# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:55:11 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-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(=NC2=O)N
#
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
 FZQ  FZQ  '[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'  ligand  46  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_FZQ
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
 FZQ  O1S  O  OS    0  -0.635   3.6924  -2.3065  -0.1337
 FZQ  O2S  O  OS    0  -0.613   3.2880  -1.2377   2.0976
 FZQ  N    N  NH2   0  -0.791   1.1201   3.2652  -0.3009
 FZQ  CA   C  CH1   0  -0.268   2.1619   2.2953  -0.4890
 FZQ  C    C  C     0   0.561   2.0174   1.0523   0.3926
 FZQ  O    O  O     0  -0.402   1.3869   1.0155   1.4175
 FZQ  CB   C  CH2   0  -0.125   3.5373   2.9071  -0.2069
 FZQ  OG   O  OH1   0  -0.660   3.7633   3.9358  -1.1336
 FZQ  C1'  C  CR15  0   0.193  -2.5559  -1.1816   0.5073
 FZQ  C2   C  CR6   0   0.639  -1.8708   0.9193  -0.6213
 FZQ  C2'  C  CR15  0  -0.036  -2.9771  -2.0244  -0.7069
 FZQ  C3'  C  CR15  0  -0.040  -1.6618  -2.6703  -1.1914
 FZQ  C4   C  CR6   0   0.537  -2.6220   2.9591   0.2064
 FZQ  C4'  C  CR15  0   0.011  -0.7502  -2.5775   0.0377
 FZQ  C5   C  CR16  0  -0.470  -3.4184   2.3231   1.2069
 FZQ  C5'  C  CH2   0  -0.205   0.6677  -2.2588  -0.3679
 FZQ  C6   C  CR16  0   0.102  -3.3690   0.9780   1.2421
 FZQ  N1   N  NR6   0  -0.553  -2.6296   0.2638   0.3578
 FZQ  N3   N  N     0  -0.574  -1.8950   2.2668  -0.6510
 FZQ  N3S  N  NC1   0  -0.836   2.7156  -0.0446  -0.0819
 FZQ  O2   O  O     0  -0.511  -1.2184   0.2567  -1.4158
 FZQ  O2'  O  OH1   0  -0.675  -3.8713  -3.0073  -0.2547
 FZQ  O3'  O  OH1   0  -0.661  -1.8221  -4.0167  -1.5598
 FZQ  O4'  O  O     0  -0.478  -1.2545  -1.5495   0.8595
 FZQ  O5'  O  OC2   0  -0.568   1.4220  -2.0413   0.8431
 FZQ  S    S  S     0   1.629   2.8945  -1.4802   0.7378
 FZQ  H1   H  HNH2  0   0.379   0.2263   2.9078  -0.6215
 FZQ  H2   H  HNH2  0   0.341   1.0128   3.4819   0.6826
 FZQ  H4   H  HCH1  0   0.274   2.1485   1.9660  -1.5338
 FZQ  H5   H  HCH2  0   0.204   3.5484   3.2756   0.8284
 FZQ  H6   H  HCH2  0   0.210   4.3079   2.1298  -0.2742
 FZQ  H7   H  HOH1  0   0.457   4.6515   4.2734  -0.9877
 FZQ  H8   H  HCR5  0   0.258  -3.2435  -1.4132   1.3255
 FZQ  H9   H  HCR5  0   0.249  -3.4380  -1.4099  -1.4874
 FZQ  H10  H  HCR5  0   0.267  -1.2578  -2.0855  -2.0179
 FZQ  H11  H  HCR5  0   0.256  -0.7740  -3.5308   0.5823
 FZQ  H12  H  HCR6  0   0.292  -4.0117   2.8821   1.9141
 FZQ  H13  H  HCH2  0   0.270   1.0900  -3.0953  -0.9277
 FZQ  H14  H  HCH2  0   0.265   0.6908  -1.3585  -0.9829
 FZQ  H15  H  HCR6  0   0.322  -3.9174   0.4095   1.9802
 FZQ  H16  H  HNC1  0   0.455   3.1701  -0.0051  -0.9872
 FZQ  H17  H  HNH2  0   0.416  -3.1267   4.8626   0.7566
 FZQ  H18  H  HNH2  0   0.405  -2.0412   4.7434  -0.5771
 FZQ  H19  H  HOH1  0   0.449  -3.6134  -3.8384  -0.6779
 FZQ  H20  H  HOH1  0   0.472  -1.9852  -4.0637  -2.5071
 FZQ  N4   N  NH2   0  -0.808  -2.5938   4.2870   0.1287

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
 FZQ  O2'  C2'  single  1.404  0.020  1.404
 FZQ  O2   C2   double  1.223  0.020  1.223
 FZQ  C2'  C1'  single  1.537  0.020  1.537
