# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 22:39:55 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3cc(CO)cc(N)c23
#
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
 RUZ  RUZ  '[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'  ligand  54  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RUZ
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
 RUZ  C1   C  CR16  0  -0.398  -11.4530  -32.8304   0.6618
 RUZ  C2   C  CR6   0   0.029  -12.2567  -32.4082   1.7317
 RUZ  C3   C  CR16  0  -0.411  -11.8710  -31.3393   2.5150
 RUZ  C4   C  CR56  0   0.137  -10.6529  -30.7272   2.2102
 RUZ  C5   C  CR56  0   0.276   -9.8377  -31.1756   1.1612
 RUZ  C6   C  CR6   0   0.291  -10.2374  -32.2394   0.3342
 RUZ  C8   C  CR15  0   0.102   -8.9578  -29.4545   2.2071
 RUZ  N    N  NH2   0  -0.773  -11.4533  -30.4862  -5.7465
 RUZ  CA   C  CH1   0  -0.259  -10.0878  -30.8743  -5.9817
 RUZ  CB   C  CH2   0  -0.159   -9.1964  -29.6506  -6.1639
 RUZ  OG   O  OH1   0  -0.660   -9.0648  -29.0237  -4.9097
 RUZ  C    C  C     0   0.569   -9.5099  -31.7579  -4.8730
 RUZ  O    O  O     0  -0.405  -10.0847  -32.0202  -3.8473
 RUZ  N3S  N  NC1   0  -0.833   -8.2392  -32.2351  -5.1396
 RUZ  S    S  S     0   1.635   -7.3537  -33.1731  -4.0945
 RUZ  O1S  O  OS    0  -0.631   -6.0735  -33.3361  -4.7351
 RUZ  O2S  O  OS    0  -0.605   -8.1095  -34.3078  -3.6457
 RUZ  O5'  O  OC2   0  -0.576   -7.2205  -32.2549  -2.8101
 RUZ  C4'  C  CH1   0   0.012   -6.4065  -30.4337  -1.5067
 RUZ  O4'  O  O2    0  -0.496   -7.6751  -30.1836  -0.9054
 RUZ  C1'  C  CH1   0   0.184   -7.4890  -30.3394   0.4812
 RUZ  C2'  C  CH1   0  -0.000   -6.6331  -31.6024   0.5845
 RUZ  O2'  O  OH1   0  -0.659   -6.0076  -31.7510   1.8220
 RUZ  C3'  C  CH1   0  -0.051   -5.6174  -31.3424  -0.5380
 RUZ  O3'  O  OH1   0  -0.662   -4.5037  -30.6182  -0.0860
 RUZ  N7   N  NR5   0  -0.566   -8.7349  -30.3253   1.1832
 RUZ  N9   N  N     0  -0.471  -10.0703  -29.6510   2.8400
 RUZ  N6   N  NH2   0  -0.872   -9.4691  -32.7140  -0.7083
 RUZ  C2M  C  CH2   0  -0.182  -13.5267  -33.1730   1.9944
 RUZ  O2M  O  OH1   0  -0.667  -14.3856  -32.4290   2.8205
 RUZ  H1   H  HCR6  0   0.248  -11.7999  -33.6521   0.0432
 RUZ  H2   H  HCR6  0   0.243  -12.4738  -30.9733   3.3342
 RUZ  H3   H  HCR5  0   0.297   -8.2343  -28.6862   2.4411
 RUZ  H5   H  HNH2  0   0.350  -11.5420  -30.0167  -4.8543
 RUZ  H7   H  HCH1  0   0.297  -10.0449  -31.4466  -6.9147
 RUZ  H8   H  HCH2  0   0.212   -8.2238  -29.9445  -6.5756
 RUZ  H9   H  HCH2  0   0.236   -9.6723  -28.9993  -6.9047
 RUZ  H10  H  HOH1  0   0.467   -8.5155  -28.2409  -5.0130
 RUZ  H11  H  HNC1  0   0.455   -7.7872  -32.0309  -6.0234
 RUZ  H12  H  HCH2  0   0.278   -5.6021  -31.0548  -3.3706
 RUZ  H13  H  HCH2  0   0.278   -7.2059  -30.2917  -3.4982
 RUZ  H14  H  HCH1  0   0.278   -5.8587  -29.4886  -1.6120
 RUZ  H15  H  HCH1  0   0.265   -6.9137  -29.4982   0.8901
 RUZ  H16  H  HCH1  0   0.257   -7.2406  -32.4740   0.3187
 RUZ  H17  H  HOH1  0   0.468   -6.5367  -32.3324   2.3748
 RUZ  H18  H  HCH1  0   0.253   -5.3098  -32.2794  -1.0153
