# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:17:54 2020
#   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  49  30  .  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_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  -0.768   0.9182   2.1219   1.5057
 G5Q  CA   C  CH1    0  -0.244   1.8101   1.5270   0.5417
 G5Q  C    C  C      0   0.577   1.9448   0.0200   0.6937
 G5Q  O    O  O      0  -0.416   1.8547  -0.5754   1.7383
 G5Q  CD   C  CH2    0  -0.560   3.2004   2.1500   0.6551
 G5Q  OD1  O  OC    -1  -0.615   3.8917   4.4144   0.8834
 G5Q  OD2  O  O      0  -0.596   2.5572   3.8896  -0.8254
 G5Q  C1'  C  CR15   0   0.190  -2.2677  -1.0595   0.0267
 G5Q  C2   C  CR6    0   0.782  -2.8556   1.2816   0.4196
 G5Q  C2'  C  CR15   0  -0.035  -2.7214  -1.9166  -1.1503
 G5Q  C3'  C  CR15   0  -0.049  -2.2482  -3.2989  -0.6924
 G5Q  C4   C  CR6    0   0.589  -1.7388   3.0590  -0.8758
 G5Q  C4'  C  CR15   0  -0.015  -0.9353  -2.9573   0.0163
 G5Q  C5   C  CR16   0  -0.497  -1.0111   2.0165  -1.5581
 G5Q  C5'  C  CH2    0  -0.197   0.2723  -3.1679  -0.8672
 G5Q  C6   C  CR16   0   0.080  -1.2149   0.7341  -1.2374
 G5Q  N1   N  NR6    0  -0.580  -2.1082   0.3485  -0.2794
 G5Q  N3   N  NR6    0  -0.601  -2.6170   2.6040   0.1132
 G5Q  N3S  N  NC1    0  -0.837   2.2276  -0.6348  -0.4958
 G5Q  O1S  O  OS     0  -0.630   2.9202  -2.4800  -1.9804
 G5Q  O2'  O  OH1    0  -0.651  -4.0992  -1.7938  -1.3247
 G5Q  O2S  O  OS     0  -0.612   3.7335  -2.4938   0.3922
 G5Q  O3'  O  OH1    0  -0.663  -3.1274  -3.8425   0.2557
 G5Q  O4'  O  O      0  -0.486  -1.0220  -1.5861   0.4054
 G5Q  O5'  O  OC2    0  -0.566   1.4470  -3.0106  -0.0441
 G5Q  S    S  S      0   1.619   2.7088  -2.2224  -0.5772
 G5Q  H1   H  HNH2   0   0.340  -0.0208   1.7651   1.3916
 G5Q  H2   H  HNH2   0   0.347   1.1994   1.8740   2.4468
 G5Q  H4   H  HCH1   0   0.269   1.4355   1.7584  -0.4583
 G5Q  H5   H  HCH2   0   0.225   3.5659   2.0478   1.6800
 G5Q  H6   H  HCH2   0   0.244   3.9080   1.6063   0.0190
 G5Q  H8   H  HCR5   0   0.282  -2.9948  -1.1257   0.8380
 G5Q  H9   H  HCR5   0   0.255  -2.1721  -1.6379  -2.0589
 G5Q  H10  H  HCR5   0   0.261  -2.0968  -3.9809  -1.5389
 G5Q  H11  H  HCH3   0   0.260  -3.2287   3.4518   1.9365
 G5Q  H12  H  HCH3   0   0.270  -3.0974   4.5710   0.5763
 G5Q  H13  H  HCH3   0   0.260  -4.4627   3.4524   0.6659
 G5Q  H14  H  HCR5   0   0.280  -0.8338  -3.5835   0.9084
 G5Q  H15  H  HCR6   0   0.298  -0.2960   2.2899  -2.3181
 G5Q  H16  H  HCH2   0   0.283   0.2834  -4.1835  -1.2622
 G5Q  H17  H  HCH2   0   0.257   0.2772  -2.4735  -1.7111
 G5Q  H18  H  HCR6   0   0.320  -0.6643  -0.0549  -1.7284
 G5Q  H19  H  HNC1   0   0.449   2.3302  -0.1064  -1.3543
