# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  9 08:15:15 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(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(=O)NC3=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
 YSU  YSU  '[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate'  ligand  55  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_YSU
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
 YSU  N    N  NH2   0  -0.765   0.9145   0.4777   2.1199
 YSU  CA   C  CH1   0  -0.208   1.3603  -0.3663   1.0470
 YSU  CB   C  CH2   0  -0.542   2.8977  -0.4246   1.0039
 YSU  CG   C  CR6   0   0.155   3.4966   0.9348   0.7855
 YSU  CD2  C  CR16  0  -0.292   3.5248   1.5060  -0.4845
 YSU  CE2  C  CR16  0  -0.314   4.0383   2.7739  -0.6996
 YSU  CZ   C  CR6   0   0.336   4.5468   3.5055   0.3709
 YSU  OH   O  OH1   0  -0.636   5.0422   4.7361   0.1179
 YSU  CE1  C  CR16  0  -0.373   4.5302   2.9491   1.6464
 YSU  CD1  C  CR16  0  -0.303   4.0053   1.6795   1.8417
 YSU  C    C  C     0   0.580   0.8009  -1.7843   1.1299
 YSU  O    O  O     0  -0.410   0.3792  -2.2863   2.1408
 YSU  NAT  N  NC1   0  -0.832   0.8317  -2.4729  -0.0681
 YSU  SBI  S  S     0   1.615   0.1655  -3.9795  -0.2753
 YSU  OAD  O  OS    0  -0.631   0.3150  -4.2593  -1.6820
 YSU  OAE  O  OS    0  -0.609   0.6509  -4.8921   0.7202
 YSU  O5'  O  OC2   0  -0.567  -1.3607  -3.7683   0.0939
 YSU  C5'  C  CH2   0  -0.224  -2.2219  -3.0029  -0.7803
 YSU  C4'  C  CH1   0   0.035  -2.7843  -1.8014  -0.0636
 YSU  O4'  O  O2    0  -0.497  -1.7747  -0.8335   0.1546
 YSU  C1'  C  CH1   0   0.190  -2.2455   0.4675  -0.0607
 YSU  C2'  C  CH1   0  -0.034  -3.6923   0.3706  -0.5710
 YSU  O2'  O  OH1   0  -0.671  -4.5347   0.7345   0.4884
 YSU  C3'  C  CH1   0  -0.040  -3.8645  -1.1227  -0.9123
 YSU  O3'  O  OH1   0  -0.658  -5.1252  -1.6193  -0.5490
 YSU  N1   N  NR6   0  -0.565  -1.3010   1.1877  -0.9067
 YSU  C6   C  CR16  0   0.083  -0.6222   2.2630  -0.3953
 YSU  C5   C  CR16  0  -0.481   0.3141   2.9381  -1.0772
 YSU  C4   C  CR6   0   0.567   0.6562   2.5254  -2.4160
 YSU  O4   O  O     0  -0.455   1.4827   3.0449  -3.1400
 YSU  N3   N  NR16  0  -0.733  -0.0631   1.4191  -2.8499
 YSU  C2   C  CR6   0   0.741  -1.0406   0.7327  -2.1831
 YSU  O2   O  O     0  -0.467  -1.6255  -0.2064  -2.6799
 YSU  H1   H  HNH2  0   0.354  -0.0938   0.4527   2.2015
 YSU  H2   H  HNH2  0   0.352   1.2741   0.1411   3.0051
 YSU  H4   H  HCH1  0   0.248   1.0264   0.0718   0.0998
 YSU  H5   H  HCH2  0   0.268   3.2618  -0.8543   1.9416
 YSU  H6   H  HCH2  0   0.268   3.2130  -1.1044   0.2087
 YSU  H7   H  HCR6  0   0.241   3.1396   0.9504  -1.3330
 YSU  H8   H  HCR6  0   0.257   4.0420   3.1989  -1.6951
 YSU  H9   H  HOH1  0   0.472   5.3495   5.1462   0.9340
 YSU  H10  H  HCR6  0   0.266   4.9243   3.5036   2.4907
 YSU  H11  H  HCR6  0   0.248   3.9978   1.2656   2.8430
 YSU  H12  H  HNC1  0   0.444   1.1591  -2.0223  -0.9139
 YSU  H13  H  HCH2  0   0.263  -1.6991  -2.6958  -1.6872
 YSU  H14  H  HCH2  0   0.282  -3.0361  -3.6699  -1.0634
 YSU  H15  H  HCH1  0   0.264  -3.2198  -2.1074   0.8960
