# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 12:24:20 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)c2N1
#
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
 T8T  T8T  2'-deoxy-5'-O-[(R)-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]guanosine  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_T8T
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
 T8T  N1    N  N     0  -0.538  46.5493  24.4602  33.7232
 T8T  C2    C  CR6   0   0.673  45.4249  24.6269  34.3657
 T8T  N2    N  NH2   0  -0.827  44.4682  23.6945  34.2914
 T8T  N3    N  NR16  0  -0.738  45.1323  25.7339  35.1146
 T8T  C4    C  CR56  0   0.643  46.0859  26.6976  35.1574
 T8T  C5    C  CR56  0  -0.115  47.2781  26.5871  34.4988
 T8T  C6    C  CR6   0   0.417  47.5530  25.3971  33.7229
 T8T  O6    O  O     0  -0.493  48.5941  25.2127  33.1033
 T8T  N7    N  N     0  -0.436  48.0281  27.7141  34.7236
 T8T  C8    C  CR15  0   0.104  47.3024  28.4634  35.4903
 T8T  N9    N  NR5   0  -0.536  46.0900  27.8862  35.8094
 T8T  PA    P  P     0   1.321  47.1170  32.7558  35.9184
 T8T  PB    P  P     0   1.481  47.2729  33.5245  38.6976
 T8T  PG    P  P     0   1.467  50.2304  33.3702  38.7273
 T8T  C1'   C  CH1   0   0.210  44.9858  28.4686  36.5372
 T8T  S1A   S  S2    0  -0.298  46.6756  34.0850  34.4125
 T8T  O1B   O  O     0  -0.657  47.1322  32.1600  39.2171
 T8T  O1G   O  OH1   0  -0.761  50.0970  31.9963  37.9805
 T8T  C2'   C  CH2   0  -0.537  45.3822  29.2342  37.7932
 T8T  O2A   O  O     0  -0.677  48.4942  32.2022  35.9607
 T8T  O2B   O  OH1   0  -0.692  46.5143  34.7178  39.3862
 T8T  O2G   O  OH1   0  -0.723  50.2835  32.8678  40.2294
 T8T  C3'   C  CH1   0  -0.012  44.2822  30.2760  37.8928
 T8T  O3'   O  OH1   0  -0.670  43.1896  29.6835  38.5536
 T8T  O3A   O  O2    0  -0.684  46.7398  33.7102  37.1670
 T8T  O3B   O  O2    0  -0.690  48.7600  34.0936  38.5649
 T8T  O3G   O  O     0  -0.675  51.2501  34.3379  38.2993
 T8T  C4'   C  CH1   0  -0.018  43.9537  30.5532  36.4145
 T8T  O4'   O  O2    0  -0.486  44.3051  29.3743  35.7060
 T8T  C5'   C  CH2   0  -0.212  44.6428  31.7557  35.8137
 T8T  O5'   O  O2    0  -0.558  46.0647  31.5807  35.9254
 T8T  HN2   H  HNH2  0   0.413  44.6894  22.8250  33.8381
 T8T  HN2A  H  HNH2  0   0.416  43.6547  23.7132  34.8820
 T8T  HN3   H  HNR6  0   0.440  44.2436  25.8225  35.5859
 T8T  H8    H  HCR5  0   0.277  47.5847  29.4368  35.8551
 T8T  H1'   H  HCH1  0   0.253  44.3235  27.6402  36.8064
 T8T  HS1A  H  HSH1  0   0.292  46.9722  33.2243  33.4265
 T8T  HO1G  H  HOH1  0   0.501  49.5657  32.0071  37.1368
 T8T  H2'   H  HCH2  0   0.291  45.4222  28.5858  38.6670
 T8T  H2'A  H  HCH2  0   0.272  46.3519  29.7190  37.6993
 T8T  HO2B  H  HOH1  0   0.523  46.0078  34.4755  40.1750
 T8T  HO2G  H  HOH1  0   0.508  50.6738  33.5032  40.8454
 T8T  H3'   H  HCH1  0   0.255  44.6190  31.1808  38.4101
 T8T  HO3'  H  HOH1  0   0.457  42.4884  30.3372  38.6410
 T8T  H4'   H  HCH1  0   0.276  42.8800  30.7372  36.2947
 T8T  H5'   H  HCH2  0   0.279  44.3868  31.8585  34.7583
 T8T  H5'A  H  HCH2  0   0.264  44.3117  32.6555  36.3368

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
 T8T  N1   C2    double    1.306  0.020  1.306
 T8T  N1   C6    single    1.373  0.020  1.373
 T8T  N2   C2    single    1.338  0.020  1.338
 T8T  C2   N3    single    1.368  0.020  1.368
 T8T  N2   HN2   single    0.860  0.020  1.020
 T8T  N2   HN2A  single    0.860  0.020  1.020
 T8T  N3   C4    single    1.356  0.020  1.356
