# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:06:57 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-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)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
 G5H  G5H  '(3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid'  ligand  46  29  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G5H
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
 G5H  C5'  C  CH2    0  -0.211  -0.0215   2.9703   1.0461
 G5H  O2'  O  OH1    0  -0.662  -3.9579   1.6195  -0.5917
 G5H  C4'  C  CH1    0   0.021  -1.1797   2.3789   0.2884
 G5H  O4'  O  O2     0  -0.497  -0.8634   1.0692  -0.1431
 G5H  C3'  C  CH1    0  -0.034  -2.4083   2.1931   1.1769
 G5H  O3'  O  OH1    0  -0.653  -3.1225   3.3882   1.2871
 G5H  C2'  C  CH1    0  -0.040  -3.1661   1.0830   0.4310
 G5H  C1'  C  CH1    0   0.161  -2.0306   0.2837  -0.2322
 G5H  C5   C  CR16   0  -0.484  -0.9708  -2.2140   2.2798
 G5H  C6   C  CR16   0   0.082  -1.2583  -1.0644   1.6580
 G5H  C4   C  CR6    0   0.595  -1.2063  -3.4692   1.6044
 G5H  O4   O  O      0  -0.464  -1.0350  -4.5752   2.0762
 G5H  C2   C  CR6    0   0.741  -1.9967  -2.1586  -0.3414
 G5H  O2   O  O      0  -0.480  -2.4337  -2.1516  -1.4739
 G5H  N    N  NH2    0  -0.773   0.9293  -1.5191  -2.2183
 G5H  CA   C  CH1    0  -0.246   1.5690  -1.0300  -1.0243
 G5H  C    C  C      0   0.585   1.8716   0.4610  -1.0753
 G5H  O    O  O      0  -0.417   1.7845   1.1513  -2.0597
 G5H  CB   C  CH2    0  -0.568   2.8288  -1.8449  -0.7418
 G5H  CG   C  C      0   0.424   2.4817  -3.3018  -0.3684
 G5H  OD1  O  O      0  -0.581   1.5425  -3.4544   0.4352
 G5H  OD2  O  OC    -1  -0.616   3.1931  -4.1948  -0.8690
 G5H  N1   N  NR6    0  -0.565  -1.7593  -1.0037   0.3836
 G5H  N3   N  NR16   0  -0.731  -1.7195  -3.3174   0.3262
 G5H  N3S  N  NC1    0  -0.834   2.2658   0.9899   0.1465
 G5H  O1S  O  OS     0  -0.633   2.8341   2.7084   1.8184
 G5H  O2S  O  OS     0  -0.612   3.3444   3.1773  -0.5904
 G5H  O5'  O  OC2    0  -0.567   1.0725   3.2453   0.1452
 G5H  S    S  S      0   1.613   2.4993   2.6055   0.4193
 G5H  H1   H  HCH2   0   0.286  -0.3186   3.9234   1.4828
 G5H  H2   H  HCH2   0   0.257   0.2847   2.3086   1.8599
 G5H  H3   H  HOH1   0   0.453  -4.3278   2.4529  -0.2736
 G5H  H4   H  HCH1   0   0.265  -1.4356   3.0204  -0.5650
 G5H  H5   H  HCH1   0   0.252  -2.0971   1.8221   2.1626
 G5H  H6   H  HOH1   0   0.473  -3.6493   3.3675   2.0928
 G5H  H7   H  HCH1   0   0.263  -3.7545   0.4551   1.1110
 G5H  H8   H  HCH1   0   0.290  -2.2871   0.0849  -1.2727
 G5H  H9   H  HCR6   0   0.290  -0.5712  -2.2118   3.2818
 G5H  H10  H  HCR6   0   0.312  -1.0913  -0.1168   2.1488
 G5H  H14  H  HCH1   0   0.274   0.8951  -1.1903  -0.1784
 G5H  H15  H  HCH2   0   0.225   3.4957  -1.8040  -1.6070
 G5H  H16  H  HCH2   0   0.240   3.3860  -1.4129   0.0964
 G5H  H18  H  HNR6   0   0.423  -1.8899  -4.1661  -0.1988
 G5H  H19  H  HNC1   0   0.448   2.3178   0.3959   0.9655
 G5H  H11  H  HNH2   0   0.348   0.0657  -1.0244  -2.3996
 G5H  H12  H  HNH2   0   0.344   1.5217  -1.3583  -3.0241

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
 G5H  OD1  CG   deloc   1.245  0.020  1.245
 G5H  CG   OD2  deloc   1.247  0.020  1.247
 G5H  CG   CB   single  1.544  0.020  1.544
 G5H  CB   CA   single  1.527  0.020  1.527
