# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 26 03:15:59 2020
#   Inital geometry file: a 170 line input string
#   Ligand name: (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-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=C\C(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)S[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=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
 HQV  HQV  '(2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-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  68  41  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HQV
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
 HQV  C15   C  CH2    0  -0.160  -1.9404  -1.3333   0.4026
 HQV  C17   C  CH1    0  -0.045  -3.9345  -1.2811   1.9657
 HQV  C21   C  CH1    0   0.185  -4.9897   0.4437   0.7328
 HQV  C24   C  CR16   0  -0.509  -6.1944  -1.5558  -2.1950
 HQV  C02   C  CH1    0   0.045   3.6539   1.6822   1.6478
 HQV  C03   C  CH1    0   0.056   4.0244   3.1670   1.7100
 HQV  C05   C  CH1    0  -0.428   3.6608   3.9128   0.4260
 HQV  C06   C  CH2    0  -0.168   3.8801   5.4116   0.5022
 HQV  C09   C  CH1    0  -0.116   4.1133   1.5256  -0.8545
 HQV  C16   C  CH1    0  -0.002  -2.8968  -0.4751   1.1916
 HQV  C19   C  CH1    0  -0.038  -5.0888  -0.2789   2.0774
 HQV  C23   C  CR16   0   0.090  -5.4028  -1.0023  -1.2600
 HQV  C25   C  CR6    0   0.566  -7.6052  -1.2655  -2.2022
 HQV  C27   C  CR6    0   0.739  -7.2059   0.1606  -0.2192
 HQV  C35   C  CH1    0  -0.090   4.3924   0.9384   0.5353
 HQV  C38   C  C1     0  -0.383   4.2499  -2.7673   0.0921
 HQV  C39   C  C1     0  -0.177   4.9771  -3.8656  -0.0986
 HQV  C40   C  CH3    0  -0.711   4.4268  -5.2457  -0.1934
 HQV  N22   N  NR6    0  -0.568  -5.8690  -0.1707  -0.2869
 HQV  N26   N  NR16   0  -0.731  -7.9926  -0.4056  -1.1847
 HQV  N36   N  NH1    0  -0.685   4.0247  -0.4531   0.5516
 HQV  O01   O  OH1    0  -0.671   3.9938   1.0518   2.8590
 HQV  O04   O  OH1    0  -0.679   3.3167   3.6966   2.8160
 HQV  O07   O  OH1    0  -0.665   5.2364   5.6691   0.7731
 HQV  O10   O  O2     0  -0.605   2.7524   1.4093  -1.1531
 HQV  O12   O  O2     0  -0.729   0.7636   0.0768  -1.7499
 HQV  O14   O  O2     0  -0.613  -1.0604  -0.5023  -0.3212
 HQV  O20   O  OH1    0  -0.665  -4.8377   0.6610   3.0857
 HQV  O29   O  O      0  -0.466  -8.4245  -1.6951  -2.9935
 HQV  O30   O  O2     0  -0.494  -3.6634   0.3556   0.3190
 HQV  O31   O  O      0  -0.781   0.3095  -2.4305  -1.3231
 HQV  O32   O  OP    -1  -0.771   1.2882  -0.9463   0.5704
 HQV  O33   O  OP    -1  -0.778   3.0924  -0.7560  -2.5034
 HQV  O34   O  O      0  -0.774   1.9356   1.3170  -3.5806
 HQV  O41   O  O      0  -0.525   6.0678  -1.2335  -0.0462
 HQV  P11   P  P      0   1.358   2.2259   0.4555  -2.3959
 HQV  P13   P  P      0   1.377   0.4348  -1.0983  -0.6614
 HQV  S08   S  S2     0   0.004   4.6526   3.2534  -0.9507
 HQV  H152  H  HCH2   0   0.232  -1.4161  -1.9749   1.1208
