# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 22:03:08 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)
#   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(Br)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
 SX0  SX0  '(2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)'  ligand  47  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SX0
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
 SX0  C     C   C     0   0.523  -7.8068   1.4311  -0.6829
 SX0  N     N   NH2   0  -0.775  -7.3764  -0.4187   0.9152
 SX0  OXT   O   OH1   0  -0.593  -7.4223   2.6586  -1.0119
 SX0  N1    N   N     0  -0.474   5.8745  -0.3782  -1.1244
 SX0  C2    C   CR16  0   0.045   5.2517  -1.5073  -1.4491
 SX0  N3    N   N     0  -0.466   3.9761  -1.8014  -1.3021
 SX0  C4    C   CR56  0   0.522   3.2794  -0.8036  -0.7564
 SX0  C5    C   CR56  0  -0.004   3.7896   0.4364  -0.3565
 SX0  C6    C   CR6   0   0.445   5.1731   0.6179  -0.5762
 SX0  N6    N   NH2   0  -0.824   5.8345   1.7329  -0.2473
 SX0  C7    C   CR5   0  -0.306   2.6799   1.1560   0.1758
 SX0  C8    C   CR15  0   0.003   1.5803   0.3580   0.0795
 SX0  N9    N   NR5   0  -0.553   1.9491  -0.8360  -0.4909
 SX0  CA    C   CH1   0  -0.206  -6.8451   0.7715   0.2989
 SX0  CB    C   CH2   0  -0.436  -5.5254   0.4661  -0.4249
 SX0  SD    S   S2    0  -0.021  -2.9639  -0.4400  -0.4156
 SX0  CG    C   CH2   0  -0.542  -4.4704  -0.0697   0.5300
 SX0  C1'   C   CH1   0   0.174   1.1012  -1.9938  -0.7515
 SX0  C2'   C   CH1   0  -0.043   1.2281  -3.0527   0.3439
 SX0  O2'   O   OH1   0  -0.664   0.9384  -4.2969  -0.2316
 SX0  C3'   C   CH1   0  -0.025   0.1146  -2.6173   1.3033
 SX0  O3'   O   OH1   0  -0.657  -0.3829  -3.6490   2.1058
 SX0  C4'   C   CH1   0   0.050  -0.9598  -2.1434   0.3271
 SX0  O4'   O   O2    0  -0.494  -0.2337  -1.5861  -0.7673
 SX0  C5'   C   CH2   0  -0.577  -1.9034  -1.1100   0.8972
 SX0  O     O   O     0  -0.438  -8.7980   0.9063  -1.1244
 SX0  HN    H   HNH2  0   0.357  -8.2022  -0.1968   1.4556
 SX0  HNA   H   HNH2  0   0.345  -7.6700  -1.0790   0.2054
 SX0  HO    H   HOH1  0   0.482  -8.0338   3.0395  -1.6602
 SX0  HN6   H   HNH2  0   0.402   6.8010   1.8210  -0.5120
 SX0  HN6A  H   HNH2  0   0.407   5.3617   2.5667   0.0516
 SX0  H8    H   HCR5  0   0.321   0.5625   0.5716   0.3590
 SX0  HA    H   HCH1  0   0.273  -6.6386   1.5033   1.0869
 SX0  HB    H   HCH2  0   0.245  -5.7119  -0.2644  -1.2183
 SX0  HBA   H   HCH2  0   0.257  -5.1536   1.3717  -0.9074
 SX0  HG    H   HCH2  0   0.261  -4.2494   0.6704   1.3020
 SX0  HGA   H   HCH2  0   0.270  -4.8180  -0.9791   1.0189
 SX0  H1'   H   HCH1  0   0.282   1.3955  -2.3936  -1.7253
 SX0  H2'   H   HCH1  0   0.260   2.2201  -3.0388   0.8115
 SX0  HO2'  H   HOH1  0   0.452   0.5600  -4.8591   0.4556
 SX0  H3'   H   HCH1  0   0.245   0.4683  -1.7709   1.9062
