# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 27 06:58:31 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-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)C1=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
 T46  T46  '(2R,3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-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  57  35  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T46
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
 T46  C4   C  C      0   0.377   6.6287   2.2373   0.2540
 T46  C5   C  CH1    0  -0.076   6.4073   1.3183  -0.9393
 T46  C6   C  CH3    0  -0.688   7.3925   0.1503  -0.9055
 T46  C21  C  CR6    0   0.744  -5.3375   0.4101  -0.6878
 T46  O21  O  O      0  -0.472  -5.1832  -0.6782  -1.2003
 T46  N31  N  NR16   0  -0.733  -5.7711   1.4936  -1.4076
 T46  C41  C  CR6    0   0.558  -5.9962   2.7820  -0.9596
 T46  O41  O  O      0  -0.456  -6.3869   3.6451  -1.7249
 T46  C51  C  CR6    0  -0.185  -5.7260   2.9789   0.4498
 T46  C5A  C  CH3    0  -0.707  -5.9312   4.3341   1.0424
 T46  C61  C  CR16   0   0.059  -5.2951   1.9219   1.1600
 T46  N11  N  NR6    0  -0.567  -5.1065   0.6660   0.6437
 T46  C1,  C  CH1    0   0.217  -4.5911  -0.3921   1.5133
 T46  C2,  C  CH2    0  -0.560  -5.4306  -1.6700   1.5900
 T46  C3,  C  CH1    0   0.021  -4.5689  -2.7502   0.9359
 T46  O3,  O  OH1    0  -0.669  -4.5852  -3.9929   1.5942
 T46  O4,  O  O2     0  -0.488  -3.3079  -0.7532   1.0934
 T46  C4,  C  CH1    0   0.015  -3.1597  -2.1614   1.0287
 T46  C5,  C  CH2    0  -0.156  -2.2962  -2.5366  -0.1499
 T46  O5,  O  O2     0  -0.621  -0.9767  -2.0796   0.0612
 T46  P    P  P      0   1.343  -0.0062  -1.9789  -1.2662
 T46  O1P  O  O      0  -0.803   0.3297  -3.3552  -1.7490
 T46  O2P  O  OP    -1  -0.792  -0.5585  -0.9566  -2.2070
 T46  OPP  O  O2     0  -0.736   1.2514  -1.3560  -0.4082
 T46  P2   P  P      0   1.338   2.7902  -1.3101  -0.9716
 T46  O4P  O  OP    -1  -0.788   3.6112  -2.3660  -0.3031
 T46  O3P  O  O      0  -0.782   2.7842  -1.1570  -2.4565
 T46  O1   O  O2     0  -0.630   3.1176   0.1517  -0.2515
 T46  C1   C  CH1    0   0.319   4.4124   0.4704   0.1014
 T46  C2   C  CH1    0  -0.051   4.3881   1.5973   1.1252
 T46  O2   O  OH1    0  -0.664   3.7871   2.7151   0.5249
 T46  C3   C  CH1    0  -0.120   5.8198   1.9511   1.5138
 T46  O3   O  OH1    0  -0.653   6.3937   0.8461   2.1737
 T46  O4   O  O      0  -0.382   7.4716   3.1023   0.2238
 T46  O5   O  O2     0  -0.495   5.0651   0.9030  -1.0703
 T46  H1   H  HCH1   0   0.276   6.6175   1.9100  -1.8342
 T46  H2   H  HCH3   0   0.241   7.2620  -0.4868  -0.0326
 T46  H3   H  HCH3   0   0.250   7.2658  -0.4593  -1.7998
 T46  H4   H  HCH3   0   0.243   8.4161   0.5251  -0.8992
 T46  H6   H  HCH3   0   0.247  -6.9652   4.6634   0.9311
 T46  H7   H  HCH3   0   0.247  -5.6927   4.3352   2.1047
 T46  H8   H  HCH3   0   0.247  -5.3008   5.0806   0.5573
