# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:19:33 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]([C@H](O)CO)[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
 LNV  LNV  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  45  24  .  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_LNV
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
 LNV  CAA   C  C      0   0.168  -0.2120  -2.1009  -0.0999
 LNV  CAB   C  C1     0  -0.367  -1.4302  -1.6784   0.2399
 LNV  CAC   C  CH1    0  -0.032  -1.7588  -0.2339   0.4839
 LNV  CAD   C  CH1    0  -0.134  -0.6027   0.6460   0.0001
 LNV  CAE   C  CH1    0   0.059   0.7136  -0.0034   0.4374
 LNV  OAF   O  O2     0  -0.477   0.8537  -1.2697  -0.1764
 LNV  CAG   C  C      0   0.368   0.1154  -3.5491  -0.4465
 LNV  OAH   O  OC    -1  -0.593   1.2964  -3.7878  -0.7464
 LNV  OAI   O  O      0  -0.592  -0.8350  -4.3520  -0.3975
 LNV  CAJ   C  CH1    0  -0.020   1.9506   0.8163   0.0796
 LNV  CAK   C  CH1    0   0.000   3.2476   0.0726   0.4569
 LNV  CAL   C  CH2    0  -0.167   4.4760   0.9270   0.1855
 LNV  OAM   O  OH1    0  -0.670   5.6249   0.1735   0.4937
 LNV  OAW   O  O2     0  -0.499   1.9316   1.1022  -1.2999
 LNV  CAX   C  CH3    0  -0.410   2.1148   2.4539  -1.6499
 LNV  OAY   O  OH1    0  -0.660   3.2074  -0.3580   1.7988
 LNV  NAZ   N  NH1    0  -0.642  -2.9783   0.1792  -0.1680
 LNV  CBA   C  C      0   0.562  -4.2047  -0.0720   0.3775
 LNV  NBB   N  N      0  -0.722  -4.3099  -0.5172   1.5772
 LNV  NBC   N  NH2    0  -0.842  -5.2582   0.2846  -0.4368
 LNV  CBE   C  CH3    0  -0.778  -1.3625   4.3138   0.5420
 LNV  OBF   O  O      0  -0.500  -1.5023   2.9364  -1.4041
 LNV  NBG   N  NH1    0  -0.635  -0.7270   1.9895   0.5015
 LNV  HAB   H  H      0   0.244  -2.2294  -2.4019   0.3101
 LNV  HAC   H  HCH1   0   0.251  -1.9060  -0.0621   1.5541
 LNV  HAD   H  HCH1   0   0.270  -0.6163   0.6969  -1.0904
 LNV  HAE   H  HCH1   0   0.234   0.6909  -0.1319   1.5291
 LNV  HAJ   H  HCH1   0   0.227   1.9031   1.7421   0.6721
 LNV  HAK   H  HCH1   0   0.241   3.3145  -0.8357  -0.1483
 LNV  HAL   H  HCH2   0   0.206   4.4784   1.2384  -0.8647
 LNV  HALA  H  HCH2   0   0.190   4.4198   1.8439   0.7936
 LNV  HOAM  H  HOH1   0   0.455   6.3936   0.7217   0.3136
 LNV  HAX   H  HCH3   0   0.207   3.1423   2.7956  -1.4852
 LNV  HAXA  H  HCH3   0   0.235   1.8924   2.5518  -2.7117
 LNV  HAXB  H  HCH3   0   0.215   1.4471   3.1198  -1.0972
 LNV  HOAY  H  HOH1   0   0.443   3.2270   0.4159   2.3729
 LNV  HNAZ  H  HNH1   0   0.376  -2.9267   0.2810  -1.1691
 LNV  HNBB  H  H      0   0.314  -5.2847  -0.5861   1.8442
 LNV  HNBC  H  HNH2   0   0.382  -5.0879   0.2920  -1.4306
 LNV  HNBA  H  HNH2   0   0.385  -6.1357  -0.1570  -0.2143
 LNV  HBE   H  HCH3   0   0.266  -2.4045   4.6323   0.5137
 LNV  HBEA  H  HCH3   0   0.248  -1.0507   4.2466   1.5825
 LNV  HBEB  H  HCH3   0   0.265  -0.7725   5.0895   0.0540
 LNV  HNBG  H  HNH1   0   0.398  -0.5940   2.1278   1.4912
 LNV  CBD   C  C      0   0.530  -1.2155   3.0192  -0.2189

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
 LNV  CAA  CAB   double  1.333  0.020  1.333
