# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:29:37 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-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)N2C=CC(=O)NC2=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
 FZK  FZK  '[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'  ligand  45  27  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FZK
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
 FZK  O2'  O  OH1   0  -0.671   3.6266  -2.5232  -0.5788
 FZK  C2'  C  CH1   0  -0.045   2.8259  -1.7795   0.3006
 FZK  C1'  C  CH1   0   0.202   2.0200  -0.7738  -0.5410
 FZK  O4'  O  O2    0  -0.476   0.7040  -1.2371  -0.6226
 FZK  C4'  C  CH1   0   0.018   0.5714  -2.5138  -0.0354
 FZK  C5'  C  CH2   0  -0.210  -0.7475  -2.6073   0.6834
 FZK  O5'  O  OC2   0  -0.568  -1.8012  -2.5128  -0.3021
 FZK  C3'  C  CH1   0  -0.037   1.7453  -2.6766   0.9325
 FZK  O3'  O  OH1   0  -0.659   2.1246  -4.0262   0.9937
 FZK  N1   N  NR6   0  -0.561   2.0410   0.6060  -0.0715
 FZK  C6   C  CR16  0   0.106   2.5766   1.5745  -0.8719
 FZK  C5   C  CR16  0  -0.498   2.6588   2.8656  -0.5193
 FZK  C4   C  CR6   0   0.563   2.1405   3.2842   0.7578
 FZK  O4   O  O     0  -0.471   2.1247   4.4249   1.1857
 FZK  N3   N  NR16  0  -0.728   1.6423   2.2410   1.5190
 FZK  C2   C  CR6   0   0.762   1.5256   0.9250   1.1664
 FZK  O2   O  O     0  -0.478   1.0352   0.1011   1.9108
 FZK  C    C  C     0   0.599  -2.1350   0.6126  -0.5364
 FZK  CA   C  CH1   0  -0.256  -1.8900   2.0199  -0.0271
 FZK  CB   C  CH2   0  -0.134  -3.1720   2.8292  -0.2680
 FZK  N    N  NH2   0  -0.760  -0.7001   2.5471  -0.6496
 FZK  N3S  N  NC1   0  -0.837  -2.6794  -0.2342   0.4083
 FZK  O    O  O     0  -0.410  -1.9301   0.2660  -1.6710
 FZK  O1S  O  OS    0  -0.608  -3.9673  -1.8661  -1.0805
 FZK  O2S  O  OS    0  -0.631  -3.6295  -2.2920   1.3679
 FZK  OG   O  OH1   0  -0.665  -2.9787   4.1021   0.2972
 FZK  S    S  S     0   1.618  -3.1530  -1.7993   0.0996
 FZK  H1   H  HOH1  0   0.450   3.6151  -3.4383  -0.2658
 FZK  H2   H  HCH1  0   0.253   3.4373  -1.2762   1.0585
 FZK  H3   H  HCH1  0   0.264   2.4688  -0.7317  -1.5370
 FZK  H4   H  HCH1  0   0.258   0.6333  -3.2930  -0.8073
 FZK  H5   H  HCH2  0   0.279  -0.8331  -3.5664   1.1952
 FZK  H6   H  HCH2  0   0.261  -0.8245  -1.8017   1.4160
 FZK  H7   H  HCH1  0   0.266   1.4858  -2.2951   1.9213
 FZK  H8   H  HOH1  0   0.472   2.4973  -4.2067   1.8622
 FZK  H9   H  HCR6  0   0.324   2.9463   1.2324  -1.8280
 FZK  H10  H  HCR6  0   0.288   3.0889   3.5928  -1.1901
 FZK  H11  H  HNR6  0   0.421   1.2620   2.4786   2.4267
 FZK  H12  H  HCH1  0   0.266  -1.7222   1.9825   1.0546
 FZK  H13  H  HCH2  0   0.212  -3.3563   2.8844  -1.3480
 FZK  H14  H  HCH2  0   0.203  -4.0302   2.3140   0.1838
 FZK  H15  H  HNH2  0   0.346  -0.7862   2.5207  -1.6582
 FZK  H16  H  HNH2  0   0.355  -0.5995   3.5213  -0.3960
 FZK  H18  H  HNC1  0   0.456  -2.8199   0.0844   1.3599
 FZK  H19  H  HOH1  0   0.462  -3.6490   4.6944  -0.0545

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
 FZK  O2'  C2'  single  1.403  0.020  1.403
 FZK  O2   C2   double  1.214  0.020  1.214
 FZK  C2'  C1'  single  1.539  0.020  1.539
