# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 09:17:03 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: [(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]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate
#   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)Cc3ccc(O)cc3)[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
 Y3U  Y3U  '[(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]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate'  ligand  58  34  .  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_Y3U
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
 Y3U  C3U  C  CH3   0  -0.531  -0.0891  -3.8877   0.1483
 Y3U  N3   N  NR6   0  -0.591   0.3952  -2.7917  -0.6834
 Y3U  C4   C  CR6   0   0.595  -0.0766  -2.6748  -1.9931
 Y3U  O4   O  O     0  -0.456  -0.7935  -3.5248  -2.4829
 Y3U  C5   C  CR16  0  -0.495   0.3477  -1.4779  -2.6800
 Y3U  C6   C  CR16  0   0.088   1.1802  -0.6203  -2.0793
 Y3U  N1   N  NR6   0  -0.575   1.6868  -0.8419  -0.8308
 Y3U  C1'  C  CR15  0   0.157   2.5018   0.1754  -0.1932
 Y3U  O4'  O  O     0  -0.495   1.7070   1.3340  -0.0557
 Y3U  C4'  C  CR15  0   0.023   2.4442   2.4855  -0.4169
 Y3U  C5'  C  CH2   0  -0.212   1.5162   3.5423  -0.9549
 Y3U  O5'  O  OC2   0  -0.566   0.7003   4.0776   0.1104
 Y3U  SBI  S  S     0   1.614  -0.8805   4.0227  -0.0021
 Y3U  OAD  O  OS    0  -0.608  -1.3477   4.7499   1.1432
 Y3U  OAE  O  OS    0  -0.629  -1.3020   4.3758  -1.3349
 Y3U  NAT  N  NC1   0  -0.834  -1.2312   2.4071   0.1484
 Y3U  C    C  C     0   0.581  -0.9520   1.6640   1.2823
 Y3U  O    O  O     0  -0.408  -0.4856   2.1680   2.2716
 Y3U  CA   C  CH1   0  -0.217  -1.3050   0.1806   1.1611
 Y3U  N    N  NH2   0  -0.755  -0.7572  -0.6190   2.2184
 Y3U  CB   C  CH2   0  -0.543  -2.8347   0.0110   1.1034
 Y3U  CG   C  CR6   0   0.149  -3.2319  -1.4072   0.8103
 Y3U  CD1  C  CR16  0  -0.295  -3.3512  -1.8575  -0.4994
 Y3U  CE1  C  CR16  0  -0.354  -3.7034  -3.1682  -0.7876
 Y3U  CZ   C  CR6   0   0.332  -3.9432  -4.0638   0.2491
 Y3U  OH   O  OH1   0  -0.637  -4.2908  -5.3518   0.0362
 Y3U  CE2  C  CR16  0  -0.327  -3.8265  -3.6306   1.5677
 Y3U  CD2  C  CR16  0  -0.282  -3.4720  -2.3190   1.8344
 Y3U  C3'  C  CR15  0  -0.031   3.4167   1.9889  -1.4851
 Y3U  O3'  O  OH1   0  -0.653   4.5172   2.8423  -1.5874
 Y3U  C2'  C  CR15  0  -0.046   3.7672   0.5829  -0.9674
 Y3U  O2'  O  OH1   0  -0.662   4.8183   0.6406  -0.0443
 Y3U  C2   C  CR6   0   0.782   1.3380  -1.9717  -0.1080
 Y3U  O2   O  O     0  -0.476   1.8219  -2.2153   0.9777
 Y3U  H1   H  HCH3  0   0.262  -0.3535  -3.5040   1.1300
 Y3U  H2   H  HCH3  0   0.269  -0.9787  -4.3010  -0.3109
