# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 12:38:01 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 (R)-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
 CSQ  CSQ  '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 (R)-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_CSQ
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
 CSQ  O1    O  OH1   0  -0.670  -4.7313   2.5277   2.7855
 CSQ  C2    C  CH2   0  -0.149  -4.2793   2.6817   1.4634
 CSQ  C3    C  CH1   0  -0.002  -3.1829   1.6620   1.2216
 CSQ  O4    O  O2    0  -0.485  -3.6597   0.3281   1.3993
 CSQ  C5    C  CH1   0  -0.092  -2.6418   1.7222  -0.2027
 CSQ  O6    O  O2    0  -0.567  -1.2848   1.2702  -0.2102
 CSQ  C7    C  CH1   0  -0.017  -3.4849   0.6663  -0.9192
 CSQ  O8    O  OH1   0  -0.653  -2.8951   0.0985  -2.0469
 CSQ  C9    C  CH1   0   0.231  -3.6128  -0.3772   0.1930
 CSQ  N10   N  NR6   0  -0.569  -4.7274  -1.2974   0.0867
 CSQ  C11   C  CR6   0   0.606  -6.0617  -0.8457   0.0419
 CSQ  N12   N  N     0  -0.540  -7.0425  -1.7678  -0.0285
 CSQ  C13   C  CR6   0   0.516  -6.7732  -3.0578  -0.0567
 CSQ  C14   C  CR16  0  -0.474  -5.4335  -3.5532  -0.0115
 CSQ  C15   C  CR16  0   0.098  -4.4592  -2.6289   0.0661
 CSQ  O16   O  O     0  -0.505  -6.2939   0.3540   0.0630
 CSQ  N17   N  NH2   0  -0.807  -7.7889  -3.9151  -0.1276
 CSQ  P18   P  P     0   1.224  -0.0927   2.1421  -0.7996
 CSQ  O19   O  O     0  -0.671   0.2497   3.3978  -0.1031
 CSQ  S20   S  S2    0  -0.356  -0.5221   2.6022  -2.7795
 CSQ  O21   O  O2    0  -0.556   0.9892   0.9710  -0.7960
 CSQ  C22   C  CH2   0  -0.208   2.3243   1.1992  -1.2514
 CSQ  C23   C  CH1   0   0.009   3.2408   1.5942  -0.1193
 CSQ  O24   O  O2    0  -0.493   3.2478   0.5882   0.8899
 CSQ  C25   C  CH1   0  -0.039   4.6951   1.7129  -0.5643
 CSQ  O26   O  OH1   0  -0.653   4.9384   2.9877  -1.0823
 CSQ  C27   C  CH1   0  -0.041   5.4415   1.4120   0.7402
 CSQ  O28   O  OH1   0  -0.662   5.4283   2.5215   1.5940
 CSQ  C29   C  CH1   0   0.187   4.5372   0.3468   1.3622
 CSQ  N30   N  NR6   0  -0.570   4.9580  -1.0208   0.9845
 CSQ  C31   C  CR6   0   0.741   6.0689  -1.5162   1.6357
 CSQ  N32   N  NR16  0  -0.731   6.4358  -2.7835   1.2742
 CSQ  C33   C  CR6   0   0.567   5.8214  -3.6158   0.3495
 CSQ  C34   C  CR16  0  -0.507   4.6571  -3.0264  -0.2608
 CSQ  C35   C  CR16  0   0.090   4.2799  -1.7827   0.0813
 CSQ  O36   O  O     0  -0.478   6.6753  -0.8709   2.4664
 CSQ  O37   O  O     0  -0.464   6.2663  -4.7259   0.1244
 CSQ  HO1   H  HOH1  0   0.458  -5.4821   3.1136   2.9144
 CSQ  H2    H  HCH2  0   0.216  -5.0885   2.5510   0.7380
 CSQ  H2A   H  HCH2  0   0.201  -3.8454   3.6767   1.2943
