# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Nov 26 00:55:46 2022
#   Inital geometry file: a 221 line input string
#   Ligand name: (2S)-2-({4-[({(6S)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2N(CC3=CN([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)C(=O)NC3=O)[C@@H](CCc2n1)CNc5ccc(cc5)C(=O)N[C@@H](CCC(O)=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
 VNM  VNM  "(2S)-2-({4-[({(6S)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)"  ligand  91  53  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VNM
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
 VNM  C2    C  CR6   0   0.733   -7.7284  53.9917   7.6272
 VNM  C4    C  CR6   0   0.564   -8.6129  53.7688   5.3275
 VNM  C5    C  CR6   0  -0.168   -7.8169  54.9226   4.9654
 VNM  C6    C  CR16  0   0.054   -7.0093  55.4647   5.8989
 VNM  C7    C  CH2   0  -0.457   -9.0924  56.4817   0.9840
 VNM  C8    C  CH2   0  -0.520  -10.4846  55.8471   1.0490
 VNM  C11   C  CH2   0  -0.353   -7.9068  55.5106   3.5916
 VNM  C12   C  CR6   0  -0.076  -12.0237  62.3323   4.7986
 VNM  C15   C  CR6   0   0.380  -10.2993  60.2687   3.9194
 VNM  C16   C  CR16  0  -0.338  -10.3164  60.6812   5.2656
 VNM  C17   C  CR16  0  -0.255  -11.1656  61.6778   5.6886
 VNM  N     N  NH1   0  -0.674  -13.4919  64.2142   4.4222
 VNM  CA    C  CH1   0  -0.165  -14.4024  65.2425   4.8461
 VNM  O     O  O     0  -0.489  -13.2111  63.4607   6.5150
 VNM  CB    C  CH2   0  -0.486  -14.8061  66.1311   3.6636
 VNM  CG    C  CH2   0  -0.594  -15.5743  65.4135   2.5615
 VNM  CD    C  C     0   0.556  -15.8077  66.2910   1.3611
 VNM  OE1   O  O     0  -0.434  -15.4424  67.4342   1.2539
 VNM  OE2   O  OH1   0  -0.593  -16.4798  65.6493   0.4104
 VNM  C1'   C  CH1   0   0.259   -6.0142  55.6178   8.1866
 VNM  C13   C  CR16  0  -0.283  -12.0018  61.9282   3.4643
 VNM  C14   C  CR16  0  -0.335  -11.1623  60.9217   3.0247
 VNM  C2"   C  CR6   0   0.503  -12.7589  55.0353   3.7499
 VNM  C2'   C  CH2   0  -0.568   -4.9467  54.6443   8.6891
 VNM  C3'   C  CH1   0   0.007   -3.7308  55.5479   8.8581
 VNM  C4"   C  CR6   0   0.470  -10.9525  55.9386   4.7870
 VNM  C4'   C  CH1   0  -0.030   -3.9215  56.5205   7.7040
 VNM  C4A   C  CR6   0   0.062  -10.2802  56.0096   3.5451
 VNM  C5'   C  CH2   0  -0.194   -3.3732  56.0121   6.3780
 VNM  C6"   C  CH1   0  -0.178   -8.7872  57.3151   2.2285
 VNM  C8A   C  CR6   0   0.280  -11.0115  55.6312   2.4392
 VNM  C9    C  CH2   0  -0.263   -9.6474  58.5762   2.2708
 VNM  CT    C  C     0   0.539  -15.6361  64.6222   5.4839
 VNM  N1    N  NR6   0  -0.579   -6.9209  55.0133   7.1816
 VNM  N1"   N  N     0  -0.507  -12.2506  55.1355   2.5274
 VNM  N3    N  NR16  0  -0.732   -8.5045  53.4126   6.6619
 VNM  N3"   N  N     0  -0.504  -12.1791  55.4395   4.8804
 VNM  N5    N  NT    0  -0.503   -8.9605  56.5295   3.4526
 VNM  NA4   N  NH2   0  -0.826  -10.3647  56.3563   5.9257
 VNM  O1    O  O     0  -0.429  -16.0803  63.5383   5.2120
 VNM  O2    O  O     0  -0.475   -7.7384  53.6216   8.7834
 VNM  O2"   O  OH1   0  -0.588  -16.2005  65.4631   6.3404
