# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 17:36:18 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2R,3S,4R)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@H](O)[C@H](O)[C@@H](O)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
 LLH  LLH  '(2R,3S,4R)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoic acid (non-preferred name)'  ligand  22  13  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LLH
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
 LLH  O5A   O  O     0  -0.436  -3.6658  -0.7409  -0.3287
 LLH  C5    C  C     0   0.517  -2.8635  -0.1251   0.3284
 LLH  O5B   O  OH1   0  -0.579  -2.9283   0.0376   1.6340
 LLH  C4    C  CH1   0  -0.089  -1.6553   0.5583  -0.2849
 LLH  O4    O  OH1   0  -0.668  -1.6903   0.4379  -1.6779
 LLH  C3    C  CH1   0  -0.027  -0.3717  -0.0693   0.2724
 LLH  O3    O  OH1   0  -0.657  -0.3328  -1.4509   0.0249
 LLH  C2    C  CH1   0  -0.108   0.8805   0.6205  -0.2930
 LLH  O2    O  OH1   0  -0.651   0.9096   1.9865   0.0105
 LLH  C1    C  C     0   0.507   2.1068  -0.0722   0.2966
 LLH  O1    O  O     0  -0.477   2.4141   0.0834   1.4659
 LLH  N     N  NH1   0  -0.364   2.7968  -0.8110  -0.5786
 LLH  ON    O  OH1   0  -0.540   3.8107  -1.6126  -0.1545
 LLH  HO5B  H  HOH1  0   0.493  -3.7031  -0.4172   1.9989
 LLH  H4    H  HCH1  0   0.279  -1.6870   1.6157   0.0048
 LLH  HO4   H  HOH1  0   0.456  -2.4311  -0.1340  -1.9183
 LLH  H3    H  HCH1  0   0.272  -0.3633   0.0529   1.3598
 LLH  HO3   H  HOH1  0   0.448  -0.4144  -1.5985  -0.9251
 LLH  H2    H  HCH1  0   0.274   0.8794   0.5413  -1.3848
 LLH  HO2   H  HOH1  0   0.451   1.0281   2.0863   0.9631
 LLH  HN    H  HNH1  0   0.421   2.4737  -0.9896  -1.5186
 LLH  HON   H  HOH1  0   0.481   4.6256  -1.1111  -0.2892

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
 LLH  O5A  C5    double  1.206  0.020  1.206
 LLH  C5   O5B   single  1.317  0.020  1.317
 LLH  C5   C4    single  1.518  0.020  1.518
 LLH  O5B  HO5B  single  0.850  0.020  0.980
 LLH  C4   O4    single  1.399  0.020  1.399
 LLH  C4   C3    single  1.534  0.020  1.534
 LLH  C4   H4    single  0.970  0.020  1.090
 LLH  O4   HO4   single  0.850  0.020  0.980
 LLH  C3   C2    single  1.537  0.020  1.537
 LLH  C3   O3    single  1.404  0.020  1.404
 LLH  C3   H3    single  0.970  0.020  1.090
 LLH  O3   HO3   single  0.850  0.020  0.980
 LLH  C2   O2    single  1.400  0.020  1.400
 LLH  C2   C1    single  1.527  0.020  1.527
 LLH  C2   H2    single  0.970  0.020  1.090
 LLH  O2   HO2   single  0.850  0.020  0.980
 LLH  C1   N     single  1.337  0.020  1.337
 LLH  C1   O1    double  1.219  0.020  1.219
 LLH  N    ON    single  1.360  0.020  1.360
 LLH  N    HN    single  0.860  0.020  1.020
 LLH  ON   HON   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
 LLH  C4    C5   O5B  112.58  3.000
 LLH  C4    C5   O5A  122.64  3.000
 LLH  O5B   C5   O5A  124.77  3.000
 LLH  HO5B  O5B  C5   110.75  3.000
 LLH  H4    C4   C3   108.83  3.000
 LLH  H4    C4   O4   110.21  3.000
 LLH  C3    C4   O4   110.34  3.000
 LLH  H4    C4   C5   107.72  3.000
 LLH  C3    C4   C5   109.58  3.000
 LLH  O4    C4   C5   110.11  3.000
 LLH  HO4   O4   C4   108.54  3.000
 LLH  H3    C3   C2   108.00  3.000
 LLH  H3    C3   O3   106.54  3.000
 LLH  C2    C3   O3   110.74  3.000
 LLH  H3    C3   C4   108.78  3.000
 LLH  O3    C3   C4   111.21  3.000
 LLH  C2    C3   C4   111.37  3.000
 LLH  HO3   O3   C3   108.76  3.000
 LLH  H2    C2   C1   110.68  3.000
 LLH  H2    C2   O2   106.67  3.000
 LLH  C1    C2   O2   110.02  3.000
 LLH  H2    C2   C3   109.48  3.000
 LLH  C1    C2   C3   107.98  3.000
 LLH  O2    C2   C3   112.03  3.000
 LLH  HO2   O2   C2   108.51  3.000
 LLH  N     C1   O1   124.63  3.000
 LLH  O1    C1   C2   120.99  3.000
 LLH  N     C1   C2   114.36  3.000
 LLH  HN    N    ON   115.11  3.000
 LLH  HN    N    C1   122.81  3.000
 LLH  ON    N    C1   120.41  3.000
 LLH  HON   ON   N    106.22  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
 LLH  CONST_01  ON    N    C1  C2   180.00  0.0  0
 LLH  CONST_02  ON    N    C1  O1     0.00  0.0  0
 LLH  CONST_03  HN    N    C1  C2     0.00  0.0  0
 LLH  CONST_04  HO5B  O5B  C5  O5A    0.00  0.0  0

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
 LLH  chir_01  C4  C5  O4  C3  positiv
 LLH  chir_02  C3  O3  C4  C2  positiv
 LLH  chir_03  C2  O2  C3  C1  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
 LLH  plan-1  C2    0.020
 LLH  plan-1  C1    0.020
 LLH  plan-1  O1    0.020
 LLH  plan-1  N     0.020
 LLH  plan-1  ON    0.020
 LLH  plan-1  HN    0.020
 LLH  plan-2  O5A   0.020
 LLH  plan-2  C5    0.020
 LLH  plan-2  O5B   0.020
 LLH  plan-2  C4    0.020
 LLH  plan-2  HO5B  0.020

