# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:41:36 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-azanyl-8-diazanyl-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
#
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
 DF8  DF8  (2~{R},3~{R},4~{S},5~{R})-2-(6-azanyl-8-diazanyl-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol  ligand  36  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DF8
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
 DF8  O3   O  OH1   0  -0.651   0.9091  -2.1132  -1.6387
 DF8  C4   C  CR56  0   0.490  -1.5873  -0.5703   0.3631
 DF8  C5   C  CH1   0   0.211   0.8868  -0.7717   0.3372
 DF8  C6   C  CH1   0  -0.031   3.1470  -0.2551   0.5396
 DF8  N1   N  NH1   0  -0.595   0.5187   2.1357  -0.3097
 DF8  C7   C  CH2   0  -0.190   3.6927   1.0445  -0.0281
 DF8  C8   C  CH1   0  -0.045   2.9990  -1.3250  -0.5450
 DF8  N2   N  N     0  -0.495  -1.7992   1.6102  -0.2520
 DF8  C9   C  CH1   0  -0.006   1.5615  -1.0621  -1.0031
 DF8  N3   N  NH2   0  -0.822  -4.7985   1.0127  -0.1900
 DF8  N4   N  N     0  -0.470  -4.1716  -1.1289   0.4232
 DF8  N    N  NH2   0  -0.648   0.2189   3.4421  -0.6841
 DF8  C    C  CR5   0   0.671  -0.5390   1.3035  -0.1173
 DF8  O    O  O2    0  -0.505   1.8374  -0.0716   1.0922
 DF8  C1   C  CR56  0   0.019  -2.4678   0.4451   0.0359
 DF8  C2   C  CR6   0   0.416  -3.8278   0.1177   0.0748
 DF8  C3   C  CR16  0   0.030  -3.2157  -2.0017   0.7187
 DF8  N5   N  N     0  -0.455  -1.9052  -1.8095   0.7127
 DF8  N6   N  NR5   0  -0.611  -0.3357  -0.0155   0.2537
 DF8  O1   O  OH1   0  -0.671   3.5083   2.0644   0.9236
 DF8  O2   O  OH1   0  -0.674   3.0556  -2.6279  -0.0353
 DF8  H1   H  HOH1  0   0.461   1.2271  -2.1687  -2.5449
 DF8  H2   H  HCH1  0   0.260   0.6099  -1.7172   0.8175
 DF8  H3   H  HCH1  0   0.258   3.8033  -0.5949   1.3475
 DF8  H4   H  HNH1  0   0.407   1.2956   2.0135   0.3296
 DF8  H5   H  HCH2  0   0.235   4.7531   0.8829  -0.2595
 DF8  H6   H  HCH2  0   0.205   3.1971   1.2902  -0.9767
 DF8  H7   H  HCH1  0   0.247   3.7254  -1.1729  -1.3547
 DF8  H8   H  HCH1  0   0.241   1.5550  -0.1520  -1.6164
 DF8  H9   H  HNH2  0   0.400  -4.5577   1.8697  -0.6579
 DF8  H10  H  HNH2  0   0.394  -5.7344   0.6729  -0.3341
 DF8  H11  H  HNH2  0   0.361   0.1769   4.0412   0.1320
 DF8  H12  H  HNH2  0   0.371   0.9717   3.7742  -1.2702
 DF8  H13  H  HCR6  0   0.246  -3.5531  -2.9944   0.9963
 DF8  H14  H  HOH1  0   0.473   3.8879   2.8765   0.5732
 DF8  H15  H  HOH1  0   0.472   3.9456  -2.7873   0.2957

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
 DF8  N   N1   single    1.392  0.020  1.392
 DF8  N3  C2   single    1.347  0.020  1.347
 DF8  N2  C1   aromatic  1.374  0.020  1.374
 DF8  N2  C    aromatic  1.304  0.020  1.304
 DF8  N1  C    single    1.360  0.020  1.360
 DF8  C2  C1   aromatic  1.399  0.020  1.399
 DF8  C2  N4   aromatic  1.339  0.020  1.339
 DF8  C1  C4   aromatic  1.383  0.020  1.383
