# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:02:04 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-fluoranyl-~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-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)CF)[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
 EEQ  EEQ  2-fluoranyl-~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  30  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EEQ
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
 EEQ  CME  C  CH2   0  -0.119   4.0711   0.1088   0.6098
 EEQ  F23  F  F     0  -0.360   5.1751   0.3930  -0.1602
 EEQ  C2N  C  C     0   0.467   2.8128   0.2433  -0.2323
 EEQ  O2N  O  O     0  -0.483   2.8468   0.6433  -1.3811
 EEQ  N2   N  NH1   0  -0.635   1.7033  -0.1292   0.4252
 EEQ  C2   C  CH1   0  -0.148   0.3681  -0.0037  -0.1017
 EEQ  C1   C  CH1   0   0.266  -0.4003  -1.3144   0.0990
 EEQ  O5   O  O2    0  -0.497  -1.7191  -1.1985  -0.3494
 EEQ  C5   C  CH1   0  -0.006  -2.4698  -0.1527   0.2466
 EEQ  C6   C  CH2   0  -0.171  -3.8825  -0.2276  -0.2885
 EEQ  O6   O  OH1   0  -0.669  -4.4803  -1.4183   0.1651
 EEQ  C4   C  CH1   0  -0.038  -1.8142   1.2030  -0.0207
 EEQ  O4   O  OH1   0  -0.672  -1.7484   1.5134  -1.3915
 EEQ  C3   C  CH1   0   0.058  -0.3883   1.1639   0.5313
 EEQ  O3   O  OH1   0  -0.660   0.3323   2.3375   0.2741
 EEQ  O1   O  OH1   0  -0.670  -0.3234  -1.6474   1.4506
 EEQ  H1   H  HCH2  0   0.246   4.1607  -0.9050   1.0063
 EEQ  H2   H  HCH2  0   0.249   4.0314   0.8046   1.4511
 EEQ  H3   H  HNH1  0   0.400   1.7900  -0.4303   1.3850
 EEQ  H4   H  HCH1  0   0.279   0.4545   0.1680  -1.1753
 EEQ  H5   H  HCH1  0   0.243   0.0482  -2.0945  -0.5254
 EEQ  H6   H  HCH1  0   0.223  -2.5183  -0.2850   1.3368
 EEQ  H7   H  HCH2  0   0.206  -4.4214   0.6592   0.0712
 EEQ  H8   H  HCH2  0   0.198  -3.8704  -0.1775  -1.3849
 EEQ  H9   H  HOH1  0   0.456  -5.3764  -1.4514  -0.1812
 EEQ  H10  H  HCH1  0   0.239  -2.3818   1.9656   0.5328
 EEQ  H11  H  HOH1  0   0.457  -2.6019   1.8476  -1.6803
 EEQ  H12  H  HCH1  0   0.221  -0.4695   0.9852   1.6135
 EEQ  H13  H  HOH1  0   0.453  -0.0297   3.0420   0.8207
 EEQ  H14  H  HOH1  0   0.467  -0.5573  -2.5745   1.5651

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
 EEQ  F23  CME  single  1.376  0.020  1.376
 EEQ  CME  C2N  single  1.520  0.020  1.520
 EEQ  C2N  N2   single  1.342  0.020  1.342
 EEQ  C2N  O2N  double  1.217  0.020  1.217
 EEQ  N2   C2   single  1.441  0.020  1.441
 EEQ  O3   C3   single  1.401  0.020  1.401
 EEQ  C3   C2   single  1.528  0.020  1.528
 EEQ  C3   C4   single  1.529  0.020  1.529
 EEQ  C2   C1   single  1.533  0.020  1.533
 EEQ  C1   O5   single  1.398  0.020  1.398
 EEQ  C4   C5   single  1.530  0.020  1.530
 EEQ  C4   O4   single  1.407  0.020  1.407
 EEQ  C5   O5   single  1.419  0.020  1.419
 EEQ  C5   C6   single  1.512  0.020  1.512
 EEQ  C6   O6   single  1.407  0.020  1.407
 EEQ  C1   O1   single  1.394  0.020  1.394
 EEQ  CME  H1   single  0.970  0.020  1.090
 EEQ  CME  H2   single  0.970  0.020  1.090
 EEQ  N2   H3   single  0.860  0.020  1.020