 YSU  H16  H  HCH1  0   0.272  -2.2583   1.0268   0.8787
 YSU  H17  H  HCH1  0   0.258  -3.8585   1.0114  -1.4436
 YSU  H18  H  HOH1  0   0.451  -5.2905   0.1308   0.4714
 YSU  H19  H  HCH1  0   0.269  -3.6739  -1.2765  -1.9750
 YSU  H20  H  HOH1  0   0.473  -5.7095  -1.5798  -1.3128
 YSU  H21  H  HCR6  0   0.332  -0.8871   2.5413   0.6144
 YSU  H22  H  HCR6  0   0.293   0.8279   3.7721  -0.6266
 YSU  H23  H  HNR6  0   0.429   0.1304   1.0883  -3.7879

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
 YSU  O2   C2   double    1.213  0.020  1.213
 YSU  C2   N3   single    1.368  0.020  1.368
 YSU  C2   N1   single    1.380  0.020  1.380
 YSU  N3   C4   single    1.389  0.020  1.389
 YSU  O4'  C1'  single    1.400  0.020  1.400
 YSU  O4'  C4'  single    1.415  0.020  1.415
 YSU  C1'  N1   single    1.458  0.020  1.458
 YSU  C1'  C2'  single    1.537  0.020  1.537
 YSU  N1   C6   single    1.371  0.020  1.371
 YSU  O3'  C3'  single    1.403  0.020  1.403
 YSU  C4   O4   double    1.215  0.020  1.215
 YSU  C4   C5   single    1.442  0.020  1.442
 YSU  C4'  C3'  single    1.532  0.020  1.532
 YSU  C4'  C5'  single    1.508  0.020  1.508
 YSU  O2'  C2'  single    1.402  0.020  1.402
 YSU  C3'  C2'  single    1.541  0.020  1.541
 YSU  C6   C5   double    1.341  0.020  1.341
 YSU  C5'  O5'  single    1.446  0.020  1.446
 YSU  O5'  SBI  single    1.584  0.020  1.584
 YSU  CE2  CD2  aromatic  1.385  0.020  1.385
 YSU  CE2  CZ   aromatic  1.393  0.020  1.393
 YSU  CD2  CG   aromatic  1.393  0.020  1.393
 YSU  SBI  NAT  single    1.660  0.020  1.660
 YSU  SBI  OAE  deloc     1.435  0.020  1.435
 YSU  SBI  OAD  deloc     1.442  0.020  1.442
 YSU  NAT  C    single    1.382  0.020  1.382
 YSU  OH   CZ   single    1.351  0.020  1.351
 YSU  CZ   CE1  aromatic  1.392  0.020  1.392
 YSU  CG   CB   single    1.501  0.020  1.501
 YSU  CG   CD1  aromatic  1.389  0.020  1.389
 YSU  CB   CA   single    1.539  0.020  1.539
 YSU  CA   C    single    1.527  0.020  1.527
 YSU  CA   N    single    1.436  0.020  1.436
 YSU  C    O    double    1.205  0.020  1.205
 YSU  CE1  CD1  aromatic  1.388  0.020  1.388
 YSU  N    H1   single    0.890  0.020  1.040
 YSU  N    H2   single    0.890  0.020  1.040
 YSU  CA   H4   single    0.970  0.020  1.090
 YSU  CB   H5   single    0.970  0.020  1.090
 YSU  CB   H6   single    0.970  0.020  1.090
 YSU  CD2  H7   single    0.930  0.020  1.080
 YSU  CE2  H8   single    0.930  0.020  1.080
 YSU  OH   H9   single    0.850  0.020  0.980
 YSU  CE1  H10  single    0.930  0.020  1.080
 YSU  CD1  H11  single    0.930  0.020  1.080
 YSU  NAT  H12  single    0.860  0.020  1.020
 YSU  C5'  H13  single    0.970  0.020  1.090
 YSU  C5'  H14  single    0.970  0.020  1.090
 YSU  C4'  H15  single    0.970  0.020  1.090
 YSU  C1'  H16  single    0.970  0.020  1.090
 YSU  C2'  H17  single    0.970  0.020  1.090
 YSU  O2'  H18  single    0.850  0.020  0.980
 YSU  C3'  H19  single    0.970  0.020  1.090
 YSU  O3'  H20  single    0.850  0.020  0.980
 YSU  C6   H21  single    0.930  0.020  1.080
