# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:32:18 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R,3R,4R,5R,6S)-2,3-difluoro-4,5-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H]1O[C@](F)([C@H](F)[C@H](O)[C@H]1O)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
 K99  K99  '(2R,3R,4R,5R,6S)-2,3-difluoro-4,5-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid'  D-saccharide  33  19  .  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_K99
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
 K99  O1A   O  O     0  -0.396   0.4398  -2.4678  -1.0810
 K99  C1    C  C     0   0.459   1.4046  -2.0036  -0.5439
 K99  O1B   O  OH1   0  -0.579   2.6562  -2.3363  -0.7862
 K99  C2    C  CT    0   0.541   1.3143  -0.9551   0.5887
 K99  C3    C  CH1   0   0.092   2.3943   0.1234   0.5338
 K99  F1    F  F     0  -0.367   2.3327   0.8141   1.7340
 K99  C4    C  CH1   0  -0.049   2.1023   1.0821  -0.6093
 K99  O4    O  OH1   0  -0.664   3.0136   2.1466  -0.6381
 K99  O6    O  O2    0  -0.502   0.0627  -0.4106   0.6634
 K99  C6    C  CH1   0  -0.020  -0.3124   0.5127  -0.3594
 K99  C5    C  CH1   0   0.041   0.6960   1.6581  -0.4576
 K99  O5    O  OH1   0  -0.669   0.3343   2.4136  -1.5836
 K99  C7    C  CH1   0  -0.028  -1.7170   0.9900   0.0061
 K99  O7    O  OH1   0  -0.659  -1.7392   1.5867   1.2793
 K99  C8    C  CH1   0  -0.026  -2.7605  -0.1338  -0.1397
 K99  O8    O  OH1   0  -0.657  -2.7694  -0.6236  -1.4608
 K99  C9    C  CH2   0  -0.159  -4.1374   0.3428   0.2966
 K99  O9    O  OH1   0  -0.670  -5.0457  -0.7247   0.1588
 K99  F2    F  F     0  -0.346   1.4696  -1.6804   1.7420
 K99  H1B   H  HOH1  0   0.498   2.7070  -3.0298  -1.4636
 K99  H3    H  HCH1  0   0.269   3.3939  -0.3088   0.4512
 K99  H4    H  HCH1  0   0.242   2.1346   0.5101  -1.5490
 K99  HA    H  HOH1  0   0.465   3.8105   1.8665  -1.0991
 K99  H5    H  HCH1  0   0.232   0.6555   2.2624   0.4578
 K99  H6    H  HCH1  0   0.258  -0.3525   0.0068  -1.3303
 K99  H7    H  HCH1  0   0.255  -1.9839   1.7819  -0.7017
 K99  HB    H  HOH1  0   0.459   0.9050   3.1876  -1.6249
 K99  HC    H  HOH1  0   0.448  -1.4823   0.9296   1.9363
 K99  H8    H  HCH1  0   0.236  -2.4708  -0.9831   0.4885
 K99  HD    H  HOH1  0   0.444  -3.0997   0.0698  -2.0437
 K99  H91C  H  HCH2  0   0.208  -4.0862   0.6958   1.3311
 K99  H92C  H  HCH2  0   0.188  -4.4312   1.2079  -0.3188
 K99  H9    H  HOH1  0   0.455  -5.8926  -0.4384   0.5115

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
 K99  O1B  C1    single  1.318  0.020  1.318
 K99  C1   O1A   double  1.198  0.020  1.198
 K99  C1   C2    single  1.546  0.020  1.546
 K99  C2   C3    single  1.527  0.020  1.527
 K99  C2   O6    single  1.367  0.020  1.367
 K99  C2   F2    single  1.371  0.020  1.371
 K99  C3   F1    single  1.386  0.020  1.386
 K99  C3   C4    single  1.520  0.020  1.520
 K99  C4   O4    single  1.402  0.020  1.402
 K99  C4   C5    single  1.527  0.020  1.527
 K99  O6   C6    single  1.428  0.020  1.428
 K99  C6   C5    single  1.529  0.020  1.529
 K99  C6   C7    single  1.528  0.020  1.528
 K99  C5   O5    single  1.403  0.020  1.403
 K99  C7   O7    single  1.406  0.020  1.406
 K99  C7   C8    single  1.540  0.020  1.540
 K99  C8   O8    single  1.409  0.020  1.409
 K99  C8   C9    single  1.521  0.020  1.521
 K99  C9   O9    single  1.408  0.020  1.408
