# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 14:00:57 2020
#   Inital geometry file: a 130 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-4-methyl-pentanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=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
 LSU  LSU  '[(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-4-methyl-pentanoyl]sulfamate'  ligand  53  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LSU
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
 LSU  N    N  NH2   0  -0.766  -1.5554   2.0432  -1.1691
 LSU  CA   C  CH1   0  -0.245  -2.3099   1.2240  -0.2567
 LSU  C    C  C     0   0.581  -2.1959  -0.2677  -0.5539
 LSU  O    O  O     0  -0.412  -2.0490  -0.7286  -1.6575
 LSU  CB   C  CH2   0  -0.412  -3.7971   1.5979  -0.2768
 LSU  CG   C  CH1   0  -0.223  -4.0789   3.0731   0.0152
 LSU  CD1  C  CH3   0  -0.653  -5.5843   3.3177  -0.0330
 LSU  CD2  C  CH3   0  -0.674  -3.5024   3.5218   1.3530
 LSU  C1'  C  CH1   0   0.191   2.2407  -0.4638  -0.0971
 LSU  C2   C  CR6   0   0.731   2.2604   1.9794  -0.2611
 LSU  C2'  C  CH1   0  -0.037   2.9209  -1.3236   0.9640
 LSU  C3'  C  CH1   0  -0.046   2.6997  -2.7241   0.3851
 LSU  C4   C  CR6   0   0.576   0.8140   3.3118   1.2516
 LSU  C4'  C  CH1   0  -0.020   1.3132  -2.5874  -0.2484
 LSU  C5   C  CR16  0  -0.515   0.4167   2.0691   1.8713
 LSU  C5'  C  CH2   0  -0.194   0.2087  -3.1081   0.6435
 LSU  C6   C  CR16  0   0.091   0.9081   0.9128   1.4056
 LSU  N1   N  NR6   0  -0.568   1.8010   0.8351   0.3715
 LSU  N3   N  NR16  0  -0.736   1.7214   3.1449   0.2158
 LSU  N3S  N  NC1   0  -0.839  -2.2983  -1.0724   0.5670
 LSU  O1S  O  OS    0  -0.628  -2.4627  -3.1634   1.8727
 LSU  O2'  O  OH1   0  -0.651   4.2570  -0.9456   1.0907
 LSU  O2S  O  OS    0  -0.610  -3.3670  -3.1450  -0.4671
 LSU  O3'  O  OH1   0  -0.664   3.6205  -2.9966  -0.6367
 LSU  O4   O  O     0  -0.451   0.4251   4.4193   1.5639
 LSU  O4'  O  O2    0  -0.486   1.1160  -1.1976  -0.5097
 LSU  O5'  O  OC2   0  -0.567  -1.0022  -3.1379  -0.1420
 LSU  S    S  S     0   1.622  -2.3887  -2.7318   0.4993
 LSU  H1   H  HNH2  0   0.348  -0.5881   1.7506  -1.2031
 LSU  H2   H  HNH2  0   0.354  -1.9123   1.9464  -2.1124
 LSU  H4   H  HCH1  0   0.260  -1.9278   1.4005   0.7527
 LSU  H5   H  HCH2  0   0.243  -4.2126   1.3404  -1.2568
 LSU  H6   H  HCH2  0   0.236  -4.3284   0.9799   0.4547
 LSU  H7   H  HCH1  0   0.226  -3.6127   3.6698  -0.7738
 LSU  H8   H  HCH3  0   0.214  -6.0996   2.7428   0.7403
 LSU  H9   H  HCH3  0   0.228  -5.8166   4.3714   0.1292
 LSU  H10  H  HCH3  0   0.225  -6.0067   3.0298  -0.9976
 LSU  H11  H  HCH3  0   0.231  -2.4140   3.4531   1.3772
 LSU  H12  H  HCH3  0   0.232  -3.7590   4.5634   1.5526
 LSU  H13  H  HCH3  0   0.215  -3.8990   2.9217   2.1762
