# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 00:46:24 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  37  20  .  2023-02-15  2023-02-15
;
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  OC    -1  -0.615  -4.4250  -0.7465  -0.5946
 9VP  C1   C  C      0   0.392  -3.5116  -0.0412  -0.1237
 9VP  O1A  O  O      0  -0.585  -3.6162   0.9431   0.6206
 9VP  C2   C  CH1    0  -0.139  -2.0953  -0.4637  -0.5726
 9VP  C3   C  CH1    0   0.183  -1.8343  -1.9327  -0.3087
 9VP  F1   F  F      0  -0.391  -2.0282  -2.1807   1.0580
 9VP  C4   C  CH2    0  -0.501  -0.4178  -2.3120  -0.6786
 9VP  O6   O  O2     0  -0.496  -1.1186   0.3336   0.0530
 9VP  C6   C  CH1    0   0.045   0.1969   0.0942  -0.3867
 9VP  C7   C  CH1    0  -0.030   1.0840   1.1219   0.3119
 9VP  C8   C  CH1    0  -0.012   0.7417   2.5663  -0.1013
 9VP  C9   C  CH2    0  -0.162   1.7107   3.5480   0.5395
 9VP  O9   O  OH1    0  -0.671   1.3276   4.8589   0.1934
 9VP  O7   O  OH1    0  -0.664   1.0328   0.9701   1.7119
 9VP  C5   C  CH1    0  -0.092   0.6080  -1.3522  -0.0768
 9VP  N5   N  NH1    0  -0.636   1.9240  -1.6217  -0.6062
 9VP  C10  C  C      0   0.523   2.9544  -2.1214   0.1017
 9VP  O10  O  O      0  -0.502   2.8867  -2.3899   1.2931
 9VP  C11  C  CH3    0  -0.781   4.2228  -2.3355  -0.6875
 9VP  O8   O  OH1    0  -0.662   0.7132   2.7074  -1.5038
 9VP  H2   H  HCH1   0   0.217  -2.0423  -0.3308  -1.6666
 9VP  H3   H  HCH1   0   0.225  -2.5539  -2.5396  -0.8595
 9VP  H4   H  HCH2   0   0.263  -0.2023  -3.3394  -0.3769
 9VP  H5   H  HCH2   0   0.238  -0.3427  -2.2824  -1.7707
 9VP  H6   H  HCH1   0   0.211   0.2695   0.2389  -1.4772
 9VP  H7   H  HCH1   0   0.238   2.1220   0.9228   0.0216
 9VP  H8   H  HCH1   0   0.233  -0.2726   2.7975   0.2405
 9VP  H9   H  HCH2   0   0.206   1.7081   3.4002   1.6242
 9VP  H10  H  HCH2   0   0.187   2.7304   3.3201   0.1907
 9VP  H11  H  HOH1   0   0.454   1.9435   5.4661   0.6125
 9VP  H12  H  HOH1   0   0.444   0.1076   1.0145   1.9803
 9VP  H13  H  HCH1   0   0.262   0.6554  -1.4892   1.0032
 9VP  H14  H  HNH1   0   0.396   2.0591  -1.4748  -1.5946
 9VP  H15  H  HCH3   0   0.247   4.1486  -2.0220  -1.7271
 9VP  H16  H  HCH3   0   0.265   5.0384  -1.7853  -0.2189
 9VP  H17  H  HCH3   0   0.266   4.4887  -3.3924  -0.6645
 9VP  H18  H  HOH1   0   0.443   1.6042   2.5715  -1.8446

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  1.410  0.020  1.410
 9VP  N5   C10  single  1.346  0.020  1.346
 9VP  N5   C5   single  1.444  0.020  1.444
 9VP  C10  O10  double  1.223  0.020  1.223
 9VP  O9   C9   single  1.409  0.020  1.409
 9VP  C6   C5   single  1.535  0.020  1.535
 9VP  C6   C7   single  1.527  0.020  1.527
 9VP  C6   O6   single  1.408  0.020  1.408
 9VP  C4   C5   single  1.528  0.020  1.528
 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  1.409  0.020  1.409
