# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:59:36 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@H]4O[P@](O)(=S)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
 SGP  SGP  2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,9-dihydro-6H-purin-6-one  ligand  35  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SGP
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
 SGP  P     P  P     0   1.194   1.6433   0.2929   2.8575
 SGP  S1P   S  S1    0  -0.450   3.1007   1.0925   3.7927
 SGP  O1P   O  OH1   0  -0.707   1.7806  -1.2645   2.5351
 SGP  O5'   O  OH1   0  -0.665  -3.7772  -1.6946   2.5458
 SGP  C5'   C  CH2   0  -0.167  -3.0743  -0.5296   2.8881
 SGP  C4'   C  CH1   0   0.002  -1.7132  -0.5728   2.2390
 SGP  O4'   O  O2    0  -0.483  -1.8494  -0.5253   0.8280
 SGP  C3'   C  CH1   0  -0.047  -0.8462   0.6448   2.5907
 SGP  O3'   O  O2    0  -0.566   0.1805   0.3466   3.5294
 SGP  C2'   C  CH1   0  -0.060  -0.1637   1.0176   1.2574
 SGP  O2'   O  O2    0  -0.565   1.2356   1.0131   1.4657
 SGP  C1'   C  CH1   0   0.204  -0.6364  -0.0845   0.2922
 SGP  N9    N  NR5   0  -0.556  -0.8665   0.3604  -1.0477
 SGP  C8    C  CR15  0   0.094  -1.8277   1.2478  -1.4772
 SGP  N7    N  N     0  -0.438  -1.7841   1.4493  -2.7557
 SGP  C5    C  CR56  0  -0.094  -0.7491   0.6665  -3.2015
 SGP  C6    C  CR6   0   0.509  -0.2255   0.4775  -4.5136
 SGP  O6    O  O     0  -0.470  -0.5905   0.9808  -5.5618
 SGP  N1    N  NR16  0  -0.728   0.8479  -0.4230  -4.4897
 SGP  C2    C  CR6   0   0.699   1.3504  -1.0499  -3.3858
 SGP  N2    N  NH2   0  -0.831   2.3659  -1.9006  -3.5752
 SGP  N3    N  N     0  -0.513   0.8632  -0.8713  -2.1813
 SGP  C4    C  CR56  0   0.511  -0.1674  -0.0200  -2.1539
 SGP  HOP1  H  HOH1  0   0.506   2.6890  -1.5675   2.3977
 SGP  HO5'  H  HOH1  0   0.462  -4.6327  -1.6694   2.9839
 SGP  H5'1  H  HCH2  0   0.218  -2.9172  -0.4428   3.9709
 SGP  H5'2  H  HCH2  0   0.210  -3.5945   0.3819   2.5642
 SGP  H4'   H  HCH1  0   0.262  -1.1888  -1.4904   2.5394
 SGP  H3'   H  HCH1  0   0.309  -1.4349   1.4700   2.9928
 SGP  H2'   H  HCH1  0   0.324  -0.4521   2.0097   0.9079
 SGP  H1'   H  HCH1  0   0.278   0.1132  -0.8848   0.2369
 SGP  H8    H  HCR5  0   0.299  -2.5303   1.7017  -0.7948
 SGP  HN1   H  HNR6  0   0.427   1.2793  -0.6111  -5.3862
 SGP  HN21  H  HNH2  0   0.414   2.8410  -2.2540  -2.7622
 SGP  HN22  H  HNH2  0   0.417   2.8790  -1.9177  -4.4399

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
 SGP  P    S1P   double    1.907  0.020  1.907
 SGP  P    O1P   single    1.596  0.020  1.596
 SGP  P    O3'   single    1.611  0.020  1.611
 SGP  P    O2'   single    1.619  0.020  1.619
 SGP  O1P  HOP1  single    0.850  0.020  0.980
 SGP  O5'  C5'   single    1.403  0.020  1.403
 SGP  O5'  HO5'  single    0.850  0.020  0.980
 SGP  C5'  C4'   single    1.509  0.020  1.509
