# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 04:50:26 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5'-O-(L-valylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N[S](=O)(=O)OC[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
 VMS  VMS  5'-O-(L-valylsulfamoyl)adenosine  L-peptide  53  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VMS
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
 VMS  CG2   C  CH3   0  -0.670   4.9459  -2.7851  -0.1727
 VMS  CB    C  CH1   0  -0.255   3.5717  -3.1991   0.3470
 VMS  CG1   C  CH3   0  -0.664   3.6984  -4.3434   1.3459
 VMS  CA    C  CH1   0  -0.192   2.8436  -2.0064   0.9933
 VMS  N     N  NH2   0  -0.785   1.5103  -2.2609   1.5063
 VMS  C     C  C     0   0.601   2.6991  -0.8851  -0.0223
 VMS  O     O  O     0  -0.415   2.0355  -0.9827  -1.0256
 VMS  NAS   N  NC1   0  -0.838   3.3729   0.2746   0.2983
 VMS  SBD   S  S     0   1.629   3.4428   1.6119  -0.6902
 VMS  OAZ   O  OS    0  -0.630   4.2105   2.5805   0.0505
 VMS  OBC   O  OS    0  -0.608   3.8075   1.2299  -2.0247
 VMS  O5'   O  OC2   0  -0.565   1.9306   2.0662  -0.8031
 VMS  C5'   C  CH2   0  -0.193   1.2536   2.5536   0.3699
 VMS  C4'   C  CH1   0  -0.038  -0.1254   2.9863  -0.0798
 VMS  O4'   O  O2    0  -0.484  -0.8221   1.8936  -0.6729
 VMS  C3'   C  CH1   0  -0.041  -0.9785   3.4578   1.0949
 VMS  O3'   O  OH1   0  -0.663  -1.8733   4.4283   0.6235
 VMS  C2'   C  CH1   0  -0.046  -1.7136   2.1654   1.4649
 VMS  O2'   O  OH1   0  -0.651  -2.9263   2.3459   2.1279
 VMS  C1'   C  CH1   0   0.211  -1.9587   1.5658   0.0824
 VMS  N9    N  NR5   0  -0.543  -2.1381   0.1407   0.0774
 VMS  C8    C  CR15  0   0.121  -1.2549  -0.8108   0.5152
 VMS  N7    N  N     0  -0.457  -1.6803  -2.0253   0.3403
 VMS  C5    C  CR56  0  -0.009  -2.9119  -1.8774  -0.2467
 VMS  C4    C  CR56  0   0.489  -3.2139  -0.5373  -0.4248
 VMS  N3    N  N     0  -0.457  -4.3206  -0.0406  -0.9695
 VMS  C2    C  CR16  0   0.046  -5.1532  -0.9975  -1.3430
 VMS  N1    N  N     0  -0.474  -5.0026  -2.3140  -1.2314
 VMS  C6    C  CR6   0   0.461  -3.8825  -2.7982  -0.6822
 VMS  N6    N  NH2   0  -0.817  -3.7284  -4.1175  -0.5682
 VMS  HG21  H  HCH3  0   0.233   4.8891  -2.0312  -0.9598
 VMS  HG22  H  HCH3  0   0.224   5.5636  -2.3815   0.6333
 VMS  HG23  H  HCH3  0   0.242   5.4725  -3.6426  -0.5916
 VMS  HB    H  HCH1  0   0.234   2.9640  -3.5413  -0.4986
 VMS  HG11  H  HCH3  0   0.221   4.2711  -4.0353   2.2243
 VMS  HG12  H  HCH3  0   0.229   2.7272  -4.7029   1.6863
 VMS  HG13  H  HCH3  0   0.239   4.2172  -5.1896   0.8946
 VMS  HA    H  HCH1  0   0.262   3.4534  -1.6597   1.8342
 VMS  H     H  HNH2  0   0.356   0.9530  -2.7665   0.8276
 VMS  H2    H  HNH2  0   0.368   1.5610  -2.8404   2.3337
 VMS  HAS   H  HNC1  0   0.456   3.8770   0.3493   1.1742
 VMS  H5'1  H  HCH2  0   0.251   1.2091   1.7646   1.1270
 VMS  H5'2  H  HCH2  0   0.280   1.7861   3.4108   0.7851
 VMS  H4'   H  HCH1  0   0.282  -0.0177   3.7851  -0.8198
 VMS  H3'   H  HCH1  0   0.262  -0.3680   3.8354   1.9257
 VMS  HO3'  H  HOH1  0   0.453  -2.5959   4.5039   1.2576
 VMS  H1    H  HCH1  0   0.252  -1.0333   1.5188   2.0343