 CSQ  H3    H  HCH1  0   0.265  -2.3766   1.8396   1.9412
 CSQ  H5    H  HCH1  0   0.295  -2.7333   2.7172  -0.6457
 CSQ  H7    H  HCH1  0   0.281  -4.4569   1.1069  -1.1445
 CSQ  HO8   H  HOH1  0   0.468  -3.2947   0.4806  -2.8328
 CSQ  H9    H  HCH1  0   0.248  -2.7186  -1.0118   0.1573
 CSQ  H14   H  HCR6  0   0.290  -5.2065  -4.6082  -0.0291
 CSQ  H15   H  HCR6  0   0.320  -3.4158  -2.9084   0.1160
 CSQ  HN17  H  HNH2  0   0.404  -8.7365  -3.5784  -0.1503
 CSQ  HN1A  H  HNH2  0   0.415  -7.6394  -4.9084  -0.1444
 CSQ  HS20  H  HSH1  0   0.264  -0.8294   1.3587  -3.1726
 CSQ  H22   H  HCH2  0   0.262   2.6471   0.2650  -1.7129
 CSQ  H22A  H  HCH2  0   0.265   2.3585   1.9712  -2.0266
 CSQ  H23   H  HCH1  0   0.264   2.9060   2.5419   0.3173
 CSQ  H25   H  HCH1  0   0.250   4.9256   0.9282  -1.2983
 CSQ  HO26  H  HOH1  0   0.472   5.7467   2.9648  -1.6054
 CSQ  H27   H  HCH1  0   0.266   6.4577   1.0471   0.5566
 CSQ  HO28  H  HOH1  0   0.453   5.5572   3.3119   1.0552
 CSQ  H29   H  HCH1  0   0.292   4.5495   0.3960   2.4524
 CSQ  H34   H  HCR6  0   0.293   4.0874  -3.5912  -0.9819
 CSQ  H35   H  HCR6  0   0.323   3.3950  -1.3415  -0.3475
 CSQ  HN32  H  HNR6  0   0.428   7.2554  -3.1468   1.7462

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
 CSQ  O1   C2    single  1.406  0.020  1.406
 CSQ  O1   HO1   single  0.850  0.020  0.980
 CSQ  C2   C3    single  1.517  0.020  1.517
 CSQ  C2   H2    single  0.970  0.020  1.090
 CSQ  C2   H2A   single  0.970  0.020  1.090
 CSQ  C5   C3    single  1.525  0.020  1.525
 CSQ  O4   C3    single  1.428  0.020  1.428
 CSQ  C3   H3    single  0.970  0.020  1.090
 CSQ  C9   O4    single  1.398  0.020  1.398
 CSQ  C5   C7    single  1.529  0.020  1.529
 CSQ  C5   O6    single  1.430  0.020  1.430
 CSQ  C5   H5    single  0.970  0.020  1.090
 CSQ  P18  O6    single  1.590  0.020  1.590
 CSQ  C9   C7    single  1.530  0.020  1.530
 CSQ  C7   O8    single  1.394  0.020  1.394
 CSQ  C7   H7    single  0.970  0.020  1.090
 CSQ  O8   HO8   single  0.850  0.020  0.980
 CSQ  N10  C9    single  1.449  0.020  1.449
 CSQ  C9   H9    single  0.970  0.020  1.090
 CSQ  C15  N10   single  1.358  0.020  1.358
 CSQ  C11  N10   single  1.409  0.020  1.409
 CSQ  N12  C11   single  1.348  0.020  1.348
 CSQ  C11  O16   double  1.222  0.020  1.222
 CSQ  C13  N12   double  1.318  0.020  1.318
 CSQ  N17  C13   single  1.331  0.020  1.331
 CSQ  C13  C14   single  1.429  0.020  1.429
 CSQ  C14  C15   double  1.345  0.020  1.345
 CSQ  C14  H14   single  0.930  0.020  1.080
 CSQ  C15  H15   single  0.930  0.020  1.080
 CSQ  N17  HN17  single  0.860  0.020  1.020
