# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 23:18:28 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: [(2~{R},3~{S},4~{S},5~{R})-5-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propyl]-3,4-bis(oxidanyl)oxan-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]1OC[C@@H](CCCn2cc(CN)nn2)[C@H](O)[C@@H]1O
#
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
 OV8  OV8  '[(2~{R},3~{S},4~{S},5~{R})-5-[3-[4-(aminomethyl)-1,2,3-triazol-1-yl]propyl]-3,4-bis(oxidanyl)oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate'  ligand  66  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OV8
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
 OV8  C13  C  CR5   0   0.143  -6.2091  -2.7458  -23.8272
 OV8  N    N  NH2   0  -0.811  -0.8524  -1.4838  -27.3719
 OV8  CA   C  CH1   0  -0.196  -2.2385  -1.1183  -27.4893
 OV8  C    C  C     0   0.571  -3.2734  -2.2360  -27.3460
 OV8  O    O  O     0  -0.396  -4.4400  -2.0281  -27.1220
 OV8  CB   C  CH2   0  -0.433  -2.5089  -0.4376  -28.8380
 OV8  CG   C  CH1   0  -0.219  -1.6175   0.7683  -29.1356
 OV8  CD1  C  CH3   0  -0.666  -1.7131   1.8348  -28.0510
 OV8  CD2  C  CH3   0  -0.652  -1.9929   1.3446  -30.4976
 OV8  C1   C  CH2   0  -0.159  -7.3354  -4.7738  -30.2823
 OV8  C14  C  CR15  0  -0.036  -6.9005  -3.2540  -24.8986
 OV8  C15  C  CH2   0  -0.350  -5.5387  -3.4734  -22.7119
 OV8  C2   C  CH1   0  -0.344  -7.7812  -3.3254  -30.0891
 OV8  C3   C  CH1   0   0.020  -6.5748  -2.4126  -29.8985
 OV8  C4   C  CH1   0   0.010  -5.5109  -2.6609  -30.9721
 OV8  C5   C  CH1   0  -0.049  -5.1821  -4.1460  -31.1328
 OV8  C6   C  CH2   0  -0.212  -4.1731  -4.6965  -30.1388
 OV8  C7   C  CH2   0  -0.432  -8.7996  -3.2507  -28.9420
 OV8  C8   C  CH2   0  -0.525  -8.2155  -3.4204  -27.5296
 OV8  C9   C  CH2   0  -0.264  -7.9880  -2.0740  -26.8583
 OV8  N10  N  NR5   0  -0.254  -7.2529  -2.1716  -25.6077
 OV8  N11  N  N     0  -0.121  -6.8203  -1.0684  -25.0290
 OV8  N12  N  N     0  -0.337  -6.1931  -1.4045  -23.9507
 OV8  N16  N  NH2   0  -0.804  -6.2881  -4.6657  -22.3521
 OV8  N3S  N  NC1   0  -0.835  -2.7735  -3.5062  -27.5581
 OV8  O1S  O  OS    0  -0.589  -4.5282  -4.9735  -26.4181
 OV8  O2S  O  OS    0  -0.644  -2.7592  -5.9439  -27.9067
 OV8  O3   O  OH1   0  -0.678  -6.9328  -1.0443  -29.8742
 OV8  O4   O  OH1   0  -0.688  -5.9479  -2.2162  -32.2383
 OV8  O5   O  O2    0  -0.485  -6.3366  -4.9335  -31.2721
 OV8  O6   O  OC2   0  -0.572  -4.6812  -4.6348  -28.7882
 OV8  S    S  S     0   1.637  -3.6885  -4.8907  -27.5775
 OV8  H2   H  HNH2  0   0.350  -0.4895  -1.9960  -28.1643
 OV8  H4   H  HCH1  0   0.269  -2.4752  -0.4122  -26.6879
 OV8  H5   H  HCH2  0   0.245  -3.5569  -0.1253  -28.8653
 OV8  H6   H  HCH2  0   0.234  -2.3840  -1.1772  -29.6390
 OV8  H7   H  HCH1  0   0.220  -0.5803   0.4244  -29.1841