 FZK  C2'  C3'  single  1.540  0.020  1.540
 FZK  C2   N3   single  1.367  0.020  1.367
 FZK  C2   N1   single  1.378  0.020  1.378
 FZK  C1'  N1   single  1.458  0.020  1.458
 FZK  C1'  O4'  single  1.398  0.020  1.398
 FZK  O3'  C3'  single  1.403  0.020  1.403
 FZK  N3   C4   single  1.384  0.020  1.384
 FZK  N1   C6   single  1.366  0.020  1.366
 FZK  C3'  C4'  single  1.530  0.020  1.530
 FZK  C4'  O4'  single  1.412  0.020  1.412
 FZK  C4'  C5'  single  1.505  0.020  1.505
 FZK  C4   O4   double  1.218  0.020  1.218
 FZK  C4   C5   single  1.440  0.020  1.440
 FZK  C6   C5   double  1.341  0.020  1.341
 FZK  C5'  O5'  single  1.446  0.020  1.446
 FZK  OG   CB   single  1.406  0.020  1.406
 FZK  O5'  S    single  1.580  0.020  1.580
 FZK  O1S  S    double  1.435  0.020  1.435
 FZK  CB   CA   single  1.535  0.020  1.535
 FZK  S    N3S  single  1.664  0.020  1.664
 FZK  S    O2S  double  1.442  0.020  1.442
 FZK  N3S  C    single  1.380  0.020  1.380
 FZK  C    CA   single  1.517  0.020  1.517
 FZK  C    O    double  1.204  0.020  1.204
 FZK  CA   N    single  1.443  0.020  1.443
 FZK  O2'  H1   single  0.850  0.020  0.980
 FZK  C2'  H2   single  0.970  0.020  1.090
 FZK  C1'  H3   single  0.970  0.020  1.090
 FZK  C4'  H4   single  0.970  0.020  1.090
 FZK  C5'  H5   single  0.970  0.020  1.090
 FZK  C5'  H6   single  0.970  0.020  1.090
 FZK  C3'  H7   single  0.970  0.020  1.090
 FZK  O3'  H8   single  0.850  0.020  0.980
 FZK  C6   H9   single  0.930  0.020  1.080
 FZK  C5   H10  single  0.930  0.020  1.080
 FZK  N3   H11  single  0.860  0.020  1.020
 FZK  CA   H12  single  0.970  0.020  1.090
 FZK  CB   H13  single  0.970  0.020  1.090
 FZK  CB   H14  single  0.970  0.020  1.090
 FZK  N    H15  single  0.890  0.020  1.040
 FZK  N    H16  single  0.890  0.020  1.040
 FZK  N3S  H18  single  0.860  0.020  1.020
 FZK  OG   H19  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
 FZK  H1   O2'  C2'  106.97  3.000
 FZK  H2   C2'  C3'  112.03  3.000
 FZK  H2   C2'  C1'  111.72  3.000
 FZK  C3'  C2'  C1'  103.75  3.000
 FZK  H2   C2'  O2'  111.01  3.000
 FZK  C3'  C2'  O2'  110.42  3.000
 FZK  C1'  C2'  O2'  107.61  3.000
 FZK  H3   C1'  N1   104.54  3.000
 FZK  H3   C1'  O4'  110.25  3.000
 FZK  N1   C1'  O4'  110.25  3.000
 FZK  H3   C1'  C2'  107.96  3.000
 FZK  O4'  C1'  C2'  107.96  3.000
 FZK  N1   C1'  C2'  115.78  3.000
 FZK  C4'  O4'  C1'  111.35  3.000
 FZK  H4   C4'  C3'  109.01  3.000
 FZK  H4   C4'  C5'  109.94  3.000
 FZK  C3'  C4'  C5'  111.32  3.000
 FZK  H4   C4'  O4'  110.11  3.000
 FZK  C5'  C4'  O4'  109.71  3.000
 FZK  C3'  C4'  O4'  106.69  3.000
 FZK  H6   C5'  H5   109.19  3.000
 FZK  H6   C5'  O5'  110.96  3.000
 FZK  H5   C5'  O5'  108.67  3.000
 FZK  H6   C5'  C4'  109.66  3.000
 FZK  H5   C5'  C4'  110.34  3.000
 FZK  O5'  C5'  C4'  108.00  3.000
 FZK  S    O5'  C5'  118.66  3.000
 FZK  H7   C3'  O3'  111.17  3.000
 FZK  H7   C3'  C4'  110.70  3.000
 FZK  O3'  C3'  C4'  109.71  3.000
 FZK  H7   C3'  C2'  109.58  3.000
 FZK  C4'  C3'  C2'  102.52  3.000
 FZK  O3'  C3'  C2'  112.86  3.000
 FZK  H8   O3'  C3'  108.94  3.000
 FZK  C2   N1   C6   120.59  3.000
 FZK  C6   N1   C1'  119.22  3.000
