# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 19 11:09:25 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: (2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-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@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(C)=O)[C@@H](O)[C@H]1NC=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
 F5G  F5G  '(2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  66  40  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F5G
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
 F5G  C15   C  CH2    0  -0.164   3.4516   2.8266  -0.0324
 F5G  C17   C  CH1    0  -0.033   5.7409   2.3276   0.8595
 F5G  C21   C  CR6    0   0.733   5.1714  -2.3091   0.4788
 F5G  C24   C  CR16   0  -0.510   2.9997  -2.0338  -1.2894
 F5G  C01   C  CH1    0  -0.107  -5.8164  -1.3393  -0.0580
 F5G  C05   C  CH1    0   0.037  -4.7157  -1.6959  -1.0651
 F5G  C06   C  CH3    0  -0.676  -4.5806  -3.1888  -1.2793
 F5G  C08   C  CH1    0   0.314  -3.4201   0.1795  -0.4318
 F5G  C16   C  CH1    0  -0.038   4.2455   2.2590   1.1325
 F5G  C18   C  CH1    0  -0.043   5.9664   0.9806   0.1613
 F5G  C19   C  CH1    0   0.220   5.0428   0.0768   0.9775
 F5G  C23   C  CR6    0   0.564   3.5808  -3.3394  -1.1207
 F5G  C25   C  CR16   0   0.075   3.5023  -0.9885  -0.6134
 F5G  C34   C  CH1    0  -0.158  -4.3970   0.6115   0.6586
 F5G  C37   C  CH3    0  -0.776  -3.7390  -0.1026   4.3178
 F5G  C39   C  CH1    0   0.023  -5.8098   0.1626   0.2689
 F5G  N02   N  NH1    0  -0.613  -7.1061  -1.7469  -0.5684
 F5G  N20   N  NR6    0  -0.569   4.5564  -1.0947   0.2520
 F5G  N22   N  NR16   0  -0.732   4.6439  -3.3563  -0.2292
 F5G  N35   N  NH1    0  -0.631  -4.0062   0.0411   1.9254
 F5G  O04   O  O      0  -0.487  -8.0462  -2.4181   1.3922
 F5G  O07   O  O2     0  -0.501  -3.4738  -1.2201  -0.5819
 F5G  O09   O  O2     0  -0.631  -2.1397   0.5160  -0.0531
 F5G  O11   O  O      0  -0.798  -1.4077   0.6946  -2.5149
 F5G  O12   O  O2     0  -0.737  -0.0932   1.6712  -0.5227
 F5G  O14   O  O2     0  -0.620   2.0933   2.4932   0.1202
 F5G  O28   O  O2     0  -0.491   3.9545   0.8729   1.3375
 F5G  O29   O  OH1    0  -0.653   7.2775   0.5040   0.2118
 F5G  O30   O  OH1    0  -0.668   6.4285   2.3815   2.0816
 F5G  O31   O  OP    -1  -0.782   0.7800   3.7696  -1.6767
 F5G  O32   O  O      0  -0.788   1.8417   1.4608  -2.2213
 F5G  O33   O  OP    -1  -0.752  -0.1379  -0.8800  -0.8637
 F5G  O38   O  O      0  -0.507  -4.9329   1.6486   3.2094
 F5G  O40   O  OH1    0  -0.666  -6.1970   0.9366  -0.8412
 F5G  P10   P  P      0   1.341  -0.8916   0.3740  -1.1488
 F5G  P13   P  P      0   1.363   1.1817   2.3930  -1.2517
 F5G  H152  H  HCH2   0   0.235   3.5986   3.9133  -0.0401
 F5G  H151  H  HCH2   0   0.209   3.8462   2.4459  -0.9816
 F5G  H171  H  HCH1   0   0.252   5.9985   3.1753   0.2096
