# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 23:31:37 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: (2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@H](O[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)C(O)=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
 HP7  HP7  '(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  62  40  .  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_HP7
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
 HP7  N1    N  NR6    0  -0.568   5.7800  -0.3551  -0.4593
 HP7  C2    C  CR6    0   0.740   7.0980  -0.7574  -0.4068
 HP7  O2    O  O      0  -0.480   7.5062  -1.5402   0.4272
 HP7  N3    N  NR16   0  -0.731   7.9095  -0.2082  -1.3616
 HP7  C4    C  CR6    0   0.567   7.5640   0.6979  -2.3538
 HP7  O4    O  O      0  -0.465   8.4019   1.1058  -3.1372
 HP7  C5    C  CR16   0  -0.508   6.1701   1.0608  -2.3324
 HP7  C6    C  CR16   0   0.089   5.3545   0.5246  -1.4082
 HP7  PA    P  P      0   1.377  -0.3954   1.0582  -0.8937
 HP7  PB    P  P      0   1.355  -2.5246  -0.4871  -2.2257
 HP7  O'P   O  O      0  -0.562  -5.8617  -4.5277   0.3293
 HP7  O'Q   O  OC    -1  -0.619  -4.9452  -4.5631   2.3594
 HP7  C1'   C  CH1    0   0.276  -4.4973  -0.8278  -0.4520
 HP7  O1A   O  O      0  -0.780  -0.0209   2.1610  -1.8273
 HP7  O1B   O  O      0  -0.777  -2.4444  -1.6594  -3.1490
 HP7  C1C   C  CH1    0   0.185   4.8744  -0.9436   0.5525
 HP7  C2'   C  CH1    0  -0.144  -4.6240   0.1717   0.7089
 HP7  N2'   N  NH1    0  -0.663  -4.0085   1.4237   0.3601
 HP7  O2A   O  OP    -1  -0.773  -1.2169   1.3552   0.3331
 HP7  O2B   O  OP    -1  -0.773  -3.1691   0.7925  -2.6482
 HP7  C2C   C  CH1    0  -0.040   5.0203  -0.2562   1.9111
 HP7  O2C   O  OH1    0  -0.664   4.7158  -1.2022   2.8988
 HP7  C3'   C  CH1    0   0.031  -4.0133  -0.4127   1.9740
 HP7  O3'   O  OH1    0  -0.672  -4.2521   0.4857   3.0332
 HP7  O3A   O  O2     0  -0.729  -0.9858  -0.2292  -1.7069
 HP7  O3B   O  O2     0  -0.635  -3.1420  -0.9795  -0.7800
 HP7  C3C   C  CH1    0  -0.043   3.9253   0.8129   1.8266
 HP7  O3C   O  OH1    0  -0.655   3.4339   1.2157   3.0732
 HP7  C4'   C  CH1    0   0.015  -4.6360  -1.7762   2.2426
 HP7  O4'   O  OH1    0  -0.710  -4.0100  -2.3518   3.3597
 HP7  C4C   C  CH1    0  -0.005   2.8392   0.0832   1.0431
 HP7  O4C   O  O2     0  -0.494   3.5519  -0.7756   0.1512
 HP7  C5'   C  CH1    0  -0.153  -4.4958  -2.6821   1.0099
 HP7  O5'   O  O2     0  -0.488  -5.0527  -2.0617  -0.1300
 HP7  C5C   C  CH2    0  -0.158   1.9325   1.0130   0.2771
 HP7  O5C   O  O2     0  -0.613   0.9621   0.2573  -0.4119
 HP7  C6'   C  C      0   0.431  -5.1775  -4.0443   1.2335
