# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 08:36:51 2020
#   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  56  34  .  2021-08-04  2021-08-04  
;
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  OP    -1  -0.787  -3.7371  -2.2191   0.2598
 3YN  P2   P  P      0   1.337  -2.9572  -1.1299   0.9231
 3YN  O3P  O  O      0  -0.785  -2.9853  -0.9506   2.4055
 3YN  O1   O  O2     0  -0.627  -3.3030   0.3086   0.1664
 3YN  C1   C  CH1    0   0.318  -4.6077   0.6129  -0.1769
 3YN  C2   C  CH2    0  -0.520  -4.6013   1.6841  -1.2523
 3YN  C3   C  CH1    0  -0.093  -6.0154   2.1125  -1.5954
 3YN  O3   O  OH1    0  -0.655  -6.6502   1.0427  -2.2699
 3YN  C4   C  C      0   0.376  -6.8281   2.3905  -0.3348
 3YN  O4   O  O      0  -0.385  -7.6860   3.2417  -0.3108
 3YN  C5   C  CH1    0  -0.083  -6.5853   1.4876   0.8658
 3YN  O5   O  O2     0  -0.492  -5.2290   1.1192   0.9871
 3YN  C6   C  CH3    0  -0.690  -7.5399   0.2942   0.8492
 3YN  OPP  O  O2     0  -0.736  -1.4045  -1.1447   0.3955
 3YN  P    P  P      0   1.342  -0.1717  -1.7855   1.2760
 3YN  O1P  O  O      0  -0.803  -0.5367  -3.1562   1.7539
 3YN  O2P  O  OP    -1  -0.792   0.3730  -0.7698   2.2290
 3YN  O5'  O  O2     0  -0.620   0.8227  -1.9005  -0.0313
 3YN  C5'  C  CH2    0  -0.156   2.1207  -2.4079   0.1981
 3YN  C4'  C  CH1    0   0.014   3.0038  -2.0934  -0.9836
 3YN  O4'  O  O2     0  -0.488   3.2089  -0.6943  -1.0767
 3YN  C3'  C  CH1    0   0.021   4.3879  -2.7357  -0.8720
 3YN  O3'  O  OH1    0  -0.669   4.3558  -3.9940  -1.4991
 3YN  C2'  C  CH2    0  -0.560   5.2935  -1.7074  -1.5500
 3YN  C1'  C  CH1    0   0.218   4.5041  -0.3959  -1.5091
 3YN  N11  N  NR6    0  -0.567   5.0628   0.6649  -0.6705
 3YN  C21  C  CR6    0   0.743   5.2859   0.4377   0.6676
 3YN  O21  O  O      0  -0.471   5.0835  -0.6270   1.2121
 3YN  N31  N  NR16   0  -0.733   5.7702   1.5210   1.3546
 3YN  C41  C  CR6    0   0.558   6.0519   2.7844   0.8686
 3YN  O41  O  O      0  -0.456   6.4825   3.6511   1.6079
 3YN  C51  C  CR6    0  -0.185   5.7870   2.9519  -0.5455
 3YN  C5A  C  CH3    0  -0.707   6.0517   4.2781  -1.1789
 3YN  C61  C  CR16   0   0.059   5.3069   1.8952  -1.2237
 3YN  H2   H  HCH1   0   0.201  -5.1357  -0.2837  -0.5270
 3YN  H3   H  HCH2   0   0.255  -4.0449   2.5527  -0.8885
 3YN  H4   H  HCH2   0   0.261  -4.1003   1.3256  -2.1544
 3YN  H5   H  HCH1   0   0.259  -5.9984   3.0206  -2.2091
 3YN  H6   H  HOH1   0   0.463  -7.4946   1.3490  -2.6178
 3YN  H7   H  HCH1   0   0.276  -6.8060   2.0811   1.7571
 3YN  H8   H  HCH3   0   0.241  -7.4068  -0.3446  -0.0221
 3YN  H9   H  HCH3   0   0.250  -7.3879  -0.3078   1.7449
 3YN  H10  H  HCH3   0   0.244  -8.5718   0.6451   0.8537
 3YN  H12  H  HCH2   0   0.216   2.5697  -1.9738   1.0983
 3YN  H13  H  HCH2   0   0.213   2.0985  -3.4964   0.3283
 3YN  H14  H  HCH1   0   0.227   2.5288  -2.4577  -1.9063
 3YN  H15  H  HCH1   0   0.234   4.6647  -2.8408   0.1804
 3YN  H16  H  HOH1   0   0.457   5.1182  -4.4975  -1.2006
 3YN  H17  H  HCH2   0   0.275   6.2800  -1.6262  -1.0966
