# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 21 08:20:34 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-5-amino-3,4-dihydroxy-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](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)[C@H](O)[C@@H](O)[C@@H]1N
#
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
 0FX  0FX  '(2R,3R,4S,5S,6R)-5-amino-3,4-dihydroxy-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  60  35  .  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_0FX
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
 0FX  O4P  O  OP    -1  -0.792  -3.7078  -1.9702  -1.4110
 0FX  P2   P  P      0   1.352  -3.1736  -1.3112  -0.1783
 0FX  O3P  O  O      0  -0.780  -3.6838  -1.6778   1.1776
 0FX  O1G  O  O2     0  -0.631  -3.2324   0.3304  -0.3811
 0FX  C1G  C  CH1    0   0.254  -4.3387   0.9046  -1.0086
 0FX  C2G  C  CH1    0  -0.022  -4.0962   2.4076  -1.1411
 0FX  O2G  O  OH1    0  -0.672  -2.8724   2.6997  -1.7711
 0FX  C3G  C  CH1    0   0.047  -4.0965   3.0851   0.2243
 0FX  O3G  O  OH1    0  -0.671  -4.0039   4.4831   0.0865
 0FX  C4G  C  CH1    0  -0.133  -5.3818   2.7440   0.9727
 0FX  N4A  N  NH2    0  -0.787  -5.3667   3.3557   2.2888
 0FX  C5G  C  CH1    0   0.035  -5.5725   1.2190   1.0034
 0FX  C6G  C  CH3    0  -0.699  -6.9068   0.8040   1.5881
 0FX  O5G  O  O2     0  -0.508  -5.5259   0.6748  -0.3133
 0FX  OPP  O  O2     0  -0.736  -1.5341  -1.3818  -0.1944
 0FX  P    P  P      0   1.345  -0.6337  -2.2413   0.8796
 0FX  O1P  O  OP    -1  -0.800  -0.4830  -1.4985   2.1693
 0FX  O2P  O  O      0  -0.797  -1.0540  -3.6769   0.8670
 0FX  O5   O  O2     0  -0.622   0.7489  -2.0681  -0.0019
 0FX  C5   C  CH2    0  -0.154   1.9739  -2.2901   0.6629
 0FX  C4   C  CH1    0   0.014   3.0863  -2.3753  -0.3519
 0FX  O4   O  O2     0  -0.489   3.2309  -1.1324  -1.0157
 0FX  C3   C  CH1    0   0.025   4.4429  -2.6869   0.2807
 0FX  O3   O  OH1    0  -0.669   4.6102  -4.0816   0.3299
 0FX  C2   C  CH2    0  -0.560   5.4191  -1.9546  -0.6408
 0FX  C1   C  CH1    0   0.221   4.5674  -0.9016  -1.3579
 0FX  N11  N  NR6    0  -0.568   4.8987   0.4935  -1.0773
 0FX  C61  C  CR16   0   0.060   5.1586   1.3397  -2.1240
 0FX  C51  C  CR6    0  -0.185   5.4599   2.6426  -1.9910
 0FX  C5A  C  CH3    0  -0.707   5.7443   3.5363  -3.1532
 0FX  C21  C  CR6    0   0.740   4.8950   0.9547   0.2187
 0FX  O21  O  O      0  -0.472   4.6490   0.2564   1.1795
 0FX  N31  N  NR16   0  -0.734   5.2053   2.2841   0.3476
 0FX  C41  C  CR6    0   0.558   5.5003   3.1937  -0.6518
 0FX  O41  O  O      0  -0.456   5.7622   4.3511  -0.3784
 0FX  H2   H  HCH1   0   0.229  -4.4931   0.4598  -1.9986
 0FX  H3   H  HCH1   0   0.221  -4.9396   2.8149  -1.7172
 0FX  H4   H  HOH1   0   0.458  -2.9698   2.5634  -2.7182
 0FX  H5   H  HCH1   0   0.199  -3.2442   2.6978   0.8063
 0FX  H6   H  HOH1   0   0.445  -3.2377   4.6673  -0.4671
 0FX  H7   H  HCH1   0   0.227  -6.2227   3.1777   0.4160
 0FX  H8   H  HNH2   0   0.351  -6.2653   3.2339   2.7367
 0FX  H9   H  HNH2   0   0.338  -4.6899   2.8882   2.8824
