# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 05:35:35 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(ccc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 7DT  7DT  '[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  48  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_7DT
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
 7DT  O3G  O  OH1   0  -0.665  21.3465    1.3769  3.5816
 7DT  PG   P  P     0   1.493  20.3313    1.1499  2.3894
 7DT  O2G  O  O     0  -0.757  20.8609    1.1013  1.0183
 7DT  O1G  O  OH1   0  -0.638  19.2426    2.2287  2.7714
 7DT  O3B  O  O2    0  -0.600  19.5674   -0.2367  2.8076
 7DT  PB   P  P     0   1.436  19.8760   -1.7064  2.2405
 7DT  O2B  O  O     0  -0.722  19.2645   -2.0508  0.9529
 7DT  O1B  O  OH1   0  -0.671  21.4456   -1.8060  2.3942
 7DT  O3A  O  O2    0  -0.724  19.3656   -2.5845  3.4941
 7DT  PA   P  P     0   1.476  17.8408   -3.0731  3.7697
 7DT  O1A  O  OH1   0  -0.658  17.9461   -4.5304  3.1487
 7DT  O2A  O  O     0  -0.814  16.8007   -2.1667  3.2683
 7DT  O5'  O  O2    0  -0.552  17.8119   -3.2034  5.3432
 7DT  C5'  C  CH2   0  -0.200  18.6584   -4.0656  6.1141
 7DT  C4'  C  CH1   0  -0.024  17.7807   -4.8710  7.0491
 7DT  O4'  O  O2    0  -0.496  16.8651   -5.6600  6.2934
 7DT  C1'  C  CH1   0   0.164  17.1128   -7.0333  6.4946
 7DT  N9   N  NR5   0  -0.558  16.9127   -7.7451  5.2689
 7DT  C8   C  CR15  0   0.050  17.6769   -7.6361  4.1233
 7DT  C20  C  CR15  0  -0.489  17.1200   -8.3682  3.1218
 7DT  C5   C  CR56  0   0.058  15.9417   -8.9616  3.6676
 7DT  C6   C  CR6   0   0.287  14.9101   -9.8105  3.2206
 7DT  N6   N  NH2   0  -0.824  14.8759  -10.3070  1.9775
 7DT  N1   N  N     0  -0.376  13.9346  -10.1520  4.0672
 7DT  C2   C  CR16  0   0.043  13.9735   -9.6758  5.3101
 7DT  N3   N  N     0  -0.428  14.8741   -8.8788  5.8493
 7DT  C4   C  CR56  0   0.455  15.8433   -8.5462  4.9959
 7DT  C2'  C  CH1   0  -0.038  18.5351   -7.1092  7.0461
 7DT  O2'  O  OH1   0  -0.669  18.7090   -8.3023  7.7492
 7DT  C3'  C  CH1   0   0.006  18.5869   -5.8437  7.9055
 7DT  O3'  O  OH1   0  -0.599  17.9120   -6.0343  9.1209
 7DT  H1   H  HOH1  0   0.529  22.2756    1.2425  3.3510
 7DT  H2   H  HOH1  0   0.536  18.5287    2.3350  2.1265
 7DT  H3   H  HOH1  0   0.534  21.8928   -2.3135  1.7013
 7DT  H4   H  HOH1  0   0.519  17.1201   -5.0355  3.1353
 7DT  H5   H  HCH2  0   0.201  19.2544   -4.7185  5.4712
 7DT  H6   H  HCH2  0   0.239  19.3430   -3.4384  6.6855
 7DT  H7   H  HCH1  0   0.247  17.2196   -4.1802  7.6866
 7DT  H8   H  HCH1  0   0.295  16.4082   -7.4578  7.2170
 7DT  H9   H  HCR5  0   0.311  18.5792   -7.0471  4.1119
 7DT  H10  H  HCR5  0   0.214  17.5144   -8.4714  2.1236
 7DT  H11  H  HNH2  0   0.363  14.0665  -10.8201  1.6726
