# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:11:11 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cc(C#N)c3c(N)ncnc23)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
 6NR  6NR  '(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid'  ligand  48  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6NR
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
 6NR  C4   C  CR56  0   0.529   3.2928   0.0365   0.4608
 6NR  C5   C  CR56  0  -0.046   3.2201  -1.3402   0.2726
 6NR  C6   C  CR6   0   0.452   4.4411  -2.0392   0.3699
 6NR  N1   N  N     0  -0.469   5.5529  -1.3487   0.6355
 6NR  C7   C  CR5   0  -0.124   1.8415  -1.6437   0.0329
 6NR  C8   C  CR15  0   0.052   1.1567  -0.4550   0.0849
 6NR  N3   N  N     0  -0.457   4.3959   0.7314   0.7254
 6NR  C    C  C     0   0.522  -6.0184  -2.5169  -0.0170
 6NR  OXT  O  OH1   0  -0.593  -5.1652  -3.5340   0.0038
 6NR  CA   C  CH1   0  -0.203  -5.4202  -1.2802  -0.6784
 6NR  N    N  NH2   0  -0.776  -6.3872  -0.2480  -0.9545
 6NR  CB   C  CH2   0  -0.438  -4.2830  -0.7403   0.2015
 6NR  CG   C  CH2   0  -0.538  -3.5822   0.4445  -0.4441
 6NR  C5'  C  CH2   0  -0.582  -1.4556   2.2093  -0.4574
 6NR  C4'  C  CR15  0  -0.009  -0.3838   2.9882   0.2909
 6NR  C3'  C  CR15  0  -0.012   0.5454   3.7300  -0.6596
 6NR  O3'  O  OH1   0  -0.666   1.1328   4.8010   0.0290
 6NR  C2'  C  CR15  0  -0.053   1.5784   2.6376  -0.9571
 6NR  O2'  O  OH1   0  -0.650   2.8242   3.1049  -1.3765
 6NR  O4'  O  O     0  -0.491   0.4692   2.1180   1.0424
 6NR  C1'  C  CR15  0   0.222   1.7060   1.9659   0.4146
 6NR  N9   N  NR5   0  -0.562   2.0310   0.5537   0.3396
 6NR  C2   C  CR16  0   0.050   5.4690  -0.0319   0.7989
 6NR  CN   C  CSP   0  -0.054   1.2632  -2.9083  -0.1916
 6NR  NN   N  NS    0  -0.254   0.8168  -3.9569  -0.3758
 6NR  N6   N  NH2   0  -0.829   4.5376  -3.3620   0.2186
 6NR  H1   H  HCR5  0   0.326   0.0932  -0.2875  -0.0067
 6NR  H2   H  HOH1  0   0.482  -5.5600  -4.2954   0.4554
 6NR  H3   H  HCH1  0   0.274  -4.9839  -1.6051  -1.6292
 6NR  H5   H  HNH2  0   0.345  -6.8431   0.0445  -0.0986
 6NR  H7   H  HCH2  0   0.247  -4.6882  -0.4490   1.1759
 6NR  H8   H  HCH2  0   0.257  -3.5553  -1.5330   0.3824
 6NR  H9   H  HCH2  0   0.263  -3.1615   0.1549  -1.4099
 6NR  H10  H  HCH2  0   0.271  -4.2756   1.2682  -0.6072
 6NR  H11  H  HCH2  0   0.267  -1.0526   1.6930  -1.3324
 6NR  H12  H  HCH2  0   0.294  -2.2100   2.9141  -0.8127
 6NR  H13  H  HCR5  0   0.276  -0.8651   3.6691   0.9971
 6NR  H14  H  HCR5  0   0.256   0.0219   4.0600  -1.5663
 6NR  H15  H  HOH1  0   0.451   1.9466   5.0408  -0.4298
 6NR  H16  H  HCR5  0   0.253   1.1523   1.9279  -1.6765
 6NR  H17  H  HOH1  0   0.470   2.7994   3.2394  -2.3291
 6NR  H18  H  HCR5  0   0.271   2.5084   2.4336   0.9936
