# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:49:10 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)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
 RSN  RSN  '(3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid'  ligand  55  33  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RSN
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
 RSN  C1   C  CR16   0  -0.382  -41.5892  -24.2957  -13.6366
 RSN  C2   C  CR6    0   0.022  -41.4191  -24.3207  -12.2396
 RSN  C3   C  CR16   0  -0.398  -42.1163  -23.4434  -11.4336
 RSN  C4   C  CR6    0   0.139  -43.0071  -22.5621  -12.0526
 RSN  C5   C  CR6    0   0.302  -43.1768  -22.5637  -13.4429
 RSN  C6   C  CR6    0   0.261  -42.4511  -23.4231  -14.2807
 RSN  N6   N  NH2    0  -0.882  -42.6350  -23.4353  -15.6747
 RSN  N    N  NH2    0  -0.773  -49.4799  -14.8283  -12.1228
 RSN  CA   C  CH1    0  -0.221  -49.8822  -16.0470  -12.7801
 RSN  C    C  C      0   0.560  -49.1278  -17.2747  -12.2854
 RSN  O    O  O      0  -0.412  -48.0292  -17.2495  -11.7867
 RSN  CB   C  CH2    0  -0.574  -49.6656  -15.9357  -14.2904
 RSN  CG   C  C      0   0.421  -50.5921  -14.9003  -14.9709
 RSN  OD1  O  O      0  -0.605  -50.0981  -14.2668  -15.9224
 RSN  OD2  O  OC    -1  -0.601  -51.7584  -14.8279  -14.5399
 RSN  C1'  C  CH1    0   0.184  -44.8185  -21.4244  -14.9610
 RSN  C2'  C  CH1    0  -0.069  -45.6868  -22.6417  -15.3542
 RSN  C2M  C  CH2    0  -0.179  -40.4218  -25.2999  -11.6791
 RSN  C3'  C  CH1    0   0.016  -47.0937  -22.1376  -15.0105
 RSN  C4'  C  CH1    0   0.019  -46.9681  -20.6448  -15.2900
 RSN  C5'  C  CH2    0  -0.231  -47.9683  -19.7589  -14.5962
 RSN  C8   C  C1     0   0.096  -44.5197  -21.1277  -12.4732
 RSN  N3S  N  NC1    0  -0.826  -49.7988  -18.4695  -12.5046
 RSN  N7   N  N      0  -0.535  -44.1594  -21.6262  -13.6839
 RSN  N9   N  N      0  -0.472  -43.8524  -21.6427  -11.4799
 RSN  O1S  O  OS     0  -0.608  -48.6077  -20.0786  -10.9182
 RSN  O2'  O  OH1    0  -0.663  -45.5886  -22.9151  -16.7194
 RSN  O2M  O  OH1    0  -0.662  -40.5998  -25.4408  -10.2938
 RSN  O2S  O  OS     0  -0.626  -50.0898  -20.9116  -12.7564
 RSN  O3'  O  OH1    0  -0.653  -48.1430  -22.6716  -15.7548
 RSN  O4'  O  O2     0  -0.497  -45.6566  -20.3096  -14.8727
 RSN  O5'  O  OC2    0  -0.570  -47.8356  -19.9382  -13.1729
 RSN  S    S  S      0   1.615  -49.1265  -19.9651  -12.2520
 RSN  H1   H  HCR6   0   0.251  -41.0146  -24.9876  -14.2442
 RSN  H2   H  HCR6   0   0.244  -41.9996  -23.4358  -10.3589
 RSN  H3   H  HNH2   0   0.386  -42.3521  -22.5673  -16.1119
 RSN  H4   H  HNH2   0   0.381  -42.1029  -24.1777  -16.1094
 RSN  H8   H  HCH1   0   0.261  -50.9507  -16.2007  -12.6046
 RSN  H9   H  HCH2   0   0.244  -49.8579  -16.9043  -14.7659
 RSN  H10  H  HCH2   0   0.224  -48.6156  -15.7035  -14.4889
 RSN  H12  H  HCH1   0   0.265  -44.0470  -21.2430  -15.7131
 RSN  H13  H  HCH1   0   0.256  -45.4166  -23.5159  -14.7509
 RSN  H14  H  HCH2   0   0.208  -40.5374  -26.2592  -12.2017
 RSN  H15  H  HCH2   0   0.217  -39.4104  -24.9432  -11.9175
 RSN  H16  H  HCH1   0   0.242  -47.2403  -22.2909  -13.9338
 RSN  H17  H  HCH1   0   0.259  -47.0877  -20.4651  -16.3676
 RSN  H18  H  HCH2   0   0.285  -47.7881  -18.7069  -14.8240
