# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:16:10 2020
#   Inital geometry file: a 136 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-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)N(C)C2=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
 L3U  L3U  '[(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-4-methyl-pentanoyl]sulfamate'  ligand  56  30  .  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_L3U
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
 L3U  N    N  NH2   0  -0.767  -1.2153   1.9573  -1.1854
 L3U  CA   C  CH1   0  -0.241  -2.1173   1.2940  -0.2794
 L3U  C    C  C     0   0.581  -2.2273  -0.2054  -0.5307
 L3U  O    O  O     0  -0.412  -2.1355  -0.7189  -1.6170
 L3U  CB   C  CH2   0  -0.416  -3.5273   1.8891  -0.3749
 L3U  CG   C  CH1   0  -0.221  -3.5956   3.3939  -0.1141
 L3U  CD1  C  CH3   0  -0.653  -5.0384   3.8658  -0.2672
 L3U  CD2  C  CH3   0  -0.677  -3.0468   3.7676   1.2581
 L3U  C1'  C  CH1   0   0.187   2.0760  -0.9919  -0.0153
 L3U  C2   C  CR6   0   0.774   2.4261   1.4218  -0.2206
 L3U  C2'  C  CH1   0  -0.037   2.6383  -1.9218   1.0562
 L3U  C3'  C  CH1   0  -0.046   2.2263  -3.2877   0.4997
 L3U  C4   C  CR6   0   0.602   1.1930   2.9582   1.2594
 L3U  C4'  C  CH1   0  -0.019   0.8698  -2.9734  -0.1352
 L3U  C5   C  CR16  0  -0.509   0.6342   1.7954   1.9049
 L3U  C5'  C  CH2   0  -0.195  -0.2940  -3.3275   0.7631
 L3U  C6   C  CR16  0   0.085   0.9527   0.5720   1.4694
 L3U  N1   N  NR6   0  -0.580   1.8211   0.3619   0.4371
 L3U  N3   N  NR6   0  -0.597   2.1090   2.6805   0.2432
 L3U  N3S  N  NC1   0  -0.839  -2.4677  -0.9473   0.6121
 L3U  O1S  O  OS    0  -0.628  -2.9544  -2.9434   1.9809
 L3U  O2'  O  OH1   0  -0.651   4.0140  -1.7273   1.1748
 L3U  O2S  O  OS    0  -0.610  -3.8354  -2.8685  -0.3658
 L3U  O3'  O  OH1   0  -0.664   3.0989  -3.7011  -0.5173
 L3U  O4   O  O     0  -0.460   0.9125   4.1036   1.5546
 L3U  O4'  O  O2    0  -0.488   0.8601  -1.5725  -0.4123
 L3U  O5'  O  OC2   0  -0.567  -1.4989  -3.2055  -0.0225
 L3U  S    S  S     0   1.622  -2.8095  -2.5749   0.5948
 L3U  H1   H  HNH2  0   0.350  -0.3214   1.4855  -1.2153
 L3U  H2   H  HNH2  0   0.354  -1.5779   1.9261  -2.1309
 L3U  H4   H  HCH1  0   0.260  -1.7496   1.4439   0.7401
 L3U  H5   H  HCH2  0   0.243  -3.9287   1.6766  -1.3713
 L3U  H6   H  HCH2  0   0.237  -4.1819   1.3741   0.3361
 L3U  H7   H  HCH1  0   0.226  -2.9900   3.8985  -0.8721
 L3U  H8   H  HCH3  0   0.225  -5.4366   3.6239  -1.2545
 L3U  H9   H  HCH3  0   0.214  -5.6875   3.3959   0.4759
 L3U  H10  H  HCH3  0   0.228  -5.1162   4.9461  -0.1350
 L3U  H11  H  HCH3  0   0.232  -1.9773   3.5713   1.3431
 L3U  H12  H  HCH3  0   0.232  -3.1906   4.8314   1.4542
 L3U  H13  H  HCH3  0   0.215  -3.5536   3.2129   2.0519
 L3U  H14  H  HCH1  0   0.284   2.7774  -0.9215  -0.8484
 L3U  H15  H  HCH1  0   0.256   2.1278  -1.7613   2.0144
 L3U  H16  H  HCH1  0   0.262   2.1451  -4.0411   1.2934