 VNM  O3'   O  OH1   0  -0.666   -3.7846  56.2981  10.0482
 VNM  O4    O  O     0  -0.448   -9.3269  53.1249   4.5815
 VNM  O4'   O  O2    0  -0.499   -5.3339  56.6884   7.6017
 VNM  O5'   O  O2    0  -0.587   -1.9461  56.0479   6.4546
 VNM  P     P  P     0   1.443   -1.0798  54.8894   5.7744
 VNM  H6    H  HCR6  0   0.316   -6.3901  56.3167   5.6593
 VNM  H71   H  HCH2  0   0.252   -8.3302  55.7068   0.8854
 VNM  H72   H  HCH2  0   0.250   -9.0048  57.0999   0.0883
 VNM  H81   H  HCH2  0   0.257  -11.2169  56.4747   0.5339
 VNM  H82   H  HCH2  0   0.268  -10.4916  54.8954   0.5129
 VNM  H101  H  HNH1  0   0.385   -9.0621  58.7073   4.2510
 VNM  H1    H  HCH2  0   0.235   -8.0305  54.7002   2.8640
 VNM  H2    H  HCH2  0   0.256   -6.9595  56.0012   3.3594
 VNM  H161  H  HCR6  0   0.257   -9.6625  60.1928   5.9789
 VNM  H171  H  HCR6  0   0.251  -11.1649  61.9579   6.7340
 VNM  H     H  HNH1  0   0.411  -13.1235  64.2579   3.4862
 VNM  HA    H  HCH1  0   0.292  -13.9253  65.8909   5.5881
 VNM  HB2   H  HCH2  0   0.272  -13.8887  66.5661   3.2615
 VNM  HB3   H  HCH2  0   0.273  -15.3953  66.9646   4.0475
 VNM  HG2   H  HCH2  0   0.290  -16.5503  65.0688   2.9138
 VNM  HG3   H  HCH2  0   0.285  -15.0531  64.5132   2.2237
 VNM  H3    H  HOH1  0   0.477  -16.6193  66.2363  -0.3480
 VNM  H1'   H  HCH1  0   0.269   -6.6431  55.9904   8.9986
 VNM  H131  H  HCR6  0   0.250  -12.6688  62.3738   2.7363
 VNM  H141  H  HCR6  0   0.269  -11.1903  60.6376   1.9815
 VNM  H2*1  H  HCH2  0   0.289   -5.2331  54.1464   9.6132
 VNM  H2*2  H  HCH2  0   0.270   -4.7490  53.8705   7.9448
 VNM  H3'   H  HCH1  0   0.251   -2.7952  54.9845   8.7775
 VNM  H4*   H  HCH1  0   0.273   -3.4845  57.4984   7.9236
 VNM  H5*1  H  HCH2  0   0.267   -3.7010  56.6637   5.5654
 VNM  H5*2  H  HCH2  0   0.244   -3.7431  55.0044   6.1657
 VNM  H61   H  HCH1  0   0.262   -7.7396  57.6294   2.2005
 VNM  H92   H  HCH2  0   0.247   -9.3495  59.2058   1.4264
 VNM  H91   H  HCH2  0   0.230  -10.7058  58.3317   2.1151
 VNM  HN3   H  HNR6  0   0.422   -9.0733  52.6345   6.9732
 VNM  HA22  H  HNH2  0   0.383  -14.3706  54.0040   3.0805
 VNM  HA21  H  HNH2  0   0.384  -14.3105  54.2151   4.7691
 VNM  HA42  H  HNH2  0   0.388  -10.9498  56.4989   6.7319
 VNM  HA41  H  HNH2  0   0.401   -9.5399  56.9281   5.8579
 VNM  H4    H  HOH1  0   0.500   -0.8600  52.8879   6.6104
 VNM  H5    H  HOH1  0   0.480  -17.0226  65.0839   6.6874
 VNM  HO3'  H  HOH1  0   0.454   -3.7835  55.6887  10.7934
 VNM  H7    H  HOH1  0   0.500    0.6345  56.0741   5.1388
 VNM  NA2   N  NH2   0  -0.826  -14.0149  54.5293   3.8607
 VNM  N10   N  NH1   0  -0.681   -9.4636  59.2740   3.5182
 VNM  C     C  C     0   0.549  -12.9435  63.3676   5.3222
 VNM  O1P   O  OH1   0  -0.733   -1.0574  53.7817   6.9223
 VNM  O2P   O  O     0  -0.699   -1.5415  54.4425   4.4466
 VNM  O3P   O  OH1   0  -0.724    0.3921  55.4904   5.8711

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
 VNM  C8   C7    single    1.531  0.020  1.531
 VNM  C8   C8A   single    1.502  0.020  1.502