 CSQ  N17  HN1A  single  0.860  0.020  1.020
 CSQ  O19  P18   double  1.476  0.020  1.476
 CSQ  P18  S20   single  2.078  0.020  2.078
 CSQ  P18  O21   single  1.594  0.020  1.594
 CSQ  S20  HS20  single  1.200  0.020  1.300
 CSQ  C22  O21   single  1.429  0.020  1.429
 CSQ  C22  C23   single  1.509  0.020  1.509
 CSQ  C22  H22   single  0.970  0.020  1.090
 CSQ  C22  H22A  single  0.970  0.020  1.090
 CSQ  C23  C25   single  1.525  0.020  1.525
 CSQ  C23  O24   single  1.425  0.020  1.425
 CSQ  C23  H23   single  0.970  0.020  1.090
 CSQ  O24  C29   single  1.394  0.020  1.394
 CSQ  C25  O26   single  1.397  0.020  1.397
 CSQ  C25  C27   single  1.533  0.020  1.533
 CSQ  C25  H25   single  0.970  0.020  1.090
 CSQ  O26  HO26  single  0.850  0.020  0.980
 CSQ  C27  C29   single  1.529  0.020  1.529
 CSQ  C27  O28   single  1.400  0.020  1.400
 CSQ  C27  H27   single  0.970  0.020  1.090
 CSQ  O28  HO28  single  0.850  0.020  0.980
 CSQ  C29  N30   single  1.480  0.020  1.480
 CSQ  C29  H29   single  0.970  0.020  1.090
 CSQ  C35  N30   single  1.362  0.020  1.362
 CSQ  N30  C31   single  1.380  0.020  1.380
 CSQ  C31  N32   single  1.368  0.020  1.368
 CSQ  C31  O36   double  1.214  0.020  1.214
 CSQ  C33  N32   single  1.387  0.020  1.387
 CSQ  C34  C33   single  1.441  0.020  1.441
 CSQ  C33  O37   double  1.217  0.020  1.217
 CSQ  C35  C34   double  1.344  0.020  1.344
 CSQ  C34  H34   single  0.930  0.020  1.080
 CSQ  C35  H35   single  0.930  0.020  1.080
 CSQ  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
 CSQ  HO1   O1   C2    108.10  3.000
 CSQ  H2A   C2   H2    107.35  3.000
 CSQ  H2A   C2   C3    107.39  3.000
 CSQ  H2    C2   C3    110.39  3.000
 CSQ  H2A   C2   O1    111.78  3.000
 CSQ  H2    C2   O1    111.87  3.000
 CSQ  C3    C2   O1    107.98  3.000
 CSQ  H3    C3   C5    110.25  3.000
 CSQ  H3    C3   O4    108.40  3.000
 CSQ  C5    C3   O4    105.77  3.000
 CSQ  H3    C3   C2    108.56  3.000
 CSQ  O4    C3   C2    111.53  3.000
 CSQ  C5    C3   C2    112.27  3.000
 CSQ  C9    O4   C3    110.65  3.000
 CSQ  H5    C5   C7    113.11  3.000
 CSQ  H5    C5   O6    111.40  3.000
 CSQ  C7    C5   O6    107.60  3.000
 CSQ  H5    C5   C3    112.63  3.000
 CSQ  O6    C5   C3    109.21  3.000
 CSQ  C7    C5   C3    102.40  3.000
 CSQ  P18   O6   C5    122.68  3.000
 CSQ  H7    C7   C9    110.55  3.000
 CSQ  H7    C7   O8    112.01  3.000
 CSQ  C9    C7   O8    110.22  3.000
 CSQ  H7    C7   C5    108.01  3.000
 CSQ  O8    C7   C5    115.28  3.000
 CSQ  C9    C7   C5    100.16  3.000
 CSQ  HO8   O8   C7    108.89  3.000
 CSQ  H9    C9   N10   104.90  3.000
 CSQ  H9    C9   C7    107.62  3.000
