# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 22:20:01 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@@H](O)[C@@H](OC)[C@@H]1OC(=C[C@H](NC(N)=N)[C@H]1NC(C)=O)C(O)=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
 LVO  LVO  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  68  33  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LVO
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
 LVO  CAA   C  C      0   0.167  -3.0597  -2.1241  -0.0870
 LVO  CAB   C  C1     0  -0.365  -4.2376  -1.6899   0.3628
 LVO  CAC   C  CH1    0  -0.035  -4.5357  -0.2409   0.6189
 LVO  CAD   C  CH1    0  -0.131  -3.4304   0.6241   0.0075
 LVO  CAE   C  CH1    0   0.055  -2.0807  -0.0255   0.3280
 LVO  OAF   O  O2     0  -0.477  -2.0012  -1.3008  -0.2768
 LVO  CAG   C  C      0   0.370  -2.7756  -3.5803  -0.4398
 LVO  OAH   O  OC    -1  -0.593  -1.6279  -3.8342  -0.8390
 LVO  OAI   O  O      0  -0.592  -3.7248  -4.3724  -0.2930
 LVO  CAJ   C  CH1    0  -0.024  -0.8829   0.7884  -0.1535
 LVO  CAK   C  CH1    0  -0.011   0.4452   0.0521   0.1203
 LVO  CAL   C  CH2    0  -0.187   1.6227   0.9386  -0.2502
 LVO  OAM   O  O2     0  -0.461   2.8171   0.1813  -0.0525
 LVO  CAN   C  C      0   0.607   3.9760   0.8060  -0.2380
 LVO  OAV   O  O      0  -0.453   4.0554   1.9745  -0.5253
 LVO  OAW   O  O2     0  -0.498  -1.0137   1.0473  -1.5313
 LVO  CAX   C  CH3    0  -0.413  -0.8822   2.3958  -1.9185
 LVO  OAY   O  OH1    0  -0.656   0.5304  -0.3790   1.4564
 LVO  NAZ   N  NH1    0  -0.642  -5.8131   0.1686   0.0899
 LVO  CBA   C  C      0   0.563  -6.9752  -0.0262   0.7789
 LVO  NBB   N  NH2    0  -0.843  -8.1066   0.3147   0.0670
 LVO  NBC   N  N      0  -0.722  -6.9556  -0.4119   2.0035
 LVO  CBE   C  CH3    0  -0.780  -4.2179   4.2778   0.5704
 LVO  OBF   O  O      0  -0.498  -4.4764   2.8768  -1.3487
 LVO  NBG   N  NH1    0  -0.633  -3.5027   1.9787   0.4883
 LVO  HAB   H  H      0   0.244  -5.0285  -2.4094   0.5186
 LVO  HAC   H  HCH1   0   0.253  -4.5749  -0.0542   1.6962
 LVO  HAD   H  HCH1   0   0.271  -3.5490   0.6514  -1.0777
 LVO  HAE   H  HCH1   0   0.236  -2.0010  -0.1396   1.4188
 LVO  HAJ   H  HCH1   0   0.234  -0.8855   1.7238   0.4250
 LVO  HAK   H  HCH1   0   0.254   0.4716  -0.8516  -0.4940
 LVO  H1AL  H  HCH2   0   0.244   1.5620   1.2547  -1.2928
 LVO  H2AL  H  HCH2   0   0.234   1.6346   1.8361   0.3774
 LVO  C15   C  CH2    0  -0.584   5.1453  -0.1254  -0.0696
 LVO  H1AX  H  HCH3   0   0.219  -1.5392   3.0565  -1.3483
 LVO  H2AX  H  HCH3   0   0.208   0.1426   2.7664  -1.8111
 LVO  H3AX  H  HCH3   0   0.237  -1.1563   2.4632  -2.9704
 LVO  HOAY  H  HOH1   0   0.447   0.5421   0.3917   2.0353
 LVO  HNAZ  H  HNH1   0   0.376  -5.8721   0.2432  -0.9130
 LVO  H1BB  H  HNH2   0   0.382  -8.0478   0.2624  -0.9383
 LVO  H2BB  H  HNH2   0   0.385  -8.9636  -0.0874   0.4104
