# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 14:26:14 2021
#   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  47  29  .  2021-08-10  2022-11-17
;
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  -0.238  -19.8886  -1.3411  -14.6807
 G5H  O2'  O  OH1   0  -0.656  -21.4785   2.7017  -15.0930
 G5H  C4'  C  CH1   0   0.022  -20.6511  -0.0441  -14.7535
 G5H  O4'  O  O2    0  -0.497  -21.9582  -0.2008  -14.2125
 G5H  C3'  C  CH1   0   0.016  -20.0691   1.1390  -13.9899
 G5H  O3'  O  OH1   0  -0.654  -18.9831   1.6686  -14.6767
 G5H  C2'  C  CH1   0  -0.067  -21.2988   2.0425  -13.8732
 G5H  C1'  C  CH1   0   0.179  -22.4053   0.9949  -13.6456
 G5H  C5   C  CR16  0  -0.510  -22.4767  -0.4508  -10.1934
 G5H  C6   C  CR16  0   0.083  -22.2280  -0.2781  -11.5031
 G5H  C4   C  CR6   0   0.566  -23.2716   0.5158   -9.4799
 G5H  O4   O  O     0  -0.464  -23.5696   0.4730   -8.3007
 G5H  C2   C  CR6   0   0.742  -23.4519   1.7674  -11.6067
 G5H  O2   O  O     0  -0.481  -23.8664   2.7346  -12.2139
 G5H  N    N  NH2   0  -0.771  -17.6879  -6.8585  -14.1112
 G5H  CA   C  CH1   0  -0.236  -17.4258  -5.4769  -14.4071
 G5H  C    C  C     0   0.570  -18.2336  -4.4989  -13.5550
 G5H  O    O  O     0  -0.402  -19.2673  -4.7804  -13.0041
 G5H  CB   C  CH2   0  -0.563  -17.7514  -5.1992  -15.8824
 G5H  CG   C  C     0   0.546  -17.0322  -6.1699  -16.7834
 G5H  OD1  O  O     0  -0.436  -17.5733  -6.9002  -17.5736
 G5H  OD2  O  OH1   0  -0.590  -15.7162  -6.1107  -16.6245
 G5H  N1   N  NR6   0  -0.566  -22.6870   0.7918  -12.2107
 G5H  N3   N  NR16  0  -0.731  -23.7044   1.5655  -10.2781
 G5H  N3S  N  NC1   0  -0.832  -17.6984  -3.2263  -13.5042
 G5H  O1S  O  OS    0  -0.602  -18.6809  -2.3948  -11.2889
 G5H  O2S  O  OS    0  -0.618  -17.5174  -0.8470  -12.8817
 G5H  O5'  O  OC2   0  -0.574  -19.7826  -1.7932  -13.3148
 G5H  S    S  S     0   1.624  -18.3681  -1.9813  -12.6267
 G5H  H1   H  HCH2  0   0.294  -20.4053  -2.1294  -15.2272
 G5H  H2   H  HCH2  0   0.275  -18.9089  -1.1944  -15.1398
 G5H  H3   H  HOH1  0   0.461  -22.2338   3.2933  -15.0123
 G5H  H4   H  HCH1  0   0.268  -20.7120   0.2058  -15.8208
 G5H  H5   H  HCH1  0   0.234  -19.7957   0.8215  -12.9747
 G5H  H6   H  HOH1  0   0.464  -18.4734   2.2217  -14.0773
 G5H  H7   H  HCH1  0   0.270  -21.2195   2.7434  -13.0358
 G5H  H8   H  HCH1  0   0.288  -23.3454   1.2975  -14.1115
 G5H  H9   H  HCR6  0   0.291  -22.0913  -1.3144   -9.6743
 G5H  H10  H  HCR6  0   0.326  -21.6512  -1.0008  -12.0559
 G5H  H12  H  HNH2  0   0.355  -18.6802  -7.0560  -14.1574