 VNM  C7   C6"   single    1.529  0.020  1.529
 VNM  N1"  C8A   aromatic  1.338  0.020  1.338
 VNM  N1"  C2"   aromatic  1.328  0.020  1.328
 VNM  C8A  C4A   aromatic  1.379  0.020  1.379
 VNM  C9   C6"   single    1.527  0.020  1.527
 VNM  C9   N10   single    1.441  0.020  1.441
 VNM  C6"  N5    single    1.465  0.020  1.465
 VNM  N10  C15   single    1.360  0.020  1.360
 VNM  C16  C15   aromatic  1.408  0.020  1.408
 VNM  C16  C17   aromatic  1.376  0.020  1.376
 VNM  NA2  C2"   single    1.359  0.020  1.359
 VNM  OE1  CD    double    1.205  0.020  1.205
 VNM  C2"  N3"   aromatic  1.333  0.020  1.333
 VNM  N5   C4A   single    1.421  0.020  1.421
 VNM  N5   C11   single    1.472  0.020  1.472
 VNM  C15  C14   aromatic  1.404  0.020  1.404
 VNM  C4A  C4"   aromatic  1.414  0.020  1.414
 VNM  C17  C12   aromatic  1.399  0.020  1.399
 VNM  CD   OE2   single    1.329  0.020  1.329
 VNM  CD   CG    single    1.505  0.020  1.505
 VNM  C11  C5    single    1.497  0.020  1.497
 VNM  CG   CB    single    1.523  0.020  1.523
 VNM  C14  C13   aromatic  1.382  0.020  1.382
 VNM  C12  C13   aromatic  1.394  0.020  1.394
 VNM  C12  C     single    1.481  0.020  1.481
 VNM  N3"  C4"   aromatic  1.328  0.020  1.328
 VNM  C4"  NA4   single    1.348  0.020  1.348
 VNM  CB   CA    single    1.533  0.020  1.533
 VNM  C    N     single    1.352  0.020  1.352
 VNM  C    O     double    1.226  0.020  1.226
 VNM  N    CA    single    1.437  0.020  1.437
 VNM  O4   C4    double    1.217  0.020  1.217
 VNM  C5   C4    single    1.448  0.020  1.448
 VNM  C5   C6    double    1.348  0.020  1.348
 VNM  CA   CT    single    1.521  0.020  1.521
 VNM  C4   N3    single    1.385  0.020  1.385
 VNM  O2P  P     double    1.475  0.020  1.475
 VNM  C6   N1    single    1.363  0.020  1.363
 VNM  CT   O1    double    1.202  0.020  1.202
 VNM  CT   O2"   single    1.326  0.020  1.326
 VNM  C5'  O5'   single    1.430  0.020  1.430
 VNM  C5'  C4'   single    1.522  0.020  1.522
 VNM  O5'  P     single    1.599  0.020  1.599
 VNM  P    O3P   single    1.593  0.020  1.593
 VNM  P    O1P   single    1.595  0.020  1.595
 VNM  N3   C2    single    1.367  0.020  1.367
 VNM  O4'  C4'   single    1.426  0.020  1.426
 VNM  O4'  C1'   single    1.397  0.020  1.397
 VNM  N1   C2    single    1.376  0.020  1.376
 VNM  N1   C1'   single    1.482  0.020  1.482
 VNM  C4'  C3'   single    1.521  0.020  1.521
 VNM  C2   O2    double    1.214  0.020  1.214
 VNM  C1'  C2'   single    1.530  0.020  1.530
 VNM  C2'  C3'   single    1.524  0.020  1.524
 VNM  C3'  O3'   single    1.408  0.020  1.408
 VNM  C6   H6    single    0.930  0.020  1.080
 VNM  C7   H71   single    0.970  0.020  1.090
 VNM  C7   H72   single    0.970  0.020  1.090
 VNM  C8   H81   single    0.970  0.020  1.090
 VNM  C8   H82   single    0.970  0.020  1.090
 VNM  N10  H101  single    0.890  0.020  1.040
 VNM  C11  H1    single    0.970  0.020  1.090
 VNM  C11  H2    single    0.970  0.020  1.090
 VNM  C16  H161  single    0.930  0.020  1.080
 VNM  C17  H171  single    0.930  0.020  1.080
