# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 20:34:26 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-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: CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)CC(O)=O)[C@@H](O)[C@H]2O)C1=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
 G5Q  G5Q  '(3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid'  ligand  50  30  .  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_G5Q
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
 G5Q  N    N  NH2   0  -0.770  -17.9407  -6.6913  -14.4045
 G5Q  CA   C  CH1   0  -0.236  -17.7074  -5.3051  -14.7015
 G5Q  C    C  C     0   0.569  -18.5890  -4.3457  -13.9022
 G5Q  O    O  O     0  -0.402  -19.6381  -4.6564  -13.3985
 G5Q  CD   C  CH2   0  -0.565  -17.9630  -5.0526  -16.1947
 G5Q  OD1  O  OH1   0  -0.590  -15.8659  -5.9149  -16.8138
 G5Q  OD2  O  O     0  -0.437  -17.6444  -6.7540  -17.8648
 G5Q  C1'  C  CH1   0   0.177  -22.8717   1.0757  -14.1847
 G5Q  C2   C  CR6   0   0.794  -23.9683   1.8518  -12.1743
 G5Q  C2'  C  CH1   0  -0.065  -21.7709   2.1338  -14.3893
 G5Q  C3'  C  CH1   0   0.016  -20.5287   1.2436  -14.4617
 G5Q  C4   C  CR6   0   0.588  -23.8532   0.6186  -10.0516
 G5Q  C4'  C  CH1   0   0.022  -21.0729   0.0469  -15.2314
 G5Q  C5   C  CR16  0  -0.508  -23.0392  -0.3488  -10.7390
 G5Q  C5'  C  CH2   0  -0.238  -20.2988  -1.2411  -15.1220
 G5Q  C6   C  CR16  0   0.077  -22.7467  -0.1922  -12.0392
 G5Q  N1   N  NR6   0  -0.579  -23.1882   0.8752  -12.7554
 G5Q  N3   N  NR6   0  -0.592  -24.2863   1.6829  -10.8471
 G5Q  N3S  N  NC1   0  -0.832  -18.0978  -3.0559  -13.8404
 G5Q  O1S  O  OS    0  -0.619  -18.0134  -0.6670  -13.2385
 G5Q  O2'  O  OH1   0  -0.658  -21.9220   2.7803  -15.6199
 G5Q  O2S  O  OS    0  -0.602  -19.1933  -2.2333  -11.6764
 G5Q  O3'  O  OH1   0  -0.654  -19.4287   1.7806  -15.1204
 G5Q  O4   O  O     0  -0.471  -24.1606   0.5466   -8.8751
 G5Q  O4'  O  O2    0  -0.498  -22.3959  -0.1181  -14.7329
 G5Q  O5'  O  OC2   0  -0.574  -20.2315  -1.6841  -13.7504
 G5Q  S    S  S     0   1.624  -18.8403  -1.8237  -13.0055
 G5Q  H1   H  HNH2  0   0.367  -17.6901  -6.9010  -13.4473
 G5Q  H2   H  HNH2  0   0.355  -18.9204  -6.9247  -14.5123
 G5Q  H4   H  HCH1  0   0.298  -16.6635  -5.0737  -14.4747
 G5Q  H5   H  HCH2  0   0.296  -17.6946  -4.0293  -16.4702
 G5Q  H6   H  HCH2  0   0.284  -19.0210  -5.1885  -16.4235
 G5Q  H7   H  HOH1  0   0.484  -15.3817  -6.5462  -17.3671
 G5Q  H8   H  HCH1  0   0.287  -23.8028   1.3640  -14.6769
 G5Q  H9   H  HCH1  0   0.268  -21.7227   2.8424  -13.5564
 G5Q  H10  H  HCH1  0   0.234  -20.2828   0.9387  -13.4359
 G5Q  H11  H  HCH3  0   0.268  -25.3614   2.4449   -9.2421
 G5Q  H12  H  HCH3  0   0.258  -24.5746   3.6760  -10.2358
