# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 03:59:08 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(=O)N[P](O)(O)=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
 GN3  GN3  '[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid'  ligand  54  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GN3
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
 GN3  O15  O  O     0  -0.472  79.7130  -61.5857  100.9102
 GN3  C9   C  CR6   0   0.505  80.3281  -61.6580  101.9602
 GN3  N5   N  NR16  0  -0.729  81.2997  -62.6489  102.1511
 GN3  C    C  CR6   0   0.694  82.0538  -62.8350  103.2751
 GN3  N    N  NH2   0  -0.834  82.9117  -63.8594  103.2691
 GN3  C2   C  CR56  0  -0.086  80.2161  -60.8364  103.1192
 GN3  N2   N  N     0  -0.440  79.3997  -59.7689  103.3832
 GN3  C3   C  CR15  0   0.084  79.7150  -59.4002  104.5868
 GN3  N3   N  NR5   0  -0.539  80.7139  -60.1695  105.1346
 GN3  C1   C  CR56  0   0.506  81.0337  -61.1046  104.2007
 GN3  N1   N  N     0  -0.519  81.9515  -62.0717  104.3370
 GN3  C4   C  CH1   0   0.160  81.3018  -60.0861  106.4673
 GN3  C8   C  CH1   0  -0.050  82.7797  -59.6766  106.4111
 GN3  O14  O  OH1   0  -0.653  83.4337  -60.0328  107.5917
 GN3  C7   C  CH1   0   0.001  82.6376  -58.1596  106.3877
 GN3  O8   O  O2    0  -0.587  83.8344  -57.5400  106.8013
 GN3  P2   P  P     0   1.447  84.2626  -56.0648  106.3230
 GN3  O10  O  O     0  -0.698  83.4937  -55.5446  105.1754
 GN3  N4   N  NH1   0  -0.962  84.1418  -55.0951  107.6700
 GN3  P3   P  P     0   1.427  83.4941  -53.5369  107.6458
 GN3  O13  O  O     0  -0.699  82.0863  -53.4683  107.2001
 GN3  O12  O  OH1   0  -0.734  84.5429  -52.7473  106.7340
 GN3  O11  O  OH1   0  -0.776  83.8122  -53.0135  109.1049
 GN3  O9   O  OH1   0  -0.717  85.8400  -56.2228  106.1781
 GN3  C5   C  CH1   0  -0.038  81.4630  -57.9354  107.3465
 GN3  O    O  O2    0  -0.485  80.6484  -59.0931  107.1973
 GN3  C6   C  CH2   0  -0.208  80.6636  -56.6946  107.0092
 GN3  O1   O  O2    0  -0.567  79.4410  -56.5920  107.7467
 GN3  P    P  P     0   1.476  79.3508  -56.5284  109.3250
 GN3  O3   O  OH1   0  -0.702  77.9470  -55.8196  109.4879
 GN3  O2   O  O     0  -0.677  79.5955  -57.7496  110.1049
 GN3  O4   O  O2    0  -0.692  80.4159  -55.3353  109.6456
 GN3  P1   P  P     0   1.524  81.4349  -55.1414  110.8709
 GN3  O7   O  O     0  -0.698  82.0263  -53.7821  110.8235
 GN3  O6   O  OH1   0  -0.719  82.4014  -56.3695  110.6527
 GN3  O5   O  OH1   0  -0.717  80.6416  -55.4906  112.1926
 GN3  H1   H  HNR6  0   0.426  81.4410  -63.2777  101.3705
 GN3  H2   H  HNH2  0   0.416  83.5345  -63.9722  104.0500
 GN3  H3   H  HNH2  0   0.418  83.1054  -64.3911  102.4385
 GN3  H4   H  HCR5  0   0.292  79.2488  -58.5956  105.1316
 GN3  H5   H  HCH1  0   0.296  81.1672  -61.0562  106.9532
 GN3  H6   H  HCH1  0   0.284  83.2835  -60.0613  105.5190