 Y3U  H3   H  HCH3  0   0.255   0.6618  -4.6696   0.2490
 Y3U  H4   H  HCR6  0   0.294  -0.0137  -1.2896  -3.6787
 Y3U  H5   H  HCR6  0   0.324   1.4995   0.2837  -2.5768
 Y3U  H6   H  HCR5  0   0.292   2.7880  -0.2180   0.7813
 Y3U  H7   H  HCR5  0   0.265   3.0055   2.8778   0.4409
 Y3U  H8   H  HCH2  0   0.287   2.0958   4.3739  -1.3549
 Y3U  H9   H  HCH2  0   0.258   0.9049   3.1360  -1.7634
 Y3U  H10  H  HNC1  0   0.446  -1.5895   1.9615  -0.6874
 Y3U  H11  H  HCH1  0   0.254  -0.8997  -0.1724   0.2056
 Y3U  H12  H  HNH2  0   0.356   0.2515  -0.5607   2.2436
 Y3U  H13  H  HNH2  0   0.349  -1.0894  -0.2907   3.1170
 Y3U  H15  H  HCH2  0   0.266  -3.2579   0.3345   2.0588
 Y3U  H16  H  HCH2  0   0.264  -3.2535   0.6725   0.3423
 Y3U  H17  H  HCR6  0   0.243  -3.1771  -1.1723  -1.3218
 Y3U  H18  H  HCR6  0   0.262  -3.7888  -3.4883  -1.8194
 Y3U  H19  H  HOH1  0   0.472  -4.3423  -5.5319  -0.9087
 Y3U  H20  H  HCR6  0   0.256  -4.0135  -4.3228   2.3798
 Y3U  H21  H  HCR6  0   0.240  -3.3895  -1.9988   2.8656
 Y3U  H22  H  HCR5  0   0.254   2.8912   1.9037  -2.4450
 Y3U  H23  H  HOH1  0   0.473   4.8823   2.7802  -2.4758
 Y3U  H24  H  HCR5  0   0.264   3.9859  -0.1164  -1.7842
 Y3U  H25  H  HOH1  0   0.453   5.4637   1.2793  -0.3726

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
 Y3U  C3U  N3   single    1.459  0.020  1.459
 Y3U  O2   C2   double    1.213  0.020  1.213
 Y3U  N3   C2   single    1.376  0.020  1.376
 Y3U  N3   C4   single    1.397  0.020  1.397
 Y3U  C2   N1   single    1.386  0.020  1.386
 Y3U  O4   C4   double    1.215  0.020  1.215
 Y3U  C4   C5   single    1.444  0.020  1.444
 Y3U  N1   C1'  single    1.451  0.020  1.451
 Y3U  N1   C6   single    1.366  0.020  1.366
 Y3U  C1'  O4'  single    1.412  0.020  1.412
 Y3U  C1'  C2'  single    1.538  0.020  1.538
 Y3U  O4'  C4'  single    1.414  0.020  1.414
 Y3U  C5   C6   double    1.338  0.020  1.338
 Y3U  O3'  C3'  single    1.396  0.020  1.396
 Y3U  C4'  C3'  single    1.528  0.020  1.528
 Y3U  C4'  C5'  single    1.506  0.020  1.506
 Y3U  O2'  C2'  single    1.400  0.020  1.400
 Y3U  C2'  C3'  single    1.539  0.020  1.539
 Y3U  C5'  O5'  single    1.445  0.020  1.445
 Y3U  O5'  SBI  single    1.586  0.020  1.586
 Y3U  CE1  CD1  aromatic  1.387  0.020  1.387
 Y3U  CE1  CZ   aromatic  1.391  0.020  1.391
 Y3U  CD1  CG   aromatic  1.390  0.020  1.390
 Y3U  SBI  NAT  single    1.660  0.020  1.660
 Y3U  SBI  OAE  deloc     1.442  0.020  1.442
 Y3U  SBI  OAD  deloc     1.435  0.020  1.435
 Y3U  NAT  C    single    1.384  0.020  1.384
 Y3U  OH   CZ   single    1.351  0.020  1.351
 Y3U  CZ   CE2  aromatic  1.393  0.020  1.393
 Y3U  CG   CB   single    1.502  0.020  1.502