 LSU  H14  H  HCH1  0   0.283   2.9297  -0.2844  -0.9247
 LSU  H15  H  HCH1  0   0.256   2.3898  -1.2473   1.9211
 LSU  H16  H  HCH1  0   0.262   2.7224  -3.4947   1.1658
 LSU  H17  H  HCH1  0   0.281   1.2913  -3.1422  -1.1917
 LSU  H18  H  HCR6  0   0.306  -0.2820   2.0794   2.6936
 LSU  H19  H  HCH2  0   0.285   0.4234  -4.1290   0.9585
 LSU  H20  H  HCH2  0   0.255   0.0911  -2.4902   1.5368
 LSU  H21  H  HCR6  0   0.322   0.6017  -0.0282   1.8394
 LSU  H22  H  HNR6  0   0.431   2.0403   3.9862  -0.2500
 LSU  H23  H  HNC1  0   0.451  -2.4445  -0.6657   1.4835
 LSU  H24  H  HOH1  0   0.472   4.5937  -1.2589   1.9363
 LSU  H25  H  HOH1  0   0.452   4.4986  -2.7551  -0.3182
 LSU  O2   O  O     0  -0.464   3.0652   1.9629  -1.1659

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
 LSU  CD2  CG   single  1.524  0.020  1.524
 LSU  O3'  C3'  single  1.402  0.020  1.402
 LSU  CG   CB   single  1.530  0.020  1.530
 LSU  CG   CD1  single  1.526  0.020  1.526
 LSU  C4'  C3'  single  1.530  0.020  1.530
 LSU  C4'  O4'  single  1.428  0.020  1.428
 LSU  C4'  C5'  single  1.512  0.020  1.512
 LSU  C3'  C2'  single  1.532  0.020  1.532
 LSU  O4'  C1'  single  1.405  0.020  1.405
 LSU  CB   CA   single  1.534  0.020  1.534
 LSU  C5'  O5'  single  1.444  0.020  1.444
 LSU  C1'  C2'  single  1.526  0.020  1.526
 LSU  C1'  N1   single  1.449  0.020  1.449
 LSU  O2'  C2'  single  1.394  0.020  1.394
 LSU  O2   C2   double  1.211  0.020  1.211
 LSU  N    CA   single  1.440  0.020  1.440
 LSU  CA   C    single  1.525  0.020  1.525
 LSU  N1   C2   single  1.386  0.020  1.386
 LSU  N1   C6   single  1.368  0.020  1.368
 LSU  O5'  S    single  1.581  0.020  1.581
 LSU  C2   N3   single  1.370  0.020  1.370
 LSU  C    O    double  1.205  0.020  1.205
 LSU  C    N3S  single  1.384  0.020  1.384
 LSU  N3S  S    single  1.663  0.020  1.663
 LSU  C6   C5   double  1.340  0.020  1.340
 LSU  O1S  S    deloc   1.442  0.020  1.442
 LSU  S    O2S  deloc   1.436  0.020  1.436
 LSU  N3   C4   single  1.387  0.020  1.387
 LSU  C5   C4   single  1.444  0.020  1.444
 LSU  C4   O4   double  1.215  0.020  1.215
 LSU  N    H1   single  0.890  0.020  1.040
 LSU  N    H2   single  0.890  0.020  1.040
 LSU  CA   H4   single  0.970  0.020  1.090
 LSU  CB   H5   single  0.970  0.020  1.090
 LSU  CB   H6   single  0.970  0.020  1.090
 LSU  CG   H7   single  0.970  0.020  1.090
 LSU  CD1  H8   single  0.970  0.020  1.090
 LSU  CD1  H9   single  0.970  0.020  1.090
 LSU  CD1  H10  single  0.970  0.020  1.090
 LSU  CD2  H11  single  0.970  0.020  1.090
 LSU  CD2  H12  single  0.970  0.020  1.090
 LSU  CD2  H13  single  0.970  0.020  1.090
 LSU  C1'  H14  single  0.970  0.020  1.090
 LSU  C2'  H15  single  0.970  0.020  1.090
 LSU  C3'  H16  single  0.970  0.020  1.090