 G5H  O3'  C3'  single  1.397  0.020  1.397
 G5H  O2'  C2'  single  1.400  0.020  1.400
 G5H  C4'  C5'  single  1.505  0.020  1.505
 G5H  C4'  C3'  single  1.528  0.020  1.528
 G5H  C4'  O4'  single  1.415  0.020  1.415
 G5H  C5'  O5'  single  1.444  0.020  1.444
 G5H  CA   N    single  1.440  0.020  1.440
 G5H  CA   C    single  1.522  0.020  1.522
 G5H  C3'  C2'  single  1.537  0.020  1.537
 G5H  O4'  C1'  single  1.410  0.020  1.410
 G5H  C2'  C1'  single  1.539  0.020  1.539
 G5H  C1'  N1   single  1.453  0.020  1.453
 G5H  C    N3S  single  1.389  0.020  1.389
 G5H  C    O    double  1.205  0.020  1.205
 G5H  N3S  S    single  1.655  0.020  1.655
 G5H  O5'  S    single  1.588  0.020  1.588
 G5H  O2S  S    deloc   1.436  0.020  1.436
 G5H  S    O1S  deloc   1.442  0.020  1.442
 G5H  O2   C2   double  1.214  0.020  1.214
 G5H  N1   C2   single  1.384  0.020  1.384
 G5H  N1   C6   single  1.371  0.020  1.371
 G5H  C2   N3   single  1.366  0.020  1.366
 G5H  C6   C5   double  1.338  0.020  1.338
 G5H  N3   C4   single  1.386  0.020  1.386
 G5H  C5   C4   single  1.445  0.020  1.445
 G5H  C4   O4   double  1.215  0.020  1.215
 G5H  C5'  H1   single  0.970  0.020  1.090
 G5H  C5'  H2   single  0.970  0.020  1.090
 G5H  O2'  H3   single  0.850  0.020  0.980
 G5H  C4'  H4   single  0.970  0.020  1.090
 G5H  C3'  H5   single  0.970  0.020  1.090
 G5H  O3'  H6   single  0.850  0.020  0.980
 G5H  C2'  H7   single  0.970  0.020  1.090
 G5H  C1'  H8   single  0.970  0.020  1.090
 G5H  C5   H9   single  0.930  0.020  1.080
 G5H  C6   H10  single  0.930  0.020  1.080
 G5H  N    H11  single  0.890  0.020  1.040
 G5H  N    H12  single  0.890  0.020  1.040
 G5H  CA   H14  single  0.970  0.020  1.090
 G5H  CB   H15  single  0.970  0.020  1.090
 G5H  CB   H16  single  0.970  0.020  1.090
 G5H  N3   H18  single  0.860  0.020  1.020
 G5H  N3S  H19  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
 G5H  H2   C5'  H1   107.92  3.000
 G5H  H2   C5'  O5'  111.58  3.000
 G5H  H1   C5'  O5'  106.86  3.000
 G5H  H2   C5'  C4'  110.65  3.000
 G5H  H1   C5'  C4'  109.61  3.000
 G5H  O5'  C5'  C4'  110.11  3.000
 G5H  H3   O2'  C2'  107.86  3.000
 G5H  H4   C4'  C3'  109.62  3.000
 G5H  H4   C4'  O4'  110.85  3.000
 G5H  C3'  C4'  O4'  104.16  3.000
 G5H  H4   C4'  C5'  109.95  3.000
 G5H  O4'  C4'  C5'  110.19  3.000
 G5H  C3'  C4'  C5'  111.95  3.000
 G5H  C1'  O4'  C4'  110.48  3.000
 G5H  H5   C3'  C2'  109.34  3.000
 G5H  H5   C3'  O3'  111.30  3.000
 G5H  C2'  C3'  O3'  113.84  3.000
 G5H  H5   C3'  C4'  109.58  3.000
 G5H  C2'  C3'  C4'  101.66  3.000
 G5H  O3'  C3'  C4'  110.68  3.000
 G5H  H6   O3'  C3'  109.12  3.000
 G5H  H7   C2'  C1'  111.46  3.000
 G5H  H7   C2'  C3'  112.15  3.000
 G5H  C1'  C2'  C3'  102.74  3.000
 G5H  H7   C2'  O2'  111.64  3.000
 G5H  C1'  C2'  O2'  107.55  3.000
 G5H  C3'  C2'  O2'  110.88  3.000
 G5H  H8   C1'  N1   106.67  3.000
 G5H  H8   C1'  C2'  109.42  3.000
 G5H  N1   C1'  C2'  114.55  3.000
 G5H  H8   C1'  O4'  110.90  3.000
 G5H  N1   C1'  O4'  108.21  3.000
 G5H  C2'  C1'  O4'  107.12  3.000
 G5H  H9   C5   C4   119.76  3.000
 G5H  H9   C5   C6   120.63  3.000
 G5H  C4   C5   C6   119.61  3.000
 G5H  H10  C6   N1   116.12  3.000
 G5H  H10  C6   C5   120.61  3.000
 G5H  N1   C6   C5   123.27  3.000