 T8T  N3   HN3   single    0.860  0.020  1.020
 T8T  C5   C4    aromatic  1.366  0.020  1.366
 T8T  C4   N9    aromatic  1.356  0.020  1.356
 T8T  C6   C5    single    1.447  0.020  1.447
 T8T  C5   N7    aromatic  1.372  0.020  1.372
 T8T  O6   C6    double    1.225  0.020  1.225
 T8T  N7   C8    aromatic  1.294  0.020  1.294
 T8T  N9   C8    aromatic  1.380  0.020  1.380
 T8T  C8   H8    single    0.930  0.020  1.080
 T8T  N9   C1'   single    1.445  0.020  1.445
 T8T  S1A  PA    single    2.057  0.020  2.057
 T8T  PA   O5'   single    1.577  0.020  1.577
 T8T  PA   O2A   double    1.485  0.020  1.485
 T8T  PA   O3A   single    1.616  0.020  1.616
 T8T  O3B  PB    single    1.598  0.020  1.598
 T8T  O3A  PB    single    1.631  0.020  1.631
 T8T  PB   O1B   double    1.467  0.020  1.467
 T8T  PB   O2B   single    1.573  0.020  1.573
 T8T  O3G  PG    double    1.470  0.020  1.470
 T8T  O3B  PG    single    1.647  0.020  1.647
 T8T  PG   O1G   single    1.569  0.020  1.569
 T8T  PG   O2G   single    1.585  0.020  1.585
 T8T  O4'  C1'   single    1.405  0.020  1.405
 T8T  C1'  C2'   single    1.523  0.020  1.523
 T8T  C1'  H1'   single    0.970  0.020  1.090
 T8T  S1A  HS1A  single    1.200  0.020  1.300
 T8T  O1G  HO1G  single    0.850  0.020  0.980
 T8T  C2'  C3'   single    1.518  0.020  1.518
 T8T  C2'  H2'   single    0.970  0.020  1.090
 T8T  C2'  H2'A  single    0.970  0.020  1.090
 T8T  O2B  HO2B  single    0.850  0.020  0.980
 T8T  O2G  HO2G  single    0.850  0.020  0.980
 T8T  C4'  C3'   single    1.539  0.020  1.539
 T8T  C3'  O3'   single    1.408  0.020  1.408
 T8T  C3'  H3'   single    0.970  0.020  1.090
 T8T  O3'  HO3'  single    0.850  0.020  0.980
 T8T  O4'  C4'   single    1.420  0.020  1.420
 T8T  C4'  C5'   single    1.511  0.020  1.511
 T8T  C4'  H4'   single    0.970  0.020  1.090
 T8T  C5'  O5'   single    1.437  0.020  1.437
 T8T  C5'  H5'   single    0.970  0.020  1.090
 T8T  C5'  H5'A  single    0.970  0.020  1.090

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
 T8T  C6    N1   C2   122.85  3.000
 T8T  N3    C2   N2   116.18  3.000
 T8T  N3    C2   N1   123.84  3.000
 T8T  N2    C2   N1   119.97  3.000
 T8T  HN2A  N2   HN2  117.32  3.000
 T8T  HN2A  N2   C2   122.21  3.000
 T8T  HN2   N2   C2   118.06  3.000
 T8T  HN3   N3   C4   122.80  3.000
 T8T  HN3   N3   C2   120.98  3.000
 T8T  C4    N3   C2   116.21  3.000
 T8T  N9    C4   C5   107.46  3.000
 T8T  N9    C4   N3   129.80  3.000
 T8T  C5    C4   N3   122.74  3.000
 T8T  N7    C5   C6   131.25  3.000
 T8T  N7    C5   C4   109.36  3.000
 T8T  C6    C5   C4   119.39  3.000
 T8T  O6    C6   C5   123.80  3.000
 T8T  O6    C6   N1   121.23  3.000
 T8T  C5    C6   N1   114.97  3.000
 T8T  C8    N7   C5   105.43  3.000
 T8T  H8    C8   N9   121.99  3.000
 T8T  H8    C8   N7   125.23  3.000
 T8T  N9    C8   N7   112.78  3.000
 T8T  C1'   N9   C8   128.25  3.000
 T8T  C1'   N9   C4   126.39  3.000
 T8T  C8    N9   C4   104.96  3.000
 T8T  O5'   PA   O3A  106.31  3.000
 T8T  O3A   PA   O2A  114.49  3.000
 T8T  O5'   PA   O2A  109.93  3.000
 T8T  O3A   PA   S1A   97.70  3.000
 T8T  O2A   PA   S1A  117.44  3.000
 T8T  O5'   PA   S1A  109.97  3.000
 T8T  O3B   PB   O3A  100.70  3.000
 T8T  O3A   PB   O2B   99.61  3.000
 T8T  O3B   PB   O2B  102.42  3.000
 T8T  O2B   PB   O1B  120.29  3.000
 T8T  O3A   PB   O1B  114.01  3.000
 T8T  O3B   PB   O1B  116.74  3.000
 T8T  O3G   PG   O3B  107.55  3.000
 T8T  O3B   PG   O2G  105.23  3.000