 FZK  C2   N1   C1'  120.20  3.000
 FZK  H9   C6   C5   121.09  3.000
 FZK  H9   C6   N1   115.35  3.000
 FZK  C5   C6   N1   123.56  3.000
 FZK  H10  C5   C4   119.92  3.000
 FZK  H10  C5   C6   120.67  3.000
 FZK  C4   C5   C6   119.40  3.000
 FZK  N3   C4   O4   120.52  3.000
 FZK  O4   C4   C5   126.02  3.000
 FZK  N3   C4   C5   113.45  3.000
 FZK  H11  N3   C2   115.15  3.000
 FZK  H11  N3   C4   116.83  3.000
 FZK  C2   N3   C4   127.90  3.000
 FZK  O2   C2   N3   121.98  3.000
 FZK  N3   C2   N1   114.99  3.000
 FZK  O2   C2   N1   123.01  3.000
 FZK  O    C    N3S  122.37  3.000
 FZK  O    C    CA   123.79  3.000
 FZK  N3S  C    CA   113.77  3.000
 FZK  H12  CA   N    108.19  3.000
 FZK  H12  CA   CB   107.51  3.000
 FZK  N    CA   CB   115.37  3.000
 FZK  H12  CA   C    108.95  3.000
 FZK  N    CA   C    109.11  3.000
 FZK  CB   CA   C    107.56  3.000
 FZK  H14  CB   H13  107.30  3.000
 FZK  H14  CB   OG   111.51  3.000
 FZK  H13  CB   OG   111.92  3.000
 FZK  H14  CB   CA   109.92  3.000
 FZK  H13  CB   CA   108.74  3.000
 FZK  OG   CB   CA   107.42  3.000
 FZK  H16  N    H15  106.45  3.000
 FZK  H16  N    CA   109.01  3.000
 FZK  H15  N    CA   110.49  3.000
 FZK  H18  N3S  S    115.49  3.000
 FZK  H18  N3S  C    120.30  3.000
 FZK  S    N3S  C    124.21  3.000
 FZK  H19  OG   CB   108.35  3.000
 FZK  O2S  S    O1S  121.32  3.000
 FZK  O2S  S    N3S  104.62  3.000
 FZK  O1S  S    N3S  110.96  3.000
 FZK  O2S  S    O5'  110.61  3.000
 FZK  N3S  S    O5'  103.20  3.000
 FZK  O1S  S    O5'  104.79  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
 FZK  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 FZK  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 FZK  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 FZK  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 FZK  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 FZK  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 FZK  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 FZK  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 FZK  CONST_09  H11  N3   C2   N1   180.00   0.0  0
 FZK  CONST_10  S    N3S  C    CA   180.00   0.0  0
 FZK  CONST_11  S    N3S  C    O      0.00   0.0  0
 FZK  CONST_12  H18  N3S  C    CA     0.00   0.0  0
 FZK  Var_01    O1S  S    O5'  C5'  179.67  30.0  3
 FZK  Var_02    C    N3S  S    O5'   63.23  30.0  3
 FZK  Var_03    H5   C5'  O5'  S     93.94  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
 FZK  chir_01  C2'  O2'  C1'  C3'  negativ
 FZK  chir_02  C1'  O4'  N1   C2'  negativ
 FZK  chir_03  C4'  O4'  C3'  C5'  negativ
 FZK  chir_04  C3'  O3'  C4'  C2'  positiv
 FZK  chir_05  CA   N    CB   C    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
 FZK  plan-1  C1'  0.020
 FZK  plan-1  N1   0.020
 FZK  plan-1  C6   0.020
 FZK  plan-1  C5   0.020
 FZK  plan-1  C4   0.020
 FZK  plan-1  O4   0.020
 FZK  plan-1  N3   0.020
 FZK  plan-1  C2   0.020
 FZK  plan-1  O2   0.020
 FZK  plan-1  H9   0.020
 FZK  plan-1  H10  0.020
 FZK  plan-1  H11  0.020
 FZK  plan-2  C    0.020
 FZK  plan-2  CA   0.020
 FZK  plan-2  N3S  0.020
 FZK  plan-2  O    0.020
 FZK  plan-2  S    0.020
 FZK  plan-2  H18  0.020

