# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:10:09 2022
#   Inital geometry file: a 154 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-4-(formylamino)-3,5-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](NC=O)[C@@H]1O
#
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
 1YF  1YF  '(2R,3R,4S,5S,6R)-4-(formylamino)-3,5-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  62  37  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1YF
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
 1YF  O1F  O  O      0  -0.498   1.4446  -3.8465   1.4872
 1YF  C1F  C  C1     0   0.250   2.3917  -4.3515   0.9081
 1YF  N3Q  N  NH1    0  -0.582   3.4598  -3.7062   0.4303
 1YF  C3Q  C  CH1    0  -0.150   3.6787  -2.2835   0.5211
 1YF  C2Q  C  CH1    0   0.032   3.7854  -1.6652  -0.8701
 1YF  O2Q  O  OH1    0  -0.659   2.5825  -1.8928  -1.5497
 1YF  C4Q  C  CH1    0   0.062   4.9442  -1.9817   1.3231
 1YF  O4Q  O  OH1    0  -0.665   4.7505  -2.4660   2.6286
 1YF  C5Q  C  CH1    0   0.014   5.2289  -0.4766   1.3239
 1YF  C6Q  C  CH3    0  -0.706   6.5496  -0.1311   1.9787
 1YF  O5Q  O  O2     0  -0.509   5.2907   0.0024  -0.0150
 1YF  C1Q  C  CH1    0   0.245   4.1212  -0.1752  -0.7584
 1YF  O3B  O  O2     0  -0.626   3.0275   0.4751  -0.1952
 1YF  PB   P  P      0   1.370   3.0486   2.1228  -0.0437
 1YF  O2B  O  O      0  -0.784   3.4805   2.5025   1.3350
 1YF  O1B  O  OP    -1  -0.792   3.7067   2.7102  -1.2523
 1YF  O3A  O  O2     0  -0.734   1.4364   2.3582  -0.2135
 1YF  PA   P  P      0   1.339   0.3524   2.4683   1.0170
 1YF  O1A  O  O      0  -0.799   0.3334   3.8612   1.5638
 1YF  O2A  O  OP    -1  -0.797   0.4542   1.2913   1.9327
 1YF  O5'  O  O2     0  -0.622  -0.9361   2.2702   0.0054
 1YF  C5'  C  CH2    0  -0.155  -2.2217   2.3302   0.5831
 1YF  C4'  C  CH1    0   0.013  -3.2628   2.2928  -0.5072
 1YF  O4'  O  O2     0  -0.490  -3.2181   1.0414  -1.1712
 1YF  C3'  C  CH1    0   0.023  -4.6871   2.4555   0.0254
 1YF  O3'  O  OH1    0  -0.669  -5.0208   3.8215   0.0157
 1YF  C2'  C  CH2    0  -0.561  -5.5073   1.5906  -0.9325
 1YF  C1'  C  CH1    0   0.219  -4.4953   0.6284  -1.5623
 1YF  N1   N  NR6    0  -0.566  -4.6640  -0.7868  -1.2343
 1YF  C2   C  CR6    0   0.742  -4.6756  -1.1903   0.0804
 1YF  O2   O  O      0  -0.472  -4.5815  -0.4268   1.0182
 1YF  C6   C  CR16   0   0.060  -4.7415  -1.7032  -2.2509
 1YF  C5   C  CR6    0  -0.186  -4.8696  -3.0289  -2.0705
 1YF  C5M  C  CH3    0  -0.707  -4.9548  -4.0038  -3.1987
 1YF  C4   C  CR6    0   0.559  -4.9180  -3.5249  -0.7102
