# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  9 00:57:31 2020
#   Inital geometry file: a 143 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-(4-hydroxyphenyl)propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=NC3=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
 YSC  YSC  '[(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-(4-hydroxyphenyl)propanoyl]sulfamate'  ligand  56  33  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YSC
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
 YSC  N    N  NH2   0  -0.772   1.2555   0.8149   1.9335
 YSC  CA   C  CH1   0  -0.253   1.5481  -0.1898   0.9457
 YSC  CB   C  CH2   0  -0.535   3.0554  -0.4361   0.6936
 YSC  CG   C  CR6   0   0.105   3.7097   0.8283   0.2125
 YSC  CD2  C  CR16  0  -0.269   3.5739   1.2342  -1.1141
 YSC  CE2  C  CR16  0  -0.344   4.1165   2.4247  -1.5690
 YSC  CZ   C  CR6   0   0.337   4.8149   3.2511  -0.6889
 YSC  OH   O  OH1   0  -0.632   5.3303   4.3973  -1.1769
 YSC  CE1  C  CR16  0  -0.368   4.9555   2.8650   0.6403
 YSC  CD1  C  CR16  0  -0.301   4.4047   1.6675   1.0767
 YSC  C    C  C     0   0.606   0.8245  -1.4730   1.3173
 YSC  O    O  O     0  -0.404   0.2470  -1.6624   2.3551
 YSC  NAT  N  NC1   0  -0.843   0.8773  -2.4407   0.3248
 YSC  SBI  S  S     0   1.622   0.0538  -3.8818   0.3887
 YSC  OAD  O  OS    0  -0.633   0.3645  -4.5429  -0.8547
 YSC  OAE  O  OS    0  -0.609   0.2608  -4.5354   1.6494
 YSC  O5'  O  OC2   0  -0.570  -1.4625  -3.4285   0.4077
 YSC  C5'  C  CH2   0  -0.209  -2.0013  -2.7964  -0.7761
 YSC  C4'  C  CH1   0   0.017  -3.1133  -1.8723  -0.3526
 YSC  O4'  O  O2    0  -0.480  -2.5917  -0.8363   0.4501
 YSC  C1'  C  CH1   0   0.200  -3.1654   0.4032   0.1358
 YSC  C2'  C  CH1   0  -0.039  -4.1090   0.2009  -1.0607
 YSC  O2'  O  OH1   0  -0.676  -5.4272   0.2382  -0.5781
 YSC  C3'  C  CH1   0  -0.040  -3.7644  -1.2122  -1.5723
 YSC  O3'  O  OH1   0  -0.661  -4.9012  -1.9448  -1.9529
 YSC  N1   N  NR6   0  -0.551  -2.1156   1.3963  -0.0206
 YSC  C6   C  CR16  0   0.101  -2.0298   2.4134   0.8726
 YSC  C5   C  CR16  0  -0.458  -1.0165   3.2986   0.8459
 YSC  C4   C  CR6   0   0.510  -0.0024   3.0653  -0.1318
 YSC  N4   N  NH2   0  -0.815   1.0949   3.8218  -0.1437
 YSC  N3   N  N     0  -0.538  -0.1024   2.1042  -1.0288
 YSC  C2   C  CR6   0   0.616  -1.1481   1.2566  -1.0253
 YSC  O2   O  O     0  -0.514  -1.2778   0.3676  -1.8574
 YSC  H1   H  HNH2  0   0.346   1.7223   0.5991   2.8066
 YSC  H2   H  HNH2  0   0.362   1.6235   1.7051   1.6250
 YSC  H4   H  HCH1  0   0.295   1.1148   0.1424  -0.0034
 YSC  H5   H  HCH2  0   0.266   3.5226  -0.7827   1.6191
 YSC  H6   H  HCH2  0   0.255   3.2040  -1.2257  -0.0479
 YSC  H7   H  HCR6  0   0.249   3.0307   0.6099  -1.8140
 YSC  H8   H  HCR6  0   0.267   4.0062   2.7149  -2.6068
 YSC  H9   H  HOH1  0   0.474   5.7832   4.8852  -0.4803
 YSC  H10  H  HCR6  0   0.271   5.4969   3.4933   1.3386
 YSC  H11  H  HCR6  0   0.255   4.5305   1.3847   2.1151
 YSC  H12  H  HNC1  0   0.452   1.3648  -2.2586  -0.5441
 YSC  H13  H  HCH2  0   0.259  -1.2328  -2.2211  -1.2968
 YSC  H14  H  HCH2  0   0.274  -2.3860  -3.5693  -1.4423