 DF8  C   N6   aromatic  1.385  0.020  1.385
 DF8  C7  O1   single    1.407  0.020  1.407
 DF8  C7  C6   single    1.520  0.020  1.520
 DF8  O   C6   single    1.433  0.020  1.433
 DF8  O   C5   single    1.401  0.020  1.401
 DF8  N4  C3   aromatic  1.328  0.020  1.328
 DF8  C4  N6   aromatic  1.373  0.020  1.373
 DF8  C4  N5   aromatic  1.326  0.020  1.326
 DF8  N6  C5   single    1.440  0.020  1.440
 DF8  C6  C8   single    1.531  0.020  1.531
 DF8  C3  N5   aromatic  1.325  0.020  1.325
 DF8  C5  C9   single    1.528  0.020  1.528
 DF8  C8  C9   single    1.531  0.020  1.531
 DF8  C8  O2   single    1.400  0.020  1.400
 DF8  C9  O3   single    1.391  0.020  1.391
 DF8  O3  H1   single    0.850  0.020  0.980
 DF8  C5  H2   single    0.970  0.020  1.090
 DF8  C6  H3   single    0.970  0.020  1.090
 DF8  N1  H4   single    0.890  0.020  1.040
 DF8  C7  H5   single    0.970  0.020  1.090
 DF8  C7  H6   single    0.970  0.020  1.090
 DF8  C8  H7   single    0.970  0.020  1.090
 DF8  C9  H8   single    0.970  0.020  1.090
 DF8  N3  H9   single    0.890  0.020  1.040
 DF8  N3  H10  single    0.890  0.020  1.040
 DF8  N   H11  single    0.890  0.020  1.040
 DF8  N   H12  single    0.890  0.020  1.040
 DF8  C3  H13  single    0.930  0.020  1.080
 DF8  O1  H14  single    0.850  0.020  0.980
 DF8  O2  H15  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
 DF8  H1   O3  C9   108.60  3.000
 DF8  N6   C4  N5   128.09  3.000
 DF8  N5   C4  C1   126.56  3.000
 DF8  N6   C4  C1   105.35  3.000
 DF8  H2   C5  N6   105.30  3.000
 DF8  H2   C5  O    111.49  3.000
 DF8  N6   C5  O    110.17  3.000
 DF8  H2   C5  C9   109.38  3.000
 DF8  N6   C5  C9   115.07  3.000
 DF8  O    C5  C9   105.54  3.000
 DF8  H3   C6  O    107.63  3.000
 DF8  H3   C6  C8   111.34  3.000
 DF8  O    C6  C8   105.92  3.000
 DF8  H3   C6  C7   109.01  3.000
 DF8  C8   C6  C7   111.58  3.000
 DF8  O    C6  C7   111.26  3.000
 DF8  H4   N1  C    115.67  3.000
 DF8  H4   N1  N    116.62  3.000
 DF8  C    N1  N    116.43  3.000
 DF8  H6   C7  H5   106.67  3.000
 DF8  H6   C7  O1   111.28  3.000
 DF8  H5   C7  O1   112.09  3.000
 DF8  H6   C7  C6   110.61  3.000
 DF8  H5   C7  C6   107.45  3.000
 DF8  O1   C7  C6   108.68  3.000
 DF8  H7   C8  O2   111.75  3.000
 DF8  H7   C8  C9   112.12  3.000
 DF8  O2   C8  C9   107.85  3.000
 DF8  H7   C8  C6   111.20  3.000
 DF8  O2   C8  C6   112.87  3.000
 DF8  C9   C8  C6   100.53  3.000
 DF8  C1   N2  C    104.43  3.000
 DF8  H8   C9  C8   108.36  3.000
 DF8  H8   C9  C5   109.26  3.000
 DF8  C8   C9  C5   100.64  3.000
 DF8  H8   C9  O3   111.63  3.000
 DF8  C8   C9  O3   116.57  3.000
 DF8  C5   C9  O3   109.72  3.000
 DF8  H10  N3  H9   116.35  3.000
 DF8  H10  N3  C2   118.31  3.000
 DF8  H9   N3  C2   119.03  3.000
 DF8  C3   N4  C2   119.02  3.000
 DF8  H12  N   H11  107.68  3.000
 DF8  H12  N   N1   107.71  3.000
 DF8  H11  N   N1   110.32  3.000
 DF8  N6   C   N2   113.17  3.000