 VNM  N    H     single    0.860  0.020  1.020
 VNM  CA   HA    single    0.970  0.020  1.090
 VNM  CB   HB2   single    0.970  0.020  1.090
 VNM  CB   HB3   single    0.970  0.020  1.090
 VNM  CG   HG2   single    0.970  0.020  1.090
 VNM  CG   HG3   single    0.970  0.020  1.090
 VNM  OE2  H3    single    0.850  0.020  0.980
 VNM  C1'  H1'   single    0.970  0.020  1.090
 VNM  C13  H131  single    0.930  0.020  1.080
 VNM  C14  H141  single    0.930  0.020  1.080
 VNM  C2'  H2*1  single    0.970  0.020  1.090
 VNM  C2'  H2*2  single    0.970  0.020  1.090
 VNM  C3'  H3'   single    0.970  0.020  1.090
 VNM  C4'  H4*   single    0.970  0.020  1.090
 VNM  C5'  H5*1  single    0.970  0.020  1.090
 VNM  C5'  H5*2  single    0.970  0.020  1.090
 VNM  C6"  H61   single    0.970  0.020  1.090
 VNM  C9   H92   single    0.970  0.020  1.090
 VNM  C9   H91   single    0.970  0.020  1.090
 VNM  N3   HN3   single    0.860  0.020  1.020
 VNM  NA2  HA22  single    0.890  0.020  1.040
 VNM  NA2  HA21  single    0.890  0.020  1.040
 VNM  NA4  HA42  single    0.890  0.020  1.040
 VNM  NA4  HA41  single    0.890  0.020  1.040
 VNM  O1P  H4    single    0.850  0.020  0.980
 VNM  O2"  H5    single    0.850  0.020  0.980
 VNM  O3'  HO3'  single    0.850  0.020  0.980
 VNM  O3P  H7    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
 VNM  O2    C2   N3    122.59  3.000
 VNM  O2    C2   N1    122.65  3.000
 VNM  N3    C2   N1    114.76  3.000
 VNM  O4    C4   N3    120.02  3.000
 VNM  N3    C4   C5    113.75  3.000
 VNM  O4    C4   C5    126.23  3.000
 VNM  C11   C5   C6    120.90  3.000
 VNM  C6    C5   C4    118.47  3.000
 VNM  C11   C5   C4    120.62  3.000
 VNM  H6    C6   N1    115.65  3.000
 VNM  H6    C6   C5    120.46  3.000
 VNM  N1    C6   C5    123.88  3.000
 VNM  H72   C7   H71   105.78  3.000
 VNM  H72   C7   C6"   110.07  3.000
 VNM  H71   C7   C6"   108.73  3.000
 VNM  H72   C7   C8    110.03  3.000
 VNM  H71   C7   C8    110.15  3.000
 VNM  C6"   C7   C8    111.89  3.000
 VNM  H82   C8   H81   105.34  3.000
 VNM  H82   C8   C8A   109.07  3.000
 VNM  H81   C8   C8A   106.47  3.000
 VNM  H82   C8   C7    110.25  3.000
 VNM  H81   C8   C7    110.55  3.000
 VNM  C8A   C8   C7    114.69  3.000
 VNM  H2    C11  H1    106.80  3.000
 VNM  H2    C11  N5    106.85  3.000
 VNM  H1    C11  N5    111.61  3.000
 VNM  H2    C11  C5    108.63  3.000
 VNM  H1    C11  C5    109.00  3.000
 VNM  N5    C11  C5    113.66  3.000
 VNM  C13   C12  C     123.43  3.000
 VNM  C     C12  C17   118.90  3.000
 VNM  C13   C12  C17   117.62  3.000
 VNM  C14   C15  C16   117.74  3.000
 VNM  C14   C15  N10   122.00  3.000
 VNM  C16   C15  N10   120.26  3.000
 VNM  H161  C16  C17   119.76  3.000
 VNM  H161  C16  C15   119.33  3.000
 VNM  C17   C16  C15   120.90  3.000
 VNM  H171  C17  C16   118.95  3.000
 VNM  H171  C17  C12   119.59  3.000
 VNM  C16   C17  C12   121.46  3.000
 VNM  H     N    C     119.85  3.000
 VNM  H     N    CA    118.36  3.000
 VNM  C     N    CA    120.57  3.000
 VNM  HA    CA   CT    108.11  3.000
 VNM  HA    CA   CB    107.11  3.000
