# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:52:48 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  21  13  .  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_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  -0.605  -3.6641  -0.5991  -0.4064
 LLH  C5   C  C      0   0.410  -2.8681  -0.0336   0.3768
 LLH  O5B  O  OC    -1  -0.590  -2.9655   0.0854   1.6060
 LLH  C4   C  CH1    0  -0.136  -1.6289   0.5897  -0.3081
 LLH  O4   O  OH1    0  -0.697  -1.6910   0.3440  -1.6918
 LLH  C3   C  CH1    0  -0.007  -0.3503  -0.0059   0.2698
 LLH  O3   O  OH1    0  -0.670  -0.2848  -1.3939   0.0377
 LLH  C2   C  CH1    0  -0.106   0.9122   0.6700  -0.2900
 LLH  O2   O  OH1    0  -0.656   0.9708   2.0356   0.0217
 LLH  C1   C  C      0   0.506   2.1332  -0.0429   0.2833
 LLH  O1   O  O      0  -0.480   2.4664   0.1111   1.4459
 LLH  N    N  NH1    0  -0.367   2.8019  -0.7963  -0.6010
 LLH  ON   O  OH1    0  -0.543   3.7832  -1.6398  -0.1741
 LLH  H4   H  HCH1   0   0.222  -1.6349   1.6691  -0.1043
 LLH  HO4  H  HOH1   0   0.434  -2.5296  -0.1529  -1.7696
 LLH  H3   H  HCH1   0   0.243  -0.3653   0.1358   1.3552
 LLH  HO3  H  HOH1   0   0.439  -0.5057  -1.5415  -0.8902
 LLH  H2   H  HCH1   0   0.262   0.9043   0.6001  -1.3831
 LLH  HO2  H  HOH1   0   0.447   1.0493   2.1244   0.9790
 LLH  HN   H  HNH1   0   0.416   2.4218  -1.0196  -1.5097
 LLH  HON  H  HOH1   0   0.480   4.6178  -1.1799  -0.3309

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   deloc   1.252  0.020  1.252
 LLH  C5   O5B  deloc   1.239  0.020  1.239
 LLH  C5   C4   single  1.547  0.020  1.547
 LLH  C4   O4   single  1.407  0.020  1.407
 LLH  C4   C3   single  1.524  0.020  1.524
 LLH  C4   H4   single  0.970  0.020  1.090
 LLH  O4   HO4  single  0.850  0.020  0.980
 LLH  C3   C2   single  1.538  0.020  1.538
 LLH  C3   O3   single  1.409  0.020  1.409
 LLH  C3   H3   single  0.970  0.020  1.090
 LLH  O3   HO3  single  0.850  0.020  0.980
 LLH  C2   O2   single  1.402  0.020  1.402
 LLH  C2   C1   single  1.526  0.020  1.526
 LLH  C2   H2   single  0.970  0.020  1.090
 LLH  O2   HO2  single  0.850  0.020  0.980
 LLH  C1   N    single  1.340  0.020  1.340
 LLH  C1   O1   double  1.219  0.020  1.219
 LLH  N    ON   single  1.363  0.020  1.363
 LLH  N    HN   single  0.890  0.020  1.040
 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  117.62  3.000
 LLH  C4   C5  O5A  114.48  3.000
 LLH  O5B  C5  O5A  127.90  3.000
 LLH  H4   C4  C3   108.55  3.000
 LLH  H4   C4  O4   110.72  3.000
 LLH  C3   C4  O4   109.98  3.000
 LLH  H4   C4  C5   108.02  3.000
 LLH  C3   C4  C5   110.28  3.000
 LLH  O4   C4  C5   109.26  3.000
 LLH  HO4  O4  C4   101.82  3.000
 LLH  H3   C3  C2   108.38  3.000
 LLH  H3   C3  O3   106.95  3.000
 LLH  C2   C3  O3   109.56  3.000
 LLH  H3   C3  C4   108.29  3.000
 LLH  O3   C3  C4   111.19  3.000
 LLH  C2   C3  C4   112.27  3.000
 LLH  HO3  O3  C3   107.36  3.000
 LLH  H2   C2  C1   110.55  3.000
 LLH  H2   C2  O2   106.52  3.000
 LLH  C1   C2  O2   109.76  3.000
 LLH  H2   C2  C3   109.23  3.000
 LLH  C1   C2  C3   108.36  3.000
 LLH  O2   C2  C3   112.43  3.000
 LLH  HO2  O2  C2   108.28  3.000
 LLH  N    C1  O1   124.31  3.000
 LLH  O1   C1  C2   121.20  3.000
 LLH  N    C1  C2   114.46  3.000
 LLH  HN   N   ON   114.58  3.000
 LLH  HN   N   C1   122.01  3.000
 LLH  ON   N   C1   120.04  3.000
 LLH  HON  ON  N    106.06  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

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