 0FX  H11  H  HCH1   0   0.215  -4.7727   0.7775   1.6117
 0FX  H12  H  HCH3   0   0.225  -7.7393   1.2684   1.0556
 0FX  H13  H  HCH3   0   0.244  -7.0241  -0.2788   1.5371
 0FX  H14  H  HCH3   0   0.227  -6.9789   1.0831   2.6383
 0FX  H16  H  HCH2   0   0.212   2.1895  -1.4841   1.3729
 0FX  H17  H  HCH2   0   0.210   1.9682  -3.2321   1.2259
 0FX  H18  H  HCH1   0   0.226   2.8580  -3.1636  -1.0841
 0FX  H19  H  HCH1   0   0.231   4.4905  -2.2590   1.2863
 0FX  H20  H  HOH1   0   0.457   5.3411  -4.2769   0.9231
 0FX  H21  H  HCH2   0   0.274   6.2749  -1.5303  -0.1187
 0FX  H22  H  HCH2   0   0.266   5.8063  -2.6541  -1.3834
 0FX  H23  H  HCH1   0   0.253   4.7020  -0.9947  -2.4382
 0FX  H24  H  HCR6   0   0.316   5.1083   0.8802  -3.1024
 0FX  H25  H  HCH3   0   0.247   5.0273   4.3564  -3.2106
 0FX  H26  H  HCH3   0   0.247   6.7379   3.9805  -3.0806
 0FX  H27  H  HCH3   0   0.247   5.6939   2.9824  -4.0893
 0FX  H28  H  HNR6   0   0.425   5.2179   2.6322   1.2987

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
 0FX  O3G  C3G  single  1.408  0.020  1.408
 0FX  N4A  C4G  single  1.451  0.020  1.451
 0FX  C3G  C4G  single  1.526  0.020  1.526
 0FX  C3G  C2G  single  1.524  0.020  1.524
 0FX  C4G  C5G  single  1.537  0.020  1.537
 0FX  O2G  C2G  single  1.407  0.020  1.407
 0FX  O41  C41  double  1.218  0.020  1.218
 0FX  C2G  C1G  single  1.528  0.020  1.528
 0FX  C5G  C6G  single  1.515  0.020  1.515
 0FX  C5G  O5G  single  1.425  0.020  1.425
 0FX  C41  N31  single  1.383  0.020  1.383
 0FX  C41  C51  single  1.449  0.020  1.449
 0FX  O1G  C1G  single  1.395  0.020  1.395
 0FX  O1G  P2   single  1.655  0.020  1.655
 0FX  N31  C21  single  1.371  0.020  1.371
 0FX  C1G  O5G  single  1.395  0.020  1.395
 0FX  O3P  P2   deloc   1.494  0.020  1.494
 0FX  C5A  C51  single  1.493  0.020  1.493
 0FX  C51  C61  double  1.344  0.020  1.344
 0FX  C21  O21  double  1.213  0.020  1.213
 0FX  C21  N11  single  1.376  0.020  1.376
 0FX  O2P  P    deloc   1.496  0.020  1.496
 0FX  P2   O4P  deloc   1.496  0.020  1.496
 0FX  P2   OPP  single  1.641  0.020  1.641
 0FX  O3   C3   single  1.406  0.020  1.406
 0FX  C61  N11  single  1.371  0.020  1.371
 0FX  N11  C1   single  1.461  0.020  1.461
 0FX  C3   C2   single  1.529  0.020  1.529
 0FX  C3   C4   single  1.529  0.020  1.529
 0FX  C2   C1   single  1.532  0.020  1.532
 0FX  O5   P    single  1.649  0.020  1.649
 0FX  O5   C5   single  1.411  0.020  1.411
 0FX  P    OPP  single  1.644  0.020  1.644
 0FX  P    O1P  deloc   1.496  0.020  1.496
 0FX  C1   O4   single  1.399  0.020  1.399
 0FX  C4   C5   single  1.508  0.020  1.508
 0FX  C4   O4   single  1.416  0.020  1.416
 0FX  C1G  H2   single  0.970  0.020  1.090
 0FX  C2G  H3   single  0.970  0.020  1.090
 0FX  O2G  H4   single  0.850  0.020  0.980
 0FX  C3G  H5   single  0.970  0.020  1.090
 0FX  O3G  H6   single  0.850  0.020  0.980
 0FX  C4G  H7   single  0.970  0.020  1.090
 0FX  N4A  H8   single  0.890  0.020  1.040
 0FX  N4A  H9   single  0.890  0.020  1.040
 0FX  C5G  H11  single  0.970  0.020  1.090