 LVO  HBC   H  H      0   0.315  -7.8970  -0.4549   2.3749
 LVO  H1BE  H  HCH3   0   0.262  -4.0376   5.1224  -0.0920
 LVO  H2BE  H  HCH3   0   0.269  -5.2403   4.3645   0.9421
 LVO  H3BE  H  HCH3   0   0.250  -3.5440   4.3471   1.4226
 LVO  HNBG  H  HNH1   0   0.398  -3.2832   2.1369   1.4596
 LVO  C16   C  CH2    0  -0.418   6.4869   0.5891  -0.0201
 LVO  C17   C  CH2    0  -0.416   7.6554  -0.3856   0.0526
 LVO  C18   C  CH2    0  -0.412   9.0036   0.3198   0.1259
 LVO  C19   C  CH2    0  -0.407  10.1851  -0.6411   0.1619
 LVO  C20   C  CH2    0  -0.419  11.5330   0.0657   0.2400
 LVO  C21   C  CH3    0  -0.663  12.7067  -0.9037   0.2660
 LVO  H23   H  HCH2   0   0.269   4.9942  -0.7323   0.8274
 LVO  H24   H  HCH2   0   0.276   5.1225  -0.8316  -0.9076
 LVO  H25   H  HCH2   0   0.225   6.6022   1.2228  -0.9028
 LVO  H26   H  HCH2   0   0.224   6.5166   1.2578   0.8450
 LVO  H27   H  HCH2   0   0.212   7.5387  -1.0388   0.9244
 LVO  H28   H  HCH2   0   0.212   7.6345  -1.0431  -0.8236
 LVO  H29   H  HCH2   0   0.208   9.1092   0.9908  -0.7339
 LVO  H30   H  HCH2   0   0.209   9.0300   0.9610   1.0142
 LVO  H31   H  HCH2   0   0.207  10.0794  -1.3161   1.0188
 LVO  H32   H  HCH2   0   0.206  10.1613  -1.2787  -0.7292
 LVO  H33   H  HCH2   0   0.210  11.6350   0.7438  -0.6133
 LVO  H34   H  HCH2   0   0.210  11.5587   0.6986   1.1328
 LVO  H35   H  HCH3   0   0.226  13.6616  -0.3795   0.3189
 LVO  H36   H  HCH3   0   0.216  12.6465  -1.5696   1.1288
 LVO  H37   H  HCH3   0   0.216  12.7211  -1.5266  -0.6303
 LVO  CBD   C  C      0   0.527  -4.0827   2.9863  -0.1973

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
 LVO  CAA  CAB   double  1.334  0.020  1.334
 LVO  CAA  OAF   single  1.354  0.020  1.354
 LVO  CAB  CAC   single  1.501  0.020  1.501
 LVO  CAB  HAB   single  0.930  0.020  1.080
 LVO  CAC  NAZ   single  1.442  0.020  1.442
 LVO  CAC  CAD   single  1.531  0.020  1.531
 LVO  CAC  HAC   single  0.970  0.020  1.090
 LVO  CAD  NBG   single  1.439  0.020  1.439
 LVO  CAD  HAD   single  0.970  0.020  1.090
 LVO  CAE  CAD   single  1.532  0.020  1.532
 LVO  CAE  CAJ   single  1.526  0.020  1.526
 LVO  CAE  HAE   single  0.970  0.020  1.090
 LVO  OAF  CAE   single  1.414  0.020  1.414
 LVO  CAG  CAA   single  1.525  0.020  1.525
 LVO  OAH  CAG   deloc   1.241  0.020  1.241
 LVO  OAI  CAG   deloc   1.245  0.020  1.245
 LVO  CAJ  OAW   single  1.408  0.020  1.408
 LVO  CAJ  HAJ   single  0.970  0.020  1.090
 LVO  CAK  CAJ   single  1.543  0.020  1.543
 LVO  CAK  CAL   single  1.520  0.020  1.520
 LVO  CAK  HAK   single  0.970  0.020  1.090
 LVO  CAL  H1AL  single  0.970  0.020  1.090
 LVO  CAL  H2AL  single  0.970  0.020  1.090
 LVO  OAM  CAL   single  1.428  0.020  1.428
 LVO  CAN  OAM   single  1.330  0.020  1.330
 LVO  CAN  OAV   double  1.206  0.020  1.206
