# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jul  7 00:05:45 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} hydrogen (S)-phosphorothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O[P@](S)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)[C@H]2O
#
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
 CSV  CSV  'O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} hydrogen (S)-phosphorothioate'  ligand  61  37  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CSV
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
 CSV  O1    O  OH1   0  -0.706  -5.9162   1.6087   0.2407
 CSV  C2    C  CH2   0  -0.228  -4.9454   1.9127  -0.7294
 CSV  C3    C  CH1   0   0.099  -3.6394   2.1923  -0.0118
 CSV  O4    O  O2    0  -0.512  -3.2193   1.0593   0.7503
 CSV  C5    C  CH1   0  -0.124  -2.4974   2.4839  -0.9790
 CSV  O6    O  O2    0  -0.600  -1.5737   3.3404  -0.2951
 CSV  C7    C  CH1   0  -0.001  -1.9285   1.0828  -1.1930
 CSV  O8    O  OH1   0  -0.662  -0.6139   1.0214  -1.6467
 CSV  C9    C  CH1   0   0.207  -2.0283   0.5358   0.2304
 CSV  N10   N  NR6   0  -0.640  -1.9770  -0.8990   0.4039
 CSV  C11   C  CR6   0   0.585  -2.7616  -1.7855  -0.3645
 CSV  N12   N  N     0  -0.486  -2.5822  -3.1088  -0.1780
 CSV  C13   C  CR6   0   0.514  -1.7969  -3.5687   0.7718
 CSV  C14   C  CR16  0  -0.485  -1.0983  -2.6985   1.6655
 CSV  C15   C  CR16  0   0.178  -1.2179  -1.3812   1.4227
 CSV  O16   O  O     0  -0.491  -3.5603  -1.3412  -1.1739
 CSV  N17   N  NH2   0  -0.775  -1.6645  -4.8881   0.9017
 CSV  P18   P  P     0   1.255  -0.1427   3.7801  -0.8551
 CSV  O19   O  O     0  -0.629   0.0723   3.7847  -2.3156
 CSV  S20   S  S2    0  -0.434   0.0512   5.7269  -0.1389
 CSV  O21   O  O2    0  -0.551   0.8460   2.9207   0.0608
 CSV  C22   C  CH2   0  -0.194   2.0545   2.3580  -0.4440
 CSV  C23   C  CH1   0  -0.006   2.6760   1.5313   0.6534
 CSV  O24   O  O2    0  -0.455   1.7825   0.5098   1.0844
 CSV  C25   C  CH1   0   0.028   3.9205   0.7792   0.1945
 CSV  O26   O  OH1   0  -0.683   5.0426   1.6108   0.2479
 CSV  C27   C  CH1   0  -0.062   3.9563  -0.3859   1.1905
 CSV  O28   O  OH1   0  -0.686   4.4527   0.0324   2.4307
 CSV  C29   C  CH1   0   0.198   2.4643  -0.6748   1.3678
 CSV  N30   N  NR6   0  -0.644   1.9859  -1.7422   0.4667
 CSV  C31   C  CR6   0   0.670   2.2342  -3.0367   0.8728
 CSV  N32   N  NR16  0  -0.689   1.7159  -4.0072   0.0600
 CSV  C33   C  CR6   0   0.540   0.9832  -3.8411  -1.1098
 CSV  C34   C  CR16  0  -0.469   0.7543  -2.4577  -1.4404
 CSV  C35   C  CR16  0   0.098   1.2575  -1.4886  -0.6577
 CSV  O36   O  O     0  -0.413   2.8659  -3.2918   1.8779
 CSV  O37   O  O     0  -0.407   0.6019  -4.8073  -1.7404
