# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 22:14:21 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: (2R,4S,5R,6R)-4-amino-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](C[C@H](N)[C@H]1O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O
#
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
 0N2  0N2  '(2R,4S,5R,6R)-4-amino-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  61  34  .  2021-08-03  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0N2
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
 0N2  O41  O  O     0  -0.436  24.8831   7.9419  -8.5516
 0N2  C41  C  CR6   0   0.520  24.8806   7.9061  -7.3351
 0N2  C51  C  CR6   0   0.003  24.7157   9.0568  -6.4679
 0N2  C5A  C  CH3   0  -0.789  24.5121  10.4019  -7.0836
 0N2  C61  C  CR16  0  -0.055  24.7383   8.8495  -5.1411
 0N2  N31  N  NR16  0  -0.660  25.0501   6.7071  -6.6676
 0N2  C21  C  CR6   0   0.729  25.0619   6.4847  -5.3161
 0N2  O21  O  O     0  -0.665  25.2055   5.3720  -4.8509
 0N2  N11  N  NR6   0  -0.482  24.9085   7.6207  -4.5537
 0N2  C1X  C  CH1   0   0.166  24.8741   7.5089  -3.1041
 0N2  O4X  O  O2    0  -0.457  23.6388   8.0131  -2.6424
 0N2  C2X  C  CH2   0  -0.553  25.9440   8.3127  -2.3850
 0N2  C3X  C  CH1   0   0.003  25.2847   8.5849  -1.0386
 0N2  O3X  O  OH1   0  -0.599  25.3545   7.4787  -0.1707
 0N2  C4X  C  CH1   0  -0.023  23.8173   8.7546  -1.4402
 0N2  C5X  C  CH2   0  -0.213  23.4204  10.1915  -1.7261
 0N2  O5X  O  O2    0  -0.672  23.3971  10.8864  -0.4661
 0N2  P    P  P     0   1.437  22.6583  12.2816  -0.3829
 0N2  O1P  O  OH1   0  -0.683  23.0472  12.7049   1.0842
 0N2  O2P  O  O     0  -0.648  22.8647  13.2346  -1.4859
 0N2  OPP  O  O2    0  -0.688  21.0886  11.8297  -0.2602
 0N2  P2   P  P     0   1.433  19.8010  12.5430  -0.9257
 0N2  O3P  O  O     0  -0.632  19.7254  12.5520  -2.3911
 0N2  O4P  O  OH1   0  -0.624  18.7090  11.7056  -0.1310
 0N2  O1   O  O2    0  -0.633  19.7818  14.0234  -0.3356
 0N2  C1   C  CR16  0   0.169  20.0052  14.3577   1.0423
 0N2  C2   C  C     0  -0.491  18.9993  15.4233   1.4724
 0N2  C3   C  CR16  0  -0.064  19.6269  16.8137   1.5212
 0N2  N3   N  NH2   0  -0.782  18.5881  17.8288   1.4362
 0N2  C4   C  CR16  0  -0.017  20.5669  16.9325   0.3282
 0N2  O4   O  OH1   0  -0.698  21.0834  18.2294   0.1596
 0N2  C5   C  CR16  0  -0.005  21.7490  15.9668   0.4987
 0N2  O5   O  O     0  -0.436  21.3196  14.7726   1.1953
 0N2  C6   C  CH3   0  -0.664  22.9047  16.5263   1.3029
 0N2  H1   H  HCH3  0   0.271  24.4273  11.1711  -6.3190
 0N2  H2   H  HCH3  0   0.282  25.3412  10.6696  -7.7400
 0N2  H3   H  HCH3  0   0.274  23.6048  10.4238  -7.6883
 0N2  H4   H  HCR6  0   0.300  24.6140   9.6811  -4.4636
 0N2  H5   H  HNR6  0   0.412  25.1773   5.8823  -7.2407
 0N2  H6   H  HCH1  0   0.297  24.9606   6.4484  -2.8710
 0N2  H7   H  HCH2  0   0.266  26.8836   7.7688  -2.3108
 0N2  H8   H  HCH2  0   0.270  26.1592   9.2514  -2.8987
 0N2  H9   H  HCH1  0   0.212  25.6923   9.4862  -0.5791
 0N2  H10  H  HOH1  0   0.466  26.2803   7.3021   0.0224
 0N2  H11  H  HCH1  0   0.235  23.1578   8.3494  -0.6674