 RUZ  H19  H  HOH1  0   0.456   -4.0442  -31.1510   0.5721
 RUZ  H20  H  HNH2  0   0.381   -8.9708  -32.0102  -1.2282
 RUZ  H21  H  HNH2  0   0.379   -9.9671  -33.3197  -1.3426
 RUZ  H22  H  HCH2  0   0.210  -14.0002  -33.4160   1.0336
 RUZ  H23  H  HCH2  0   0.219  -13.2632  -34.1338   2.4569
 RUZ  H24  H  HOH1  0   0.460  -15.1071  -33.0030   3.0919
 RUZ  C5'  C  CH2   0  -0.242   -6.5843  -30.9649  -2.9033
 RUZ  H4   H  HNH2  0   0.360  -12.0522  -31.3002  -5.7060

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
 RUZ  N    CA   single    1.439  0.020  1.439
 RUZ  CA   CB   single    1.525  0.020  1.525
 RUZ  CA   C    single    1.531  0.020  1.531
 RUZ  CB   OG   single    1.408  0.020  1.408
 RUZ  C    O    double    1.205  0.020  1.205
 RUZ  C    N3S  single    1.383  0.020  1.383
 RUZ  N3S  S    single    1.660  0.020  1.660
 RUZ  S    O2S  double    1.435  0.020  1.435
 RUZ  S    O1S  double    1.441  0.020  1.441
 RUZ  S    O5'  single    1.584  0.020  1.584
 RUZ  C5'  O5'  single    1.441  0.020  1.441
 RUZ  C5'  C4'  single    1.505  0.020  1.505
 RUZ  C4'  C3'  single    1.545  0.020  1.545
 RUZ  C4'  O4'  single    1.426  0.020  1.426
 RUZ  O3'  C3'  single    1.403  0.020  1.403
 RUZ  C3'  C2'  single    1.536  0.020  1.536
 RUZ  O4'  C1'  single    1.408  0.020  1.408
 RUZ  N6   C6   single    1.379  0.020  1.379
 RUZ  C2'  C1'  single    1.529  0.020  1.529
 RUZ  C2'  O2'  single    1.395  0.020  1.395
 RUZ  C1'  N7   single    1.430  0.020  1.430
 RUZ  C6   C1   aromatic  1.391  0.020  1.391
 RUZ  C6   C5   aromatic  1.406  0.020  1.406
 RUZ  C1   C2   aromatic  1.403  0.020  1.403
 RUZ  N7   C5   aromatic  1.393  0.020  1.393
 RUZ  N7   C8   aromatic  1.362  0.020  1.362
 RUZ  C5   C4   aromatic  1.402  0.020  1.402
 RUZ  C8   N9   aromatic  1.295  0.020  1.295
 RUZ  C2   C2M  single    1.506  0.020  1.506
 RUZ  C2   C3   aromatic  1.380  0.020  1.380
 RUZ  C4   C3   aromatic  1.397  0.020  1.397
 RUZ  C4   N9   aromatic  1.376  0.020  1.376
 RUZ  C2M  O2M  single    1.405  0.020  1.405
 RUZ  C1   H1   single    0.930  0.020  1.080
 RUZ  C3   H2   single    0.930  0.020  1.080
 RUZ  C8   H3   single    0.930  0.020  1.080
 RUZ  N    H4   single    0.890  0.020  1.040
 RUZ  N    H5   single    0.890  0.020  1.040
 RUZ  CA   H7   single    0.970  0.020  1.090
 RUZ  CB   H8   single    0.970  0.020  1.090
 RUZ  CB   H9   single    0.970  0.020  1.090
 RUZ  OG   H10  single    0.850  0.020  0.980
 RUZ  N3S  H11  single    0.860  0.020  1.020
 RUZ  C5'  H12  single    0.970  0.020  1.090
 RUZ  C5'  H13  single    0.970  0.020  1.090
 RUZ  C4'  H14  single    0.970  0.020  1.090
 RUZ  C1'  H15  single    0.970  0.020  1.090
 RUZ  C2'  H16  single    0.970  0.020  1.090
 RUZ  O2'  H17  single    0.850  0.020  0.980
 RUZ  C3'  H18  single    0.970  0.020  1.090
 RUZ  O3'  H19  single    0.850  0.020  0.980
 RUZ  N6   H20  single    0.890  0.020  1.040
 RUZ  N6   H21  single    0.890  0.020  1.040
 RUZ  C2M  H22  single    0.970  0.020  1.090
 RUZ  C2M  H23  single    0.970  0.020  1.090
 RUZ  O2M  H24  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
