# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 03:20:47 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S,3aR,4R,6R,6aR)-4-(6-amino-9H-purin-9-yl)-6-({[(R)-hydroxy(sulfooxy)phosphoryl]oxy}methyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[S](O)(=O)=O)[C@H]4O[P@@](O)(=O)O[C@@H]34
#
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
 GGZ  GGZ  '(2S,3aR,4R,6R,6aR)-4-(6-amino-9H-purin-9-yl)-6-({[(R)-hydroxy(sulfooxy)phosphoryl]oxy}methyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-oxide'  ligand  43  30  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GGZ
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
 GGZ  C2    C  CR16  0  -0.006  20.3859   -7.2087  20.1588
 GGZ  C4    C  CR56  0   0.439  19.5162   -9.0946  19.4375
 GGZ  C5    C  CR56  0   0.095  20.7366   -9.7213  19.2809
 GGZ  C6    C  CR6   0   0.338  21.8899   -8.9805  19.5788
 GGZ  C8    C  CR15  0   0.107  19.2997  -11.1201  18.6605
 GGZ  N1    N  N     0  -0.508  21.6329   -7.7295  20.0325
 GGZ  P1    P  P     0   1.428  14.0654   -9.3387  20.9182
 GGZ  O2'   O  O2    0  -0.533  15.3255  -10.2405  20.4666
 GGZ  O1P   O  O     0  -0.696  12.8282   -9.5718  20.1602
 GGZ  O3'   O  O2    0  -0.563  14.7923   -7.9110  20.7479
 GGZ  C3'   C  CH1   0  -0.073  16.0766   -8.0263  20.1592
 GGZ  C4'   C  CH1   0  -0.001  16.0544   -7.7957  18.6415
 GGZ  C5'   C  CH2   0  -0.349  16.5738   -6.4244  18.2830
 GGZ  O5'   O  O2    0  -0.432  16.5504   -6.2611  16.8658
 GGZ  P2    P  P     0   1.465  17.8169   -5.7197  16.0626
 GGZ  O4P   O  O     0  -0.742  17.4825   -5.5321  14.6426
 GGZ  O5P   O  OH1   0  -0.615  18.3002   -4.4051  16.8158
 GGZ  O6P   O  OC2   0  -0.620  18.9340   -6.8396  16.3839
 GGZ  S2    S  S     0   1.641  20.5914   -6.5445  16.5370
 GGZ  OS3   O  OS    0  -0.668  20.9959   -6.0807  15.2214
 GGZ  OS2   O  OS    0  -0.600  20.6327   -5.5132  17.5871
 GGZ  OS1   O  OS    0  -0.798  21.0726   -7.8508  16.9398
 GGZ  C2'   C  CH1   0   0.026  16.5192   -9.4902  20.3002
 GGZ  C1'   C  CH1   0   0.014  17.1626   -9.8334  18.9521
 GGZ  O4'   O  O2    0  -0.497  16.8864   -8.7902  18.0709
 GGZ  N9    N  NR5   0  -0.282  18.5958  -10.0091  19.0423
 GGZ  N7    N  N     0  -0.345  20.5845  -10.9852  18.7946
 GGZ  N6    N  NH2   0  -0.883  23.1189   -9.4173  19.4520
 GGZ  N3    N  N     0  -0.376  19.2991   -7.8506  19.8854
 GGZ  H2    H  HCR6  0   0.242  20.3481   -6.1972  20.5344
 GGZ  H8    H  HCR5  0   0.208  18.7950  -12.0010  18.2931
 GGZ  HO3P  H  HOH1  0   0.515  13.0991   -9.8286  22.7981
 GGZ  H3'   H  HCH1  0   0.323  16.7529   -7.3455  20.6751
 GGZ  H4'   H  HCH1  0   0.309  15.0308   -7.9148  18.2641