 VNM  CT    CA   CB    110.25  3.000
 VNM  HA    CA   N     110.34  3.000
 VNM  CT    CA   N     110.22  3.000
 VNM  CB    CA   N     110.73  3.000
 VNM  HB3   CB   HB2   106.21  3.000
 VNM  HB3   CB   CG    110.02  3.000
 VNM  HB2   CB   CG    110.18  3.000
 VNM  HB3   CB   CA    108.28  3.000
 VNM  HB2   CB   CA    107.08  3.000
 VNM  CG    CB   CA    114.70  3.000
 VNM  HG3   CG   HG2   105.39  3.000
 VNM  HG3   CG   CD    107.91  3.000
 VNM  HG2   CG   CD    107.61  3.000
 VNM  HG3   CG   CB    111.77  3.000
 VNM  HG2   CG   CB    111.44  3.000
 VNM  CD    CG   CB    112.37  3.000
 VNM  OE2   CD   OE1   123.21  3.000
 VNM  OE2   CD   CG    111.55  3.000
 VNM  OE1   CD   CG    125.25  3.000
 VNM  H3    OE2  CD    109.88  3.000
 VNM  H1'   C1'  O4'   109.28  3.000
 VNM  H1'   C1'  N1    106.91  3.000
 VNM  O4'   C1'  N1    109.06  3.000
 VNM  H1'   C1'  C2'   112.00  3.000
 VNM  N1    C1'  C2'   112.96  3.000
 VNM  O4'   C1'  C2'   106.59  3.000
 VNM  H131  C13  C14   117.37  3.000
 VNM  H131  C13  C12   120.95  3.000
 VNM  C14   C13  C12   121.66  3.000
 VNM  H141  C14  C13   118.83  3.000
 VNM  H141  C14  C15   120.55  3.000
 VNM  C13   C14  C15   120.61  3.000
 VNM  NA2   C2"  N3"   116.47  3.000
 VNM  N3"   C2"  N1"   126.26  3.000
 VNM  NA2   C2"  N1"   117.20  3.000
 VNM  H2*2  C2'  H2*1  107.60  3.000
 VNM  H2*2  C2'  C3'   110.56  3.000
 VNM  H2*1  C2'  C3'   112.77  3.000
 VNM  H2*2  C2'  C1'   110.70  3.000
 VNM  H2*1  C2'  C1'   112.74  3.000
 VNM  C3'   C2'  C1'   102.46  3.000
 VNM  H3'   C3'  O3'   111.66  3.000
 VNM  H3'   C3'  C4'   112.35  3.000
 VNM  O3'   C3'  C4'   107.21  3.000
 VNM  H3'   C3'  C2'   111.61  3.000
 VNM  O3'   C3'  C2'   112.28  3.000
 VNM  C4'   C3'  C2'   101.24  3.000
 VNM  NA4   C4"  N3"   117.39  3.000
 VNM  NA4   C4"  C4A   121.27  3.000
 VNM  N3"   C4"  C4A   121.33  3.000
 VNM  H4*   C4'  O4'   107.76  3.000
 VNM  H4*   C4'  C5'   109.25  3.000
 VNM  O4'   C4'  C5'   109.49  3.000
 VNM  H4*   C4'  C3'   111.67  3.000
 VNM  O4'   C4'  C3'   104.71  3.000
 VNM  C5'   C4'  C3'   113.71  3.000
 VNM  N5    C4A  C8A   122.72  3.000
 VNM  N5    C4A  C4"   121.13  3.000
 VNM  C8A   C4A  C4"   116.01  3.000
 VNM  H5*2  C5'  H5*1  107.68  3.000
 VNM  H5*2  C5'  O5'   111.77  3.000
 VNM  H5*1  C5'  O5'   108.94  3.000
 VNM  H5*2  C5'  C4'   110.78  3.000
 VNM  H5*1  C5'  C4'   109.93  3.000
 VNM  O5'   C5'  C4'   107.73  3.000
 VNM  H61   C6"  N5    106.79  3.000
 VNM  H61   C6"  C9    107.62  3.000
 VNM  N5    C6"  C9    110.68  3.000
 VNM  H61   C6"  C7    109.09  3.000
 VNM  N5    C6"  C7    111.37  3.000
 VNM  C9    C6"  C7    111.12  3.000
 VNM  N1"   C8A  C4A   122.70  3.000
 VNM  C4A   C8A  C8    121.12  3.000
 VNM  N1"   C8A  C8    116.05  3.000
 VNM  H91   C9   H92   106.34  3.000
 VNM  H91   C9   C6"   110.81  3.000
 VNM  H92   C9   C6"   107.48  3.000
 VNM  H91   C9   N10   110.72  3.000
 VNM  H92   C9   N10   110.76  3.000
 VNM  C6"   C9   N10   110.61  3.000
 VNM  O2"   CT   O1    124.08  3.000
 VNM  O2"   CT   CA    110.94  3.000
