# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 23 04:30:11 2020
#   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  59  34  .  2021-08-03  2021-08-03  
;
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  -0.470   1.1226  -3.4427  -1.8363
 0N2  C41  C  CR6    0   0.569   1.4708  -2.6332  -0.9937
 0N2  C51  C  CR6    0  -0.171   1.1690  -2.7225   0.4191
 0N2  C5A  C  CH3    0  -0.726   0.3633  -3.8758   0.9150
 0N2  C61  C  CR16   0   0.055   1.5850  -1.7224   1.2126
 0N2  N31  N  NR16   0  -0.725   2.2435  -1.5459  -1.3396
 0N2  C21  C  CR6    0   0.770   2.6670  -0.5206  -0.5383
 0N2  O21  O  O      0  -0.485   3.3436   0.3892  -0.9683
 0N2  N11  N  NR6    0  -0.564   2.3120  -0.6416   0.7857
 0N2  C1X  C  CH1    0   0.204   2.5555   0.4524   1.7315
 0N2  O4X  O  O2     0  -0.472   1.6927   1.5156   1.4670
 0N2  C2X  C  CH2    0  -0.551   3.9706   1.0252   1.7874
 0N2  C3X  C  CH1    0   0.012   3.8774   2.4005   1.1230
 0N2  O3X  O  OH1    0  -0.673   4.5975   3.4153   1.7838
 0N2  C4X  C  CH1    0   0.016   2.3825   2.7276   1.2072
 0N2  C5X  C  CH2    0  -0.178   1.8369   3.3693  -0.0488
 0N2  O5X  O  O2     0  -0.624   0.5189   3.8265   0.1912
 0N2  P    P  P      0   1.350  -0.6630   3.5734  -0.9153
 0N2  O1P  O  OP    -1  -0.792  -1.8882   4.1809  -0.3107
 0N2  O2P  O  O      0  -0.811  -0.1895   3.9658  -2.2811
 0N2  OPP  O  O2     0  -0.741  -0.7962   1.9441  -0.8220
 0N2  P2   P  P      0   1.371  -0.6870   0.8695  -2.0620
 0N2  O3P  O  O      0  -0.808  -1.8835   1.0410  -2.9479
 0N2  O4P  O  OP    -1  -0.768   0.6922   0.8190  -2.6278
 0N2  O1   O  O2     0  -0.612  -0.8527  -0.5005  -1.1619
 0N2  C1   C  CH1    0   0.332  -2.0739  -0.8184  -0.5819
 0N2  C2   C  CH2    0  -0.499  -2.0011  -0.7569   0.9313
 0N2  C3   C  CH1    0  -0.119  -3.3067  -1.2388   1.5508
 0N2  N3   N  NH2    0  -0.800  -3.1749  -1.2965   2.9986
 0N2  C4   C  CH1    0   0.055  -3.6094  -2.6258   1.0046
 0N2  O4   O  OH1    0  -0.673  -4.8499  -3.0550   1.5179
 0N2  C5   C  CH1    0  -0.033  -3.5955  -2.6425  -0.5342
 0N2  O5   O  O2     0  -0.492  -2.3648  -2.1283  -1.0113
 0N2  C6   C  CH3    0  -0.688  -4.8040  -1.9706  -1.1781
 0N2  H1   H  HCH3   0   0.248  -0.6310  -3.8702   0.4658
 0N2  H2   H  HCH3   0   0.244   0.8290  -4.8306   0.6669
 0N2  H3   H  HCH3   0   0.239   0.2438  -3.8326   1.9968
 0N2  H4   H  HCR6   0   0.307   1.3604  -1.7295   2.2712
 0N2  H5   H  HNR6   0   0.411   2.4197  -1.4077  -2.3257
 0N2  H6   H  HCH1   0   0.246   2.3016   0.0165   2.6999
 0N2  H7   H  HCH2   0   0.262   4.2298   1.1655   2.8389
 0N2  H8   H  HCH2   0   0.270   4.7222   0.3727   1.3478
 0N2  H9   H  HCH1   0   0.235   4.1923   2.3327   0.0797
 0N2  H10  H  HOH1   0   0.454   5.5255   3.3233   1.5502
 0N2  H11  H  HCH1   0   0.222   2.2296   3.4088   2.0562
 0N2  H12  H  HCH2   0   0.209   2.4755   4.2197  -0.3146
 0N2  H13  H  HCH2   0   0.237   1.8841   2.6467  -0.8681
 0N2  H16  H  HCH1   0   0.182  -2.8622  -0.1354  -0.9335
 0N2  H17  H  HCH2   0   0.239  -1.1765  -1.3811   1.2858
 0N2  H18  H  HCH2   0   0.244  -1.7883   0.2703   1.2378
 0N2  H19  H  HCH1   0   0.206  -4.1135  -0.5560   1.2349