 LNV  CAA  OAF   single  1.354  0.020  1.354
 LNV  CAA  CAG   single  1.525  0.020  1.525
 LNV  CAB  CAC   single  1.501  0.020  1.501
 LNV  CAC  CAD   single  1.531  0.020  1.531
 LNV  CAC  NAZ   single  1.443  0.020  1.443
 LNV  CAD  CAE   single  1.531  0.020  1.531
 LNV  CAD  NBG   single  1.439  0.020  1.439
 LNV  CAE  OAF   single  1.414  0.020  1.414
 LNV  CAE  CAJ   single  1.527  0.020  1.527
 LNV  CAG  OAH   deloc   1.242  0.020  1.242
 LNV  CAG  OAI   deloc   1.245  0.020  1.245
 LNV  CAJ  CAK   single  1.542  0.020  1.542
 LNV  CAJ  OAW   single  1.409  0.020  1.409
 LNV  CAK  CAL   single  1.521  0.020  1.521
 LNV  CAK  OAY   single  1.410  0.020  1.410
 LNV  CAL  OAM   single  1.408  0.020  1.408
 LNV  OAW  CAX   single  1.408  0.020  1.408
 LNV  NAZ  CBA   single  1.366  0.020  1.366
 LNV  CBA  NBB   double  1.284  0.020  1.284
 LNV  CBA  NBC   single  1.378  0.020  1.378
 LNV  CBD  CBE   single  1.509  0.020  1.509
 LNV  CBD  OBF   double  1.222  0.020  1.222
 LNV  CBD  NBG   single  1.348  0.020  1.348
 LNV  CAB  HAB   single  0.930  0.020  1.080
 LNV  CAC  HAC   single  0.970  0.020  1.090
 LNV  CAD  HAD   single  0.970  0.020  1.090
 LNV  CAE  HAE   single  0.970  0.020  1.090
 LNV  CAJ  HAJ   single  0.970  0.020  1.090
 LNV  CAK  HAK   single  0.970  0.020  1.090
 LNV  CAL  HAL   single  0.970  0.020  1.090
 LNV  CAL  HALA  single  0.970  0.020  1.090
 LNV  OAM  HOAM  single  0.850  0.020  0.980
 LNV  CAX  HAX   single  0.970  0.020  1.090
 LNV  CAX  HAXA  single  0.970  0.020  1.090
 LNV  CAX  HAXB  single  0.970  0.020  1.090
 LNV  OAY  HOAY  single  0.850  0.020  0.980
 LNV  NAZ  HNAZ  single  0.890  0.020  1.040
 LNV  NBB  HNBB  single  0.890  0.020  1.040
 LNV  NBC  HNBC  single  0.890  0.020  1.040
 LNV  NBC  HNBA  single  0.890  0.020  1.040
 LNV  CBE  HBE   single  0.970  0.020  1.090
 LNV  CBE  HBEA  single  0.970  0.020  1.090
 LNV  CBE  HBEB  single  0.970  0.020  1.090
 LNV  NBG  HNBG  single  0.860  0.020  1.020

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
 LNV  CAG   CAA  OAF   113.67  3.000
 LNV  CAG   CAA  CAB   123.71  3.000
 LNV  OAF   CAA  CAB   122.62  3.000
 LNV  HAB   CAB  CAC   118.16  3.000
 LNV  HAB   CAB  CAA   118.70  3.000
 LNV  CAC   CAB  CAA   123.11  3.000
 LNV  HAC   CAC  NAZ   106.45  3.000
 LNV  HAC   CAC  CAD   108.69  3.000
 LNV  NAZ   CAC  CAD   109.32  3.000
 LNV  HAC   CAC  CAB   109.85  3.000
 LNV  NAZ   CAC  CAB   112.77  3.000
 LNV  CAD   CAC  CAB   109.65  3.000
 LNV  HAD   CAD  NBG   107.66  3.000
 LNV  HAD   CAD  CAE   108.40  3.000
 LNV  NBG   CAD  CAE   111.75  3.000
 LNV  HAD   CAD  CAC   109.44  3.000
 LNV  NBG   CAD  CAC   111.17  3.000
 LNV  CAE   CAD  CAC   108.36  3.000
 LNV  HAE   CAE  CAJ   108.19  3.000
 LNV  HAE   CAE  OAF   109.17  3.000
 LNV  CAJ   CAE  OAF   107.39  3.000
 LNV  HAE   CAE  CAD   108.38  3.000
 LNV  CAJ   CAE  CAD   113.69  3.000
 LNV  OAF   CAE  CAD   109.93  3.000
 LNV  CAE   OAF  CAA   116.57  3.000
 LNV  OAI   CAG  OAH   127.71  3.000
 LNV  OAI   CAG  CAA   116.08  3.000
 LNV  OAH   CAG  CAA   116.21  3.000
 LNV  HAJ   CAJ  OAW   110.85  3.000
