# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 03:19:20 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=S)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
#
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
 SGT  SGT  2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione  ligand  47  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SGT
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
 SGT  PG   P  P     0   1.467  -12.3377   0.4786  69.0881
 SGT  O1G  O  OH1   0  -0.710  -10.9931  -0.3359  69.2675
 SGT  O2G  O  O     0  -0.669  -13.5973  -0.2182  69.3779
 SGT  O3G  O  OH1   0  -0.742  -12.0456   1.8565  69.8240
 SGT  O3B  O  O2    0  -0.670  -12.2018   0.9738  67.5399
 SGT  PB   P  P     0   1.534  -12.8209   2.2493  66.7995
 SGT  O1B  O  O     0  -0.656  -12.8692   2.0432  65.3418
 SGT  O2B  O  OH1   0  -0.726  -14.1595   2.6183  67.5486
 SGT  O3A  O  O2    0  -0.699  -11.8281   3.4120  67.2356
 SGT  PA   P  P     0   1.507  -11.7213   4.8349  68.0221
 SGT  O1A  O  OH1   0  -0.724  -13.0095   4.9263  68.9344
 SGT  O2A  O  O     0  -0.652  -10.3949   4.9649  68.6304
 SGT  O5'  O  O2    0  -0.576  -12.0059   5.9058  66.9000
 SGT  C5'  C  CH2   0  -0.227  -13.2506   6.1065  66.2149
 SGT  C4'  C  CH1   0   0.018  -13.0072   6.3158  64.7427
 SGT  O4'  O  O2    0  -0.496  -12.1600   7.4389  64.5365
 SGT  C3'  C  CH1   0   0.000  -12.3526   5.1644  63.9699
 SGT  O3'  O  OH1   0  -0.690  -13.2655   4.1787  63.5922
 SGT  C2'  C  CH2   0  -0.539  -11.7881   5.9252  62.7777
 SGT  C1'  C  CH1   0   0.192  -11.3740   7.2560  63.3931
 SGT  N9   N  NR5   0  -0.530   -9.9661   7.2729  63.7887
 SGT  C8   C  CR15  0   0.089   -9.4095   7.1067  65.0343
 SGT  N7   N  N     0  -0.434   -8.1125   7.1572  65.0225
 SGT  C5   C  CR56  0   0.028   -7.7816   7.3641  63.7097
 SGT  C6   C  CR6   0   0.160   -6.5374   7.5031  63.0766
 SGT  N1   N  NR16  0  -0.682   -6.6733   7.7011  61.7183
 SGT  C2   C  CR6   0   0.695   -7.8512   7.7601  61.0294
 SGT  N2   N  NH2   0  -0.831   -7.7770   7.9265  59.7053
 SGT  N3   N  N     0  -0.500   -9.0205   7.6306  61.6130
 SGT  C4   C  CR56  0   0.516   -8.9319   7.4388  62.9298
 SGT  S6   S  S1    0  -0.382   -5.0272   7.4515  63.7767
 SGT  H1   H  HOH1  0   0.513  -11.0905  -1.2959  69.1945
 SGT  H2   H  HOH1  0   0.517  -12.2418   1.8539  70.7725
 SGT  H3   H  HOH1  0   0.522  -14.9626   2.2073  67.1936
 SGT  H4   H  HOH1  0   0.506  -13.0025   4.4010  69.7470
 SGT  H5   H  HCH2  0   0.288  -13.7381   6.9758  66.6572
 SGT  H6   H  HCH2  0   0.248  -13.9300   5.2583  66.3310
 SGT  H7   H  HCH1  0   0.252  -13.9949   6.5053  64.2996
 SGT  H8   H  HCH1  0   0.231  -11.5257   4.7430  64.5558
 SGT  H9   H  HOH1  0   0.462  -13.1580   3.4054  64.1682
 SGT  H10  H  HCH2  0   0.268  -12.5818   6.0965  62.0466
 SGT  H11  H  HCH2  0   0.283  -10.9681   5.4168  62.2730
 SGT  H12  H  HCH1  0   0.278  -11.5091   8.0895  62.7002
 SGT  H13  H  HCR5  0   0.295  -10.0145   6.9630  65.9141
 SGT  H14  H  HNR6  0   0.428   -5.8091   7.8087  61.2022
 SGT  H15  H  HNH2  0   0.418   -8.6298   8.1142  59.2058
 SGT  H16  H  HNH2  0   0.420   -6.9199   8.2034  59.2575

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
 SGT  N2   C2   single    1.337  0.020  1.337
 SGT  C2   N1   single    1.366  0.020  1.366
 SGT  C2   N3   double    1.313  0.020  1.313
 SGT  N1   C6   single    1.379  0.020  1.379
