# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:05:45 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](O)[C@@H]1O[C@@H]([C@H](F)C(=O)[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
 9T1  9T1  '5-(acetylamino)-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid'  L-saccharide  36  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_9T1
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
 9T1  O10  O  O     0  -0.492   3.3683  -1.4041   1.2420
 9T1  C10  C  C     0   0.531   3.4163  -0.9105   0.1261
 9T1  C11  C  CH3   0  -0.780   4.7121  -0.7429  -0.6228
 9T1  N5   N  NH1   0  -0.631   2.3185  -0.4611  -0.5196
 9T1  C5   C  CH1   0  -0.205   0.9964  -0.5984   0.0042
 9T1  C4   C  C     0   0.363   0.3070  -1.8402  -0.5263
 9T1  O4   O  O     0  -0.344   0.8463  -2.6534  -1.2283
 9T1  C3   C  CH1   0   0.096  -1.1643  -1.9511  -0.1539
 9T1  F1   F  F     0  -0.361  -1.2409  -2.1370   1.2200
 9T1  C6   C  CH1   0   0.002   0.1282   0.6315  -0.3525
 9T1  C7   C  CH1   0   0.006   0.6544   1.9042   0.3135
 9T1  O7   O  OH1   0  -0.659   0.7260   1.7562   1.7086
 9T1  C8   C  CH1   0   0.025  -0.1571   3.1456  -0.0783
 9T1  O8   O  OH1   0  -0.675  -0.1171   3.2181  -1.4893
 9T1  C9   C  CH3   0  -0.686   0.4086   4.4048   0.5605
 9T1  O6   O  O2    0  -0.486  -1.1886   0.4318   0.1064
 9T1  C2   C  CH1   0  -0.135  -1.8513  -0.6348  -0.4974
 9T1  C1   C  C     0   0.522  -3.2898  -0.6127  -0.0062
 9T1  O1B  O  OH1   0  -0.588  -3.9758  -1.6082  -0.5402
 9T1  O1A  O  O     0  -0.405  -3.7321   0.2046   0.7505
 9T1  H1   H  HCH3  0   0.270   5.3859  -0.1121  -0.0435
 9T1  H2   H  HCH3  0   0.269   5.1913  -1.7154  -0.7339
 9T1  H3   H  HCH3  0   0.251   4.5904  -0.3034  -1.6108
 9T1  H4   H  HNH1  0   0.408   2.4131  -0.1633  -1.4784
 9T1  H5   H  HCH1  0   0.311   1.0479  -0.6752   1.0943
 9T1  H6   H  HCH1  0   0.282  -1.6240  -2.8004  -0.6607
 9T1  H7   H  HCH1  0   0.261   0.1382   0.7625  -1.4437
 9T1  H8   H  HCH1  0   0.253   1.6820   2.0545  -0.0324
 9T1  H9   H  HOH1  0   0.447  -0.1666   1.6488   2.0566
 9T1  H10  H  HCH1  0   0.209  -1.1921   3.0124   0.2685
 9T1  H11  H  HOH1  0   0.455  -0.6669   3.9571  -1.7677
 9T1  H12  H  HCH3  0   0.224   1.4587   4.5442   0.2957
 9T1  H13  H  HCH3  0   0.234  -0.1468   5.2819   0.2222
 9T1  H14  H  HCH3  0   0.231   0.3314   4.3708   1.6461
 9T1  H15  H  HCH1  0   0.302  -1.8632  -0.5392  -1.5956
 9T1  H16  H  HOH1  0   0.495  -4.8942  -1.5971  -0.2292

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
 9T1  C11  C10  single  1.506  0.020  1.506
 9T1  O8   C8   single  1.414  0.020  1.414
 9T1  N5   C10  single  1.351  0.020  1.351
 9T1  N5   C5   single  1.429  0.020  1.429
 9T1  C10  O10  double  1.221  0.020  1.221
 9T1  C6   C7   single  1.530  0.020  1.530
 9T1  C6   C5   single  1.547  0.020  1.547
 9T1  C6   O6   single  1.409  0.020  1.409
 9T1  C7   C8   single  1.534  0.020  1.534
 9T1  C7   O7   single  1.405  0.020  1.405
 9T1  C8   C9   single  1.521  0.020  1.521
 9T1  C2   C3   single  1.524  0.020  1.524
 9T1  C2   O6   single  1.393  0.020  1.393
 9T1  C2   C1   single  1.520  0.020  1.520
 9T1  C5   C4   single  1.516  0.020  1.516
 9T1  C3   C4   single  1.522  0.020  1.522
 9T1  C3   F1   single  1.389  0.020  1.389
 9T1  C4   O4   double  1.202  0.020  1.202
 9T1  C1   O1A  double  1.198  0.020  1.198
 9T1  C1   O1B  single  1.322  0.020  1.322
 9T1  C11  H1   single  0.970  0.020  1.090
 9T1  C11  H2   single  0.970  0.020  1.090
 9T1  C11  H3   single  0.970  0.020  1.090
 9T1  N5   H4   single  0.860  0.020  1.020
 9T1  C5   H5   single  0.970  0.020  1.090
 9T1  C3   H6   single  0.970  0.020  1.090
 9T1  C6   H7   single  0.970  0.020  1.090