 T46  H10  H  HCH1   0   0.253  -4.5434   0.0753   2.4997
 T46  H11  H  HCH2   0   0.267  -5.5774  -1.9238   2.6413
 T46  H12  H  HCH2   0   0.275  -6.4159  -1.5621   1.1394
 T46  H13  H  HCH1   0   0.233  -4.8528  -2.8706  -0.1129
 T46  H14  H  HOH1   0   0.456  -5.3727  -4.4688   1.3162
 T46  H15  H  HCH1   0   0.227  -2.6953  -2.5245   1.9572
 T46  H16  H  HCH2   0   0.212  -2.3202  -3.6278  -0.2565
 T46  H17  H  HCH2   0   0.216  -2.7324  -2.1037  -1.0567
 T46  H20  H  HCH1   0   0.210   4.9262  -0.3988   0.5333
 T46  H21  H  HCH1   0   0.249   3.8461   1.2564   2.0174
 T46  H22  H  HOH1   0   0.460   3.6202   3.3745   1.2058
 T46  H23  H  HCH1   0   0.263   5.8230   2.8470   2.1486
 T46  H24  H  HOH1   0   0.468   7.2305   1.1150   2.5667
 T46  H5   H  HNR6   0   0.425  -5.9461   1.3159  -2.3893
 T46  H9   H  HCR6   0   0.316  -5.0746   2.0172   2.2150

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
 T46  O3,  C3,  single  1.406  0.020  1.406
 T46  C3,  C2,  single  1.529  0.020  1.529
 T46  C3,  C4,  single  1.530  0.020  1.530
 T46  O1P  P    deloc   1.497  0.020  1.497
 T46  C2,  C1,  single  1.531  0.020  1.531
 T46  C4,  C5,  single  1.508  0.020  1.508
 T46  C4,  O4,  single  1.417  0.020  1.417
 T46  C5,  O5,  single  1.412  0.020  1.412
 T46  O5,  P    single  1.647  0.020  1.647
 T46  P    O2P  deloc   1.495  0.020  1.495
 T46  P    OPP  single  1.645  0.020  1.645
 T46  C1,  O4,  single  1.398  0.020  1.398
 T46  C1,  N11  single  1.463  0.020  1.463
 T46  O3P  P2   deloc   1.493  0.020  1.493
 T46  O21  C21  double  1.213  0.020  1.213
 T46  N11  C21  single  1.375  0.020  1.375
 T46  N11  C61  single  1.371  0.020  1.371
 T46  OPP  P2   single  1.639  0.020  1.639
 T46  C21  N31  single  1.371  0.020  1.371
 T46  P2   O1   single  1.662  0.020  1.662
 T46  P2   O4P  deloc   1.495  0.020  1.495
 T46  C61  C51  double  1.344  0.020  1.344
 T46  O2   C2   single  1.404  0.020  1.404
 T46  O1   C1   single  1.379  0.020  1.379
 T46  N31  C41  single  1.383  0.020  1.383
 T46  C51  C41  single  1.449  0.020  1.449
 T46  C51  C5A  single  1.493  0.020  1.493
 T46  C41  O41  double  1.218  0.020  1.218
 T46  C3   C2   single  1.525  0.020  1.525
 T46  C3   O3   single  1.409  0.020  1.409
 T46  C3   C4   single  1.524  0.020  1.524
 T46  C2   C1   single  1.523  0.020  1.523
 T46  C1   O5   single  1.409  0.020  1.409
 T46  C4   C5   single  1.522  0.020  1.522
 T46  C4   O4   double  1.208  0.020  1.208
 T46  O5   C5   single  1.411  0.020  1.411
 T46  C5   C6   single  1.528  0.020  1.528
 T46  C5   H1   single  0.970  0.020  1.090
 T46  C6   H2   single  0.970  0.020  1.090
 T46  C6   H3   single  0.970  0.020  1.090
 T46  C6   H4   single  0.970  0.020  1.090
 T46  N31  H5   single  0.860  0.020  1.020
 T46  C5A  H6   single  0.970  0.020  1.090
 T46  C5A  H7   single  0.970  0.020  1.090
 T46  C5A  H8   single  0.970  0.020  1.090