 9VP  C2   C3   single  1.515  0.020  1.515
 9VP  C2   O6   single  1.407  0.020  1.407
 9VP  C2   C1   single  1.545  0.020  1.545
 9VP  C3   F1   single  1.403  0.020  1.403
 9VP  C1   O1A  deloc   1.238  0.020  1.238
 9VP  C1   O1B  deloc   1.246  0.020  1.246
 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  C2   C1   O1A  118.00  3.000
 9VP  O1A  C1   O1B  127.95  3.000
 9VP  C2   C1   O1B  114.04  3.000
 9VP  H2   C2   O6   109.82  3.000
 9VP  H2   C2   C3   106.33  3.000
 9VP  O6   C2   C3   110.63  3.000
 9VP  H2   C2   C1   107.41  3.000
 9VP  O6   C2   C1   110.62  3.000
 9VP  C3   C2   C1   111.87  3.000
 9VP  H3   C3   C4   110.79  3.000
 9VP  H3   C3   F1   107.61  3.000
 9VP  C4   C3   F1   108.87  3.000
 9VP  H3   C3   C2   109.75  3.000
 9VP  F1   C3   C2   108.50  3.000
 9VP  C4   C3   C2   111.22  3.000
 9VP  H5   C4   H4   106.70  3.000
 9VP  H5   C4   C5   109.25  3.000
 9VP  H4   C4   C5   110.46  3.000
 9VP  H5   C4   C3   107.54  3.000
 9VP  H4   C4   C3   110.68  3.000
 9VP  C5   C4   C3   112.01  3.000
 9VP  C6   O6   C2   114.41  3.000
 9VP  H6   C6   C5   107.80  3.000
 9VP  H6   C6   C7   109.03  3.000
 9VP  C5   C6   C7   112.72  3.000
 9VP  H6   C6   O6   110.38  3.000
 9VP  C7   C6   O6   106.59  3.000
 9VP  C5   C6   O6   110.33  3.000
 9VP  H7   C7   O7   106.14  3.000
 9VP  H7   C7   C8   108.03  3.000
 9VP  O7   C7   C8   111.06  3.000
 9VP  H7   C7   C6   107.86  3.000
 9VP  O7   C7   C6   111.16  3.000
 9VP  C8   C7   C6   112.29  3.000
 9VP  H8   C8   O8   105.70  3.000
 9VP  H8   C8   C9   108.80  3.000
 9VP  O8   C8   C9   111.55  3.000
 9VP  H8   C8   C7   108.66  3.000
 9VP  C9   C8   C7   110.52  3.000
 9VP  O8   C8   C7   111.41  3.000
 9VP  H10  C9   H9   106.74  3.000
 9VP  H10  C9   O9   111.49  3.000
 9VP  H9   C9   O9   111.62  3.000
 9VP  H10  C9   C8   108.83  3.000
 9VP  H9   C9   C8   109.20  3.000
 9VP  O9   C9   C8   108.90  3.000
 9VP  H11  O9   C9   107.85  3.000
 9VP  H12  O7   C7   107.85  3.000
 9VP  H13  C5   N5   107.47  3.000
 9VP  H13  C5   C6   109.28  3.000
 9VP  N5   C5   C6   110.24  3.000
 9VP  H13  C5   C4   109.91  3.000
 9VP  C6   C5   C4   109.42  3.000
 9VP  N5   C5   C4   110.49  3.000
 9VP  H14  N5   C10  117.83  3.000
 9VP  H14  N5   C5   117.02  3.000
 9VP  C10  N5   C5   125.03  3.000
 9VP  C11  C10  O10  121.65  3.000
 9VP  O10  C10  N5   123.46  3.000
 9VP  C11  C10  N5   114.89  3.000
 9VP  H17  C11  H16  107.34  3.000
 9VP  H17  C11  H15  108.42  3.000
 9VP  H16  C11  H15  108.45  3.000
 9VP  H17  C11  C10  109.36  3.000
 9VP  H16  C11  C10  109.42  3.000
 9VP  H15  C11  C10  113.66  3.000
 9VP  H18  O8   C8   108.60  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  H14  N5   C10  O10  180.00   0.0  0
 9VP  Var_01    H15  C11  C10  N5     2.06  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