 0N2  H12  H  HCH2  0   0.260  24.1238  10.6871  -2.3972
 0N2  H13  H  HCH2  0   0.258  22.4299  10.2065  -2.1870
 0N2  H14  H  HOH1  0   0.504  22.5522  13.5059   1.3762
 0N2  H15  H  HOH1  0   0.527  17.8286  11.7313  -0.5287
 0N2  H16  H  HCR6  0   0.261  19.9048  13.4670   1.6657
 0N2  H17  H  H     0   0.270  18.1541  15.4280   0.7806
 0N2  H18  H  H     0   0.248  18.6055  15.1583   2.4548
 0N2  H19  H  HCR6  0   0.237  20.2142  16.9006   2.4470
 0N2  H20  H  HNH2  0   0.368  17.8395  17.6031   2.0801
 0N2  H21  H  HNH2  0   0.307  18.9548  18.7148   1.7605
 0N2  H23  H  HCR6  0   0.252  19.9990  16.6440  -0.5675
 0N2  H24  H  HOH1  0   0.437  20.3778  18.7744  -0.2022
 0N2  H25  H  HCR6  0   0.271  22.1133  15.6681  -0.4881
 0N2  H26  H  HCH3  0   0.223  23.3660  17.3579   0.7761
 0N2  H27  H  HCH3  0   0.244  22.5963  16.8669   2.2915
 0N2  H28  H  HCH3  0   0.258  23.6743  15.7646   1.4343

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
 0N2  O41  C41  double  1.217  0.020  1.217
 0N2  C41  N31  single  1.383  0.020  1.383
 0N2  C41  C51  single  1.450  0.020  1.450
 0N2  C5A  C51  single  1.493  0.020  1.493
 0N2  N31  C21  single  1.370  0.020  1.370
 0N2  C51  C61  double  1.343  0.020  1.343
 0N2  C21  O21  double  1.215  0.020  1.215
 0N2  C21  N11  single  1.377  0.020  1.377
 0N2  C61  N11  single  1.373  0.020  1.373
 0N2  N11  C1X  single  1.454  0.020  1.454
 0N2  O2P  P    double  1.472  0.020  1.472
 0N2  O4X  C1X  single  1.412  0.020  1.412
 0N2  O4X  C4X  single  1.424  0.020  1.424
 0N2  C1X  C2X  single  1.519  0.020  1.519
 0N2  C5X  C4X  single  1.518  0.020  1.518
 0N2  C5X  O5X  single  1.439  0.020  1.439
 0N2  P    O1P  single  1.576  0.020  1.576
 0N2  P    O5X  single  1.581  0.020  1.581
 0N2  P    OPP  single  1.638  0.020  1.638
 0N2  C4X  C3X  single  1.531  0.020  1.531
 0N2  C2X  C3X  single  1.524  0.020  1.524
 0N2  O3P  P2   double  1.467  0.020  1.467
 0N2  OPP  P2   single  1.615  0.020  1.615
 0N2  C3X  O3X  single  1.408  0.020  1.408
 0N2  P2   O4P  single  1.589  0.020  1.589
 0N2  P2   O1   single  1.594  0.020  1.594
 0N2  C5   C6   single  1.515  0.020  1.515
 0N2  C5   O5   single  1.448  0.020  1.448
 0N2  C5   C4   single  1.536  0.020  1.536
 0N2  O1   C1   single  1.435  0.020  1.435
 0N2  O5   C1   single  1.387  0.020  1.387
 0N2  O4   C4   single  1.406  0.020  1.406
 0N2  C4   C3   single  1.524  0.020  1.524
 0N2  C1   C2   single  1.527  0.020  1.527
 0N2  C3   C2   single  1.526  0.020  1.526
 0N2  C3   N3   single  1.455  0.020  1.455
 0N2  C5A  H1   single  0.970  0.020  1.090
 0N2  C5A  H2   single  0.970  0.020  1.090
 0N2  C5A  H3   single  0.970  0.020  1.090
 0N2  C61  H4   single  0.930  0.020  1.080
 0N2  N31  H5   single  0.860  0.020  1.020
 0N2  C1X  H6   single  0.970  0.020  1.090
 0N2  C2X  H7   single  0.970  0.020  1.090
 0N2  C2X  H8   single  0.970  0.020  1.090
 0N2  C3X  H9   single  0.970  0.020  1.090
 0N2  O3X  H10  single  0.850  0.020  0.980
 0N2  C4X  H11  single  0.970  0.020  1.090
 0N2  C5X  H12  single  0.970  0.020  1.090
