# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 04:05:26 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,4,5-trideoxy-3-fluoro-D-erythro-L-gluco-nononic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1C[C@@H](F)[C@H](O[C@H]1[C@H](O)[C@H](O)CO)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
 9VP  9VP  '5-(acetylamino)-2,6-anhydro-3,4,5-trideoxy-3-fluoro-D-erythro-L-gluco-nononic acid'  D-saccharide  38  20  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9VP
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
 9VP  O1B  O  OH1   0  -0.592  -4.3946  -0.6703  -0.6374
 9VP  C1   C  C     0   0.513  -3.4138  -0.0077  -0.0434
 9VP  O1A  O  O     0  -0.414  -3.5694   0.8267   0.8043
 9VP  C2   C  CH1   0  -0.105  -2.0671  -0.4419  -0.5908
 9VP  C3   C  CH1   0   0.174  -1.8162  -1.9233  -0.3451
 9VP  F1   F  F     0  -0.378  -2.0178  -2.1722   1.0147
 9VP  C4   C  CH2   0  -0.510  -0.3983  -2.2860  -0.7231
 9VP  O6   O  O2    0  -0.495  -1.0987   0.3524   0.0240
 9VP  C6   C  CH1   0   0.035   0.2232   0.1146  -0.4185
 9VP  C7   C  CH1   0  -0.032   1.1063   1.1435   0.2825
 9VP  C8   C  CH1   0  -0.014   0.7538   2.5889  -0.1198
 9VP  C9   C  CH2   0  -0.162   1.7360   3.5692   0.5029
 9VP  O9   O  OH1   0  -0.671   1.3420   4.8797   0.1700
 9VP  O7   O  OH1   0  -0.660   1.0773   0.9791   1.6805
 9VP  C5   C  CH1   0  -0.091   0.6246  -1.3323  -0.1057
 9VP  N5   N  NH1   0  -0.639   1.9441  -1.6050  -0.6191
 9VP  C10  C  C     0   0.525   2.9609  -2.1130   0.1058
 9VP  O10  O  O     0  -0.498   2.8707  -2.3787   1.2955
 9VP  C11  C  CH3   0  -0.781   4.2390  -2.3374  -0.6635
 9VP  O8   O  OH1   0  -0.660   0.6944   2.7306  -1.5208
 9VP  H1   H  HOH1  0   0.491  -5.2531  -0.3982  -0.2787
 9VP  H2   H  HCH1  0   0.277  -2.0778  -0.2898  -1.6822
 9VP  H3   H  HCH1  0   0.255  -2.5299  -2.5289  -0.9058
 9VP  H4   H  HCH2  0   0.279  -0.1865  -3.3168  -0.4329
 9VP  H5   H  HCH2  0   0.252  -0.3248  -2.2443  -1.8145
 9VP  H6   H  HCH1  0   0.229   0.2908   0.2636  -1.5072
 9VP  H7   H  HCH1  0   0.245   2.1403   0.9497  -0.0238
 9VP  H8   H  HCH1  0   0.235  -0.2523   2.8217   0.2445
 9VP  H9   H  HCH2  0   0.207   1.7583   3.4173   1.5869
 9VP  H10  H  HCH2  0   0.189   2.7477   3.3438   0.1298
 9VP  H11  H  HOH1  0   0.455   1.9654   5.4875   0.5771
 9VP  H12  H  HOH1  0   0.446   0.1648   1.0732   1.9772
 9VP  H13  H  HCH1  0   0.270   0.6564  -1.4717   0.9746
 9VP  H14  H  HNH1  0   0.399   2.0924  -1.4661  -1.6068
 9VP  H15  H  HCH3  0   0.248   4.1836  -2.0224  -1.7037
 9VP  H16  H  HCH3  0   0.267   5.0522  -1.7956  -0.1813
 9VP  H17  H  HCH3  0   0.267   4.4937  -3.3970  -0.6379
 9VP  H18  H  HOH1  0   0.445   1.5806   2.6118  -1.8797

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
 9VP  C11  C10  single  1.509  0.020  1.509
 9VP  O8   C8   single  1.409  0.020  1.409
 9VP  N5   C10  single  1.348  0.020  1.348
 9VP  N5   C5   single  1.442  0.020  1.442
 9VP  C10  O10  double  1.222  0.020  1.222
 9VP  O9   C9   single  1.408  0.020  1.408
 9VP  C6   C5   single  1.534  0.020  1.534
 9VP  C6   C7   single  1.526  0.020  1.526
 9VP  C6   O6   single  1.414  0.020  1.414
 9VP  C4   C5   single  1.529  0.020  1.529
 9VP  C4   C3   single  1.512  0.020  1.512
 9VP  C8   C7   single  1.541  0.020  1.541
 9VP  C8   C9   single  1.521  0.020  1.521
 9VP  C7   O7   single  1.408  0.020  1.408
 9VP  C2   C3   single  1.522  0.020  1.522
 9VP  C2   O6   single  1.395  0.020  1.395
 9VP  C2   C1   single  1.517  0.020  1.517
 9VP  C3   F1   single  1.397  0.020  1.397
 9VP  C1   O1A  double  1.200  0.020  1.200
 9VP  C1   O1B  single  1.324  0.020  1.324
 9VP  O1B  H1   single  0.850  0.020  0.980
 9VP  C2   H2   single  0.970  0.020  1.090
 9VP  C3   H3   single  0.970  0.020  1.090
 9VP  C4   H4   single  0.970  0.020  1.090
 9VP  C4   H5   single  0.970  0.020  1.090