 CSQ  N10   C9   C7    116.35  3.000
 CSQ  H9    C9   O4    110.31  3.000
 CSQ  N10   C9   O4    110.97  3.000
 CSQ  C7    C9   O4    106.61  3.000
 CSQ  C15   N10  C11   120.04  3.000
 CSQ  C11   N10  C9    121.80  3.000
 CSQ  C15   N10  C9    118.14  3.000
 CSQ  O16   C11  N12   122.28  3.000
 CSQ  O16   C11  N10   119.60  3.000
 CSQ  N12   C11  N10   118.11  3.000
 CSQ  C13   N12  C11   121.46  3.000
 CSQ  N17   C13  C14   119.59  3.000
 CSQ  C14   C13  N12   122.02  3.000
 CSQ  N17   C13  N12   118.39  3.000
 CSQ  H14   C14  C15   121.35  3.000
 CSQ  H14   C14  C13   122.38  3.000
 CSQ  C15   C14  C13   116.27  3.000
 CSQ  H15   C15  C14   121.60  3.000
 CSQ  H15   C15  N10   116.31  3.000
 CSQ  C14   C15  N10   122.10  3.000
 CSQ  HN1A  N17  HN17  118.08  3.000
 CSQ  HN1A  N17  C13   121.61  3.000
 CSQ  HN17  N17  C13   120.30  3.000
 CSQ  O21   P18  S20   107.76  3.000
 CSQ  O21   P18  O19   117.80  3.000
 CSQ  S20   P18  O19   108.01  3.000
 CSQ  O21   P18  O6     96.03  3.000
 CSQ  S20   P18  O6    108.64  3.000
 CSQ  O19   P18  O6    117.74  3.000
 CSQ  HS20  S20  P18    96.98  3.000
 CSQ  C22   O21  P18   121.06  3.000
 CSQ  H22A  C22  H22   107.16  3.000
 CSQ  H22A  C22  C23   109.13  3.000
 CSQ  H22   C22  C23   111.21  3.000
 CSQ  H22A  C22  O21   111.57  3.000
 CSQ  H22   C22  O21   105.93  3.000
 CSQ  C23   C22  O21   111.73  3.000
 CSQ  H23   C23  C25   109.89  3.000
 CSQ  H23   C23  O24   109.26  3.000
 CSQ  C25   C23  O24   104.89  3.000
 CSQ  H23   C23  C22   109.85  3.000
 CSQ  O24   C23  C22   110.45  3.000
 CSQ  C25   C23  C22   112.37  3.000
 CSQ  C29   O24  C23   111.51  3.000
 CSQ  H25   C25  C27   109.03  3.000
 CSQ  H25   C25  O26   111.55  3.000
 CSQ  C27   C25  O26   114.20  3.000
 CSQ  H25   C25  C23   109.83  3.000
 CSQ  C27   C25  C23   101.57  3.000
 CSQ  O26   C25  C23   110.19  3.000
 CSQ  HO26  O26  C25   109.02  3.000
 CSQ  H27   C27  C29   112.63  3.000
 CSQ  H27   C27  O28   112.02  3.000
 CSQ  C29   C27  O28   107.36  3.000
 CSQ  H27   C27  C25   112.00  3.000
 CSQ  O28   C27  C25   111.03  3.000
 CSQ  C29   C27  C25   101.24  3.000
 CSQ  HO28  O28  C27   107.89  3.000
 CSQ  H29   C29  N30   107.06  3.000
 CSQ  H29   C29  C27   111.61  3.000
 CSQ  N30   C29  C27   111.82  3.000
 CSQ  H29   C29  O24   109.93  3.000
 CSQ  N30   C29  O24   109.66  3.000
 CSQ  C27   C29  O24   106.77  3.000
 CSQ  C35   N30  C31   120.85  3.000
 CSQ  C31   N30  C29   116.13  3.000
 CSQ  C35   N30  C29   122.99  3.000
 CSQ  O36   C31  N32   122.63  3.000
 CSQ  O36   C31  N30   122.29  3.000
 CSQ  N32   C31  N30   115.08  3.000
 CSQ  HN32  N32  C33   116.97  3.000
 CSQ  HN32  N32  C31   115.22  3.000