 Y3U  CG   CD2  aromatic  1.392  0.020  1.392
 Y3U  CB   CA   single    1.540  0.020  1.540
 Y3U  CA   C    single    1.530  0.020  1.530
 Y3U  CA   N    single    1.434  0.020  1.434
 Y3U  C    O    double    1.204  0.020  1.204
 Y3U  CE2  CD2  aromatic  1.385  0.020  1.385
 Y3U  C3U  H1   single    0.970  0.020  1.090
 Y3U  C3U  H2   single    0.970  0.020  1.090
 Y3U  C3U  H3   single    0.970  0.020  1.090
 Y3U  C5   H4   single    0.930  0.020  1.080
 Y3U  C6   H5   single    0.930  0.020  1.080
 Y3U  C1'  H6   single    0.970  0.020  1.090
 Y3U  C4'  H7   single    0.970  0.020  1.090
 Y3U  C5'  H8   single    0.970  0.020  1.090
 Y3U  C5'  H9   single    0.970  0.020  1.090
 Y3U  NAT  H10  single    0.860  0.020  1.020
 Y3U  CA   H11  single    0.970  0.020  1.090
 Y3U  N    H12  single    0.890  0.020  1.040
 Y3U  N    H13  single    0.890  0.020  1.040
 Y3U  CB   H15  single    0.970  0.020  1.090
 Y3U  CB   H16  single    0.970  0.020  1.090
 Y3U  CD1  H17  single    0.930  0.020  1.080
 Y3U  CE1  H18  single    0.930  0.020  1.080
 Y3U  OH   H19  single    0.850  0.020  0.980
 Y3U  CE2  H20  single    0.930  0.020  1.080
 Y3U  CD2  H21  single    0.930  0.020  1.080
 Y3U  C3'  H22  single    0.970  0.020  1.090
 Y3U  O3'  H23  single    0.850  0.020  0.980
 Y3U  C2'  H24  single    0.970  0.020  1.090
 Y3U  O2'  H25  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
 Y3U  H3   C3U  H2   109.37  3.000
 Y3U  H3   C3U  H1   109.75  3.000
 Y3U  H2   C3U  H1   108.54  3.000
 Y3U  H3   C3U  N3   111.31  3.000
 Y3U  H2   C3U  N3   108.52  3.000
 Y3U  H1   C3U  N3   109.31  3.000
 Y3U  C2   N3   C4   125.01  3.000
 Y3U  C4   N3   C3U  119.04  3.000
 Y3U  C2   N3   C3U  115.91  3.000
 Y3U  C5   C4   O4   124.17  3.000
 Y3U  C5   C4   N3   114.59  3.000
 Y3U  O4   C4   N3   121.24  3.000
 Y3U  H4   C5   C6   120.82  3.000
 Y3U  H4   C5   C4   119.13  3.000
 Y3U  C6   C5   C4   120.05  3.000
 Y3U  H5   C6   N1   116.57  3.000
 Y3U  H5   C6   C5   120.91  3.000
 Y3U  N1   C6   C5   122.51  3.000
 Y3U  C2   N1   C1'  118.93  3.000
 Y3U  C1'  N1   C6   119.76  3.000
 Y3U  C2   N1   C6   121.05  3.000
 Y3U  H6   C1'  C2'  109.25  3.000
 Y3U  H6   C1'  O4'  110.93  3.000
 Y3U  C2'  C1'  O4'  107.15  3.000
 Y3U  H6   C1'  N1   106.71  3.000
 Y3U  C2'  C1'  N1   115.25  3.000
 Y3U  O4'  C1'  N1   107.57  3.000
 Y3U  C4'  O4'  C1'  110.47  3.000
 Y3U  H7   C4'  C3'  109.70  3.000
 Y3U  H7   C4'  C5'  110.09  3.000
 Y3U  C3'  C4'  C5'  111.76  3.000
 Y3U  H7   C4'  O4'  110.97  3.000
 Y3U  C5'  C4'  O4'  109.96  3.000
 Y3U  C3'  C4'  O4'  104.23  3.000
 Y3U  H9   C5'  H8   108.06  3.000