 VNM  O1    CT   CA    124.92  3.000
 VNM  C1'   N1   C6    122.87  3.000
 VNM  C1'   N1   C2    116.23  3.000
 VNM  C6    N1   C2    120.84  3.000
 VNM  C8A   N1"  C2"   116.31  3.000
 VNM  HN3   N3   C4    116.72  3.000
 VNM  HN3   N3   C2    115.29  3.000
 VNM  C4    N3   C2    127.99  3.000
 VNM  C4"   N3"  C2"   117.14  3.000
 VNM  C6"   N5   C4A   111.13  3.000
 VNM  C4A   N5   C11   113.90  3.000
 VNM  C6"   N5   C11   111.43  3.000
 VNM  HA41  NA4  HA42  116.76  3.000
 VNM  HA41  NA4  C4"   118.47  3.000
 VNM  HA42  NA4  C4"   117.85  3.000
 VNM  H5    O2"  CT    110.12  3.000
 VNM  HO3'  O3'  C3'   108.48  3.000
 VNM  C4'   O4'  C1'   111.23  3.000
 VNM  P     O5'  C5'   120.00  3.000
 VNM  O5'   P    O3P   101.62  3.000
 VNM  O3P   P    O2P   117.27  3.000
 VNM  O5'   P    O2P   115.66  3.000
 VNM  O3P   P    O1P   101.85  3.000
 VNM  O5'   P    O1P   101.81  3.000
 VNM  O2P   P    O1P   116.22  3.000
 VNM  HA21  NA2  HA22  115.70  3.000
 VNM  HA21  NA2  C2"   117.51  3.000
 VNM  HA22  NA2  C2"   117.28  3.000
 VNM  H101  N10  C9    114.04  3.000
 VNM  H101  N10  C15   116.15  3.000
 VNM  C9    N10  C15   122.09  3.000
 VNM  O     C    N     120.78  3.000
 VNM  O     C    C12   122.19  3.000
 VNM  N     C    C12   117.03  3.000
 VNM  H4    O1P  P     114.36  3.000
 VNM  H7    O3P  P     114.42  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
 VNM  CONST_01  C15   C16  C17  C12     0.00   0.0  0
 VNM  CONST_02  C15   C14  C13  C12     0.00   0.0  0
 VNM  CONST_03  C13   C14  C15  C16     0.00   0.0  0
 VNM  CONST_04  C13   C12  C17  C16     0.00   0.0  0
 VNM  CONST_05  C14   C15  C16  C17     0.00   0.0  0
 VNM  CONST_06  C14   C13  C12  C17     0.00   0.0  0
 VNM  CONST_07  C4A   C8A  N1"  C2"     0.00   0.0  0
 VNM  CONST_08  C4A   C4"  N3"  C2"     0.00   0.0  0
 VNM  CONST_09  N1"   C8A  C4A  C4"     0.00   0.0  0
 VNM  CONST_10  N1"   C2"  N3"  C4"     0.00   0.0  0
 VNM  CONST_11  N3"   C2"  N1"  C8A     0.00   0.0  0
 VNM  CONST_12  N3"   C4"  C4A  C8A     0.00   0.0  0
 VNM  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 VNM  CONST_14  N1    C2   N3   C4      0.00   0.0  0
 VNM  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 VNM  CONST_16  N3    C2   N1   C1'   180.00   0.0  0
 VNM  CONST_17  C17   C16  C15  N10   180.00   0.0  0
 VNM  CONST_18  C13   C14  C15  N10   180.00   0.0  0
 VNM  CONST_19  C     C12  C17  C16   180.00   0.0  0
 VNM  CONST_20  C14   C13  C12  C     180.00   0.0  0
 VNM  CONST_21  NA4   C4"  N3"  C2"   180.00   0.0  0
 VNM  CONST_22  NA2   C2"  N3"  C4"   180.00   0.0  0
 VNM  CONST_23  NA2   C2"  N1"  C8A   180.00   0.0  0
 VNM  CONST_24  NA4   C4"  C4A  C8A   180.00   0.0  0
 VNM  CONST_25  NA4   C4"  C4A  N5      0.00   0.0  0
 VNM  CONST_26  O4    C4   N3   C2    180.00   0.0  0
 VNM  CONST_27  O2    C2   N3   C4    180.00   0.0  0
 VNM  CONST_28  O2    C2   N1   C6    180.00   0.0  0
 VNM  CONST_29  O2    C2   N1   C1'     0.00   0.0  0
 VNM  CONST_30  H161  C16  C17  C12   180.00   0.0  0
 VNM  CONST_31  H141  C14  C13  C12   180.00   0.0  0