 1YF  N3   N  NR16   0  -0.734  -4.8118  -2.5431   0.2582
 1YF  O4   O  O      0  -0.456  -5.0361  -4.6955  -0.3963
 1YF  H2   H  H      0   0.197   2.4552  -5.4334   0.7167
 1YF  H3   H  HCH1   0   0.269   2.8193  -1.8496   1.0382
 1YF  H4   H  HCH1   0   0.219   4.6310  -2.1374  -1.3935
 1YF  H5   H  HOH1   0   0.455   2.7142  -1.6928  -2.4816
 1YF  H6   H  HCH1   0   0.209   5.7902  -2.4911   0.8353
 1YF  H7   H  HOH1   0   0.456   5.6090  -2.6278   3.0293
 1YF  H8   H  HCH1   0   0.229   4.4232   0.0314   1.8666
 1YF  H9   H  HCH3   0   0.227   7.3848  -0.6415   1.4951
 1YF  H10  H  HCH3   0   0.246   6.7279   0.9435   1.9317
 1YF  H11  H  HCH3   0   0.231   6.5438  -0.4082   3.0325
 1YF  H12  H  HCH1   0   0.234   4.3481   0.2301  -1.7516
 1YF  H15  H  HCH2   0   0.211  -2.3909   1.4923   1.2700
 1YF  H16  H  HCH2   0   0.211  -2.3601   3.2572   1.1526
 1YF  H17  H  HCH1   0   0.227  -3.0699   3.1005  -1.2282
 1YF  H18  H  HCH1   0   0.233  -4.7536   2.0541   1.0404
 1YF  H19  H  HOH1   0   0.457  -5.8101   3.9412   0.5515
 1YF  H20  H  HCH2   0   0.275  -6.3409   1.0800  -0.4536
 1YF  H21  H  HCH2   0   0.267  -5.9196   2.2228  -1.7207
 1YF  H22  H  HCH1   0   0.253  -4.5845   0.6619  -2.6510
 1YF  H23  H  HCR6   0   0.316  -4.6953  -1.2808  -3.2459
 1YF  H24  H  HCH3   0   0.247  -4.1344  -4.7217  -3.1651
 1YF  H25  H  HCH3   0   0.247  -5.8848  -4.5728  -3.1639
 1YF  H26  H  HCH3   0   0.247  -4.9121  -3.4927  -4.1591
 1YF  H27  H  HNR6   0   0.425  -4.8321  -2.8505   1.2232
 1YF  H1   H  HNH1   0   0.401   4.1634  -4.2618  -0.0319

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
 1YF  O2Q  C2Q  single  1.400  0.020  1.400
 1YF  O1F  C1F  double  1.220  0.020  1.220
 1YF  C1F  N3Q  single  1.336  0.020  1.336
 1YF  C2Q  C1Q  single  1.531  0.020  1.531
 1YF  C2Q  C3Q  single  1.526  0.020  1.526
 1YF  O3'  C3'  single  1.406  0.020  1.406
 1YF  O2B  PB   deloc   1.494  0.020  1.494
 1YF  N3Q  C3Q  single  1.442  0.020  1.442
 1YF  C1Q  O3B  single  1.391  0.020  1.391
 1YF  C1Q  O5Q  single  1.397  0.020  1.397
 1YF  O1B  PB   deloc   1.496  0.020  1.496
 1YF  C2'  C3'  single  1.529  0.020  1.529
 1YF  C2'  C1'  single  1.532  0.020  1.532
 1YF  O3B  PB   single  1.655  0.020  1.655
 1YF  C3Q  C4Q  single  1.528  0.020  1.528
 1YF  PB   O3A  single  1.638  0.020  1.638
 1YF  C3'  C4'  single  1.529  0.020  1.529
 1YF  O2   C2   double  1.213  0.020  1.213
 1YF  O5Q  C5Q  single  1.423  0.020  1.423
 1YF  C4Q  C5Q  single  1.532  0.020  1.532
 1YF  C4Q  O4Q  single  1.406  0.020  1.406
 1YF  C2   N3   single  1.371  0.020  1.371