 GGZ  H5'1  H  HCH2  0   0.291  15.9257   -5.6681  18.7303
 GGZ  H5'2  H  HCH2  0   0.269  17.5773   -6.2966  18.6947
 GGZ  HO5P  H  HOH1  0   0.512  19.1453   -4.5044  17.3067
 GGZ  HOS2  H  H     0   0.564  22.4114   -7.1243  20.2647
 GGZ  H2'   H  HCH1  0   0.289  17.1873   -9.6698  21.1442
 GGZ  H1'   H  HCH1  0   0.361  16.7696  -10.7840  18.5810
 GGZ  HN61  H  HNH2  0   0.381  23.9213   -8.8513  19.6774
 GGZ  HN62  H  HNH2  0   0.394  23.2895  -10.3515  19.1155
 GGZ  O3P   O  OH1   0  -0.625  13.9560   -9.5008  22.4920

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
 GGZ  C2   N3    aromatic  1.291  0.020  1.291
 GGZ  C2   N1    aromatic  1.357  0.020  1.357
 GGZ  C2   H2    single    0.930  0.020  1.080
 GGZ  C4   N9    single    1.356  0.020  1.356
 GGZ  C4   C5    aromatic  1.381  0.020  1.381
 GGZ  C4   N3    aromatic  1.340  0.020  1.340
 GGZ  C5   N7    single    1.363  0.020  1.363
 GGZ  C5   C6    aromatic  1.403  0.020  1.403
 GGZ  C6   N6    single    1.310  0.020  1.310
 GGZ  C6   N1    aromatic  1.355  0.020  1.355
 GGZ  C8   N7    double    1.299  0.020  1.299
 GGZ  C8   N9    single    1.370  0.020  1.370
 GGZ  C8   H8    single    0.930  0.020  1.080
 GGZ  O3P  P1    single    1.586  0.020  1.586
 GGZ  O3P  HO3P  single    0.850  0.020  0.980
 GGZ  P1   O3'   single    1.611  0.020  1.611
 GGZ  P1   O1P   double    1.470  0.020  1.470
 GGZ  P1   O2'   single    1.614  0.020  1.614
 GGZ  O2'  C2'   single    1.420  0.020  1.420
 GGZ  O3'  C3'   single    1.417  0.020  1.417
 GGZ  C3'  C4'   single    1.535  0.020  1.535
 GGZ  C3'  C2'   single    1.536  0.020  1.536
 GGZ  C3'  H3'   single    0.970  0.020  1.090
 GGZ  C4'  O4'   single    1.417  0.020  1.417
 GGZ  C4'  C5'   single    1.510  0.020  1.510
 GGZ  C4'  H4'   single    0.970  0.020  1.090
 GGZ  C5'  O5'   single    1.427  0.020  1.427
 GGZ  C5'  H5'1  single    0.970  0.020  1.090
 GGZ  C5'  H5'2  single    0.970  0.020  1.090
 GGZ  O5'  P2    single    1.594  0.020  1.594
 GGZ  P2   O4P   double    1.471  0.020  1.471
 GGZ  P2   O6P   single    1.614  0.020  1.614
 GGZ  P2   O5P   single    1.590  0.020  1.590
 GGZ  O5P  HO5P  single    0.850  0.020  0.980
 GGZ  O6P  S2    single    1.690  0.020  1.690
 GGZ  S2   OS1   double    1.449  0.020  1.449
 GGZ  S2   OS3   double    1.452  0.020  1.452
 GGZ  S2   OS2   single    1.472  0.020  1.472
 GGZ  OS2  HOS2  single    0.850  0.020  0.980
 GGZ  C2'  C1'   single    1.533  0.020  1.533
 GGZ  C2'  H2'   single    0.970  0.020  1.090
 GGZ  C1'  O4'   single    1.393  0.020  1.393
 GGZ  C1'  N9    single    1.447  0.020  1.447