 0FX  C6G  H12  single  0.970  0.020  1.090
 0FX  C6G  H13  single  0.970  0.020  1.090
 0FX  C6G  H14  single  0.970  0.020  1.090
 0FX  C5   H16  single  0.970  0.020  1.090
 0FX  C5   H17  single  0.970  0.020  1.090
 0FX  C4   H18  single  0.970  0.020  1.090
 0FX  C3   H19  single  0.970  0.020  1.090
 0FX  O3   H20  single  0.850  0.020  0.980
 0FX  C2   H21  single  0.970  0.020  1.090
 0FX  C2   H22  single  0.970  0.020  1.090
 0FX  C1   H23  single  0.970  0.020  1.090
 0FX  C61  H24  single  0.930  0.020  1.080
 0FX  C5A  H25  single  0.970  0.020  1.090
 0FX  C5A  H26  single  0.970  0.020  1.090
 0FX  C5A  H27  single  0.970  0.020  1.090
 0FX  N31  H28  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
 0FX  OPP  P2   O1G   94.41  3.000
 0FX  OPP  P2   O3P  109.85  3.000
 0FX  O1G  P2   O3P  110.02  3.000
 0FX  OPP  P2   O4P  109.25  3.000
 0FX  O3P  P2   O4P  121.17  3.000
 0FX  O1G  P2   O4P  108.85  3.000
 0FX  C1G  O1G  P2   119.44  3.000
 0FX  H2   C1G  O5G  105.27  3.000
 0FX  H2   C1G  C2G  110.06  3.000
 0FX  O5G  C1G  C2G  109.90  3.000
 0FX  H2   C1G  O1G  110.54  3.000
 0FX  O5G  C1G  O1G  112.51  3.000
 0FX  C2G  C1G  O1G  108.54  3.000
 0FX  H3   C2G  C3G  107.73  3.000
 0FX  H3   C2G  O2G  110.83  3.000
 0FX  C3G  C2G  O2G  108.00  3.000
 0FX  H3   C2G  C1G  106.75  3.000
 0FX  O2G  C2G  C1G  112.39  3.000
 0FX  C3G  C2G  C1G  111.07  3.000
 0FX  H4   O2G  C2G  108.87  3.000
 0FX  H5   C3G  C4G  108.29  3.000
 0FX  H5   C3G  O3G  110.47  3.000
 0FX  C4G  C3G  O3G  108.99  3.000
 0FX  H5   C3G  C2G  108.46  3.000
 0FX  C4G  C3G  C2G  109.88  3.000
 0FX  O3G  C3G  C2G  110.71  3.000
 0FX  H6   O3G  C3G  107.37  3.000
 0FX  H7   C4G  C5G  107.88  3.000
 0FX  H7   C4G  N4A  107.54  3.000
 0FX  C5G  C4G  N4A  113.66  3.000
 0FX  H7   C4G  C3G  107.95  3.000
 0FX  C5G  C4G  C3G  109.64  3.000
 0FX  N4A  C4G  C3G  109.98  3.000
 0FX  H9   N4A  H8   106.15  3.000
 0FX  H9   N4A  C4G  110.08  3.000
 0FX  H8   N4A  C4G  109.97  3.000
 0FX  H11  C5G  O5G  109.54  3.000
 0FX  H11  C5G  C6G  108.53  3.000
 0FX  O5G  C5G  C6G  106.31  3.000
 0FX  H11  C5G  C4G  108.65  3.000
 0FX  O5G  C5G  C4G  110.87  3.000
 0FX  C6G  C5G  C4G  112.88  3.000
 0FX  H14  C6G  H13  107.01  3.000
 0FX  H14  C6G  H12  108.11  3.000
 0FX  H13  C6G  H12  108.52  3.000
 0FX  H14  C6G  C5G  111.12  3.000
 0FX  H13  C6G  C5G  110.41  3.000
 0FX  H12  C6G  C5G  111.52  3.000
 0FX  C5G  O5G  C1G  115.17  3.000
 0FX  P    OPP  P2   124.28  3.000
 0FX  O5   P    O2P  109.39  3.000
 0FX  O5   P    O1P  108.93  3.000
 0FX  O2P  P    O1P  120.80  3.000
 0FX  O1P  P    OPP  111.03  3.000
 0FX  O5   P    OPP   93.16  3.000
 0FX  O2P  P    OPP  110.02  3.000
 0FX  C5   O5   P    117.36  3.000
 0FX  H17  C5   H16  107.45  3.000
 0FX  H17  C5   C4   107.49  3.000
 0FX  H16  C5   C4   109.42  3.000
 0FX  H17  C5   O5   111.85  3.000
 0FX  H16  C5   O5   111.13  3.000
 0FX  C4   C5   O5   109.40  3.000
 0FX  H18  C4   C3   108.28  3.000
 0FX  H18  C4   O4   109.76  3.000
 0FX  C3   C4   O4   106.39  3.000
 0FX  H18  C4   C5   109.59  3.000