 OV8  H8   H  HCH3  0   0.230  -1.3311   1.4811  -27.0929
 OV8  H9   H  HCH3  0   0.227  -1.1314   2.7163  -28.3260
 OV8  H10  H  HCH3  0   0.213  -2.7472   2.1561  -27.9029
 OV8  H11  H  HCH3  0   0.225  -1.3413   2.1770  -30.7678
 OV8  H12  H  HCH3  0   0.224  -1.9152   0.5937  -31.2861
 OV8  H13  H  HCH3  0   0.213  -3.0203   1.7168  -30.4945
 OV8  H14  H  HCH2  0   0.236  -8.1888  -5.3612  -30.6261
 OV8  H15  H  HCH2  0   0.216  -7.0215  -5.2094  -29.3279
 OV8  H16  H  HCR5  0   0.286  -7.1398  -4.2608  -25.1867
 OV8  H17  H  HCH2  0   0.235  -4.5443  -3.7905  -23.0387
 OV8  H18  H  HCH2  0   0.206  -5.3764  -2.7693  -21.8852
 OV8  H19  H  HCH1  0   0.238  -8.2920  -3.0208  -31.0112
 OV8  H20  H  HCH1  0   0.259  -6.1189  -2.6112  -28.9285
 OV8  H21  H  HCH1  0   0.228  -4.5899  -2.1341  -30.6788
 OV8  H22  H  HCH1  0   0.273  -4.6469  -4.2418  -32.0851
 OV8  H23  H  HCH2  0   0.274  -3.9500  -5.7353  -30.3843
 OV8  H24  H  HCH2  0   0.255  -3.2529  -4.1114  -30.2230
 OV8  H25  H  HCH2  0   0.242  -9.3506  -2.3082  -28.9987
 OV8  H26  H  HCH2  0   0.241  -9.5483  -4.0275  -29.1152
 OV8  H27  H  HCH2  0   0.251  -8.9025  -4.0117  -26.9209
 OV8  H28  H  HCH2  0   0.261  -7.2805  -3.9858  -27.5634
 OV8  H29  H  HCH2  0   0.281  -7.4283  -1.4024  -27.5056
 OV8  H30  H  HCH2  0   0.260  -8.9514  -1.6025  -26.6542
 OV8  H31  H  HNH2  0   0.359  -5.7618  -5.1978  -21.6713
 OV8  H32  H  HNH2  0   0.351  -7.1492  -4.3981  -21.8919
 OV8  H34  H  HNC1  0   0.450  -1.7783  -3.6324  -27.7007
 OV8  H35  H  HOH1  0   0.458  -7.6230  -0.8856  -30.5268
 OV8  H36  H  HOH1  0   0.467  -6.0753  -1.2632  -32.1947
 OV8  H1   H  HNH2  0   0.392  -0.6280  -1.9670  -26.5140

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
 OV8  CD2  CG   single    1.526  0.020  1.526
 OV8  O4   C4   single    1.411  0.020  1.411
 OV8  O5   C5   single    1.404  0.020  1.404
 OV8  O5   C1   single    1.415  0.020  1.415
 OV8  C5   C4   single    1.530  0.020  1.530
 OV8  C5   C6   single    1.520  0.020  1.520
 OV8  CG   CB   single    1.529  0.020  1.529
 OV8  CG   CD1  single    1.524  0.020  1.524
 OV8  C4   C3   single    1.532  0.020  1.532
 OV8  CB   CA   single    1.535  0.020  1.535
 OV8  C6   O6   single    1.444  0.020  1.444
 OV8  C1   C2   single    1.528  0.020  1.528
 OV8  C2   C3   single    1.525  0.020  1.525
 OV8  C2   C7   single    1.536  0.020  1.536
 OV8  C3   O3   single    1.415  0.020  1.415
 OV8  N    CA   single    1.438  0.020  1.438
 OV8  CA   C    single    1.530  0.020  1.530
 OV8  C7   C8   single    1.538  0.020  1.538
 OV8  O6   S    single    1.586  0.020  1.586
 OV8  C    N3S  single    1.381  0.020  1.381
 OV8  C    O    double    1.206  0.020  1.206
 OV8  N3S  S    single    1.660  0.020  1.660
 OV8  O2S  S    double    1.443  0.020  1.443