 GN3  H7   H  HOH1  0   0.467  83.6325  -60.9742  107.5631
 GN3  H8   H  HCH1  0   0.280  82.3701  -57.8428  105.3739
 GN3  H9   H  HNH1  0   0.439  84.6897  -55.3479  108.4849
 GN3  H10  H  HOH1  0   0.497  84.1889  -51.9342  106.3489
 GN3  H11  H  HOH1  0   0.501  83.1285  -53.2587  109.7900
 GN3  H12  H  HOH1  0   0.503  86.1224  -56.8584  105.5050
 GN3  H13  H  HCH1  0   0.266  81.8396  -57.8887  108.3744
 GN3  H14  H  HCH2  0   0.276  81.2653  -55.7977  107.1675
 GN3  H15  H  HCH2  0   0.263  80.3616  -56.7068  105.9620
 GN3  H16  H  HOH1  0   0.514  77.3955  -56.1939  110.1891
 GN3  H17  H  HOH1  0   0.517  83.1611  -56.4166  111.2518
 GN3  H18  H  HOH1  0   0.514  80.2247  -54.7381  112.6367

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
 GN3  O15  C9   double    1.219  0.020  1.219
 GN3  N5   C9   single    1.401  0.020  1.401
 GN3  N5   C    single    1.366  0.020  1.366
 GN3  C9   C2   single    1.425  0.020  1.425
 GN3  N    C    single    1.336  0.020  1.336
 GN3  C    N1   double    1.312  0.020  1.312
 GN3  C2   N2   aromatic  1.370  0.020  1.370
 GN3  C2   C1   aromatic  1.382  0.020  1.382
 GN3  N2   C3   aromatic  1.298  0.020  1.298
 GN3  N1   C1   single    1.340  0.020  1.340
 GN3  C1   N3   aromatic  1.360  0.020  1.360
 GN3  O10  P2   double    1.476  0.020  1.476
 GN3  C3   N3   aromatic  1.375  0.020  1.375
 GN3  N3   C4   single    1.459  0.020  1.459
 GN3  O13  P3   double    1.478  0.020  1.478
 GN3  P2   O9   single    1.592  0.020  1.592
 GN3  P2   O8   single    1.609  0.020  1.609
 GN3  P2   N4   single    1.664  0.020  1.664
 GN3  O12  P3   single    1.598  0.020  1.598
 GN3  C7   C8   single    1.524  0.020  1.524
 GN3  C7   O8   single    1.410  0.020  1.410
 GN3  C7   C5   single    1.533  0.020  1.533
 GN3  C8   C4   single    1.535  0.020  1.535
 GN3  C8   O14  single    1.396  0.020  1.396
 GN3  C4   O    single    1.395  0.020  1.395
 GN3  P3   N4   single    1.688  0.020  1.688
 GN3  P3   O11  single    1.582  0.020  1.582
 GN3  C6   C5   single    1.514  0.020  1.514
 GN3  C6   O1   single    1.431  0.020  1.431
 GN3  O    C5   single    1.423  0.020  1.423
 GN3  O1   P    single    1.582  0.020  1.582
 GN3  P    O4   single    1.631  0.020  1.631
 GN3  P    O2   double    1.469  0.020  1.469
 GN3  P    O3   single    1.581  0.020  1.581
 GN3  O4   P1   single    1.605  0.020  1.605
 GN3  O7   P1   double    1.483  0.020  1.483
 GN3  P1   O6   single    1.578  0.020  1.578
 GN3  P1   O5   single    1.581  0.020  1.581
 GN3  N5   H1   single    0.860  0.020  1.020
 GN3  N    H2   single    0.860  0.020  1.020
 GN3  N    H3   single    0.860  0.020  1.020
 GN3  C3   H4   single    0.930  0.020  1.080
 GN3  C4   H5   single    0.970  0.020  1.090
 GN3  C8   H6   single    0.970  0.020  1.090
 GN3  O14  H7   single    0.850  0.020  0.980
 GN3  C7   H8   single    0.970  0.020  1.090
 GN3  N4   H9   single    0.860  0.020  1.020