 1YF  C2   N1   single  1.375  0.020  1.375
 1YF  C1'  N1   single  1.463  0.020  1.463
 1YF  C1'  O4'  single  1.398  0.020  1.398
 1YF  N3   C4   single  1.383  0.020  1.383
 1YF  N1   C6   single  1.371  0.020  1.371
 1YF  C4'  O4'  single  1.417  0.020  1.417
 1YF  C4'  C5'  single  1.508  0.020  1.508
 1YF  O3A  PA   single  1.644  0.020  1.644
 1YF  C5Q  C6Q  single  1.514  0.020  1.514
 1YF  C4   O4   double  1.218  0.020  1.218
 1YF  C4   C5   single  1.449  0.020  1.449
 1YF  C6   C5   double  1.344  0.020  1.344
 1YF  C5   C5M  single  1.494  0.020  1.494
 1YF  C5'  O5'  single  1.411  0.020  1.411
 1YF  O5'  PA   single  1.650  0.020  1.650
 1YF  PA   O1A  deloc   1.496  0.020  1.496
 1YF  PA   O2A  deloc   1.495  0.020  1.495
 1YF  C1F  H2   single  0.930  0.020  1.080
 1YF  C3Q  H3   single  0.970  0.020  1.090
 1YF  C2Q  H4   single  0.970  0.020  1.090
 1YF  O2Q  H5   single  0.850  0.020  0.980
 1YF  C4Q  H6   single  0.970  0.020  1.090
 1YF  O4Q  H7   single  0.850  0.020  0.980
 1YF  C5Q  H8   single  0.970  0.020  1.090
 1YF  C6Q  H9   single  0.970  0.020  1.090
 1YF  C6Q  H10  single  0.970  0.020  1.090
 1YF  C6Q  H11  single  0.970  0.020  1.090
 1YF  C1Q  H12  single  0.970  0.020  1.090
 1YF  C5'  H15  single  0.970  0.020  1.090
 1YF  C5'  H16  single  0.970  0.020  1.090
 1YF  C4'  H17  single  0.970  0.020  1.090
 1YF  C3'  H18  single  0.970  0.020  1.090
 1YF  O3'  H19  single  0.850  0.020  0.980
 1YF  C2'  H20  single  0.970  0.020  1.090
 1YF  C2'  H21  single  0.970  0.020  1.090
 1YF  C1'  H22  single  0.970  0.020  1.090
 1YF  C6   H23  single  0.930  0.020  1.080
 1YF  C5M  H24  single  0.970  0.020  1.090
 1YF  C5M  H25  single  0.970  0.020  1.090
 1YF  C5M  H26  single  0.970  0.020  1.090
 1YF  N3   H27  single  0.860  0.020  1.020
 1YF  N3Q  H1   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
 1YF  H2   C1F  N3Q  111.50  3.000
 1YF  H2   C1F  O1F  122.31  3.000
 1YF  N3Q  C1F  O1F  126.19  3.000
 1YF  H1   N3Q  C3Q  117.79  3.000
 1YF  H1   N3Q  C1F  117.09  3.000
 1YF  C3Q  N3Q  C1F  125.12  3.000
 1YF  H3   C3Q  C4Q  108.93  3.000
 1YF  H3   C3Q  C2Q  109.00  3.000
 1YF  C4Q  C3Q  C2Q  109.91  3.000
 1YF  H3   C3Q  N3Q  107.58  3.000
 1YF  C4Q  C3Q  N3Q  110.70  3.000
 1YF  C2Q  C3Q  N3Q  110.66  3.000
 1YF  H4   C2Q  C1Q  106.47  3.000
 1YF  H4   C2Q  O2Q  111.07  3.000
 1YF  C1Q  C2Q  O2Q  112.45  3.000
 1YF  H4   C2Q  C3Q  108.26  3.000
 1YF  C1Q  C2Q  C3Q  110.06  3.000
 1YF  O2Q  C2Q  C3Q  108.45  3.000
 1YF  H5   O2Q  C2Q  108.59  3.000
 1YF  H6   C4Q  C5Q  108.18  3.000