 9T1  C7   H8   single  0.970  0.020  1.090
 9T1  O7   H9   single  0.850  0.020  0.980
 9T1  C8   H10  single  0.970  0.020  1.090
 9T1  O8   H11  single  0.850  0.020  0.980
 9T1  C9   H12  single  0.970  0.020  1.090
 9T1  C9   H13  single  0.970  0.020  1.090
 9T1  C9   H14  single  0.970  0.020  1.090
 9T1  C2   H15  single  0.970  0.020  1.090
 9T1  O1B  H16  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
 9T1  N5   C10  C11  115.12  3.000
 9T1  N5   C10  O10  122.65  3.000
 9T1  C11  C10  O10  122.23  3.000
 9T1  H3   C11  H2   108.49  3.000
 9T1  H3   C11  H1   108.54  3.000
 9T1  H2   C11  H1   107.39  3.000
 9T1  H3   C11  C10  113.60  3.000
 9T1  H2   C11  C10  109.26  3.000
 9T1  H1   C11  C10  109.39  3.000
 9T1  H4   N5   C5   117.63  3.000
 9T1  H4   N5   C10  118.46  3.000
 9T1  C5   N5   C10  123.02  3.000
 9T1  H5   C5   C6   108.18  3.000
 9T1  H5   C5   C4   108.21  3.000
 9T1  C6   C5   C4   108.38  3.000
 9T1  H5   C5   N5   109.18  3.000
 9T1  C4   C5   N5   111.79  3.000
 9T1  C6   C5   N5   111.00  3.000
 9T1  C3   C4   O4   121.83  3.000
 9T1  O4   C4   C5   123.67  3.000
 9T1  C3   C4   C5   114.44  3.000
 9T1  H6   C3   C2   112.20  3.000
 9T1  H6   C3   F1   109.40  3.000
 9T1  C2   C3   F1   108.29  3.000
 9T1  H6   C3   C4   110.52  3.000
 9T1  F1   C3   C4   107.78  3.000
 9T1  C2   C3   C4   108.53  3.000
 9T1  H7   C6   O6   110.41  3.000
 9T1  H7   C6   C7   109.27  3.000
 9T1  O6   C6   C7   107.31  3.000
 9T1  H7   C6   C5   108.58  3.000
 9T1  O6   C6   C5   109.68  3.000
 9T1  C7   C6   C5   111.59  3.000
 9T1  H8   C7   C8   107.74  3.000
 9T1  H8   C7   O7   106.29  3.000
 9T1  C8   C7   O7   111.46  3.000
 9T1  H8   C7   C6   107.43  3.000
 9T1  O7   C7   C6   111.24  3.000
 9T1  C8   C7   C6   112.34  3.000
 9T1  H9   O7   C7   108.84  3.000
 9T1  H10  C8   C9   108.54  3.000
 9T1  H10  C8   O8   110.35  3.000
 9T1  C9   C8   O8   111.48  3.000
 9T1  H10  C8   C7   108.62  3.000
 9T1  C9   C8   C7   111.47  3.000
 9T1  O8   C8   C7   106.35  3.000
 9T1  H11  O8   C8   108.18  3.000
 9T1  H14  C9   H13  107.33  3.000
 9T1  H14  C9   H12  108.29  3.000
 9T1  H13  C9   H12  108.14  3.000
 9T1  H14  C9   C8   111.50  3.000
 9T1  H13  C9   C8   110.23  3.000
 9T1  H12  C9   C8   111.19  3.000
 9T1  C2   O6   C6   114.33  3.000
 9T1  H15  C2   C1   108.09  3.000
 9T1  H15  C2   O6   111.74  3.000
 9T1  C1   C2   O6   107.39  3.000
 9T1  H15  C2   C3   107.72  3.000
 9T1  C1   C2   C3   111.48  3.000
 9T1  O6   C2   C3   110.43  3.000
 9T1  O1A  C1   O1B  125.26  3.000
 9T1  O1B  C1   C2   110.47  3.000
 9T1  O1A  C1   C2   124.27  3.000
 9T1  H16  O1B  C1   110.69  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
 9T1  CONST_01  C5   N5   C10  O10    0.00   0.0  0
 9T1  CONST_02  C5   N5   C10  C11  180.00   0.0  0
 9T1  CONST_03  H16  O1B  C1   C2   180.00   0.0  0
 9T1  CONST_04  H4   N5   C10  O10  180.00   0.0  0
 9T1  Var_01    H1   C11  C10  O10  -59.54  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
 9T1  chir_01  C5  N5  C6  C4  negativ
 9T1  chir_02  C3  F1  C4  C2  positiv
 9T1  chir_03  C6  O6  C5  C7  positiv
 9T1  chir_04  C7  O7  C8  C6  positiv
 9T1  chir_05  C8  O8  C7  C9  negativ
 9T1  chir_06  C2  O6  C1  C3  positiv

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
 9T1  plan-1  O10  0.020
 9T1  plan-1  C10  0.020
 9T1  plan-1  C11  0.020
 9T1  plan-1  N5   0.020
 9T1  plan-1  C5   0.020
 9T1  plan-1  H4   0.020
 9T1  plan-2  C5   0.020
 9T1  plan-2  C4   0.020
 9T1  plan-2  O4   0.020
 9T1  plan-2  C3   0.020
 9T1  plan-3  C2   0.020
 9T1  plan-3  C1   0.020
 9T1  plan-3  O1B  0.020
 9T1  plan-3  O1A  0.020
 9T1  plan-3  H16  0.020