 G5H  H14  H  HCH1  0   0.298  -16.3648  -5.2807  -14.2344
 G5H  H15  H  HCH2  0   0.296  -17.4661  -4.1815  -16.1606
 G5H  H16  H  HCH2  0   0.284  -18.8235  -5.3011  -16.0562
 G5H  H17  H  HOH1  0   0.484  -15.2809  -6.7513  -17.2069
 G5H  H18  H  HNR6  0   0.427  -24.2650   2.2808   -9.8309
 G5H  H19  H  HNC1  0   0.460  -16.7861  -3.0320  -13.9028
 G5H  H11  H  HNH2  0   0.367  -17.3832  -7.0899  -13.1749

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   double  1.204  0.020  1.204
 G5H  CG   OD2  single  1.327  0.020  1.327
 G5H  CG   CB   single  1.507  0.020  1.507
 G5H  CB   CA   single  1.536  0.020  1.536
 G5H  O3'  C3'  single  1.390  0.020  1.390
 G5H  O2'  C2'  single  1.398  0.020  1.398
 G5H  C4'  C5'  single  1.506  0.020  1.506
 G5H  C4'  C3'  single  1.524  0.020  1.524
 G5H  C4'  O4'  single  1.423  0.020  1.423
 G5H  C5'  O5'  single  1.443  0.020  1.443
 G5H  CA   N    single  1.437  0.020  1.437
 G5H  CA   C    single  1.528  0.020  1.528
 G5H  C3'  C2'  single  1.530  0.020  1.530
 G5H  O4'  C1'  single  1.397  0.020  1.397
 G5H  C2'  C1'  single  1.541  0.020  1.541
 G5H  C1'  N1   single  1.476  0.020  1.476
 G5H  C    N3S  single  1.382  0.020  1.382
 G5H  C    O    double  1.205  0.020  1.205
 G5H  N3S  S    single  1.664  0.020  1.664
 G5H  O5'  S    single  1.584  0.020  1.584
 G5H  O2S  S    double  1.441  0.020  1.441
 G5H  S    O1S  double  1.435  0.020  1.435
 G5H  O2   C2   double  1.215  0.020  1.215
 G5H  N1   C2   single  1.379  0.020  1.379
 G5H  N1   C6   single  1.362  0.020  1.362
 G5H  C2   N3   single  1.367  0.020  1.367
 G5H  C6   C5   double  1.344  0.020  1.344
 G5H  N3   C4   single  1.388  0.020  1.388
 G5H  C5   C4   single  1.441  0.020  1.441
 G5H  C4   O4   double  1.217  0.020  1.217
 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  OD2  H17  single  0.850  0.020  0.980
 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   108.17  3.000
 G5H  H2   C5'  O5'  111.98  3.000
 G5H  H1   C5'  O5'  106.44  3.000
 G5H  H2   C5'  C4'  108.56  3.000
 G5H  H1   C5'  C4'  111.02  3.000
 G5H  O5'  C5'  C4'  110.65  3.000
 G5H  H3   O2'  C2'  108.51  3.000
 G5H  H4   C4'  C3'  109.37  3.000
 G5H  H4   C4'  O4'  110.10  3.000
 G5H  C3'  C4'  O4'  104.23  3.000
 G5H  H4   C4'  C5'  105.73  3.000
 G5H  O4'  C4'  C5'  110.60  3.000
 G5H  C3'  C4'  C5'  116.81  3.000
 G5H  C1'  O4'  C4'  110.73  3.000
 G5H  H5   C3'  C2'  107.47  3.000
 G5H  H5   C3'  O3'  111.87  3.000
 G5H  C2'  C3'  O3'  116.14  3.000
 G5H  H5   C3'  C4'  109.50  3.000
 G5H  C2'  C3'  C4'  100.94  3.000
 G5H  O3'  C3'  C4'  110.29  3.000
