# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:34:20 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1C[C@H](O)[C@@H](O)[C@@H]1CO
#
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
 LXE  LXE  '[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]azanium'  ligand  24  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LXE
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
 LXE  C1'   C  CH2   0  -0.487   1.6361   0.7433   0.3570
 LXE  C2'   C  CR15  0  -0.013   1.4804  -0.7124  -0.0616
 LXE  O2'   O  OH1   0  -0.668   1.4806  -0.8530  -1.4649
 LXE  C3'   C  CR15  0   0.041   0.0626  -1.0522   0.4150
 LXE  O3'   O  OH1   0  -0.673   0.0448  -1.2907   1.8039
 LXE  C4'   C  CR15  0  -0.302  -0.7518   0.2283   0.1520
 LXE  C5'   C  CH2   0  -0.141  -1.6957   0.1371  -1.0349
 LXE  O5'   O  OH1   0  -0.668  -2.6900  -0.8131  -0.7387
 LXE  C6'   C  CR15  0  -0.119   0.2954   1.3399  -0.0537
 LXE  N1'   N  NT3   1  -0.788  -0.0307   2.5613   0.7295
 LXE  H1'   H  HCH2  0   0.259   1.7650   0.7962   1.4407
 LXE  H1    H  HCH2  0   0.281   2.4879   1.2470  -0.1024
 LXE  H2'   H  HCR5  0   0.242   2.2350  -1.3592   0.4043
 LXE  HB    H  HOH1  0   0.457   2.3171  -0.5217  -1.8071
 LXE  H3'   H  HCR5  0   0.240  -0.3372  -1.9096  -0.1404
 LXE  HC    H  HOH1  0   0.453   0.5837  -2.0677   1.9852
 LXE  H4'   H  HCR5  0   0.277  -1.3536   0.4389   1.0430
 LXE  H5'1  H  HCH2  0   0.209  -2.1313   1.1297  -1.2183
 LXE  H5'2  H  HCH2  0   0.210  -1.1280  -0.1328  -1.9335
 LXE  H5'   H  HOH1  0   0.458  -3.2118  -0.9618  -1.5322
 LXE  H6'   H  HCR5  0   0.313   0.3217   1.6688  -1.0928
 LXE  HN1'  H  HNT3  0   0.468  -0.0780   2.3769   1.7320
 LXE  HN11  H  HNT3  0   0.477   0.6672   3.2929   0.5923
 LXE  HN12  H  HNT3  0   0.475  -0.9275   2.9638   0.4560

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
 LXE  N1'  C6'   single  1.487  0.020  1.487
 LXE  C4'  C6'   single  1.541  0.020  1.541
 LXE  C4'  C5'   single  1.519  0.020  1.519
 LXE  C4'  C3'   single  1.540  0.020  1.540
 LXE  O3'  C3'   single  1.409  0.020  1.409
 LXE  C6'  C1'   single  1.524  0.020  1.524
 LXE  C5'  O5'   single  1.407  0.020  1.407
 LXE  C2'  C3'   single  1.534  0.020  1.534
 LXE  C2'  C1'   single  1.523  0.020  1.523
 LXE  C2'  O2'   single  1.410  0.020  1.410
 LXE  C1'  H1'   single  0.970  0.020  1.090
 LXE  C1'  H1    single  0.970  0.020  1.090
 LXE  C2'  H2'   single  0.970  0.020  1.090
 LXE  O2'  HB    single  0.850  0.020  0.980
 LXE  C3'  H3'   single  0.970  0.020  1.090
 LXE  O3'  HC    single  0.850  0.020  0.980
 LXE  C4'  H4'   single  0.970  0.020  1.090
 LXE  C5'  H5'1  single  0.970  0.020  1.090
 LXE  C5'  H5'2  single  0.970  0.020  1.090
 LXE  O5'  H5'   single  0.850  0.020  0.980
 LXE  C6'  H6'   single  0.970  0.020  1.090
 LXE  N1'  HN1'  single  0.890  0.020  1.040
 LXE  N1'  HN11  single  0.890  0.020  1.040
 LXE  N1'  HN12  single  0.890  0.020  1.040

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
 LXE  H1    C1'  H1'   107.65  3.000
 LXE  H1    C1'  C6'   113.13  3.000
 LXE  H1'   C1'  C6'   110.62  3.000
 LXE  H1    C1'  C2'   113.92  3.000
 LXE  H1'   C1'  C2'   109.32  3.000
 LXE  C6'   C1'  C2'   102.13  3.000
 LXE  H2'   C2'  C3'   111.90  3.000
 LXE  H2'   C2'  O2'   111.31  3.000
 LXE  C3'   C2'  O2'   106.69  3.000
 LXE  H2'   C2'  C1'   112.11  3.000
 LXE  O2'   C2'  C1'   111.64  3.000
 LXE  C3'   C2'  C1'   102.77  3.000
 LXE  HB    O2'  C2'   108.63  3.000
 LXE  H3'   C3'  C4'   111.75  3.000
 LXE  H3'   C3'  O3'   111.23  3.000
 LXE  C4'   C3'  O3'   107.60  3.000
 LXE  H3'   C3'  C2'   110.65  3.000
 LXE  O3'   C3'  C2'   110.82  3.000
 LXE  C4'   C3'  C2'   104.56  3.000
 LXE  HC    O3'  C3'   108.36  3.000
 LXE  H4'   C4'  C6'   110.07  3.000
 LXE  H4'   C4'  C5'   107.80  3.000
 LXE  C6'   C4'  C5'   111.18  3.000
 LXE  H4'   C4'  C3'   108.14  3.000
 LXE  C5'   C4'  C3'   114.33  3.000
 LXE  C6'   C4'  C3'   105.26  3.000
 LXE  H5'2  C5'  H5'1  106.90  3.000
 LXE  H5'2  C5'  O5'   111.85  3.000
 LXE  H5'1  C5'  O5'   111.40  3.000
 LXE  H5'2  C5'  C4'   109.47  3.000
 LXE  H5'1  C5'  C4'   108.80  3.000
 LXE  O5'   C5'  C4'   108.37  3.000
 LXE  H5'   O5'  C5'   108.31  3.000
 LXE  H6'   C6'  N1'   105.04  3.000
 LXE  H6'   C6'  C4'   111.18  3.000
 LXE  N1'   C6'  C4'   111.91  3.000
 LXE  H6'   C6'  C1'   110.71  3.000
 LXE  C4'   C6'  C1'   106.23  3.000
 LXE  N1'   C6'  C1'   111.87  3.000
 LXE  HN12  N1'  HN11  106.40  3.000
 LXE  HN12  N1'  HN1'  107.10  3.000
 LXE  HN11  N1'  HN1'  107.06  3.000
 LXE  HN12  N1'  C6'   112.06  3.000
 LXE  HN11  N1'  C6'   111.60  3.000
 LXE  HN1'  N1'  C6'   112.28  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
 LXE  chir_01  C2'  C3'  C1'  O2'  positiv
 LXE  chir_02  C3'  O3'  C4'  C2'  negativ
 LXE  chir_03  C4'  C3'  C5'  C6'  positiv
 LXE  chir_04  C6'  N1'  C4'  C1'  positiv