 YSC  H15  H  HCH1  0   0.256  -3.8745  -2.4352   0.2043
 YSC  H16  H  HCH1  0   0.256  -3.7663   0.7598   0.9769
 YSC  H17  H  HCH1  0   0.250  -3.9544   0.9633  -1.8313
 YSC  H18  H  HOH1  0   0.449  -5.9029  -0.4879  -1.0058
 YSC  H19  H  HCH1  0   0.267  -3.0525  -1.1375  -2.3942
 YSC  H20  H  HOH1  0   0.472  -5.0494  -1.8204  -2.8958
 YSC  H21  H  HCR6  0   0.319  -2.8184   2.4755   1.6097
 YSC  H22  H  HCR6  0   0.288  -0.9524   4.1007   1.5647
 YSC  H23  H  HNH2  0   0.414   1.2302   4.5653   0.5187
 YSC  H24  H  HNH2  0   0.408   1.8426   3.6102  -0.7848

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
 YSC  O2   C2   double    1.225  0.020  1.225
 YSC  C2   N3   single    1.346  0.020  1.346
 YSC  C2   N1   single    1.402  0.020  1.402
 YSC  N3   C4   double    1.318  0.020  1.318
 YSC  O4'  C1'  single    1.402  0.020  1.402
 YSC  O4'  C4'  single    1.411  0.020  1.411
 YSC  C1'  N1   single    1.454  0.020  1.454
 YSC  C1'  C2'  single    1.537  0.020  1.537
 YSC  N1   C6   single    1.356  0.020  1.356
 YSC  O3'  C3'  single    1.405  0.020  1.405
 YSC  C4   N4   single    1.333  0.020  1.333
 YSC  C4   C5   single    1.428  0.020  1.428
 YSC  C4'  C3'  single    1.532  0.020  1.532
 YSC  C4'  C5'  single    1.507  0.020  1.507
 YSC  O2'  C2'  single    1.404  0.020  1.404
 YSC  C3'  C2'  single    1.542  0.020  1.542
 YSC  C6   C5   double    1.346  0.020  1.346
 YSC  C5'  O5'  single    1.446  0.020  1.446
 YSC  O5'  SBI  single    1.583  0.020  1.583
 YSC  CE2  CD2  aromatic  1.385  0.020  1.385
 YSC  CE2  CZ   aromatic  1.395  0.020  1.395
 YSC  CD2  CG   aromatic  1.394  0.020  1.394
 YSC  SBI  OAE  deloc     1.435  0.020  1.435
 YSC  SBI  NAT  single    1.661  0.020  1.661
 YSC  SBI  OAD  deloc     1.442  0.020  1.442
 YSC  NAT  C    single    1.387  0.020  1.387
 YSC  OH   CZ   single    1.348  0.020  1.348
 YSC  CZ   CE1  aromatic  1.391  0.020  1.391
 YSC  CB   CG   single    1.503  0.020  1.503
 YSC  CB   CA   single    1.548  0.020  1.548
 YSC  CG   CD1  aromatic  1.391  0.020  1.391
 YSC  CA   C    single    1.519  0.020  1.519
 YSC  CA   N    single    1.439  0.020  1.439
 YSC  C    O    double    1.203  0.020  1.203
 YSC  CE1  CD1  aromatic  1.388  0.020  1.388
 YSC  N    H1   single    0.890  0.020  1.040
 YSC  N    H2   single    0.890  0.020  1.040
 YSC  CA   H4   single    0.970  0.020  1.090
 YSC  CB   H5   single    0.970  0.020  1.090
 YSC  CB   H6   single    0.970  0.020  1.090
 YSC  CD2  H7   single    0.930  0.020  1.080
 YSC  CE2  H8   single    0.930  0.020  1.080
 YSC  OH   H9   single    0.850  0.020  0.980
 YSC  CE1  H10  single    0.930  0.020  1.080
 YSC  CD1  H11  single    0.930  0.020  1.080
 YSC  NAT  H12  single    0.860  0.020  1.020
 YSC  C5'  H13  single    0.970  0.020  1.090
 YSC  C5'  H14  single    0.970  0.020  1.090
 YSC  C4'  H15  single    0.970  0.020  1.090
 YSC  C1'  H16  single    0.970  0.020  1.090
 YSC  C2'  H17  single    0.970  0.020  1.090
 YSC  O2'  H18  single    0.850  0.020  0.980
 YSC  C3'  H19  single    0.970  0.020  1.090
 YSC  O3'  H20  single    0.850  0.020  0.980
 YSC  C6   H21  single    0.930  0.020  1.080
 YSC  C5   H22  single    0.930  0.020  1.080
