
 8ZB  H31  C31  C36  106.94  3.000
 8ZB  H35  C31  C36  110.08  3.000
 8ZB  H31  C31  C28  109.34  3.000
 8ZB  H35  C31  C28  110.03  3.000
 8ZB  C36  C31  C28  113.94  3.000
 8ZB  H61  C36  O37  108.58  3.000
 8ZB  H61  C36  C40  109.10  3.000
 8ZB  O37  C36  C40  104.43  3.000
 8ZB  H61  C36  C31  108.91  3.000
 8ZB  C40  C36  C31  114.87  3.000
 8ZB  O37  C36  C31  110.73  3.000
 8ZB  H62  C38  O37  110.84  3.000
 8ZB  H62  C38  N47  106.92  3.000
 8ZB  O37  C38  N47  109.05  3.000
 8ZB  H62  C38  C39  111.42  3.000
 8ZB  O37  C38  C39  107.07  3.000
 8ZB  N47  C38  C39  111.56  3.000
 8ZB  H44  C39  O41  111.79  3.000
 8ZB  H44  C39  C40  112.81  3.000
 8ZB  O41  C39  C40  111.10  3.000
 8ZB  H44  C39  C38  111.94  3.000
 8ZB  C40  C39  C38  100.81  3.000
 8ZB  O41  C39  C38  107.79  3.000
 8ZB  H43  C40  O42  111.51  3.000
 8ZB  H43  C40  C39  109.08  3.000
 8ZB  O42  C40  C39  113.86  3.000
 8ZB  H43  C40  C36  109.90  3.000
 8ZB  O42  C40  C36  110.15  3.000
 8ZB  C39  C40  C36  101.90  3.000
 8ZB  H58  C49  N48  124.63  3.000
 8ZB  H58  C49  N47  122.01  3.000
 8ZB  N48  C49  N47  113.35  3.000
 8ZB  N48  C50  C55  133.10  3.000
 8ZB  N48  C50  C51  110.73  3.000
 8ZB  C55  C50  C51  116.17  3.000
 8ZB  N52  C51  N47  128.02  3.000
 8ZB  N52  C51  C50  126.68  3.000
 8ZB  N47  C51  C50  105.30  3.000
 8ZB  H56  C53  N54  115.41  3.000
 8ZB  H56  C53  N52  116.15  3.000
 8ZB  N54  C53  N52  128.43  3.000
 8ZB  N57  C55  N54  119.33  3.000
 8ZB  N54  C55  C50  117.91  3.000
 8ZB  N57  C55  C50  122.76  3.000
 8ZB  C51  N47  C49  106.24  3.000
 8ZB  C51  N47  C38  124.98  3.000
 8ZB  C49  N47  C38  128.78  3.000
 8ZB  C50  N48  C49  104.38  3.000
 8ZB  C53  N52  C51  111.55  3.000
 8ZB  C55  N54  C53  119.25  3.000
 8ZB  H59  N57  H60  118.22  3.000
 8ZB  H59  N57  C55  120.21  3.000
 8ZB  H60  N57  C55  120.98  3.000
 8ZB  C38  O37  C36  111.40  3.000
 8ZB  H46  O41  C39  107.75  3.000
 8ZB  H45  O42  C40  108.96  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
 8ZB  CONST_01  C55  C50  N48  C49  180.00   0.0  0
 8ZB  CONST_02  C51  C50  N48  C49    0.00   0.0  0
 8ZB  CONST_03  C50  C51  N47  C49    0.00   0.0  0
 8ZB  CONST_04  N52  C51  N47  C49  180.00   0.0  0
 8ZB  CONST_05  C53  N54  C55  C50    0.00   0.0  0
 8ZB  CONST_06  N47  C49  N48  C50    0.00   0.0  0
 8ZB  CONST_07  C53  N52  C51  C50    0.00   0.0  0
 8ZB  CONST_08  N54  C55  C50  C51    0.00   0.0  0
 8ZB  CONST_09  N48  C49  N47  C51    0.00   0.0  0
 8ZB  CONST_10  N54  C53  N52  C51    0.00   0.0  0
 8ZB  CONST_11  N47  C51  N52  C53  180.00   0.0  0
 8ZB  CONST_12  N47  C51  C50  C55  180.00   0.0  0
 8ZB  CONST_13  N52  C51  C50  C55    0.00   0.0  0
 8ZB  CONST_14  N52  C53  N54  C55    0.00   0.0  0
 8ZB  CONST_15  N48  C50  C51  N47    0.00   0.0  0
 8ZB  CONST_16  N54  C55  C50  N48  180.00   0.0  0
 8ZB  CONST_17  N52  C51  C50  N48  180.00   0.0  0
 8ZB  CONST_18  N48  C49  N47  C38  180.00   0.0  0
 8ZB  CONST_19  C50  C51  N47  C38  180.00   0.0  0
 8ZB  CONST_20  N52  C51  N47  C38    0.00   0.0  0
 8ZB  CONST_21  N57  C55  C50  C51  180.00   0.0  0
 8ZB  CONST_22  N57  C55  N54  C53  180.00   0.0  0
 8ZB  CONST_23  N57  C55  C50  N48    0.00   0.0  0
 8ZB  CONST_24  H58  C49  N47  C38    0.00   0.0  0
 8ZB  CONST_25  H56  C53  N52  C51  180.00   0.0  0
 8ZB  CONST_26  H60  N57  C55  C50    0.00   0.0  0
 8ZB  CONST_27  H59  N57  C55  C50  180.00   0.0  0
 8ZB  Var_01    C36  C31  C28  C24  174.35  30.0  2
 8ZB  Var_02    H2   C24  C28  C31  -60.81  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
 8ZB  chir_01  C36  O37  C31  C40  positiv
 8ZB  chir_02  C38  O37  N47  C39  negativ
 8ZB  chir_03  C39  O41  C38  C40  negativ
 8ZB  chir_04  C40  O42  C39  C36  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
 8ZB  plan-1  C38  0.020
 8ZB  plan-1  C49  0.020
 8ZB  plan-1  C50  0.020
 8ZB  plan-1  C51  0.020
 8ZB  plan-1  C53  0.020
 8ZB  plan-1  C55  0.020
 8ZB  plan-1  N47  0.020
 8ZB  plan-1  N48  0.020
 8ZB  plan-1  N52  0.020
 8ZB  plan-1  N54  0.020
 8ZB  plan-1  N57  0.020
 8ZB  plan-1  H58  0.020
 8ZB  plan-1  H56  0.020
 8ZB  plan-2  C55  0.020
 8ZB  plan-2  N57  0.020
 8ZB  plan-2  H60  0.020
 8ZB  plan-2  H59  0.020