 HQV  H151  H  HCH2   0   0.217  -2.4929  -1.9964  -0.2744
 HQV  H171  H  HCH1   0   0.250  -4.2598  -2.1439   1.3684
 HQV  H211  H  HCH1   0   0.287  -5.2889   1.4897   0.8188
 HQV  H241  H  HCR6   0   0.292  -5.7764  -2.2061  -2.9475
 HQV  H021  H  HCH1   0   0.210   2.5707   1.6054   1.4637
 HQV  H031  H  HCH1   0   0.227   5.1073   3.2463   1.8702
 HQV  H051  H  HCH1   0   0.284   2.6026   3.7591   0.1921
 HQV  H062  H  HCH2   0   0.220   3.2209   5.8179   1.2792
 HQV  H091  H  HCH1   0   0.279   4.7429   0.9990  -1.5785
 HQV  H161  H  HCH1   0   0.252  -2.3281   0.1583   1.8835
 HQV  H191  H  HCH1   0   0.261  -6.0574  -0.7731   2.2138
 HQV  H231  H  HCR6   0   0.328  -4.3417  -1.1951  -1.2550
 HQV  H351  H  HCH1   0   0.253   5.4672   1.0203   0.7129
 HQV  H381  H  H      0   0.253   3.1711  -2.8310   0.1885
 HQV  H391  H  H      0   0.246   6.0542  -3.7680  -0.1959
 HQV  H1    H  HCH3   0   0.244   4.8564  -5.8876   0.5788
 HQV  H2    H  HCH3   0   0.239   3.3423  -5.2657  -0.0908
 HQV  H3    H  HCH3   0   0.245   4.6896  -5.7005  -1.1511
 HQV  H261  H  HNR6   0   0.427  -8.9746  -0.1616  -1.1395
 HQV  H361  H  HNH1   0   0.441   3.0188  -0.6666   0.5783
 HQV  H011  H  HOH1   0   0.445   3.6015   1.5731   3.5680
 HQV  H041  H  HOH1   0   0.462   3.8270   4.4178   3.1953
 HQV  H071  H  HOH1   0   0.459   5.3563   6.6211   0.8326
 HQV  H201  H  HOH1   0   0.452  -4.3919   0.2028   3.8093
 HQV  O18   O  OH1    0  -0.655  -3.4149  -1.6830   3.2012
 HQV  C37   C  C      0   0.543   4.8728  -1.4226   0.1771
 HQV  H181  H  HOH1   0   0.470  -3.9497  -2.4067   3.5439
 HQV  O28   O  O      0  -0.480  -7.6498   0.8999   0.6358
 HQV  H061  H  HCH2   0   0.224   3.5610   5.8629  -0.4456

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
 HQV  C06  O07   single  1.407  0.020  1.407
 HQV  C06  C05   single  1.517  0.020  1.517
 HQV  O31  P13   deloc   1.493  0.020  1.493
 HQV  O41  C37   double  1.230  0.020  1.230
 HQV  O14  P13   single  1.645  0.020  1.645
 HQV  O14  C15   single  1.410  0.020  1.410
 HQV  S08  C05   single  1.820  0.020  1.820
 HQV  S08  C09   single  1.813  0.020  1.813
 HQV  O32  P13   deloc   1.506  0.020  1.506
 HQV  P13  O12   single  1.635  0.020  1.635
 HQV  O30  C16   single  1.428  0.020  1.428
 HQV  O30  C21   single  1.392  0.020  1.392
 HQV  C05  C03   single  1.529  0.020  1.529
 HQV  C37  N36   single  1.341  0.020  1.341
 HQV  C37  C38   single  1.484  0.020  1.484
 HQV  C16  C15   single  1.508  0.020  1.508
 HQV  C16  C17   single  1.525  0.020  1.525
 HQV  C35  C09   single  1.534  0.020  1.534
 HQV  C35  N36   single  1.439  0.020  1.439
 HQV  C35  C02   single  1.528  0.020  1.528
 HQV  C39  C38   double  1.331  0.020  1.331
 HQV  C39  C40   single  1.489  0.020  1.489
 HQV  C09  O10   single  1.398  0.020  1.398
 HQV  O28  C27   double  1.214  0.020  1.214
 HQV  C03  C02   single  1.532  0.020  1.532
 HQV  C03  O04   single  1.416  0.020  1.416