 RSN  H19  H  HCH2   0   0.271  -48.9679  -20.0227  -14.9475
 RSN  H20  H  H      0   0.288  -45.2855  -20.3750  -12.3720
 RSN  H21  H  HNC1   0   0.454  -50.7181  -18.4689  -12.9333
 RSN  H22  H  HOH1   0   0.454  -44.6931  -23.2569  -16.8526
 RSN  H23  H  HOH1   0   0.458  -39.8523  -25.9328   -9.9429
 RSN  H24  H  HOH1   0   0.461  -48.3531  -23.5469  -15.4153
 RSN  H5   H  HNH2   0   0.351  -49.6537  -14.8850  -11.1274
 RSN  H6   H  HNH2   0   0.343  -48.4835  -14.6842  -12.2332

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
 RSN  O2'  C2'  single    1.396  0.020  1.396
 RSN  O3'  C3'  single    1.393  0.020  1.393
 RSN  C4'  C3'  single    1.524  0.020  1.524
 RSN  C4'  C5'  single    1.505  0.020  1.505
 RSN  C4'  O4'  single    1.417  0.020  1.417
 RSN  N6   C6   single    1.406  0.020  1.406
 RSN  C2'  C3'  single    1.533  0.020  1.533
 RSN  C2'  C1'  single    1.546  0.020  1.546
 RSN  OD1  CG   deloc     1.245  0.020  1.245
 RSN  C1'  O4'  single    1.398  0.020  1.398
 RSN  C1'  N7   single    1.451  0.020  1.451
 RSN  C5'  O5'  single    1.441  0.020  1.441
 RSN  CG   CB   single    1.547  0.020  1.547
 RSN  CG   OD2  deloc     1.245  0.020  1.245
 RSN  C6   C1   aromatic  1.385  0.020  1.385
 RSN  C6   C5   aromatic  1.403  0.020  1.403
 RSN  CB   CA   single    1.530  0.020  1.530
 RSN  N7   C5   aromatic  1.379  0.020  1.379
 RSN  N7   C8   aromatic  1.358  0.020  1.358
 RSN  O5'  S    single    1.586  0.020  1.586
 RSN  C1   C2   aromatic  1.408  0.020  1.408
 RSN  C5   C4   aromatic  1.401  0.020  1.401
 RSN  O2S  S    deloc     1.442  0.020  1.442
 RSN  N3S  S    single    1.659  0.020  1.659
 RSN  N3S  C    single    1.388  0.020  1.388
 RSN  CA   C    single    1.524  0.020  1.524
 RSN  CA   N    single    1.442  0.020  1.442
 RSN  S    O1S  deloc     1.436  0.020  1.436
 RSN  C8   N9   aromatic  1.303  0.020  1.303
 RSN  C    O    double    1.207  0.020  1.207
 RSN  C2   C2M  single    1.506  0.020  1.506
 RSN  C2   C3   aromatic  1.380  0.020  1.380
 RSN  C4   N9   aromatic  1.374  0.020  1.374
 RSN  C4   C3   aromatic  1.398  0.020  1.398
 RSN  C2M  O2M  single    1.404  0.020  1.404
 RSN  C1   H1   single    0.930  0.020  1.080
 RSN  C3   H2   single    0.930  0.020  1.080
 RSN  N6   H3   single    0.890  0.020  1.040
 RSN  N6   H4   single    0.890  0.020  1.040
 RSN  N    H5   single    0.890  0.020  1.040
 RSN  N    H6   single    0.890  0.020  1.040
 RSN  CA   H8   single    0.970  0.020  1.090
 RSN  CB   H9   single    0.970  0.020  1.090
 RSN  CB   H10  single    0.970  0.020  1.090
 RSN  C1'  H12  single    0.970  0.020  1.090
 RSN  C2'  H13  single    0.970  0.020  1.090
 RSN  C2M  H14  single    0.970  0.020  1.090
 RSN  C2M  H15  single    0.970  0.020  1.090
 RSN  C3'  H16  single    0.970  0.020  1.090
 RSN  C4'  H17  single    0.970  0.020  1.090
 RSN  C5'  H18  single    0.970  0.020  1.090
 RSN  C5'  H19  single    0.970  0.020  1.090
 RSN  C8   H20  single    0.930  0.020  1.080
 RSN  N3S  H21  single    0.860  0.020  1.020
 RSN  O2'  H22  single    0.850  0.020  0.980
 RSN  O2M  H23  single    0.850  0.020  0.980
 RSN  O3'  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
 RSN  H1   C1   C6   118.08  3.000