 GN3  O12  H10  single    0.850  0.020  0.980
 GN3  O11  H11  single    0.850  0.020  0.980
 GN3  O9   H12  single    0.850  0.020  0.980
 GN3  C5   H13  single    0.970  0.020  1.090
 GN3  C6   H14  single    0.970  0.020  1.090
 GN3  C6   H15  single    0.970  0.020  1.090
 GN3  O3   H16  single    0.850  0.020  0.980
 GN3  O6   H17  single    0.850  0.020  0.980
 GN3  O5   H18  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
 GN3  C2   C9   N5   110.58  3.000
 GN3  C2   C9   O15  128.81  3.000
 GN3  N5   C9   O15  120.61  3.000
 GN3  H1   N5   C    118.21  3.000
 GN3  H1   N5   C9   115.54  3.000
 GN3  C    N5   C9   126.25  3.000
 GN3  N1   C    N    119.99  3.000
 GN3  N1   C    N5   122.93  3.000
 GN3  N    C    N5   117.07  3.000
 GN3  H3   N    H2   117.60  3.000
 GN3  H3   N    C    122.21  3.000
 GN3  H2   N    C    118.71  3.000
 GN3  C1   C2   N2   110.67  3.000
 GN3  C1   C2   C9   118.56  3.000
 GN3  N2   C2   C9   130.77  3.000
 GN3  C3   N2   C2   104.80  3.000
 GN3  H4   C3   N3   122.05  3.000
 GN3  H4   C3   N2   125.16  3.000
 GN3  N3   C3   N2   112.77  3.000
 GN3  C4   N3   C1   124.88  3.000
 GN3  C4   N3   C3   128.67  3.000
 GN3  C1   N3   C3   106.39  3.000
 GN3  N1   C1   N3   125.98  3.000
 GN3  N3   C1   C2   105.36  3.000
 GN3  N1   C1   C2   128.66  3.000
 GN3  C1   N1   C    113.02  3.000
 GN3  H5   C4   O    109.96  3.000
 GN3  H5   C4   C8   111.82  3.000
 GN3  O    C4   C8   106.28  3.000
 GN3  H5   C4   N3   107.80  3.000
 GN3  O    C4   N3   109.26  3.000
 GN3  C8   C4   N3   111.71  3.000
 GN3  H6   C8   C7   112.36  3.000
 GN3  H6   C8   O14  112.59  3.000
 GN3  C7   C8   O14  108.10  3.000
 GN3  H6   C8   C4   112.30  3.000
 GN3  O14  C8   C4   110.62  3.000
 GN3  C7   C8   C4   100.16  3.000
 GN3  H7   O14  C8   108.73  3.000
 GN3  H8   C7   C5   110.46  3.000
 GN3  H8   C7   O8   110.60  3.000
 GN3  C5   C7   O8   113.75  3.000
 GN3  H8   C7   C8   108.96  3.000
 GN3  C5   C7   C8   101.98  3.000
 GN3  O8   C7   C8   110.73  3.000
 GN3  P2   O8   C7   122.80  3.000
 GN3  O9   P2   N4   101.74  3.000
 GN3  N4   P2   O10  112.72  3.000
 GN3  O9   P2   O10  118.71  3.000
 GN3  N4   P2   O8   105.92  3.000
 GN3  O9   P2   O8   101.52  3.000
 GN3  O10  P2   O8   114.56  3.000
 GN3  H9   N4   P3   116.68  3.000
 GN3  H9   N4   P2   117.78  3.000
 GN3  P3   N4   P2   123.66  3.000
 GN3  O11  P3   O12  103.34  3.000
 GN3  O11  P3   O13  117.01  3.000
 GN3  O12  P3   O13  115.46  3.000
 GN3  O11  P3   N4   102.42  3.000
 GN3  O12  P3   N4   102.26  3.000
 GN3  O13  P3   N4   114.37  3.000
 GN3  H10  O12  P3   113.73  3.000
 GN3  H11  O11  P3   114.44  3.000
 GN3  H12  O9   P2   114.69  3.000
 GN3  H13  C5   C6   110.83  3.000
 GN3  H13  C5   O    109.25  3.000
 GN3  C6   C5   O    109.94  3.000
 GN3  H13  C5   C7   109.25  3.000
 GN3  O    C5   C7   104.72  3.000