 T46  C61  H9   single  0.930  0.020  1.080
 T46  C1,  H10  single  0.970  0.020  1.090
 T46  C2,  H11  single  0.970  0.020  1.090
 T46  C2,  H12  single  0.970  0.020  1.090
 T46  C3,  H13  single  0.970  0.020  1.090
 T46  O3,  H14  single  0.850  0.020  0.980
 T46  C4,  H15  single  0.970  0.020  1.090
 T46  C5,  H16  single  0.970  0.020  1.090
 T46  C5,  H17  single  0.970  0.020  1.090
 T46  C1   H20  single  0.970  0.020  1.090
 T46  C2   H21  single  0.970  0.020  1.090
 T46  O2   H22  single  0.850  0.020  0.980
 T46  C3   H23  single  0.970  0.020  1.090
 T46  O3   H24  single  0.850  0.020  0.980

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
 T46  O4   C4   C3   121.69  3.000
 T46  O4   C4   C5   120.93  3.000
 T46  C3   C4   C5   117.22  3.000
 T46  H1   C5   O5   105.44  3.000
 T46  H1   C5   C6   107.93  3.000
 T46  O5   C5   C6   112.97  3.000
 T46  H1   C5   C4   106.68  3.000
 T46  C6   C5   C4   110.50  3.000
 T46  O5   C5   C4   112.87  3.000
 T46  H4   C6   H3   107.83  3.000
 T46  H4   C6   H2   108.01  3.000
 T46  H3   C6   H2   108.46  3.000
 T46  H4   C6   C5   110.04  3.000
 T46  H3   C6   C5   109.54  3.000
 T46  H2   C6   C5   112.82  3.000
 T46  N11  C21  N31  114.48  3.000
 T46  N31  C21  O21  121.84  3.000
 T46  N11  C21  O21  123.69  3.000
 T46  H5   N31  C41  116.71  3.000
 T46  H5   N31  C21  115.14  3.000
 T46  C41  N31  C21  128.15  3.000
 T46  C51  C41  O41  125.10  3.000
 T46  O41  C41  N31  120.60  3.000
 T46  C51  C41  N31  114.31  3.000
 T46  C61  C51  C5A  123.23  3.000
 T46  C5A  C51  C41  118.94  3.000
 T46  C61  C51  C41  117.83  3.000
 T46  H8   C5A  H7   107.86  3.000
 T46  H8   C5A  H6   107.21  3.000
 T46  H7   C5A  H6   107.87  3.000
 T46  H8   C5A  C51  111.42  3.000
 T46  H7   C5A  C51  110.98  3.000
 T46  H6   C5A  C51  111.33  3.000
 T46  H9   C61  N11  114.82  3.000
 T46  H9   C61  C51  120.75  3.000
 T46  N11  C61  C51  124.44  3.000
 T46  C1,  N11  C61  119.15  3.000
 T46  C61  N11  C21  120.79  3.000
 T46  C1,  N11  C21  119.99  3.000
 T46  H10  C1,  O4,  109.98  3.000
 T46  H10  C1,  C2,  109.63  3.000
 T46  O4,  C1,  C2,  107.63  3.000
 T46  H10  C1,  N11  104.03  3.000
 T46  O4,  C1,  N11  109.37  3.000
 T46  C2,  C1,  N11  116.12  3.000
 T46  H12  C2,  H11  107.46  3.000
 T46  H12  C2,  C3,  113.77  3.000
 T46  H11  C2,  C3,  108.88  3.000
 T46  H12  C2,  C1,  113.13  3.000
 T46  H11  C2,  C1,  108.43  3.000
 T46  C3,  C2,  C1,  105.02  3.000
 T46  H13  C3,  C4,  109.86  3.000
 T46  H13  C3,  O3,  110.41  3.000
 T46  C4,  C3,  O3,  108.80  3.000
 T46  H13  C3,  C2,  109.99  3.000
 T46  C4,  C3,  C2,  102.79  3.000
 T46  O3,  C3,  C2,  114.68  3.000
 T46  H14  O3,  C3,  108.16  3.000
 T46  C4,  O4,  C1,  111.49  3.000
 T46  H15  C4,  C5,  109.62  3.000
 T46  H15  C4,  O4,  109.49  3.000
 T46  C5,  C4,  O4,  110.04  3.000
 T46  H15  C4,  C3,  108.24  3.000
 T46  O4,  C4,  C3,  106.79  3.000