 9VP  C6   H6   single  0.970  0.020  1.090
 9VP  C7   H7   single  0.970  0.020  1.090
 9VP  C8   H8   single  0.970  0.020  1.090
 9VP  C9   H9   single  0.970  0.020  1.090
 9VP  C9   H10  single  0.970  0.020  1.090
 9VP  O9   H11  single  0.850  0.020  0.980
 9VP  O7   H12  single  0.850  0.020  0.980
 9VP  C5   H13  single  0.970  0.020  1.090
 9VP  N5   H14  single  0.860  0.020  1.020
 9VP  C11  H15  single  0.970  0.020  1.090
 9VP  C11  H16  single  0.970  0.020  1.090
 9VP  C11  H17  single  0.970  0.020  1.090
 9VP  O8   H18  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
 9VP  H1   O1B  C1   110.46  3.000
 9VP  C2   C1   O1A  124.69  3.000
 9VP  O1A  C1   O1B  124.67  3.000
 9VP  C2   C1   O1B  110.63  3.000
 9VP  H2   C2   O6   111.38  3.000
 9VP  H2   C2   C3   107.20  3.000
 9VP  O6   C2   C3   111.62  3.000
 9VP  H2   C2   C1   108.01  3.000
 9VP  O6   C2   C1   107.11  3.000
 9VP  C3   C2   C1   111.50  3.000
 9VP  H3   C3   C4   110.61  3.000
 9VP  H3   C3   F1   107.87  3.000
 9VP  C4   C3   F1   109.64  3.000
 9VP  H3   C3   C2   110.44  3.000
 9VP  F1   C3   C2   107.86  3.000
 9VP  C4   C3   C2   110.35  3.000
 9VP  H5   C4   H4   106.74  3.000
 9VP  H5   C4   C5   109.51  3.000
 9VP  H4   C4   C5   110.60  3.000
 9VP  H5   C4   C3   107.65  3.000
 9VP  H4   C4   C3   110.00  3.000
 9VP  C5   C4   C3   112.14  3.000
 9VP  C6   O6   C2   114.53  3.000
 9VP  H6   C6   C5   108.26  3.000
 9VP  H6   C6   C7   109.11  3.000
 9VP  C5   C6   C7   113.01  3.000
 9VP  H6   C6   O6   110.12  3.000
 9VP  C7   C6   O6   106.49  3.000
 9VP  C5   C6   O6   109.84  3.000
 9VP  H7   C7   O7   106.04  3.000
 9VP  H7   C7   C8   107.99  3.000
 9VP  O7   C7   C8   111.35  3.000
 9VP  H7   C7   C6   107.35  3.000
 9VP  O7   C7   C6   111.43  3.000
 9VP  C8   C7   C6   112.33  3.000
 9VP  H8   C8   O8   105.69  3.000
 9VP  H8   C8   C9   108.67  3.000
 9VP  O8   C8   C9   111.68  3.000
 9VP  H8   C8   C7   108.83  3.000
 9VP  C9   C8   C7   110.48  3.000
 9VP  O8   C8   C7   111.31  3.000
 9VP  H10  C9   H9   106.75  3.000
 9VP  H10  C9   O9   111.55  3.000
 9VP  H9   C9   O9   111.65  3.000
 9VP  H10  C9   C8   108.81  3.000
 9VP  H9   C9   C8   109.21  3.000
 9VP  O9   C9   C8   108.80  3.000
 9VP  H11  O9   C9   107.87  3.000
 9VP  H12  O7   C7   108.28  3.000
 9VP  H13  C5   N5   107.58  3.000
 9VP  H13  C5   C6   109.30  3.000
 9VP  N5   C5   C6   110.20  3.000
 9VP  H13  C5   C4   109.88  3.000
 9VP  C6   C5   C4   109.34  3.000
 9VP  N5   C5   C4   110.52  3.000
 9VP  H14  N5   C10  117.88  3.000
 9VP  H14  N5   C5   117.21  3.000
 9VP  C10  N5   C5   124.75  3.000
 9VP  C11  C10  O10  121.77  3.000
 9VP  O10  C10  N5   123.34  3.000
 9VP  C11  C10  N5   114.89  3.000
 9VP  H17  C11  H16  107.37  3.000
 9VP  H17  C11  H15  108.40  3.000
 9VP  H16  C11  H15  108.48  3.000
 9VP  H17  C11  C10  109.31  3.000
 9VP  H16  C11  C10  109.43  3.000
 9VP  H15  C11  C10  113.65  3.000
 9VP  H18  O8   C8   108.61  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
 9VP  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9VP  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9VP  CONST_03  H1   O1B  C1   C2   180.00   0.0  0
 9VP  CONST_04  H14  N5   C10  O10  180.00   0.0  0
 9VP  Var_01    H15  C11  C10  N5     2.17  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
 9VP  chir_01  C2  C3  O6  C1  positiv
 9VP  chir_02  C3  F1  C2  C4  negativ
 9VP  chir_03  C6  O6  C5  C7  positiv
 9VP  chir_04  C7  O7  C6  C8  negativ
 9VP  chir_05  C8  O8  C7  C9  negativ
 9VP  chir_06  C5  N5  C6  C4  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
 9VP  plan-1  C5   0.020
 9VP  plan-1  N5   0.020
 9VP  plan-1  C10  0.020
 9VP  plan-1  O10  0.020
 9VP  plan-1  C11  0.020
 9VP  plan-1  H14  0.020
 9VP  plan-2  O1B  0.020
 9VP  plan-2  C1   0.020
 9VP  plan-2  O1A  0.020
 9VP  plan-2  C2   0.020
 9VP  plan-2  H1   0.020