 SGP  C5'  H5'1  single    0.970  0.020  1.090
 SGP  C5'  H5'2  single    0.970  0.020  1.090
 SGP  C4'  O4'   single    1.418  0.020  1.418
 SGP  C4'  C3'   single    1.536  0.020  1.536
 SGP  C4'  H4'   single    0.970  0.020  1.090
 SGP  O4'  C1'   single    1.397  0.020  1.397
 SGP  C3'  O3'   single    1.423  0.020  1.423
 SGP  C3'  C2'   single    1.544  0.020  1.544
 SGP  C3'  H3'   single    0.970  0.020  1.090
 SGP  C2'  O2'   single    1.415  0.020  1.415
 SGP  C2'  C1'   single    1.539  0.020  1.539
 SGP  C2'  H2'   single    0.970  0.020  1.090
 SGP  C1'  N9    single    1.430  0.020  1.430
 SGP  C1'  H1'   single    0.970  0.020  1.090
 SGP  N9   C8    aromatic  1.377  0.020  1.377
 SGP  N9   C4    aromatic  1.363  0.020  1.363
 SGP  C8   N7    aromatic  1.295  0.020  1.295
 SGP  C8   H8    single    0.930  0.020  1.080
 SGP  N7   C5    aromatic  1.372  0.020  1.372
 SGP  C5   C6    single    1.425  0.020  1.425
 SGP  C5   C4    aromatic  1.381  0.020  1.381
 SGP  C6   O6    double    1.219  0.020  1.219
 SGP  C6   N1    single    1.401  0.020  1.401
 SGP  N1   C2    single    1.365  0.020  1.365
 SGP  N1   HN1   single    0.860  0.020  1.020
 SGP  C2   N2    single    1.338  0.020  1.338
 SGP  C2   N3    double    1.311  0.020  1.311
 SGP  N2   HN21  single    0.890  0.020  1.040
 SGP  N2   HN22  single    0.890  0.020  1.040
 SGP  N3   C4    single    1.337  0.020  1.337

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
 SGP  O2'   P    O3'    96.60  3.000
 SGP  O2'   P    O1P   106.38  3.000
 SGP  O3'   P    O1P   101.23  3.000
 SGP  O2'   P    S1P   115.30  3.000
 SGP  O3'   P    S1P   118.39  3.000
 SGP  O1P   P    S1P   116.25  3.000
 SGP  HOP1  O1P  P     114.52  3.000
 SGP  HO5'  O5'  C5'   108.23  3.000
 SGP  H5'2  C5'  H5'1  107.04  3.000
 SGP  H5'2  C5'  C4'   108.92  3.000
 SGP  H5'1  C5'  C4'   107.31  3.000
 SGP  H5'2  C5'  O5'   112.33  3.000
 SGP  H5'1  C5'  O5'   112.21  3.000
 SGP  C4'   C5'  O5'   108.86  3.000
 SGP  H4'   C4'  C3'   109.27  3.000
 SGP  H4'   C4'  O4'   110.23  3.000
 SGP  C3'   C4'  O4'   104.81  3.000
 SGP  H4'   C4'  C5'   109.69  3.000
 SGP  C3'   C4'  C5'   112.84  3.000
 SGP  O4'   C4'  C5'   109.90  3.000
 SGP  C1'   O4'  C4'   107.98  3.000
 SGP  H3'   C3'  C2'   111.99  3.000
 SGP  H3'   C3'  O3'   107.76  3.000
 SGP  C2'   C3'  O3'   107.55  3.000
 SGP  H3'   C3'  C4'   112.31  3.000
 SGP  C2'   C3'  C4'   104.08  3.000
 SGP  O3'   C3'  C4'   113.10  3.000
 SGP  C3'   O3'  P     112.78  3.000
 SGP  H2'   C2'  C1'   111.66  3.000
 SGP  H2'   C2'  O2'   108.16  3.000
 SGP  C1'   C2'  O2'   113.19  3.000
 SGP  H2'   C2'  C3'   112.31  3.000
 SGP  C1'   C2'  C3'   103.47  3.000
 SGP  O2'   C2'  C3'   108.02  3.000
 SGP  C2'   O2'  P     112.15  3.000
 SGP  H1'   C1'  N9    106.82  3.000
 SGP  H1'   C1'  C2'   110.10  3.000