 RSN  H1   C1   C2   118.70  3.000
 RSN  C6   C1   C2   123.22  3.000
 RSN  C2M  C2   C3   122.04  3.000
 RSN  C3   C2   C1   120.48  3.000
 RSN  C2M  C2   C1   117.45  3.000
 RSN  H2   C3   C4   120.31  3.000
 RSN  H2   C3   C2   122.03  3.000
 RSN  C4   C3   C2   117.65  3.000
 RSN  N9   C4   C5   109.87  3.000
 RSN  N9   C4   C3   129.01  3.000
 RSN  C5   C4   C3   121.08  3.000
 RSN  N7   C5   C6   132.90  3.000
 RSN  N7   C5   C4   105.01  3.000
 RSN  C6   C5   C4   122.07  3.000
 RSN  N6   C6   C5   122.00  3.000
 RSN  C5   C6   C1   115.48  3.000
 RSN  N6   C6   C1   122.47  3.000
 RSN  H4   N6   H3   107.26  3.000
 RSN  H4   N6   C6   111.32  3.000
 RSN  H3   N6   C6   112.59  3.000
 RSN  H6   N    H5   106.50  3.000
 RSN  H6   N    CA   110.19  3.000
 RSN  H5   N    CA   110.67  3.000
 RSN  H8   CA   CB   107.88  3.000
 RSN  H8   CA   C    108.57  3.000
 RSN  CB   CA   C    108.01  3.000
 RSN  H8   CA   N    108.56  3.000
 RSN  C    CA   N    113.26  3.000
 RSN  CB   CA   N    110.42  3.000
 RSN  N3S  C    O    121.56  3.000
 RSN  O    C    CA   124.62  3.000
 RSN  N3S  C    CA   113.77  3.000
 RSN  H10  CB   H9   106.09  3.000
 RSN  H10  CB   CG   110.68  3.000
 RSN  H9   CB   CG   107.19  3.000
 RSN  H10  CB   CA   109.31  3.000
 RSN  H9   CB   CA   109.83  3.000
 RSN  CG   CB   CA   113.47  3.000
 RSN  OD2  CG   OD1  127.32  3.000
 RSN  OD2  CG   CB   116.58  3.000
 RSN  OD1  CG   CB   116.04  3.000
 RSN  H12  C1'  O4'  109.55  3.000
 RSN  H12  C1'  N7   107.95  3.000
 RSN  O4'  C1'  N7   109.13  3.000
 RSN  H12  C1'  C2'  110.63  3.000
 RSN  N7   C1'  C2'  111.68  3.000
 RSN  O4'  C1'  C2'  107.90  3.000
 RSN  H13  C2'  O2'  111.40  3.000
 RSN  H13  C2'  C3'  111.41  3.000
 RSN  O2'  C2'  C3'  110.38  3.000
 RSN  H13  C2'  C1'  110.46  3.000
 RSN  C3'  C2'  C1'  101.50  3.000
 RSN  O2'  C2'  C1'  111.31  3.000
 RSN  H15  C2M  H14  106.09  3.000
 RSN  H15  C2M  O2M  111.32  3.000
 RSN  H14  C2M  O2M  111.63  3.000
 RSN  H15  C2M  C2   108.53  3.000
 RSN  H14  C2M  C2   108.73  3.000
 RSN  O2M  C2M  C2   110.40  3.000
 RSN  H16  C3'  O3'  111.72  3.000
 RSN  H16  C3'  C4'  109.14  3.000
 RSN  O3'  C3'  C4'  109.86  3.000
 RSN  H16  C3'  C2'  107.25  3.000
 RSN  C4'  C3'  C2'  101.85  3.000
 RSN  O3'  C3'  C2'  116.44  3.000
 RSN  H17  C4'  O4'  110.54  3.000
 RSN  H17  C4'  C5'  106.46  3.000
 RSN  O4'  C4'  C5'  109.88  3.000
 RSN  H17  C4'  C3'  109.33  3.000
 RSN  O4'  C4'  C3'  104.72  3.000
 RSN  C5'  C4'  C3'  115.92  3.000
 RSN  H19  C5'  H18  108.47  3.000
 RSN  H19  C5'  O5'  111.84  3.000
 RSN  H18  C5'  O5'  108.12  3.000
 RSN  H19  C5'  C4'  108.53  3.000
 RSN  H18  C5'  C4'  111.18  3.000
 RSN  O5'  C5'  C4'  108.71  3.000
 RSN  H20  C8   N9   124.61  3.000
 RSN  H20  C8   N7   121.89  3.000
 RSN  N9   C8   N7   113.50  3.000
 RSN  H21  N3S  S    115.61  3.000
 RSN  H21  N3S  C    120.29  3.000
 RSN  S    N3S  C    123.79  3.000
 RSN  C8   N7   C1'  127.80  3.000
 RSN  C8   N7   C5   106.43  3.000
 RSN  C1'  N7   C5   124.88  3.000
 RSN  C8   N9   C4   105.18  3.000
 RSN  H22  O2'  C2'  105.60  3.000
 RSN  H23  O2M  C2M  108.24  3.000
 RSN  H24  O3'  C3'  108.95  3.000
 RSN  C4'  O4'  C1'  110.36  3.000
 RSN  S    O5'  C5'  120.05  3.000
