# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:46:49 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-3-azanyl-propane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 VMX  VMX  N-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-3-azanyl-propane-1-sulfonamide  ligand  47  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VMX
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
 VMX  S     S  S     0   1.369  -3.7697   0.4760   0.8673
 VMX  N1    N  N     0  -0.474   5.0292  -2.1169   0.4833
 VMX  C2    C  CR16  0   0.048   5.0854  -0.8001   0.6618
 VMX  N3    N  N     0  -0.457   4.1241   0.0930   0.5011
 VMX  C4    C  CR56  0   0.495   2.9859  -0.4755   0.1137
 VMX  C5    C  CR56  0  -0.012   2.7724  -1.8260  -0.1101
 VMX  C6    C  CR6   0   0.461   3.8774  -2.6739   0.0920
 VMX  N6    N  NH2   0  -0.815   3.8210  -3.9920  -0.0987
 VMX  N7    N  N     0  -0.444   1.4757  -2.0581  -0.4934
 VMX  C8    C  CR15  0   0.121   0.9283  -0.8814  -0.5049
 VMX  N9    N  NR5   0  -0.540   1.7868   0.1243  -0.1497
 VMX  C1'   C  CH1   0   0.212   1.4941   1.5298  -0.0547
 VMX  C10   C  CH2   0  -0.438  -4.6009  -1.8370  -0.3594
 VMX  C11   C  CH2   0  -0.269  -4.2207  -3.1166  -1.0944
 VMX  N12   N  NH2   0  -0.799  -5.4090  -3.9044  -1.3769
 VMX  C1S   C  CH2   0  -0.634  -3.3672  -0.9921  -0.0761
 VMX  C2'   C  CH1   0  -0.054   1.0637   2.1635  -1.3787
 VMX  O2'   O  OH1   0  -0.651   2.1922   2.5289  -2.1121
 VMX  O2S   O  OS    0  -0.670  -4.6552   1.3078   0.0653
 VMX  C3'   C  CH1   0  -0.020   0.2037   3.3286  -0.8835
 VMX  O3'   O  OH1   0  -0.666   1.0051   4.3762  -0.4065
 VMX  O3S   O  OS    0  -0.665  -4.1869   0.0597   2.1971
 VMX  C4'   C  CH1   0  -0.037  -0.5011   2.6848   0.3030
 VMX  O4'   O  O2    0  -0.496   0.4253   1.7301   0.8325
 VMX  C5'   C  CH2   0  -0.288  -1.7942   1.9985  -0.1038
 VMX  N5'   N  NC1   0  -0.740  -2.3631   1.3172   1.0522
 VMX  HN6   H  HNH2  0   0.404   4.6164  -4.5681   0.1163
 VMX  HN6A  H  HNH2  0   0.412   2.9580  -4.4454  -0.3420
 VMX  H8    H  HCR5  0   0.275  -0.1011  -0.6843  -0.7649
 VMX  H1'   H  HCH1  0   0.270   2.4086   2.0069   0.3120
 VMX  H10   H  HCH2  0   0.250  -5.3131  -1.2717  -0.9628
 VMX  H10A  H  HCH2  0   0.246  -5.0951  -2.0954   0.5806
 VMX  H11   H  HCH2  0   0.224  -3.7467  -2.8565  -2.0442
 VMX  H11A  H  HCH2  0   0.200  -3.4638  -3.6534  -0.5047
 VMX  HN12  H  HNH2  0   0.351  -5.1470  -4.7260  -1.9063
 VMX  HN1A  H  HNH2  0   0.341  -5.7937  -4.2529  -0.5072
 VMX  H1S   H  HCH2  0   0.292  -2.8969  -0.6613  -1.0051
 VMX  H1SA  H  HCH2  0   0.294  -2.6308  -1.5456   0.5107
 VMX  H2'   H  HCH1  0   0.253   0.4289   1.4650  -1.9387
 VMX  HO2'  H  HOH1  0   0.471   1.9408   2.6487  -3.0336
 VMX  H3'   H  HCH1  0   0.259  -0.5075   3.6712  -1.6464
 VMX  HO3'  H  HOH1  0   0.452   1.6940   4.5465  -1.0596
 VMX  H4'   H  HCH1  0   0.281  -0.7170   3.4210   1.0818
 VMX  H5'   H  HCH2  0   0.287  -2.4898   2.7634  -0.4466
 VMX  H5'A  H  HCH2  0   0.234  -1.6170   1.3188  -0.9469
 VMX  HN5'  H  HNC1  0   0.413  -1.6889   0.8070   1.6153
 VMX  H2    H  HCR6  0   0.254   6.0476  -0.4135   0.9797

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
 VMX  S    C1S   single    1.791  0.020  1.791
 VMX  S    O2S   double    1.456  0.020  1.456
 VMX  S    O3S   double    1.455  0.020  1.455
 VMX  S    N5'   single    1.649  0.020  1.649
 VMX  N1   C2    aromatic  1.330  0.020  1.330
 VMX  N1   C6    aromatic  1.338  0.020  1.338
 VMX  C2   N3    aromatic  1.322  0.020  1.322
 VMX  N3   C4    aromatic  1.330  0.020  1.330
 VMX  C4   C5    aromatic  1.386  0.020  1.386
 VMX  C4   N9    aromatic  1.366  0.020  1.366
 VMX  C5   C6    aromatic  1.407  0.020  1.407
 VMX  C5   N7    aromatic  1.372  0.020  1.372
 VMX  C6   N6    single    1.333  0.020  1.333
