# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 00:56:57 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl 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](O)C1=O)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
 3YN  3YN  '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  58  34  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3YN
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
 3YN  O4P  O  OH1   0  -0.705  -22.6461  5.5790  14.4020
 3YN  P2   P  P     0   1.513  -22.5473  5.1132  12.8957
 3YN  O3P  O  O     0  -0.692  -21.6980  5.8903  11.9743
 3YN  O1   O  O2    0  -0.590  -24.0684  4.9542  12.4556
 3YN  C1   C  CH1   0   0.236  -24.4201  4.8825  11.0602
 3YN  C2   C  CH2   0  -0.517  -25.9297  4.9152  10.9669
 3YN  C3   C  CH1   0  -0.041  -26.5602  3.6185  11.4649
 3YN  O3   O  OH1   0  -0.652  -27.9282  3.6630  11.2034
 3YN  C4   C  C     0   0.366  -25.8627  2.4508  10.7956
 3YN  O4   O  O     0  -0.374  -26.4630  1.5493  10.2673
 3YN  C5   C  CH1   0  -0.089  -24.3453  2.4867  10.8980
 3YN  O5   O  O2    0  -0.477  -23.8578  3.7644  10.4784
 3YN  C6   C  CH3   0  -0.693  -23.6462  1.4375  10.0674
 3YN  OPP  O  O2    0  -0.682  -22.0850  3.5840  13.1282
 3YN  P    P  P     0   1.490  -20.6328  2.9144  12.8568
 3YN  O1P  O  O     0  -0.671  -20.3170  2.6430  11.4458
 3YN  O2P  O  OH1   0  -0.707  -20.7235  1.6578  13.8186
 3YN  O5'  O  O2    0  -0.586  -19.7198  3.9409  13.6430
 3YN  C5'  C  CH2   0  -0.212  -18.3440  4.2134  13.3406
 3YN  C4'  C  CH1   0   0.006  -18.2541  5.6278  12.7871
 3YN  O4'  O  O2    0  -0.501  -16.9156  6.0819  12.9432
 3YN  C3'  C  CH1   0  -0.037  -18.5890  5.7468  11.2854
 3YN  O3'  O  OH1   0  -0.694  -19.2416  6.9549  10.9924
 3YN  C2'  C  CH2   0  -0.525  -17.2080  5.7568  10.6538
 3YN  C1'  C  CH1   0   0.200  -16.3759  6.4749  11.7036
 3YN  N11  N  NR6   0  -0.564  -14.9625  6.1346  11.6939
 3YN  C21  C  CR6   0   0.734  -14.0274  7.1192  11.4651
 3YN  O21  O  O     0  -0.481  -14.3076  8.2800  11.2469
 3YN  N31  N  NR16  0  -0.736  -12.7301  6.6795  11.4951
 3YN  C41  C  CR6   0   0.562  -12.2671  5.3973  11.7294
 3YN  O41  O  O     0  -0.450  -11.0742  5.1582  11.7232
 3YN  C51  C  CR6   0  -0.186  -13.3096  4.4189  11.9749
 3YN  C5A  C  CH3   0  -0.707  -12.9210  3.0041  12.2514
 3YN  C61  C  CR16  0   0.072  -14.5836  4.8410  11.9483
 3YN  H1   H  HOH1  0   0.514  -22.7720  6.5311  14.5244
 3YN  H2   H  HCH1  0   0.288  -23.9907  5.7431  10.5444
 3YN  H3   H  HCH2  0   0.284  -26.3212  5.7711  11.5183
 3YN  H4   H  HCH2  0   0.276  -26.1872  5.0584   9.9143
 3YN  H5   H  HCH1  0   0.257  -26.3541  3.5143  12.5427
 3YN  H6   H  HOH1  0   0.459  -28.3357  2.8523  11.5258
 3YN  H7   H  HCH1  0   0.268  -24.1026  2.3226  11.9572
 3YN  H8   H  HCH3  0   0.245  -23.9405  0.4407  10.3892
 3YN  H9   H  HCH3  0   0.241  -23.8781  1.5405   9.0076
 3YN  H10  H  HCH3  0   0.252  -22.5682  1.5242  10.1990
