# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:48:35 2020
#   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  41  30  .  2021-08-10  2021-08-10  
;
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  C1     0   0.050   1.5363   1.9512  -2.9723
 GGZ  C4    C  CR5    0   0.501   2.1590   1.4692  -0.9187
 GGZ  C5    C  CR5    0   0.030   2.9979   2.5684  -0.8581
 GGZ  C6    C  C      0   0.465   3.0759   3.3572  -2.0172
 GGZ  C8    C  CR15   0   0.113   3.1493   1.6364   1.0237
 GGZ  N1    N  N      0  -0.474   2.2962   3.0359  -3.0517
 GGZ  P1    P  P      0   1.450  -0.8200  -2.9597   0.5290
 GGZ  O2'   O  O      0  -0.589  -0.4045  -1.4889   1.0339
 GGZ  O1P   O  O      0  -0.672  -0.5342  -4.0567   1.4666
 GGZ  O3'   O  O      0  -0.589   0.0017  -2.9222  -0.8514
 GGZ  C3'   C  CR15   0  -0.038   0.8833  -1.8074  -0.9339
 GGZ  C4'   C  CH1    0  -0.045   2.3146  -2.1619  -0.4978
 GGZ  C5'   C  CH2    0  -0.161   3.3429  -1.8519  -1.5678
 GGZ  O5'   O  O2     0  -0.615   4.6073  -2.2276  -1.0705
 GGZ  P2    P  P      0   1.359   5.9553  -1.7284  -1.8574
 GGZ  O4P   O  O      0  -0.778   7.0968  -2.3588  -1.1320
 GGZ  O5P   O  OP    -1  -0.792   5.7691  -1.8581  -3.3313
 GGZ  O6P   O  OC2    0  -0.749   5.9152  -0.1251  -1.4059
 GGZ  S2    S  S      0   1.594   6.0655   1.1492  -2.4335
 GGZ  OS3   O  OS     0  -0.721   4.8443   1.1634  -3.2367
 GGZ  OS2   O  OS    -1  -0.731   6.1965   2.2602  -1.4913
 GGZ  OS1   O  OS     0  -0.754   7.2871   0.8903  -3.2019
 GGZ  C2'   C  CR15   0  -0.029   0.4071  -0.7739   0.1085
 GGZ  C1'   C  CH1    0   0.139   1.6905  -0.3580   0.8246
 GGZ  O4'   O  O2     0  -0.466   2.5539  -1.4451   0.7080
 GGZ  N9    N  NR5    0  -0.542   2.2633   0.8690   0.3094
 GGZ  N7    N  N      0  -0.445   3.6042   2.6562   0.3678
 GGZ  N6    N  NH2    0  -0.814   3.8589   4.4438  -2.0985
 GGZ  N3    N  N      0  -0.477   1.4122   1.1106  -1.9594
 GGZ  H2    H  H      0   0.249   0.9378   1.7299  -3.8498
 GGZ  H8    H  HCR5   0   0.297   3.4054   1.3821   2.0422
 GGZ  HO3P  H  HOH1   0   0.507  -2.9219  -3.4856   0.4723
 GGZ  H3'   H  HCR5   0   0.308   0.8352  -1.4146  -1.9477
 GGZ  H4'   H  HCH1   0   0.273   2.3808  -3.2271  -0.2573
 GGZ  H5'1  H  HCH2   0   0.238   3.3153  -0.7956  -1.8504
 GGZ  H5'2  H  HCH2   0   0.223   3.0791  -2.4300  -2.4609
 GGZ  H2'   H  HCR5   0   0.309  -0.1643   0.0529  -0.3089
 GGZ  H1'   H  HCH1   0   0.303   1.5038  -0.1847   1.8855
 GGZ  HN61  H  HNH2   0   0.400   4.6482   4.4940  -1.4759
 GGZ  HN62  H  HNH2   0   0.391   4.0055   4.8394  -3.0130
 GGZ  O3P   O  OH1    0  -0.716  -2.3332  -2.8370   0.0632

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  1.322  0.020  1.322