 0N2  C5X  H13  single  0.970  0.020  1.090
 0N2  O1P  H14  single  0.850  0.020  0.980
 0N2  O4P  H15  single  0.850  0.020  0.980
 0N2  C1   H16  single  0.970  0.020  1.090
 0N2  C2   H17  single  0.970  0.020  1.090
 0N2  C2   H18  single  0.970  0.020  1.090
 0N2  C3   H19  single  0.970  0.020  1.090
 0N2  N3   H20  single  0.890  0.020  1.040
 0N2  N3   H21  single  0.890  0.020  1.040
 0N2  C4   H23  single  0.970  0.020  1.090
 0N2  O4   H24  single  0.850  0.020  0.980
 0N2  C5   H25  single  0.970  0.020  1.090
 0N2  C6   H26  single  0.970  0.020  1.090
 0N2  C6   H27  single  0.970  0.020  1.090
 0N2  C6   H28  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
 0N2  N31  C41  C51  114.41  3.000
 0N2  C51  C41  O41  125.07  3.000
 0N2  N31  C41  O41  120.52  3.000
 0N2  C61  C51  C5A  123.28  3.000
 0N2  C61  C51  C41  117.80  3.000
 0N2  C5A  C51  C41  118.92  3.000
 0N2  H3   C5A  H2   107.08  3.000
 0N2  H3   C5A  H1   108.10  3.000
 0N2  H2   C5A  H1   107.98  3.000
 0N2  H3   C5A  C51  111.11  3.000
 0N2  H2   C5A  C51  111.44  3.000
 0N2  H1   C5A  C51  110.96  3.000
 0N2  H4   C61  N11  115.80  3.000
 0N2  H4   C61  C51  119.93  3.000
 0N2  N11  C61  C51  124.27  3.000
 0N2  H5   N31  C21  115.16  3.000
 0N2  H5   N31  C41  116.65  3.000
 0N2  C21  N31  C41  128.19  3.000
 0N2  N11  C21  O21  123.85  3.000
 0N2  N11  C21  N31  114.30  3.000
 0N2  O21  C21  N31  121.85  3.000
 0N2  C1X  N11  C21  119.42  3.000
 0N2  C1X  N11  C61  119.50  3.000
 0N2  C21  N11  C61  121.03  3.000
 0N2  H6   C1X  C2X  110.97  3.000
 0N2  H6   C1X  O4X  110.32  3.000
 0N2  C2X  C1X  O4X  105.81  3.000
 0N2  H6   C1X  N11  106.63  3.000
 0N2  C2X  C1X  N11  114.49  3.000
 0N2  O4X  C1X  N11  108.62  3.000
 0N2  C4X  O4X  C1X  110.64  3.000
 0N2  H8   C2X  H7   106.96  3.000
 0N2  H8   C2X  C3X  110.34  3.000
 0N2  H7   C2X  C3X  113.74  3.000
 0N2  H8   C2X  C1X  111.78  3.000
 0N2  H7   C2X  C1X  112.08  3.000
 0N2  C3X  C2X  C1X  102.01  3.000
 0N2  H9   C3X  C4X  112.15  3.000
 0N2  H9   C3X  O3X  111.78  3.000
 0N2  C4X  C3X  O3X  107.24  3.000
 0N2  H9   C3X  C2X  110.99  3.000
 0N2  O3X  C3X  C2X  112.52  3.000
 0N2  C4X  C3X  C2X  101.70  3.000
 0N2  H10  O3X  C3X  108.40  3.000
 0N2  H11  C4X  C5X  109.04  3.000
 0N2  H11  C4X  C3X  110.58  3.000
 0N2  C5X  C4X  C3X  113.89  3.000
 0N2  H11  C4X  O4X  109.15  3.000
 0N2  C3X  C4X  O4X  106.50  3.000
 0N2  C5X  C4X  O4X  107.53  3.000
 0N2  H13  C5X  H12  108.59  3.000
 0N2  H13  C5X  O5X  110.36  3.000
 0N2  H12  C5X  O5X  109.25  3.000
 0N2  H13  C5X  C4X  109.24  3.000
 0N2  H12  C5X  C4X  112.16  3.000
 0N2  O5X  C5X  C4X  107.24  3.000
 0N2  P    O5X  C5X  118.67  3.000
 0N2  OPP  P    O2P  111.66  3.000
 0N2  OPP  P    O1P  103.94  3.000
 0N2  O2P  P    O1P  119.28  3.000
 0N2  OPP  P    O5X  102.02  3.000
 0N2  O1P  P    O5X   99.83  3.000
 0N2  O2P  P    O5X  117.80  3.000
 0N2  H14  O1P  P    111.72  3.000
 0N2  P2   OPP  P    127.67  3.000
 0N2  O1   P2   O4P  107.22  3.000
 0N2  O1   P2   O3P  111.31  3.000
 0N2  O4P  P2   O3P  117.86  3.000
 0N2  O1   P2   OPP  105.50  3.000