 F5G  H241  H  HCR6   0   0.285   2.1336  -1.8959  -1.9164
 F5G  H011  H  HCH1   0   0.262  -5.6315  -1.8921   0.8671
 F5G  H031  H  H      0   0.209  -8.9776  -2.5069  -0.4146
 F5G  H051  H  HCH1   0   0.219  -4.9471  -1.2113  -2.0270
 F5G  H063  H  HCH3   0   0.246  -3.7867  -3.4027  -1.9950
 F5G  H061  H  HCH3   0   0.231  -4.3490  -3.6983  -0.3425
 F5G  H081  H  HCH1   0   0.217  -3.7028   0.6614  -1.3785
 F5G  H161  H  HCH1   0   0.263   3.9815   2.7941   2.0492
 F5G  H181  H  HCH1   0   0.247   5.6020   1.0435  -0.8725
 F5G  H191  H  HCH1   0   0.267   5.5682  -0.2970   1.8595
 F5G  H251  H  HCR6   0   0.344   3.0600  -0.0106  -0.7344
 F5G  H341  H  HCH1   0   0.278  -4.3861   1.7011   0.7401
 F5G  H372  H  HCH3   0   0.264  -4.5312  -0.2408   5.0525
 F5G  H373  H  HCH3   0   0.249  -3.3013  -1.0725   4.0893
 F5G  H371  H  HCH3   0   0.268  -2.9712   0.5187   4.7802
 F5G  H391  H  HCH1   0   0.246  -6.4819   0.3351   1.1184
 F5G  H021  H  HNH1   0   0.409  -7.2811  -1.6638  -1.5586
 F5G  H221  H  HNR6   0   0.424   5.0926  -4.2500  -0.0697
 F5G  H351  H  HNH1   0   0.399  -3.4576  -0.8043   1.9195
 F5G  H291  H  HOH1   0   0.469   7.7832   0.9140  -0.4972
 F5G  H301  H  HOH1   0   0.449   7.3375   2.1000   1.9252
 F5G  H401  H  HOH1   0   0.454  -7.1284   0.7737  -1.0212
 F5G  O26   O  O      0  -0.471   3.2226  -4.3658  -1.6707
 F5G  C36   C  C      0   0.527  -4.2885   0.6129   3.1094
 F5G  C03   C  C1     0   0.255  -8.0931  -2.2511   0.1868
 F5G  O27   O  O      0  -0.481   6.1053  -2.4541   1.2406
 F5G  H062  H  HCH3   0   0.236  -5.5039  -3.6097  -1.6744

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
 F5G  O29  C18   single  1.396  0.020  1.396
 F5G  O30  C17   single  1.403  0.020  1.403
 F5G  C16  C17   single  1.522  0.020  1.522
 F5G  C16  O28   single  1.431  0.020  1.431
 F5G  C16  C15   single  1.520  0.020  1.520
 F5G  C18  C17   single  1.534  0.020  1.534
 F5G  C18  C19   single  1.528  0.020  1.528
 F5G  O28  C19   single  1.396  0.020  1.396
 F5G  C19  N20   single  1.461  0.020  1.461
 F5G  C15  O14   single  1.407  0.020  1.407
 F5G  O27  C21   double  1.214  0.020  1.214
 F5G  N20  C21   single  1.380  0.020  1.380
 F5G  N20  C25   single  1.368  0.020  1.368
 F5G  O14  P13   single  1.650  0.020  1.650
 F5G  C21  N22   single  1.370  0.020  1.370
 F5G  O12  P13   single  1.636  0.020  1.636
 F5G  O12  P10   single  1.647  0.020  1.647
 F5G  C25  C24   double  1.343  0.020  1.343
 F5G  O11  P10   deloc   1.495  0.020  1.495
 F5G  P13  O32   deloc   1.498  0.020  1.498
 F5G  P13  O31   deloc   1.496  0.020  1.496
 F5G  N22  C23   single  1.388  0.020  1.388
 F5G  P10  O33   deloc   1.491  0.020  1.491
 F5G  P10  O09   single  1.667  0.020  1.667
 F5G  C24  C23   single  1.439  0.020  1.439
 F5G  C23  O26   double  1.218  0.020  1.218