 GGZ  C2   N1    aromatic  1.327  0.020  1.327
 GGZ  C2   H2    single    0.930  0.020  1.080
 GGZ  C4   N9    single    1.371  0.020  1.371
 GGZ  C4   C5    aromatic  1.384  0.020  1.384
 GGZ  C4   N3    aromatic  1.330  0.020  1.330
 GGZ  C5   N7    single    1.370  0.020  1.370
 GGZ  C5   C6    aromatic  1.404  0.020  1.404
 GGZ  C6   N6    single    1.342  0.020  1.342
 GGZ  C6   N1    aromatic  1.335  0.020  1.335
 GGZ  C8   N7    double    1.295  0.020  1.295
 GGZ  C8   N9    single    1.373  0.020  1.373
 GGZ  C8   H8    single    0.930  0.020  1.080
 GGZ  O3P  P1    single    1.588  0.020  1.588
 GGZ  O3P  HO3P  single    0.850  0.020  0.980
 GGZ  P1   O3'   single    1.607  0.020  1.607
 GGZ  P1   O1P   double    1.471  0.020  1.471
 GGZ  P1   O2'   single    1.610  0.020  1.610
 GGZ  O2'  C2'   single    1.423  0.020  1.423
 GGZ  O3'  C3'   single    1.424  0.020  1.424
 GGZ  C3'  C4'   single    1.538  0.020  1.538
 GGZ  C3'  C2'   single    1.543  0.020  1.543
 GGZ  C3'  H3'   single    0.970  0.020  1.090
 GGZ  C4'  O4'   single    1.423  0.020  1.423
 GGZ  C4'  C5'   single    1.516  0.020  1.516
 GGZ  C4'  H4'   single    0.970  0.020  1.090
 GGZ  C5'  O5'   single    1.410  0.020  1.410
 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    1.639  0.020  1.639
 GGZ  P2   O4P   deloc     1.492  0.020  1.492
 GGZ  P2   O6P   single    1.666  0.020  1.666
 GGZ  P2   O5P   deloc     1.491  0.020  1.491
 GGZ  O6P  S2    single    1.644  0.020  1.644
 GGZ  S2   OS1   deloc     1.466  0.020  1.466
 GGZ  S2   OS3   deloc     1.462  0.020  1.462
 GGZ  S2   OS2   deloc     1.463  0.020  1.463
 GGZ  C2'  C1'   single    1.527  0.020  1.527
 GGZ  C2'  H2'   single    0.970  0.020  1.090
 GGZ  C1'  O4'   single    1.393  0.020  1.393
 GGZ  C1'  N9    single    1.449  0.020  1.449
 GGZ  C1'  H1'   single    0.970  0.020  1.090
 GGZ  N6   HN61  single    0.890  0.020  1.040
 GGZ  N6   HN62  single    0.890  0.020  1.040

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    115.99  3.000
 GGZ  H2    C2   N1    115.74  3.000
 GGZ  N3    C2   N1    128.27  3.000
 GGZ  N3    C4   N9    128.73  3.000
 GGZ  N3    C4   C5    126.06  3.000
 GGZ  N9    C4   C5    105.21  3.000
 GGZ  N7    C5   C6    132.67  3.000
 GGZ  C6    C5   C4    116.34  3.000
 GGZ  N7    C5   C4    110.99  3.000
 GGZ  N6    C6   N1    119.27  3.000
 GGZ  N1    C6   C5    118.17  3.000
 GGZ  N6    C6   C5    122.50  3.000
 GGZ  H8    C8   N7    125.41  3.000
 GGZ  H8    C8   N9    120.79  3.000
 GGZ  N7    C8   N9    113.79  3.000
 GGZ  C6    N1   C2    119.02  3.000
 GGZ  O3'   P1   O1P   117.75  3.000