 LVO  CAN  C15   single  1.504  0.020  1.504
 LVO  OAW  CAX   single  1.409  0.020  1.409
 LVO  CAX  H1AX  single  0.970  0.020  1.090
 LVO  CAX  H2AX  single  0.970  0.020  1.090
 LVO  CAX  H3AX  single  0.970  0.020  1.090
 LVO  OAY  CAK   single  1.407  0.020  1.407
 LVO  OAY  HOAY  single  0.850  0.020  0.980
 LVO  NAZ  CBA   single  1.365  0.020  1.365
 LVO  NAZ  HNAZ  single  0.890  0.020  1.040
 LVO  CBA  NBB   single  1.380  0.020  1.380
 LVO  NBB  H1BB  single  0.890  0.020  1.040
 LVO  NBB  H2BB  single  0.890  0.020  1.040
 LVO  NBC  CBA   double  1.284  0.020  1.284
 LVO  NBC  HBC   single  0.890  0.020  1.040
 LVO  CBD  OBF   double  1.222  0.020  1.222
 LVO  CBD  CBE   single  1.509  0.020  1.509
 LVO  CBE  H1BE  single  0.970  0.020  1.090
 LVO  CBE  H2BE  single  0.970  0.020  1.090
 LVO  CBE  H3BE  single  0.970  0.020  1.090
 LVO  NBG  CBD   single  1.350  0.020  1.350
 LVO  NBG  HNBG  single  0.860  0.020  1.020
 LVO  C15  C16   single  1.521  0.020  1.521
 LVO  C16  C17   single  1.523  0.020  1.523
 LVO  C17  C18   single  1.523  0.020  1.523
 LVO  C18  C19   single  1.523  0.020  1.523
 LVO  C19  C20   single  1.524  0.020  1.524
 LVO  C20  C21   single  1.523  0.020  1.523
 LVO  C15  H23   single  0.970  0.020  1.090
 LVO  C15  H24   single  0.970  0.020  1.090
 LVO  C16  H25   single  0.970  0.020  1.090
 LVO  C16  H26   single  0.970  0.020  1.090
 LVO  C17  H27   single  0.970  0.020  1.090
 LVO  C17  H28   single  0.970  0.020  1.090
 LVO  C18  H29   single  0.970  0.020  1.090
 LVO  C18  H30   single  0.970  0.020  1.090
 LVO  C19  H31   single  0.970  0.020  1.090
 LVO  C19  H32   single  0.970  0.020  1.090
 LVO  C20  H33   single  0.970  0.020  1.090
 LVO  C20  H34   single  0.970  0.020  1.090
 LVO  C21  H35   single  0.970  0.020  1.090
 LVO  C21  H36   single  0.970  0.020  1.090
 LVO  C21  H37   single  0.970  0.020  1.090

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
 LVO  CAG   CAA  OAF   113.73  3.000
 LVO  CAG   CAA  CAB   123.61  3.000
 LVO  OAF   CAA  CAB   122.66  3.000
 LVO  HAB   CAB  CAC   118.22  3.000
 LVO  HAB   CAB  CAA   118.58  3.000
 LVO  CAC   CAB  CAA   123.17  3.000
 LVO  HAC   CAC  NAZ   106.32  3.000
 LVO  HAC   CAC  CAD   108.83  3.000
 LVO  NAZ   CAC  CAD   109.43  3.000
 LVO  HAC   CAC  CAB   109.86  3.000
 LVO  CAD   CAC  CAB   109.50  3.000
 LVO  NAZ   CAC  CAB   112.79  3.000
 LVO  HAD   CAD  NBG   107.64  3.000
 LVO  HAD   CAD  CAE   108.31  3.000
 LVO  NBG   CAD  CAE   111.93  3.000
 LVO  CAE   CAD  CAC   108.24  3.000
 LVO  HAD   CAD  CAC   109.43  3.000
 LVO  NBG   CAD  CAC   111.23  3.000
 LVO  HAE   CAE  CAJ   108.15  3.000
 LVO  HAE   CAE  OAF   109.07  3.000
 LVO  CAJ   CAE  OAF   107.58  3.000
 LVO  OAF   CAE  CAD   110.03  3.000
 LVO  HAE   CAE  CAD   108.38  3.000
