# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:52:06 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2,2-bis(fluoranyl)-N-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](NC(=O)C(F)F)[C@@H](O)[C@H]1O
#
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
 SIZ  SIZ  2,2-bis(fluoranyl)-N-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  30  17  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SIZ
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
 SIZ  F2   F  F     0  -0.334  32.8980   3.3886  -15.4703
 SIZ  C8   C  CH1   0   0.482  32.2385   2.5879  -14.6001
 SIZ  F1   F  F     0  -0.335  31.1852   2.0451  -15.2644
 SIZ  C7   C  C     0   0.413  33.2140   1.5234  -14.0887
 SIZ  O7   O  O     0  -0.474  34.2751   1.9033  -13.6253
 SIZ  N2   N  NH1   0  -0.644  32.7910   0.2640  -14.1690
 SIZ  C2   C  CH1   0  -0.141  33.4946  -0.8979  -13.6630
 SIZ  C3   C  CH1   0   0.038  33.6830  -0.8678  -12.1438
 SIZ  O3   O  OH1   0  -0.661  32.4295  -0.6660  -11.5531
 SIZ  C4   C  CH1   0  -0.026  34.3672  -2.1601  -11.6889
 SIZ  O4   O  OH1   0  -0.669  33.4878  -3.2391  -11.8942
 SIZ  C5   C  CH1   0  -0.011  35.6699  -2.3136  -12.4766
 SIZ  C6   C  CH2   0  -0.166  36.4214  -3.5764  -12.1150
 SIZ  O6   O  OH1   0  -0.664  37.6978  -3.5338  -12.7061
 SIZ  O5   O  O2    0  -0.492  35.4003  -2.3318  -13.8634
 SIZ  C1   C  CH1   0   0.299  34.8522  -1.1269  -14.3392
 SIZ  O1   O  OH1   0  -0.651  34.6510  -1.2380  -15.6965
 SIZ  H81  H  HCH1  0   0.228  31.8581   3.1947  -13.7767
 SIZ  HN2  H  HNH1  0   0.415  31.8953   0.0889  -14.5939
 SIZ  H2   H  HCH1  0   0.283  32.8591  -1.7498  -13.9184
 SIZ  H3   H  HCH1  0   0.226  34.3719  -0.0500  -11.8942
 SIZ  H1   H  HCH1  0   0.195  35.5401  -0.3027  -14.0951
 SIZ  HO3  H  HOH1  0   0.452  32.5581  -0.4855  -10.6165
 SIZ  H4   H  HCH1  0   0.239  34.6214  -2.0515  -10.6245
 SIZ  HO4  H  HOH1  0   0.457  33.7076  -3.9461  -11.2814
 SIZ  H5   H  HCH1  0   0.219  36.3107  -1.4519  -12.2240
 SIZ  H61  H  HCH2  0   0.202  36.4838  -3.6288  -11.0195
 SIZ  H62  H  HCH2  0   0.202  35.8495  -4.4515  -12.4477
 SIZ  HO6  H  HOH1  0   0.454  38.1414  -4.3655  -12.5186
 SIZ  HO1  H  HOH1  0   0.463  35.4843  -1.0926  -16.1567

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
 SIZ  F2  C8   single  1.354  0.020  1.354
 SIZ  C8  F1   single  1.358  0.020  1.358
 SIZ  C8  C7   single  1.532  0.020  1.532
 SIZ  C7  O7   double  1.219  0.020  1.219
 SIZ  C7  N2   single  1.331  0.020  1.331
 SIZ  N2  C2   single  1.449  0.020  1.449
 SIZ  C2  C3   single  1.531  0.020  1.531
 SIZ  C2  C1   single  1.534  0.020  1.534
 SIZ  C3  O3   single  1.400  0.020  1.400
 SIZ  C3  C4   single  1.531  0.020  1.531
 SIZ  C4  O4   single  1.407  0.020  1.407
 SIZ  C4  C5   single  1.530  0.020  1.530
 SIZ  C5  C6   single  1.513  0.020  1.513
 SIZ  C5  O5   single  1.413  0.020  1.413
 SIZ  C6  O6   single  1.407  0.020  1.407
 SIZ  O5  C1   single  1.407  0.020  1.407
 SIZ  C1  O1   single  1.377  0.020  1.377
 SIZ  C8  H81  single  0.970  0.020  1.090