 T8T  O3G   PG   O2G  117.49  3.000
 T8T  O2G   PG   O1G  100.16  3.000
 T8T  O3B   PG   O1G  105.17  3.000
 T8T  O3G   PG   O1G  119.79  3.000
 T8T  H1'   C1'  O4'  109.89  3.000
 T8T  H1'   C1'  C2'  109.58  3.000
 T8T  O4'   C1'  C2'  106.85  3.000
 T8T  H1'   C1'  N9   106.34  3.000
 T8T  C2'   C1'  N9   114.77  3.000
 T8T  O4'   C1'  N9   109.39  3.000
 T8T  HS1A  S1A  PA    94.36  3.000
 T8T  HO1G  O1G  PG   116.01  3.000
 T8T  H2'A  C2'  H2'  107.57  3.000
 T8T  H2'A  C2'  C3'  110.22  3.000
 T8T  H2'   C2'  C3'  112.49  3.000
 T8T  H2'A  C2'  C1'  112.62  3.000
 T8T  H2'   C2'  C1'  111.83  3.000
 T8T  C3'   C2'  C1'  102.15  3.000
 T8T  HO2B  O2B  PB   114.78  3.000
 T8T  HO2G  O2G  PG   114.14  3.000
 T8T  H3'   C3'  C4'  111.74  3.000
 T8T  H3'   C3'  O3'  111.38  3.000
 T8T  C4'   C3'  O3'  111.15  3.000
 T8T  H3'   C3'  C2'  112.03  3.000
 T8T  O3'   C3'  C2'  107.72  3.000
 T8T  C4'   C3'  C2'  102.43  3.000
 T8T  HO3'  O3'  C3'  108.80  3.000
 T8T  PB    O3A  PA   125.55  3.000
 T8T  PG    O3B  PB   131.79  3.000
 T8T  H4'   C4'  C5'  105.65  3.000
 T8T  H4'   C4'  O4'  109.11  3.000
 T8T  C5'   C4'  O4'  110.46  3.000
 T8T  H4'   C4'  C3'  110.14  3.000
 T8T  C5'   C4'  C3'  115.33  3.000
 T8T  O4'   C4'  C3'  106.08  3.000
 T8T  C4'   O4'  C1'  111.09  3.000
 T8T  H5'A  C5'  H5'  108.33  3.000
 T8T  H5'A  C5'  O5'  111.28  3.000
 T8T  H5'   C5'  O5'  108.60  3.000
 T8T  H5'A  C5'  C4'  109.09  3.000
 T8T  H5'   C5'  C4'  110.66  3.000
 T8T  O5'   C5'  C4'  108.88  3.000
 T8T  C5'   O5'  PA   124.69  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
 T8T  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 T8T  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 T8T  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 T8T  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 T8T  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 T8T  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 T8T  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 T8T  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 T8T  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 T8T  CONST_10  C6    N1   C2   N3     0.00   0.0  0
 T8T  CONST_11  C6    N1   C2   N2   180.00   0.0  0
 T8T  CONST_12  C4    N3   C2   N2   180.00   0.0  0
 T8T  CONST_13  H8    C8   N9   C4   180.00   0.0  0
 T8T  CONST_14  HN3   N3   C2   N1   180.00   0.0  0
 T8T  CONST_15  HN2   N2   C2   N1     0.00   0.0  0
 T8T  CONST_16  HN2A  N2   C2   N1   180.00   0.0  0
 T8T  Var_01    C4'   C5'  O5'  PA  -156.77  30.0  1
 T8T  Var_02    O3B   PB   O3A  PA    77.06  30.0  3
 T8T  Var_03    O3G   PG   O3B  PB   171.79  30.0  3
 T8T  Var_04    S1A   PA   O3A  PB  -159.02  30.0  1
 T8T  Var_05    O3A   PB   O3B  PG  -115.08  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
 T8T  chir_03  C1'  N9   O4'  C2'  positiv
 T8T  chir_04  C3'  O3'  C4'  C2'  positiv
 T8T  chir_05  C4'  O4'  C3'  C5'  negativ
 T8T  chir_06  PA   O5'  O2A  O3A  both
 T8T  chir_07  PB   O3A  O1B  O2B  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
 T8T  plan-1  N1    0.020
 T8T  plan-1  C2    0.020
 T8T  plan-1  N2    0.020
 T8T  plan-1  N3    0.020
 T8T  plan-1  C4    0.020
 T8T  plan-1  C5    0.020
 T8T  plan-1  C6    0.020
 T8T  plan-1  O6    0.020
 T8T  plan-1  N7    0.020
 T8T  plan-1  C8    0.020
 T8T  plan-1  N9    0.020
 T8T  plan-1  C1'   0.020
 T8T  plan-1  HN2   0.020
 T8T  plan-1  HN2A  0.020
 T8T  plan-1  HN3   0.020
 T8T  plan-1  H8    0.020