 LVO  CAJ   CAE  CAD   113.54  3.000
 LVO  CAE   OAF  CAA   116.39  3.000
 LVO  OAI   CAG  OAH   127.78  3.000
 LVO  OAI   CAG  CAA   115.99  3.000
 LVO  OAH   CAG  CAA   116.23  3.000
 LVO  HAJ   CAJ  OAW   110.99  3.000
 LVO  HAJ   CAJ  CAK   108.33  3.000
 LVO  OAW   CAJ  CAK   109.96  3.000
 LVO  CAK   CAJ  CAE   111.41  3.000
 LVO  HAJ   CAJ  CAE   106.61  3.000
 LVO  OAW   CAJ  CAE   109.51  3.000
 LVO  HAK   CAK  OAY   106.20  3.000
 LVO  OAY   CAK  CAL   111.31  3.000
 LVO  HAK   CAK  CAL   109.06  3.000
 LVO  OAY   CAK  CAJ   111.53  3.000
 LVO  HAK   CAK  CAJ   108.40  3.000
 LVO  CAL   CAK  CAJ   110.20  3.000
 LVO  H2AL  CAL  H1AL  108.10  3.000
 LVO  H2AL  CAL  OAM   110.25  3.000
 LVO  H1AL  CAL  OAM   109.42  3.000
 LVO  OAM   CAL  CAK   107.76  3.000
 LVO  H2AL  CAL  CAK   110.29  3.000
 LVO  H1AL  CAL  CAK   111.03  3.000
 LVO  CAN   OAM  CAL   117.42  3.000
 LVO  C15   CAN  OAV   125.13  3.000
 LVO  C15   CAN  OAM   111.77  3.000
 LVO  OAV   CAN  OAM   123.09  3.000
 LVO  CAX   OAW  CAJ   115.86  3.000
 LVO  H3AX  CAX  H2AX  108.02  3.000
 LVO  H3AX  CAX  H1AX  108.38  3.000
 LVO  H2AX  CAX  H1AX  107.88  3.000
 LVO  H3AX  CAX  OAW   107.52  3.000
 LVO  H2AX  CAX  OAW   112.60  3.000
 LVO  H1AX  CAX  OAW   112.29  3.000
 LVO  HOAY  OAY  CAK   109.03  3.000
 LVO  HNAZ  NAZ  CBA   117.60  3.000
 LVO  HNAZ  NAZ  CAC   115.98  3.000
 LVO  CBA   NAZ  CAC   121.90  3.000
 LVO  NBC   CBA  NBB   125.38  3.000
 LVO  NBC   CBA  NAZ   120.75  3.000
 LVO  NBB   CBA  NAZ   113.73  3.000
 LVO  H2BB  NBB  H1BB  111.64  3.000
 LVO  H2BB  NBB  CBA   115.04  3.000
 LVO  H1BB  NBB  CBA   117.00  3.000
 LVO  HBC   NBC  CBA   110.38  3.000
 LVO  H3BE  CBE  H2BE  107.96  3.000
 LVO  H3BE  CBE  H1BE  108.93  3.000
 LVO  H2BE  CBE  H1BE  107.51  3.000
 LVO  H3BE  CBE  CBD   113.41  3.000
 LVO  H2BE  CBE  CBD   108.98  3.000
 LVO  H1BE  CBE  CBD   109.86  3.000
 LVO  HNBG  NBG  CBD   117.76  3.000
 LVO  HNBG  NBG  CAD   117.29  3.000
 LVO  CBD   NBG  CAD   123.68  3.000
 LVO  H24   C15  H23   105.47  3.000
 LVO  H24   C15  C16   110.24  3.000
 LVO  H23   C15  C16   110.85  3.000
 LVO  H24   C15  CAN   107.29  3.000
 LVO  H23   C15  CAN   109.15  3.000
 LVO  C16   C15  CAN   113.48  3.000
 LVO  H26   C16  H25   106.35  3.000
 LVO  H26   C16  C17   109.43  3.000
 LVO  H25   C16  C17   109.19  3.000
 LVO  H26   C16  C15   109.69  3.000
 LVO  H25   C16  C15   109.83  3.000
 LVO  C17   C16  C15   112.19  3.000
 LVO  H28   C17  H27   106.06  3.000
 LVO  H28   C17  C18   109.46  3.000
 LVO  H27   C17  C18   109.39  3.000
 LVO  H28   C17  C16   109.34  3.000
 LVO  H27   C17  C16   109.74  3.000
 LVO  C18   C17  C16   112.63  3.000
 LVO  H30   C18  H29   105.99  3.000
 LVO  H30   C18  C19   109.35  3.000
 LVO  H29   C18  C19   109.27  3.000
 LVO  H30   C18  C17   109.35  3.000