 G5Q  H20  H  HOH1   0   0.472  -4.3307  -2.0885  -2.2114
 G5Q  H21  H  HOH1   0   0.452  -4.0258  -3.7476  -0.0829
 G5Q  CG   C  C      0   0.417   3.2062   3.6262   0.2033
 G5Q  O2   O  O      0  -0.471  -3.6690   0.9615   1.2592
 G5Q  C3U  C  CH3    0  -0.532  -3.4011   3.5743   0.8701
 G5Q  O4   O  O      0  -0.455  -1.6208   4.2437  -1.1173

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   deloc   1.245  0.020  1.245
 G5Q  CG   OD1  deloc   1.246  0.020  1.246
 G5Q  CG   CD   single  1.544  0.020  1.544
 G5Q  CD   CA   single  1.528  0.020  1.528
 G5Q  O3'  C3'  single  1.403  0.020  1.403
 G5Q  O2'  C2'  single  1.394  0.020  1.394
 G5Q  C4'  C5'  single  1.511  0.020  1.511
 G5Q  C4'  C3'  single  1.531  0.020  1.531
 G5Q  C4'  O4'  single  1.428  0.020  1.428
 G5Q  C5'  O5'  single  1.443  0.020  1.443
 G5Q  CA   N    single  1.442  0.020  1.442
 G5Q  CA   C    single  1.521  0.020  1.521
 G5Q  C3'  C2'  single  1.531  0.020  1.531
 G5Q  O4'  C1'  single  1.404  0.020  1.404
 G5Q  C2'  C1'  single  1.525  0.020  1.525
 G5Q  C    N3S  single  1.387  0.020  1.387
 G5Q  C    O    double  1.206  0.020  1.206
 G5Q  C1'  N1   single  1.450  0.020  1.450
 G5Q  N3S  S    single  1.661  0.020  1.661
 G5Q  O5'  S    single  1.580  0.020  1.580
 G5Q  O1S  S    deloc   1.442  0.020  1.442
 G5Q  O2   C2   double  1.212  0.020  1.212
 G5Q  S    O2S  deloc   1.436  0.020  1.436
 G5Q  N1   C2   single  1.385  0.020  1.385
 G5Q  N1   C6   single  1.365  0.020  1.365
 G5Q  C2   N3   single  1.378  0.020  1.378
 G5Q  C6   C5   double  1.338  0.020  1.338
 G5Q  N3   C3U  single  1.459  0.020  1.459
 G5Q  N3   C4   single  1.399  0.020  1.399
 G5Q  C5   C4   single  1.443  0.020  1.443
 G5Q  C4   O4   double  1.215  0.020  1.215
 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  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   106.04  3.000
 G5Q  H2   N    CA   110.39  3.000
 G5Q  H1   N    CA   110.70  3.000
 G5Q  H4   CA   CD   107.07  3.000
 G5Q  H4   CA   C    109.38  3.000
 G5Q  CD   CA   C    108.43  3.000
 G5Q  H4   CA   N    108.21  3.000
 G5Q  C    CA   N    113.38  3.000
 G5Q  CD   CA   N    110.19  3.000
 G5Q  N3S  C    O    121.68  3.000
 G5Q  O    C    CA   124.71  3.000
 G5Q  N3S  C    CA   113.59  3.000
 G5Q  H6   CD   H5   106.37  3.000
 G5Q  H6   CD   CG   107.58  3.000
 G5Q  H5   CD   CG   111.26  3.000
 G5Q  H6   CD   CA   110.01  3.000
 G5Q  H5   CD   CA   109.62  3.000
 G5Q  CG   CD   CA   111.82  3.000
 G5Q  H8   C1'  O4'  111.57  3.000
 G5Q  H8   C1'  N1   106.81  3.000
 G5Q  O4'  C1'  N1   108.87  3.000
 G5Q  H8   C1'  C2'  109.97  3.000
 G5Q  N1   C1'  C2'  114.56  3.000
 G5Q  O4'  C1'  C2'  105.15  3.000
 G5Q  O2   C2   N3   121.57  3.000