 G5H  H6   O3'  C3'  108.99  3.000
 G5H  H7   C2'  C1'  111.98  3.000
 G5H  H7   C2'  C3'  112.22  3.000
 G5H  C1'  C2'  C3'  100.77  3.000
 G5H  H7   C2'  O2'  112.01  3.000
 G5H  C1'  C2'  O2'  110.92  3.000
 G5H  C3'  C2'  O2'  108.37  3.000
 G5H  H8   C1'  N1   106.76  3.000
 G5H  H8   C1'  C2'  111.52  3.000
 G5H  N1   C1'  C2'  111.97  3.000
 G5H  H8   C1'  O4'  109.86  3.000
 G5H  N1   C1'  O4'  109.74  3.000
 G5H  C2'  C1'  O4'  106.99  3.000
 G5H  H9   C5   C4   119.73  3.000
 G5H  H9   C5   C6   120.37  3.000
 G5H  C4   C5   C6   119.90  3.000
 G5H  H10  C6   N1   116.15  3.000
 G5H  H10  C6   C5   120.85  3.000
 G5H  N1   C6   C5   122.99  3.000
 G5H  N3   C4   O4   120.49  3.000
 G5H  O4   C4   C5   126.26  3.000
 G5H  N3   C4   C5   113.25  3.000
 G5H  N3   C2   N1   115.06  3.000
 G5H  N3   C2   O2   122.70  3.000
 G5H  N1   C2   O2   122.24  3.000
 G5H  H12  N    H11  107.02  3.000
 G5H  H12  N    CA   110.90  3.000
 G5H  H11  N    CA   110.83  3.000
 G5H  H14  CA   CB   108.98  3.000
 G5H  H14  CA   C    108.07  3.000
 G5H  CB   CA   C    107.93  3.000
 G5H  H14  CA   N    108.49  3.000
 G5H  C    CA   N    113.83  3.000
 G5H  CB   CA   N    109.44  3.000
 G5H  N3S  C    O    122.06  3.000
 G5H  O    C    CA   123.99  3.000
 G5H  N3S  C    CA   113.91  3.000
 G5H  H16  CB   H15  107.63  3.000
 G5H  H16  CB   CG   108.28  3.000
 G5H  H15  CB   CG   108.85  3.000
 G5H  H16  CB   CA   110.15  3.000
 G5H  H15  CB   CA   110.94  3.000
 G5H  CG   CB   CA   110.89  3.000
 G5H  OD2  CG   OD1  123.45  3.000
 G5H  OD2  CG   CB   111.90  3.000
 G5H  OD1  CG   CB   124.64  3.000
 G5H  H17  OD2  CG   110.12  3.000
 G5H  C2   N1   C6   121.00  3.000
 G5H  C6   N1   C1'  123.26  3.000
 G5H  C2   N1   C1'  115.74  3.000
 G5H  H18  N3   C2   115.28  3.000
 G5H  H18  N3   C4   116.92  3.000
 G5H  C2   N3   C4   127.79  3.000
 G5H  H19  N3S  S    115.21  3.000
 G5H  H19  N3S  C    120.69  3.000
 G5H  S    N3S  C    123.55  3.000
 G5H  S    O5'  C5'  120.93  3.000
 G5H  O5'  S    O2S  110.91  3.000
 G5H  O2S  S    O1S  121.38  3.000
 G5H  O5'  S    O1S  104.16  3.000
 G5H  O1S  S    N3S  111.33  3.000
 G5H  O2S  S    N3S  104.96  3.000
 G5H  O5'  S    N3S  102.66  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  CONST_13  H17  OD2  CG   CB   180.00   0.0  0
 G5H  Var_01    N3S  S    O5'  C5'  -65.44  30.0  3
 G5H  Var_02    OD1  CG   CB   CA   122.51  30.0  2
 G5H  Var_03    O5'  S    N3S  C    -62.64  30.0  3
 G5H  Var_04    H1   C5'  O5'  S    119.89  30.0  2

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
 G5H  plan-3  H17  0.020