 RUZ  H1   C1   C6   117.82  3.000
 RUZ  H1   C1   C2   118.64  3.000
 RUZ  C6   C1   C2   123.53  3.000
 RUZ  C2M  C2   C3   122.01  3.000
 RUZ  C3   C2   C1   120.38  3.000
 RUZ  C2M  C2   C1   117.60  3.000
 RUZ  H2   C3   C4   120.22  3.000
 RUZ  H2   C3   C2   122.45  3.000
 RUZ  C4   C3   C2   117.33  3.000
 RUZ  N9   C4   C5   110.26  3.000
 RUZ  N9   C4   C3   127.72  3.000
 RUZ  C5   C4   C3   122.01  3.000
 RUZ  N7   C5   C6   134.15  3.000
 RUZ  N7   C5   C4   104.67  3.000
 RUZ  C6   C5   C4   121.13  3.000
 RUZ  N6   C6   C5   123.15  3.000
 RUZ  C5   C6   C1   115.57  3.000
 RUZ  N6   C6   C1   121.24  3.000
 RUZ  H3   C8   N9   125.24  3.000
 RUZ  H3   C8   N7   120.49  3.000
 RUZ  N9   C8   N7   114.26  3.000
 RUZ  H5   N    H4   106.63  3.000
 RUZ  H5   N    CA   110.63  3.000
 RUZ  H4   N    CA   110.58  3.000
 RUZ  H7   CA   C    107.48  3.000
 RUZ  H7   CA   CB   107.13  3.000
 RUZ  C    CA   CB   109.21  3.000
 RUZ  H7   CA   N    108.50  3.000
 RUZ  C    CA   N    113.30  3.000
 RUZ  CB   CA   N    110.97  3.000
 RUZ  H9   CB   H8   106.91  3.000
 RUZ  H9   CB   OG   112.23  3.000
 RUZ  H8   CB   OG   111.77  3.000
 RUZ  H9   CB   CA   107.70  3.000
 RUZ  H8   CB   CA   110.39  3.000
 RUZ  OG   CB   CA   107.79  3.000
 RUZ  H10  OG   CB   108.66  3.000
 RUZ  N3S  C    O    121.82  3.000
 RUZ  N3S  C    CA   113.97  3.000
 RUZ  O    C    CA   124.20  3.000
 RUZ  H11  N3S  S    115.15  3.000
 RUZ  H11  N3S  C    120.55  3.000
 RUZ  S    N3S  C    124.30  3.000
 RUZ  O5'  S    O2S  104.41  3.000
 RUZ  O5'  S    O1S  110.57  3.000
 RUZ  O2S  S    O1S  121.16  3.000
 RUZ  O5'  S    N3S  103.17  3.000
 RUZ  O1S  S    N3S  104.95  3.000
 RUZ  O2S  S    N3S  111.26  3.000
 RUZ  C5'  O5'  S    120.22  3.000
 RUZ  H14  C4'  C3'  108.16  3.000
 RUZ  H14  C4'  O4'  109.48  3.000
 RUZ  C3'  C4'  O4'  107.04  3.000
 RUZ  H14  C4'  C5'  105.90  3.000
 RUZ  O4'  C4'  C5'  110.37  3.000
 RUZ  C3'  C4'  C5'  115.77  3.000
 RUZ  C1'  O4'  C4'  106.16  3.000
 RUZ  H15  C1'  N7   105.43  3.000
 RUZ  H15  C1'  C2'  108.32  3.000
 RUZ  N7   C1'  C2'  117.55  3.000
 RUZ  H15  C1'  O4'  110.56  3.000
 RUZ  N7   C1'  O4'  111.54  3.000
 RUZ  C2'  C1'  O4'  103.41  3.000
 RUZ  H16  C2'  C3'  108.91  3.000
 RUZ  H16  C2'  O2'  112.29  3.000
 RUZ  C3'  C2'  O2'  111.71  3.000
 RUZ  H16  C2'  C1'  109.30  3.000
 RUZ  O2'  C2'  C1'  113.52  3.000
 RUZ  C3'  C2'  C1'  100.42  3.000
 RUZ  H17  O2'  C2'  109.14  3.000
 RUZ  H18  C3'  O3'  111.03  3.000
 RUZ  H18  C3'  C2'  111.06  3.000
 RUZ  O3'  C3'  C2'  112.13  3.000
 RUZ  H18  C3'  C4'  111.91  3.000
 RUZ  C2'  C3'  C4'  102.71  3.000
 RUZ  O3'  C3'  C4'  107.69  3.000
 RUZ  H19  O3'  C3'  108.25  3.000
 RUZ  C1'  N7   C8   121.18  3.000
 RUZ  C8   N7   C5   105.81  3.000
 RUZ  C1'  N7   C5   132.54  3.000
 RUZ  C8   N9   C4   104.99  3.000
 RUZ  H21  N6   H20  109.84  3.000
 RUZ  H21  N6   C6   114.02  3.000
 RUZ  H20  N6   C6   115.17  3.000
 RUZ  H23  C2M  H22  106.15  3.000
 RUZ  H23  C2M  O2M  111.25  3.000
 RUZ  H22  C2M  O2M  111.59  3.000
 RUZ  H23  C2M  C2   108.39  3.000
 RUZ  H22  C2M  C2   108.87  3.000