 Y3U  H9   C5'  O5'  111.57  3.000
 Y3U  H8   C5'  O5'  106.76  3.000
 Y3U  H9   C5'  C4'  110.39  3.000
 Y3U  H8   C5'  C4'  109.81  3.000
 Y3U  O5'  C5'  C4'  110.16  3.000
 Y3U  SBI  O5'  C5'  119.86  3.000
 Y3U  NAT  SBI  OAE  105.09  3.000
 Y3U  OAE  SBI  OAD  121.24  3.000
 Y3U  NAT  SBI  OAD  110.62  3.000
 Y3U  OAD  SBI  O5'  104.50  3.000
 Y3U  OAE  SBI  O5'  110.40  3.000
 Y3U  NAT  SBI  O5'  103.76  3.000
 Y3U  H10  NAT  C    120.75  3.000
 Y3U  H10  NAT  SBI  115.35  3.000
 Y3U  C    NAT  SBI  123.65  3.000
 Y3U  CA   C    O    124.07  3.000
 Y3U  O    C    NAT  121.76  3.000
 Y3U  CA   C    NAT  114.16  3.000
 Y3U  H11  CA   CB   107.40  3.000
 Y3U  H11  CA   N    108.77  3.000
 Y3U  CB   CA   N    110.21  3.000
 Y3U  H11  CA   C    107.22  3.000
 Y3U  N    CA   C    113.21  3.000
 Y3U  CB   CA   C    109.82  3.000
 Y3U  H13  N    H12  106.66  3.000
 Y3U  H13  N    CA   110.37  3.000
 Y3U  H12  N    CA   111.55  3.000
 Y3U  H16  CB   H15  106.33  3.000
 Y3U  H16  CB   CG   109.56  3.000
 Y3U  H15  CB   CG   110.33  3.000
 Y3U  H16  CB   CA   109.90  3.000
 Y3U  H15  CB   CA   108.60  3.000
 Y3U  CG   CB   CA   111.97  3.000
 Y3U  CD2  CG   CD1  117.78  3.000
 Y3U  CD2  CG   CB   121.38  3.000
 Y3U  CD1  CG   CB   120.83  3.000
 Y3U  H17  CD1  CE1  118.69  3.000
 Y3U  H17  CD1  CG   119.73  3.000
 Y3U  CE1  CD1  CG   121.57  3.000
 Y3U  H18  CE1  CZ   120.39  3.000
 Y3U  H18  CE1  CD1  119.79  3.000
 Y3U  CZ   CE1  CD1  119.82  3.000
 Y3U  CE2  CZ   OH   117.86  3.000
 Y3U  CE2  CZ   CE1  119.40  3.000
 Y3U  OH   CZ   CE1  122.74  3.000
 Y3U  H19  OH   CZ   110.27  3.000
 Y3U  H20  CE2  CD2  120.33  3.000
 Y3U  H20  CE2  CZ   119.77  3.000
 Y3U  CD2  CE2  CZ   119.90  3.000
 Y3U  H21  CD2  CE2  118.89  3.000
 Y3U  H21  CD2  CG   119.58  3.000
 Y3U  CE2  CD2  CG   121.53  3.000
 Y3U  H22  C3'  C2'  109.41  3.000
 Y3U  H22  C3'  O3'  111.14  3.000
 Y3U  C2'  C3'  O3'  113.80  3.000
 Y3U  H22  C3'  C4'  109.39  3.000
 Y3U  C2'  C3'  C4'  101.93  3.000
 Y3U  O3'  C3'  C4'  110.75  3.000
 Y3U  H23  O3'  C3'  109.10  3.000
 Y3U  H24  C2'  O2'  111.55  3.000
 Y3U  H24  C2'  C3'  112.16  3.000
 Y3U  O2'  C2'  C3'  110.80  3.000
 Y3U  H24  C2'  C1'  111.70  3.000
 Y3U  C3'  C2'  C1'  102.94  3.000
 Y3U  O2'  C2'  C1'  107.26  3.000
 Y3U  H25  O2'  C2'  107.75  3.000
 Y3U  O2   C2   N1   122.00  3.000
 Y3U  N1   C2   N3   116.12  3.000
 Y3U  O2   C2   N3   121.87  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
 Y3U  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 Y3U  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 Y3U  CONST_03  CE2  CZ   CE1  CD1     0.00   0.0  0
 Y3U  CONST_04  CE2  CD2  CG   CD1     0.00   0.0  0