 G5Q  H13  H  HCH3  0   0.259  -26.0301   2.8559  -10.8243
 G5Q  H14  H  HCH1  0   0.267  -21.1012   0.2854  -16.3027
 G5Q  H15  H  HCR6  0   0.289  -22.6728  -1.2050  -10.1944
 G5Q  H16  H  HCH2  0   0.294  -20.7886  -2.0399  -15.6780
 G5Q  H17  H  HCH2  0   0.275  -19.3063  -1.0876  -15.5506
 G5Q  H18  H  HCR6  0   0.327  -22.1520  -0.9159  -12.5705
 G5Q  H19  H  HNC1  0   0.460  -17.1806  -2.8338  -14.2119
 G5Q  H20  H  HOH1  0   0.462  -22.6940   3.3537  -15.5706
 G5Q  H21  H  HOH1  0   0.464  -18.9409   2.3405  -14.5091
 G5Q  CG   C  C     0   0.547  -17.1687  -6.0087  -17.0468
 G5Q  O2   O  O     0  -0.489  -24.3505   2.8142  -12.8118
 G5Q  C3U  C  CH3   0  -0.532  -25.1117   2.7295  -10.2565

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
 G5Q  OD2  CG   double  1.205  0.020  1.205
 G5Q  CG   OD1  single  1.327  0.020  1.327
 G5Q  CG   CD   single  1.507  0.020  1.507
 G5Q  CD   CA   single  1.536  0.020  1.536
 G5Q  O3'  C3'  single  1.390  0.020  1.390
 G5Q  O2'  C2'  single  1.398  0.020  1.398
 G5Q  C4'  C5'  single  1.507  0.020  1.507
 G5Q  C4'  C3'  single  1.523  0.020  1.523
 G5Q  C4'  O4'  single  1.423  0.020  1.423
 G5Q  C5'  O5'  single  1.443  0.020  1.443
 G5Q  CA   N    single  1.437  0.020  1.437
 G5Q  CA   C    single  1.528  0.020  1.528
 G5Q  C3'  C2'  single  1.530  0.020  1.530
 G5Q  O4'  C1'  single  1.397  0.020  1.397
 G5Q  C2'  C1'  single  1.540  0.020  1.540
 G5Q  C    N3S  single  1.382  0.020  1.382
 G5Q  C    O    double  1.204  0.020  1.204
 G5Q  C1'  N1   single  1.478  0.020  1.478
 G5Q  N3S  S    single  1.663  0.020  1.663
 G5Q  O5'  S    single  1.584  0.020  1.584
 G5Q  O1S  S    double  1.441  0.020  1.441
 G5Q  O2   C2   double  1.216  0.020  1.216
 G5Q  S    O2S  double  1.435  0.020  1.435
 G5Q  N1   C2   single  1.378  0.020  1.378
 G5Q  N1   C6   single  1.359  0.020  1.359
 G5Q  C2   N3   single  1.375  0.020  1.375
 G5Q  C6   C5   double  1.342  0.020  1.342
 G5Q  N3   C3U  single  1.458  0.020  1.458
 G5Q  N3   C4   single  1.398  0.020  1.398
 G5Q  C5   C4   single  1.439  0.020  1.439
 G5Q  C4   O4   double  1.218  0.020  1.218
 G5Q  N    H1   single  0.890  0.020  1.040
 G5Q  N    H2   single  0.890  0.020  1.040
 G5Q  CA   H4   single  0.970  0.020  1.090
 G5Q  CD   H5   single  0.970  0.020  1.090
 G5Q  CD   H6   single  0.970  0.020  1.090
 G5Q  OD1  H7   single  0.850  0.020  0.980
 G5Q  C1'  H8   single  0.970  0.020  1.090
 G5Q  C2'  H9   single  0.970  0.020  1.090
 G5Q  C3'  H10  single  0.970  0.020  1.090
 G5Q  C3U  H11  single  0.970  0.020  1.090
 G5Q  C3U  H12  single  0.970  0.020  1.090
 G5Q  C3U  H13  single  0.970  0.020  1.090
 G5Q  C4'  H14  single  0.970  0.020  1.090