 SGP  N9    C1'  C2'   114.46  3.000
 SGP  H1'   C1'  O4'   112.46  3.000
 SGP  N9    C1'  O4'   108.52  3.000
 SGP  C2'   C1'  O4'   104.60  3.000
 SGP  C4    N9   C8    106.55  3.000
 SGP  C4    N9   C1'   126.23  3.000
 SGP  C8    N9   C1'   127.22  3.000
 SGP  H8    C8   N7    125.49  3.000
 SGP  H8    C8   N9    121.89  3.000
 SGP  N7    C8   N9    112.63  3.000
 SGP  C5    N7   C8    104.92  3.000
 SGP  C4    C5   C6    118.53  3.000
 SGP  C4    C5   N7    110.78  3.000
 SGP  C6    C5   N7    130.69  3.000
 SGP  N1    C6   O6    120.63  3.000
 SGP  N1    C6   C5    110.55  3.000
 SGP  O6    C6   C5    128.83  3.000
 SGP  HN1   N1   C2    118.28  3.000
 SGP  HN1   N1   C6    115.51  3.000
 SGP  C2    N1   C6    126.21  3.000
 SGP  N3    C2   N2    119.90  3.000
 SGP  N3    C2   N1    122.91  3.000
 SGP  N2    C2   N1    117.17  3.000
 SGP  HN22  N2   HN21  116.62  3.000
 SGP  HN22  N2   C2    121.31  3.000
 SGP  HN21  N2   C2    117.87  3.000
 SGP  C4    N3   C2    113.07  3.000
 SGP  N3    C4   C5    128.73  3.000
 SGP  N3    C4   N9    126.14  3.000
 SGP  C5    C4   N9    105.13  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
 SGP  CONST_01  C5    N7  C8   N9     0.00   0.0  0
 SGP  CONST_02  N7    C5  C4   N9     0.00   0.0  0
 SGP  CONST_03  C5    C4  N9   C8     0.00   0.0  0
 SGP  CONST_04  C4    C5  N7   C8     0.00   0.0  0
 SGP  CONST_05  C4    N9  C8   N7     0.00   0.0  0
 SGP  CONST_06  N7    C8  N9   C1'  180.00   0.0  0
 SGP  CONST_07  C5    C4  N9   C1'  180.00   0.0  0
 SGP  CONST_08  N3    C4  N9   C1'    0.00   0.0  0
 SGP  CONST_09  C2    N1  C6   C5     0.00   0.0  0
 SGP  CONST_10  N3    C2  N1   C6     0.00   0.0  0
 SGP  CONST_11  C4    N3  C2   N1     0.00   0.0  0
 SGP  CONST_12  N2    C2  N1   C6   180.00   0.0  0
 SGP  CONST_13  C2    N1  C6   O6   180.00   0.0  0
 SGP  CONST_14  C4    N3  C2   N2   180.00   0.0  0
 SGP  CONST_15  H8    C8  N9   C1'    0.00   0.0  0
 SGP  CONST_16  HN1   N1  C6   C5   180.00   0.0  0
 SGP  CONST_17  HN21  N2  C2   N1   180.00   0.0  0
 SGP  CONST_18  HN22  N2  C2   N1     0.00   0.0  0
 SGP  Var_01    O2'   P   O3'  C3'   14.54  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
 SGP  chir_02  C4'  C5'  O4'  C3'  negativ
 SGP  chir_03  C3'  O3'  C2'  C4'  negativ
 SGP  chir_04  C2'  O2'  C1'  C3'  negativ
 SGP  chir_05  C1'  O4'  N9   C2'  negativ
 SGP  chir_06  P    O1P  O3'  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
 SGP  plan-1  C1'   0.020
 SGP  plan-1  N9    0.020
 SGP  plan-1  C8    0.020
 SGP  plan-1  N7    0.020
 SGP  plan-1  C5    0.020
 SGP  plan-1  C6    0.020
 SGP  plan-1  O6    0.020
 SGP  plan-1  N1    0.020
 SGP  plan-1  C2    0.020
 SGP  plan-1  N2    0.020
 SGP  plan-1  N3    0.020
 SGP  plan-1  C4    0.020
 SGP  plan-1  H8    0.020
 SGP  plan-1  HN1   0.020
 SGP  plan-1  HN21  0.020
 SGP  plan-1  HN22  0.020