 F5G  O09  C08   single  1.377  0.020  1.377
 F5G  C08  C34   single  1.526  0.020  1.526
 F5G  C08  O07   single  1.409  0.020  1.409
 F5G  C34  N35   single  1.443  0.020  1.443
 F5G  C34  C39   single  1.533  0.020  1.533
 F5G  O07  C05   single  1.415  0.020  1.415
 F5G  N35  C36   single  1.345  0.020  1.345
 F5G  C37  C36   single  1.508  0.020  1.508
 F5G  O40  C39   single  1.408  0.020  1.408
 F5G  C36  O38   double  1.224  0.020  1.224
 F5G  C39  C01   single  1.537  0.020  1.537
 F5G  C05  C01   single  1.534  0.020  1.534
 F5G  C05  C06   single  1.514  0.020  1.514
 F5G  C01  N02   single  1.446  0.020  1.446
 F5G  C03  N02   single  1.341  0.020  1.341
 F5G  C03  O04   double  1.218  0.020  1.218
 F5G  C15  H152  single  0.970  0.020  1.090
 F5G  C15  H151  single  0.970  0.020  1.090
 F5G  C17  H171  single  0.970  0.020  1.090
 F5G  C24  H241  single  0.930  0.020  1.080
 F5G  C01  H011  single  0.970  0.020  1.090
 F5G  C03  H031  single  0.930  0.020  1.080
 F5G  C05  H051  single  0.970  0.020  1.090
 F5G  C06  H062  single  0.970  0.020  1.090
 F5G  C06  H063  single  0.970  0.020  1.090
 F5G  C06  H061  single  0.970  0.020  1.090
 F5G  C08  H081  single  0.970  0.020  1.090
 F5G  C16  H161  single  0.970  0.020  1.090
 F5G  C18  H181  single  0.970  0.020  1.090
 F5G  C19  H191  single  0.970  0.020  1.090
 F5G  C25  H251  single  0.930  0.020  1.080
 F5G  C34  H341  single  0.970  0.020  1.090
 F5G  C37  H372  single  0.970  0.020  1.090
 F5G  C37  H373  single  0.970  0.020  1.090
 F5G  C37  H371  single  0.970  0.020  1.090
 F5G  C39  H391  single  0.970  0.020  1.090
 F5G  N02  H021  single  0.860  0.020  1.020
 F5G  N22  H221  single  0.860  0.020  1.020
 F5G  N35  H351  single  0.860  0.020  1.020
 F5G  O29  H291  single  0.850  0.020  0.980
 F5G  O30  H301  single  0.850  0.020  0.980
 F5G  O40  H401  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
 F5G  H151  C15  H152  106.84  3.000
 F5G  H151  C15  O14   111.05  3.000
 F5G  H152  C15  O14   111.40  3.000
 F5G  H151  C15  C16   110.25  3.000
 F5G  H152  C15  C16   107.79  3.000
 F5G  O14   C15  C16   109.44  3.000
 F5G  H171  C17  O30   111.75  3.000
 F5G  H171  C17  C18   111.95  3.000
 F5G  O30   C17  C18   110.99  3.000
 F5G  H171  C17  C16   111.79  3.000
 F5G  C18   C17  C16   100.75  3.000
 F5G  O30   C17  C16   109.09  3.000
 F5G  O27   C21  N22   121.96  3.000
 F5G  N22   C21  N20   114.60  3.000
 F5G  O27   C21  N20   123.44  3.000
 F5G  H241  C24  C25   119.61  3.000
 F5G  H241  C24  C23   120.57  3.000
 F5G  C25   C24  C23   119.75  3.000
 F5G  H011  C01  N02   107.88  3.000
 F5G  H011  C01  C39   108.26  3.000
 F5G  N02   C01  C39   110.76  3.000
 F5G  H011  C01  C05   108.46  3.000
 F5G  N02   C01  C05   110.05  3.000
 F5G  C39   C01  C05   111.33  3.000
 F5G  H051  C05  O07   109.55  3.000
 F5G  H051  C05  C06   109.21  3.000