 CSV  HO1   H  HOH1  0   0.424  -6.7380   1.4086  -0.2153
 CSV  H2    H  HCH2  0   0.250  -4.8161   1.0932  -1.4448
 CSV  H2A   H  HCH2  0   0.247  -5.2083   2.8115  -1.3022
 CSV  H3    H  HCH1  0   0.282  -3.7867   3.0356   0.6705
 CSV  H5    H  HCH1  0   0.313  -2.8253   2.9626  -1.9047
 CSV  H7    H  HCH1  0   0.232  -2.6102   0.5543  -1.8615
 CSV  HO8   H  HOH1  0   0.447  -0.5987   1.1784  -2.5964
 CSV  H9    H  HCH1  0   0.259  -1.1634   0.9136   0.7902
 CSV  H14   H  HCR6  0   0.285  -0.5011  -3.0667   2.4863
 CSV  H15   H  HCR6  0   0.286  -0.7047  -0.6454   2.0269
 CSV  HN17  H  HNH2  0   0.415  -2.0848  -5.5022   0.2252
 CSV  HN1A  H  HNH2  0   0.425  -1.0293  -5.2878   1.5690
 CSV  HS20  H  HSH1  0   0.261  -0.0600   5.4453   1.1666
 CSV  H22   H  HCH2  0   0.234   1.8539   1.7485  -1.3266
 CSV  H22A  H  HCH2  0   0.251   2.7596   3.1447  -0.7261
 CSV  H23   H  HCH1  0   0.239   2.9221   2.1806   1.5022
 CSV  H25   H  HCH1  0   0.285   3.7583   0.3824  -0.8178
 CSV  HO26  H  HOH1  0   0.458   5.7382   1.2325  -0.2993
 CSV  H27   H  HCH1  0   0.305   4.5035  -1.2513   0.7993
 CSV  HO28  H  HOH1  0   0.428   5.2021   0.6180   2.2681
 CSV  H29   H  HCH1  0   0.302   2.2466  -0.9982   2.3877
 CSV  H34   H  HCR6  0   0.300   0.1742  -2.2054  -2.3142
 CSV  H35   H  HCR6  0   0.302   1.0665  -0.4523  -0.8836
 CSV  HN32  H  HNR6  0   0.428   1.9134  -4.9585   0.3446

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
 CSV  O1   C2    single  1.406  0.020  1.406
 CSV  O1   HO1   single  0.850  0.020  0.980
 CSV  C2   C3    single  1.516  0.020  1.516
 CSV  C2   H2    single  0.970  0.020  1.090
 CSV  C2   H2A   single  0.970  0.020  1.090
 CSV  C5   C3    single  1.525  0.020  1.525
 CSV  O4   C3    single  1.429  0.020  1.429
 CSV  C3   H3    single  0.970  0.020  1.090
 CSV  C9   O4    single  1.401  0.020  1.401
 CSV  C5   C7    single  1.527  0.020  1.527
 CSV  C5   O6    single  1.433  0.020  1.433
 CSV  C5   H5    single  0.970  0.020  1.090
 CSV  P18  O6    single  1.598  0.020  1.598
 CSV  C9   C7    single  1.528  0.020  1.528
 CSV  C7   O8    single  1.392  0.020  1.392
 CSV  C7   H7    single  0.970  0.020  1.090
 CSV  O8   HO8   single  0.850  0.020  0.980
 CSV  N10  C9    single  1.446  0.020  1.446
 CSV  C9   H9    single  0.970  0.020  1.090
 CSV  C15  N10   single  1.359  0.020  1.359
 CSV  C11  N10   single  1.411  0.020  1.411
 CSV  N12  C11   single  1.348  0.020  1.348
 CSV  C11  O16   double  1.221  0.020  1.221
 CSV  C13  N12   double  1.315  0.020  1.315
 CSV  N17  C13   single  1.332  0.020  1.332
 CSV  C13  C14   single  1.430  0.020  1.430
 CSV  C14  C15   double  1.345  0.020  1.345
 CSV  C14  H14   single  0.930  0.020  1.080