 T46  C5,  C4,  C3,  112.59  3.000
 T46  H17  C5,  H16  107.70  3.000
 T46  H17  C5,  O5,  111.59  3.000
 T46  H16  C5,  O5,  110.91  3.000
 T46  H17  C5,  C4,  108.70  3.000
 T46  H16  C5,  C4,  108.12  3.000
 T46  O5,  C5,  C4,  109.73  3.000
 T46  P    O5,  C5,  116.73  3.000
 T46  OPP  P    O2P  110.59  3.000
 T46  OPP  P    O1P  110.18  3.000
 T46  O2P  P    O1P  120.58  3.000
 T46  OPP  P    O5,   93.05  3.000
 T46  O2P  P    O5,  109.34  3.000
 T46  O1P  P    O5,  109.63  3.000
 T46  P2   OPP  P    123.29  3.000
 T46  O1   P2   O3P  109.97  3.000
 T46  O1   P2   O4P  108.61  3.000
 T46  O3P  P2   O4P  121.29  3.000
 T46  O4P  P2   OPP  109.99  3.000
 T46  O1   P2   OPP   93.48  3.000
 T46  O3P  P2   OPP  109.94  3.000
 T46  C1   O1   P2   119.93  3.000
 T46  H20  C1   O5   110.69  3.000
 T46  H20  C1   C2   109.20  3.000
 T46  O5   C1   C2   109.83  3.000
 T46  H20  C1   O1   110.91  3.000
 T46  O5   C1   O1   107.03  3.000
 T46  C2   C1   O1   109.15  3.000
 T46  H21  C2   C3   109.16  3.000
 T46  H21  C2   O2   112.54  3.000
 T46  C3   C2   O2   109.03  3.000
 T46  H21  C2   C1   108.93  3.000
 T46  C3   C2   C1   109.15  3.000
 T46  O2   C2   C1   107.98  3.000
 T46  H22  O2   C2   108.50  3.000
 T46  H23  C3   O3   111.59  3.000
 T46  H23  C3   C2   109.84  3.000
 T46  O3   C3   C2   108.64  3.000
 T46  H23  C3   C4   108.85  3.000
 T46  O3   C3   C4   108.55  3.000
 T46  C2   C3   C4   109.34  3.000
 T46  H24  O3   C3   109.03  3.000
 T46  C1   O5   C5   116.98  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
 T46  CONST_01  C1,  N11  C21  N31  180.00   0.0  0
 T46  CONST_02  C61  N11  C21  N31    0.00   0.0  0
 T46  CONST_03  N11  C21  N31  C41    0.00   0.0  0
 T46  CONST_04  C1,  N11  C21  O21    0.00   0.0  0
 T46  CONST_05  C61  N11  C21  O21  180.00   0.0  0
 T46  CONST_06  C41  N31  C21  O21  180.00   0.0  0
 T46  CONST_07  H5   N31  C21  N11  180.00   0.0  0
 T46  Var_01    H6   C5A  C51  C41   59.72  30.0  3
 T46  Var_02    O1P  P    O5,  C5,  -70.04  30.0  3
 T46  Var_03    O3P  P2   OPP  P     31.46  30.0  3
 T46  Var_04    H16  C5,  O5,  P     78.58  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
 T46  chir_01  C5   C4   O5   C6   positiv
 T46  chir_02  C1,  C2,  O4,  N11  negativ
 T46  chir_03  C3,  O3,  C2,  C4,  negativ
 T46  chir_04  C4,  O4,  C3,  C5,  negativ
 T46  chir_07  C1   O1   C2   O5   positiv
 T46  chir_08  C2   O2   C1   C3   negativ
 T46  chir_09  C3   O3   C2   C4   positiv

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
 T46  plan-1  C21  0.020
 T46  plan-1  O21  0.020
 T46  plan-1  N31  0.020
 T46  plan-1  C41  0.020
 T46  plan-1  O41  0.020
 T46  plan-1  C51  0.020
 T46  plan-1  C5A  0.020
 T46  plan-1  C61  0.020
 T46  plan-1  N11  0.020
 T46  plan-1  C1,  0.020
 T46  plan-1  H5   0.020
 T46  plan-1  H9   0.020
 T46  plan-2  C4   0.020
 T46  plan-2  C5   0.020
 T46  plan-2  C3   0.020
 T46  plan-2  O4   0.020

