# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:37:39 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3S,4S)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoate (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
 XYH  XYH  '(2R,3S,4S)-2,3,4-trihydroxy-5-(hydroxyamino)-5-oxopentanoate (non-preferred name)'  ligand  21  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XYH
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
 XYH  O1B  O  O      0  -0.587  -2.5016   1.9129  -0.7181
 XYH  O1A  O  OC    -1  -0.606  -3.6513   0.4343   0.5052
 XYH  C1   C  C      0   0.407  -2.6876   0.8010  -0.2046
 XYH  C2   C  CH1    0  -0.133  -1.6312  -0.3016  -0.4688
 XYH  OH2  O  OH1    0  -0.688  -2.0052  -1.4621   0.2286
 XYH  C3   C  CH1    0   0.006  -0.2404   0.1661  -0.0294
 XYH  OH3  O  OH1    0  -0.673  -0.1423   0.1532   1.3734
 XYH  C4   C  CH1    0  -0.110   0.8940  -0.6392  -0.6834
 XYH  OH4  O  OH1    0  -0.655   0.7850  -2.0218  -0.5191
 XYH  C5   C  C      0   0.484   2.2361  -0.1636  -0.1222
 XYH  OH5  O  O      0  -0.468   2.8640  -0.8252   0.6841
 XYH  N6   N  NH1    0  -0.370   2.6125   1.0500  -0.5563
 XYH  OH6  O  OH1    0  -0.541   3.8381   1.5416  -0.2211
 XYH  H21  H  HCH1   0   0.220  -1.6128  -0.4819  -1.5538
 XYH  HO2  H  HOH1   0   0.433  -2.8568  -1.1867   0.6261
 XYH  H31  H  HCH1   0   0.241  -0.1218   1.2023  -0.3598
 XYH  HO3  H  HOH1   0   0.438  -0.6127  -0.6353   1.6743
 XYH  H41  H  HCH1   0   0.263   0.8563  -0.4386  -1.7599
 XYH  HO4  H  HOH1   0   0.442   1.1346  -2.2489   0.3510
 XYH  HN6  H  HNH1   0   0.418   2.1851   1.4937  -1.3568
 XYH  HO6  H  HOH1   0   0.479   3.6915   2.1470   0.5173

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
 XYH  O1B  C1   deloc   1.239  0.020  1.239
 XYH  O1A  C1   deloc   1.252  0.020  1.252
 XYH  C1   C2   single  1.550  0.020  1.550
 XYH  C2   OH2  single  1.405  0.020  1.405
 XYH  C2   C3   single  1.532  0.020  1.532
 XYH  C2   H21  single  0.970  0.020  1.090
 XYH  OH2  HO2  single  0.850  0.020  0.980
 XYH  C3   OH3  single  1.406  0.020  1.406
 XYH  C3   C4   single  1.537  0.020  1.537
 XYH  C3   H31  single  0.970  0.020  1.090
 XYH  OH3  HO3  single  0.850  0.020  0.980
 XYH  C4   OH4  single  1.397  0.020  1.397
 XYH  C4   C5   single  1.530  0.020  1.530
 XYH  C4   H41  single  0.970  0.020  1.090
 XYH  OH4  HO4  single  0.850  0.020  0.980
 XYH  C5   OH5  double  1.217  0.020  1.217
 XYH  C5   N6   single  1.343  0.020  1.343
 XYH  N6   OH6  single  1.362  0.020  1.362
 XYH  N6   HN6  single  0.890  0.020  1.040
 XYH  OH6  HO6  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
 XYH  C2   C1   O1A  114.40  3.000
 XYH  C2   C1   O1B  117.75  3.000
 XYH  O1A  C1   O1B  127.85  3.000
 XYH  H21  C2   C3   108.53  3.000
 XYH  H21  C2   OH2  111.02  3.000
 XYH  C3   C2   OH2  110.59  3.000
 XYH  H21  C2   C1   107.22  3.000
 XYH  C3   C2   C1   110.66  3.000
 XYH  OH2  C2   C1   108.76  3.000
 XYH  HO2  OH2  C2   101.58  3.000
 XYH  H31  C3   C4   106.72  3.000
 XYH  H31  C3   OH3  107.60  3.000
 XYH  C4   C3   OH3  111.60  3.000
 XYH  H31  C3   C2   107.52  3.000
 XYH  C4   C3   C2   112.83  3.000
 XYH  OH3  C3   C2   110.28  3.000
 XYH  HO3  OH3  C3   106.52  3.000
 XYH  H41  C4   C5   109.49  3.000
 XYH  H41  C4   OH4  107.11  3.000
 XYH  C5   C4   OH4  109.45  3.000
 XYH  H41  C4   C3   107.26  3.000
 XYH  C5   C4   C3   109.17  3.000
 XYH  OH4  C4   C3   114.27  3.000
 XYH  HO4  OH4  C4   108.12  3.000
 XYH  N6   C5   OH5  124.10  3.000
 XYH  N6   C5   C4   114.09  3.000
 XYH  OH5  C5   C4   121.75  3.000
 XYH  HN6  N6   OH6  114.65  3.000
 XYH  HN6  N6   C5   122.32  3.000
 XYH  OH6  N6   C5   119.92  3.000
 XYH  HO6  OH6  N6   106.12  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
 XYH  CONST_01  OH6  N6  C5  C4   180.00  0.0  0
 XYH  CONST_02  OH6  N6  C5  OH5    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
 XYH  chir_01  C2  C1   OH2  C3  positiv
 XYH  chir_02  C3  OH3  C2   C4  positiv
 XYH  chir_03  C4  OH4  C3   C5  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
 XYH  plan-1  C4   0.020
 XYH  plan-1  C5   0.020
 XYH  plan-1  OH5  0.020
 XYH  plan-1  N6   0.020
 XYH  plan-1  OH6  0.020
 XYH  plan-1  HN6  0.020
 XYH  plan-2  O1B  0.020
 XYH  plan-2  O1A  0.020
 XYH  plan-2  C1   0.020
 XYH  plan-2  C2   0.020