 VMX  N7   C8    aromatic  1.298  0.020  1.298
 VMX  C8   N9    aromatic  1.369  0.020  1.369
 VMX  N9   C1'   single    1.439  0.020  1.439
 VMX  C1'  C2'   single    1.530  0.020  1.530
 VMX  C1'  O4'   single    1.403  0.020  1.403
 VMX  C10  C11   single    1.524  0.020  1.524
 VMX  C10  C1S   single    1.522  0.020  1.522
 VMX  C11  N12   single    1.453  0.020  1.453
 VMX  C2'  O2'   single    1.395  0.020  1.395
 VMX  C2'  C3'   single    1.530  0.020  1.530
 VMX  C3'  O3'   single    1.403  0.020  1.403
 VMX  C3'  C4'   single    1.523  0.020  1.523
 VMX  C4'  O4'   single    1.432  0.020  1.432
 VMX  C4'  C5'   single    1.519  0.020  1.519
 VMX  C5'  N5'   single    1.457  0.020  1.457
 VMX  C2   H2    single    0.930  0.020  1.080
 VMX  N6   HN6   single    0.860  0.020  1.020
 VMX  N6   HN6A  single    0.860  0.020  1.020
 VMX  C8   H8    single    0.930  0.020  1.080
 VMX  C1'  H1'   single    0.970  0.020  1.090
 VMX  C10  H10   single    0.970  0.020  1.090
 VMX  C10  H10A  single    0.970  0.020  1.090
 VMX  C11  H11   single    0.970  0.020  1.090
 VMX  C11  H11A  single    0.970  0.020  1.090
 VMX  N12  HN12  single    0.890  0.020  1.040
 VMX  N12  HN1A  single    0.890  0.020  1.040
 VMX  C1S  H1S   single    0.970  0.020  1.090
 VMX  C1S  H1SA  single    0.970  0.020  1.090
 VMX  C2'  H2'   single    0.970  0.020  1.090
 VMX  O2'  HO2'  single    0.850  0.020  0.980
 VMX  C3'  H3'   single    0.970  0.020  1.090
 VMX  O3'  HO3'  single    0.850  0.020  0.980
 VMX  C4'  H4'   single    0.970  0.020  1.090
 VMX  C5'  H5'   single    0.970  0.020  1.090
 VMX  C5'  H5'A  single    0.970  0.020  1.090
 VMX  N5'  HN5'  single    0.890  0.020  1.040

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
 VMX  N5'   S    O3S   106.75  3.000
 VMX  N5'   S    O2S   106.81  3.000
 VMX  O3S   S    O2S   119.52  3.000
 VMX  N5'   S    C1S   106.59  3.000
 VMX  O3S   S    C1S   108.15  3.000
 VMX  O2S   S    C1S   108.35  3.000
 VMX  C6    N1   C2    119.19  3.000
 VMX  H2    C2   N3    116.10  3.000
 VMX  H2    C2   N1    115.45  3.000
 VMX  N3    C2   N1    128.45  3.000
 VMX  C4    N3   C2    111.65  3.000
 VMX  N9    C4   C5    105.16  3.000
 VMX  N9    C4   N3    128.28  3.000
 VMX  C5    C4   N3    126.56  3.000
 VMX  N7    C5   C6    132.87  3.000
 VMX  N7    C5   C4    110.83  3.000
 VMX  C6    C5   C4    116.30  3.000
 VMX  N6    C6   C5    122.82  3.000
 VMX  N6    C6   N1    119.33  3.000
 VMX  C5    C6   N1    117.85  3.000
 VMX  HN6A  N6   HN6   118.21  3.000
 VMX  HN6A  N6   C6    121.14  3.000
 VMX  HN6   N6   C6    120.18  3.000
 VMX  C8    N7   C5    104.35  3.000
 VMX  H8    C8   N9    121.74  3.000
 VMX  H8    C8   N7    124.73  3.000
 VMX  N9    C8   N7    113.53  3.000
 VMX  C1'   N9   C8    127.38  3.000
 VMX  C1'   N9   C4    126.49  3.000
 VMX  C8    N9   C4    106.13  3.000
 VMX  H1'   C1'  O4'   111.24  3.000
 VMX  H1'   C1'  C2'   110.15  3.000
 VMX  O4'   C1'  C2'   105.89  3.000
 VMX  H1'   C1'  N9    106.13  3.000
 VMX  O4'   C1'  N9    109.64  3.000
 VMX  C2'   C1'  N9    113.88  3.000
 VMX  H10A  C10  H10   107.63  3.000
 VMX  H10A  C10  C1S   109.74  3.000
 VMX  H10   C10  C1S   110.15  3.000
 VMX  H10A  C10  C11   109.21  3.000
 VMX  H10   C10  C11   109.34  3.000
 VMX  C1S   C10  C11   110.72  3.000
 VMX  H11A  C11  H11   106.48  3.000
 VMX  H11A  C11  N12   113.74  3.000
 VMX  H11   C11  N12   108.34  3.000
 VMX  H11A  C11  C10   108.85  3.000
 VMX  H11   C11  C10   109.11  3.000
 VMX  N12   C11  C10   110.18  3.000
 VMX  HN1A  N12  HN12  105.56  3.000
 VMX  HN1A  N12  C11   109.28  3.000
 VMX  HN12  N12  C11   109.27  3.000
 VMX  H1SA  C1S  H1S   108.67  3.000
 VMX  H1SA  C1S  C10   111.43  3.000
 VMX  H1S   C1S  C10   111.02  3.000
 VMX  H1SA  C1S  S     106.49  3.000
 VMX  H1S   C1S  S     107.24  3.000