 OV8  S    O1S  double    1.434  0.020  1.434
 OV8  C8   C9   single    1.522  0.020  1.522
 OV8  C9   N10  single    1.454  0.020  1.454
 OV8  N10  N11  aromatic  1.319  0.020  1.319
 OV8  N10  C14  aromatic  1.341  0.020  1.341
 OV8  N11  N12  aromatic  1.292  0.020  1.292
 OV8  C14  C13  aromatic  1.373  0.020  1.373
 OV8  N12  C13  aromatic  1.347  0.020  1.347
 OV8  C13  C15  single    1.491  0.020  1.491
 OV8  N16  C15  single    1.454  0.020  1.454
 OV8  N    H1   single    0.890  0.020  1.040
 OV8  N    H2   single    0.890  0.020  1.040
 OV8  CA   H4   single    0.970  0.020  1.090
 OV8  CB   H5   single    0.970  0.020  1.090
 OV8  CB   H6   single    0.970  0.020  1.090
 OV8  CG   H7   single    0.970  0.020  1.090
 OV8  CD1  H8   single    0.970  0.020  1.090
 OV8  CD1  H9   single    0.970  0.020  1.090
 OV8  CD1  H10  single    0.970  0.020  1.090
 OV8  CD2  H11  single    0.970  0.020  1.090
 OV8  CD2  H12  single    0.970  0.020  1.090
 OV8  CD2  H13  single    0.970  0.020  1.090
 OV8  C1   H14  single    0.970  0.020  1.090
 OV8  C1   H15  single    0.970  0.020  1.090
 OV8  C14  H16  single    0.930  0.020  1.080
 OV8  C15  H17  single    0.970  0.020  1.090
 OV8  C15  H18  single    0.970  0.020  1.090
 OV8  C2   H19  single    0.970  0.020  1.090
 OV8  C3   H20  single    0.970  0.020  1.090
 OV8  C4   H21  single    0.970  0.020  1.090
 OV8  C5   H22  single    0.970  0.020  1.090
 OV8  C6   H23  single    0.970  0.020  1.090
 OV8  C6   H24  single    0.970  0.020  1.090
 OV8  C7   H25  single    0.970  0.020  1.090
 OV8  C7   H26  single    0.970  0.020  1.090
 OV8  C8   H27  single    0.970  0.020  1.090
 OV8  C8   H28  single    0.970  0.020  1.090
 OV8  C9   H29  single    0.970  0.020  1.090
 OV8  C9   H30  single    0.970  0.020  1.090
 OV8  N16  H31  single    0.890  0.020  1.040
 OV8  N16  H32  single    0.890  0.020  1.040
 OV8  N3S  H34  single    0.860  0.020  1.020
 OV8  O3   H35  single    0.850  0.020  0.980
 OV8  O4   H36  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
 OV8  N12  C13  C15  123.31  3.000
 OV8  C15  C13  C14  129.03  3.000
 OV8  N12  C13  C14  107.64  3.000
 OV8  H2   N    H1   110.11  3.000
 OV8  H2   N    CA   114.25  3.000
 OV8  H1   N    CA   113.89  3.000
 OV8  H4   CA   CB   108.62  3.000
 OV8  H4   CA   C    104.87  3.000
 OV8  CB   CA   C    106.69  3.000
 OV8  H4   CA   N    108.22  3.000
 OV8  C    CA   N    117.30  3.000
 OV8  CB   CA   N    110.75  3.000
 OV8  N3S  C    O    122.49  3.000
 OV8  O    C    CA   123.08  3.000
 OV8  N3S  C    CA   114.36  3.000
 OV8  H6   CB   H5   106.45  3.000
 OV8  H6   CB   CG   108.86  3.000
 OV8  H5   CB   CG   109.18  3.000
 OV8  H6   CB   CA   108.81  3.000
 OV8  H5   CB   CA   108.50  3.000
 OV8  CG   CB   CA   114.72  3.000