 L3U  H17  H  HCH3  0   0.260   2.2123   4.0463  -1.3610
 L3U  H18  H  HCH3  0   0.267   2.7311   4.6671   0.2114
 L3U  H19  H  HCH3  0   0.264   3.7723   3.5573  -0.6798
 L3U  H20  H  HCH1  0   0.281   0.7724  -3.5306  -1.0723
 L3U  H21  H  HCR6  0   0.302  -0.0589   1.9289   2.7210
 L3U  H22  H  HCH2  0   0.285  -0.2226  -4.3628   1.0949
 L3U  H23  H  HCH2  0   0.255  -0.3244  -2.6841   1.6457
 L3U  H24  H  HCR6  0   0.321   0.5152  -0.3082   1.9172
 L3U  H25  H  HNC1  0   0.451  -2.5772  -0.4880   1.5088
 L3U  H26  H  HOH1  0   0.472   4.3083  -2.0752   2.0227
 L3U  H27  H  HOH1  0   0.452   4.0026  -3.5722  -0.2052
 L3U  O2   O  O     0  -0.471   3.1835   1.2543  -1.1520
 L3U  C3U  C  CH3   0  -0.532   2.7429   3.8024  -0.4414

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
 L3U  CD2  CG   single  1.524  0.020  1.524
 L3U  O3'  C3'  single  1.402  0.020  1.402
 L3U  CG   CB   single  1.529  0.020  1.529
 L3U  CG   CD1  single  1.526  0.020  1.526
 L3U  C4'  C3'  single  1.530  0.020  1.530
 L3U  C4'  O4'  single  1.428  0.020  1.428
 L3U  C4'  C5'  single  1.512  0.020  1.512
 L3U  C3'  C2'  single  1.531  0.020  1.531
 L3U  CB   CA   single  1.533  0.020  1.533
 L3U  O2   C2   double  1.212  0.020  1.212
 L3U  O4'  C1'  single  1.405  0.020  1.405
 L3U  C5'  O5'  single  1.444  0.020  1.444
 L3U  C1'  C2'  single  1.526  0.020  1.526
 L3U  C1'  N1   single  1.450  0.020  1.450
 L3U  O2'  C2'  single  1.395  0.020  1.395
 L3U  C2   N1   single  1.386  0.020  1.386
 L3U  C2   N3   single  1.378  0.020  1.378
 L3U  N    CA   single  1.440  0.020  1.440
 L3U  CA   C    single  1.524  0.020  1.524
 L3U  N1   C6   single  1.365  0.020  1.365
 L3U  O5'  S    single  1.580  0.020  1.580
 L3U  C3U  N3   single  1.459  0.020  1.459
 L3U  C    N3S  single  1.384  0.020  1.384
 L3U  C    O    double  1.205  0.020  1.205
 L3U  N3   C4   single  1.396  0.020  1.396
 L3U  N3S  S    single  1.663  0.020  1.663
 L3U  C6   C5   double  1.337  0.020  1.337
 L3U  O2S  S    deloc   1.436  0.020  1.436
 L3U  S    O1S  deloc   1.442  0.020  1.442
 L3U  C4   C5   single  1.443  0.020  1.443
 L3U  C4   O4   double  1.216  0.020  1.216
 L3U  N    H1   single  0.890  0.020  1.040
 L3U  N    H2   single  0.890  0.020  1.040
 L3U  CA   H4   single  0.970  0.020  1.090
 L3U  CB   H5   single  0.970  0.020  1.090
 L3U  CB   H6   single  0.970  0.020  1.090
 L3U  CG   H7   single  0.970  0.020  1.090
 L3U  CD1  H8   single  0.970  0.020  1.090
 L3U  CD1  H9   single  0.970  0.020  1.090
 L3U  CD1  H10  single  0.970  0.020  1.090
 L3U  CD2  H11  single  0.970  0.020  1.090
 L3U  CD2  H12  single  0.970  0.020  1.090
 L3U  CD2  H13  single  0.970  0.020  1.090
 L3U  C1'  H14  single  0.970  0.020  1.090
 L3U  C2'  H15  single  0.970  0.020  1.090
 L3U  C3'  H16  single  0.970  0.020  1.090
 L3U  C3U  H17  single  0.970  0.020  1.090
 L3U  C3U  H18  single  0.970  0.020  1.090
 L3U  C3U  H19  single  0.970  0.020  1.090
 L3U  C4'  H20  single  0.970  0.020  1.090