 0N2  H20  H  HNH2   0   0.343  -2.9604  -0.3702   3.3481
 0N2  H21  H  HNH2   0   0.342  -4.0672  -1.5407   3.4097
 0N2  H23  H  HCH1   0   0.211  -2.7999  -3.2861   1.3523
 0N2  H24  H  HOH1   0   0.452  -4.9605  -3.9887   1.3127
 0N2  H25  H  HCH1   0   0.236  -3.5975  -3.6905  -0.8522
 0N2  H26  H  HCH3   0   0.237  -4.7169  -2.0161  -2.2643
 0N2  H27  H  HCH3   0   0.235  -5.7196  -2.4903  -0.8997
 0N2  H28  H  HCH3   0   0.226  -4.9227  -0.9241  -0.8964

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  1.219  0.020  1.219
 0N2  C41  N31  single  1.378  0.020  1.378
 0N2  C41  C51  single  1.447  0.020  1.447
 0N2  C5A  C51  single  1.492  0.020  1.492
 0N2  N31  C21  single  1.368  0.020  1.368
 0N2  C51  C61  double  1.343  0.020  1.343
 0N2  C21  O21  double  1.213  0.020  1.213
 0N2  C21  N11  single  1.376  0.020  1.376
 0N2  C61  N11  single  1.371  0.020  1.371
 0N2  N11  C1X  single  1.466  0.020  1.466
 0N2  O2P  P    deloc   1.498  0.020  1.498
 0N2  O4X  C1X  single  1.395  0.020  1.395
 0N2  O4X  C4X  single  1.419  0.020  1.419
 0N2  C1X  C2X  single  1.528  0.020  1.528
 0N2  C5X  C4X  single  1.512  0.020  1.512
 0N2  C5X  O5X  single  1.416  0.020  1.416
 0N2  P    O1P  deloc   1.495  0.020  1.495
 0N2  P    O5X  single  1.639  0.020  1.639
 0N2  P    OPP  single  1.637  0.020  1.637
 0N2  C4X  C3X  single  1.533  0.020  1.533
 0N2  C2X  C3X  single  1.530  0.020  1.530
 0N2  O3P  P2   deloc   1.499  0.020  1.499
 0N2  OPP  P2   single  1.644  0.020  1.644
 0N2  C3X  O3X  single  1.409  0.020  1.409
 0N2  P2   O4P  deloc   1.492  0.020  1.492
 0N2  P2   O1   single  1.648  0.020  1.648
 0N2  C5   C6   single  1.525  0.020  1.525
 0N2  C5   O5   single  1.417  0.020  1.417
 0N2  C5   C4   single  1.539  0.020  1.539
 0N2  O1   C1   single  1.389  0.020  1.389
 0N2  O5   C1   single  1.409  0.020  1.409
 0N2  O4   C4   single  1.409  0.020  1.409
 0N2  C4   C3   single  1.521  0.020  1.521
 0N2  C1   C2   single  1.516  0.020  1.516
 0N2  C3   C2   single  1.523  0.020  1.523
 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  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  114.24  3.000
 0N2  C51  C41  O41  125.03  3.000
 0N2  N31  C41  O41  120.70  3.000
 0N2  C61  C51  C5A  123.14  3.000
 0N2  C61  C51  C41  117.80  3.000
 0N2  C5A  C51  C41  119.00  3.000
 0N2  H3   C5A  H2   107.90  3.000
 0N2  H3   C5A  H1   107.98  3.000
 0N2  H2   C5A  H1   107.45  3.000
 0N2  H3   C5A  C51  111.03  3.000
 0N2  H2   C5A  C51  111.74  3.000
 0N2  H1   C5A  C51  110.58  3.000
 0N2  H4   C61  N11  114.83  3.000
 0N2  H4   C61  C51  120.59  3.000
 0N2  N11  C61  C51  124.58  3.000
 0N2  H5   N31  C21  114.50  3.000
 0N2  H5   N31  C41  116.76  3.000
 0N2  C21  N31  C41  128.15  3.000
 0N2  N11  C21  O21  123.44  3.000
 0N2  N11  C21  N31  114.69  3.000
 0N2  O21  C21  N31  121.82  3.000
 0N2  C1X  N11  C21  120.81  3.000
 0N2  C1X  N11  C61  118.39  3.000
 0N2  C21  N11  C61  120.38  3.000
 0N2  H6   C1X  C2X  109.43  3.000
 0N2  H6   C1X  O4X  109.19  3.000
 0N2  C2X  C1X  O4X  107.11  3.000
 0N2  H6   C1X  N11  103.63  3.000
 0N2  C2X  C1X  N11  117.20  3.000
 0N2  O4X  C1X  N11  110.10  3.000