 SX0  HO3'  H   HOH1  0   0.469   0.1795  -3.7388   2.8816
 SX0  H4'   H   HCH1  0   0.250  -1.5435  -3.0011  -0.0278
 SX0  H5'   H   HCH2  0   0.265  -1.3557  -0.3055   1.3930
 SX0  H5'A  H   HCH2  0   0.289  -2.5337  -1.5958   1.6444
 SX0  H2    H   HCR6  0   0.252   5.8770  -2.2775  -1.8884
 SX0  BR    BR  BR    0  -0.048   2.6739   2.8845   0.8766

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
 SX0  CA   C     single    1.524  0.020  1.524
 SX0  C    O     double    1.205  0.020  1.205
 SX0  C    OXT   single    1.328  0.020  1.328
 SX0  CA   N     single    1.442  0.020  1.442
 SX0  N    HN    single    0.890  0.020  1.040
 SX0  N    HNA   single    0.890  0.020  1.040
 SX0  OXT  HO    single    0.850  0.020  0.980
 SX0  BR   C7    single    1.865  0.020  1.865
 SX0  C6   N1    aromatic  1.336  0.020  1.336
 SX0  N1   C2    aromatic  1.330  0.020  1.330
 SX0  C2   N3    aromatic  1.317  0.020  1.317
 SX0  C2   H2    single    0.930  0.020  1.080
 SX0  C4   N3    aromatic  1.334  0.020  1.334
 SX0  C5   C4    aromatic  1.399  0.020  1.399
 SX0  C4   N9    aromatic  1.357  0.020  1.357
 SX0  C6   C5    aromatic  1.413  0.020  1.413
 SX0  C7   C5    aromatic  1.426  0.020  1.426
 SX0  N6   C6    single    1.337  0.020  1.337
 SX0  N6   HN6   single    0.860  0.020  1.020
 SX0  N6   HN6A  single    0.860  0.020  1.020
 SX0  C7   C8    aromatic  1.362  0.020  1.362
 SX0  C8   N9    aromatic  1.374  0.020  1.374
 SX0  C8   H8    single    0.930  0.020  1.080
 SX0  N9   C1'   single    1.459  0.020  1.459
 SX0  CB   CA    single    1.536  0.020  1.536
 SX0  CA   HA    single    0.970  0.020  1.090
 SX0  CB   CG    single    1.520  0.020  1.520
 SX0  CB   HB    single    0.970  0.020  1.090
 SX0  CB   HBA   single    0.970  0.020  1.090
 SX0  C5'  SD    single    1.816  0.020  1.816
 SX0  SD   CG    single    1.817  0.020  1.817
 SX0  CG   HG    single    0.970  0.020  1.090
 SX0  CG   HGA   single    0.970  0.020  1.090
 SX0  C2'  C1'   single    1.529  0.020  1.529
 SX0  C1'  O4'   single    1.396  0.020  1.396
 SX0  C1'  H1'   single    0.970  0.020  1.090
 SX0  O2'  C2'   single    1.401  0.020  1.401
 SX0  C2'  C3'   single    1.533  0.020  1.533
 SX0  C2'  H2'   single    0.970  0.020  1.090
 SX0  O2'  HO2'  single    0.850  0.020  0.980
 SX0  O3'  C3'   single    1.399  0.020  1.399
 SX0  C3'  C4'   single    1.527  0.020  1.527
 SX0  C3'  H3'   single    0.970  0.020  1.090
 SX0  O3'  HO3'  single    0.850  0.020  0.980
 SX0  O4'  C4'   single    1.427  0.020  1.427
 SX0  C4'  C5'   single    1.511  0.020  1.511
 SX0  C4'  H4'   single    0.970  0.020  1.090
 SX0  C5'  H5'   single    0.970  0.020  1.090
 SX0  C5'  H5'A  single    0.970  0.020  1.090

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
 SX0  O     C    CA   124.49  3.000