 3YN  H18  H  HCH2   0   0.267   5.4350  -1.9932  -2.5937
 3YN  H19  H  HCH1   0   0.253   4.4720   0.0446  -2.5083
 3YN  H20  H  HNR6   0   0.425   5.9417   1.3632   2.3402
 3YN  H21  H  HCH3   0   0.247   5.4620   5.0676  -0.7112
 3YN  H22  H  HCH3   0   0.247   7.1012   4.5602  -1.0850
 3YN  H23  H  HCH3   0   0.247   5.8044   4.2595  -2.2389
 3YN  H24  H  HCR6   0   0.316   5.0877   1.9695  -2.2807

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  1.413  0.020  1.413
 3YN  O5   C5   single  1.411  0.020  1.411
 3YN  C2   C1   single  1.518  0.020  1.518
 3YN  C2   C3   single  1.517  0.020  1.517
 3YN  C6   C5   single  1.528  0.020  1.528
 3YN  C2'  C3'  single  1.529  0.020  1.529
 3YN  C2'  C1'  single  1.531  0.020  1.531
 3YN  O1P  P    deloc   1.497  0.020  1.497
 3YN  C1   O1   single  1.383  0.020  1.383
 3YN  O3   C3   single  1.415  0.020  1.415
 3YN  O4   C4   double  1.209  0.020  1.209
 3YN  C3'  O3'  single  1.406  0.020  1.406
 3YN  C3'  C4'  single  1.530  0.020  1.530
 3YN  C4   C5   single  1.522  0.020  1.522
 3YN  C4   C3   single  1.525  0.020  1.525
 3YN  C5A  C51  single  1.493  0.020  1.493
 3YN  C51  C61  double  1.344  0.020  1.344
 3YN  C51  C41  single  1.448  0.020  1.448
 3YN  C61  N11  single  1.371  0.020  1.371
 3YN  N11  C1'  single  1.463  0.020  1.463
 3YN  N11  C21  single  1.375  0.020  1.375
 3YN  O41  C41  double  1.218  0.020  1.218
 3YN  C41  N31  single  1.383  0.020  1.383
 3YN  C1'  O4'  single  1.398  0.020  1.398
 3YN  OPP  P    single  1.645  0.020  1.645
 3YN  OPP  P2   single  1.640  0.020  1.640
 3YN  P    O5'  single  1.646  0.020  1.646
 3YN  P    O2P  deloc   1.495  0.020  1.495
 3YN  N31  C21  single  1.371  0.020  1.371
 3YN  C21  O21  double  1.213  0.020  1.213
 3YN  O1   P2   single  1.662  0.020  1.662
 3YN  O5'  C5'  single  1.412  0.020  1.412
 3YN  C4'  C5'  single  1.508  0.020  1.508
 3YN  C4'  O4'  single  1.417  0.020  1.417
 3YN  O3P  P2   deloc   1.493  0.020  1.493
 3YN  P2   O4P  deloc   1.495  0.020  1.495
 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  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  OPP  P2   O1    93.34  3.000
 3YN  O1   P2   O3P  110.13  3.000
 3YN  OPP  P2   O3P  109.77  3.000
 3YN  O3P  P2   O4P  121.21  3.000
 3YN  O1   P2   O4P  108.67  3.000
 3YN  OPP  P2   O4P  110.16  3.000
 3YN  C1   O1   P2   119.99  3.000
 3YN  H2   C1   O5   110.11  3.000
 3YN  H2   C1   C2   110.63  3.000
 3YN  O5   C1   C2   109.43  3.000
 3YN  H2   C1   O1   110.68  3.000
 3YN  C2   C1   O1   109.10  3.000
 3YN  O5   C1   O1   106.80  3.000
 3YN  H4   C2   H3   107.57  3.000
 3YN  H4   C2   C3   109.48  3.000
 3YN  H3   C2   C3   108.98  3.000
 3YN  H4   C2   C1   110.82  3.000
 3YN  H3   C2   C1   109.08  3.000
 3YN  C3   C2   C1   110.83  3.000
 3YN  H5   C3   C4   108.67  3.000
 3YN  H5   C3   O3   111.49  3.000
 3YN  C4   C3   O3   107.02  3.000
 3YN  H5   C3   C2   110.25  3.000
 3YN  C4   C3   C2   111.18  3.000
 3YN  O3   C3   C2   108.21  3.000
 3YN  H6   O3   C3   108.97  3.000
 3YN  C5   C4   O4   121.02  3.000
 3YN  C5   C4   C3   117.31  3.000
