# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 02:06:32 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CNC(=O)[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
 IFL  IFL  (3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-one  ligand  22  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IFL
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
 IFL  O4    O  OH1   0  -0.670  -2.2768   0.1428   0.4547
 IFL  C4    C  CH1   0   0.057  -0.9830  -0.2601   0.0798
 IFL  C3    C  CH1   0  -0.069  -0.6010   0.3252  -1.2717
 IFL  O3    O  OH1   0  -0.668  -1.4640  -0.1890  -2.2468
 IFL  C2    C  C     0   0.492   0.8528   0.0587  -1.6473
 IFL  N     N  NH1   0  -0.627   1.7207  -0.0940  -0.6428
 IFL  C7    C  CH2   0  -0.237   1.3961  -0.3117   0.7551
 IFL  C5    C  CH1   0  -0.362   0.0177   0.2255   1.1200
 IFL  C6    C  CH2   0  -0.129  -0.3726  -0.2174   2.5223
 IFL  O6    O  OH1   0  -0.672   0.6229   0.2145   3.4236
 IFL  O2    O  O     0  -0.502   1.1805   0.0550  -2.8277
 IFL  H4    H  HOH1  0   0.455  -2.9037  -0.2058  -0.1872
 IFL  HA    H  HCH1  0   0.217  -0.9194  -1.3590   0.0177
 IFL  H3    H  HCH1  0   0.241  -0.6946   1.4220  -1.1955
 IFL  HB    H  HOH1  0   0.453  -1.1325   0.0775  -3.1122
 IFL  H     H  HNH1  0   0.400   2.6843  -0.2433  -0.9070
 IFL  H7C1  H  HCH2  0   0.266   2.1630   0.1738   1.3555
 IFL  H7C2  H  HCH2  0   0.235   1.4410  -1.3840   0.9777
 IFL  H5    H  HCH1  0   0.253   0.0467   1.3220   1.0917
 IFL  H6C1  H  HCH2  0   0.191  -0.4790  -1.3117   2.5362
 IFL  H6C2  H  HCH2  0   0.220  -1.3481   0.2055   2.7800
 IFL  H6    H  HOH1  0   0.457   0.3684  -0.0676   4.3067

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
 IFL  O4  C4    single  1.406  0.020  1.406
 IFL  O4  H4    single  0.850  0.020  0.980
 IFL  C4  C3    single  1.522  0.020  1.522
 IFL  C4  C5    single  1.523  0.020  1.523
 IFL  C4  HA    single  0.970  0.020  1.090
 IFL  C3  O3    single  1.400  0.020  1.400
 IFL  C3  C2    single  1.525  0.020  1.525
 IFL  C3  H3    single  0.970  0.020  1.090
 IFL  O3  HB    single  0.850  0.020  0.980
 IFL  C2  N     single  1.336  0.020  1.336
 IFL  C2  O2    double  1.225  0.020  1.225
 IFL  N   C7    single  1.452  0.020  1.452
 IFL  N   H     single  0.860  0.020  1.020
 IFL  C7  C5    single  1.524  0.020  1.524
 IFL  C7  H7C1  single  0.970  0.020  1.090
 IFL  C7  H7C2  single  0.970  0.020  1.090
 IFL  C5  C6    single  1.521  0.020  1.521
 IFL  C5  H5    single  0.970  0.020  1.090
 IFL  C6  O6    single  1.411  0.020  1.411
 IFL  C6  H6C1  single  0.970  0.020  1.090
 IFL  C6  H6C2  single  0.970  0.020  1.090
 IFL  O6  H6    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
 IFL  H4    O4  C4    108.53  3.000
 IFL  HA    C4  C5    108.56  3.000
 IFL  HA    C4  C3    108.60  3.000
 IFL  C5    C4  C3    108.61  3.000
 IFL  HA    C4  O4    110.71  3.000
 IFL  C5    C4  O4    109.34  3.000
 IFL  C3    C4  O4    110.96  3.000
 IFL  H3    C3  C2    105.76  3.000
 IFL  H3    C3  O3    111.15  3.000
 IFL  C2    C3  O3    110.60  3.000
 IFL  H3    C3  C4    107.45  3.000
 IFL  C2    C3  C4    113.01  3.000
 IFL  O3    C3  C4    108.82  3.000
 IFL  HB    O3  C3    108.16  3.000
 IFL  O2    C2  N     123.38  3.000
 IFL  O2    C2  C3    119.53  3.000
 IFL  N     C2  C3    117.00  3.000
 IFL  H     N   C7    116.30  3.000
 IFL  H     N   C2    116.09  3.000
 IFL  C7    N   C2    126.57  3.000
 IFL  H7C2  C7  H7C1  107.19  3.000
 IFL  H7C2  C7  C5    109.47  3.000
 IFL  H7C1  C7  C5    110.37  3.000
 IFL  H7C2  C7  N     109.46  3.000
 IFL  H7C1  C7  N     107.86  3.000
 IFL  C5    C7  N     112.34  3.000
 IFL  H5    C5  C6    108.75  3.000
 IFL  H5    C5  C7    108.80  3.000
 IFL  C6    C5  C7    110.50  3.000
 IFL  H5    C5  C4    108.56  3.000
 IFL  C6    C5  C4    111.60  3.000
 IFL  C7    C5  C4    108.57  3.000
 IFL  H6C2  C6  H6C1  107.18  3.000
 IFL  H6C2  C6  O6    111.13  3.000
 IFL  H6C1  C6  O6    111.40  3.000
 IFL  H6C2  C6  C5    109.47  3.000
 IFL  H6C1  C6  C5    109.04  3.000
 IFL  O6    C6  C5    108.59  3.000
 IFL  H6    O6  C6    108.07  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
 IFL  CONST_01  C7  N   C2  C3    0.00   0.0  0
 IFL  CONST_02  O2  C2  N   C7  180.00   0.0  0
 IFL  CONST_03  H   N   C2  C3  180.00   0.0  0
 IFL  Var_01    C5  C7  N   C2  -24.81  30.0  1

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
 IFL  chir_01  C4  O4  C3  C5  negativ
 IFL  chir_02  C3  O3  C4  C2  negativ
 IFL  chir_03  C5  C4  C7  C6  positiv

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
 IFL  plan-1  C3  0.020
 IFL  plan-1  C2  0.020
 IFL  plan-1  N   0.020
 IFL  plan-1  C7  0.020
 IFL  plan-1  O2  0.020
 IFL  plan-1  H   0.020