 SX0  O     C    OXT  123.37  3.000
 SX0  CA    C    OXT  112.14  3.000
 SX0  HNA   N    HN   106.30  3.000
 SX0  HNA   N    CA   110.21  3.000
 SX0  HN    N    CA   110.38  3.000
 SX0  HO    OXT  C    110.27  3.000
 SX0  C6    N1   C2   119.17  3.000
 SX0  H2    C2   N3   116.41  3.000
 SX0  H2    C2   N1   115.58  3.000
 SX0  N3    C2   N1   128.01  3.000
 SX0  C4    N3   C2   112.61  3.000
 SX0  N9    C4   C5   108.83  3.000
 SX0  N9    C4   N3   125.05  3.000
 SX0  C5    C4   N3   126.12  3.000
 SX0  C7    C5   C6   139.08  3.000
 SX0  C7    C5   C4   105.68  3.000
 SX0  C6    C5   C4   115.25  3.000
 SX0  N6    C6   C5   123.59  3.000
 SX0  N6    C6   N1   117.57  3.000
 SX0  C5    C6   N1   118.83  3.000
 SX0  HN6A  N6   HN6  117.26  3.000
 SX0  HN6A  N6   C6   122.19  3.000
 SX0  HN6   N6   C6   118.91  3.000
 SX0  C8    C7   C5   107.83  3.000
 SX0  C8    C7   BR   124.53  3.000
 SX0  C5    C7   BR   127.63  3.000
 SX0  H8    C8   N9   122.27  3.000
 SX0  H8    C8   C7   128.94  3.000
 SX0  N9    C8   C7   108.78  3.000
 SX0  C1'   N9   C8   127.45  3.000
 SX0  C1'   N9   C4   123.64  3.000
 SX0  C8    N9   C4   108.89  3.000
 SX0  HA    CA   CB   108.06  3.000
 SX0  HA    CA   N    108.28  3.000
 SX0  CB    CA   N    110.73  3.000
 SX0  HA    CA   C    107.06  3.000
 SX0  CB    CA   C    108.94  3.000
 SX0  N     CA   C    113.58  3.000
 SX0  HBA   CB   HB   106.93  3.000
 SX0  HBA   CB   CG   109.49  3.000
 SX0  HB    CB   CG   109.78  3.000
 SX0  HBA   CB   CA   109.64  3.000
 SX0  HB    CB   CA   109.14  3.000
 SX0  CG    CB   CA   111.74  3.000
 SX0  C5'   SD   CG   100.55  3.000
 SX0  HGA   CG   HG   108.25  3.000
 SX0  HGA   CG   SD   109.14  3.000
 SX0  HG    CG   SD   109.77  3.000
 SX0  HGA   CG   CB   110.77  3.000
 SX0  HG    CG   CB   110.22  3.000
 SX0  SD    CG   CB   108.68  3.000
 SX0  H1'   C1'  O4'  110.75  3.000
 SX0  H1'   C1'  C2'  111.26  3.000
 SX0  O4'   C1'  C2'  106.85  3.000
 SX0  H1'   C1'  N9   107.04  3.000
 SX0  O4'   C1'  N9   109.04  3.000
 SX0  C2'   C1'  N9   111.94  3.000
 SX0  H2'   C2'  C3'  112.74  3.000
 SX0  H2'   C2'  O2'  111.92  3.000
 SX0  C3'   C2'  O2'  111.04  3.000
 SX0  H2'   C2'  C1'  111.83  3.000
 SX0  C3'   C2'  C1'  101.03  3.000
 SX0  O2'   C2'  C1'  107.68  3.000
 SX0  HO2'  O2'  C2'  107.81  3.000
 SX0  H3'   C3'  C4'  109.79  3.000
 SX0  H3'   C3'  O3'  111.61  3.000
 SX0  C4'   C3'  O3'  110.21  3.000
 SX0  H3'   C3'  C2'  109.19  3.000
 SX0  C4'   C3'  C2'  101.48  3.000
 SX0  O3'   C3'  C2'  114.08  3.000
 SX0  HO3'  O3'  C3'  108.87  3.000
 SX0  H4'   C4'  C5'  108.95  3.000
 SX0  H4'   C4'  O4'  109.16  3.000
 SX0  C5'   C4'  O4'  109.88  3.000
 SX0  H4'   C4'  C3'  109.80  3.000
 SX0  C5'   C4'  C3'  114.23  3.000
 SX0  O4'   C4'  C3'  104.68  3.000
 SX0  C4'   O4'  C1'  111.34  3.000