 CSQ  C33   N32  C31   127.81  3.000
 CSQ  O37   C33  C34   126.17  3.000
 CSQ  O37   C33  N32   120.57  3.000
 CSQ  C34   C33  N32   113.25  3.000
 CSQ  H34   C34  C35   120.44  3.000
 CSQ  H34   C34  C33   119.72  3.000
 CSQ  C35   C34  C33   119.84  3.000
 CSQ  H35   C35  C34   120.53  3.000
 CSQ  H35   C35  N30   116.32  3.000
 CSQ  C34   C35  N30   123.14  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
 CSQ  CONST_01  N12   C11  N10  C9   180.00   0.0  0
 CSQ  CONST_02  C13   N12  C11  N10    0.00   0.0  0
 CSQ  CONST_03  C14   C13  N12  C11    0.00   0.0  0
 CSQ  CONST_04  C15   N10  C11  N12    0.00   0.0  0
 CSQ  CONST_05  N32   C31  N30  C29  180.00   0.0  0
 CSQ  CONST_06  C33   N32  C31  N30    0.00   0.0  0
 CSQ  CONST_07  C34   C33  N32  C31    0.00   0.0  0
 CSQ  CONST_08  C35   N30  C31  N32    0.00   0.0  0
 CSQ  CONST_09  O16   C11  N10  C9     0.00   0.0  0
 CSQ  CONST_10  N17   C13  N12  C11  180.00   0.0  0
 CSQ  CONST_11  O16   C11  N12  C13  180.00   0.0  0
 CSQ  CONST_12  O16   C11  N10  C15  180.00   0.0  0
 CSQ  CONST_13  O36   C31  N30  C29    0.00   0.0  0
 CSQ  CONST_14  O37   C33  N32  C31  180.00   0.0  0
 CSQ  CONST_15  O36   C31  N32  C33  180.00   0.0  0
 CSQ  CONST_16  O36   C31  N30  C35  180.00   0.0  0
 CSQ  CONST_17  HN32  N32  C31  N30  180.00   0.0  0
 CSQ  CONST_18  HN17  N17  C13  N12    0.00   0.0  0
 CSQ  CONST_19  HN1A  N17  C13  N12  180.00   0.0  0
 CSQ  Var_01    O19   P18  O6   C5    66.04  30.0  1
 CSQ  Var_02    C23   C22  O21  P18   92.20  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
 CSQ  chir_01  C3   C2   C5   O4   positiv
 CSQ  chir_02  C5   O6   C7   C3   negativ
 CSQ  chir_03  C7   O8   C9   C5   negativ
 CSQ  chir_04  C9   O4   N10  C7   negativ
 CSQ  chir_06  C23  C22  C25  O24  positiv
 CSQ  chir_07  C25  O26  C27  C23  negativ
 CSQ  chir_08  C27  O28  C29  C25  negativ
 CSQ  chir_09  C29  O24  N30  C27  negativ
 CSQ  chir_10  P18  O19  S20  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
 CSQ  plan-1  C9    0.020
 CSQ  plan-1  N10   0.020
 CSQ  plan-1  C11   0.020
 CSQ  plan-1  N12   0.020
 CSQ  plan-1  C13   0.020
 CSQ  plan-1  C14   0.020
 CSQ  plan-1  C15   0.020
 CSQ  plan-1  O16   0.020
 CSQ  plan-1  N17   0.020
 CSQ  plan-1  H14   0.020
 CSQ  plan-1  H15   0.020
 CSQ  plan-1  HN17  0.020
 CSQ  plan-1  HN1A  0.020
 CSQ  plan-2  C29   0.020
 CSQ  plan-2  N30   0.020
 CSQ  plan-2  C31   0.020
 CSQ  plan-2  N32   0.020
 CSQ  plan-2  C33   0.020
 CSQ  plan-2  C34   0.020
 CSQ  plan-2  C35   0.020
 CSQ  plan-2  O36   0.020
 CSQ  plan-2  O37   0.020
 CSQ  plan-2  H34   0.020
 CSQ  plan-2  H35   0.020
 CSQ  plan-2  HN32  0.020