 7DT  H12  H  HNH2  0   0.368  15.5106   -9.9810  1.2702
 7DT  H13  H  HCR6  0   0.295  13.1573   -9.9852  5.9548
 7DT  H14  H  HCH1  0   0.287  19.2612   -7.0123  6.2294
 7DT  H15  H  HOH1  0   0.449  19.6476   -8.5113  7.7900
 7DT  H16  H  HCH1  0   0.195  19.6162   -5.4939  8.0635
 7DT  H17  H  HOH1  0   0.453  18.1999   -6.8779  9.4902

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
 7DT  O2B  PB   double    1.466  0.020  1.466
 7DT  O2A  PA   double    1.468  0.020  1.468
 7DT  O1A  PA   single    1.588  0.020  1.588
 7DT  PA   O3A  single    1.625  0.020  1.625
 7DT  PA   O5'  single    1.579  0.020  1.579
 7DT  PB   O3A  single    1.613  0.020  1.613
 7DT  PB   O1B  single    1.580  0.020  1.580
 7DT  PB   O3B  single    1.605  0.020  1.605
 7DT  O3B  PG   single    1.637  0.020  1.637
 7DT  O2G  PG   double    1.471  0.020  1.471
 7DT  O5'  C5'  single    1.433  0.020  1.433
 7DT  C20  C8   aromatic  1.360  0.020  1.360
 7DT  C20  C5   aromatic  1.428  0.020  1.428
 7DT  N6   C6   single    1.339  0.020  1.339
 7DT  C8   N9   aromatic  1.381  0.020  1.381
 7DT  PG   O1G  single    1.580  0.020  1.580
 7DT  PG   O3G  single    1.582  0.020  1.582
 7DT  C5   C6   aromatic  1.409  0.020  1.409
 7DT  C5   C4   aromatic  1.395  0.020  1.395
 7DT  C6   N1   aromatic  1.336  0.020  1.336
 7DT  C5'  C4'  single    1.514  0.020  1.514
 7DT  O4'  C4'  single    1.425  0.020  1.425
 7DT  O4'  C1'  single    1.410  0.020  1.410
 7DT  N9   C4   aromatic  1.364  0.020  1.364
 7DT  N9   C1'  single    1.431  0.020  1.431
 7DT  C4   N3   aromatic  1.334  0.020  1.334
 7DT  N1   C2   aromatic  1.332  0.020  1.332
 7DT  C4'  C3'  single    1.526  0.020  1.526
 7DT  C1'  C2'  single    1.527  0.020  1.527
 7DT  N3   C2   aromatic  1.318  0.020  1.318
 7DT  C2'  C3'  single    1.531  0.020  1.531
 7DT  C2'  O2'  single    1.396  0.020  1.396
 7DT  C3'  O3'  single    1.403  0.020  1.403
 7DT  O3G  H1   single    0.850  0.020  0.980
 7DT  O1G  H2   single    0.850  0.020  0.980
 7DT  O1B  H3   single    0.850  0.020  0.980
 7DT  O1A  H4   single    0.850  0.020  0.980
 7DT  C5'  H5   single    0.970  0.020  1.090
 7DT  C5'  H6   single    0.970  0.020  1.090
 7DT  C4'  H7   single    0.970  0.020  1.090
 7DT  C1'  H8   single    0.970  0.020  1.090
 7DT  C8   H9   single    0.930  0.020  1.080
 7DT  C20  H10  single    0.930  0.020  1.080
 7DT  N6   H11  single    0.860  0.020  1.020
 7DT  N6   H12  single    0.860  0.020  1.020
 7DT  C2   H13  single    0.930  0.020  1.080
 7DT  C2'  H14  single    0.970  0.020  1.090
 7DT  O2'  H15  single    0.850  0.020  0.980
 7DT  C3'  H16  single    0.970  0.020  1.090
 7DT  O3'  H17  single    0.850  0.020  0.980

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