 SX0  H5'A  C5'  H5'  107.86  3.000
 SX0  H5'A  C5'  C4'  108.33  3.000
 SX0  H5'   C5'  C4'  111.22  3.000
 SX0  H5'A  C5'  SD   108.77  3.000
 SX0  H5'   C5'  SD   110.44  3.000
 SX0  C4'   C5'  SD   110.14  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
 SX0  CONST_01  C4    C5   C6  N1    0.00   0.0  0
 SX0  CONST_02  C7    C5   C6  N1  180.00   0.0  0
 SX0  CONST_03  C4    N3   C2  N1    0.00   0.0  0
 SX0  CONST_04  C5    C6   N1  C2    0.00   0.0  0
 SX0  CONST_05  C5    C4   N3  C2    0.00   0.0  0
 SX0  CONST_06  N9    C4   N3  C2  180.00   0.0  0
 SX0  CONST_07  C6    N1   C2  N3    0.00   0.0  0
 SX0  CONST_08  C6    C5   C4  N3    0.00   0.0  0
 SX0  CONST_09  C7    C5   C4  N3  180.00   0.0  0
 SX0  CONST_10  C8    N9   C4  N3  180.00   0.0  0
 SX0  CONST_11  C8    C7   C5  C4    0.00   0.0  0
 SX0  CONST_12  C7    C8   N9  C4    0.00   0.0  0
 SX0  CONST_13  C8    N9   C4  C5    0.00   0.0  0
 SX0  CONST_14  N9    C8   C7  C5    0.00   0.0  0
 SX0  CONST_15  N9    C4   C5  C6  180.00   0.0  0
 SX0  CONST_16  C8    C7   C5  C6  180.00   0.0  0
 SX0  CONST_17  N9    C4   C5  C7    0.00   0.0  0
 SX0  CONST_18  C1'   N9   C4  N3    0.00   0.0  0
 SX0  CONST_19  C1'   N9   C4  C5  180.00   0.0  0
 SX0  CONST_20  C1'   N9   C8  C7  180.00   0.0  0
 SX0  CONST_21  C4    C5   C7  BR  180.00   0.0  0
 SX0  CONST_22  C6    C5   C7  BR    0.00   0.0  0
 SX0  CONST_23  N9    C8   C7  BR  180.00   0.0  0
 SX0  CONST_24  N6    C6   N1  C2  180.00   0.0  0
 SX0  CONST_25  N6    C6   C5  C4  180.00   0.0  0
 SX0  CONST_26  C7    C5   C6  N6    0.00   0.0  0
 SX0  CONST_27  H2    C2   N3  C4  180.00   0.0  0
 SX0  CONST_28  H8    C8   N9  C4  180.00   0.0  0
 SX0  CONST_29  HN6   N6   C6  N1    0.00   0.0  0
 SX0  CONST_30  HN6A  N6   C6  N1  180.00   0.0  0
 SX0  CONST_31  HO    OXT  C   CA  180.00   0.0  0
 SX0  Var_01    C4'   C5'  SD  CG  148.92  30.0  1
 SX0  Var_02    SD    CG   CB  CA  178.62  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
 SX0  chir_01  CA   C    N    CB   negativ
 SX0  chir_02  C1'  N9   C2'  O4'  negativ
 SX0  chir_03  C2'  O2'  C3'  C1'  positiv
 SX0  chir_04  C3'  O3'  C2'  C4'  negativ
 SX0  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
 SX0  plan-1  N1    0.020
 SX0  plan-1  C2    0.020
 SX0  plan-1  N3    0.020
 SX0  plan-1  C4    0.020
 SX0  plan-1  C5    0.020
 SX0  plan-1  C6    0.020
 SX0  plan-1  N6    0.020
 SX0  plan-1  C7    0.020
 SX0  plan-1  C8    0.020
 SX0  plan-1  N9    0.020
 SX0  plan-1  C1'   0.020
 SX0  plan-1  H8    0.020
 SX0  plan-1  H2    0.020
 SX0  plan-1  BR    0.020
 SX0  plan-2  C6    0.020
 SX0  plan-2  N6    0.020
 SX0  plan-2  HN6   0.020
 SX0  plan-2  HN6A  0.020
 SX0  plan-3  C     0.020
 SX0  plan-3  OXT   0.020
 SX0  plan-3  CA    0.020
 SX0  plan-3  O     0.020
 SX0  plan-3  HO    0.020