 DF8  N6   C   N1   120.44  3.000
 DF8  N2   C   N1   126.39  3.000
 DF8  C6   O   C5   110.37  3.000
 DF8  C2   C1  N2   132.62  3.000
 DF8  C2   C1  C4   116.13  3.000
 DF8  N2   C1  C4   111.24  3.000
 DF8  C1   C2  N4   118.32  3.000
 DF8  N4   C2  N3   119.00  3.000
 DF8  C1   C2  N3   122.66  3.000
 DF8  H13  C3  N5   116.21  3.000
 DF8  H13  C3  N4   115.77  3.000
 DF8  N5   C3  N4   128.02  3.000
 DF8  C3   N5  C4   111.96  3.000
 DF8  C    N6  C5   129.81  3.000
 DF8  C5   N6  C4   123.84  3.000
 DF8  C    N6  C4   105.80  3.000
 DF8  H14  O1  C7   108.28  3.000
 DF8  H15  O2  C8   108.45  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
 DF8  CONST_01  C    N2  C1  C4    0.00  0.0  0
 DF8  CONST_02  N4   C2  C1  C4    0.00  0.0  0
 DF8  CONST_03  N2   C   N6  C4    0.00  0.0  0
 DF8  CONST_04  N4   C3  N5  C4    0.00  0.0  0
 DF8  CONST_05  N4   C2  C1  N2  180.00  0.0  0
 DF8  CONST_06  N6   C4  C1  N2    0.00  0.0  0
 DF8  CONST_07  N5   C4  C1  N2  180.00  0.0  0
 DF8  CONST_08  C2   C1  N2  C   180.00  0.0  0
 DF8  CONST_09  C1   C4  N6  C     0.00  0.0  0
 DF8  CONST_10  N5   C4  N6  C   180.00  0.0  0
 DF8  CONST_11  N6   C   N2  C1    0.00  0.0  0
 DF8  CONST_12  C3   N4  C2  C1    0.00  0.0  0
 DF8  CONST_13  C3   N5  C4  C1    0.00  0.0  0
 DF8  CONST_14  N6   C4  C1  C2  180.00  0.0  0
 DF8  CONST_15  N5   C4  C1  C2    0.00  0.0  0
 DF8  CONST_16  N5   C3  N4  C2    0.00  0.0  0
 DF8  CONST_17  N6   C4  N5  C3  180.00  0.0  0
 DF8  CONST_18  N2   C   N6  C5  180.00  0.0  0
 DF8  CONST_19  C1   C4  N6  C5  180.00  0.0  0
 DF8  CONST_20  N5   C4  N6  C5    0.00  0.0  0
 DF8  CONST_21  N3   C2  C1  C4  180.00  0.0  0
 DF8  CONST_22  N1   C   N6  C4  180.00  0.0  0
 DF8  CONST_23  N1   C   N6  C5    0.00  0.0  0
 DF8  CONST_24  C1   N2  C   N1  180.00  0.0  0
 DF8  CONST_25  N3   C2  C1  N2    0.00  0.0  0
 DF8  CONST_26  C3   N4  C2  N3  180.00  0.0  0
 DF8  CONST_27  H13  C3  N5  C4  180.00  0.0  0
 DF8  CONST_28  N    N1  C   N2    0.00  0.0  0
 DF8  CONST_29  N6   C   N1  N   180.00  0.0  0
 DF8  CONST_31  H9   N3  C2  N4  180.00  0.0  0
 DF8  CONST_32  H10  N3  C2  N4    0.00  0.0  0

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
 DF8  chir_01  C5  O   N6  C9  negativ
 DF8  chir_02  C6  O   C7  C8  positiv
 DF8  chir_03  C8  O2  C6  C9  positiv
 DF8  chir_04  C9  O3  C8  C5  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
 DF8  plan-1  C4   0.020
 DF8  plan-1  C5   0.020
 DF8  plan-1  N1   0.020
 DF8  plan-1  N2   0.020
 DF8  plan-1  N3   0.020
 DF8  plan-1  N4   0.020
 DF8  plan-1  C    0.020
 DF8  plan-1  C1   0.020
 DF8  plan-1  C2   0.020
 DF8  plan-1  C3   0.020
 DF8  plan-1  N5   0.020
 DF8  plan-1  N6   0.020
 DF8  plan-1  H13  0.020
 DF8  plan-2  N1   0.020
 DF8  plan-2  N    0.020
 DF8  plan-2  C    0.020
 DF8  plan-2  H4   0.020
 DF8  plan-3  N3   0.020
 DF8  plan-3  C2   0.020
 DF8  plan-3  H9   0.020
 DF8  plan-3  H10  0.020