 0N2  C4X  O4X  C1X  112.66  3.000
 0N2  H8   C2X  H7   107.58  3.000
 0N2  H8   C2X  C3X  113.92  3.000
 0N2  H7   C2X  C3X  108.49  3.000
 0N2  H8   C2X  C1X  113.59  3.000
 0N2  H7   C2X  C1X  107.66  3.000
 0N2  C3X  C2X  C1X  105.35  3.000
 0N2  H9   C3X  C4X  110.30  3.000
 0N2  H9   C3X  O3X  110.21  3.000
 0N2  C4X  C3X  O3X  108.60  3.000
 0N2  H9   C3X  C2X  109.97  3.000
 0N2  O3X  C3X  C2X  114.37  3.000
 0N2  C4X  C3X  C2X  103.14  3.000
 0N2  H10  O3X  C3X  108.08  3.000
 0N2  H11  C4X  C5X  109.17  3.000
 0N2  H11  C4X  C3X  108.09  3.000
 0N2  C5X  C4X  C3X  113.38  3.000
 0N2  H11  C4X  O4X  108.68  3.000
 0N2  C3X  C4X  O4X  107.58  3.000
 0N2  C5X  C4X  O4X  109.83  3.000
 0N2  H13  C5X  H12  107.81  3.000
 0N2  H13  C5X  O5X  112.37  3.000
 0N2  H12  C5X  O5X  109.45  3.000
 0N2  H13  C5X  C4X  109.04  3.000
 0N2  H12  C5X  C4X  108.69  3.000
 0N2  O5X  C5X  C4X  109.40  3.000
 0N2  P    O5X  C5X  120.48  3.000
 0N2  OPP  P    O2P  109.78  3.000
 0N2  OPP  P    O1P  108.34  3.000
 0N2  O2P  P    O1P  121.42  3.000
 0N2  OPP  P    O5X  100.01  3.000
 0N2  O1P  P    O5X  104.78  3.000
 0N2  O2P  P    O5X  110.32  3.000
 0N2  P2   OPP  P    127.00  3.000
 0N2  O1   P2   O4P  105.79  3.000
 0N2  O1   P2   O3P  109.74  3.000
 0N2  O4P  P2   O3P  121.19  3.000
 0N2  O1   P2   OPP   97.16  3.000
 0N2  O4P  P2   OPP  111.69  3.000
 0N2  O3P  P2   OPP  108.54  3.000
 0N2  C1   O1   P2   120.46  3.000
 0N2  H16  C1   O5   109.37  3.000
 0N2  H16  C1   C2   109.15  3.000
 0N2  O5   C1   C2   110.60  3.000
 0N2  H16  C1   O1   110.75  3.000
 0N2  C2   C1   O1   111.42  3.000
 0N2  O5   C1   O1   105.49  3.000
 0N2  H18  C2   H17  107.39  3.000
 0N2  H18  C2   C3   110.50  3.000
 0N2  H17  C2   C3   109.51  3.000
 0N2  H18  C2   C1   109.11  3.000
 0N2  H17  C2   C1   109.67  3.000
 0N2  C3   C2   C1   110.60  3.000
 0N2  H19  C3   C4   108.42  3.000
 0N2  H19  C3   N3   112.07  3.000
 0N2  C4   C3   N3   109.83  3.000
 0N2  H19  C3   C2   108.34  3.000
 0N2  N3   C3   C2   109.85  3.000
 0N2  C4   C3   C2   108.24  3.000
 0N2  H21  N3   H20  105.49  3.000
 0N2  H21  N3   C3   109.51  3.000
 0N2  H20  N3   C3   109.04  3.000
 0N2  H23  C4   C5   107.62  3.000
 0N2  H23  C4   O4   110.46  3.000
 0N2  C5   C4   O4   111.64  3.000
 0N2  H23  C4   C3   106.68  3.000
 0N2  O4   C4   C3   108.79  3.000
 0N2  C5   C4   C3   111.54  3.000
 0N2  H24  O4   C4   108.59  3.000
 0N2  H25  C5   C6   107.31  3.000
 0N2  H25  C5   O5   104.54  3.000
 0N2  C6   C5   O5   112.72  3.000
 0N2  H25  C5   C4   107.50  3.000
 0N2  O5   C5   C4   109.92  3.000
 0N2  C6   C5   C4   114.22  3.000
 0N2  C5   O5   C1   114.47  3.000
 0N2  H28  C6   H27  107.48  3.000
 0N2  H28  C6   H26  107.82  3.000
 0N2  H27  C6   H26  107.57  3.000
 0N2  H28  C6   C5   113.58  3.000
 0N2  H27  C6   C5   110.37  3.000
 0N2  H26  C6   C5   109.80  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  -62.14  30.0  3
 0N2  Var_02    O2P  P    O5X  C5X  -48.03  30.0  1
 0N2  Var_03    O3P  P2   OPP  P    -68.79  30.0  3
 0N2  Var_04    H12  C5X  O5X  P    104.78  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

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