 3YN  O4   C4   C3   121.53  3.000
 3YN  H7   C5   C6   107.86  3.000
 3YN  H7   C5   O5   105.41  3.000
 3YN  C6   C5   O5   113.42  3.000
 3YN  H7   C5   C4   106.79  3.000
 3YN  C6   C5   C4   110.80  3.000
 3YN  O5   C5   C4   112.10  3.000
 3YN  C5   O5   C1   116.45  3.000
 3YN  H10  C6   H9   107.85  3.000
 3YN  H10  C6   H8   107.94  3.000
 3YN  H9   C6   H8   108.46  3.000
 3YN  H10  C6   C5   109.87  3.000
 3YN  H9   C6   C5   109.59  3.000
 3YN  H8   C6   C5   112.99  3.000
 3YN  P    OPP  P2   122.74  3.000
 3YN  O5'  P    O2P  109.48  3.000
 3YN  O2P  P    O1P  120.49  3.000
 3YN  O5'  P    O1P  109.68  3.000
 3YN  O2P  P    OPP  110.46  3.000
 3YN  O5'  P    OPP   93.14  3.000
 3YN  O1P  P    OPP  110.17  3.000
 3YN  C5'  O5'  P    116.82  3.000
 3YN  H13  C5'  H12  107.71  3.000
 3YN  H13  C5'  C4'  108.17  3.000
 3YN  H12  C5'  C4'  108.73  3.000
 3YN  H13  C5'  O5'  110.93  3.000
 3YN  H12  C5'  O5'  111.58  3.000
 3YN  C4'  C5'  O5'  109.63  3.000
 3YN  H14  C4'  C3'  108.23  3.000
 3YN  H14  C4'  O4'  109.54  3.000
 3YN  C3'  C4'  O4'  106.76  3.000
 3YN  H14  C4'  C5'  109.60  3.000
 3YN  O4'  C4'  C5'  110.00  3.000
 3YN  C3'  C4'  C5'  112.64  3.000
 3YN  C1'  O4'  C4'  111.42  3.000
 3YN  H15  C3'  C2'  109.98  3.000
 3YN  H15  C3'  O3'  110.42  3.000
 3YN  C2'  C3'  O3'  114.68  3.000
 3YN  H15  C3'  C4'  109.86  3.000
 3YN  O3'  C3'  C4'  108.81  3.000
 3YN  C2'  C3'  C4'  102.78  3.000
 3YN  H16  O3'  C3'  108.19  3.000
 3YN  H18  C2'  H17  107.48  3.000
 3YN  H18  C2'  C1'  108.46  3.000
 3YN  H17  C2'  C1'  113.09  3.000
 3YN  H18  C2'  C3'  108.95  3.000
 3YN  H17  C2'  C3'  113.71  3.000
 3YN  C1'  C2'  C3'  105.00  3.000
 3YN  H19  C1'  N11  104.07  3.000
 3YN  H19  C1'  C2'  109.64  3.000
 3YN  N11  C1'  C2'  116.07  3.000
 3YN  H19  C1'  O4'  109.98  3.000
 3YN  N11  C1'  O4'  109.35  3.000
 3YN  C2'  C1'  O4'  107.65  3.000
 3YN  C61  N11  C21  120.79  3.000
 3YN  C21  N11  C1'  119.98  3.000
 3YN  C61  N11  C1'  119.17  3.000
 3YN  N31  C21  O21  121.84  3.000
 3YN  O21  C21  N11  123.69  3.000
 3YN  N31  C21  N11  114.47  3.000
 3YN  H20  N31  C41  116.74  3.000
 3YN  H20  N31  C21  115.10  3.000
 3YN  C41  N31  C21  128.16  3.000
 3YN  C51  C41  O41  125.11  3.000
 3YN  O41  C41  N31  120.59  3.000
 3YN  C51  C41  N31  114.30  3.000
 3YN  C61  C51  C5A  123.19  3.000
 3YN  C61  C51  C41  117.84  3.000
 3YN  C5A  C51  C41  118.96  3.000
 3YN  H23  C5A  H22  107.87  3.000
 3YN  H23  C5A  H21  107.88  3.000
 3YN  H22  C5A  H21  107.22  3.000
 3YN  H23  C5A  C51  110.95  3.000
 3YN  H22  C5A  C51  111.33  3.000
 3YN  H21  C5A  C51  111.42  3.000
 3YN  H24  C61  C51  120.74  3.000
 3YN  H24  C61  N11  114.82  3.000
 3YN  C51  C61  N11  124.43  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   -59.54  30.0  3
 3YN  Var_02    OPP  P2   O1   C1    155.40  30.0  3
 3YN  Var_03    C4'  C5'  O5'  P    -164.37  30.0  3
 3YN  Var_04    O1P  P    OPP  P2     49.58  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

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

