# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 04:21:27 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]pentanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
#
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
 VPU  VPU  'N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]pentanamide (non-preferred name)'  ligand  53  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPU
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
 VPU  C3    C  CH3   0  -0.663   0.9598   7.4016  -0.3731
 VPU  C2    C  CH2   0  -0.422   0.0985   6.4385   0.4313
 VPU  C1    C  CH2   0  -0.410  -0.2605   5.1846  -0.3564
 VPU  CAH   C  CH2   0  -0.589  -1.1205   4.2244   0.4532
 VPU  CAG   C  C     0   0.574  -1.5777   3.0171  -0.3335
 VPU  OAN   O  O     0  -0.493  -1.8107   3.0635  -1.5317
 VPU  NAI   N  NH1   0  -0.636  -1.7423   1.8970   0.4000
 VPU  CAB   C  CH1   0  -0.200  -2.2459   0.6700  -0.1339
 VPU  CAC   C  CH1   0   0.051  -3.5172   0.2135   0.5762
 VPU  OAJ   O  OH1   0  -0.657  -4.4794   1.2095   0.3881
 VPU  CAD   C  CH1   0  -0.024  -3.9569  -1.1230  -0.0068
 VPU  OAK   O  OH1   0  -0.666  -5.1166  -1.5272   0.6789
 VPU  CAE   C  CH1   0  -0.022  -2.8460  -2.1540   0.1825
 VPU  CAF   C  CH2   0  -0.157  -3.1439  -3.4592  -0.5178
 VPU  OAM   O  OH1   0  -0.665  -2.1496  -4.3944  -0.1853
 VPU  OAL   O  O2    0  -0.456  -1.5958  -1.6802  -0.3441
 VPU  CAA   C  C     0   0.502  -1.2092  -0.4304  -0.1236
 VPU  NAY   N  N     0  -0.173   0.0118  -0.0976  -0.0153
 VPU  OAQ   O  O2    0  -0.406   0.8314  -1.2062  -0.0903
 VPU  CAP   C  C     0   0.750   2.1383  -0.9094   0.0916
 VPU  OAR   O  O     0  -0.464   2.5698   0.1869   0.3323
 VPU  NAO   N  NH1   0  -0.776   2.8395  -2.0604  -0.0445
 VPU  CAS   C  CR6   0   0.373   4.2174  -2.2557   0.0849
 VPU  CAT   C  CR16  0  -0.317   5.1492  -1.2325   0.2618
 VPU  CAU   C  CR16  0  -0.245   6.4983  -1.5469   0.3697
 VPU  CAV   C  CR16  0  -0.273   6.9431  -2.8584   0.3021
 VPU  CAW   C  CR16  0  -0.245   6.0126  -3.8739   0.1229
 VPU  CAX   C  CR16  0  -0.342   4.6649  -3.5778   0.0164
 VPU  H3    H  HCH3  0   0.218   1.9065   6.9387  -0.6572
 VPU  H3A   H  HCH3  0   0.217   0.4546   7.7063  -1.2914
 VPU  H3B   H  HCH3  0   0.228   1.1893   8.3044   0.1936
 VPU  H2    H  HCH2  0   0.215   0.6214   6.1575   1.3505
 VPU  H2A   H  HCH2  0   0.215  -0.8208   6.9411   0.7478
 VPU  H1    H  HCH2  0   0.223  -0.7879   5.4695  -1.2697
 VPU  H1A   H  HCH2  0   0.222   0.6568   4.6796  -0.6746
 VPU  HAH   H  HCH2  0   0.252  -0.5917   3.9139   1.3580
 VPU  HAHA  H  HCH2  0   0.271  -2.0242   4.7408   0.7967
 VPU  HNAI  H  HNH1  0   0.403  -1.4884   1.9157   1.3752
 VPU  HAB   H  HCH1  0   0.308  -2.5000   0.8480  -1.1847
 VPU  HAC   H  HCH1  0   0.230  -3.2978   0.0681   1.6471
 VPU  HOAJ  H  HOH1  0   0.456  -5.2831   0.9357   0.8433
 VPU  HAD   H  HCH1  0   0.246  -4.1532  -0.9891  -1.0797
 VPU  HOAK  H  HOH1  0   0.467  -5.7143  -1.9635   0.0658
 VPU  HAE   H  HCH1  0   0.257  -2.7152  -2.3356   1.2565