 HQV  O18  C17   single  1.399  0.020  1.399
 HQV  C27  N22   single  1.379  0.020  1.379
 HQV  C27  N26   single  1.368  0.020  1.368
 HQV  C21  N22   single  1.480  0.020  1.480
 HQV  C21  C19   single  1.530  0.020  1.530
 HQV  C02  O01   single  1.407  0.020  1.407
 HQV  N22  C23   single  1.362  0.020  1.362
 HQV  N26  C25   single  1.387  0.020  1.387
 HQV  O12  P11   single  1.643  0.020  1.643
 HQV  C17  C19   single  1.533  0.020  1.533
 HQV  O34  P11   deloc   1.493  0.020  1.493
 HQV  O10  P11   single  1.653  0.020  1.653
 HQV  C23  C24   double  1.344  0.020  1.344
 HQV  C25  O29   double  1.217  0.020  1.217
 HQV  C25  C24   single  1.440  0.020  1.440
 HQV  P11  O33   deloc   1.493  0.020  1.493
 HQV  C19  O20   single  1.401  0.020  1.401
 HQV  C15  H152  single  0.970  0.020  1.090
 HQV  C15  H151  single  0.970  0.020  1.090
 HQV  C17  H171  single  0.970  0.020  1.090
 HQV  C21  H211  single  0.970  0.020  1.090
 HQV  C24  H241  single  0.930  0.020  1.080
 HQV  C02  H021  single  0.970  0.020  1.090
 HQV  C03  H031  single  0.970  0.020  1.090
 HQV  C05  H051  single  0.970  0.020  1.090
 HQV  C06  H061  single  0.970  0.020  1.090
 HQV  C06  H062  single  0.970  0.020  1.090
 HQV  C09  H091  single  0.970  0.020  1.090
 HQV  C16  H161  single  0.970  0.020  1.090
 HQV  C19  H191  single  0.970  0.020  1.090
 HQV  C23  H231  single  0.930  0.020  1.080
 HQV  C35  H351  single  0.970  0.020  1.090
 HQV  C38  H381  single  0.930  0.020  1.080
 HQV  C39  H391  single  0.930  0.020  1.080
 HQV  C40  H1    single  0.970  0.020  1.090
 HQV  C40  H2    single  0.970  0.020  1.090
 HQV  C40  H3    single  0.970  0.020  1.090
 HQV  N26  H261  single  0.860  0.020  1.020
 HQV  N36  H361  single  0.860  0.020  1.020
 HQV  O01  H011  single  0.850  0.020  0.980
 HQV  O04  H041  single  0.850  0.020  0.980
 HQV  O07  H071  single  0.850  0.020  0.980
 HQV  O18  H181  single  0.850  0.020  0.980
 HQV  O20  H201  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
 HQV  H151  C15  H152  106.94  3.000
 HQV  H151  C15  O14   110.72  3.000
 HQV  H152  C15  O14   112.49  3.000
 HQV  H151  C15  C16   110.33  3.000
 HQV  H152  C15  C16   107.07  3.000
 HQV  O14   C15  C16   109.21  3.000
 HQV  H171  C17  O18   111.37  3.000
 HQV  H171  C17  C19   109.28  3.000
 HQV  O18   C17  C19   113.77  3.000
 HQV  H171  C17  C16   109.91  3.000
 HQV  C19   C17  C16   101.77  3.000
 HQV  O18   C17  C16   110.32  3.000
 HQV  H211  C21  O30   110.20  3.000
 HQV  H211  C21  N22   106.82  3.000
 HQV  O30   C21  N22   109.57  3.000
 HQV  H211  C21  C19   111.45  3.000
 HQV  N22   C21  C19   111.78  3.000
 HQV  O30   C21  C19   107.04  3.000
 HQV  H241  C24  C25   119.83  3.000
 HQV  H241  C24  C23   120.34  3.000
 HQV  C25   C24  C23   119.82  3.000
 HQV  H021  C02  O01   110.50  3.000
 HQV  H021  C02  C35   108.63  3.000
 HQV  O01   C02  C35   106.97  3.000
 HQV  H021  C02  C03   108.20  3.000