 YSC  N4   H23  single    0.860  0.020  1.020
 YSC  N4   H24  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
 YSC  H2   N    H1   106.42  3.000
 YSC  H2   N    CA   109.34  3.000
 YSC  H1   N    CA   110.43  3.000
 YSC  H4   CA   C    106.25  3.000
 YSC  H4   CA   CB   107.01  3.000
 YSC  C    CA   CB   111.67  3.000
 YSC  H4   CA   N    107.62  3.000
 YSC  C    CA   N    108.96  3.000
 YSC  CB   CA   N    114.89  3.000
 YSC  H6   CB   H5   106.68  3.000
 YSC  H6   CB   CG   109.35  3.000
 YSC  H5   CB   CG   110.59  3.000
 YSC  H6   CB   CA   110.96  3.000
 YSC  H5   CB   CA   109.19  3.000
 YSC  CG   CB   CA   110.01  3.000
 YSC  CD1  CG   CD2  117.67  3.000
 YSC  CD1  CG   CB   121.76  3.000
 YSC  CD2  CG   CB   120.48  3.000
 YSC  H7   CD2  CE2  118.64  3.000
 YSC  H7   CD2  CG   119.71  3.000
 YSC  CE2  CD2  CG   121.65  3.000
 YSC  H8   CE2  CZ   119.79  3.000
 YSC  H8   CE2  CD2  120.33  3.000
 YSC  CZ   CE2  CD2  119.88  3.000
 YSC  CE1  CZ   OH   122.89  3.000
 YSC  CE1  CZ   CE2  119.28  3.000
 YSC  OH   CZ   CE2  117.83  3.000
 YSC  H9   OH   CZ   110.39  3.000
 YSC  H10  CE1  CD1  119.70  3.000
 YSC  H10  CE1  CZ   120.33  3.000
 YSC  CD1  CE1  CZ   119.97  3.000
 YSC  H11  CD1  CE1  118.70  3.000
 YSC  H11  CD1  CG   119.74  3.000
 YSC  CE1  CD1  CG   121.56  3.000
 YSC  NAT  C    O    121.72  3.000
 YSC  O    C    CA   124.94  3.000
 YSC  NAT  C    CA   113.33  3.000
 YSC  H12  NAT  SBI  115.32  3.000
 YSC  H12  NAT  C    120.44  3.000
 YSC  SBI  NAT  C    123.98  3.000
 YSC  O5'  SBI  OAE  104.95  3.000
 YSC  OAE  SBI  OAD  121.17  3.000
 YSC  O5'  SBI  OAD  110.37  3.000
 YSC  OAD  SBI  NAT  104.94  3.000
 YSC  OAE  SBI  NAT  110.94  3.000
 YSC  O5'  SBI  NAT  103.12  3.000
 YSC  C5'  O5'  SBI  118.18  3.000
 YSC  H14  C5'  H13  109.29  3.000
 YSC  H14  C5'  C4'  110.24  3.000
 YSC  H13  C5'  C4'  109.29  3.000
 YSC  H14  C5'  O5'  108.77  3.000
 YSC  H13  C5'  O5'  111.00  3.000
 YSC  C4'  C5'  O5'  108.24  3.000
 YSC  H15  C4'  C3'  109.26  3.000
 YSC  H15  C4'  O4'  110.13  3.000
 YSC  C3'  C4'  O4'  107.08  3.000
 YSC  H15  C4'  C5'  109.86  3.000
 YSC  C3'  C4'  C5'  110.74  3.000
 YSC  O4'  C4'  C5'  109.72  3.000
 YSC  C1'  O4'  C4'  111.75  3.000
 YSC  H16  C1'  N1   104.88  3.000
 YSC  H16  C1'  C2'  107.72  3.000
 YSC  N1   C1'  C2'  116.71  3.000
 YSC  H16  C1'  O4'  109.93  3.000
 YSC  C2'  C1'  O4'  108.03  3.000
 YSC  N1   C1'  O4'  109.43  3.000
 YSC  H17  C2'  C3'  111.90  3.000
 YSC  H17  C2'  O2'  110.85  3.000
 YSC  C3'  C2'  O2'  110.38  3.000
 YSC  H17  C2'  C1'  111.69  3.000
 YSC  C3'  C2'  C1'  103.99  3.000
 YSC  O2'  C2'  C1'  107.77  3.000
 YSC  H18  O2'  C2'  106.83  3.000
 YSC  H19  C3'  O3'  111.10  3.000
 YSC  H19  C3'  C2'  109.47  3.000
 YSC  O3'  C3'  C2'  112.77  3.000
 YSC  H19  C3'  C4'  110.62  3.000
 YSC  C2'  C3'  C4'  103.05  3.000
 YSC  O3'  C3'  C4'  109.56  3.000
 YSC  H20  O3'  C3'  108.81  3.000
 YSC  C2   N1   C6   120.20  3.000
 YSC  C6   N1   C1'  119.16  3.000
 YSC  C2   N1   C1'  120.50  3.000
 YSC  H21  C6   C5   121.67  3.000
 YSC  H21  C6   N1   116.47  3.000
 YSC  C5   C6   N1   121.86  3.000
 YSC  H22  C5   C4   122.37  3.000
