# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:34:00 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  32  19  .  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_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  -0.571   0.3330  -2.6431  -0.6805
 K99  C1    C  C      0   0.336   1.3728  -2.0031  -0.4840
 K99  O1B   O  OC    -1  -0.580   2.4769  -2.1153  -1.0451
 K99  C2    C  CT     0   0.474   1.3032  -0.9435   0.6607
 K99  C3    C  CH1    0   0.111   2.3944   0.1144   0.5932
 K99  F1    F  F      0  -0.383   2.3714   0.8394   1.7844
 K99  C4    C  CH1    0  -0.053   2.1163   1.0654  -0.5606
 K99  O4    O  OH1    0  -0.672   3.0236   2.1402  -0.5894
 K99  O6    O  O2     0  -0.511   0.0638  -0.3377   0.7748
 K99  C6    C  CH1    0  -0.016  -0.2957   0.4930  -0.3156
 K99  C5    C  CH1    0   0.046   0.7067   1.6410  -0.4487
 K99  O5    O  OH1    0  -0.674   0.3616   2.3669  -1.6021
 K99  C7    C  CH1    0  -0.020  -1.7191   0.9720  -0.0364
 K99  O7    O  OH1    0  -0.664  -1.8045   1.6134   1.2140
 K99  C8    C  CH1    0  -0.027  -2.7364  -0.1744  -0.1913
 K99  O8    O  OH1    0  -0.658  -2.7373  -0.6415  -1.5216
 K99  C9    C  CH2    0  -0.159  -4.1247   0.2574   0.2548
 K99  O9    O  OH1    0  -0.671  -5.0094  -0.8255   0.0804
 K99  F2    F  F      0  -0.371   1.4489  -1.6435   1.8418
 K99  H3    H  HCH1   0   0.240   3.3822  -0.3407   0.5028
 K99  H4    H  HCH1   0   0.234   2.1704   0.4799  -1.4875
 K99  HA    H  HOH1   0   0.460   3.8321   1.8520  -1.0237
 K99  H5    H  HCH1   0   0.216   0.6495   2.2715   0.4491
 K99  H6    H  HCH1   0   0.242  -0.2984  -0.0784  -1.2527
 K99  H7    H  HCH1   0   0.247  -1.9679   1.7353  -0.7816
 K99  HB    H  HOH1   0   0.454   0.9729   3.1058  -1.6847
 K99  HC    H  HOH1   0   0.446  -1.5073   0.9979   1.8935
 K99  H8    H  HCH1   0   0.234  -2.4188  -1.0270   0.4184
 K99  HD    H  HOH1   0   0.442  -3.0806   0.0573  -2.0900
 K99  H91C  H  HCH2   0   0.206  -4.0858   0.5785   1.3001
 K99  H92C  H  HCH2   0   0.186  -4.4363   1.1341  -0.3349
 K99  H9    H  HOH1   0   0.454  -5.8662  -0.5630   0.4276

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    deloc   1.244  0.020  1.244
 K99  C1   O1A   deloc   1.237  0.020  1.237
 K99  C1   C2    single  1.561  0.020  1.561
 K99  C2   C3    single  1.521  0.020  1.521
 K99  C2   O6    single  1.384  0.020  1.384
 K99  C2   F2    single  1.381  0.020  1.381
 K99  C3   F1    single  1.395  0.020  1.395
 K99  C3   C4    single  1.521  0.020  1.521
 K99  C4   O4    single  1.407  0.020  1.407
 K99  C4   C5    single  1.527  0.020  1.527
 K99  O6   C6    single  1.417  0.020  1.417
 K99  C6   C5    single  1.530  0.020  1.530
 K99  C6   C7    single  1.528  0.020  1.528
 K99  C5   O5    single  1.406  0.020  1.406
 K99  C7   O7    single  1.408  0.020  1.408
 K99  C7   C8    single  1.541  0.020  1.541
 K99  C8   O8    single  1.410  0.020  1.410
 K99  C8   C9    single  1.521  0.020  1.521
 K99  C9   O9    single  1.409  0.020  1.409
 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   115.57  3.000
 K99  C2    C1  O1A   115.48  3.000
 K99  O1B   C1  O1A   128.91  3.000
 K99  F2    C2  O6    104.23  3.000
 K99  F2    C2  C3    108.35  3.000
 K99  O6    C2  C3    109.97  3.000
 K99  F2    C2  C1    106.16  3.000
 K99  O6    C2  C1    113.41  3.000
 K99  C3    C2  C1    114.04  3.000
 K99  H3    C3  C4    111.31  3.000
 K99  H3    C3  F1    107.61  3.000
 K99  C4    C3  F1    108.66  3.000
 K99  H3    C3  C2    111.28  3.000
 K99  C4    C3  C2    109.71  3.000
 K99  F1    C3  C2    108.17  3.000
 K99  H4    C4  C5    107.97  3.000
 K99  H4    C4  O4    111.00  3.000
 K99  C5    C4  O4    108.00  3.000
 K99  H4    C4  C3    107.34  3.000
 K99  C5    C4  C3    110.42  3.000
 K99  O4    C4  C3    112.04  3.000
 K99  HA    O4  C4    108.81  3.000
 K99  C6    O6  C2    114.85  3.000
 K99  H6    C6  C7    108.48  3.000
 K99  H6    C6  C5    108.54  3.000
 K99  C7    C6  C5    113.02  3.000
 K99  H6    C6  O6    110.64  3.000
 K99  C7    C6  O6    106.23  3.000
 K99  C5    C6  O6    109.91  3.000
 K99  H5    C5  O5    111.19  3.000
 K99  H5    C5  C6    109.00  3.000
 K99  O5    C5  C6    107.34  3.000
 K99  H5    C5  C4    108.92  3.000
 K99  O5    C5  C4    111.17  3.000
 K99  C6    C5  C4    109.17  3.000
 K99  HB    O5  C5    108.11  3.000
 K99  H7    C7  C8    107.47  3.000
 K99  H7    C7  O7    105.84  3.000
 K99  C8    C7  O7    112.85  3.000
 K99  H7    C7  C6    107.81  3.000
 K99  C8    C7  C6    111.32  3.000
 K99  O7    C7  C6    111.21  3.000
 K99  HC    O7  C7    108.45  3.000
 K99  H8    C8  C9    108.82  3.000
 K99  H8    C8  O8    105.52  3.000
 K99  C9    C8  O8    111.73  3.000
 K99  H8    C8  C7    109.38  3.000
 K99  C9    C8  C7    111.22  3.000
 K99  O8    C8  C7    109.98  3.000
 K99  HD    O8  C8    108.45  3.000
 K99  H92C  C9  H91C  106.73  3.000
 K99  H92C  C9  O9    111.58  3.000
 K99  H91C  C9  O9    111.47  3.000
 K99  H92C  C9  C8    109.10  3.000
 K99  H91C  C9  C8    109.34  3.000
 K99  O9    C9  C8    108.58  3.000
 K99  H9    O9  C9    107.77  3.000

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