 GGZ  C1'  H1'   single    0.970  0.020  1.090
 GGZ  N6   HN61  single    0.860  0.020  1.020
 GGZ  N6   HN62  single    0.860  0.020  1.020

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
 GGZ  H2    C2   N3    120.65  3.000
 GGZ  H2    C2   N1    115.09  3.000
 GGZ  N3    C2   N1    124.24  3.000
 GGZ  N3    C4   N9    127.84  3.000
 GGZ  N3    C4   C5    127.05  3.000
 GGZ  N9    C4   C5    105.12  3.000
 GGZ  N7    C5   C6    131.10  3.000
 GGZ  C6    C5   C4    117.58  3.000
 GGZ  N7    C5   C4    111.27  3.000
 GGZ  N6    C6   N1    121.19  3.000
 GGZ  N1    C6   C5    113.74  3.000
 GGZ  N6    C6   C5    125.06  3.000
 GGZ  H8    C8   N7    125.62  3.000
 GGZ  H8    C8   N9    121.10  3.000
 GGZ  N7    C8   N9    113.29  3.000
 GGZ  C6    N1   C2    124.03  3.000
 GGZ  O3'   P1   O1P   117.77  3.000
 GGZ  O1P   P1   O2'   115.11  3.000
 GGZ  O3'   P1   O2'    96.51  3.000
 GGZ  O2'   P1   O3P   105.92  3.000
 GGZ  O1P   P1   O3P   115.95  3.000
 GGZ  O3'   P1   O3P   103.09  3.000
 GGZ  C2'   O2'  P1    113.20  3.000
 GGZ  C3'   O3'  P1    112.37  3.000
 GGZ  H3'   C3'  C2'   111.91  3.000
 GGZ  H3'   C3'  C4'   112.53  3.000
 GGZ  C2'   C3'  C4'   103.78  3.000
 GGZ  H3'   C3'  O3'   108.36  3.000
 GGZ  C2'   C3'  O3'   107.49  3.000
 GGZ  C4'   C3'  O3'   112.66  3.000
 GGZ  H4'   C4'  O4'   109.45  3.000
 GGZ  H4'   C4'  C5'   109.75  3.000
 GGZ  O4'   C4'  C5'   109.88  3.000
 GGZ  H4'   C4'  C3'   109.70  3.000
 GGZ  C5'   C4'  C3'   111.49  3.000
 GGZ  O4'   C4'  C3'   106.51  3.000
 GGZ  H5'2  C5'  H5'1  108.06  3.000
 GGZ  H5'2  C5'  O5'   112.09  3.000
 GGZ  H5'1  C5'  O5'   108.54  3.000
 GGZ  H5'2  C5'  C4'   109.44  3.000
 GGZ  H5'1  C5'  C4'   109.13  3.000
 GGZ  O5'   C5'  C4'   109.53  3.000
 GGZ  P2    O5'  C5'   121.75  3.000
 GGZ  O6P   P2   O5P   105.60  3.000
 GGZ  O5P   P2   O4P   114.89  3.000
 GGZ  O6P   P2   O4P   115.98  3.000
 GGZ  O5P   P2   O5'   106.47  3.000
 GGZ  O6P   P2   O5'   102.35  3.000
 GGZ  O4P   P2   O5'   110.43  3.000
 GGZ  HO5P  O5P  P2    114.49  3.000
 GGZ  S2    O6P  P2    125.13  3.000
 GGZ  OS1   S2   OS2   115.08  3.000
 GGZ  OS2   S2   OS3   114.49  3.000
 GGZ  OS1   S2   OS3   116.56  3.000
 GGZ  OS2   S2   O6P   102.38  3.000
 GGZ  OS3   S2   O6P   104.29  3.000
 GGZ  OS1   S2   O6P   101.15  3.000
 GGZ  HOS2  OS2  S2    103.36  3.000
 GGZ  H2'   C2'  C1'   112.73  3.000
 GGZ  H2'   C2'  C3'   113.85  3.000
 GGZ  C1'   C2'  C3'   104.69  3.000
 GGZ  H2'   C2'  O2'   109.71  3.000
 GGZ  C1'   C2'  O2'   109.74  3.000
 GGZ  C3'   C2'  O2'   105.79  3.000
 GGZ  H1'   C1'  N9    105.76  3.000
 GGZ  H1'   C1'  O4'   111.41  3.000