 L3U  C5   H21  single  0.930  0.020  1.080
 L3U  C5'  H22  single  0.970  0.020  1.090
 L3U  C5'  H23  single  0.970  0.020  1.090
 L3U  C6   H24  single  0.930  0.020  1.080
 L3U  N3S  H25  single  0.860  0.020  1.020
 L3U  O2'  H26  single  0.850  0.020  0.980
 L3U  O3'  H27  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
 L3U  H2   N    H1   105.92  3.000
 L3U  H2   N    CA   110.41  3.000
 L3U  H1   N    CA   110.94  3.000
 L3U  H4   CA   CB   108.30  3.000
 L3U  H4   CA   C    108.22  3.000
 L3U  CB   CA   C    107.77  3.000
 L3U  H4   CA   N    108.21  3.000
 L3U  C    CA   N    113.23  3.000
 L3U  CB   CA   N    110.97  3.000
 L3U  N3S  C    O    121.96  3.000
 L3U  O    C    CA   124.22  3.000
 L3U  N3S  C    CA   113.82  3.000
 L3U  H6   CB   H5   106.28  3.000
 L3U  H6   CB   CG   109.00  3.000
 L3U  H5   CB   CG   109.26  3.000
 L3U  H6   CB   CA   109.06  3.000
 L3U  H5   CB   CA   108.57  3.000
 L3U  CG   CB   CA   114.36  3.000
 L3U  H7   CG   CD2  108.15  3.000
 L3U  H7   CG   CD1  108.14  3.000
 L3U  CD2  CG   CD1  110.79  3.000
 L3U  H7   CG   CB   108.14  3.000
 L3U  CD1  CG   CB   109.24  3.000
 L3U  CD2  CG   CB   112.26  3.000
 L3U  H10  CD1  H9   107.52  3.000
 L3U  H10  CD1  H8   107.63  3.000
 L3U  H9   CD1  H8   107.64  3.000
 L3U  H10  CD1  CG   111.19  3.000
 L3U  H9   CD1  CG   111.13  3.000
 L3U  H8   CD1  CG   111.54  3.000
 L3U  H13  CD2  H12  107.65  3.000
 L3U  H13  CD2  H11  107.86  3.000
 L3U  H12  CD2  H11  106.89  3.000
 L3U  H13  CD2  CG   111.25  3.000
 L3U  H12  CD2  CG   110.69  3.000
 L3U  H11  CD2  CG   112.27  3.000
 L3U  H14  C1'  O4'  111.55  3.000
 L3U  H14  C1'  N1   106.91  3.000
 L3U  O4'  C1'  N1   108.78  3.000
 L3U  H14  C1'  C2'  109.79  3.000
 L3U  N1   C1'  C2'  114.49  3.000
 L3U  O4'  C1'  C2'  105.40  3.000
 L3U  O2   C2   N3   121.91  3.000
 L3U  N3   C2   N1   115.98  3.000
 L3U  O2   C2   N1   122.11  3.000
 L3U  H15  C2'  O2'  111.36  3.000
 L3U  H15  C2'  C3'  108.82  3.000
 L3U  O2'  C2'  C3'  114.88  3.000
 L3U  H15  C2'  C1'  110.65  3.000
 L3U  O2'  C2'  C1'  109.77  3.000
 L3U  C3'  C2'  C1'  100.91  3.000
 L3U  H16  C3'  O3'  111.60  3.000
 L3U  H16  C3'  C4'  112.06  3.000
 L3U  O3'  C3'  C4'  108.13  3.000
 L3U  H16  C3'  C2'  111.69  3.000
 L3U  C4'  C3'  C2'  101.89  3.000
 L3U  O3'  C3'  C2'  111.04  3.000
 L3U  O4   C4   N3   121.04  3.000
 L3U  O4   C4   C5   124.15  3.000
 L3U  N3   C4   C5   114.81  3.000
 L3U  H20  C4'  O4'  109.43  3.000
 L3U  H20  C4'  C5'  108.72  3.000
 L3U  O4'  C4'  C5'  109.86  3.000
 L3U  H20  C4'  C3'  109.24  3.000
 L3U  C5'  C4'  C3'  112.80  3.000
 L3U  O4'  C4'  C3'  106.74  3.000
 L3U  H21  C5   C6   120.84  3.000
 L3U  H21  C5   C4   119.18  3.000
 L3U  C6   C5   C4   119.96  3.000
 L3U  H23  C5'  H22  108.38  3.000
 L3U  H23  C5'  O5'  111.51  3.000
 L3U  H22  C5'  O5'  107.50  3.000
 L3U  H23  C5'  C4'  111.31  3.000
 L3U  H22  C5'  C4'  110.67  3.000