 6NR  H19  H  HCR6  0   0.256   6.4035   0.4731   1.0186
 6NR  H20  H  HNH2  0   0.412   3.7535  -3.9341  -0.0399
 6NR  H21  H  HNH2  0   0.407   5.4414  -3.8018   0.2561
 6NR  SD   S  S2    0  -0.016  -2.2322   0.9945   0.6409
 6NR  H4   H  HNH2  0   0.357  -7.1170  -0.5979  -1.5617
 6NR  O    O  O     0  -0.438  -7.1314  -2.5749   0.4419

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
 6NR  O2'  C2'  single    1.395  0.020  1.395
 6NR  NN   CN   triple    1.154  0.020  1.154
 6NR  N6   C6   single    1.335  0.020  1.335
 6NR  CN   C7   single    1.409  0.020  1.409
 6NR  C7   C5   aromatic  1.432  0.020  1.432
 6NR  C7   C8   aromatic  1.373  0.020  1.373
 6NR  C6   C5   aromatic  1.410  0.020  1.410
 6NR  C6   N1   aromatic  1.336  0.020  1.336
 6NR  C2'  C1'  single    1.533  0.020  1.533
 6NR  C2'  C3'  single    1.533  0.020  1.533
 6NR  C5   C4   aromatic  1.391  0.020  1.391
 6NR  C8   N9   aromatic  1.359  0.020  1.359
 6NR  N1   C2   aromatic  1.329  0.020  1.329
 6NR  C4   N9   aromatic  1.369  0.020  1.369
 6NR  C4   N3   aromatic  1.330  0.020  1.330
 6NR  N9   C1'  single    1.451  0.020  1.451
 6NR  C2   N3   aromatic  1.319  0.020  1.319
 6NR  O3'  C3'  single    1.402  0.020  1.402
 6NR  C1'  O4'  single    1.395  0.020  1.395
 6NR  C3'  C4'  single    1.522  0.020  1.522
 6NR  O4'  C4'  single    1.432  0.020  1.432
 6NR  C4'  C5'  single    1.522  0.020  1.522
 6NR  C5'  SD   single    1.812  0.020  1.812
 6NR  SD   CG   single    1.817  0.020  1.817
 6NR  CB   CG   single    1.520  0.020  1.520
 6NR  CB   CA   single    1.536  0.020  1.536
 6NR  CA   N    single    1.441  0.020  1.441
 6NR  CA   C    single    1.525  0.020  1.525
 6NR  C    O    double    1.205  0.020  1.205
 6NR  C    OXT  single    1.328  0.020  1.328
 6NR  C8   H1   single    0.930  0.020  1.080
 6NR  OXT  H2   single    0.850  0.020  0.980
 6NR  CA   H3   single    0.970  0.020  1.090
 6NR  N    H4   single    0.890  0.020  1.040
 6NR  N    H5   single    0.890  0.020  1.040
 6NR  CB   H7   single    0.970  0.020  1.090
 6NR  CB   H8   single    0.970  0.020  1.090
 6NR  CG   H9   single    0.970  0.020  1.090
 6NR  CG   H10  single    0.970  0.020  1.090
 6NR  C5'  H11  single    0.970  0.020  1.090
 6NR  C5'  H12  single    0.970  0.020  1.090
 6NR  C4'  H13  single    0.970  0.020  1.090
 6NR  C3'  H14  single    0.970  0.020  1.090
 6NR  O3'  H15  single    0.850  0.020  0.980
 6NR  C2'  H16  single    0.970  0.020  1.090
 6NR  O2'  H17  single    0.850  0.020  0.980
 6NR  C1'  H18  single    0.970  0.020  1.090
 6NR  C2   H19  single    0.930  0.020  1.080
 6NR  N6   H20  single    0.860  0.020  1.020
 6NR  N6   H21  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
 6NR  N9   C4   N3   125.77  3.000
 6NR  N3   C4   C5   125.95  3.000