 Y3U  CONST_05  CD2  CG   CD1  CE1     0.00   0.0  0
 Y3U  CONST_06  CD2  CE2  CZ   CE1     0.00   0.0  0
 Y3U  CONST_07  C1'  N1   C2   N3    180.00   0.0  0
 Y3U  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 Y3U  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 Y3U  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 Y3U  CONST_11  CE1  CD1  CG   CB    180.00   0.0  0
 Y3U  CONST_12  CE2  CD2  CG   CB    180.00   0.0  0
 Y3U  CONST_13  OH   CZ   CE1  CD1   180.00   0.0  0
 Y3U  CONST_14  CD2  CE2  CZ   OH    180.00   0.0  0
 Y3U  CONST_15  N1   C2   N3   C3U   180.00   0.0  0
 Y3U  CONST_16  C5   C4   N3   C3U   180.00   0.0  0
 Y3U  CONST_17  O2   C2   N3   C4    180.00   0.0  0
 Y3U  CONST_18  C2   N3   C4   O4    180.00   0.0  0
 Y3U  CONST_19  O2   C2   N1   C6    180.00   0.0  0
 Y3U  CONST_20  O2   C2   N1   C1'     0.00   0.0  0
 Y3U  CONST_21  H18  CE1  CD1  CG    180.00   0.0  0
 Y3U  CONST_22  H20  CE2  CD2  CG    180.00   0.0  0
 Y3U  CONST_23  H21  CD2  CG   CD1   180.00   0.0  0
 Y3U  CONST_24  H17  CD1  CE1  CZ    180.00   0.0  0
 Y3U  CONST_25  O2   C2   N3   C3U     0.00   0.0  0
 Y3U  CONST_26  O4   C4   N3   C3U     0.00   0.0  0
 Y3U  CONST_27  CA   C    NAT  SBI   180.00   0.0  0
 Y3U  CONST_28  O    C    NAT  SBI     0.00   0.0  0
 Y3U  CONST_29  H10  NAT  C    O     180.00   0.0  0
 Y3U  Var_01    CD1  CG   CB   CA    -87.44  30.0  2
 Y3U  Var_02    H1   C3U  N3   C4   -134.15  30.0  3
 Y3U  Var_03    NAT  SBI  O5'  C5'    69.66  30.0  3
 Y3U  Var_04    C    NAT  SBI  O5'    62.57  30.0  3
 Y3U  Var_05    H8   C5'  O5'  SBI   117.78  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
 Y3U  chir_01  C1'  N1   O4'  C2'  positiv
 Y3U  chir_02  C4'  O4'  C3'  C5'  negativ
 Y3U  chir_03  CA   N    CB   C    negativ
 Y3U  chir_04  C3'  O3'  C4'  C2'  positiv
 Y3U  chir_05  C2'  O2'  C3'  C1'  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
 Y3U  plan-1  C3U  0.020
 Y3U  plan-1  N3   0.020
 Y3U  plan-1  C4   0.020
 Y3U  plan-1  O4   0.020
 Y3U  plan-1  C5   0.020
 Y3U  plan-1  C6   0.020
 Y3U  plan-1  N1   0.020
 Y3U  plan-1  C1'  0.020
 Y3U  plan-1  C2   0.020
 Y3U  plan-1  O2   0.020
 Y3U  plan-1  H4   0.020
 Y3U  plan-1  H5   0.020
 Y3U  plan-2  CB   0.020
 Y3U  plan-2  CG   0.020
 Y3U  plan-2  CD1  0.020
 Y3U  plan-2  CE1  0.020
 Y3U  plan-2  CZ   0.020
 Y3U  plan-2  OH   0.020
 Y3U  plan-2  CE2  0.020
 Y3U  plan-2  CD2  0.020
 Y3U  plan-2  H17  0.020
 Y3U  plan-2  H18  0.020
 Y3U  plan-2  H20  0.020
 Y3U  plan-2  H21  0.020
 Y3U  plan-3  SBI  0.020
 Y3U  plan-3  NAT  0.020
 Y3U  plan-3  C    0.020
 Y3U  plan-3  O    0.020
 Y3U  plan-3  CA   0.020
 Y3U  plan-3  H10  0.020