 G5Q  C5   H15  single  0.930  0.020  1.080
 G5Q  C5'  H16  single  0.970  0.020  1.090
 G5Q  C5'  H17  single  0.970  0.020  1.090
 G5Q  C6   H18  single  0.930  0.020  1.080
 G5Q  N3S  H19  single  0.860  0.020  1.020
 G5Q  O2'  H20  single  0.850  0.020  0.980
 G5Q  O3'  H21  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
 G5Q  H2   N    H1   107.01  3.000
 G5Q  H2   N    CA   110.94  3.000
 G5Q  H1   N    CA   110.82  3.000
 G5Q  H4   CA   CD   109.02  3.000
 G5Q  H4   CA   C    108.02  3.000
 G5Q  CD   CA   C    108.02  3.000
 G5Q  H4   CA   N    108.44  3.000
 G5Q  C    CA   N    113.81  3.000
 G5Q  CD   CA   N    109.43  3.000
 G5Q  N3S  C    O    122.12  3.000
 G5Q  O    C    CA   124.00  3.000
 G5Q  N3S  C    CA   113.85  3.000
 G5Q  H6   CD   H5   107.57  3.000
 G5Q  H6   CD   CG   108.27  3.000
 G5Q  H5   CD   CG   108.78  3.000
 G5Q  H6   CD   CA   110.17  3.000
 G5Q  H5   CD   CA   110.98  3.000
 G5Q  CG   CD   CA   110.96  3.000
 G5Q  H7   OD1  CG   110.13  3.000
 G5Q  H8   C1'  O4'  109.82  3.000
 G5Q  H8   C1'  N1   106.81  3.000
 G5Q  O4'  C1'  N1   109.67  3.000
 G5Q  H8   C1'  C2'  111.60  3.000
 G5Q  N1   C1'  C2'  112.01  3.000
 G5Q  O4'  C1'  C2'  106.95  3.000
 G5Q  O2   C2   N3   122.04  3.000
 G5Q  N3   C2   N1   116.79  3.000
 G5Q  O2   C2   N1   121.17  3.000
 G5Q  H9   C2'  O2'  112.03  3.000
 G5Q  H9   C2'  C3'  112.14  3.000
 G5Q  O2'  C2'  C3'  108.37  3.000
 G5Q  H9   C2'  C1'  112.03  3.000
 G5Q  C3'  C2'  C1'  100.77  3.000
 G5Q  O2'  C2'  C1'  110.93  3.000
 G5Q  H10  C3'  O3'  111.89  3.000
 G5Q  H10  C3'  C4'  109.50  3.000
 G5Q  O3'  C3'  C4'  110.28  3.000
 G5Q  H10  C3'  C2'  107.41  3.000
 G5Q  C4'  C3'  C2'  101.01  3.000
 G5Q  O3'  C3'  C2'  116.12  3.000
 G5Q  O4   C4   N3   121.10  3.000
 G5Q  O4   C4   C5   124.36  3.000
 G5Q  N3   C4   C5   114.54  3.000
 G5Q  H14  C4'  O4'  110.05  3.000
 G5Q  H14  C4'  C5'  105.65  3.000
 G5Q  O4'  C4'  C5'  110.68  3.000
 G5Q  H14  C4'  C3'  109.37  3.000
 G5Q  O4'  C4'  C3'  104.25  3.000
 G5Q  C5'  C4'  C3'  116.83  3.000
 G5Q  H15  C5   C6   120.51  3.000
 G5Q  H15  C5   C4   118.98  3.000
 G5Q  C6   C5   C4   120.51  3.000
 G5Q  H17  C5'  H16  108.14  3.000
 G5Q  H17  C5'  O5'  111.95  3.000
 G5Q  H16  C5'  O5'  106.31  3.000
 G5Q  H17  C5'  C4'  108.57  3.000
 G5Q  H16  C5'  C4'  111.02  3.000
 G5Q  O5'  C5'  C4'  110.82  3.000
 G5Q  H18  C6   N1   116.56  3.000
 G5Q  H18  C6   C5   121.33  3.000
 G5Q  N1   C6   C5   122.11  3.000
 G5Q  C6   N1   C2   121.20  3.000
 G5Q  C6   N1   C1'  123.15  3.000
 G5Q  C2   N1   C1'  115.65  3.000
 G5Q  C4   N3   C3U  119.45  3.000
 G5Q  C4   N3   C2   124.83  3.000
 G5Q  C3U  N3   C2   115.70  3.000
 G5Q  H19  N3S  S    115.17  3.000
 G5Q  H19  N3S  C    120.63  3.000