 VMS  H2'   H  HOH1  0   0.471  -2.7590   2.4131   3.0732
 VMS  H1'   H  HCH1  0   0.265  -2.8695   1.9882  -0.3563
 VMS  H8    H  HCR5  0   0.287  -0.3018  -0.5609   0.9577
 VMS  H3    H  HCR6  0   0.253  -6.0817  -0.6716  -1.7993
 VMS  HN61  H  HNH2  0   0.412  -2.8979  -4.5118  -0.1633
 VMS  HN62  H  HNH2  0   0.404  -4.4468  -4.7430  -0.8895

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
 VMS  CG2  CB    single    1.526  0.020  1.526
 VMS  CG2  HG21  single    0.970  0.020  1.090
 VMS  CG2  HG22  single    0.970  0.020  1.090
 VMS  CG2  HG23  single    0.970  0.020  1.090
 VMS  CB   CG1   single    1.524  0.020  1.524
 VMS  CB   CA    single    1.521  0.033  1.521
 VMS  CB   HB    single    0.970  0.020  1.090
 VMS  CG1  HG11  single    0.970  0.020  1.090
 VMS  CG1  HG12  single    0.970  0.020  1.090
 VMS  CG1  HG13  single    0.970  0.020  1.090
 VMS  CA   N     single    1.458  0.019  1.458
 VMS  CA   C     single    1.525  0.021  1.525
 VMS  CA   HA    single    0.970  0.020  0.970
 VMS  N    H     single    0.860  0.020  0.860
 VMS  N    H2    single    0.890  0.020  1.040
 VMS  C    O     double    1.231  0.020  1.231
 VMS  C    NAS   single    1.379  0.020  1.379
 VMS  NAS  SBD   single    1.664  0.020  1.664
 VMS  NAS  HAS   single    0.860  0.020  1.020
 VMS  SBD  OAZ   deloc     1.441  0.020  1.441
 VMS  SBD  OBC   deloc     1.435  0.020  1.435
 VMS  SBD  O5'   single    1.583  0.020  1.583
 VMS  O5'  C5'   single    1.439  0.020  1.439
 VMS  C5'  C4'   single    1.514  0.020  1.514
 VMS  C5'  H5'1  single    0.970  0.020  1.090
 VMS  C5'  H5'2  single    0.970  0.020  1.090
 VMS  C4'  O4'   single    1.425  0.020  1.425
 VMS  C4'  C3'   single    1.526  0.020  1.526
 VMS  C4'  H4'   single    0.970  0.020  1.090
 VMS  O4'  C1'   single    1.403  0.020  1.403
 VMS  C3'  O3'   single    1.402  0.020  1.402
 VMS  C3'  C2'   single    1.532  0.020  1.532
 VMS  C3'  H3'   single    0.970  0.020  1.090
 VMS  O3'  HO3'  single    0.850  0.020  0.980
 VMS  C2'  O2'   single    1.394  0.020  1.394
 VMS  C2'  C1'   single    1.527  0.020  1.527
 VMS  C2'  H1    single    0.970  0.020  1.090
 VMS  O2'  H2'   single    0.850  0.020  0.980
 VMS  C1'  N9    single    1.436  0.020  1.436
 VMS  C1'  H1'   single    0.970  0.020  1.090
 VMS  N9   C8    aromatic  1.370  0.020  1.370
 VMS  N9   C4    aromatic  1.367  0.020  1.367
 VMS  C8   N7    aromatic  1.299  0.020  1.299
 VMS  C8   H8    single    0.930  0.020  1.080
 VMS  N7   C5    aromatic  1.372  0.020  1.372
 VMS  C5   C4    aromatic  1.385  0.020  1.385
 VMS  C5   C6    aromatic  1.407  0.020  1.407
 VMS  C4   N3    aromatic  1.330  0.020  1.330
 VMS  N3   C2    aromatic  1.322  0.020  1.322
 VMS  C2   N1    aromatic  1.330  0.020  1.330
 VMS  C2   H3    single    0.930  0.020  1.080
 VMS  N1   C6    aromatic  1.338  0.020  1.338
 VMS  C6   N6    single    1.333  0.020  1.333
 VMS  N6   HN61  single    0.860  0.020  1.020
 VMS  N6   HN62  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
 VMS  HG23  CG2  HG22  107.51  3.000
 VMS  HG23  CG2  HG21  106.94  3.000
 VMS  HG22  CG2  HG21  107.84  3.000
 VMS  HG23  CG2  CB    110.63  3.000