 HP7  C7'   C  C      0   0.523  -4.6509   2.3643  -0.3453
 HP7  O7'   O  O      0  -0.533  -5.8563   2.3349  -0.5829
 HP7  C8'   C  CH3    0  -0.773  -3.7924   3.5145  -0.8092
 HP7  H5    H  HCR6   0   0.292   5.7838   1.7517  -3.0653
 HP7  H6    H  HCR6   0   0.325   4.3046   0.7703  -1.3932
 HP7  H1'   H  HCH1   0   0.235  -5.0721  -0.4546  -1.3054
 HP7  H1C   H  HCH1   0   0.288   5.1166  -2.0059   0.6137
 HP7  H2'   H  HCH1   0   0.249  -5.6908   0.3381   0.8837
 HP7  HN2'  H  HNH1   0   0.435  -2.9818   1.4448   0.3651
 HP7  H2C   H  HCH1   0   0.262   6.0168   0.1765   2.0555
 HP7  HO2C  H  HOH1   0   0.452   4.3086  -0.7339   3.6385
 HP7  H3'   H  HCH1   0   0.204  -2.9321  -0.5485   1.8210
 HP7  HO3'  H  HOH1   0   0.448  -3.8266   0.1317   3.8206
 HP7  H3C   H  HCH1   0   0.246   4.2940   1.6696   1.2460
 HP7  HO3C  H  HOH1   0   0.471   3.9992   1.9126   3.4222
 HP7  H4'   H  HCH1   0   0.187  -5.7135  -1.6183   2.4285
 HP7  HO4'  H  HOH1   0   0.438  -4.2513  -3.3050   3.2832
 HP7  H4C   H  HCH1   0   0.254   2.2371  -0.5278   1.7269
 HP7  H5'   H  HCH1   0   0.230  -3.4228  -2.8778   0.8577
 HP7  H5C   H  HCH2   0   0.227   1.4771   1.6947   1.0059
 HP7  H5CA  H  HCH2   0   0.213   2.5185   1.6299  -0.4159
 HP7  H8'   H  HCH3   0   0.239  -2.7406   3.3935  -0.5629
 HP7  H8'A  H  HCH3   0   0.252  -3.8787   3.6034  -1.8913
 HP7  H8'B  H  HCH3   0   0.244  -4.1566   4.4439  -0.3708
 HP7  HN3   H  HNR6   0   0.427   8.8774  -0.5041  -1.3277

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
 HP7  C6   N1    single  1.362  0.020  1.362
 HP7  C1C  N1    single  1.480  0.020  1.480
 HP7  N1   C2    single  1.379  0.020  1.379
 HP7  C2   N3    single  1.368  0.020  1.368
 HP7  C2   O2    double  1.214  0.020  1.214
 HP7  C4   N3    single  1.387  0.020  1.387
 HP7  C5   C4    single  1.441  0.020  1.441
 HP7  C4   O4    double  1.217  0.020  1.217
 HP7  C6   C5    double  1.344  0.020  1.344
 HP7  C5   H5    single  0.930  0.020  1.080
 HP7  C6   H6    single  0.930  0.020  1.080
 HP7  O1A  PA    deloc   1.493  0.020  1.493
 HP7  O2A  PA    deloc   1.506  0.020  1.506
 HP7  PA   O3A   single  1.633  0.020  1.633
 HP7  PA   O5C   single  1.648  0.020  1.648
 HP7  O1B  PB    deloc   1.494  0.020  1.494
 HP7  O3A  PB    single  1.644  0.020  1.644
 HP7  PB   O3B   single  1.647  0.020  1.647
 HP7  PB   O2B   deloc   1.494  0.020  1.494
 HP7  O'P  C6'   deloc   1.233  0.020  1.233
 HP7  C6'  O'Q   deloc   1.261  0.020  1.261
 HP7  O5'  C1'   single  1.391  0.020  1.391
 HP7  C2'  C1'   single  1.537  0.020  1.537
 HP7  C1'  O3B   single  1.403  0.020  1.403
 HP7  C1'  H1'   single  0.970  0.020  1.090