 3YN  H11  H  HOH1  0   0.511  -20.7399  0.8044  13.3639
 3YN  H12  H  HCH2  0   0.278  -17.7942  4.1347  14.2779
 3YN  H13  H  HCH2  0   0.245  -17.9353  3.4750  12.6455
 3YN  H14  H  HCH1  0   0.257  -18.9192  6.2676  13.3769
 3YN  H15  H  HCH1  0   0.250  -19.1723  4.8898  10.9360
 3YN  H16  H  HOH1  0   0.456  -20.1479  6.8605  11.3179
 3YN  H17  H  HCH2  0   0.270  -16.8548  4.7347  10.4973
 3YN  H18  H  HCH2  0   0.285  -17.1898  6.2612   9.6889
 3YN  H19  H  HCH1  0   0.276  -16.4381  7.5562  11.5788
 3YN  H20  H  HNR6  0   0.427  -12.0302  7.3910  11.3219
 3YN  H21  H  HCH3  0   0.248  -12.3732  2.5718  11.4130
 3YN  H22  H  HCH3  0   0.248  -12.2765  2.9337  13.1285
 3YN  H23  H  HCH3  0   0.247  -13.8001  2.3873  12.4298
 3YN  H24  H  HCR6  0   0.305  -15.3915  4.1487  12.1389

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
 3YN  O5   C1   single  1.380  0.020  1.380
 3YN  O5   C5   single  1.430  0.020  1.430
 3YN  C2   C1   single  1.513  0.020  1.513
 3YN  C2   C3   single  1.525  0.020  1.525
 3YN  C6   C5   single  1.510  0.020  1.510
 3YN  C2'  C3'  single  1.519  0.020  1.519
 3YN  C2'  C1'  single  1.520  0.020  1.520
 3YN  O1P  P    double  1.471  0.020  1.471
 3YN  C1   O1   single  1.441  0.020  1.441
 3YN  O3   C3   single  1.394  0.020  1.394
 3YN  O4   C4   double  1.205  0.020  1.205
 3YN  C3'  O3'  single  1.404  0.020  1.404
 3YN  C3'  C4'  single  1.543  0.020  1.543
 3YN  C4   C5   single  1.521  0.020  1.521
 3YN  C4   C3   single  1.516  0.020  1.516
 3YN  C5A  C51  single  1.493  0.020  1.493
 3YN  C51  C61  double  1.342  0.020  1.342
 3YN  C51  C41  single  1.451  0.020  1.451
 3YN  C61  N11  single  1.372  0.020  1.372
 3YN  N11  C1'  single  1.454  0.020  1.454
 3YN  N11  C21  single  1.377  0.020  1.377
 3YN  O41  C41  double  1.217  0.020  1.217
 3YN  C41  N31  single  1.383  0.020  1.383
 3YN  C1'  O4'  single  1.408  0.020  1.408
 3YN  OPP  P    single  1.622  0.020  1.622
 3YN  OPP  P2   single  1.614  0.020  1.614
 3YN  P    O5'  single  1.583  0.020  1.583
 3YN  P    O2P  single  1.585  0.020  1.585
 3YN  N31  C21  single  1.370  0.020  1.370
 3YN  C21  O21  double  1.214  0.020  1.214
 3YN  O1   P2   single  1.591  0.020  1.591
 3YN  O5'  C5'  single  1.435  0.020  1.435
 3YN  C4'  C5'  single  1.522  0.020  1.522
 3YN  C4'  O4'  single  1.422  0.020  1.422
 3YN  O3P  P2   double  1.475  0.020  1.475
 3YN  P2   O4P  single  1.580  0.020  1.580
 3YN  O4P  H1   single  0.850  0.020  0.980
 3YN  C1   H2   single  0.970  0.020  1.090
 3YN  C2   H3   single  0.970  0.020  1.090
 3YN  C2   H4   single  0.970  0.020  1.090
 3YN  C3   H5   single  0.970  0.020  1.090
 3YN  O3   H6   single  0.850  0.020  0.980
 3YN  C5   H7   single  0.970  0.020  1.090
 3YN  C6   H8   single  0.970  0.020  1.090
 3YN  C6   H9   single  0.970  0.020  1.090
 3YN  C6   H10  single  0.970  0.020  1.090
 3YN  O2P  H11  single  0.850  0.020  0.980
 3YN  C5'  H12  single  0.970  0.020  1.090