 VPU  HAF   H  HCH2  0   0.211  -4.1370  -3.7956  -0.1973
 VPU  HAFA  H  HCH2  0   0.210  -3.1971  -3.2784  -1.6001
 VPU  HOAM  H  HOH1  0   0.460  -2.3659  -5.2240  -0.6204
 VPU  HNAO  H  HNH1  0   0.419   2.3003  -2.8932  -0.2327
 VPU  HAT   H  HCR6  0   0.278   4.8429  -0.2006   0.3140
 VPU  HAU   H  HCR6  0   0.259   7.2092  -0.7422   0.5062
 VPU  HAV   H  HCR6  0   0.255   7.9974  -3.0858   0.3858
 VPU  HAW   H  HCR6  0   0.260   6.3327  -4.9063   0.0657
 VPU  HAX   H  HCR6  0   0.271   3.9497  -4.3807  -0.1203

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
 VPU  C3   C2    single    1.522  0.020  1.522
 VPU  C2   C1    single    1.524  0.020  1.524
 VPU  C1   CAH   single    1.522  0.020  1.522
 VPU  CAH  CAG   single    1.512  0.020  1.512
 VPU  CAG  OAN   double    1.222  0.020  1.222
 VPU  CAG  NAI   single    1.349  0.020  1.349
 VPU  NAI  CAB   single    1.430  0.020  1.430
 VPU  CAB  CAC   single    1.526  0.020  1.526
 VPU  CAB  CAA   single    1.512  0.020  1.512
 VPU  CAC  OAJ   single    1.398  0.020  1.398
 VPU  CAC  CAD   single    1.523  0.020  1.523
 VPU  CAD  OAK   single    1.407  0.020  1.407
 VPU  CAD  CAE   single    1.527  0.020  1.527
 VPU  CAE  CAF   single    1.511  0.020  1.511
 VPU  CAE  OAL   single    1.437  0.020  1.437
 VPU  CAF  OAM   single    1.405  0.020  1.405
 VPU  OAL  CAA   single    1.327  0.020  1.327
 VPU  CAA  NAY   double    1.270  0.020  1.270
 VPU  NAY  OAQ   single    1.381  0.020  1.381
 VPU  OAQ  CAP   single    1.353  0.020  1.353
 VPU  CAP  OAR   double    1.203  0.020  1.203
 VPU  CAP  NAO   single    1.355  0.020  1.355
 VPU  NAO  CAS   single    1.398  0.020  1.398
 VPU  CAS  CAT   aromatic  1.395  0.020  1.395
 VPU  CAS  CAX   aromatic  1.397  0.020  1.397
 VPU  CAT  CAU   aromatic  1.389  0.020  1.389
 VPU  CAU  CAV   aromatic  1.387  0.020  1.387
 VPU  CAV  CAW   aromatic  1.389  0.020  1.389
 VPU  CAW  CAX   aromatic  1.384  0.020  1.384
 VPU  C3   H3    single    0.970  0.020  1.090
 VPU  C3   H3A   single    0.970  0.020  1.090
 VPU  C3   H3B   single    0.970  0.020  1.090
 VPU  C2   H2    single    0.970  0.020  1.090
 VPU  C2   H2A   single    0.970  0.020  1.090
 VPU  C1   H1    single    0.970  0.020  1.090
 VPU  C1   H1A   single    0.970  0.020  1.090
 VPU  CAH  HAH   single    0.970  0.020  1.090
 VPU  CAH  HAHA  single    0.970  0.020  1.090
 VPU  NAI  HNAI  single    0.860  0.020  1.020
 VPU  CAB  HAB   single    0.970  0.020  1.090
 VPU  CAC  HAC   single    0.970  0.020  1.090
 VPU  OAJ  HOAJ  single    0.850  0.020  0.980
 VPU  CAD  HAD   single    0.970  0.020  1.090
 VPU  OAK  HOAK  single    0.850  0.020  0.980
 VPU  CAE  HAE   single    0.970  0.020  1.090
 VPU  CAF  HAF   single    0.970  0.020  1.090
 VPU  CAF  HAFA  single    0.970  0.020  1.090
 VPU  OAM  HOAM  single    0.850  0.020  0.980
 VPU  NAO  HNAO  single    0.860  0.020  1.020
 VPU  CAT  HAT   single    0.930  0.020  1.080
 VPU  CAU  HAU   single    0.930  0.020  1.080
 VPU  CAV  HAV   single    0.930  0.020  1.080