 VMX  C10   C1S  S     111.78  3.000
 VMX  H2'   C2'  C3'   108.94  3.000
 VMX  H2'   C2'  O2'   111.50  3.000
 VMX  C3'   C2'  O2'   115.18  3.000
 VMX  H2'   C2'  C1'   109.92  3.000
 VMX  C3'   C2'  C1'   101.15  3.000
 VMX  O2'   C2'  C1'   109.64  3.000
 VMX  HO2'  O2'  C2'   108.95  3.000
 VMX  H3'   C3'  C4'   111.94  3.000
 VMX  H3'   C3'  O3'   111.93  3.000
 VMX  C4'   C3'  O3'   108.37  3.000
 VMX  H3'   C3'  C2'   112.13  3.000
 VMX  C4'   C3'  C2'   100.97  3.000
 VMX  O3'   C3'  C2'   110.95  3.000
 VMX  HO3'  O3'  C3'   108.04  3.000
 VMX  H4'   C4'  C5'   109.08  3.000
 VMX  H4'   C4'  O4'   108.26  3.000
 VMX  C5'   C4'  O4'   110.39  3.000
 VMX  H4'   C4'  C3'   111.21  3.000
 VMX  C5'   C4'  C3'   112.10  3.000
 VMX  O4'   C4'  C3'   105.70  3.000
 VMX  C4'   O4'  C1'   110.74  3.000
 VMX  H5'A  C5'  H5'   107.23  3.000
 VMX  H5'A  C5'  N5'   112.51  3.000
 VMX  H5'   C5'  N5'   109.19  3.000
 VMX  H5'A  C5'  C4'   110.37  3.000
 VMX  H5'   C5'  C4'   108.09  3.000
 VMX  N5'   C5'  C4'   109.33  3.000
 VMX  HN5'  N5'  C5'   114.54  3.000
 VMX  HN5'  N5'  S     111.84  3.000
 VMX  C5'   N5'  S     118.84  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
 VMX  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 VMX  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 VMX  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 VMX  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 VMX  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 VMX  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 VMX  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 VMX  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 VMX  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 VMX  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 VMX  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 VMX  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 VMX  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 VMX  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 VMX  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 VMX  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 VMX  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 VMX  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 VMX  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 VMX  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 VMX  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 VMX  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 VMX  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 VMX  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 VMX  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 VMX  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 VMX  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 VMX  Var_01    C4'   C5'  N5'  S    -179.30  30.0  1
 VMX  Var_02    C11   C10  C1S  S    -176.83  30.0  2
 VMX  Var_03    O2S   S    C1S  C10   -63.35  30.0  1
 VMX  Var_04    C1S   C10  C11  N12  -179.14  30.0  2
 VMX  Var_05    C5'   N5'  S    C1S    71.95  30.0  3
 VMX  Var_06    HN12  N12  C11  C10   177.09  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
 VMX  chir_01  C1'  N9   C2'  O4'  negativ
 VMX  chir_02  C2'  O2'  C3'  C1'  positiv
 VMX  chir_03  C3'  O3'  C4'  C2'  positiv
 VMX  chir_04  C4'  O4'  C3'  C5'  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
 VMX  plan-1  N1    0.020
 VMX  plan-1  C2    0.020
 VMX  plan-1  N3    0.020
 VMX  plan-1  C4    0.020
 VMX  plan-1  C5    0.020
 VMX  plan-1  C6    0.020
 VMX  plan-1  N6    0.020
 VMX  plan-1  N7    0.020
 VMX  plan-1  C8    0.020
 VMX  plan-1  N9    0.020
 VMX  plan-1  C1'   0.020
 VMX  plan-1  H8    0.020
 VMX  plan-1  H2    0.020
 VMX  plan-2  C6    0.020
 VMX  plan-2  N6    0.020
 VMX  plan-2  HN6   0.020
 VMX  plan-2  HN6A  0.020