 HQV  O01   C02  C03   109.93  3.000
 HQV  C35   C02  C03   112.61  3.000
 HQV  H031  C03  O04   110.62  3.000
 HQV  H031  C03  C05   108.79  3.000
 HQV  O04   C03  C05   110.78  3.000
 HQV  H031  C03  C02   108.34  3.000
 HQV  O04   C03  C02   105.87  3.000
 HQV  C05   C03  C02   112.42  3.000
 HQV  H051  C05  S08   108.31  3.000
 HQV  H051  C05  C06   106.82  3.000
 HQV  S08   C05  C06   108.49  3.000
 HQV  H051  C05  C03   109.93  3.000
 HQV  S08   C05  C03   109.20  3.000
 HQV  C06   C05  C03   113.92  3.000
 HQV  H062  C06  H061  106.55  3.000
 HQV  H062  C06  O07   112.03  3.000
 HQV  H061  C06  O07   111.80  3.000
 HQV  H062  C06  C05   108.34  3.000
 HQV  H061  C06  C05   108.73  3.000
 HQV  O07   C06  C05   109.27  3.000
 HQV  H091  C09  S08   104.62  3.000
 HQV  H091  C09  O10   112.25  3.000
 HQV  S08   C09  O10   110.95  3.000
 HQV  H091  C09  C35   108.09  3.000
 HQV  O10   C09  C35   109.80  3.000
 HQV  S08   C09  C35   111.02  3.000
 HQV  H161  C16  O30   109.14  3.000
 HQV  H161  C16  C17   109.74  3.000
 HQV  O30   C16  C17   104.61  3.000
 HQV  H161  C16  C15   109.26  3.000
 HQV  C17   C16  C15   113.35  3.000
 HQV  O30   C16  C15   110.60  3.000
 HQV  H191  C19  O20   111.79  3.000
 HQV  H191  C19  C21   112.31  3.000
 HQV  O20   C19  C21   107.70  3.000
 HQV  H191  C19  C17   112.32  3.000
 HQV  O20   C19  C17   110.86  3.000
 HQV  C21   C19  C17   101.31  3.000
 HQV  H231  C23  N22   116.27  3.000
 HQV  H231  C23  C24   120.59  3.000
 HQV  N22   C23  C24   123.14  3.000
 HQV  O29   C25  N26   120.50  3.000
 HQV  O29   C25  C24   126.25  3.000
 HQV  N26   C25  C24   113.25  3.000
 HQV  O28   C27  N26   122.59  3.000
 HQV  N26   C27  N22   115.05  3.000
 HQV  O28   C27  N22   122.36  3.000
 HQV  H351  C35  N36   108.78  3.000
 HQV  H351  C35  C09   107.31  3.000
 HQV  N36   C35  C09   109.50  3.000
 HQV  H351  C35  C02   108.69  3.000
 HQV  N36   C35  C02   109.80  3.000
 HQV  C09   C35  C02   112.65  3.000
 HQV  H381  C38  C39   120.50  3.000
 HQV  H381  C38  C37   117.73  3.000
 HQV  C39   C38  C37   121.77  3.000
 HQV  H391  C39  C40   116.38  3.000
 HQV  H391  C39  C38   118.72  3.000
 HQV  C40   C39  C38   124.90  3.000
 HQV  H3    C40  H2    108.33  3.000
 HQV  H3    C40  H1    106.29  3.000
 HQV  H2    C40  H1    108.31  3.000
 HQV  H3    C40  C39   110.67  3.000
 HQV  H2    C40  C39   112.27  3.000
 HQV  H1    C40  C39   110.76  3.000
 HQV  C27   N22  C23   120.89  3.000
 HQV  C23   N22  C21   122.84  3.000
 HQV  C27   N22  C21   116.26  3.000
 HQV  H261  N26  C27   115.24  3.000
 HQV  H261  N26  C25   116.92  3.000
 HQV  C27   N26  C25   127.84  3.000
 HQV  H361  N36  C37   118.39  3.000
 HQV  H361  N36  C35   116.80  3.000
 HQV  C37   N36  C35   122.28  3.000
 HQV  H011  O01  C02   107.02  3.000
 HQV  H041  O04  C03   108.87  3.000
 HQV  H071  O07  C06   108.26  3.000
 HQV  P11   O10  C09   121.25  3.000
 HQV  P13   O12  P11   127.33  3.000
 HQV  P13   O14  C15   117.37  3.000