 VPU  CAW  HAW   single    0.930  0.020  1.080
 VPU  CAX  HAX   single    0.930  0.020  1.080

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
 VPU  H3B   C3   H3A  107.67  3.000
 VPU  H3B   C3   H3   107.69  3.000
 VPU  H3A   C3   H3   107.51  3.000
 VPU  H3B   C3   C2   111.62  3.000
 VPU  H3A   C3   C2   111.06  3.000
 VPU  H3    C3   C2   111.11  3.000
 VPU  H2A   C2   H2   106.05  3.000
 VPU  H2A   C2   C1   109.24  3.000
 VPU  H2    C2   C1   109.60  3.000
 VPU  H2A   C2   C3   109.73  3.000
 VPU  H2    C2   C3   109.64  3.000
 VPU  C1    C2   C3   112.39  3.000
 VPU  H1A   C1   H1   106.37  3.000
 VPU  H1A   C1   CAH  109.70  3.000
 VPU  H1    C1   CAH  109.66  3.000
 VPU  H1A   C1   C2   109.42  3.000
 VPU  H1    C1   C2   109.35  3.000
 VPU  CAH   C1   C2   112.17  3.000
 VPU  HAHA  CAH  HAH  105.86  3.000
 VPU  HAHA  CAH  CAG  106.86  3.000
 VPU  HAH   CAH  CAG  110.50  3.000
 VPU  HAHA  CAH  C1   109.59  3.000
 VPU  HAH   CAH  C1   110.25  3.000
 VPU  CAG   CAH  C1   113.45  3.000
 VPU  NAI   CAG  OAN  122.79  3.000
 VPU  NAI   CAG  CAH  114.65  3.000
 VPU  OAN   CAG  CAH  122.53  3.000
 VPU  HNAI  NAI  CAB  117.77  3.000
 VPU  HNAI  NAI  CAG  118.68  3.000
 VPU  CAB   NAI  CAG  123.54  3.000
 VPU  HAB   CAB  CAA  106.48  3.000
 VPU  HAB   CAB  CAC  107.56  3.000
 VPU  CAA   CAB  CAC  110.51  3.000
 VPU  HAB   CAB  NAI  107.48  3.000
 VPU  CAA   CAB  NAI  112.37  3.000
 VPU  CAC   CAB  NAI  112.11  3.000
 VPU  HAC   CAC  CAD  108.27  3.000
 VPU  HAC   CAC  OAJ  111.20  3.000
 VPU  CAD   CAC  OAJ  112.03  3.000
 VPU  HAC   CAC  CAB  109.00  3.000
 VPU  CAD   CAC  CAB  108.96  3.000
 VPU  OAJ   CAC  CAB  107.32  3.000
 VPU  HOAJ  OAJ  CAC  107.95  3.000
 VPU  HAD   CAD  CAE  109.46  3.000
 VPU  HAD   CAD  OAK  111.33  3.000
 VPU  CAE   CAD  OAK  110.19  3.000
 VPU  HAD   CAD  CAC  108.57  3.000
 VPU  CAE   CAD  CAC  109.57  3.000
 VPU  OAK   CAD  CAC  107.68  3.000
 VPU  HOAK  OAK  CAD  109.40  3.000
 VPU  HAE   CAE  OAL  108.03  3.000
 VPU  HAE   CAE  CAF  109.53  3.000
 VPU  OAL   CAE  CAF  106.65  3.000
 VPU  HAE   CAE  CAD  108.65  3.000
 VPU  OAL   CAE  CAD  111.40  3.000
 VPU  CAF   CAE  CAD  112.48  3.000
 VPU  HAFA  CAF  HAF  107.14  3.000
 VPU  HAFA  CAF  OAM  112.14  3.000
 VPU  HAF   CAF  OAM  111.57  3.000
 VPU  HAFA  CAF  CAE  108.91  3.000
 VPU  HAF   CAF  CAE  107.95  3.000
 VPU  OAM   CAF  CAE  109.01  3.000
 VPU  HOAM  OAM  CAF  107.94  3.000
 VPU  CAA   OAL  CAE  120.21  3.000
 VPU  NAY   CAA  OAL  122.75  3.000
 VPU  NAY   CAA  CAB  117.97  3.000
 VPU  OAL   CAA  CAB  119.00  3.000
 VPU  OAQ   NAY  CAA  110.83  3.000
 VPU  CAP   OAQ  NAY  112.96  3.000
 VPU  NAO   CAP  OAR  127.52  3.000
 VPU  NAO   CAP  OAQ  107.47  3.000
 VPU  OAR   CAP  OAQ  125.01  3.000
 VPU  HNAO  NAO  CAS  115.37  3.000
 VPU  HNAO  NAO  CAP  116.30  3.000
 VPU  CAS   NAO  CAP  128.30  3.000
 VPU  CAX   CAS  CAT  119.10  3.000
 VPU  CAX   CAS  NAO  116.32  3.000
 VPU  CAT   CAS  NAO  124.59  3.000
 VPU  HAT   CAT  CAU  119.27  3.000
 VPU  HAT   CAT  CAS  121.24  3.000