 GGZ  N9    C1'  O4'   109.07  3.000
 GGZ  H1'   C1'  C2'   110.01  3.000
 GGZ  N9    C1'  C2'   112.84  3.000
 GGZ  O4'   C1'  C2'   107.79  3.000
 GGZ  C1'   O4'  C4'   112.79  3.000
 GGZ  C1'   N9   C8    126.18  3.000
 GGZ  C1'   N9   C4    127.49  3.000
 GGZ  C8    N9   C4    106.22  3.000
 GGZ  C8    N7   C5    104.10  3.000
 GGZ  HN62  N6   HN61  117.43  3.000
 GGZ  HN62  N6   C6    120.02  3.000
 GGZ  HN61  N6   C6    122.55  3.000
 GGZ  C4    N3   C2    113.32  3.000
 GGZ  HO3P  O3P  P1    114.20  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
 GGZ  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 GGZ  CONST_02  C5    C6   N1   C2      0.00   0.0  0
 GGZ  CONST_03  N1    C6   C5   C4      0.00   0.0  0
 GGZ  CONST_04  N1    C2   N3   C4      0.00   0.0  0
 GGZ  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 GGZ  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 GGZ  CONST_07  N7    C8   N9   C4      0.00   0.0  0
 GGZ  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 GGZ  CONST_09  C8    N9   C4   C5      0.00   0.0  0
 GGZ  CONST_10  C1'   N9   C4   C5    180.00   0.0  0
 GGZ  CONST_11  N9    C8   N7   C5      0.00   0.0  0
 GGZ  CONST_12  N7    C8   N9   C1'   180.00   0.0  0
 GGZ  CONST_13  N7    C5   C4   N9      0.00   0.0  0
 GGZ  CONST_14  N6    C6   N1   C2    180.00   0.0  0
 GGZ  CONST_15  N6    C6   C5   C4    180.00   0.0  0
 GGZ  CONST_16  N6    C6   C5   N7      0.00   0.0  0
 GGZ  CONST_17  H2    C2   N3   C4    180.00   0.0  0
 GGZ  CONST_18  H8    C8   N9   C4    180.00   0.0  0
 GGZ  CONST_19  HN61  N6   C6   C5    180.00   0.0  0
 GGZ  CONST_20  HN62  N6   C6   C5      0.00   0.0  0
 GGZ  Var_01    O4P   P2   O5'  C5'  -174.81  30.0  3
 GGZ  Var_02    OS1   S2   O6P  P2    174.94  30.0  3
 GGZ  Var_03    H5'1  C5'  O5'  P2    109.97  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
 GGZ  chir_02  C3'  O3'  C4'  C2'  positiv
 GGZ  chir_03  C4'  O4'  C3'  C5'  negativ
 GGZ  chir_05  C2'  O2'  C3'  C1'  positiv
 GGZ  chir_06  C1'  O4'  N9   C2'  negativ
 GGZ  chir_07  P2   O4P  O6P  O5P  both
 GGZ  chir_08  P1   O1P  O3'  O3P  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
 GGZ  plan-1  C2    0.020
 GGZ  plan-1  C4    0.020
 GGZ  plan-1  C5    0.020
 GGZ  plan-1  C6    0.020
 GGZ  plan-1  C8    0.020
 GGZ  plan-1  N1    0.020
 GGZ  plan-1  C1'   0.020
 GGZ  plan-1  N9    0.020
 GGZ  plan-1  N7    0.020
 GGZ  plan-1  N6    0.020
 GGZ  plan-1  N3    0.020
 GGZ  plan-1  H2    0.020
 GGZ  plan-1  H8    0.020
 GGZ  plan-2  C6    0.020
 GGZ  plan-2  N6    0.020
 GGZ  plan-2  HN61  0.020
 GGZ  plan-2  HN62  0.020