 VNM  CONST_32  H171  C17  C16  C15   180.00   0.0  0
 VNM  CONST_33  H131  C13  C14  C15   180.00   0.0  0
 VNM  CONST_34  H141  C14  C15  C16   180.00   0.0  0
 VNM  CONST_35  H131  C13  C12  C17   180.00   0.0  0
 VNM  CONST_36  H171  C17  C12  C13   180.00   0.0  0
 VNM  CONST_37  H161  C16  C15  C14   180.00   0.0  0
 VNM  CONST_38  HN3   N3   C4   C5    180.00   0.0  0
 VNM  CONST_39  HN3   N3   C2   N1    180.00   0.0  0
 VNM  CONST_44  HA42  NA4  C4"  C4A   180.00   0.0  0
 VNM  CONST_51  HA41  NA4  C4"  N3"   180.00   0.0  0
 VNM  CONST_52  HN3   N3   C2   O2      0.00   0.0  0
 VNM  CONST_53  HN3   N3   C4   O4      0.00   0.0  0
 VNM  CONST_54  CA    N    C    C12   180.00   0.0  0
 VNM  CONST_55  H     N    C    C12     0.00   0.0  0
 VNM  CONST_56  O     C    N    CA      0.00   0.0  0
 VNM  CONST_57  H     N    C    O     180.00   0.0  0
 VNM  CONST_58  H5    O2"  CT   CA    180.00   0.0  0
 VNM  CONST_59  H3    OE2  CD   CG    180.00   0.0  0
 VNM  CONST_60  H3    OE2  CD   OE1     0.00   0.0  0
 VNM  CONST_61  H5    O2"  CT   O1      0.00   0.0  0
 VNM  Var_01    N1"   C8A  C8   C7    177.02  30.0  1
 VNM  Var_02    C4A   C8A  C8   C7      1.09  30.0  1
 VNM  Var_03    C6"   N5   C4A  C4"  -142.19  30.0  1
 VNM  Var_04    C8A   C8   C7   C6"   -25.52  30.0  1
 VNM  Var_05    C8A   C4A  N5   C6"    33.39  30.0  1
 VNM  Var_06    N5    C11  C5   C4     88.34  30.0  1
 VNM  Var_07    C6"   N5   C11  C5    165.06  30.0  2
 VNM  Var_08    C4A   N5   C11  C5    -68.26  30.0  2
 VNM  Var_09    N5    C11  C5   C6    -90.71  30.0  1
 VNM  Var_10    C8A   C4A  N5   C11   -93.45  30.0  1
 VNM  Var_11    C4"   C4A  N5   C11    90.96  30.0  1
 VNM  Var_12    N3    C4   C5   C11  -174.83  30.0  1
 VNM  Var_13    N1    C6   C5   C11   177.24  30.0  1
 VNM  Var_14    H6    C6   N1   C2    175.60  30.0  1
 VNM  Var_15    H6    C6   C5   C4    179.07  30.0  1
 VNM  Var_16    H6    C6   N1   C1'    -1.50  30.0  1
 VNM  Var_17    H81   C8   C8A  C4A  -121.51  30.0  1
 VNM  Var_18    H82   C8   C8A  C4A   125.28  30.0  1
 VNM  Var_19    H81   C8   C7   C6"    94.86  30.0  1
 VNM  Var_20    H82   C8   C7   C6"  -149.08  30.0  1
 VNM  Var_21    H71   C7   C8   C8A    95.56  30.0  1
 VNM  Var_22    H72   C7   C8   C8A  -148.21  30.0  1
 VNM  Var_23    H81   C8   C8A  N1"    54.42  30.0  1
 VNM  Var_24    H82   C8   C8A  N1"   -58.79  30.0  1
 VNM  Var_25    O4    C4   C5   C11     5.38  30.0  1
 VNM  Var_26    C6"   C9   N10  C15  -166.63  30.0  2
 VNM  Var_27    N     C    C12  C17   163.02  30.0  2
 VNM  Var_28    O     C    C12  C17   -17.37  30.0  2
 VNM  Var_29    C13   C12  C    N     -19.77  30.0  2
 VNM  Var_30    C13   C12  C    O     159.84  30.0  2
 VNM  Var_31    H1    C11  C5   C4    -36.84  30.0  1
 VNM  Var_32    H2    C11  C5   C4   -152.86  30.0  1
 VNM  Var_33    H1    C11  C5   C6    144.11  30.0  1
 VNM  Var_34    H2    C11  C5   C6     28.09  30.0  1
 VNM  Var_35    H6    C6   C5   C11    -1.87  30.0  1
 VNM  Var_36    H1    C11  N5   C4A    55.52  30.0  3
 VNM  Var_37    H2    C11  N5   C4A   171.93  30.0  3