 CSV  C15  H15   single  0.930  0.020  1.080
 CSV  N17  HN17  single  0.860  0.020  1.020
 CSV  N17  HN1A  single  0.860  0.020  1.020
 CSV  S20  P18   single  2.083  0.020  2.083
 CSV  P18  O19   double  1.476  0.020  1.476
 CSV  P18  O21   single  1.598  0.020  1.598
 CSV  S20  HS20  single  1.200  0.020  1.300
 CSV  O21  C22   single  1.425  0.020  1.425
 CSV  C22  C23   single  1.508  0.020  1.508
 CSV  C22  H22   single  0.970  0.020  1.090
 CSV  C22  H22A  single  0.970  0.020  1.090
 CSV  C23  C25   single  1.525  0.020  1.525
 CSV  C23  O24   single  1.424  0.020  1.424
 CSV  C23  H23   single  0.970  0.020  1.090
 CSV  O24  C29   single  1.396  0.020  1.396
 CSV  C25  O26   single  1.398  0.020  1.398
 CSV  C25  C27   single  1.533  0.020  1.533
 CSV  C25  H25   single  0.970  0.020  1.090
 CSV  O26  HO26  single  0.850  0.020  0.980
 CSV  C27  C29   single  1.530  0.020  1.530
 CSV  C27  O28   single  1.400  0.020  1.400
 CSV  C27  H27   single  0.970  0.020  1.090
 CSV  O28  HO28  single  0.850  0.020  0.980
 CSV  C29  N30   single  1.477  0.020  1.477
 CSV  C29  H29   single  0.970  0.020  1.090
 CSV  C35  N30   single  1.364  0.020  1.364
 CSV  N30  C31   single  1.379  0.020  1.379
 CSV  C31  N32   single  1.368  0.020  1.368
 CSV  C31  O36   double  1.214  0.020  1.214
 CSV  C33  N32   single  1.390  0.020  1.390
 CSV  C34  C33   single  1.441  0.020  1.441
 CSV  C33  O37   double  1.215  0.020  1.215
 CSV  C35  C34   double  1.344  0.020  1.344
 CSV  C34  H34   single  0.930  0.020  1.080
 CSV  C35  H35   single  0.930  0.020  1.080
 CSV  N32  HN32  single  0.860  0.020  1.020

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
 CSV  HO1   O1   C2    107.95  3.000
 CSV  H2A   C2   H2    107.46  3.000
 CSV  H2A   C2   C3    107.59  3.000
 CSV  H2    C2   C3    110.20  3.000
 CSV  H2A   C2   O1    111.83  3.000
 CSV  H2    C2   O1    111.74  3.000
 CSV  C3    C2   O1    107.95  3.000
 CSV  H3    C3   C5    110.42  3.000
 CSV  H3    C3   O4    108.54  3.000
 CSV  C5    C3   O4    105.65  3.000
 CSV  H3    C3   C2    108.73  3.000
 CSV  O4    C3   C2    111.06  3.000
 CSV  C5    C3   C2    112.35  3.000
 CSV  C9    O4   C3    110.39  3.000
 CSV  H5    C5   C7    113.27  3.000
 CSV  H5    C5   O6    109.62  3.000
 CSV  C7    C5   O6    112.02  3.000
 CSV  H5    C5   C3    113.36  3.000
 CSV  O6    C5   C3    107.11  3.000
 CSV  C7    C5   C3    101.10  3.000
 CSV  P18   O6   C5    125.04  3.000
 CSV  H7    C7   C9    110.89  3.000
 CSV  H7    C7   O8    111.65  3.000
 CSV  C9    C7   O8    110.45  3.000
 CSV  H7    C7   C5    107.30  3.000
 CSV  O8    C7   C5    115.97  3.000
 CSV  C9    C7   C5     99.99  3.000
 CSV  HO8   O8   C7    109.22  3.000