 K99  O1B  H1B   single  0.850  0.020  0.980
 K99  C3   H3    single  0.970  0.020  1.090
 K99  C4   H4    single  0.970  0.020  1.090
 K99  O4   HA    single  0.850  0.020  0.980
 K99  C5   H5    single  0.970  0.020  1.090
 K99  C6   H6    single  0.970  0.020  1.090
 K99  C7   H7    single  0.970  0.020  1.090
 K99  O5   HB    single  0.850  0.020  0.980
 K99  O7   HC    single  0.850  0.020  0.980
 K99  C8   H8    single  0.970  0.020  1.090
 K99  O8   HD    single  0.850  0.020  0.980
 K99  C9   H91C  single  0.970  0.020  1.090
 K99  C9   H92C  single  0.970  0.020  1.090
 K99  O9   H9    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
 K99  C2    C1   O1B   111.19  3.000
 K99  C2    C1   O1A   122.97  3.000
 K99  O1B   C1   O1A   125.79  3.000
 K99  H1B   O1B  C1    111.00  3.000
 K99  F2    C2   O6    105.58  3.000
 K99  F2    C2   C3    108.89  3.000
 K99  O6    C2   C3    111.60  3.000
 K99  F2    C2   C1    104.53  3.000
 K99  O6    C2   C1    111.32  3.000
 K99  C3    C2   C1    114.28  3.000
 K99  H3    C3   C4    111.62  3.000
 K99  H3    C3   F1    107.65  3.000
 K99  C4    C3   F1    109.17  3.000
 K99  H3    C3   C2    111.74  3.000
 K99  C4    C3   C2    109.67  3.000
 K99  F1    C3   C2    106.82  3.000
 K99  H4    C4   C5    107.93  3.000
 K99  H4    C4   O4    110.99  3.000
 K99  C5    C4   O4    108.32  3.000
 K99  H4    C4   C3    107.98  3.000
 K99  C5    C4   C3    109.87  3.000
 K99  O4    C4   C3    111.68  3.000
 K99  HA    O4   C4    109.10  3.000
 K99  C6    O6   C2    117.32  3.000
 K99  H6    C6   C7    108.82  3.000
 K99  H6    C6   C5    108.25  3.000
 K99  C7    C6   C5    112.81  3.000
 K99  H6    C6   O6    110.23  3.000
 K99  C7    C6   O6    105.79  3.000
 K99  C5    C6   O6    110.92  3.000
 K99  H5    C5   O5    111.30  3.000
 K99  H5    C5   C6    109.54  3.000
 K99  O5    C5   C6    106.55  3.000
 K99  H5    C5   C4    108.94  3.000
 K99  O5    C5   C4    111.14  3.000
 K99  C6    C5   C4    109.34  3.000
 K99  HB    O5   C5    108.33  3.000
 K99  H7    C7   C8    107.53  3.000
 K99  H7    C7   O7    105.93  3.000
 K99  C8    C7   O7    112.62  3.000
 K99  H7    C7   C6    107.18  3.000
 K99  C8    C7   C6    111.85  3.000
 K99  O7    C7   C6    111.32  3.000
 K99  HC    O7   C7    108.88  3.000
 K99  H8    C8   C9    108.53  3.000
 K99  H8    C8   O8    105.66  3.000
 K99  C9    C8   O8    111.85  3.000
 K99  H8    C8   C7    109.40  3.000
 K99  C9    C8   C7    110.94  3.000
 K99  O8    C8   C7    110.28  3.000
 K99  HD    O8   C8    108.60  3.000
 K99  H92C  C9   H91C  106.69  3.000
 K99  H92C  C9   O9    111.63  3.000
 K99  H91C  C9   O9    111.55  3.000
 K99  H92C  C9   C8    109.10  3.000
 K99  H91C  C9   C8    109.27  3.000
 K99  O9    C9   C8    108.56  3.000
 K99  H9    O9   C9    107.85  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
 K99  CONST_01  H1B  O1B  C1  C2  180.00  0.0  0

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
 K99  chir_01  C2  C3  O6  F2  positiv
 K99  chir_02  C3  F1  C4  C2  positiv
 K99  chir_03  C4  O4  C3  C5  negativ
 K99  chir_04  C6  O6  C5  C7  positiv
 K99  chir_05  C5  O5  C6  C4  negativ
 K99  chir_06  C7  O7  C8  C6  positiv
 K99  chir_07  C8  O8  C7  C9  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
 K99  plan-1  O1A  0.020
 K99  plan-1  C1   0.020
 K99  plan-1  O1B  0.020
 K99  plan-1  C2   0.020
 K99  plan-1  H1B  0.020