 LVO  H29   C18  C17   109.33  3.000
 LVO  C19   C18  C17   113.29  3.000
 LVO  H32   C19  H31   105.98  3.000
 LVO  H32   C19  C20   109.31  3.000
 LVO  H31   C19  C20   109.32  3.000
 LVO  H32   C19  C18   109.33  3.000
 LVO  H31   C19  C18   109.40  3.000
 LVO  C20   C19  C18   113.24  3.000
 LVO  H34   C20  H33   105.99  3.000
 LVO  H34   C20  C21   109.64  3.000
 LVO  H33   C20  C21   109.63  3.000
 LVO  H34   C20  C19   109.31  3.000
 LVO  H33   C20  C19   109.25  3.000
 LVO  C21   C20  C19   112.79  3.000
 LVO  H37   C21  H36   107.56  3.000
 LVO  H37   C21  H35   107.61  3.000
 LVO  H36   C21  H35   107.65  3.000
 LVO  H37   C21  C20   111.07  3.000
 LVO  H36   C21  C20   111.07  3.000
 LVO  H35   C21  C20   111.70  3.000
 LVO  NBG   CBD  OBF   123.39  3.000
 LVO  NBG   CBD  CBE   114.78  3.000
 LVO  OBF   CBD  CBE   121.84  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
 LVO  CONST_01  OBF   CBD  NBG  CAD     0.00   0.0  0
 LVO  CONST_02  CBE   CBD  NBG  CAD   180.00   0.0  0
 LVO  CONST_03  NBB   CBA  NAZ  CAC   180.00   0.0  0
 LVO  CONST_04  NBC   CBA  NAZ  CAC     0.00   0.0  0
 LVO  CONST_05  HNBG  NBG  CBD  CBE     0.00   0.0  0
 LVO  CONST_08  HBC   NBC  CBA  NAZ   180.00   0.0  0
 LVO  Var_01    OAF   CAA  CAB  CAC     4.05  30.0  1
 LVO  Var_02    OAH   CAG  CAA  CAB  -179.59  30.0  2
 LVO  Var_03    OAV   CAN  OAM  CAL     2.07  30.0  2
 LVO  Var_04    C16   C15  CAN  OAM  -169.44  30.0  3
 LVO  Var_05    C17   C16  C15  CAN  -176.00  30.0  3
 LVO  Var_06    C18   C17  C16  C15  -179.05  30.0  3
 LVO  Var_07    C19   C18  C17  C16  -178.47  30.0  3
 LVO  Var_08    C20   C19  C18  C17  -179.80  30.0  3
 LVO  Var_09    C21   C20  C19  C18  -179.62  30.0  3
 LVO  Var_10    H1AX  CAX  OAW  CAJ   -52.31  30.0  3
 LVO  Var_11    H1AL  CAL  OAM  CAN    63.46  30.0  3
 LVO  Var_12    H1BE  CBE  CBD  OBF   -37.98  30.0  3
 LVO  Var_13    H35   C21  C20  C19   179.83  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
 LVO  chir_01  CAC  CAB  NAZ  CAD  positiv
 LVO  chir_02  CAD  NBG  CAE  CAC  negativ
 LVO  chir_03  CAE  OAF  CAD  CAJ  positiv
 LVO  chir_04  CAJ  OAW  CAK  CAE  positiv
 LVO  chir_05  CAK  OAY  CAJ  CAL  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
 LVO  plan-1  CAD   0.020
 LVO  plan-1  CBE   0.020
 LVO  plan-1  OBF   0.020
 LVO  plan-1  NBG   0.020
 LVO  plan-1  HNBG  0.020
 LVO  plan-1  CBD   0.020
 LVO  plan-2  CAC   0.020
 LVO  plan-2  NAZ   0.020
 LVO  plan-2  CBA   0.020
 LVO  plan-2  NBB   0.020
 LVO  plan-2  NBC   0.020
 LVO  plan-2  HNAZ  0.020
 LVO  plan-2  H1BB  0.020
 LVO  plan-2  H2BB  0.020
 LVO  plan-2  HBC   0.020
 LVO  plan-3  CAA   0.020
 LVO  plan-3  CAG   0.020
 LVO  plan-3  OAH   0.020
 LVO  plan-3  OAI   0.020
 LVO  plan-4  OAM   0.020
 LVO  plan-4  CAN   0.020
 LVO  plan-4  OAV   0.020
 LVO  plan-4  C15   0.020