 FZQ  C2'  C3'  single  1.543  0.020  1.543
 FZQ  O3'  C3'  single  1.405  0.020  1.405
 FZQ  C2   N3   single  1.348  0.020  1.348
 FZQ  C2   N1   single  1.401  0.020  1.401
 FZQ  C1'  N1   single  1.455  0.020  1.455
 FZQ  C1'  O4'  single  1.398  0.020  1.398
 FZQ  N3   C4   double  1.320  0.020  1.320
 FZQ  C3'  C4'  single  1.533  0.020  1.533
 FZQ  N1   C6   single  1.356  0.020  1.356
 FZQ  C4'  O4'  single  1.409  0.020  1.409
 FZQ  C4'  C5'  single  1.509  0.020  1.509
 FZQ  C4   N4   single  1.330  0.020  1.330
 FZQ  C4   C5   single  1.428  0.020  1.428
 FZQ  C6   C5   double  1.346  0.020  1.346
 FZQ  C5'  O5'  single  1.443  0.020  1.443
 FZQ  OG   CB   single  1.403  0.020  1.403
 FZQ  O5'  S    single  1.579  0.020  1.579
 FZQ  O2S  S    double  1.436  0.020  1.436
 FZQ  CB   CA   single  1.532  0.020  1.532
 FZQ  S    N3S  single  1.663  0.020  1.663
 FZQ  S    O1S  double  1.442  0.020  1.442
 FZQ  N3S  C    single  1.384  0.020  1.384
 FZQ  C    CA   single  1.531  0.020  1.531
 FZQ  C    O    double  1.204  0.020  1.204
 FZQ  CA   N    single  1.436  0.020  1.436
 FZQ  N    H1   single  0.890  0.020  1.040
 FZQ  N    H2   single  0.890  0.020  1.040
 FZQ  CA   H4   single  0.970  0.020  1.090
 FZQ  CB   H5   single  0.970  0.020  1.090
 FZQ  CB   H6   single  0.970  0.020  1.090
 FZQ  OG   H7   single  0.850  0.020  0.980
 FZQ  C1'  H8   single  0.970  0.020  1.090
 FZQ  C2'  H9   single  0.970  0.020  1.090
 FZQ  C3'  H10  single  0.970  0.020  1.090
 FZQ  C4'  H11  single  0.970  0.020  1.090
 FZQ  C5   H12  single  0.930  0.020  1.080
 FZQ  C5'  H13  single  0.970  0.020  1.090
 FZQ  C5'  H14  single  0.970  0.020  1.090
 FZQ  C6   H15  single  0.930  0.020  1.080
 FZQ  N3S  H16  single  0.860  0.020  1.020
 FZQ  N4   H17  single  0.860  0.020  1.020
 FZQ  N4   H18  single  0.860  0.020  1.020
 FZQ  O2'  H19  single  0.850  0.020  0.980
 FZQ  O3'  H20  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
 FZQ  H2   N    H1   106.79  3.000
 FZQ  H2   N    CA   110.41  3.000
 FZQ  H1   N    CA   111.09  3.000
 FZQ  H4   CA   CB   107.86  3.000
 FZQ  H4   CA   C    107.69  3.000
 FZQ  CB   CA   C    107.64  3.000
 FZQ  H4   CA   N    108.61  3.000
 FZQ  C    CA   N    113.87  3.000
 FZQ  CB   CA   N    110.96  3.000
 FZQ  N3S  C    O    122.13  3.000
 FZQ  O    C    CA   124.37  3.000
 FZQ  N3S  C    CA   113.48  3.000
 FZQ  H6   CB   H5   106.76  3.000
 FZQ  H6   CB   OG   111.47  3.000
 FZQ  H5   CB   OG   112.01  3.000
 FZQ  H6   CB   CA   109.68  3.000
 FZQ  H5   CB   CA   108.45  3.000
 FZQ  OG   CB   CA   108.42  3.000
 FZQ  H7   OG   CB   107.82  3.000
 FZQ  H8   C1'  O4'  109.95  3.000
 FZQ  H8   C1'  N1   104.80  3.000
 FZQ  O4'  C1'  N1   109.55  3.000
 FZQ  H8   C1'  C2'  107.61  3.000
 FZQ  O4'  C1'  C2'  108.06  3.000
 FZQ  N1   C1'  C2'  116.73  3.000
 FZQ  O2   C2   N3   122.46  3.000
 FZQ  N3   C2   N1   118.25  3.000
 FZQ  O2   C2   N1   119.29  3.000
 FZQ  H9   C2'  O2'  110.76  3.000
 FZQ  H9   C2'  C3'  111.70  3.000
 FZQ  O2'  C2'  C3'  110.54  3.000
 FZQ  H9   C2'  C1'  111.76  3.000
 FZQ  C3'  C2'  C1'  104.12  3.000
 FZQ  O2'  C2'  C1'  107.71  3.000
 FZQ  H10  C3'  O3'  110.96  3.000
 FZQ  H10  C3'  C4'  110.79  3.000
 FZQ  O3'  C3'  C4'  109.63  3.000