 G5H  N3   C4   O4   120.69  3.000
 G5H  O4   C4   C5   125.91  3.000
 G5H  N3   C4   C5   113.35  3.000
 G5H  N3   C2   N1   114.65  3.000
 G5H  N3   C2   O2   122.27  3.000
 G5H  N1   C2   O2   123.07  3.000
 G5H  H12  N    H11  106.20  3.000
 G5H  H12  N    CA   110.23  3.000
 G5H  H11  N    CA   111.21  3.000
 G5H  H14  CA   CB   106.68  3.000
 G5H  H14  CA   C    106.98  3.000
 G5H  CB   CA   C    111.40  3.000
 G5H  H14  CA   N    108.54  3.000
 G5H  C    CA   N    113.15  3.000
 G5H  CB   CA   N    109.79  3.000
 G5H  N3S  C    O    121.40  3.000
 G5H  O    C    CA   125.02  3.000
 G5H  N3S  C    CA   113.58  3.000
 G5H  H16  CB   H15  106.30  3.000
 G5H  H16  CB   CG   107.55  3.000
 G5H  H15  CB   CG   111.35  3.000
 G5H  H16  CB   CA   110.54  3.000
 G5H  H15  CB   CA   109.69  3.000
 G5H  CG   CB   CA   111.28  3.000
 G5H  OD2  CG   OD1  126.99  3.000
 G5H  OD2  CG   CB   116.79  3.000
 G5H  OD1  CG   CB   116.19  3.000
 G5H  C2   N1   C6   120.85  3.000
 G5H  C6   N1   C1'  120.11  3.000
 G5H  C2   N1   C1'  119.04  3.000
 G5H  H18  N3   C2   115.06  3.000
 G5H  H18  N3   C4   116.67  3.000
 G5H  C2   N3   C4   128.24  3.000
 G5H  H19  N3S  S    115.59  3.000
 G5H  H19  N3S  C    120.17  3.000
 G5H  S    N3S  C    123.84  3.000
 G5H  S    O5'  C5'  119.77  3.000
 G5H  O5'  S    O2S  104.31  3.000
 G5H  O2S  S    O1S  121.14  3.000
 G5H  O5'  S    O1S  110.32  3.000
 G5H  O1S  S    N3S  105.21  3.000
 G5H  O2S  S    N3S  110.86  3.000
 G5H  O5'  S    N3S  103.78  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
 G5H  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 G5H  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 G5H  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 G5H  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 G5H  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 G5H  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 G5H  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 G5H  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 G5H  CONST_09  H18  N3   C4   C5   180.00   0.0  0
 G5H  CONST_10  S    N3S  C    CA   180.00   0.0  0
 G5H  CONST_11  S    N3S  C    O      0.00   0.0  0
 G5H  CONST_12  H19  N3S  C    CA     0.00   0.0  0
 G5H  Var_01    N3S  S    O5'  C5'   68.55  30.0  3
 G5H  Var_02    OD1  CG   CB   CA   -44.38  30.0  3
 G5H  Var_03    O5'  S    N3S  C     61.40  30.0  3
 G5H  Var_04    H1   C5'  O5'  S    117.56  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
 G5H  chir_01  C4'  C5'  C3'  O4'  positiv
 G5H  chir_02  C3'  O3'  C4'  C2'  positiv
 G5H  chir_03  C2'  O2'  C3'  C1'  positiv
 G5H  chir_04  C1'  O4'  N1   C2'  negativ
 G5H  chir_05  CA   CB   N    C    positiv

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
 G5H  plan-1  C1'  0.020
 G5H  plan-1  C5   0.020
 G5H  plan-1  C6   0.020
 G5H  plan-1  C4   0.020
 G5H  plan-1  O4   0.020
 G5H  plan-1  C2   0.020
 G5H  plan-1  O2   0.020
 G5H  plan-1  N1   0.020
 G5H  plan-1  N3   0.020
 G5H  plan-1  H9   0.020
 G5H  plan-1  H10  0.020
 G5H  plan-1  H18  0.020
 G5H  plan-2  CA   0.020
 G5H  plan-2  C    0.020
 G5H  plan-2  O    0.020
 G5H  plan-2  N3S  0.020
 G5H  plan-2  S    0.020
 G5H  plan-2  H19  0.020
 G5H  plan-3  CB   0.020
 G5H  plan-3  CG   0.020
 G5H  plan-3  OD1  0.020
 G5H  plan-3  OD2  0.020