 7DT  H1   O3G  PG   114.64  3.000
 7DT  O3B  PG   O1G  101.24  3.000
 7DT  O1G  PG   O2G  119.75  3.000
 7DT  O3B  PG   O2G  112.22  3.000
 7DT  O1G  PG   O3G   99.33  3.000
 7DT  O2G  PG   O3G  118.44  3.000
 7DT  O3B  PG   O3G  103.20  3.000
 7DT  H2   O1G  PG   114.97  3.000
 7DT  PB   O3B  PG   126.54  3.000
 7DT  O3A  PB   O1B  101.79  3.000
 7DT  O1B  PB   O2B  119.00  3.000
 7DT  O3A  PB   O2B  114.99  3.000
 7DT  O1B  PB   O3B  102.37  3.000
 7DT  O3A  PB   O3B   99.38  3.000
 7DT  O2B  PB   O3B  116.43  3.000
 7DT  H3   O1B  PB   114.97  3.000
 7DT  PA   O3A  PB   126.33  3.000
 7DT  O5'  PA   O2A  112.23  3.000
 7DT  O5'  PA   O1A  108.37  3.000
 7DT  O2A  PA   O1A  118.70  3.000
 7DT  O5'  PA   O3A  102.18  3.000
 7DT  O1A  PA   O3A   98.48  3.000
 7DT  O2A  PA   O3A  114.92  3.000
 7DT  H4   O1A  PA   115.32  3.000
 7DT  C5'  O5'  PA   125.08  3.000
 7DT  H6   C5'  H5   108.03  3.000
 7DT  H6   C5'  C4'  110.26  3.000
 7DT  H5   C5'  C4'  111.20  3.000
 7DT  H6   C5'  O5'  107.86  3.000
 7DT  H5   C5'  O5'  111.41  3.000
 7DT  C4'  C5'  O5'  108.04  3.000
 7DT  H7   C4'  C3'  110.25  3.000
 7DT  H7   C4'  O4'  109.19  3.000
 7DT  C3'  C4'  O4'  106.50  3.000
 7DT  H7   C4'  C5'  108.73  3.000
 7DT  C3'  C4'  C5'  112.29  3.000
 7DT  O4'  C4'  C5'  109.84  3.000
 7DT  C1'  O4'  C4'  110.53  3.000
 7DT  H8   C1'  C2'  109.99  3.000
 7DT  H8   C1'  N9   106.40  3.000
 7DT  C2'  C1'  N9   114.50  3.000
 7DT  H8   C1'  O4'  111.02  3.000
 7DT  C2'  C1'  O4'  105.28  3.000
 7DT  N9   C1'  O4'  109.73  3.000
 7DT  C4   N9   C8   108.31  3.000
 7DT  C4   N9   C1'  124.96  3.000
 7DT  C8   N9   C1'  126.41  3.000
 7DT  H9   C8   C20  129.00  3.000
 7DT  H9   C8   N9   121.01  3.000
 7DT  C20  C8   N9   109.98  3.000
 7DT  H10  C20  C5   128.02  3.000
 7DT  H10  C20  C8   125.71  3.000
 7DT  C5   C20  C8   106.27  3.000
 7DT  C4   C5   C6   115.45  3.000
 7DT  C4   C5   C20  107.36  3.000
 7DT  C6   C5   C20  137.18  3.000
 7DT  N1   C6   N6   118.35  3.000
 7DT  N1   C6   C5   119.19  3.000
 7DT  N6   C6   C5   122.45  3.000
 7DT  H12  N6   H11  117.43  3.000
 7DT  H12  N6   C6   121.14  3.000
 7DT  H11  N6   C6   119.41  3.000
 7DT  C2   N1   C6   118.60  3.000
 7DT  H13  C2   N3   116.31  3.000
 7DT  H13  C2   N1   115.51  3.000
 7DT  N3   C2   N1   128.18  3.000
 7DT  C4   N3   C2   112.68  3.000
 7DT  N3   C4   C5   125.89  3.000
 7DT  N3   C4   N9   126.04  3.000
 7DT  C5   C4   N9   108.07  3.000
 7DT  H14  C2'  C3'  108.81  3.000
 7DT  H14  C2'  O2'  111.59  3.000
 7DT  C3'  C2'  O2'  114.82  3.000
 7DT  H14  C2'  C1'  110.07  3.000
 7DT  O2'  C2'  C1'  109.90  3.000
 7DT  C3'  C2'  C1'  101.14  3.000
 7DT  H15  O2'  C2'  109.18  3.000
 7DT  H16  C3'  O3'  111.67  3.000