 YSU  C5   H22  single    0.930  0.020  1.080
 YSU  N3   H23  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
 YSU  H2   N    H1   105.97  3.000
 YSU  H2   N    CA   110.33  3.000
 YSU  H1   N    CA   110.80  3.000
 YSU  H4   CA   C    107.86  3.000
 YSU  H4   CA   CB   107.18  3.000
 YSU  C    CA   CB   109.41  3.000
 YSU  H4   CA   N    108.44  3.000
 YSU  C    CA   N    113.05  3.000
 YSU  CB   CA   N    110.68  3.000
 YSU  H6   CB   H5   106.47  3.000
 YSU  H6   CB   CG   110.02  3.000
 YSU  H5   CB   CG   110.34  3.000
 YSU  H6   CB   CA   109.40  3.000
 YSU  H5   CB   CA   108.87  3.000
 YSU  CG   CB   CA   111.60  3.000
 YSU  CD1  CG   CD2  117.79  3.000
 YSU  CD1  CG   CB   121.39  3.000
 YSU  CD2  CG   CB   120.80  3.000
 YSU  H7   CD2  CE2  118.62  3.000
 YSU  H7   CD2  CG   119.74  3.000
 YSU  CE2  CD2  CG   121.64  3.000
 YSU  H8   CE2  CZ   119.96  3.000
 YSU  H8   CE2  CD2  120.24  3.000
 YSU  CZ   CE2  CD2  119.80  3.000
 YSU  CE1  CZ   OH   122.71  3.000
 YSU  CE1  CZ   CE2  119.35  3.000
 YSU  OH   CZ   CE2  117.95  3.000
 YSU  H9   OH   CZ   110.25  3.000
 YSU  H10  CE1  CD1  119.72  3.000
 YSU  H10  CE1  CZ   120.32  3.000
 YSU  CD1  CE1  CZ   119.96  3.000
 YSU  H11  CD1  CE1  118.83  3.000
 YSU  H11  CD1  CG   119.70  3.000
 YSU  CE1  CD1  CG   121.47  3.000
 YSU  NAT  C    O    121.83  3.000
 YSU  O    C    CA   124.12  3.000
 YSU  NAT  C    CA   114.05  3.000
 YSU  H12  NAT  SBI  115.41  3.000
 YSU  H12  NAT  C    120.63  3.000
 YSU  SBI  NAT  C    123.46  3.000
 YSU  O5'  SBI  OAE  104.41  3.000
 YSU  OAE  SBI  OAD  121.22  3.000
 YSU  O5'  SBI  OAD  110.68  3.000
 YSU  OAD  SBI  NAT  104.85  3.000
 YSU  OAE  SBI  NAT  110.78  3.000
 YSU  O5'  SBI  NAT  103.68  3.000
 YSU  C5'  O5'  SBI  120.22  3.000
 YSU  H14  C5'  H13  108.32  3.000
 YSU  H14  C5'  C4'  109.42  3.000
 YSU  H13  C5'  C4'  110.46  3.000
 YSU  H14  C5'  O5'  106.14  3.000
 YSU  H13  C5'  O5'  111.48  3.000
 YSU  C4'  C5'  O5'  110.89  3.000
 YSU  H15  C4'  C3'  109.15  3.000
 YSU  H15  C4'  O4'  109.81  3.000
 YSU  C3'  C4'  O4'  106.58  3.000
 YSU  H15  C4'  C5'  109.96  3.000
 YSU  C3'  C4'  C5'  110.65  3.000
 YSU  O4'  C4'  C5'  110.62  3.000
 YSU  C1'  O4'  C4'  111.83  3.000
 YSU  H16  C1'  N1   104.67  3.000
 YSU  H16  C1'  C2'  107.84  3.000
 YSU  N1   C1'  C2'  116.62  3.000
 YSU  H16  C1'  O4'  110.31  3.000
 YSU  C2'  C1'  O4'  108.00  3.000
 YSU  N1   C1'  O4'  109.29  3.000
 YSU  H17  C2'  C3'  111.93  3.000
 YSU  H17  C2'  O2'  111.04  3.000
 YSU  C3'  C2'  O2'  110.59  3.000
 YSU  H17  C2'  C1'  111.74  3.000
 YSU  C3'  C2'  C1'  103.87  3.000
 YSU  O2'  C2'  C1'  107.36  3.000
 YSU  H18  O2'  C2'  107.11  3.000
 YSU  H19  C3'  O3'  111.07  3.000
 YSU  H19  C3'  C2'  109.44  3.000
 YSU  O3'  C3'  C2'  112.71  3.000
 YSU  H19  C3'  C4'  110.73  3.000
 YSU  C2'  C3'  C4'  103.16  3.000
 YSU  O3'  C3'  C4'  109.47  3.000
 YSU  H20  O3'  C3'  109.00  3.000
 YSU  C2   N1   C6   120.69  3.000
 YSU  C6   N1   C1'  119.46  3.000
 YSU  C2   N1   C1'  119.73  3.000
 YSU  H21  C6   C5   121.12  3.000
 YSU  H21  C6   N1   115.43  3.000