 HP7  C2C  C1C   single  1.530  0.020  1.530
 HP7  C1C  O4C   single  1.392  0.020  1.392
 HP7  C1C  H1C   single  0.970  0.020  1.090
 HP7  C2'  N2'   single  1.438  0.020  1.438
 HP7  C2'  C3'   single  1.521  0.020  1.521
 HP7  C2'  H2'   single  0.970  0.020  1.090
 HP7  C7'  N2'   single  1.340  0.020  1.340
 HP7  N2'  HN2'  single  0.890  0.020  1.040
 HP7  O2C  C2C   single  1.401  0.020  1.401
 HP7  C2C  C3C   single  1.533  0.020  1.533
 HP7  C2C  H2C   single  0.970  0.020  1.090
 HP7  O2C  HO2C  single  0.850  0.020  0.980
 HP7  O3'  C3'   single  1.409  0.020  1.409
 HP7  C4'  C3'   single  1.523  0.020  1.523
 HP7  C3'  H3'   single  0.970  0.020  1.090
 HP7  O3'  HO3'  single  0.850  0.020  0.980
 HP7  C3C  O3C   single  1.399  0.020  1.399
 HP7  C3C  C4C   single  1.525  0.020  1.525
 HP7  C3C  H3C   single  0.970  0.020  1.090
 HP7  O3C  HO3C  single  0.850  0.020  0.980
 HP7  C4'  C5'   single  1.536  0.020  1.536
 HP7  C4'  O4'   single  1.404  0.020  1.404
 HP7  C4'  H4'   single  0.970  0.020  1.090
 HP7  O4'  HO4'  single  0.850  0.020  0.980
 HP7  C5C  C4C   single  1.508  0.020  1.508
 HP7  C4C  O4C   single  1.429  0.020  1.429
 HP7  C4C  H4C   single  0.970  0.020  1.090
 HP7  O5'  C5'   single  1.412  0.020  1.412
 HP7  C6'  C5'   single  1.540  0.020  1.540
 HP7  C5'  H5'   single  0.970  0.020  1.090
 HP7  O5C  C5C   single  1.410  0.020  1.410
 HP7  C5C  H5C   single  0.970  0.020  1.090
 HP7  C5C  H5CA  single  0.970  0.020  1.090
 HP7  O7'  C7'   double  1.229  0.020  1.229
 HP7  C7'  C8'   single  1.508  0.020  1.508
 HP7  C8'  H8'   single  0.970  0.020  1.090
 HP7  C8'  H8'A  single  0.970  0.020  1.090
 HP7  C8'  H8'B  single  0.970  0.020  1.090
 HP7  N3   HN3   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
 HP7  C1C   N1   C6    122.82  3.000
 HP7  C1C   N1   C2    116.28  3.000
 HP7  C6    N1   C2    120.90  3.000
 HP7  N3    C2   O2    122.59  3.000
 HP7  O2    C2   N1    122.37  3.000
 HP7  N3    C2   N1    115.04  3.000
 HP7  HN3   N3   C4    116.92  3.000
 HP7  HN3   N3   C2    115.23  3.000
 HP7  C4    N3   C2    127.85  3.000
 HP7  C5    C4   O4    126.24  3.000
 HP7  O4    C4   N3    120.51  3.000
 HP7  C5    C4   N3    113.25  3.000
 HP7  H5    C5   C6    120.34  3.000
 HP7  H5    C5   C4    119.85  3.000
 HP7  C6    C5   C4    119.80  3.000
 HP7  H6    C6   C5    120.63  3.000
 HP7  H6    C6   N1    116.21  3.000
 HP7  C5    C6   N1    123.16  3.000
 HP7  O5C   PA   O3A    93.46  3.000
 HP7  O5C   PA   O2A   107.88  3.000
 HP7  O3A   PA   O2A   111.34  3.000
 HP7  O5C   PA   O1A   109.59  3.000
 HP7  O3A   PA   O1A   111.20  3.000
 HP7  O2A   PA   O1A   120.04  3.000