 0FX  O4   C4   C5   109.94  3.000
 0FX  C3   C4   C5   112.80  3.000
 0FX  C1   O4   C4   110.91  3.000
 0FX  H19  C3   C2   109.81  3.000
 0FX  H19  C3   O3   110.54  3.000
 0FX  C2   C3   O3   114.85  3.000
 0FX  H19  C3   C4   109.83  3.000
 0FX  C2   C3   C4   102.68  3.000
 0FX  O3   C3   C4   108.80  3.000
 0FX  H20  O3   C3   108.27  3.000
 0FX  H22  C2   H21  107.29  3.000
 0FX  H22  C2   C1   108.62  3.000
 0FX  H21  C2   C1   113.17  3.000
 0FX  H22  C2   C3   109.25  3.000
 0FX  H21  C2   C3   113.55  3.000
 0FX  C1   C2   C3   104.85  3.000
 0FX  H23  C1   N11  104.08  3.000
 0FX  H23  C1   C2   109.61  3.000
 0FX  N11  C1   C2   116.12  3.000
 0FX  H23  C1   O4   110.22  3.000
 0FX  C2   C1   O4   107.65  3.000
 0FX  N11  C1   O4   109.10  3.000
 0FX  C21  N11  C61  120.85  3.000
 0FX  C61  N11  C1   119.07  3.000
 0FX  C21  N11  C1   120.03  3.000
 0FX  H24  C61  C51  120.77  3.000
 0FX  H24  C61  N11  114.79  3.000
 0FX  C51  C61  N11  124.43  3.000
 0FX  C41  C51  C5A  119.11  3.000
 0FX  C5A  C51  C61  123.08  3.000
 0FX  C41  C51  C61  117.81  3.000
 0FX  H27  C5A  H26  107.85  3.000
 0FX  H27  C5A  H25  107.87  3.000
 0FX  H26  C5A  H25  107.22  3.000
 0FX  H27  C5A  C51  110.84  3.000
 0FX  H26  C5A  C51  111.43  3.000
 0FX  H25  C5A  C51  111.45  3.000
 0FX  N31  C21  O21  121.97  3.000
 0FX  O21  C21  N11  123.63  3.000
 0FX  N31  C21  N11  114.40  3.000
 0FX  H28  N31  C41  116.74  3.000
 0FX  H28  N31  C21  115.10  3.000
 0FX  C41  N31  C21  128.16  3.000
 0FX  O41  C41  N31  120.57  3.000
 0FX  N31  C41  C51  114.32  3.000
 0FX  O41  C41  C51  125.10  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
 0FX  CONST_01  N31  C21  N11  C1   180.00   0.0  0
 0FX  CONST_02  C41  N31  C21  N11    0.00   0.0  0
 0FX  CONST_03  N31  C21  N11  C61    0.00   0.0  0
 0FX  CONST_04  C21  N31  C41  C51    0.00   0.0  0
 0FX  CONST_05  O21  C21  N11  C1     0.00   0.0  0
 0FX  CONST_06  O21  C21  N11  C61  180.00   0.0  0
 0FX  CONST_07  O41  C41  N31  C21  180.00   0.0  0
 0FX  CONST_08  C41  N31  C21  O21  180.00   0.0  0
 0FX  CONST_09  H28  N31  C21  N11  180.00   0.0  0
 0FX  Var_01    H25  C5A  C51  C61  118.89  30.0  3
 0FX  Var_02    OPP  P2   O1G  C1G  152.11  30.0  3
 0FX  Var_03    C4   C5   O5   P    168.07  30.0  3
 0FX  Var_04    O2P  P    OPP  P2    56.18  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
 0FX  chir_02  C1G  C2G  O1G  O5G  negativ
 0FX  chir_03  C2G  O2G  C1G  C3G  negativ
 0FX  chir_04  C3G  O3G  C2G  C4G  positiv
 0FX  chir_05  C4G  N4A  C3G  C5G  negativ
 0FX  chir_06  C5G  O5G  C4G  C6G  negativ
 0FX  chir_08  C4   C3   C5   O4   negativ
 0FX  chir_09  C3   O3   C2   C4   negativ
 0FX  chir_10  C1   O4   N11  C2   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
 0FX  plan-1  C1   0.020
 0FX  plan-1  N11  0.020
 0FX  plan-1  C61  0.020
 0FX  plan-1  C51  0.020
 0FX  plan-1  C5A  0.020
 0FX  plan-1  C21  0.020
 0FX  plan-1  O21  0.020
 0FX  plan-1  N31  0.020
 0FX  plan-1  C41  0.020
 0FX  plan-1  O41  0.020
 0FX  plan-1  H24  0.020
 0FX  plan-1  H28  0.020