 6NR  N9   C4   C5   108.28  3.000
 6NR  C7   C5   C6   137.74  3.000
 6NR  C6   C5   C4   115.84  3.000
 6NR  C7   C5   C4   106.42  3.000
 6NR  N6   C6   N1   118.34  3.000
 6NR  N1   C6   C5   118.57  3.000
 6NR  N6   C6   C5   123.09  3.000
 6NR  C2   N1   C6   118.95  3.000
 6NR  CN   C7   C8   125.35  3.000
 6NR  C8   C7   C5   106.89  3.000
 6NR  CN   C7   C5   127.75  3.000
 6NR  H1   C8   N9   122.28  3.000
 6NR  H1   C8   C7   128.46  3.000
 6NR  N9   C8   C7   109.20  3.000
 6NR  C2   N3   C4   112.54  3.000
 6NR  CA   C    OXT  112.09  3.000
 6NR  OXT  C    O    123.41  3.000
 6NR  CA   C    O    124.50  3.000
 6NR  H2   OXT  C    110.32  3.000
 6NR  H3   CA   CB   107.85  3.000
 6NR  H3   CA   N    108.26  3.000
 6NR  CB   CA   N    110.78  3.000
 6NR  H3   CA   C    106.99  3.000
 6NR  N    CA   C    113.63  3.000
 6NR  CB   CA   C    109.10  3.000
 6NR  H5   N    H4   106.40  3.000
 6NR  H5   N    CA   110.30  3.000
 6NR  H4   N    CA   110.56  3.000
 6NR  H8   CB   H7   107.01  3.000
 6NR  H8   CB   CG   109.22  3.000
 6NR  H7   CB   CG   109.95  3.000
 6NR  H8   CB   CA   109.47  3.000
 6NR  H7   CB   CA   109.23  3.000
 6NR  CG   CB   CA   111.84  3.000
 6NR  H10  CG   H9   108.26  3.000
 6NR  H10  CG   SD   109.48  3.000
 6NR  H9   CG   SD   108.78  3.000
 6NR  H10  CG   CB   111.07  3.000
 6NR  H9   CG   CB   110.26  3.000
 6NR  SD   CG   CB   108.95  3.000
 6NR  H12  C5'  H11  107.41  3.000
 6NR  H12  C5'  C4'  108.43  3.000
 6NR  H11  C5'  C4'  112.07  3.000
 6NR  H12  C5'  SD   109.50  3.000
 6NR  H11  C5'  SD   109.05  3.000
 6NR  C4'  C5'  SD   110.30  3.000
 6NR  H13  C4'  O4'  107.57  3.000
 6NR  H13  C4'  C3'  111.64  3.000
 6NR  O4'  C4'  C3'  105.09  3.000
 6NR  H13  C4'  C5'  109.06  3.000
 6NR  O4'  C4'  C5'  111.51  3.000
 6NR  C3'  C4'  C5'  111.86  3.000
 6NR  H14  C3'  C2'  112.04  3.000
 6NR  H14  C3'  O3'  112.07  3.000
 6NR  C2'  C3'  O3'  110.94  3.000
 6NR  H14  C3'  C4'  111.78  3.000
 6NR  O3'  C3'  C4'  108.74  3.000
 6NR  C2'  C3'  C4'  100.68  3.000
 6NR  H15  O3'  C3'  108.05  3.000
 6NR  H16  C2'  C1'  109.63  3.000
 6NR  H16  C2'  O2'  111.50  3.000
 6NR  C1'  C2'  O2'  109.97  3.000
 6NR  H16  C2'  C3'  109.07  3.000
 6NR  C1'  C2'  C3'  101.23  3.000
 6NR  O2'  C2'  C3'  114.92  3.000
 6NR  H17  O2'  C2'  108.74  3.000
 6NR  C1'  O4'  C4'  110.99  3.000
 6NR  H18  C1'  N9   106.20  3.000
 6NR  H18  C1'  O4'  111.43  3.000
 6NR  N9   C1'  O4'  109.14  3.000
 6NR  H18  C1'  C2'  110.32  3.000
 6NR  O4'  C1'  C2'  106.33  3.000
 6NR  N9   C1'  C2'  113.51  3.000
 6NR  C1'  N9   C8   126.01  3.000
 6NR  C1'  N9   C4   124.72  3.000
 6NR  C8   N9   C4   109.22  3.000
 6NR  H19  C2   N3   116.28  3.000
 6NR  H19  C2   N1   115.57  3.000
 6NR  N3   C2   N1   128.15  3.000