 1YF  H6   C4Q  O4Q  110.96  3.000
 1YF  C5Q  C4Q  O4Q  111.32  3.000
 1YF  H6   C4Q  C3Q  108.20  3.000
 1YF  O4Q  C4Q  C3Q  107.77  3.000
 1YF  C5Q  C4Q  C3Q  110.38  3.000
 1YF  H7   O4Q  C4Q  108.79  3.000
 1YF  H8   C5Q  O5Q  109.98  3.000
 1YF  H8   C5Q  C6Q  108.74  3.000
 1YF  O5Q  C5Q  C6Q  106.99  3.000
 1YF  H8   C5Q  C4Q  108.61  3.000
 1YF  C6Q  C5Q  C4Q  112.74  3.000
 1YF  O5Q  C5Q  C4Q  109.77  3.000
 1YF  H11  C6Q  H10  107.05  3.000
 1YF  H11  C6Q  H9   108.27  3.000
 1YF  H10  C6Q  H9   108.46  3.000
 1YF  H11  C6Q  C5Q  110.83  3.000
 1YF  H10  C6Q  C5Q  110.42  3.000
 1YF  H9   C6Q  C5Q  111.66  3.000
 1YF  C1Q  O5Q  C5Q  114.92  3.000
 1YF  H12  C1Q  O3B  110.88  3.000
 1YF  H12  C1Q  O5Q  105.18  3.000
 1YF  O3B  C1Q  O5Q  112.53  3.000
 1YF  H12  C1Q  C2Q  109.81  3.000
 1YF  O5Q  C1Q  C2Q  110.25  3.000
 1YF  O3B  C1Q  C2Q  108.18  3.000
 1YF  PB   O3B  C1Q  119.50  3.000
 1YF  O3A  PB   O1B  107.02  3.000
 1YF  O3A  PB   O2B  110.10  3.000
 1YF  O1B  PB   O2B  121.24  3.000
 1YF  O3A  PB   O3B   96.95  3.000
 1YF  O1B  PB   O3B  108.82  3.000
 1YF  O2B  PB   O3B  109.96  3.000
 1YF  PA   O3A  PB   125.53  3.000
 1YF  O5'  PA   O2A  109.52  3.000
 1YF  O2A  PA   O1A  120.66  3.000
 1YF  O5'  PA   O1A  109.02  3.000
 1YF  O2A  PA   O3A  111.16  3.000
 1YF  O1A  PA   O3A  110.14  3.000
 1YF  O5'  PA   O3A   92.75  3.000
 1YF  C5'  O5'  PA   117.10  3.000
 1YF  H16  C5'  H15  107.52  3.000
 1YF  H16  C5'  C4'  108.02  3.000
 1YF  H15  C5'  C4'  109.12  3.000
 1YF  H16  C5'  O5'  111.32  3.000
 1YF  H15  C5'  O5'  111.39  3.000
 1YF  C4'  C5'  O5'  109.39  3.000
 1YF  H17  C4'  C3'  108.27  3.000
 1YF  H17  C4'  O4'  109.62  3.000
 1YF  C3'  C4'  O4'  106.64  3.000
 1YF  H17  C4'  C5'  109.55  3.000
 1YF  O4'  C4'  C5'  109.81  3.000
 1YF  C3'  C4'  C5'  112.87  3.000
 1YF  C1'  O4'  C4'  111.28  3.000
 1YF  H18  C3'  C2'  109.95  3.000
 1YF  H18  C3'  O3'  110.39  3.000
 1YF  C2'  C3'  O3'  114.70  3.000
 1YF  H18  C3'  C4'  109.93  3.000
 1YF  C2'  C3'  C4'  102.78  3.000
 1YF  O3'  C3'  C4'  108.78  3.000
 1YF  H19  O3'  C3'  108.18  3.000
 1YF  H21  C2'  H20  107.46  3.000
 1YF  H21  C2'  C1'  108.45  3.000
 1YF  H20  C2'  C1'  113.09  3.000
 1YF  H21  C2'  C3'  109.11  3.000
 1YF  H20  C2'  C3'  113.61  3.000
 1YF  C1'  C2'  C3'  104.98  3.000
 1YF  H22  C1'  N1   104.10  3.000
 1YF  H22  C1'  C2'  109.66  3.000
 1YF  N1   C1'  C2'  116.07  3.000
 1YF  H22  C1'  O4'  110.13  3.000
 1YF  N1   C1'  O4'  109.17  3.000
 1YF  C2'  C1'  O4'  107.64  3.000
 1YF  C6   N1   C2   120.82  3.000