 HP7  O3B   PB   O3A    96.93  3.000
 HP7  O3B   PB   O2B   110.04  3.000
 HP7  O3A   PB   O2B   111.01  3.000
 HP7  O2B   PB   O1B   121.36  3.000
 HP7  O3B   PB   O1B   109.14  3.000
 HP7  O3A   PB   O1B   105.53  3.000
 HP7  H1'   C1'  O5'   105.86  3.000
 HP7  H1'   C1'  O3B   111.22  3.000
 HP7  O5'   C1'  O3B   110.12  3.000
 HP7  H1'   C1'  C2'   108.90  3.000
 HP7  O3B   C1'  C2'   109.06  3.000
 HP7  O5'   C1'  C2'   111.66  3.000
 HP7  H1C   C1C  O4C   110.15  3.000
 HP7  H1C   C1C  C2C   111.50  3.000
 HP7  O4C   C1C  C2C   107.00  3.000
 HP7  H1C   C1C  N1    106.83  3.000
 HP7  O4C   C1C  N1    109.64  3.000
 HP7  C2C   C1C  N1    111.73  3.000
 HP7  H2'   C2'  C3'   108.48  3.000
 HP7  H2'   C2'  N2'   108.89  3.000
 HP7  C3'   C2'  N2'   111.36  3.000
 HP7  H2'   C2'  C1'   107.46  3.000
 HP7  C3'   C2'  C1'   110.19  3.000
 HP7  N2'   C2'  C1'   110.35  3.000
 HP7  HN2'  N2'  C7'   117.87  3.000
 HP7  HN2'  N2'  C2'   116.40  3.000
 HP7  C7'   N2'  C2'   122.26  3.000
 HP7  H2C   C2C  C3C   112.42  3.000
 HP7  H2C   C2C  O2C   111.80  3.000
 HP7  C3C   C2C  O2C   110.77  3.000
 HP7  H2C   C2C  C1C   112.41  3.000
 HP7  C3C   C2C  C1C   101.32  3.000
 HP7  O2C   C2C  C1C   107.57  3.000
 HP7  HO2C  O2C  C2C   107.71  3.000
 HP7  H3'   C3'  C4'   108.41  3.000
 HP7  H3'   C3'  O3'   110.47  3.000
 HP7  C4'   C3'  O3'   111.65  3.000
 HP7  H3'   C3'  C2'   109.04  3.000
 HP7  C4'   C3'  C2'   109.05  3.000
 HP7  O3'   C3'  C2'   108.19  3.000
 HP7  HO3'  O3'  C3'   107.79  3.000
 HP7  PB    O3A  PA    128.25  3.000
 HP7  C1'   O3B  PB    122.34  3.000
 HP7  H3C   C3C  C4C   109.91  3.000
 HP7  H3C   C3C  O3C   111.36  3.000
 HP7  C4C   C3C  O3C   110.20  3.000
 HP7  H3C   C3C  C2C   109.47  3.000
 HP7  C4C   C3C  C2C   101.74  3.000
 HP7  O3C   C3C  C2C   113.74  3.000
 HP7  HO3C  O3C  C3C   108.97  3.000
 HP7  H4'   C4'  C5'   107.96  3.000
 HP7  H4'   C4'  O4'   111.08  3.000
 HP7  C5'   C4'  O4'   110.85  3.000
 HP7  H4'   C4'  C3'   107.49  3.000
 HP7  O4'   C4'  C3'   108.97  3.000
 HP7  C5'   C4'  C3'   110.44  3.000
 HP7  HO4'  O4'  C4'   103.03  3.000
 HP7  H4C   C4C  C5C   109.28  3.000
 HP7  H4C   C4C  O4C   109.16  3.000
 HP7  C5C   C4C  O4C   110.71  3.000
 HP7  H4C   C4C  C3C   109.70  3.000
 HP7  O4C   C4C  C3C   104.66  3.000
 HP7  C5C   C4C  C3C   113.21  3.000
 HP7  C4C   O4C  C1C   111.50  3.000
 HP7  H5'   C5'  C6'   107.11  3.000
 HP7  H5'   C5'  O5'   110.53  3.000
 HP7  C6'   C5'  O5'   109.35  3.000
 HP7  H5'   C5'  C4'   107.74  3.000
 HP7  C6'   C5'  C4'   111.40  3.000
 HP7  O5'   C5'  C4'   110.65  3.000
 HP7  C5'   O5'  C1'   114.78  3.000
 HP7  H5CA  C5C  H5C   106.97  3.000