 F5G  O07   C05  C06   107.54  3.000
 F5G  H051  C05  C01   108.68  3.000
 F5G  C06   C05  C01   112.71  3.000
 F5G  O07   C05  C01   109.11  3.000
 F5G  H061  C06  H063  108.51  3.000
 F5G  H061  C06  H062  108.12  3.000
 F5G  H063  C06  H062  107.66  3.000
 F5G  H061  C06  C05   110.97  3.000
 F5G  H063  C06  C05   110.57  3.000
 F5G  H062  C06  C05   110.90  3.000
 F5G  H081  C08  O09   111.65  3.000
 F5G  H081  C08  O07   109.52  3.000
 F5G  O09   C08  O07   107.91  3.000
 F5G  H081  C08  C34   109.06  3.000
 F5G  O07   C08  C34   109.44  3.000
 F5G  O09   C08  C34   109.24  3.000
 F5G  H161  C16  O28   107.74  3.000
 F5G  H161  C16  C17   111.44  3.000
 F5G  O28   C16  C17   105.62  3.000
 F5G  H161  C16  C15   109.49  3.000
 F5G  O28   C16  C15   111.43  3.000
 F5G  C17   C16  C15   111.04  3.000
 F5G  H181  C18  O29   111.43  3.000
 F5G  H181  C18  C19   109.64  3.000
 F5G  O29   C18  C19   110.26  3.000
 F5G  H181  C18  C17   109.24  3.000
 F5G  C19   C18  C17   100.80  3.000
 F5G  O29   C18  C17   114.93  3.000
 F5G  H191  C19  O28   111.22  3.000
 F5G  H191  C19  N20   106.65  3.000
 F5G  O28   C19  N20   109.01  3.000
 F5G  H191  C19  C18   110.05  3.000
 F5G  N20   C19  C18   114.21  3.000
 F5G  O28   C19  C18   105.76  3.000
 F5G  O26   C23  N22   120.33  3.000
 F5G  O26   C23  C24   126.35  3.000
 F5G  N22   C23  C24   113.32  3.000
 F5G  H251  C25  N20   117.18  3.000
 F5G  H251  C25  C24   119.69  3.000
 F5G  N20   C25  C24   123.13  3.000
 F5G  H341  C34  N35   109.03  3.000
 F5G  H341  C34  C39   108.68  3.000
 F5G  N35   C34  C39   110.92  3.000
 F5G  H341  C34  C08   109.21  3.000
 F5G  C39   C34  C08   108.99  3.000
 F5G  N35   C34  C08   109.99  3.000
 F5G  H371  C37  H373  108.28  3.000
 F5G  H371  C37  H372  107.36  3.000
 F5G  H373  C37  H372  108.73  3.000
 F5G  H371  C37  C36   109.02  3.000
 F5G  H373  C37  C36   113.65  3.000
 F5G  H372  C37  C36   109.61  3.000
 F5G  H391  C39  O40   110.84  3.000
 F5G  H391  C39  C34   108.77  3.000
 F5G  O40   C39  C34   107.04  3.000
 F5G  H391  C39  C01   108.40  3.000
 F5G  O40   C39  C01   111.62  3.000
 F5G  C34   C39  C01   110.13  3.000
 F5G  H021  N02  C03   117.13  3.000
 F5G  H021  N02  C01   118.55  3.000
 F5G  C03   N02  C01   124.31  3.000
 F5G  C25   N20  C19   120.55  3.000
 F5G  C25   N20  C21   121.04  3.000
 F5G  C19   N20  C21   118.39  3.000
 F5G  H221  N22  C23   116.84  3.000
 F5G  H221  N22  C21   115.00  3.000
 F5G  C23   N22  C21   128.16  3.000
 F5G  H351  N35  C36   118.43  3.000
 F5G  H351  N35  C34   118.28  3.000
 F5G  C36   N35  C34   123.22  3.000
 F5G  C08   O07  C05   113.82  3.000
 F5G  P10   O09  C08   119.65  3.000
 F5G  P13   O12  P10   123.76  3.000
 F5G  P13   O14  C15   117.23  3.000
 F5G  C19   O28  C16   110.91  3.000
 F5G  H291  O29  C18   108.75  3.000
 F5G  H301  O30  C17   108.02  3.000