 GGZ  O1P   P1   O2'   115.55  3.000
 GGZ  O3'   P1   O2'    96.67  3.000
 GGZ  O2'   P1   O3P   105.51  3.000
 GGZ  O1P   P1   O3P   115.45  3.000
 GGZ  O3'   P1   O3P   103.50  3.000
 GGZ  C2'   O2'  P1    113.72  3.000
 GGZ  C3'   O3'  P1    112.63  3.000
 GGZ  H3'   C3'  C2'   111.96  3.000
 GGZ  H3'   C3'  C4'   112.86  3.000
 GGZ  C2'   C3'  C4'   104.48  3.000
 GGZ  H3'   C3'  O3'   108.02  3.000
 GGZ  C2'   C3'  O3'   107.11  3.000
 GGZ  C4'   C3'  O3'   112.30  3.000
 GGZ  H4'   C4'  O4'   107.10  3.000
 GGZ  H4'   C4'  C5'   108.26  3.000
 GGZ  O4'   C4'  C5'   112.39  3.000
 GGZ  H4'   C4'  C3'   110.07  3.000
 GGZ  C5'   C4'  C3'   112.59  3.000
 GGZ  O4'   C4'  C3'   106.30  3.000
 GGZ  H5'2  C5'  H5'1  107.02  3.000
 GGZ  H5'2  C5'  O5'   111.27  3.000
 GGZ  H5'1  C5'  O5'   111.79  3.000
 GGZ  H5'2  C5'  C4'   107.70  3.000
 GGZ  H5'1  C5'  C4'   111.27  3.000
 GGZ  O5'   C5'  C4'   107.76  3.000
 GGZ  P2    O5'  C5'   119.16  3.000
 GGZ  O6P   P2   O5P   110.40  3.000
 GGZ  O5P   P2   O4P   122.63  3.000
 GGZ  O6P   P2   O4P   107.05  3.000
 GGZ  O5P   P2   O5'   110.20  3.000
 GGZ  O6P   P2   O5'    98.23  3.000
 GGZ  O4P   P2   O5'   105.50  3.000
 GGZ  S2    O6P  P2    125.05  3.000
 GGZ  OS1   S2   OS2   113.40  3.000
 GGZ  OS2   S2   OS3   114.92  3.000
 GGZ  OS1   S2   OS3   114.19  3.000
 GGZ  OS2   S2   O6P   101.21  3.000
 GGZ  OS3   S2   O6P   105.94  3.000
 GGZ  OS1   S2   O6P   105.48  3.000
 GGZ  H2'   C2'  C1'   114.46  3.000
 GGZ  H2'   C2'  C3'   114.31  3.000
 GGZ  C1'   C2'  C3'   103.87  3.000
 GGZ  H2'   C2'  O2'   109.37  3.000
 GGZ  C1'   C2'  O2'   108.13  3.000
 GGZ  C3'   C2'  O2'   106.18  3.000
 GGZ  H1'   C1'  N9    106.20  3.000
 GGZ  H1'   C1'  O4'   108.14  3.000
 GGZ  N9    C1'  O4'   112.71  3.000
 GGZ  H1'   C1'  C2'   110.81  3.000
 GGZ  N9    C1'  C2'   113.34  3.000
 GGZ  O4'   C1'  C2'   105.61  3.000
 GGZ  C1'   O4'  C4'   111.09  3.000
 GGZ  C1'   N9   C8    122.93  3.000
 GGZ  C1'   N9   C4    131.24  3.000
 GGZ  C8    N9   C4    105.70  3.000
 GGZ  C8    N7   C5    104.31  3.000
 GGZ  HN62  N6   HN61  115.33  3.000
 GGZ  HN62  N6   C6    117.26  3.000
 GGZ  HN61  N6   C6    117.42  3.000
 GGZ  C4    N3   C2    112.05  3.000
 GGZ  HO3P  O3P  P1    113.84  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_20  HN62  N6   C6   C5    180.00   0.0  0
 GGZ  Var_01    O4P   P2   O5'  C5'  -176.63  30.0  3
 GGZ  Var_02    OS1   S2   O6P  P2    -52.04  30.0  3
 GGZ  Var_03    H5'1  C5'  O5'  P2    -44.50  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
 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  P1   O3'  O1P  O2'  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