 0N2  O4P  P2   OPP   96.26  3.000
 0N2  O3P  P2   OPP  117.08  3.000
 0N2  H15  O4P  P2   113.97  3.000
 0N2  C1   O1   P2   124.74  3.000
 0N2  H16  C1   O5   105.56  3.000
 0N2  H16  C1   C2   110.36  3.000
 0N2  O5   C1   C2   112.61  3.000
 0N2  H16  C1   O1   110.11  3.000
 0N2  C2   C1   O1   109.29  3.000
 0N2  O5   C1   O1   108.85  3.000
 0N2  H18  C2   H17  106.99  3.000
 0N2  H18  C2   C3   109.93  3.000
 0N2  H17  C2   C3   109.54  3.000
 0N2  H18  C2   C1   108.77  3.000
 0N2  H17  C2   C1   109.53  3.000
 0N2  C3   C2   C1   111.95  3.000
 0N2  H19  C3   C4   108.87  3.000
 0N2  H19  C3   N3   112.05  3.000
 0N2  C4   C3   N3   109.90  3.000
 0N2  H19  C3   C2   108.57  3.000
 0N2  N3   C3   C2   109.89  3.000
 0N2  C4   C3   C2   107.44  3.000
 0N2  H21  N3   H20  105.02  3.000
 0N2  H21  N3   C3   109.47  3.000
 0N2  H20  N3   C3   109.57  3.000
 0N2  H23  C4   C5   108.85  3.000
 0N2  H23  C4   O4   109.52  3.000
 0N2  C5   C4   O4   108.09  3.000
 0N2  H23  C4   C3   107.39  3.000
 0N2  O4   C4   C3   113.11  3.000
 0N2  C5   C4   C3   109.81  3.000
 0N2  H24  O4   C4   107.35  3.000
 0N2  H25  C5   C6   109.02  3.000
 0N2  H25  C5   O5   107.93  3.000
 0N2  C6   C5   O5   105.99  3.000
 0N2  H25  C5   C4   109.14  3.000
 0N2  O5   C5   C4   110.10  3.000
 0N2  C6   C5   C4   114.44  3.000
 0N2  C5   O5   C1   118.35  3.000
 0N2  H28  C6   H27  107.97  3.000
 0N2  H28  C6   H26  107.05  3.000
 0N2  H27  C6   H26  108.69  3.000
 0N2  H28  C6   C5   110.13  3.000
 0N2  H27  C6   C5   112.39  3.000
 0N2  H26  C6   C5   110.42  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
 0N2  CONST_01  N11  C21  N31  C41     0.00   0.0  0
 0N2  CONST_02  C21  N31  C41  C51     0.00   0.0  0
 0N2  CONST_03  N31  C21  N11  C61     0.00   0.0  0
 0N2  CONST_04  C1X  N11  C21  N31   180.00   0.0  0
 0N2  CONST_05  C21  N31  C41  O41   180.00   0.0  0
 0N2  CONST_06  O21  C21  N31  C41   180.00   0.0  0
 0N2  CONST_07  O21  C21  N11  C61   180.00   0.0  0
 0N2  CONST_08  C1X  N11  C21  O21     0.00   0.0  0
 0N2  CONST_09  H5   N31  C41  C51   180.00   0.0  0
 0N2  Var_01    H1   C5A  C51  C41  -178.65  30.0  3
 0N2  Var_02    O2P  P    O5X  C5X   -42.80  30.0  2
 0N2  Var_03    O3P  P2   OPP  P      64.33  30.0  3
 0N2  Var_04    H12  C5X  O5X  P      74.21  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
 0N2  chir_01  C1X  N11  O4X  C2X  positiv
 0N2  chir_02  C3X  O3X  C4X  C2X  positiv
 0N2  chir_03  C4X  O4X  C3X  C5X  negativ
 0N2  chir_06  C1   O1   O5   C2   negativ
 0N2  chir_07  C3   N3   C4   C2   positiv
 0N2  chir_08  C4   O4   C5   C3   negativ
 0N2  chir_09  C5   O5   C4   C6   negativ
 0N2  chir_10  P    O1P  O5X  OPP  both
 0N2  chir_11  P2   O4P  OPP  O3P  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
 0N2  plan-1  O41  0.020
 0N2  plan-1  C41  0.020
 0N2  plan-1  C51  0.020
 0N2  plan-1  C5A  0.020
 0N2  plan-1  C61  0.020
 0N2  plan-1  N31  0.020
 0N2  plan-1  C21  0.020
 0N2  plan-1  O21  0.020
 0N2  plan-1  N11  0.020
 0N2  plan-1  C1X  0.020
 0N2  plan-1  H4   0.020
 0N2  plan-1  H5   0.020