 F5G  H401  O40  C39   108.70  3.000
 F5G  O33   P10  O12   110.17  3.000
 F5G  O33   P10  O11   121.99  3.000
 F5G  O12   P10  O11   110.23  3.000
 F5G  O33   P10  O09   108.93  3.000
 F5G  O11   P10  O09   108.90  3.000
 F5G  O12   P10  O09    92.64  3.000
 F5G  O32   P13  O31   120.47  3.000
 F5G  O31   P13  O14   109.19  3.000
 F5G  O32   P13  O14   109.42  3.000
 F5G  O31   P13  O12   108.86  3.000
 F5G  O32   P13  O12   110.92  3.000
 F5G  O14   P13  O12    94.98  3.000
 F5G  O38   C36  N35   122.84  3.000
 F5G  O38   C36  C37   121.87  3.000
 F5G  N35   C36  C37   115.29  3.000
 F5G  H031  C03  O04   122.71  3.000
 F5G  H031  C03  N02   111.80  3.000
 F5G  O04   C03  N02   125.49  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
 F5G  CONST_01  C24   C23  N22  C21     0.00   0.0  0
 F5G  CONST_02  N22   C21  N20  C19   180.00   0.0  0
 F5G  CONST_03  N20   C21  N22  C23     0.00   0.0  0
 F5G  CONST_04  N22   C21  N20  C25     0.00   0.0  0
 F5G  CONST_05  O26   C23  N22  C21   180.00   0.0  0
 F5G  CONST_06  O27   C21  N20  C19     0.00   0.0  0
 F5G  CONST_07  O27   C21  N22  C23   180.00   0.0  0
 F5G  CONST_08  O27   C21  N20  C25   180.00   0.0  0
 F5G  CONST_09  H221  N22  C23  C24   180.00   0.0  0
 F5G  CONST_10  O04   C03  N02  C01     0.00   0.0  0
 F5G  CONST_11  C37   C36  N35  C34   180.00   0.0  0
 F5G  CONST_12  O38   C36  N35  C34     0.00   0.0  0
 F5G  CONST_13  H351  N35  C36  C37     0.00   0.0  0
 F5G  CONST_14  H021  N02  C03  O04   180.00   0.0  0
 F5G  Var_01    O12   P10  O09  C08   146.63  30.0  2
 F5G  Var_02    O12   P13  O14  C15   167.63  30.0  3
 F5G  Var_03    H372  C37  C36  N35  -130.15  30.0  3
 F5G  Var_04    H152  C15  O14  P13    87.32  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
 F5G  chir_01  C17  O30  C16  C18  positiv
 F5G  chir_02  C01  C39  C05  N02  positiv
 F5G  chir_03  C05  O07  C01  C06  positiv
 F5G  chir_04  C08  O07  O09  C34  positiv
 F5G  chir_05  C16  C17  O28  C15  positiv
 F5G  chir_06  C18  O29  C17  C19  positiv
 F5G  chir_07  C19  O28  N20  C18  negativ
 F5G  chir_08  C34  C08  N35  C39  positiv
 F5G  chir_09  C39  O40  C34  C01  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
 F5G  plan-1  C01   0.020
 F5G  plan-1  N02   0.020
 F5G  plan-1  O04   0.020
 F5G  plan-1  H031  0.020
 F5G  plan-1  H021  0.020
 F5G  plan-1  C03   0.020
 F5G  plan-2  C34   0.020
 F5G  plan-2  C37   0.020
 F5G  plan-2  N35   0.020
 F5G  plan-2  O38   0.020
 F5G  plan-2  H351  0.020
 F5G  plan-2  C36   0.020
 F5G  plan-3  C21   0.020
 F5G  plan-3  C24   0.020
 F5G  plan-3  C19   0.020
 F5G  plan-3  C23   0.020
 F5G  plan-3  C25   0.020
 F5G  plan-3  N20   0.020
 F5G  plan-3  N22   0.020
 F5G  plan-3  H241  0.020
 F5G  plan-3  H251  0.020
 F5G  plan-3  H221  0.020
 F5G  plan-3  O26   0.020
 F5G  plan-3  O27   0.020