 HP7  H5CA  C5C  O5C   111.12  3.000
 HP7  H5C   C5C  O5C   111.85  3.000
 HP7  H5CA  C5C  C4C   110.26  3.000
 HP7  H5C   C5C  C4C   107.18  3.000
 HP7  O5C   C5C  C4C   109.37  3.000
 HP7  C5C   O5C  PA    116.70  3.000
 HP7  C5'   C6'  O'Q   114.33  3.000
 HP7  C5'   C6'  O'P   119.09  3.000
 HP7  O'Q   C6'  O'P   126.57  3.000
 HP7  C8'   C7'  O7'   121.14  3.000
 HP7  C8'   C7'  N2'   115.11  3.000
 HP7  O7'   C7'  N2'   123.73  3.000
 HP7  H8'B  C8'  H8'A  107.67  3.000
 HP7  H8'B  C8'  H8'   109.09  3.000
 HP7  H8'A  C8'  H8'   108.11  3.000
 HP7  H8'B  C8'  C7'   109.65  3.000
 HP7  H8'A  C8'  C7'   108.83  3.000
 HP7  H8'   C8'  C7'   113.34  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
 HP7  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 HP7  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 HP7  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 HP7  CONST_04  C1C   N1   C2   N3   180.00   0.0  0
 HP7  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 HP7  CONST_06  C6    N1   C2   O2   180.00   0.0  0
 HP7  CONST_07  C1C   N1   C2   O2     0.00   0.0  0
 HP7  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 HP7  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 HP7  CONST_10  O7'   C7'  N2'  C2'    0.00   0.0  0
 HP7  CONST_11  C8'   C7'  N2'  C2'  180.00   0.0  0
 HP7  CONST_12  HN2'  N2'  C7'  O7'  180.00   0.0  0
 HP7  Var_01    C4C   C5C  O5C  PA   160.50  30.0  3
 HP7  Var_02    O1B   PB   O3B  C1'  -97.62  30.0  1
 HP7  Var_03    O1A   PA   O3A  PB   -84.46  30.0  1
 HP7  Var_04    H8'   C8'  C7'  N2'    3.86  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
 HP7  chir_03  C1'  O5'  C2'  O3B  negativ
 HP7  chir_04  C1C  N1   C2C  O4C  negativ
 HP7  chir_05  C2'  N2'  C3'  C1'  positiv
 HP7  chir_06  C2C  C1C  O2C  C3C  positiv
 HP7  chir_07  C3'  O3'  C2'  C4'  positiv
 HP7  chir_08  C3C  O3C  C4C  C2C  positiv
 HP7  chir_09  C4'  O4'  C3'  C5'  negativ
 HP7  chir_10  C4C  C3C  C5C  O4C  negativ
 HP7  chir_11  C5'  C4'  O5'  C6'  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
 HP7  plan-1  N1    0.020
 HP7  plan-1  C2    0.020
 HP7  plan-1  O2    0.020
 HP7  plan-1  N3    0.020
 HP7  plan-1  C4    0.020
 HP7  plan-1  O4    0.020
 HP7  plan-1  C5    0.020
 HP7  plan-1  C6    0.020
 HP7  plan-1  C1C   0.020
 HP7  plan-1  H5    0.020
 HP7  plan-1  H6    0.020
 HP7  plan-1  HN3   0.020
 HP7  plan-2  C2'   0.020
 HP7  plan-2  N2'   0.020
 HP7  plan-2  C7'   0.020
 HP7  plan-2  O7'   0.020
 HP7  plan-2  C8'   0.020
 HP7  plan-2  HN2'  0.020
 HP7  plan-3  O'P   0.020
 HP7  plan-3  O'Q   0.020
 HP7  plan-3  C5'   0.020
 HP7  plan-3  C6'   0.020