 VPU  CAU   CAT  CAS  119.49  3.000
 VPU  HAU   CAU  CAV  119.91  3.000
 VPU  HAU   CAU  CAT  118.64  3.000
 VPU  CAV   CAU  CAT  121.45  3.000
 VPU  HAV   CAV  CAW  120.61  3.000
 VPU  HAV   CAV  CAU  120.52  3.000
 VPU  CAW   CAV  CAU  118.87  3.000
 VPU  HAW   CAW  CAX  119.21  3.000
 VPU  HAW   CAW  CAV  120.40  3.000
 VPU  CAX   CAW  CAV  120.39  3.000
 VPU  HAX   CAX  CAW  119.59  3.000
 VPU  HAX   CAX  CAS  119.72  3.000
 VPU  CAW   CAX  CAS  120.69  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
 VPU  CONST_01  CAV   CAU  CAT  CAS    0.00   0.0  0
 VPU  CONST_02  CAV   CAW  CAX  CAS    0.00   0.0  0
 VPU  CONST_03  CAW   CAX  CAS  CAT    0.00   0.0  0
 VPU  CONST_04  CAW   CAV  CAU  CAT    0.00   0.0  0
 VPU  CONST_05  CAX   CAS  CAT  CAU    0.00   0.0  0
 VPU  CONST_06  CAX   CAW  CAV  CAU    0.00   0.0  0
 VPU  CONST_07  CAU   CAT  CAS  NAO  180.00   0.0  0
 VPU  CONST_08  CAW   CAX  CAS  NAO  180.00   0.0  0
 VPU  CONST_09  HAU   CAU  CAT  CAS  180.00   0.0  0
 VPU  CONST_10  HAW   CAW  CAX  CAS  180.00   0.0  0
 VPU  CONST_11  HAX   CAX  CAS  CAT  180.00   0.0  0
 VPU  CONST_12  HAV   CAV  CAU  CAT  180.00   0.0  0
 VPU  CONST_13  HAT   CAT  CAU  CAV  180.00   0.0  0
 VPU  CONST_14  CAT   CAS  NAO  CAP    0.00   0.0  0
 VPU  CONST_15  CAX   CAS  NAO  CAP  180.00   0.0  0
 VPU  CONST_16  HNAO  NAO  CAS  CAT  180.00   0.0  0
 VPU  CONST_17  CAB   NAI  CAG  CAH  180.00   0.0  0
 VPU  CONST_18  CAB   NAI  CAG  OAN    0.00   0.0  0
 VPU  CONST_19  CAS   NAO  CAP  OAQ  180.00   0.0  0
 VPU  CONST_20  CAS   NAO  CAP  OAR    0.00   0.0  0
 VPU  CONST_21  HNAI  NAI  CAG  CAH    0.00   0.0  0
 VPU  Var_01    NAY   CAA  OAL  CAE  148.44  30.0  1
 VPU  Var_02    CAH   C1   C2   C3   179.94  30.0  3
 VPU  Var_03    CAG   CAH  C1   C2   175.80  30.0  3
 VPU  Var_04    OAN   CAG  CAH  C1   -32.56  30.0  3
 VPU  Var_05    OAR   CAP  OAQ  NAY    1.99  30.0  3
 VPU  Var_06    H3    C3   C2   C1   -61.14  30.0  3

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
 VPU  chir_01  CAB  NAI  CAC  CAA  positiv
 VPU  chir_02  CAC  OAJ  CAB  CAD  positiv
 VPU  chir_03  CAD  OAK  CAE  CAC  positiv
 VPU  chir_04  CAE  OAL  CAD  CAF  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
 VPU  plan-1  NAO   0.020
 VPU  plan-1  CAS   0.020
 VPU  plan-1  CAT   0.020
 VPU  plan-1  CAU   0.020
 VPU  plan-1  CAV   0.020
 VPU  plan-1  CAW   0.020
 VPU  plan-1  CAX   0.020
 VPU  plan-1  HAT   0.020
 VPU  plan-1  HAU   0.020
 VPU  plan-1  HAV   0.020
 VPU  plan-1  HAW   0.020
 VPU  plan-1  HAX   0.020
 VPU  plan-2  CAP   0.020
 VPU  plan-2  NAO   0.020
 VPU  plan-2  CAS   0.020
 VPU  plan-2  HNAO  0.020
 VPU  plan-3  CAH   0.020
 VPU  plan-3  CAG   0.020
 VPU  plan-3  OAN   0.020
 VPU  plan-3  NAI   0.020
 VPU  plan-3  CAB   0.020
 VPU  plan-3  HNAI  0.020
 VPU  plan-4  CAB   0.020
 VPU  plan-4  OAL   0.020
 VPU  plan-4  CAA   0.020
 VPU  plan-4  NAY   0.020
 VPU  plan-4  OAQ   0.020
 VPU  plan-5  OAQ   0.020
 VPU  plan-5  CAP   0.020
 VPU  plan-5  OAR   0.020
 VPU  plan-5  NAO   0.020