 VNM  Var_38    H1    C11  N5   C6"   -71.17  30.0  3
 VNM  Var_39    H2    C11  N5   C6"    45.25  30.0  3
 VNM  Var_40    P     O5'  C5'  C4'   142.64  30.0  3
 VNM  Var_41    H92   C9   N10  C15    74.31  30.0  2
 VNM  Var_42    H91   C9   N10  C15   -43.39  30.0  2
 VNM  Var_43    H101  N10  C9   C6"   -18.50  30.0  3
 VNM  Var_44    CD    CG   CB   CA   -173.51  30.0  1
 VNM  Var_45    OE1   CD   CG   CB     -0.06  30.0  3
 VNM  Var_46    OE2   CD   CG   CB   -179.95  30.0  3
 VNM  Var_47    O2P   P    O5'  C5'    41.49  30.0  3
 VNM  Var_48    O3P   P    O5'  C5'   169.64  30.0  3
 VNM  Var_49    O1P   P    O5'  C5'   -85.46  30.0  3
 VNM  Var_50    HG2   CG   CB   CA     65.63  30.0  1
 VNM  Var_51    HG3   CG   CB   CA    -52.01  30.0  1
 VNM  Var_52    HB2   CB   CG   CD    -52.62  30.0  3
 VNM  Var_53    HB3   CB   CG   CD     64.15  30.0  3
 VNM  Var_54    HG2   CG   CD   OE1   122.99  30.0  3
 VNM  Var_55    HG3   CG   CD   OE1  -123.73  30.0  3
 VNM  Var_56    HG2   CG   CD   OE2   -56.90  30.0  3
 VNM  Var_57    HG3   CG   CD   OE2    56.37  30.0  3
 VNM  Var_58    H5*1  C5'  O5'  P     -98.16  30.0  1
 VNM  Var_59    H5*2  C5'  O5'  P      20.72  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
 VNM  chir_01  CA   CB   N    CT   positiv
 VNM  chir_02  C1'  O4'  N1   C2'  negativ
 VNM  chir_03  C3'  O3'  C4'  C2'  positiv
 VNM  chir_04  C4'  O4'  C3'  C5'  negativ
 VNM  chir_05  C6"  C7   C9   N5   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
 VNM  plan-1  C2    0.020
 VNM  plan-1  C4    0.020
 VNM  plan-1  C5    0.020
 VNM  plan-1  C6    0.020
 VNM  plan-1  C1'   0.020
 VNM  plan-1  N1    0.020
 VNM  plan-1  N3    0.020
 VNM  plan-1  O2    0.020
 VNM  plan-1  O4    0.020
 VNM  plan-1  HN3   0.020
 VNM  plan-2  CG    0.020
 VNM  plan-2  CD    0.020
 VNM  plan-2  OE1   0.020
 VNM  plan-2  OE2   0.020
 VNM  plan-2  H3    0.020
 VNM  plan-3  CA    0.020
 VNM  plan-3  CT    0.020
 VNM  plan-3  O1    0.020
 VNM  plan-3  O2"   0.020
 VNM  plan-3  H5    0.020
 VNM  plan-4  C12   0.020
 VNM  plan-4  C15   0.020
 VNM  plan-4  C16   0.020
 VNM  plan-4  C17   0.020
 VNM  plan-4  C13   0.020
 VNM  plan-4  C14   0.020
 VNM  plan-4  H161  0.020
 VNM  plan-4  H171  0.020
 VNM  plan-4  H131  0.020
 VNM  plan-4  H141  0.020
 VNM  plan-4  N10   0.020
 VNM  plan-4  C     0.020
 VNM  plan-5  C4"   0.020
 VNM  plan-5  NA4   0.020
 VNM  plan-5  HA42  0.020
 VNM  plan-5  HA41  0.020
 VNM  plan-6  C2"   0.020
 VNM  plan-6  HA22  0.020
 VNM  plan-6  HA21  0.020
 VNM  plan-6  NA2   0.020
 VNM  plan-7  C8    0.020
 VNM  plan-7  C2"   0.020
 VNM  plan-7  C4"   0.020
 VNM  plan-7  C4A   0.020
 VNM  plan-7  C8A   0.020
 VNM  plan-7  N1"   0.020
 VNM  plan-7  N3"   0.020
 VNM  plan-7  N5    0.020
 VNM  plan-7  NA4   0.020
 VNM  plan-7  NA2   0.020
 VNM  plan-8  C15   0.020
 VNM  plan-8  C9    0.020
 VNM  plan-8  H101  0.020
 VNM  plan-8  N10   0.020
 VNM  plan-9  C12   0.020
 VNM  plan-9  N     0.020
 VNM  plan-9  CA    0.020
 VNM  plan-9  O     0.020
 VNM  plan-9  H     0.020
 VNM  plan-9  C     0.020