 3YN  C5'  H13  single  0.970  0.020  1.090
 3YN  C4'  H14  single  0.970  0.020  1.090
 3YN  C3'  H15  single  0.970  0.020  1.090
 3YN  O3'  H16  single  0.850  0.020  0.980
 3YN  C2'  H17  single  0.970  0.020  1.090
 3YN  C2'  H18  single  0.970  0.020  1.090
 3YN  C1'  H19  single  0.970  0.020  1.090
 3YN  N31  H20  single  0.860  0.020  1.020
 3YN  C5A  H21  single  0.970  0.020  1.090
 3YN  C5A  H22  single  0.970  0.020  1.090
 3YN  C5A  H23  single  0.970  0.020  1.090
 3YN  C61  H24  single  0.930  0.020  1.080

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
 3YN  H1   O4P  P2   114.75  3.000
 3YN  OPP  P2   O1   102.64  3.000
 3YN  O1   P2   O3P  115.49  3.000
 3YN  OPP  P2   O3P  115.11  3.000
 3YN  O3P  P2   O4P  118.45  3.000
 3YN  O1   P2   O4P  103.49  3.000
 3YN  OPP  P2   O4P   99.20  3.000
 3YN  C1   O1   P2   120.40  3.000
 3YN  H2   C1   O5   106.23  3.000
 3YN  H2   C1   C2   110.27  3.000
 3YN  O5   C1   C2   113.45  3.000
 3YN  H2   C1   O1   108.81  3.000
 3YN  C2   C1   O1   107.59  3.000
 3YN  O5   C1   O1   110.44  3.000
 3YN  H4   C2   H3   107.42  3.000
 3YN  H4   C2   C3   109.17  3.000
 3YN  H3   C2   C3   110.71  3.000
 3YN  H4   C2   C1   107.29  3.000
 3YN  H3   C2   C1   110.12  3.000
 3YN  C3   C2   C1   111.96  3.000
 3YN  H5   C3   C4   105.83  3.000
 3YN  H5   C3   O3   111.72  3.000
 3YN  C4   C3   O3   113.17  3.000
 3YN  H5   C3   C2   108.80  3.000
 3YN  C4   C3   C2   108.69  3.000
 3YN  O3   C3   C2   108.50  3.000
 3YN  H6   O3   C3   109.01  3.000
 3YN  C5   C4   O4   122.96  3.000
 3YN  C5   C4   C3   114.27  3.000
 3YN  O4   C4   C3   122.73  3.000
 3YN  H7   C5   C6   108.92  3.000
 3YN  H7   C5   O5   109.92  3.000
 3YN  C6   C5   O5   107.55  3.000
 3YN  H7   C5   C4   106.36  3.000
 3YN  C6   C5   C4   114.11  3.000
 3YN  O5   C5   C4   109.95  3.000
 3YN  C5   O5   C1   117.46  3.000
 3YN  H10  C6   H9   108.69  3.000
 3YN  H10  C6   H8   107.75  3.000
 3YN  H9   C6   H8   108.47  3.000
 3YN  H10  C6   C5   109.66  3.000
 3YN  H9   C6   C5   111.76  3.000
 3YN  H8   C6   C5   110.41  3.000
 3YN  P    OPP  P2   128.56  3.000
 3YN  O5'  P    O2P  104.22  3.000
 3YN  O2P  P    O1P  116.62  3.000
 3YN  O5'  P    O1P  118.17  3.000
 3YN  O2P  P    OPP  100.05  3.000
 3YN  O5'  P    OPP   99.53  3.000
 3YN  O1P  P    OPP  115.39  3.000
 3YN  H11  O2P  P    114.53  3.000
 3YN  C5'  O5'  P    124.86  3.000
 3YN  H13  C5'  H12  108.03  3.000
 3YN  H13  C5'  C4'  111.99  3.000
 3YN  H12  C5'  C4'  110.50  3.000
 3YN  H13  C5'  O5'  111.36  3.000
 3YN  H12  C5'  O5'  106.79  3.000
 3YN  C4'  C5'  O5'  108.05  3.000
 3YN  H14  C4'  C3'  110.31  3.000
 3YN  H14  C4'  O4'  109.02  3.000
 3YN  C3'  C4'  O4'  106.65  3.000
 3YN  H14  C4'  C5'  108.13  3.000
 3YN  O4'  C4'  C5'  108.22  3.000
 3YN  C3'  C4'  C5'  114.39  3.000
 3YN  C1'  O4'  C4'  110.69  3.000
 3YN  H15  C3'  C2'  110.93  3.000
 3YN  H15  C3'  O3'  111.08  3.000
 3YN  C2'  C3'  O3'  109.28  3.000