 RSN  O5'  S    O2S  110.60  3.000
 RSN  O2S  S    O1S  120.97  3.000
 RSN  O5'  S    O1S  104.28  3.000
 RSN  O1S  S    N3S  111.05  3.000
 RSN  O2S  S    N3S  105.53  3.000
 RSN  O5'  S    N3S  103.07  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
 RSN  CONST_01  N7   C5   C6   C1    180.00   0.0  0
 RSN  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 RSN  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 RSN  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 RSN  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 RSN  CONST_06  N9   C4   C3   C2    180.00   0.0  0
 RSN  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 RSN  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 RSN  CONST_09  N7   C5   C4   C3    180.00   0.0  0
 RSN  CONST_10  C8   N9   C4   C3    180.00   0.0  0
 RSN  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 RSN  CONST_12  N7   C8   N9   C4      0.00   0.0  0
 RSN  CONST_13  N9   C8   N7   C5      0.00   0.0  0
 RSN  CONST_14  C8   N9   C4   C5      0.00   0.0  0
 RSN  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 RSN  CONST_16  N9   C4   C5   C6    180.00   0.0  0
 RSN  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 RSN  CONST_18  C1'  N7   C5   C4    180.00   0.0  0
 RSN  CONST_19  C1'  N7   C5   C6      0.00   0.0  0
 RSN  CONST_20  N9   C8   N7   C1'   180.00   0.0  0
 RSN  CONST_21  N6   C6   C1   C2    180.00   0.0  0
 RSN  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 RSN  CONST_23  C2M  C2   C3   C4    180.00   0.0  0
 RSN  CONST_24  C2M  C2   C1   C6    180.00   0.0  0
 RSN  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 RSN  CONST_26  H2   C3   C2   C1    180.00   0.0  0
 RSN  CONST_27  H1   C1   C2   C3    180.00   0.0  0
 RSN  CONST_28  H20  C8   N9   C4    180.00   0.0  0
 RSN  CONST_30  H4   N6   C6   C1      0.00   0.0  0
 RSN  CONST_31  S    N3S  C    CA    180.00   0.0  0
 RSN  CONST_32  S    N3S  C    O       0.00   0.0  0
 RSN  CONST_33  H21  N3S  C    CA      0.00   0.0  0
 RSN  Var_01    O2M  C2M  C2   C1   -165.49  30.0  2
 RSN  Var_02    OD1  CG   CB   CA    144.71  30.0  2
 RSN  Var_03    O5'  S    N3S  C     -56.89  30.0  3
 RSN  Var_04    H18  C5'  O5'  S      98.12  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
 RSN  chir_01  CA   CB   C    N    negativ
 RSN  chir_02  C1'  C2'  O4'  N7   negativ
 RSN  chir_03  C2'  O2'  C3'  C1'  positiv
 RSN  chir_04  C3'  O3'  C2'  C4'  negativ
 RSN  chir_05  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
 RSN  plan-1  C1   0.020
 RSN  plan-1  C2   0.020
 RSN  plan-1  C3   0.020
 RSN  plan-1  C4   0.020
 RSN  plan-1  C5   0.020
 RSN  plan-1  C6   0.020
 RSN  plan-1  N6   0.020
 RSN  plan-1  C1'  0.020
 RSN  plan-1  C2M  0.020
 RSN  plan-1  C8   0.020
 RSN  plan-1  N7   0.020
 RSN  plan-1  N9   0.020
 RSN  plan-1  H1   0.020
 RSN  plan-1  H2   0.020
 RSN  plan-1  H20  0.020
 RSN  plan-2  C6   0.020
 RSN  plan-2  N6   0.020
 RSN  plan-2  H3   0.020
 RSN  plan-2  H4   0.020
 RSN  plan-3  CA   0.020
 RSN  plan-3  C    0.020
 RSN  plan-3  O    0.020
 RSN  plan-3  N3S  0.020
 RSN  plan-3  S    0.020
 RSN  plan-3  H21  0.020
 RSN  plan-4  CB   0.020
 RSN  plan-4  CG   0.020
 RSN  plan-4  OD1  0.020
 RSN  plan-4  OD2  0.020