 OV8  H7   CG   CD2  108.21  3.000
 OV8  H7   CG   CD1  108.12  3.000
 OV8  CD2  CG   CD1  110.83  3.000
 OV8  H7   CG   CB   108.27  3.000
 OV8  CD1  CG   CB   112.14  3.000
 OV8  CD2  CG   CB   109.16  3.000
 OV8  H10  CD1  H9   107.52  3.000
 OV8  H10  CD1  H8   107.93  3.000
 OV8  H9   CD1  H8   107.26  3.000
 OV8  H10  CD1  CG   111.19  3.000
 OV8  H9   CD1  CG   110.63  3.000
 OV8  H8   CD1  CG   112.10  3.000
 OV8  H13  CD2  H12  107.66  3.000
 OV8  H13  CD2  H11  107.59  3.000
 OV8  H12  CD2  H11  107.66  3.000
 OV8  H13  CD2  CG   110.94  3.000
 OV8  H12  CD2  CG   111.56  3.000
 OV8  H11  CD2  CG   111.24  3.000
 OV8  H15  C1   H14  106.53  3.000
 OV8  H15  C1   O5   111.25  3.000
 OV8  H14  C1   O5   105.71  3.000
 OV8  H15  C1   C2   110.52  3.000
 OV8  H14  C1   C2   108.77  3.000
 OV8  O5   C1   C2   113.67  3.000
 OV8  H16  C14  N10  123.78  3.000
 OV8  H16  C14  C13  131.96  3.000
 OV8  N10  C14  C13  104.26  3.000
 OV8  H18  C15  H17  106.05  3.000
 OV8  H18  C15  N16  114.57  3.000
 OV8  H17  C15  N16  107.75  3.000
 OV8  H18  C15  C13  108.47  3.000
 OV8  H17  C15  C13  109.08  3.000
 OV8  N16  C15  C13  110.71  3.000
 OV8  H19  C2   C7   107.79  3.000
 OV8  H19  C2   C3   107.89  3.000
 OV8  C7   C2   C3   113.71  3.000
 OV8  H19  C2   C1   107.02  3.000
 OV8  C7   C2   C1   109.52  3.000
 OV8  C3   C2   C1   110.64  3.000
 OV8  H20  C3   O3   105.47  3.000
 OV8  H20  C3   C4   107.68  3.000
 OV8  O3   C3   C4   110.16  3.000
 OV8  H20  C3   C2   109.46  3.000
 OV8  O3   C3   C2   112.39  3.000
 OV8  C4   C3   C2   111.40  3.000
 OV8  H21  C4   O4   110.33  3.000
 OV8  H21  C4   C5   108.22  3.000
 OV8  O4   C4   C5   106.16  3.000
 OV8  H21  C4   C3   108.47  3.000
 OV8  C5   C4   C3   112.35  3.000
 OV8  O4   C4   C3   111.27  3.000
 OV8  H22  C5   O5   105.43  3.000
 OV8  H22  C5   C6   102.26  3.000
 OV8  O5   C5   C6   114.06  3.000
 OV8  H22  C5   C4   106.31  3.000
 OV8  C6   C5   C4   115.20  3.000
 OV8  O5   C5   C4   112.22  3.000
 OV8  H24  C6   H23  108.67  3.000
 OV8  H24  C6   O6   110.18  3.000
 OV8  H23  C6   O6   108.86  3.000
 OV8  H24  C6   C5   108.33  3.000
 OV8  H23  C6   C5   109.49  3.000
 OV8  O6   C6   C5   111.26  3.000
 OV8  H26  C7   H25  105.03  3.000
 OV8  H26  C7   C8   109.11  3.000
 OV8  H25  C7   C8   109.53  3.000
 OV8  H26  C7   C2   107.54  3.000
 OV8  H25  C7   C2   109.72  3.000
 OV8  C8   C7   C2   115.39  3.000
 OV8  H28  C8   H27  105.98  3.000
 OV8  H28  C8   C9   110.09  3.000
 OV8  H27  C8   C9   109.11  3.000
 OV8  H28  C8   C7   110.70  3.000
 OV8  H27  C8   C7   109.44  3.000
 OV8  C9   C8   C7   111.37  3.000
 OV8  H30  C9   H29  107.37  3.000
 OV8  H30  C9   N10  108.33  3.000
 OV8  H29  C9   N10  107.05  3.000
 OV8  H30  C9   C8   109.43  3.000
 OV8  H29  C9   C8   111.14  3.000