 HQV  H201  O20  C19   107.68  3.000
 HQV  C16   O30  C21   111.51  3.000
 HQV  O34   P11  O33   121.58  3.000
 HQV  O33   P11  O12   110.96  3.000
 HQV  O34   P11  O12   105.78  3.000
 HQV  O33   P11  O10   109.72  3.000
 HQV  O34   P11  O10   109.00  3.000
 HQV  O12   P11  O10    96.94  3.000
 HQV  O32   P13  O31   120.01  3.000
 HQV  O32   P13  O14   108.02  3.000
 HQV  O31   P13  O14   109.80  3.000
 HQV  O32   P13  O12   110.97  3.000
 HQV  O14   P13  O12    93.44  3.000
 HQV  O31   P13  O12   111.29  3.000
 HQV  C09   S08  C05    98.23  3.000
 HQV  H181  O18  C17   108.90  3.000
 HQV  O41   C37  N36   123.62  3.000
 HQV  N36   C37  C38   113.92  3.000
 HQV  O41   C37  C38   122.44  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
 HQV  CONST_01  N26   C27  N22  C21   180.00   0.0  0
 HQV  CONST_02  C27   N26  C25  C24     0.00   0.0  0
 HQV  CONST_03  N26   C27  N22  C23     0.00   0.0  0
 HQV  CONST_04  N22   C27  N26  C25     0.00   0.0  0
 HQV  CONST_05  O28   C27  N22  C21     0.00   0.0  0
 HQV  CONST_06  O28   C27  N22  C23   180.00   0.0  0
 HQV  CONST_07  O28   C27  N26  C25   180.00   0.0  0
 HQV  CONST_08  O29   C25  N26  C27   180.00   0.0  0
 HQV  CONST_09  H261  N26  C25  C24   180.00   0.0  0
 HQV  CONST_10  O41   C37  N36  C35     0.00   0.0  0
 HQV  CONST_11  C38   C37  N36  C35   180.00   0.0  0
 HQV  CONST_12  C40   C39  C38  C37   180.00   0.0  0
 HQV  CONST_13  H361  N36  C37  C38     0.00   0.0  0
 HQV  CONST_14  H391  C39  C38  C37     0.00   0.0  0
 HQV  CONST_15  H381  C38  C39  C40     0.00   0.0  0
 HQV  Var_01    O12   P11  O10  C09   150.53  30.0  3
 HQV  Var_02    O31   P13  O14  C15    52.69  30.0  3
 HQV  Var_03    O41   C37  C38  C39     6.93  30.0  2
 HQV  Var_04    H1    C40  C39  C38  -121.07  30.0  3
 HQV  Var_05    H152  C15  O14  P13    33.14  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
 HQV  chir_01  C17  C16  O18  C19  negativ
 HQV  chir_02  C21  O30  N22  C19  negativ
 HQV  chir_03  C02  C35  C03  O01  positiv
 HQV  chir_04  C03  O04  C05  C02  positiv
 HQV  chir_05  C05  S08  C03  C06  negativ
 HQV  chir_06  C09  S08  O10  C35  positiv
 HQV  chir_07  C16  O30  C15  C17  positiv
 HQV  chir_08  C19  O20  C17  C21  positiv
 HQV  chir_09  C35  C09  N36  C02  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
 HQV  plan-1  C38   0.020
 HQV  plan-1  C39   0.020
 HQV  plan-1  C40   0.020
 HQV  plan-1  H381  0.020
 HQV  plan-1  H391  0.020
 HQV  plan-1  C37   0.020
 HQV  plan-2  C21   0.020
 HQV  plan-2  C24   0.020
 HQV  plan-2  C23   0.020
 HQV  plan-2  C25   0.020
 HQV  plan-2  C27   0.020
 HQV  plan-2  N22   0.020
 HQV  plan-2  N26   0.020
 HQV  plan-2  O29   0.020
 HQV  plan-2  H241  0.020
 HQV  plan-2  H231  0.020
 HQV  plan-2  H261  0.020
 HQV  plan-2  O28   0.020
 HQV  plan-3  C35   0.020
 HQV  plan-3  C38   0.020
 HQV  plan-3  N36   0.020
 HQV  plan-3  O41   0.020
 HQV  plan-3  H361  0.020
 HQV  plan-3  C37   0.020