 L3U  O5'  C5'  C4'  107.41  3.000
 L3U  H24  C6   N1   116.47  3.000
 L3U  H24  C6   C5   120.94  3.000
 L3U  N1   C6   C5   122.59  3.000
 L3U  C6   N1   C2   121.24  3.000
 L3U  C6   N1   C1'  119.43  3.000
 L3U  C2   N1   C1'  119.28  3.000
 L3U  C4   N3   C3U  118.28  3.000
 L3U  C4   N3   C2   125.28  3.000
 L3U  C3U  N3   C2   116.37  3.000
 L3U  H25  N3S  S    115.50  3.000
 L3U  H25  N3S  C    120.44  3.000
 L3U  S    N3S  C    123.50  3.000
 L3U  H26  O2'  C2'  109.04  3.000
 L3U  H27  O3'  C3'  107.99  3.000
 L3U  C4'  O4'  C1'  110.16  3.000
 L3U  S    O5'  C5'  120.90  3.000
 L3U  O5'  S    O2S  104.46  3.000
 L3U  O2S  S    O1S  121.28  3.000
 L3U  O5'  S    O1S  110.92  3.000
 L3U  O1S  S    N3S  105.12  3.000
 L3U  O2S  S    N3S  110.72  3.000
 L3U  O5'  S    N3S  102.95  3.000
 L3U  H19  C3U  H18  108.85  3.000
 L3U  H19  C3U  H17  109.11  3.000
 L3U  H18  C3U  H17  108.94  3.000
 L3U  H19  C3U  N3   109.98  3.000
 L3U  H18  C3U  N3   109.04  3.000
 L3U  H17  C3U  N3   110.90  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
 L3U  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 L3U  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 L3U  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 L3U  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 L3U  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 L3U  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 L3U  CONST_07  N1   C2   N3   C3U  180.00   0.0  0
 L3U  CONST_08  C5   C4   N3   C3U  180.00   0.0  0
 L3U  CONST_09  O2   C2   N3   C4   180.00   0.0  0
 L3U  CONST_10  O2   C2   N1   C6   180.00   0.0  0
 L3U  CONST_11  O2   C2   N3   C3U    0.00   0.0  0
 L3U  CONST_12  O4   C4   N3   C3U    0.00   0.0  0
 L3U  CONST_13  S    N3S  C    CA   180.00   0.0  0
 L3U  CONST_14  S    N3S  C    O      0.00   0.0  0
 L3U  CONST_15  H25  N3S  C    CA     0.00   0.0  0
 L3U  Var_01    H17  C3U  N3   C2    81.34  30.0  3
 L3U  Var_02    CD2  CG   CB   CA   -57.89  30.0  2
 L3U  Var_03    O5'  S    N3S  C     62.39  30.0  3
 L3U  Var_04    N3S  S    O5'  C5'   75.49  30.0  3
 L3U  Var_05    H11  CD2  CG   CB    65.79  30.0  3
 L3U  Var_06    H8   CD1  CG   CB   -57.10  30.0  3
 L3U  Var_07    H22  C5'  O5'  S    101.29  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
 L3U  chir_01  CA   CB   N    C    positiv
 L3U  chir_02  C1'  O4'  C2'  N1   positiv
 L3U  chir_03  C2'  O2'  C1'  C3'  negativ
 L3U  chir_04  C3'  O3'  C4'  C2'  positiv
 L3U  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
 L3U  plan-1  C1'  0.020
 L3U  plan-1  C2   0.020
 L3U  plan-1  C4   0.020
 L3U  plan-1  C5   0.020
 L3U  plan-1  C6   0.020
 L3U  plan-1  N1   0.020
 L3U  plan-1  N3   0.020
 L3U  plan-1  O4   0.020
 L3U  plan-1  H21  0.020
 L3U  plan-1  H24  0.020
 L3U  plan-1  O2   0.020
 L3U  plan-1  C3U  0.020
 L3U  plan-2  CA   0.020
 L3U  plan-2  C    0.020
 L3U  plan-2  O    0.020
 L3U  plan-2  N3S  0.020
 L3U  plan-2  S    0.020
 L3U  plan-2  H25  0.020