 G5Q  N3   C2   N1   116.16  3.000
 G5Q  O2   C2   N1   122.27  3.000
 G5Q  H9   C2'  O2'  111.63  3.000
 G5Q  H9   C2'  C3'  108.79  3.000
 G5Q  O2'  C2'  C3'  114.98  3.000
 G5Q  H9   C2'  C1'  110.32  3.000
 G5Q  C3'  C2'  C1'  100.64  3.000
 G5Q  O2'  C2'  C1'  109.94  3.000
 G5Q  H10  C3'  O3'  111.53  3.000
 G5Q  H10  C3'  C4'  112.18  3.000
 G5Q  O3'  C3'  C4'  108.13  3.000
 G5Q  H10  C3'  C2'  111.90  3.000
 G5Q  C4'  C3'  C2'  101.66  3.000
 G5Q  O3'  C3'  C2'  110.99  3.000
 G5Q  O4   C4   N3   121.26  3.000
 G5Q  O4   C4   C5   124.16  3.000
 G5Q  N3   C4   C5   114.58  3.000
 G5Q  H14  C4'  O4'  109.45  3.000
 G5Q  H14  C4'  C5'  108.82  3.000
 G5Q  O4'  C4'  C5'  109.98  3.000
 G5Q  H14  C4'  C3'  109.22  3.000
 G5Q  O4'  C4'  C3'  106.76  3.000
 G5Q  C5'  C4'  C3'  112.57  3.000
 G5Q  H15  C5   C6   120.86  3.000
 G5Q  H15  C5   C4   118.98  3.000
 G5Q  C6   C5   C4   120.16  3.000
 G5Q  H17  C5'  H16  108.19  3.000
 G5Q  H17  C5'  O5'  111.57  3.000
 G5Q  H16  C5'  O5'  107.47  3.000
 G5Q  H17  C5'  C4'  111.50  3.000
 G5Q  H16  C5'  C4'  110.48  3.000
 G5Q  O5'  C5'  C4'  107.58  3.000
 G5Q  H18  C6   N1   116.49  3.000
 G5Q  H18  C6   C5   120.91  3.000
 G5Q  N1   C6   C5   122.60  3.000
 G5Q  C6   N1   C2   121.12  3.000
 G5Q  C6   N1   C1'  119.63  3.000
 G5Q  C2   N1   C1'  119.24  3.000
 G5Q  C4   N3   C3U  119.20  3.000
 G5Q  C4   N3   C2   125.31  3.000
 G5Q  C3U  N3   C2   115.45  3.000
 G5Q  H19  N3S  S    115.31  3.000
 G5Q  H19  N3S  C    120.07  3.000
 G5Q  S    N3S  C    123.53  3.000
 G5Q  H20  O2'  C2'  109.02  3.000
 G5Q  H21  O3'  C3'  107.96  3.000
 G5Q  C4'  O4'  C1'  109.90  3.000
 G5Q  S    O5'  C5'  120.79  3.000
 G5Q  O5'  S    O2S  104.34  3.000
 G5Q  O2S  S    O1S  121.22  3.000
 G5Q  O5'  S    O1S  110.87  3.000
 G5Q  O2S  S    N3S  110.74  3.000
 G5Q  O1S  S    N3S  105.12  3.000
 G5Q  O5'  S    N3S  103.23  3.000
 G5Q  OD2  CG   OD1  127.15  3.000
 G5Q  OD1  CG   CD   116.56  3.000
 G5Q  OD2  CG   CD   116.25  3.000
 G5Q  H13  C3U  H12  109.02  3.000
 G5Q  H13  C3U  H11  109.04  3.000
 G5Q  H12  C3U  H11  108.99  3.000
 G5Q  H13  C3U  N3   110.65  3.000
 G5Q  H12  C3U  N3   108.71  3.000
 G5Q  H11  C3U  N3   110.40  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  Var_01    H11  C3U  N3   C2    58.00  30.0  3
 G5Q  Var_02    OD2  CG   CD   CA   -42.49  30.0  2
 G5Q  Var_03    O5'  S    N3S  C     64.99  30.0  3
 G5Q  Var_04    N3S  S    O5'  C5'   74.69  30.0  3
 G5Q  Var_05    H16  C5'  O5'  S    102.74  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  H15  0.020
 G5Q  plan-1  H18  0.020
 G5Q  plan-1  O2   0.020
 G5Q  plan-1  C3U  0.020
 G5Q  plan-1  O4   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  CG   0.020