 6NR  NN   CN   C7   180.00  3.000
 6NR  H21  N6   H20  117.52  3.000
 6NR  H21  N6   C6   119.60  3.000
 6NR  H20  N6   C6   122.49  3.000
 6NR  C5'  SD   CG    99.17  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
 6NR  CONST_01  C8   C7   C5  C4     0.00   0.0  0
 6NR  CONST_02  N1   C6   C5  C4     0.00   0.0  0
 6NR  CONST_03  C7   C8   N9  C4     0.00   0.0  0
 6NR  CONST_04  N1   C2   N3  C4     0.00   0.0  0
 6NR  CONST_05  N9   C8   C7  C5     0.00   0.0  0
 6NR  CONST_06  C2   N1   C6  C5     0.00   0.0  0
 6NR  CONST_07  C8   N9   C4  C5     0.00   0.0  0
 6NR  CONST_08  C2   N3   C4  C5     0.00   0.0  0
 6NR  CONST_09  C8   C7   C5  C6   180.00   0.0  0
 6NR  CONST_10  N9   C4   C5  C6   180.00   0.0  0
 6NR  CONST_11  N3   C4   C5  C6     0.00   0.0  0
 6NR  CONST_12  N3   C2   N1  C6     0.00   0.0  0
 6NR  CONST_13  C7   C5   C6  N1   180.00   0.0  0
 6NR  CONST_14  N9   C4   C5  C7     0.00   0.0  0
 6NR  CONST_15  N3   C4   C5  C7   180.00   0.0  0
 6NR  CONST_16  N3   C4   N9  C8   180.00   0.0  0
 6NR  CONST_17  C2   N3   C4  N9   180.00   0.0  0
 6NR  CONST_18  C1'  N9   C4  C5   180.00   0.0  0
 6NR  CONST_19  C1'  N9   C8  C7   180.00   0.0  0
 6NR  CONST_20  C1'  N9   C4  N3     0.00   0.0  0
 6NR  CONST_21  CN   C7   C5  C4   180.00   0.0  0
 6NR  CONST_22  N6   C6   C5  C4   180.00   0.0  0
 6NR  CONST_23  CN   C7   C5  C6     0.00   0.0  0
 6NR  CONST_24  N6   C6   C5  C7     0.00   0.0  0
 6NR  CONST_25  CN   C7   C8  N9   180.00   0.0  0
 6NR  CONST_26  N6   C6   N1  C2   180.00   0.0  0
 6NR  CONST_27  H1   C8   N9  C4   180.00   0.0  0
 6NR  CONST_28  H19  C2   N3  C4   180.00   0.0  0
 6NR  CONST_29  H20  N6   C6  C5     0.00   0.0  0
 6NR  CONST_30  H21  N6   C6  C5   180.00   0.0  0
 6NR  CONST_31  H2   OXT  C   O      0.00   0.0  0
 6NR  Var_01    C4'  C5'  SD  CG   171.84  30.0  1
 6NR  Var_02    SD   CG   CB  CA  -178.72  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
 6NR  chir_01  CA   CB   N    C    positiv
 6NR  chir_02  C4'  O4'  C3'  C5'  negativ
 6NR  chir_03  C3'  O3'  C4'  C2'  positiv
 6NR  chir_04  C2'  O2'  C3'  C1'  positiv
 6NR  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
 6NR  plan-1  C4   0.020
 6NR  plan-1  C5   0.020
 6NR  plan-1  C6   0.020
 6NR  plan-1  N1   0.020
 6NR  plan-1  C7   0.020
 6NR  plan-1  C8   0.020
 6NR  plan-1  N3   0.020
 6NR  plan-1  C1'  0.020
 6NR  plan-1  N9   0.020
 6NR  plan-1  C2   0.020
 6NR  plan-1  CN   0.020
 6NR  plan-1  NN   0.020
 6NR  plan-1  N6   0.020
 6NR  plan-1  H1   0.020
 6NR  plan-1  H19  0.020
 6NR  plan-2  C6   0.020
 6NR  plan-2  N6   0.020
 6NR  plan-2  H20  0.020
 6NR  plan-2  H21  0.020
 6NR  plan-3  C    0.020
 6NR  plan-3  OXT  0.020
 6NR  plan-3  CA   0.020
 6NR  plan-3  H2   0.020
 6NR  plan-3  O    0.020