 EEQ  C2   H4   single  0.970  0.020  1.090
 EEQ  C1   H5   single  0.970  0.020  1.090
 EEQ  C5   H6   single  0.970  0.020  1.090
 EEQ  C6   H7   single  0.970  0.020  1.090
 EEQ  C6   H8   single  0.970  0.020  1.090
 EEQ  O6   H9   single  0.850  0.020  0.980
 EEQ  C4   H10  single  0.970  0.020  1.090
 EEQ  O4   H11  single  0.850  0.020  0.980
 EEQ  C3   H12  single  0.970  0.020  1.090
 EEQ  O3   H13  single  0.850  0.020  0.980
 EEQ  O1   H14  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
 EEQ  H2   CME  H1   108.34  3.000
 EEQ  H2   CME  C2N  109.89  3.000
 EEQ  H1   CME  C2N  110.56  3.000
 EEQ  H2   CME  F23  109.18  3.000
 EEQ  H1   CME  F23  109.21  3.000
 EEQ  C2N  CME  F23  109.63  3.000
 EEQ  N2   C2N  O2N  125.22  3.000
 EEQ  O2N  C2N  CME  121.93  3.000
 EEQ  N2   C2N  CME  112.85  3.000
 EEQ  H3   N2   C2   116.95  3.000
 EEQ  H3   N2   C2N  118.52  3.000
 EEQ  C2   N2   C2N  124.24  3.000
 EEQ  H4   C2   C3   109.07  3.000
 EEQ  H4   C2   C1   107.65  3.000
 EEQ  C3   C2   C1   110.55  3.000
 EEQ  H4   C2   N2   107.47  3.000
 EEQ  C1   C2   N2   110.01  3.000
 EEQ  C3   C2   N2   111.94  3.000
 EEQ  H5   C1   O1   111.10  3.000
 EEQ  H5   C1   O5   105.22  3.000
 EEQ  O1   C1   O5   112.51  3.000
 EEQ  H5   C1   C2   109.22  3.000
 EEQ  O1   C1   C2   107.67  3.000
 EEQ  O5   C1   C2   111.11  3.000
 EEQ  C5   O5   C1   115.19  3.000
 EEQ  H6   C5   C4   107.39  3.000
 EEQ  H6   C5   C6   107.68  3.000
 EEQ  C4   C5   C6   112.48  3.000
 EEQ  H6   C5   O5   110.57  3.000
 EEQ  C6   C5   O5   108.01  3.000
 EEQ  C4   C5   O5   110.68  3.000
 EEQ  H8   C6   H7   107.20  3.000
 EEQ  H8   C6   O6   111.42  3.000
 EEQ  H7   C6   O6   111.66  3.000
 EEQ  H8   C6   C5   109.93  3.000
 EEQ  H7   C6   C5   107.61  3.000
 EEQ  O6   C6   C5   108.94  3.000
 EEQ  H9   O6   C6   108.00  3.000
 EEQ  H10  C4   C3   108.49  3.000
 EEQ  H10  C4   O4   111.19  3.000
 EEQ  C3   C4   O4   108.28  3.000
 EEQ  H10  C4   C5   107.78  3.000
 EEQ  O4   C4   C5   112.69  3.000
 EEQ  C3   C4   C5   108.29  3.000
 EEQ  H11  O4   C4   109.14  3.000
 EEQ  H12  C3   O3   110.77  3.000
 EEQ  H12  C3   C4   106.89  3.000
 EEQ  O3   C3   C4   113.07  3.000
 EEQ  H12  C3   C2   108.66  3.000
 EEQ  C4   C3   C2   109.35  3.000
 EEQ  O3   C3   C2   108.02  3.000
 EEQ  H13  O3   C3   108.39  3.000
 EEQ  H14  O1   C1   109.38  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
 EEQ  CONST_01  C2  N2   C2N  CME  180.00   0.0  0
 EEQ  CONST_02  C2  N2   C2N  O2N    0.00   0.0  0
 EEQ  CONST_03  H3  N2   C2N  CME    0.00   0.0  0
 EEQ  Var_01    N2  C2N  CME  F23  174.73  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
 EEQ  chir_01  C2  N2  C3  C1  positiv
 EEQ  chir_02  C1  O5  O1  C2  positiv
 EEQ  chir_03  C5  O5  C4  C6  negativ
 EEQ  chir_04  C4  O4  C5  C3  negativ
 EEQ  chir_05  C3  O3  C4  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
 EEQ  plan-1  CME  0.020
 EEQ  plan-1  C2N  0.020
 EEQ  plan-1  O2N  0.020
 EEQ  plan-1  N2   0.020
 EEQ  plan-1  C2   0.020
 EEQ  plan-1  H3   0.020