 OV8  N10  C9   C8   113.31  3.000
 OV8  N11  N10  C9   119.15  3.000
 OV8  N11  N10  C14  110.91  3.000
 OV8  C9   N10  C14  129.93  3.000
 OV8  N12  N11  N10  107.93  3.000
 OV8  N11  N12  C13  109.25  3.000
 OV8  H32  N16  H31  105.99  3.000
 OV8  H32  N16  C15  109.53  3.000
 OV8  H31  N16  C15  109.26  3.000
 OV8  H34  N3S  S    115.84  3.000
 OV8  H34  N3S  C    119.45  3.000
 OV8  S    N3S  C    124.71  3.000
 OV8  H35  O3   C3   109.22  3.000
 OV8  H36  O4   C4   108.20  3.000
 OV8  C5   O5   C1   116.58  3.000
 OV8  S    O6   C6   119.12  3.000
 OV8  O6   S    O2S  110.29  3.000
 OV8  O2S  S    O1S  121.30  3.000
 OV8  O6   S    O1S  105.06  3.000
 OV8  O1S  S    N3S  111.19  3.000
 OV8  O2S  S    N3S  104.87  3.000
 OV8  O6   S    N3S  102.67  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
 OV8  CONST_01  N11  N10  C14  C13     0.00   0.0  0
 OV8  CONST_02  N10  N11  N12  C13     0.00   0.0  0
 OV8  CONST_03  N12  N11  N10  C14     0.00   0.0  0
 OV8  CONST_04  N11  N12  C13  C14     0.00   0.0  0
 OV8  CONST_05  N12  C13  C14  N10     0.00   0.0  0
 OV8  CONST_06  C9   N10  C14  C13   180.00   0.0  0
 OV8  CONST_07  N10  C14  C13  C15   180.00   0.0  0
 OV8  CONST_08  N11  N12  C13  C15   180.00   0.0  0
 OV8  CONST_09  N12  N11  N10  C9    180.00   0.0  0
 OV8  CONST_10  H16  C14  N10  N11   180.00   0.0  0
 OV8  CONST_11  S    N3S  C    CA    180.00   0.0  0
 OV8  CONST_12  S    N3S  C    O       0.00   0.0  0
 OV8  CONST_13  H34  N3S  C    CA      0.00   0.0  0
 OV8  Var_01    H14  C1   O5   C5    173.02  30.0  1
 OV8  Var_02    C8   C9   N10  C14    -9.02  30.0  1
 OV8  Var_03    N16  C15  C13  C14   -35.32  30.0  2
 OV8  Var_04    C9   C8   C7   C2     98.01  30.0  3
 OV8  Var_05    N10  C9   C8   C7   -171.24  30.0  3
 OV8  Var_06    H31  N16  C15  C13   173.49  30.0  3
 OV8  Var_07    CD2  CG   CB   CA   -179.94  30.0  2
 OV8  Var_08    O6   S    N3S  C      61.52  30.0  3
 OV8  Var_09    N3S  S    O6   C6     72.66  30.0  3
 OV8  Var_10    H11  CD2  CG   CB   -177.03  30.0  3
 OV8  Var_11    H8   CD1  CG   CB     64.87  30.0  3
 OV8  Var_12    H23  C6   O6   S      71.14  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
 OV8  chir_01  CA  CB  N   C   positiv
 OV8  chir_02  C2  C1  C3  C7  positiv
 OV8  chir_03  C3  O3  C2  C4  negativ
 OV8  chir_04  C4  O4  C5  C3  positiv
 OV8  chir_05  C5  O5  C6  C4  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
 OV8  plan-1  C13  0.020
 OV8  plan-1  C14  0.020
 OV8  plan-1  C15  0.020
 OV8  plan-1  C9   0.020
 OV8  plan-1  N10  0.020
 OV8  plan-1  N11  0.020
 OV8  plan-1  N12  0.020
 OV8  plan-1  H16  0.020
 OV8  plan-2  CA   0.020
 OV8  plan-2  C    0.020
 OV8  plan-2  O    0.020
 OV8  plan-2  N3S  0.020
 OV8  plan-2  S    0.020
 OV8  plan-2  H34  0.020