 SGT  N3   C4   single    1.334  0.020  1.334
 SGT  C2'  C1'  single    1.524  0.020  1.524
 SGT  C2'  C3'  single    1.523  0.020  1.523
 SGT  C6   S6   double    1.665  0.020  1.665
 SGT  C6   C5   single    1.403  0.020  1.403
 SGT  C4   C5   aromatic  1.392  0.020  1.392
 SGT  C4   N9   aromatic  1.355  0.020  1.355
 SGT  C1'  N9   single    1.463  0.020  1.463
 SGT  C1'  O4'  single    1.400  0.020  1.400
 SGT  C5   N7   aromatic  1.370  0.020  1.370
 SGT  N9   C8   aromatic  1.374  0.020  1.374
 SGT  O3'  C3'  single    1.396  0.020  1.396
 SGT  C3'  C4'  single    1.533  0.020  1.533
 SGT  O4'  C4'  single    1.422  0.020  1.422
 SGT  N7   C8   aromatic  1.298  0.020  1.298
 SGT  C4'  C5'  single    1.507  0.020  1.507
 SGT  O1B  PB   double    1.473  0.020  1.473
 SGT  C5'  O5'  single    1.435  0.020  1.435
 SGT  O5'  PA   single    1.577  0.020  1.577
 SGT  PB   O3A  single    1.590  0.020  1.590
 SGT  PB   O2B  single    1.578  0.020  1.578
 SGT  PB   O3B  single    1.599  0.020  1.599
 SGT  O3A  PA   single    1.629  0.020  1.629
 SGT  O3B  PG   single    1.631  0.020  1.631
 SGT  PA   O2A  double    1.465  0.020  1.465
 SGT  PA   O1A  single    1.581  0.020  1.581
 SGT  PG   O2G  double    1.468  0.020  1.468
 SGT  PG   O3G  single    1.589  0.020  1.589
 SGT  PG   O1G  single    1.582  0.020  1.582
 SGT  O1G  H1   single    0.850  0.020  0.980
 SGT  O3G  H2   single    0.850  0.020  0.980
 SGT  O2B  H3   single    0.850  0.020  0.980
 SGT  O1A  H4   single    0.850  0.020  0.980
 SGT  C5'  H5   single    0.970  0.020  1.090
 SGT  C5'  H6   single    0.970  0.020  1.090
 SGT  C4'  H7   single    0.970  0.020  1.090
 SGT  C3'  H8   single    0.970  0.020  1.090
 SGT  O3'  H9   single    0.850  0.020  0.980
 SGT  C2'  H10  single    0.970  0.020  1.090
 SGT  C2'  H11  single    0.970  0.020  1.090
 SGT  C1'  H12  single    0.970  0.020  1.090
 SGT  C8   H13  single    0.930  0.020  1.080
 SGT  N1   H14  single    0.860  0.020  1.020
 SGT  N2   H15  single    0.890  0.020  1.040
 SGT  N2   H16  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
 SGT  O3B  PG   O3G   99.26  3.000
 SGT  O3G  PG   O2G  118.54  3.000
 SGT  O3B  PG   O2G  113.76  3.000
 SGT  O3G  PG   O1G  103.75  3.000
 SGT  O2G  PG   O1G  117.53  3.000
 SGT  O3B  PG   O1G  101.14  3.000
 SGT  H1   O1G  PG   114.62  3.000
 SGT  H2   O3G  PG   114.45  3.000
 SGT  PB   O3B  PG   130.48  3.000
 SGT  O3A  PB   O2B  103.21  3.000
 SGT  O2B  PB   O1B  118.34  3.000
 SGT  O3A  PB   O1B  113.22  3.000
 SGT  O2B  PB   O3B  107.17  3.000
 SGT  O3A  PB   O3B  102.39  3.000
 SGT  O1B  PB   O3B  111.05  3.000
 SGT  H3   O2B  PB   115.45  3.000
 SGT  PA   O3A  PB   144.29  3.000
 SGT  O5'  PA   O2A  113.49  3.000
 SGT  O2A  PA   O1A  119.53  3.000
 SGT  O5'  PA   O1A  102.96  3.000
 SGT  O1A  PA   O3A  106.00  3.000
 SGT  O2A  PA   O3A  109.71  3.000
 SGT  O5'  PA   O3A  103.75  3.000
 SGT  H4   O1A  PA   116.57  3.000
 SGT  C5'  O5'  PA   126.25  3.000
 SGT  H6   C5'  H5   107.32  3.000
 SGT  H6   C5'  C4'  108.18  3.000
 SGT  H5   C5'  C4'  110.97  3.000
 SGT  H6   C5'  O5'  112.33  3.000
 SGT  H5   C5'  O5'  107.80  3.000
 SGT  C4'  C5'  O5'  110.23  3.000
 SGT  H7   C4'  C3'  108.05  3.000
 SGT  H7   C4'  O4'  109.93  3.000
 SGT  C3'  C4'  O4'  105.41  3.000
 SGT  H7   C4'  C5'  105.83  3.000
 SGT  O4'  C4'  C5'  110.35  3.000
 SGT  C3'  C4'  C5'  117.20  3.000