 FZQ  H10  C3'  C2'  109.23  3.000
 FZQ  C4'  C3'  C2'  103.28  3.000
 FZQ  O3'  C3'  C2'  112.72  3.000
 FZQ  N4   C4   N3   118.28  3.000
 FZQ  N4   C4   C5   119.82  3.000
 FZQ  N3   C4   C5   121.90  3.000
 FZQ  H11  C4'  O4'  109.64  3.000
 FZQ  H11  C4'  C5'  109.70  3.000
 FZQ  O4'  C4'  C5'  109.81  3.000
 FZQ  H11  C4'  C3'  109.40  3.000
 FZQ  C5'  C4'  C3'  110.86  3.000
 FZQ  O4'  C4'  C3'  107.39  3.000
 FZQ  H12  C5   C6   121.36  3.000
 FZQ  H12  C5   C4   122.34  3.000
 FZQ  C6   C5   C4   116.28  3.000
 FZQ  H14  C5'  H13  109.59  3.000
 FZQ  H14  C5'  O5'  109.74  3.000
 FZQ  H13  C5'  O5'  110.09  3.000
 FZQ  H14  C5'  C4'  110.24  3.000
 FZQ  H13  C5'  C4'  109.85  3.000
 FZQ  O5'  C5'  C4'  107.30  3.000
 FZQ  H15  C6   N1   116.41  3.000
 FZQ  H15  C6   C5   121.64  3.000
 FZQ  N1   C6   C5   121.94  3.000
 FZQ  C6   N1   C2   120.29  3.000
 FZQ  C6   N1   C1'  118.94  3.000
 FZQ  C2   N1   C1'  120.60  3.000
 FZQ  C4   N3   C2   121.32  3.000
 FZQ  H16  N3S  S    115.19  3.000
 FZQ  H16  N3S  C    120.10  3.000
 FZQ  S    N3S  C    124.71  3.000
 FZQ  H19  O2'  C2'  106.91  3.000
 FZQ  H20  O3'  C3'  108.91  3.000
 FZQ  C4'  O4'  C1'  112.23  3.000
 FZQ  S    O5'  C5'  119.01  3.000
 FZQ  O5'  S    N3S  103.85  3.000
 FZQ  N3S  S    O2S  110.51  3.000
 FZQ  O5'  S    O2S  104.61  3.000
 FZQ  N3S  S    O1S  104.85  3.000
 FZQ  O2S  S    O1S  121.16  3.000
 FZQ  O5'  S    O1S  110.65  3.000
 FZQ  H18  N4   H17  118.03  3.000
 FZQ  H18  N4   C4   120.36  3.000
 FZQ  H17  N4   C4   121.60  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
 FZQ  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 FZQ  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 FZQ  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 FZQ  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 FZQ  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 FZQ  CONST_06  N4   C4   N3   C2    180.00   0.0  0
 FZQ  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 FZQ  CONST_08  O2   C2   N1   C6    180.00   0.0  0
 FZQ  CONST_09  H17  N4   C4   C5      0.00   0.0  0
 FZQ  CONST_10  H18  N4   C4   C5    180.00   0.0  0
 FZQ  CONST_11  S    N3S  C    CA    180.00   0.0  0
 FZQ  CONST_12  S    N3S  C    O       0.00   0.0  0
 FZQ  CONST_13  H16  N3S  C    CA      0.00   0.0  0
 FZQ  Var_01    C    N3S  S    O1S  -179.67  30.0  3
 FZQ  Var_02    N3S  S    O5'  C5'    57.53  30.0  3
 FZQ  Var_03    H13  C5'  O5'  S      69.38  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
 FZQ  chir_01  CA   CB   C    N    negativ
 FZQ  chir_02  C1'  C2'  N1   O4'  positiv
 FZQ  chir_03  C2'  O2'  C3'  C1'  positiv
 FZQ  chir_04  C3'  O3'  C4'  C2'  positiv
 FZQ  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
 FZQ  plan-1  C1'  0.020
 FZQ  plan-1  C2   0.020
 FZQ  plan-1  C4   0.020
 FZQ  plan-1  C5   0.020
 FZQ  plan-1  C6   0.020
 FZQ  plan-1  N1   0.020
 FZQ  plan-1  N3   0.020
 FZQ  plan-1  O2   0.020
 FZQ  plan-1  H12  0.020
 FZQ  plan-1  H15  0.020
 FZQ  plan-1  H17  0.020
 FZQ  plan-1  H18  0.020
 FZQ  plan-1  N4   0.020
 FZQ  plan-2  CA   0.020
 FZQ  plan-2  C    0.020
 FZQ  plan-2  O    0.020
 FZQ  plan-2  N3S  0.020
 FZQ  plan-2  S    0.020
 FZQ  plan-2  H16  0.020