 RUZ  O2M  C2M  C2   110.45  3.000
 RUZ  H24  O2M  C2M  107.98  3.000
 RUZ  H13  C5'  H12  109.25  3.000
 RUZ  H13  C5'  C4'  110.80  3.000
 RUZ  H12  C5'  C4'  108.67  3.000
 RUZ  H13  C5'  O5'  109.61  3.000
 RUZ  H12  C5'  O5'  110.56  3.000
 RUZ  C4'  C5'  O5'  107.94  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
 RUZ  CONST_01  N7   C5   C6   C1    180.00   0.0  0
 RUZ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 RUZ  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 RUZ  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 RUZ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 RUZ  CONST_06  N9   C4   C3   C2    180.00   0.0  0
 RUZ  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 RUZ  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 RUZ  CONST_09  N7   C5   C4   C3    180.00   0.0  0
 RUZ  CONST_10  C8   N9   C4   C3    180.00   0.0  0
 RUZ  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 RUZ  CONST_12  N7   C8   N9   C4      0.00   0.0  0
 RUZ  CONST_13  N9   C8   N7   C5      0.00   0.0  0
 RUZ  CONST_14  C8   N9   C4   C5      0.00   0.0  0
 RUZ  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 RUZ  CONST_16  N9   C4   C5   C6    180.00   0.0  0
 RUZ  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 RUZ  CONST_18  C1'  N7   C5   C4    180.00   0.0  0
 RUZ  CONST_19  C1'  N7   C5   C6      0.00   0.0  0
 RUZ  CONST_20  N9   C8   N7   C1'   180.00   0.0  0
 RUZ  CONST_21  N6   C6   C1   C2    180.00   0.0  0
 RUZ  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 RUZ  CONST_23  C2M  C2   C3   C4    180.00   0.0  0
 RUZ  CONST_24  C2M  C2   C1   C6    180.00   0.0  0
 RUZ  CONST_25  N6   C6   C5   N7      0.00   0.0  0
 RUZ  CONST_26  H2   C3   C2   C1    180.00   0.0  0
 RUZ  CONST_27  H1   C1   C2   C3    180.00   0.0  0
 RUZ  CONST_28  H3   C8   N9   C4    180.00   0.0  0
 RUZ  CONST_31  S    N3S  C    CA    180.00   0.0  0
 RUZ  CONST_32  S    N3S  C    O       0.00   0.0  0
 RUZ  CONST_33  H11  N3S  C    CA      0.00   0.0  0
 RUZ  Var_01    O2M  C2M  C2   C1   -163.47  30.0  2
 RUZ  Var_02    C4'  C5'  O5'  S    -170.94  30.0  1
 RUZ  Var_03    O2S  S    N3S  C      51.85  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
 RUZ  chir_01  CA   N    CB   C    negativ
 RUZ  chir_02  C4'  O4'  C5'  C3'  positiv
 RUZ  chir_03  C1'  O4'  N7   C2'  negativ
 RUZ  chir_04  C2'  O2'  C1'  C3'  negativ
 RUZ  chir_05  C3'  O3'  C4'  C2'  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
 RUZ  plan-1  C1   0.020
 RUZ  plan-1  C2   0.020
 RUZ  plan-1  C3   0.020
 RUZ  plan-1  C4   0.020
 RUZ  plan-1  C5   0.020
 RUZ  plan-1  C6   0.020
 RUZ  plan-1  C8   0.020
 RUZ  plan-1  C1'  0.020
 RUZ  plan-1  N7   0.020
 RUZ  plan-1  N9   0.020
 RUZ  plan-1  N6   0.020
 RUZ  plan-1  C2M  0.020
 RUZ  plan-1  H1   0.020
 RUZ  plan-1  H2   0.020
 RUZ  plan-1  H3   0.020
 RUZ  plan-2  C6   0.020
 RUZ  plan-2  N6   0.020
 RUZ  plan-2  H20  0.020
 RUZ  plan-2  H21  0.020
 RUZ  plan-3  CA   0.020
 RUZ  plan-3  C    0.020
 RUZ  plan-3  O    0.020
 RUZ  plan-3  N3S  0.020
 RUZ  plan-3  S    0.020
 RUZ  plan-3  H11  0.020