 GN3  C6   C5   C7   112.65  3.000
 GN3  C5   O    C4   111.45  3.000
 GN3  H15  C6   H14  107.54  3.000
 GN3  H15  C6   O1   105.02  3.000
 GN3  H14  C6   O1   109.70  3.000
 GN3  H15  C6   C5   110.56  3.000
 GN3  H14  C6   C5   110.49  3.000
 GN3  O1   C6   C5   113.26  3.000
 GN3  P    O1   C6   124.44  3.000
 GN3  O4   P    O2   113.26  3.000
 GN3  O2   P    O3   117.76  3.000
 GN3  O4   P    O3   103.39  3.000
 GN3  O3   P    O1    99.87  3.000
 GN3  O2   P    O1   119.12  3.000
 GN3  O4   P    O1   100.85  3.000
 GN3  H16  O3   P    114.04  3.000
 GN3  P1   O4   P    130.75  3.000
 GN3  O5   P1   O6   104.55  3.000
 GN3  O5   P1   O7   115.43  3.000
 GN3  O6   P1   O7   117.68  3.000
 GN3  O5   P1   O4   107.04  3.000
 GN3  O6   P1   O4   100.91  3.000
 GN3  O7   P1   O4   109.84  3.000
 GN3  H17  O6   P1   115.64  3.000
 GN3  H18  O5   P1   115.34  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
 GN3  CONST_01  N3   C3  N2  C2      0.00   0.0  0
 GN3  CONST_02  C3   N3  C1  C2      0.00   0.0  0
 GN3  CONST_03  N3   C1  C2  N2      0.00   0.0  0
 GN3  CONST_04  C1   N3  C3  N2      0.00   0.0  0
 GN3  CONST_05  C1   C2  N2  C3      0.00   0.0  0
 GN3  CONST_06  C4   N3  C1  C2    180.00   0.0  0
 GN3  CONST_07  C4   N3  C3  N2    180.00   0.0  0
 GN3  CONST_08  C4   N3  C1  N1      0.00   0.0  0
 GN3  CONST_09  N1   C   N5  C9      0.00   0.0  0
 GN3  CONST_10  C1   N1  C   N5      0.00   0.0  0
 GN3  CONST_11  C2   C9  N5  C       0.00   0.0  0
 GN3  CONST_12  C    N5  C9  O15   180.00   0.0  0
 GN3  CONST_13  N    C   N5  C9    180.00   0.0  0
 GN3  CONST_14  C1   N1  C   N     180.00   0.0  0
 GN3  CONST_15  H4   C3  N2  C2    180.00   0.0  0
 GN3  CONST_16  H1   N5  C9  C2    180.00   0.0  0
 GN3  CONST_17  H2   N   C   N5    180.00   0.0  0
 GN3  CONST_18  H3   N   C   N5      0.00   0.0  0
 GN3  Var_01    O10  P2  O8  C7    -14.36  30.0  2
 GN3  Var_02    P3   N4  P2  O8   -138.20  30.0  3
 GN3  Var_03    O13  P3  N4  P2     60.21  30.0  2
 GN3  Var_04    O4   P   O1  C6     50.94  30.0  3
 GN3  Var_05    O7   P1  O4  P    -170.55  30.0  3
 GN3  Var_06    H14  C6  O1  P     -64.28  30.0  1

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
 GN3  chir_01  C4  N3   C8  O   negativ
 GN3  chir_02  C8  O14  C7  C4  positiv
 GN3  chir_03  C7  O8   C5  C8  positiv
 GN3  chir_05  C5  C7   C6  O   negativ
 GN3  chir_06  P2  O9   O8  N4  both
 GN3  chir_07  P   O2   O4  O1  both

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
 GN3  plan-1  O15  0.020
 GN3  plan-1  C9   0.020
 GN3  plan-1  N5   0.020
 GN3  plan-1  C    0.020
 GN3  plan-1  N    0.020
 GN3  plan-1  C2   0.020
 GN3  plan-1  N2   0.020
 GN3  plan-1  C3   0.020
 GN3  plan-1  N3   0.020
 GN3  plan-1  C1   0.020
 GN3  plan-1  N1   0.020
 GN3  plan-1  C4   0.020
 GN3  plan-1  H1   0.020
 GN3  plan-1  H2   0.020
 GN3  plan-1  H3   0.020
 GN3  plan-1  H4   0.020