 SGT  C1'  O4'  C4'  110.48  3.000
 SGT  H8   C3'  C2'  109.30  3.000
 SGT  H8   C3'  O3'  111.48  3.000
 SGT  C2'  C3'  O3'  112.55  3.000
 SGT  H8   C3'  C4'  109.93  3.000
 SGT  O3'  C3'  C4'  112.80  3.000
 SGT  C2'  C3'  C4'  100.23  3.000
 SGT  H9   O3'  C3'  109.25  3.000
 SGT  H11  C2'  H10  108.07  3.000
 SGT  H11  C2'  C1'  112.97  3.000
 SGT  H10  C2'  C1'  109.32  3.000
 SGT  H11  C2'  C3'  114.13  3.000
 SGT  H10  C2'  C3'  109.45  3.000
 SGT  C1'  C2'  C3'  102.76  3.000
 SGT  H12  C1'  N9   106.37  3.000
 SGT  H12  C1'  C2'  112.13  3.000
 SGT  N9   C1'  C2'  112.40  3.000
 SGT  H12  C1'  O4'  110.43  3.000
 SGT  N9   C1'  O4'  108.55  3.000
 SGT  C2'  C1'  O4'  106.95  3.000
 SGT  C4   N9   C8   106.28  3.000
 SGT  C8   N9   C1'  129.31  3.000
 SGT  C4   N9   C1'  124.40  3.000
 SGT  H13  C8   N7   125.00  3.000
 SGT  H13  C8   N9   121.93  3.000
 SGT  N7   C8   N9   113.06  3.000
 SGT  C5   N7   C8   104.83  3.000
 SGT  C4   C5   C6   118.35  3.000
 SGT  C4   C5   N7   110.22  3.000
 SGT  C6   C5   N7   131.44  3.000
 SGT  S6   C6   N1   120.52  3.000
 SGT  S6   C6   C5   127.69  3.000
 SGT  N1   C6   C5   111.79  3.000
 SGT  H14  N1   C2   118.32  3.000
 SGT  H14  N1   C6   115.67  3.000
 SGT  C2   N1   C6   126.01  3.000
 SGT  N3   C2   N2   120.13  3.000
 SGT  N3   C2   N1   122.64  3.000
 SGT  N2   C2   N1   117.21  3.000
 SGT  H16  N2   H15  116.74  3.000
 SGT  H16  N2   C2   121.51  3.000
 SGT  H15  N2   C2   117.91  3.000
 SGT  C4   N3   C2   113.19  3.000
 SGT  N3   C4   C5   128.02  3.000
 SGT  C5   C4   N9   105.61  3.000
 SGT  N3   C4   N9   126.36  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
 SGT  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 SGT  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 SGT  CONST_03  C5   C4   N9   C8      0.00   0.0  0
 SGT  CONST_04  C4   C5   N7   C8      0.00   0.0  0
 SGT  CONST_05  C4   N9   C8   N7      0.00   0.0  0
 SGT  CONST_06  N3   C4   N9   C1'     0.00   0.0  0
 SGT  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 SGT  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 SGT  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 SGT  CONST_10  C4   N3   C2   N1      0.00   0.0  0
 SGT  CONST_11  N2   C2   N1   C6    180.00   0.0  0
 SGT  CONST_12  C4   N3   C2   N2    180.00   0.0  0
 SGT  CONST_13  H13  C8   N9   C1'     0.00   0.0  0
 SGT  CONST_14  H14  N1   C2   N3    180.00   0.0  0
 SGT  CONST_15  H15  N2   C2   N1    180.00   0.0  0
 SGT  CONST_16  H16  N2   C2   N1      0.00   0.0  0
 SGT  Var_01    C4'  C5'  O5'  PA   -137.28  30.0  1
 SGT  Var_02    O1B  PB   O3B  PG   -158.60  30.0  1
 SGT  Var_03    O5'  PA   O3A  PB    -89.56  30.0  3

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
 SGT  chir_03  C4'  C3'  O4'  C5'  positiv
 SGT  chir_04  C3'  O3'  C2'  C4'  negativ
 SGT  chir_05  C1'  O4'  N9   C2'  negativ
 SGT  chir_06  PB   O3A  O2B  O3B  both
 SGT  chir_07  PA   O2A  O3A  O5'  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
 SGT  plan-1  C1'  0.020
 SGT  plan-1  N9   0.020
 SGT  plan-1  C8   0.020
 SGT  plan-1  N7   0.020
 SGT  plan-1  C5   0.020
 SGT  plan-1  C6   0.020
 SGT  plan-1  N1   0.020
 SGT  plan-1  C2   0.020
 SGT  plan-1  N2   0.020
 SGT  plan-1  N3   0.020
 SGT  plan-1  C4   0.020
 SGT  plan-1  S6   0.020
 SGT  plan-1  H13  0.020
 SGT  plan-1  H14  0.020
 SGT  plan-1  H15  0.020
 SGT  plan-1  H16  0.020