 LSU  C4'  H17  single  0.970  0.020  1.090
 LSU  C5   H18  single  0.930  0.020  1.080
 LSU  C5'  H19  single  0.970  0.020  1.090
 LSU  C5'  H20  single  0.970  0.020  1.090
 LSU  C6   H21  single  0.930  0.020  1.080
 LSU  N3   H22  single  0.860  0.020  1.020
 LSU  N3S  H23  single  0.860  0.020  1.020
 LSU  O2'  H24  single  0.850  0.020  0.980
 LSU  O3'  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
 LSU  H2   N    H1   106.14  3.000
 LSU  H2   N    CA   110.55  3.000
 LSU  H1   N    CA   110.98  3.000
 LSU  H4   CA   CB   108.16  3.000
 LSU  H4   CA   C    108.15  3.000
 LSU  CB   CA   C    107.96  3.000
 LSU  H4   CA   N    108.06  3.000
 LSU  C    CA   N    113.19  3.000
 LSU  CB   CA   N    111.17  3.000
 LSU  N3S  C    O    121.90  3.000
 LSU  N3S  C    CA   113.92  3.000
 LSU  O    C    CA   124.17  3.000
 LSU  H6   CB   H5   106.32  3.000
 LSU  H6   CB   CG   109.10  3.000
 LSU  H5   CB   CG   109.13  3.000
 LSU  H6   CB   CA   108.91  3.000
 LSU  H5   CB   CA   108.81  3.000
 LSU  CG   CB   CA   114.28  3.000
 LSU  H7   CG   CD2  108.14  3.000
 LSU  H7   CG   CD1  108.08  3.000
 LSU  CD2  CG   CD1  110.71  3.000
 LSU  H7   CG   CB   108.05  3.000
 LSU  CD1  CG   CB   109.28  3.000
 LSU  CD2  CG   CB   112.44  3.000
 LSU  H10  CD1  H9   107.68  3.000
 LSU  H10  CD1  H8   107.70  3.000
 LSU  H9   CD1  H8   107.61  3.000
 LSU  H10  CD1  CG   111.55  3.000
 LSU  H9   CD1  CG   111.11  3.000
 LSU  H8   CD1  CG   111.01  3.000
 LSU  H13  CD2  H12  107.51  3.000
 LSU  H13  CD2  H11  108.10  3.000
 LSU  H12  CD2  H11  106.90  3.000
 LSU  H13  CD2  CG   111.23  3.000
 LSU  H12  CD2  CG   110.65  3.000
 LSU  H11  CD2  CG   112.23  3.000
 LSU  H14  C1'  O4'  111.62  3.000
 LSU  H14  C1'  N1   106.82  3.000
 LSU  O4'  C1'  N1   108.68  3.000
 LSU  H14  C1'  C2'  109.78  3.000
 LSU  N1   C1'  C2'  114.54  3.000
 LSU  O4'  C1'  C2'  105.48  3.000
 LSU  O2   C2   N3   122.22  3.000
 LSU  N3   C2   N1   114.40  3.000
 LSU  O2   C2   N1   123.38  3.000
 LSU  H15  C2'  O2'  111.45  3.000
 LSU  H15  C2'  C3'  108.87  3.000
 LSU  O2'  C2'  C3'  114.87  3.000
 LSU  H15  C2'  C1'  110.59  3.000
 LSU  O2'  C2'  C1'  109.73  3.000
 LSU  C3'  C2'  C1'  100.83  3.000
 LSU  H16  C3'  O3'  111.62  3.000
 LSU  H16  C3'  C4'  112.09  3.000
 LSU  O3'  C3'  C4'  108.10  3.000
 LSU  H16  C3'  C2'  111.73  3.000
 LSU  C4'  C3'  C2'  101.87  3.000
 LSU  O3'  C3'  C2'  111.00  3.000
 LSU  O4   C4   N3   120.74  3.000
 LSU  O4   C4   C5   125.88  3.000
 LSU  N3   C4   C5   113.38  3.000
 LSU  H17  C4'  O4'  109.44  3.000
 LSU  H17  C4'  C5'  108.62  3.000
 LSU  O4'  C4'  C5'  110.01  3.000
 LSU  H17  C4'  C3'  109.24  3.000
 LSU  C5'  C4'  C3'  112.76  3.000
 LSU  O4'  C4'  C3'  106.72  3.000
 LSU  H18  C5   C6   120.70  3.000
 LSU  H18  C5   C4   119.79  3.000