 VMS  HG22  CG2  CB    110.97  3.000
 VMS  HG21  CG2  CB    112.71  3.000
 VMS  HB    CB   CA    107.67  3.000
 VMS  HB    CB   CG1   108.50  3.000
 VMS  CA    CB   CG1   110.23  3.000
 VMS  HB    CB   CG2   108.74  3.000
 VMS  CA    CB   CG2   111.01  3.000
 VMS  CG1   CB   CG2   110.61  3.000
 VMS  HG13  CG1  HG12  107.28  3.000
 VMS  HG13  CG1  HG11  107.58  3.000
 VMS  HG12  CG1  HG11  107.99  3.000
 VMS  HG13  CG1  CB    110.54  3.000
 VMS  HG12  CG1  CB    112.22  3.000
 VMS  HG11  CG1  CB    111.02  3.000
 VMS  HA    CA   C     110.00  3.000
 VMS  HA    CA   N     110.00  3.000
 VMS  C     CA   N     111.00  2.800
 VMS  HA    CA   CB    109.00  3.000
 VMS  C     CA   CB    110.50  1.500
 VMS  N     CA   CB    110.40  1.500
 VMS  H2    N    H     106.84  3.000
 VMS  H2    N    CA    110.10  3.000
 VMS  H     N    CA    114.00  3.000
 VMS  NAS   C    O     122.00  3.000
 VMS  NAS   C    CA    114.75  3.000
 VMS  O     C    CA    120.80  1.700
 VMS  HAS   NAS  SBD   115.67  3.000
 VMS  HAS   NAS  C     120.39  3.000
 VMS  SBD   NAS  C     123.93  3.000
 VMS  O5'   SBD  OBC   104.64  3.000
 VMS  O5'   SBD  OAZ   110.65  3.000
 VMS  OBC   SBD  OAZ   121.43  3.000
 VMS  O5'   SBD  NAS   103.46  3.000
 VMS  OBC   SBD  NAS   110.43  3.000
 VMS  OAZ   SBD  NAS   104.91  3.000
 VMS  C5'   O5'  SBD   119.23  3.000
 VMS  H5'2  C5'  H5'1  108.85  3.000
 VMS  H5'2  C5'  C4'   109.45  3.000
 VMS  H5'1  C5'  C4'   111.99  3.000
 VMS  H5'2  C5'  O5'   110.28  3.000
 VMS  H5'1  C5'  O5'   109.80  3.000
 VMS  C4'   C5'  O5'   106.45  3.000
 VMS  H4'   C4'  C3'   110.49  3.000
 VMS  H4'   C4'  O4'   109.05  3.000
 VMS  C3'   C4'  O4'   106.49  3.000
 VMS  H4'   C4'  C5'   108.66  3.000
 VMS  C3'   C4'  C5'   111.64  3.000
 VMS  O4'   C4'  C5'   110.48  3.000
 VMS  C1'   O4'  C4'   110.55  3.000
 VMS  H3'   C3'  C2'   111.97  3.000
 VMS  H3'   C3'  O3'   111.80  3.000
 VMS  C2'   C3'  O3'   111.04  3.000
 VMS  H3'   C3'  C4'   112.19  3.000
 VMS  C2'   C3'  C4'   101.16  3.000
 VMS  O3'   C3'  C4'   108.17  3.000
 VMS  HO3'  O3'  C3'   108.14  3.000
 VMS  H1    C2'  C1'   109.74  3.000
 VMS  H1    C2'  O2'   111.64  3.000
 VMS  C1'   C2'  O2'   109.99  3.000
 VMS  H1    C2'  C3'   108.95  3.000
 VMS  C1'   C2'  C3'   100.93  3.000
 VMS  O2'   C2'  C3'   115.03  3.000
 VMS  H2'   O2'  C2'   108.97  3.000
 VMS  H1'   C1'  N9    106.10  3.000
 VMS  H1'   C1'  C2'   110.15  3.000
 VMS  N9    C1'  C2'   114.38  3.000
 VMS  H1'   C1'  O4'   111.57  3.000
 VMS  N9    C1'  O4'   109.33  3.000
 VMS  C2'   C1'  O4'   105.40  3.000
 VMS  C4    N9   C8    106.27  3.000
 VMS  C4    N9   C1'   126.27  3.000
 VMS  C8    N9   C1'   127.40  3.000
 VMS  H8    C8   N7    124.09  3.000
 VMS  H8    C8   N9    122.62  3.000
 VMS  N7    C8   N9    113.28  3.000
 VMS  C5    N7   C8    104.52  3.000
 VMS  C6    C5   C4    116.29  3.000
 VMS  C6    C5   N7    132.92  3.000
 VMS  C4    C5   N7    110.79  3.000
 VMS  N3    C4   C5    126.55  3.000
 VMS  N3    C4   N9    128.32  3.000
 VMS  C5    C4   N9    105.13  3.000
 VMS  C2    N3   C4    111.68  3.000
 VMS  H3    C2   N1    115.45  3.000
 VMS  H3    C2   N3    116.13  3.000