 7DT  H16  C3'  C2'  112.07  3.000
 7DT  O3'  C3'  C2'  110.96  3.000
 7DT  H16  C3'  C4'  111.88  3.000
 7DT  O3'  C3'  C4'  108.57  3.000
 7DT  C2'  C3'  C4'  101.19  3.000
 7DT  H17  O3'  C3'  107.86  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
 7DT  CONST_01  C5   C20  C8   N9      0.00   0.0  0
 7DT  CONST_02  C20  C5   C4   N9      0.00   0.0  0
 7DT  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 7DT  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 7DT  CONST_05  C6   C5   C20  C8    180.00   0.0  0
 7DT  CONST_06  C4   C5   C20  C8      0.00   0.0  0
 7DT  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 7DT  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 7DT  CONST_09  C4   N9   C8   C20     0.00   0.0  0
 7DT  CONST_10  N1   C6   C5   C20   180.00   0.0  0
 7DT  CONST_11  N3   C4   C5   C20   180.00   0.0  0
 7DT  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 7DT  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 7DT  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 7DT  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 7DT  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 7DT  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 7DT  CONST_18  C20  C8   N9   C1'   180.00   0.0  0
 7DT  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 7DT  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 7DT  CONST_21  N6   C6   C5   C20     0.00   0.0  0
 7DT  CONST_22  C4   C5   C6   N6    180.00   0.0  0
 7DT  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 7DT  CONST_24  H9   C8   N9   C1'     0.00   0.0  0
 7DT  CONST_25  H10  C20  C8   N9    180.00   0.0  0
 7DT  CONST_26  H13  C2   N1   C6    180.00   0.0  0
 7DT  CONST_27  H11  N6   C6   C5    180.00   0.0  0
 7DT  CONST_28  H12  N6   C6   C5      0.00   0.0  0
 7DT  Var_01    C4'  C5'  O5'  PA   -129.19  30.0  3
 7DT  Var_02    O2B  PB   O3B  PG    -82.35  30.0  1
 7DT  Var_03    O2A  PA   O3A  PB    -30.91  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
 7DT  chir_03  C4'  C5'  O4'  C3'  negativ
 7DT  chir_04  C1'  O4'  N9   C2'  negativ
 7DT  chir_05  C2'  O2'  C1'  C3'  negativ
 7DT  chir_06  C3'  O3'  C4'  C2'  positiv
 7DT  chir_07  PB   O3A  O1B  O3B  both
 7DT  chir_08  PA   O1A  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
 7DT  plan-1  C1'  0.020
 7DT  plan-1  N9   0.020
 7DT  plan-1  C8   0.020
 7DT  plan-1  C20  0.020
 7DT  plan-1  C5   0.020
 7DT  plan-1  C6   0.020
 7DT  plan-1  N6   0.020
 7DT  plan-1  N1   0.020
 7DT  plan-1  C2   0.020
 7DT  plan-1  N3   0.020
 7DT  plan-1  C4   0.020
 7DT  plan-1  H9   0.020
 7DT  plan-1  H10  0.020
 7DT  plan-1  H13  0.020
 7DT  plan-2  C6   0.020
 7DT  plan-2  N6   0.020
 7DT  plan-2  H11  0.020
 7DT  plan-2  H12  0.020