 3YN  H15  C3'  C4'  111.47  3.000
 3YN  O3'  C3'  C4'  111.74  3.000
 3YN  C2'  C3'  C4'  101.99  3.000
 3YN  H16  O3'  C3'  106.33  3.000
 3YN  H18  C2'  H17  107.51  3.000
 3YN  H18  C2'  C1'  112.58  3.000
 3YN  H17  C2'  C1'  111.34  3.000
 3YN  H18  C2'  C3'  112.76  3.000
 3YN  H17  C2'  C3'  110.33  3.000
 3YN  C1'  C2'  C3'  102.34  3.000
 3YN  H19  C1'  N11  106.67  3.000
 3YN  H19  C1'  C2'  111.00  3.000
 3YN  N11  C1'  C2'  114.65  3.000
 3YN  H19  C1'  O4'  110.84  3.000
 3YN  N11  C1'  O4'  108.25  3.000
 3YN  C2'  C1'  O4'  105.44  3.000
 3YN  C61  N11  C21  121.16  3.000
 3YN  C21  N11  C1'  119.60  3.000
 3YN  C61  N11  C1'  119.21  3.000
 3YN  N31  C21  O21  121.96  3.000
 3YN  O21  C21  N11  123.84  3.000
 3YN  N31  C21  N11  114.20  3.000
 3YN  H20  N31  C41  116.67  3.000
 3YN  H20  N31  C21  115.15  3.000
 3YN  C41  N31  C21  128.18  3.000
 3YN  C51  C41  O41  124.96  3.000
 3YN  O41  C41  N31  120.63  3.000
 3YN  C51  C41  N31  114.42  3.000
 3YN  C61  C51  C5A  123.27  3.000
 3YN  C61  C51  C41  117.82  3.000
 3YN  C5A  C51  C41  118.91  3.000
 3YN  H23  C5A  H22  107.99  3.000
 3YN  H23  C5A  H21  107.88  3.000
 3YN  H22  C5A  H21  107.20  3.000
 3YN  H23  C5A  C51  110.92  3.000
 3YN  H22  C5A  C51  111.33  3.000
 3YN  H21  C5A  C51  111.34  3.000
 3YN  H24  C61  C51  120.29  3.000
 3YN  H24  C61  N11  115.49  3.000
 3YN  C51  C61  N11  124.22  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
 3YN  CONST_01  N31  C21  N11  C1'  180.00   0.0  0
 3YN  CONST_02  C41  N31  C21  N11    0.00   0.0  0
 3YN  CONST_03  C51  C41  N31  C21    0.00   0.0  0
 3YN  CONST_04  C61  N11  C21  N31    0.00   0.0  0
 3YN  CONST_05  O21  C21  N11  C1'    0.00   0.0  0
 3YN  CONST_06  O41  C41  N31  C21  180.00   0.0  0
 3YN  CONST_07  C61  N11  C21  O21  180.00   0.0  0
 3YN  CONST_08  C41  N31  C21  O21  180.00   0.0  0
 3YN  CONST_09  H20  N31  C21  N11  180.00   0.0  0
 3YN  Var_01    H21  C5A  C51  C41  -60.64  30.0  3
 3YN  Var_02    OPP  P2   O1   C1   -93.50  30.0  3
 3YN  Var_03    C4'  C5'  O5'  P    110.97  30.0  3
 3YN  Var_04    O1P  P    OPP  P2   -76.14  30.0  3

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
 3YN  chir_02  C1   O5   C2   O1   negativ
 3YN  chir_03  C3   O3   C4   C2   negativ
 3YN  chir_04  C5   O5   C4   C6   negativ
 3YN  chir_06  C4'  C3'  C5'  O4'  negativ
 3YN  chir_07  C3'  O3'  C2'  C4'  negativ
 3YN  chir_08  C1'  O4'  N11  C2'  negativ
 3YN  chir_09  P2   O1   O3P  O4P  both
 3YN  chir_10  P    OPP  O5'  O2P  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
 3YN  plan-1  C3   0.020
 3YN  plan-1  C4   0.020
 3YN  plan-1  O4   0.020
 3YN  plan-1  C5   0.020
 3YN  plan-2  C1'  0.020
 3YN  plan-2  N11  0.020
 3YN  plan-2  C21  0.020
 3YN  plan-2  O21  0.020
 3YN  plan-2  N31  0.020
 3YN  plan-2  C41  0.020
 3YN  plan-2  O41  0.020
 3YN  plan-2  C51  0.020
 3YN  plan-2  C5A  0.020
 3YN  plan-2  C61  0.020
 3YN  plan-2  H20  0.020
 3YN  plan-2  H24  0.020