 YSC  H22  C5   C6   121.37  3.000
 YSC  C4   C5   C6   116.16  3.000
 YSC  N3   C4   N4   118.04  3.000
 YSC  N4   C4   C5   119.88  3.000
 YSC  N3   C4   C5   122.07  3.000
 YSC  H24  N4   H23  118.36  3.000
 YSC  H24  N4   C4   119.84  3.000
 YSC  H23  N4   C4   121.66  3.000
 YSC  C2   N3   C4   121.08  3.000
 YSC  O2   C2   N3   122.53  3.000
 YSC  N3   C2   N1   118.37  3.000
 YSC  O2   C2   N1   119.10  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
 YSC  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 YSC  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 YSC  CONST_03  CE1  CZ   CE2  CD2     0.00   0.0  0
 YSC  CONST_04  CE1  CD1  CG   CD2     0.00   0.0  0
 YSC  CONST_05  CD1  CG   CD2  CE2     0.00   0.0  0
 YSC  CONST_06  CD1  CE1  CZ   CE2     0.00   0.0  0
 YSC  CONST_07  N3   C2   N1   C1'   180.00   0.0  0
 YSC  CONST_08  C4   N3   C2   N1      0.00   0.0  0
 YSC  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 YSC  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 YSC  CONST_11  CE2  CD2  CG   CB    180.00   0.0  0
 YSC  CONST_12  CE1  CD1  CG   CB    180.00   0.0  0
 YSC  CONST_13  OH   CZ   CE2  CD2   180.00   0.0  0
 YSC  CONST_14  CD1  CE1  CZ   OH    180.00   0.0  0
 YSC  CONST_15  O2   C2   N1   C1'     0.00   0.0  0
 YSC  CONST_16  O2   C2   N1   C6    180.00   0.0  0
 YSC  CONST_17  O2   C2   N3   C4    180.00   0.0  0
 YSC  CONST_18  C2   N3   C4   N4    180.00   0.0  0
 YSC  CONST_19  H8   CE2  CD2  CG    180.00   0.0  0
 YSC  CONST_20  H10  CE1  CD1  CG    180.00   0.0  0
 YSC  CONST_21  H11  CD1  CG   CD2   180.00   0.0  0
 YSC  CONST_22  H7   CD2  CE2  CZ    180.00   0.0  0
 YSC  CONST_23  H23  N4   C4   C5      0.00   0.0  0
 YSC  CONST_24  H24  N4   C4   C5    180.00   0.0  0
 YSC  CONST_25  SBI  NAT  C    CA    180.00   0.0  0
 YSC  CONST_26  SBI  NAT  C    O       0.00   0.0  0
 YSC  CONST_27  H12  NAT  C    CA      0.00   0.0  0
 YSC  Var_01    CD2  CG   CB   CA    -78.62  30.0  2
 YSC  Var_02    C4'  C5'  O5'  SBI  -151.88  30.0  2
 YSC  Var_03    O5'  SBI  NAT  C      62.60  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
 YSC  chir_01  CA   CB   C    N    negativ
 YSC  chir_02  C4'  O4'  C3'  C5'  negativ
 YSC  chir_03  C1'  O4'  N1   C2'  negativ
 YSC  chir_04  C2'  O2'  C1'  C3'  negativ
 YSC  chir_05  C3'  O3'  C4'  C2'  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
 YSC  plan-1  CB   0.020
 YSC  plan-1  CG   0.020
 YSC  plan-1  CD2  0.020
 YSC  plan-1  CE2  0.020
 YSC  plan-1  CZ   0.020
 YSC  plan-1  OH   0.020
 YSC  plan-1  CE1  0.020
 YSC  plan-1  CD1  0.020
 YSC  plan-1  H7   0.020
 YSC  plan-1  H8   0.020
 YSC  plan-1  H10  0.020
 YSC  plan-1  H11  0.020
 YSC  plan-2  C1'  0.020
 YSC  plan-2  N1   0.020
 YSC  plan-2  C6   0.020
 YSC  plan-2  C5   0.020
 YSC  plan-2  C4   0.020
 YSC  plan-2  N4   0.020
 YSC  plan-2  N3   0.020
 YSC  plan-2  C2   0.020
 YSC  plan-2  O2   0.020
 YSC  plan-2  H21  0.020
 YSC  plan-2  H22  0.020
 YSC  plan-2  H23  0.020
 YSC  plan-2  H24  0.020
 YSC  plan-3  CA   0.020
 YSC  plan-3  C    0.020
 YSC  plan-3  O    0.020
 YSC  plan-3  NAT  0.020
 YSC  plan-3  SBI  0.020
 YSC  plan-3  H12  0.020