 CSV  H9    C9   N10   104.62  3.000
 CSV  H9    C9   C7    107.49  3.000
 CSV  N10   C9   C7    117.68  3.000
 CSV  H9    C9   O4    110.62  3.000
 CSV  N10   C9   O4    110.87  3.000
 CSV  C7    C9   O4    105.51  3.000
 CSV  C15   N10  C11   119.72  3.000
 CSV  C11   N10  C9    122.56  3.000
 CSV  C15   N10  C9    117.50  3.000
 CSV  O16   C11  N12   122.40  3.000
 CSV  O16   C11  N10   119.74  3.000
 CSV  N12   C11  N10   117.85  3.000
 CSV  C13   N12  C11   121.50  3.000
 CSV  N17   C13  C14   119.56  3.000
 CSV  C14   C13  N12   122.02  3.000
 CSV  N17   C13  N12   118.42  3.000
 CSV  H14   C14  C15   121.36  3.000
 CSV  H14   C14  C13   122.53  3.000
 CSV  C15   C14  C13   116.10  3.000
 CSV  H15   C15  C14   121.56  3.000
 CSV  H15   C15  N10   116.26  3.000
 CSV  C14   C15  N10   122.18  3.000
 CSV  HN1A  N17  HN17  117.92  3.000
 CSV  HN1A  N17  C13   121.45  3.000
 CSV  HN17  N17  C13   119.84  3.000
 CSV  O21   P18  S20   104.35  3.000
 CSV  O21   P18  O19   118.58  3.000
 CSV  S20   P18  O19   108.88  3.000
 CSV  O21   P18  O6    101.83  3.000
 CSV  O19   P18  O6    118.55  3.000
 CSV  S20   P18  O6    102.71  3.000
 CSV  HS20  S20  P18    97.52  3.000
 CSV  C22   O21  P18   122.26  3.000
 CSV  H22A  C22  H22   108.17  3.000
 CSV  H22A  C22  C23   108.44  3.000
 CSV  H22   C22  C23   110.99  3.000
 CSV  H22A  C22  O21   110.74  3.000
 CSV  H22   C22  O21   110.55  3.000
 CSV  C23   C22  O21   107.94  3.000
 CSV  H23   C23  C25   109.99  3.000
 CSV  H23   C23  O24   109.35  3.000
 CSV  C25   C23  O24   104.44  3.000
 CSV  H23   C23  C22   109.33  3.000
 CSV  O24   C23  C22   110.79  3.000
 CSV  C25   C23  C22   112.82  3.000
 CSV  C29   O24  C23   111.33  3.000
 CSV  H25   C25  C27   109.11  3.000
 CSV  H25   C25  O26   111.61  3.000
 CSV  C27   C25  O26   114.12  3.000
 CSV  H25   C25  C23   109.56  3.000
 CSV  C27   C25  C23   101.44  3.000
 CSV  O26   C25  C23   110.50  3.000
 CSV  HO26  O26  C25   108.94  3.000
 CSV  H27   C27  C29   112.28  3.000
 CSV  H27   C27  O28   112.03  3.000
 CSV  C29   C27  O28   107.43  3.000
 CSV  H27   C27  C25   112.32  3.000
 CSV  O28   C27  C25   110.90  3.000
 CSV  C29   C27  C25   101.30  3.000
 CSV  HO28  O28  C27   107.91  3.000
 CSV  H29   C29  N30   106.94  3.000
 CSV  H29   C29  C27   111.01  3.000
 CSV  N30   C29  C27   112.44  3.000
 CSV  H29   C29  O24   110.10  3.000
 CSV  N30   C29  O24   109.35  3.000
 CSV  C27   C29  O24   107.01  3.000
 CSV  C35   N30  C31   120.90  3.000
 CSV  C31   N30  C29   116.14  3.000
 CSV  C35   N30  C29   122.81  3.000
 CSV  O36   C31  N32   122.68  3.000
 CSV  O36   C31  N30   122.31  3.000
 CSV  N32   C31  N30   115.01  3.000
 CSV  HN32  N32  C33   116.84  3.000