 VMS  N1    C2   N3    128.42  3.000
 VMS  C6    N1   C2    119.17  3.000
 VMS  N6    C6   N1    119.34  3.000
 VMS  N6    C6   C5    122.78  3.000
 VMS  N1    C6   C5    117.88  3.000
 VMS  HN62  N6   HN61  118.38  3.000
 VMS  HN62  N6   C6    120.39  3.000
 VMS  HN61  N6   C6    121.23  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
 VMS  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 VMS  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 VMS  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 VMS  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 VMS  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 VMS  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 VMS  CONST_07  C4    C5   N7   C8     0.00   0.0  0
 VMS  CONST_08  C6    C5   N7   C8   180.00   0.0  0
 VMS  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 VMS  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 VMS  CONST_11  N1    C6   C5   N7   180.00   0.0  0
 VMS  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 VMS  CONST_13  C2    N1   C6   C5     0.00   0.0  0
 VMS  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 VMS  CONST_15  N1    C2   N3   C4     0.00   0.0  0
 VMS  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 VMS  CONST_17  C6    N1   C2   N3     0.00   0.0  0
 VMS  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 VMS  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 VMS  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 VMS  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 VMS  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 VMS  CONST_23  N6    C6   N1   C2   180.00   0.0  0
 VMS  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 VMS  CONST_25  H3    C2   N3   C4   180.00   0.0  0
 VMS  CONST_26  HN61  N6   C6   C5     0.00   0.0  0
 VMS  CONST_27  HN62  N6   C6   C5   180.00   0.0  0
 VMS  CONST_28  SBD   NAS  C    CA   180.00   0.0  0
 VMS  CONST_29  SBD   NAS  C    O      0.00   0.0  0
 VMS  CONST_30  HAS   NAS  C    CA     0.00   0.0  0
 VMS  Var_01    C4'   C5'  O5'  SBD  176.37  30.0  3
 VMS  Var_02    OAZ   SBD  NAS  C    178.59  30.0  3
 VMS  Var_03    HG11  CG1  CB   CG2   62.69  30.0  3
 VMS  Var_04    HG21  CG2  CB   CG1  174.64  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
 VMS  chir_01  CA   CB   N    C    positiv
 VMS  chir_02  C4'  O4'  C5'  C3'  positiv
 VMS  chir_03  C3'  O3'  C4'  C2'  positiv
 VMS  chir_04  C2'  O2'  C3'  C1'  positiv
 VMS  chir_05  C1'  O4'  N9   C2'  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
 VMS  plan-1  C1'   0.020
 VMS  plan-1  N9    0.020
 VMS  plan-1  C8    0.020
 VMS  plan-1  N7    0.020
 VMS  plan-1  C5    0.020
 VMS  plan-1  C4    0.020
 VMS  plan-1  N3    0.020
 VMS  plan-1  C2    0.020
 VMS  plan-1  N1    0.020
 VMS  plan-1  C6    0.020
 VMS  plan-1  N6    0.020
 VMS  plan-1  H8    0.020
 VMS  plan-1  H3    0.020
 VMS  plan-2  C6    0.020
 VMS  plan-2  N6    0.020
 VMS  plan-2  HN61  0.020
 VMS  plan-2  HN62  0.020
 VMS  plan-3  CA    0.020
 VMS  plan-3  C     0.020
 VMS  plan-3  O     0.020
 VMS  plan-3  NAS   0.020
 VMS  plan-3  SBD   0.020
 VMS  plan-3  HAS   0.020