 G5Q  S    N3S  C    123.74  3.000
 G5Q  H20  O2'  C2'  108.48  3.000
 G5Q  H21  O3'  C3'  108.96  3.000
 G5Q  C4'  O4'  C1'  110.79  3.000
 G5Q  S    O5'  C5'  121.00  3.000
 G5Q  O5'  S    O2S  104.16  3.000
 G5Q  O2S  S    O1S  121.34  3.000
 G5Q  O5'  S    O1S  110.93  3.000
 G5Q  O2S  S    N3S  111.30  3.000
 G5Q  O1S  S    N3S  104.91  3.000
 G5Q  O5'  S    N3S  102.78  3.000
 G5Q  OD2  CG   OD1  123.43  3.000
 G5Q  OD1  CG   CD   111.92  3.000
 G5Q  OD2  CG   CD   124.63  3.000
 G5Q  H13  C3U  H12  109.01  3.000
 G5Q  H13  C3U  H11  108.96  3.000
 G5Q  H12  C3U  H11  108.94  3.000
 G5Q  H13  C3U  N3   110.50  3.000
 G5Q  H12  C3U  N3   110.65  3.000
 G5Q  H11  C3U  N3   108.75  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
 G5Q  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 G5Q  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 G5Q  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 G5Q  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 G5Q  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 G5Q  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 G5Q  CONST_07  N1   C2   N3   C3U  180.00   0.0  0
 G5Q  CONST_08  C5   C4   N3   C3U  180.00   0.0  0
 G5Q  CONST_09  O2   C2   N3   C4   180.00   0.0  0
 G5Q  CONST_10  O2   C2   N1   C6   180.00   0.0  0
 G5Q  CONST_11  O2   C2   N3   C3U    0.00   0.0  0
 G5Q  CONST_12  O4   C4   N3   C3U    0.00   0.0  0
 G5Q  CONST_13  S    N3S  C    CA   180.00   0.0  0
 G5Q  CONST_14  S    N3S  C    O      0.00   0.0  0
 G5Q  CONST_15  H19  N3S  C    CA     0.00   0.0  0
 G5Q  CONST_16  H7   OD1  CG   CD   180.00   0.0  0
 G5Q  Var_01    H11  C3U  N3   C2   175.32  30.0  3
 G5Q  Var_02    OD2  CG   CD   CA   123.22  30.0  2
 G5Q  Var_03    O5'  S    N3S  C    -62.55  30.0  3
 G5Q  Var_04    N3S  S    O5'  C5'  -65.79  30.0  3
 G5Q  Var_05    H16  C5'  O5'  S    121.14  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
 G5Q  chir_01  CA   CD   N    C    positiv
 G5Q  chir_02  C1'  O4'  C2'  N1   positiv
 G5Q  chir_03  C2'  O2'  C1'  C3'  negativ
 G5Q  chir_04  C3'  O3'  C4'  C2'  positiv
 G5Q  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
 G5Q  plan-1  C1'  0.020
 G5Q  plan-1  C2   0.020
 G5Q  plan-1  C4   0.020
 G5Q  plan-1  C5   0.020
 G5Q  plan-1  C6   0.020
 G5Q  plan-1  N1   0.020
 G5Q  plan-1  N3   0.020
 G5Q  plan-1  O4   0.020
 G5Q  plan-1  H15  0.020
 G5Q  plan-1  H18  0.020
 G5Q  plan-1  O2   0.020
 G5Q  plan-1  C3U  0.020
 G5Q  plan-2  CA   0.020
 G5Q  plan-2  C    0.020
 G5Q  plan-2  O    0.020
 G5Q  plan-2  N3S  0.020
 G5Q  plan-2  S    0.020
 G5Q  plan-2  H19  0.020
 G5Q  plan-3  CD   0.020
 G5Q  plan-3  OD1  0.020
 G5Q  plan-3  OD2  0.020
 G5Q  plan-3  H7   0.020
 G5Q  plan-3  CG   0.020