 1YF  C6   N1   C1'  119.15  3.000
 1YF  C2   N1   C1'  119.95  3.000
 1YF  N3   C2   O2   121.90  3.000
 1YF  N3   C2   N1   114.47  3.000
 1YF  O2   C2   N1   123.62  3.000
 1YF  H23  C6   C5   120.84  3.000
 1YF  H23  C6   N1   114.75  3.000
 1YF  C5   C6   N1   124.41  3.000
 1YF  C4   C5   C5M  118.94  3.000
 1YF  C5M  C5   C6   123.22  3.000
 1YF  C4   C5   C6   117.84  3.000
 1YF  H26  C5M  H25  107.84  3.000
 1YF  H26  C5M  H24  107.87  3.000
 1YF  H25  C5M  H24  107.27  3.000
 1YF  H26  C5M  C5   110.96  3.000
 1YF  H25  C5M  C5   111.41  3.000
 1YF  H24  C5M  C5   111.31  3.000
 1YF  O4   C4   N3   120.62  3.000
 1YF  O4   C4   C5   125.06  3.000
 1YF  N3   C4   C5   114.32  3.000
 1YF  H27  N3   C4   116.75  3.000
 1YF  H27  N3   C2   115.14  3.000
 1YF  C4   N3   C2   128.11  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
 1YF  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 1YF  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 1YF  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 1YF  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 1YF  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 1YF  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 1YF  CONST_07  C4   N3   C2   O2    180.00   0.0  0
 1YF  CONST_08  C6   N1   C2   O2    180.00   0.0  0
 1YF  CONST_09  H27  N3   C2   N1    180.00   0.0  0
 1YF  CONST_10  C3Q  N3Q  C1F  O1F     0.00   0.0  0
 1YF  CONST_11  H1   N3Q  C1F  O1F   180.00   0.0  0
 1YF  Var_01    H24  C5M  C5   C6    119.40  30.0  3
 1YF  Var_02    O2B  PB   O3B  C1Q   -96.81  30.0  3
 1YF  Var_03    C4'  C5'  O5'  PA    173.35  30.0  1
 1YF  Var_04    O5'  PA   O3A  PB   -165.48  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
 1YF  chir_01  C3Q  C2Q  N3Q  C4Q  negativ
 1YF  chir_02  C2Q  O2Q  C3Q  C1Q  positiv
 1YF  chir_03  C4Q  O4Q  C3Q  C5Q  negativ
 1YF  chir_04  C5Q  O5Q  C4Q  C6Q  negativ
 1YF  chir_05  C1Q  O5Q  O3B  C2Q  positiv
 1YF  chir_08  C4'  C3'  O4'  C5'  positiv
 1YF  chir_09  C3'  O3'  C2'  C4'  negativ
 1YF  chir_10  C1'  O4'  N1   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
 1YF  plan-1  O1F  0.020
 1YF  plan-1  C1F  0.020
 1YF  plan-1  N3Q  0.020
 1YF  plan-1  C3Q  0.020
 1YF  plan-1  H2   0.020
 1YF  plan-1  H1   0.020
 1YF  plan-2  C1'  0.020
 1YF  plan-2  N1   0.020
 1YF  plan-2  C2   0.020
 1YF  plan-2  O2   0.020
 1YF  plan-2  C6   0.020
 1YF  plan-2  C5   0.020
 1YF  plan-2  C5M  0.020
 1YF  plan-2  C4   0.020
 1YF  plan-2  N3   0.020
 1YF  plan-2  O4   0.020
 1YF  plan-2  H23  0.020
 1YF  plan-2  H27  0.020