 LSU  C6   C5   C4   119.51  3.000
 LSU  H20  C5'  H19  108.35  3.000
 LSU  H20  C5'  O5'  111.48  3.000
 LSU  H19  C5'  O5'  107.65  3.000
 LSU  H20  C5'  C4'  111.48  3.000
 LSU  H19  C5'  C4'  110.44  3.000
 LSU  O5'  C5'  C4'  107.39  3.000
 LSU  H21  C6   N1   116.04  3.000
 LSU  H21  C6   C5   120.53  3.000
 LSU  N1   C6   C5   123.43  3.000
 LSU  C6   N1   C2   120.96  3.000
 LSU  C6   N1   C1'  119.55  3.000
 LSU  C2   N1   C1'  119.46  3.000
 LSU  H22  N3   C4   116.70  3.000
 LSU  H22  N3   C2   115.00  3.000
 LSU  C4   N3   C2   128.30  3.000
 LSU  H23  N3S  S    115.43  3.000
 LSU  H23  N3S  C    120.66  3.000
 LSU  S    N3S  C    123.46  3.000
 LSU  H24  O2'  C2'  109.07  3.000
 LSU  H25  O3'  C3'  107.97  3.000
 LSU  C4'  O4'  C1'  110.13  3.000
 LSU  S    O5'  C5'  120.64  3.000
 LSU  O5'  S    O2S  104.52  3.000
 LSU  O2S  S    O1S  121.34  3.000
 LSU  O5'  S    O1S  110.77  3.000
 LSU  O2S  S    N3S  110.58  3.000
 LSU  O1S  S    N3S  105.23  3.000
 LSU  O5'  S    N3S  103.01  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
 LSU  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 LSU  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 LSU  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 LSU  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 LSU  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 LSU  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 LSU  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 LSU  CONST_08  O2   C2   N1   C6   180.00   0.0  0
 LSU  CONST_09  H22  N3   C4   C5   180.00   0.0  0
 LSU  CONST_10  S    N3S  C    CA   180.00   0.0  0
 LSU  CONST_11  S    N3S  C    O      0.00   0.0  0
 LSU  CONST_12  H23  N3S  C    CA     0.00   0.0  0
 LSU  Var_01    CD2  CG   CB   CA   -56.62  30.0  3
 LSU  Var_02    O5'  S    N3S  C     63.06  30.0  3
 LSU  Var_03    N3S  S    O5'  C5'   75.98  30.0  3
 LSU  Var_04    H11  CD2  CG   CB    63.28  30.0  3
 LSU  Var_05    H8   CD1  CG   CB    62.73  30.0  3
 LSU  Var_06    H19  C5'  O5'  S     99.95  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
 LSU  chir_01  CA   CB   N    C    positiv
 LSU  chir_02  C1'  O4'  C2'  N1   positiv
 LSU  chir_03  C2'  O2'  C1'  C3'  negativ
 LSU  chir_04  C3'  O3'  C4'  C2'  positiv
 LSU  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
 LSU  plan-1  C1'  0.020
 LSU  plan-1  C2   0.020
 LSU  plan-1  C4   0.020
 LSU  plan-1  C5   0.020
 LSU  plan-1  C6   0.020
 LSU  plan-1  N1   0.020
 LSU  plan-1  N3   0.020
 LSU  plan-1  O4   0.020
 LSU  plan-1  H18  0.020
 LSU  plan-1  H21  0.020
 LSU  plan-1  H22  0.020
 LSU  plan-1  O2   0.020
 LSU  plan-2  CA   0.020
 LSU  plan-2  C    0.020
 LSU  plan-2  O    0.020
 LSU  plan-2  N3S  0.020
 LSU  plan-2  S    0.020
 LSU  plan-2  H23  0.020