 YSU  C5   C6   N1   123.44  3.000
 YSU  H22  C5   C4   119.76  3.000
 YSU  H22  C5   C6   120.64  3.000
 YSU  C4   C5   C6   119.59  3.000
 YSU  N3   C4   O4   120.43  3.000
 YSU  O4   C4   C5   126.30  3.000
 YSU  N3   C4   C5   113.27  3.000
 YSU  H23  N3   C2   115.08  3.000
 YSU  H23  N3   C4   116.76  3.000
 YSU  C2   N3   C4   128.12  3.000
 YSU  O2   C2   N3   122.24  3.000
 YSU  N3   C2   N1   114.85  3.000
 YSU  O2   C2   N1   122.91  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
 YSU  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 YSU  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 YSU  CONST_03  CE1  CZ   CE2  CD2     0.00   0.0  0
 YSU  CONST_04  CE1  CD1  CG   CD2     0.00   0.0  0
 YSU  CONST_05  CD1  CG   CD2  CE2     0.00   0.0  0
 YSU  CONST_06  CD1  CE1  CZ   CE2     0.00   0.0  0
 YSU  CONST_07  N3   C2   N1   C1'   180.00   0.0  0
 YSU  CONST_08  C4   N3   C2   N1      0.00   0.0  0
 YSU  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 YSU  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 YSU  CONST_11  CE2  CD2  CG   CB    180.00   0.0  0
 YSU  CONST_12  CE1  CD1  CG   CB    180.00   0.0  0
 YSU  CONST_13  OH   CZ   CE2  CD2   180.00   0.0  0
 YSU  CONST_14  CD1  CE1  CZ   OH    180.00   0.0  0
 YSU  CONST_15  O2   C2   N1   C1'     0.00   0.0  0
 YSU  CONST_16  O2   C2   N1   C6    180.00   0.0  0
 YSU  CONST_17  O2   C2   N3   C4    180.00   0.0  0
 YSU  CONST_18  C2   N3   C4   O4    180.00   0.0  0
 YSU  CONST_19  H8   CE2  CD2  CG    180.00   0.0  0
 YSU  CONST_20  H10  CE1  CD1  CG    180.00   0.0  0
 YSU  CONST_21  H11  CD1  CG   CD2   180.00   0.0  0
 YSU  CONST_22  H7   CD2  CE2  CZ    180.00   0.0  0
 YSU  CONST_23  H23  N3   C2   N1    180.00   0.0  0
 YSU  CONST_24  SBI  NAT  C    CA    180.00   0.0  0
 YSU  CONST_25  SBI  NAT  C    O       0.00   0.0  0
 YSU  CONST_26  H12  NAT  C    CA      0.00   0.0  0
 YSU  Var_01    CD2  CG   CB   CA    -78.56  30.0  2
 YSU  Var_02    C4'  C5'  O5'  SBI  -119.44  30.0  1
 YSU  Var_03    O5'  SBI  NAT  C      58.77  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
 YSU  chir_01  CA   CB   C    N    negativ
 YSU  chir_02  C4'  O4'  C3'  C5'  negativ
 YSU  chir_03  C1'  O4'  N1   C2'  negativ
 YSU  chir_04  C2'  O2'  C1'  C3'  negativ
 YSU  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
 YSU  plan-1  CB   0.020
 YSU  plan-1  CG   0.020
 YSU  plan-1  CD2  0.020
 YSU  plan-1  CE2  0.020
 YSU  plan-1  CZ   0.020
 YSU  plan-1  OH   0.020
 YSU  plan-1  CE1  0.020
 YSU  plan-1  CD1  0.020
 YSU  plan-1  H7   0.020
 YSU  plan-1  H8   0.020
 YSU  plan-1  H10  0.020
 YSU  plan-1  H11  0.020
 YSU  plan-2  C1'  0.020
 YSU  plan-2  N1   0.020
 YSU  plan-2  C6   0.020
 YSU  plan-2  C5   0.020
 YSU  plan-2  C4   0.020
 YSU  plan-2  O4   0.020
 YSU  plan-2  N3   0.020
 YSU  plan-2  C2   0.020
 YSU  plan-2  O2   0.020
 YSU  plan-2  H21  0.020
 YSU  plan-2  H22  0.020
 YSU  plan-2  H23  0.020
 YSU  plan-3  CA   0.020
 YSU  plan-3  C    0.020
 YSU  plan-3  O    0.020
 YSU  plan-3  NAT  0.020
 YSU  plan-3  SBI  0.020
 YSU  plan-3  H12  0.020