 LNV  HAJ   CAJ  CAK   108.08  3.000
 LNV  OAW   CAJ  CAK   110.42  3.000
 LNV  HAJ   CAJ  CAE   106.89  3.000
 LNV  OAW   CAJ  CAE   109.12  3.000
 LNV  CAK   CAJ  CAE   111.42  3.000
 LNV  HAK   CAK  OAY   105.95  3.000
 LNV  HAK   CAK  CAL   108.57  3.000
 LNV  OAY   CAK  CAL   111.37  3.000
 LNV  HAK   CAK  CAJ   108.46  3.000
 LNV  OAY   CAK  CAJ   110.87  3.000
 LNV  CAL   CAK  CAJ   111.40  3.000
 LNV  HALA  CAL  HAL   107.02  3.000
 LNV  HALA  CAL  OAM   111.48  3.000
 LNV  HAL   CAL  OAM   111.11  3.000
 LNV  HALA  CAL  CAK   109.14  3.000
 LNV  HAL   CAL  CAK   109.43  3.000
 LNV  OAM   CAL  CAK   108.63  3.000
 LNV  HOAM  OAM  CAL   107.84  3.000
 LNV  CAX   OAW  CAJ   115.87  3.000
 LNV  HAXB  CAX  HAXA  108.27  3.000
 LNV  HAXB  CAX  HAX   107.87  3.000
 LNV  HAXA  CAX  HAX   108.06  3.000
 LNV  HAXB  CAX  OAW   112.31  3.000
 LNV  HAXA  CAX  OAW   107.58  3.000
 LNV  HAX   CAX  OAW   112.59  3.000
 LNV  HOAY  OAY  CAK   108.73  3.000
 LNV  HNAZ  NAZ  CBA   117.48  3.000
 LNV  HNAZ  NAZ  CAC   115.74  3.000
 LNV  CBA   NAZ  CAC   121.72  3.000
 LNV  NBC   CBA  NBB   125.39  3.000
 LNV  NBC   CBA  NAZ   113.76  3.000
 LNV  NBB   CBA  NAZ   120.70  3.000
 LNV  HNBB  NBB  CBA   110.40  3.000
 LNV  HNBA  NBC  HNBC  111.59  3.000
 LNV  HNBA  NBC  CBA   114.95  3.000
 LNV  HNBC  NBC  CBA   117.07  3.000
 LNV  HBEB  CBE  HBEA  108.47  3.000
 LNV  HBEB  CBE  HBE   107.33  3.000
 LNV  HBEA  CBE  HBE   108.47  3.000
 LNV  HBEB  CBE  CBD   109.40  3.000
 LNV  HBEA  CBE  CBD   113.66  3.000
 LNV  HBE   CBE  CBD   109.31  3.000
 LNV  HNBG  NBG  CBD   117.88  3.000
 LNV  HNBG  NBG  CAD   117.29  3.000
 LNV  CBD   NBG  CAD   123.92  3.000
 LNV  NBG   CBD  OBF   123.46  3.000
 LNV  NBG   CBD  CBE   114.90  3.000
 LNV  OBF   CBD  CBE   121.62  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
 LNV  CONST_01  CBE   CBD  NBG  CAD  180.00   0.0  0
 LNV  CONST_02  OBF   CBD  NBG  CAD    0.00   0.0  0
 LNV  CONST_03  NBB   CBA  NAZ  CAC    0.00   0.0  0
 LNV  CONST_04  NBC   CBA  NAZ  CAC  180.00   0.0  0
 LNV  CONST_05  HNBG  NBG  CBD  CBE    0.00   0.0  0
 LNV  CONST_06  HNBB  NBB  CBA  NAZ  180.00   0.0  0
 LNV  Var_01    OAF   CAA  CAB  CAC    4.04  30.0  1
 LNV  Var_02    OAH   CAG  CAA  CAB  179.84  30.0  2
 LNV  Var_03    HAX   CAX  OAW  CAJ   71.45  30.0  3
 LNV  Var_04    HBE   CBE  CBD  OBF   59.88  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
 LNV  chir_01  CAC  CAB  CAD  NAZ  negativ
 LNV  chir_02  CAD  NBG  CAE  CAC  negativ
 LNV  chir_03  CAE  OAF  CAD  CAJ  positiv
 LNV  chir_04  CAJ  OAW  CAK  CAE  positiv
 LNV  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
 LNV  plan-1  CAD   0.020
 LNV  plan-1  CBE   0.020
 LNV  plan-1  OBF   0.020
 LNV  plan-1  NBG   0.020
 LNV  plan-1  HNBG  0.020
 LNV  plan-1  CBD   0.020
 LNV  plan-2  CAC   0.020
 LNV  plan-2  NAZ   0.020
 LNV  plan-2  CBA   0.020
 LNV  plan-2  NBB   0.020
 LNV  plan-2  NBC   0.020
 LNV  plan-2  HNAZ  0.020
 LNV  plan-2  HNBB  0.020
 LNV  plan-2  HNBC  0.020
 LNV  plan-2  HNBA  0.020
 LNV  plan-3  CAA   0.020
 LNV  plan-3  CAG   0.020
 LNV  plan-3  OAH   0.020
 LNV  plan-3  OAI   0.020