 SIZ  N2  HN2  single  0.860  0.020  1.020
 SIZ  C2  H2   single  0.970  0.020  1.090
 SIZ  C3  H3   single  0.970  0.020  1.090
 SIZ  C1  H1   single  0.970  0.020  1.090
 SIZ  O3  HO3  single  0.850  0.020  0.980
 SIZ  C4  H4   single  0.970  0.020  1.090
 SIZ  O4  HO4  single  0.850  0.020  0.980
 SIZ  C5  H5   single  0.970  0.020  1.090
 SIZ  C6  H61  single  0.970  0.020  1.090
 SIZ  C6  H62  single  0.970  0.020  1.090
 SIZ  O6  HO6  single  0.850  0.020  0.980
 SIZ  O1  HO1  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
 SIZ  H81  C8  C7   110.88  3.000
 SIZ  H81  C8  F1   108.72  3.000
 SIZ  C7   C8  F1   112.30  3.000
 SIZ  H81  C8  F2   109.01  3.000
 SIZ  C7   C8  F2   108.38  3.000
 SIZ  F1   C8  F2   107.44  3.000
 SIZ  N2   C7  O7   126.49  3.000
 SIZ  N2   C7  C8   115.79  3.000
 SIZ  O7   C7  C8   117.70  3.000
 SIZ  HN2  N2  C2   116.09  3.000
 SIZ  HN2  N2  C7   118.22  3.000
 SIZ  C2   N2  C7   125.67  3.000
 SIZ  H2   C2  C1   107.17  3.000
 SIZ  H2   C2  C3   108.58  3.000
 SIZ  C1   C2  C3   109.36  3.000
 SIZ  H2   C2  N2   105.13  3.000
 SIZ  C1   C2  N2   113.29  3.000
 SIZ  C3   C2  N2   112.98  3.000
 SIZ  H3   C3  C4   106.30  3.000
 SIZ  H3   C3  O3   111.00  3.000
 SIZ  C4   C3  O3   113.35  3.000
 SIZ  H3   C3  C2   108.50  3.000
 SIZ  C4   C3  C2   109.46  3.000
 SIZ  O3   C3  C2   108.14  3.000
 SIZ  HO3  O3  C3   108.54  3.000
 SIZ  H4   C4  C5   108.15  3.000
 SIZ  H4   C4  O4   111.19  3.000
 SIZ  C5   C4  O4   112.33  3.000
 SIZ  H4   C4  C3   107.91  3.000
 SIZ  C5   C4  C3   108.19  3.000
 SIZ  O4   C4  C3   108.94  3.000
 SIZ  HO4  O4  C4   109.15  3.000
 SIZ  H5   C5  O5   110.22  3.000
 SIZ  H5   C5  C6   107.97  3.000
 SIZ  O5   C5  C6   108.58  3.000
 SIZ  H5   C5  C4   107.35  3.000
 SIZ  O5   C5  C4   110.13  3.000
 SIZ  C6   C5  C4   112.55  3.000
 SIZ  H62  C6  H61  107.10  3.000
 SIZ  H62  C6  O6   111.69  3.000
 SIZ  H61  C6  O6   111.64  3.000
 SIZ  H62  C6  C5   109.53  3.000
 SIZ  H61  C6  C5   107.84  3.000
 SIZ  O6   C6  C5   108.95  3.000
 SIZ  HO6  O6  C6   108.09  3.000
 SIZ  C1   O5  C5   113.29  3.000
 SIZ  H1   C1  O1   111.74  3.000
 SIZ  H1   C1  O5   108.83  3.000
 SIZ  O1   C1  O5   108.74  3.000
 SIZ  H1   C1  C2   110.09  3.000
 SIZ  O1   C1  C2   108.50  3.000
 SIZ  O5   C1  C2   108.88  3.000
 SIZ  HO1  O1  C1   109.43  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
 SIZ  CONST_01  C2   N2  C7  C8  180.00   0.0  0
 SIZ  CONST_02  C2   N2  C7  O7    0.00   0.0  0
 SIZ  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 SIZ  Var_01    O7   C7  C8  F2   52.56  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
 SIZ  chir_01  C2  N2  C3  C1  positiv
 SIZ  chir_02  C3  O3  C2  C4  positiv
 SIZ  chir_03  C4  O4  C5  C3  negativ
 SIZ  chir_04  C5  O5  C4  C6  negativ
 SIZ  chir_05  C1  O5  O1  C2  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
 SIZ  plan-1  C8   0.020
 SIZ  plan-1  C7   0.020
 SIZ  plan-1  O7   0.020
 SIZ  plan-1  N2   0.020
 SIZ  plan-1  C2   0.020
 SIZ  plan-1  HN2  0.020