 CSV  HN32  N32  C31   115.20  3.000
 CSV  C33   N32  C31   127.95  3.000
 CSV  O37   C33  C34   126.48  3.000
 CSV  O37   C33  N32   120.47  3.000
 CSV  C34   C33  N32   113.05  3.000
 CSV  H34   C34  C35   120.31  3.000
 CSV  H34   C34  C33   119.73  3.000
 CSV  C35   C34  C33   119.96  3.000
 CSV  H35   C35  C34   120.34  3.000
 CSV  H35   C35  N30   116.51  3.000
 CSV  C34   C35  N30   123.12  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
 CSV  CONST_01  N12   C11  N10  C9    180.00   0.0  0
 CSV  CONST_02  C13   N12  C11  N10     0.00   0.0  0
 CSV  CONST_03  C14   C13  N12  C11     0.00   0.0  0
 CSV  CONST_04  C15   N10  C11  N12     0.00   0.0  0
 CSV  CONST_05  N32   C31  N30  C29   180.00   0.0  0
 CSV  CONST_06  C33   N32  C31  N30     0.00   0.0  0
 CSV  CONST_07  C34   C33  N32  C31     0.00   0.0  0
 CSV  CONST_08  C35   N30  C31  N32     0.00   0.0  0
 CSV  CONST_09  O16   C11  N10  C9      0.00   0.0  0
 CSV  CONST_10  N17   C13  N12  C11   180.00   0.0  0
 CSV  CONST_11  O16   C11  N12  C13   180.00   0.0  0
 CSV  CONST_12  O16   C11  N10  C15   180.00   0.0  0
 CSV  CONST_13  O36   C31  N30  C29     0.00   0.0  0
 CSV  CONST_14  O37   C33  N32  C31   180.00   0.0  0
 CSV  CONST_15  O36   C31  N32  C33   180.00   0.0  0
 CSV  CONST_16  O36   C31  N30  C35   180.00   0.0  0
 CSV  CONST_17  HN32  N32  C31  N30   180.00   0.0  0
 CSV  CONST_18  HN17  N17  C13  N12     0.00   0.0  0
 CSV  CONST_19  HN1A  N17  C13  N12   180.00   0.0  0
 CSV  Var_01    S20   P18  O6   C5    145.23  30.0  2
 CSV  Var_02    C23   C22  O21  P18  -175.67  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
 CSV  chir_01  C3   C2   C5   O4   positiv
 CSV  chir_02  C5   O6   C7   C3   negativ
 CSV  chir_03  C7   O8   C9   C5   negativ
 CSV  chir_04  C9   O4   N10  C7   negativ
 CSV  chir_06  C23  C22  C25  O24  positiv
 CSV  chir_07  C25  O26  C27  C23  negativ
 CSV  chir_08  C27  O28  C29  C25  negativ
 CSV  chir_09  C29  O24  N30  C27  negativ
 CSV  chir_10  P18  S20  O19  O21  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
 CSV  plan-1  C9    0.020
 CSV  plan-1  N10   0.020
 CSV  plan-1  C11   0.020
 CSV  plan-1  N12   0.020
 CSV  plan-1  C13   0.020
 CSV  plan-1  C14   0.020
 CSV  plan-1  C15   0.020
 CSV  plan-1  O16   0.020
 CSV  plan-1  N17   0.020
 CSV  plan-1  H14   0.020
 CSV  plan-1  H15   0.020
 CSV  plan-1  HN17  0.020
 CSV  plan-1  HN1A  0.020
 CSV  plan-2  C29   0.020
 CSV  plan-2  N30   0.020
 CSV  plan-2  C31   0.020
 CSV  plan-2  N32   0.020
 CSV  plan-2  C33   0.020
 CSV  plan-2  C34   0.020
 CSV  plan-2  C35   0.020
 CSV  plan-2  O36   0.020
 CSV  plan-2  O37   0.020
 CSV  plan-2  H34   0.020
 CSV  plan-2  H35   0.020
 CSV  plan-2  HN32  0.020

