# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 13:58:21 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R,3R,4R)-N,2,3,4,5-pentahydroxypentanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)C(=O)NO
#
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
 0YR  0YR  '(2R,3R,4R)-N,2,3,4,5-pentahydroxypentanamide (non-preferred name)'  ligand  23  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0YR
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
 0YR  CAG  C  CH2   0  -0.159  -2.9322   0.7361  -0.5511
 0YR  NAH  N  NH1   0  -0.368   2.6584   0.5737   0.7332
 0YR  CAI  C  C     0   0.511   1.9737  -0.1097  -0.1907
 0YR  CAJ  C  CH1   0  -0.013  -1.8418   0.1646   0.3423
 0YR  CAK  C  CH1   0  -0.118   0.6077  -0.6089   0.2765
 0YR  CAL  C  CH1   0  -0.029  -0.4770   0.2826  -0.3614
 0YR  OAB  O  OH1   0  -0.671  -4.1316   0.8142   0.1812
 0YR  OAD  O  OH1   0  -0.656  -2.1447  -1.1385   0.7727
 0YR  OAF  O  OH1   0  -0.655  -0.0677   1.6295  -0.4131
 0YR  OAE  O  OH1   0  -0.652   0.4667  -1.9573  -0.0796
 0YR  OAC  O  OH1   0  -0.541   3.9271   0.9942   0.4801
 0YR  H1   H  HCH2  0   0.205  -2.6149   1.7196  -0.9168
 0YR  H2   H  HCH2  0   0.193  -3.0348   0.0865  -1.4335
 0YR  H3   H  HNH1  0   0.420   2.3741   0.6236   1.7008
 0YR  H4   H  HCH1  0   0.231  -1.7902   0.7653   1.2598
 0YR  H5   H  HCH1  0   0.267   0.5314  -0.5604   1.3686
 0YR  H6   H  HCH1  0   0.243  -0.5776  -0.0328  -1.4076
 0YR  H7   H  HOH1  0   0.455  -4.7896   1.2478  -0.3689
 0YR  H8   H  HOH1  0   0.442  -2.0875  -1.7385   0.0215
 0YR  H9   H  HOH1  0   0.449  -0.0702   1.9947   0.4789
 0YR  H10  H  HOH1  0   0.447   0.7074  -2.0479  -1.0100
 0YR  H11  H  HOH1  0   0.480   3.8556   1.9127   0.1886
 0YR  OAA  O  O     0  -0.479   2.3688  -0.3306  -1.3225

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
 0YR  OAC  NAH  single  1.360  0.020  1.360
 0YR  NAH  CAI  single  1.338  0.020  1.338
 0YR  CAI  OAA  double  1.219  0.020  1.219
 0YR  CAI  CAK  single  1.528  0.020  1.528
 0YR  CAK  OAE  single  1.402  0.020  1.402
 0YR  CAK  CAL  single  1.542  0.020  1.542
 0YR  OAF  CAL  single  1.409  0.020  1.409
 0YR  CAL  CAJ  single  1.540  0.020  1.540
 0YR  CAJ  OAD  single  1.405  0.020  1.405
 0YR  CAJ  CAG  single  1.521  0.020  1.521
 0YR  CAG  OAB  single  1.407  0.020  1.407
 0YR  CAG  H1   single  0.970  0.020  1.090
 0YR  CAG  H2   single  0.970  0.020  1.090
 0YR  NAH  H3   single  0.860  0.020  1.020
 0YR  CAJ  H4   single  0.970  0.020  1.090
 0YR  CAK  H5   single  0.970  0.020  1.090
 0YR  CAL  H6   single  0.970  0.020  1.090
 0YR  OAB  H7   single  0.850  0.020  0.980
 0YR  OAD  H8   single  0.850  0.020  0.980
 0YR  OAF  H9   single  0.850  0.020  0.980
 0YR  OAE  H10  single  0.850  0.020  0.980
 0YR  OAC  H11  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
 0YR  H2   CAG  H1   106.80  3.000
 0YR  H2   CAG  OAB  111.75  3.000
 0YR  H1   CAG  OAB  111.74  3.000
 0YR  H2   CAG  CAJ  108.42  3.000
 0YR  H1   CAG  CAJ  109.00  3.000
 0YR  OAB  CAG  CAJ  109.03  3.000
 0YR  H3   NAH  OAC  115.19  3.000
 0YR  H3   NAH  CAI  122.88  3.000
 0YR  OAC  NAH  CAI  120.45  3.000
 0YR  OAA  CAI  CAK  120.97  3.000
 0YR  CAK  CAI  NAH  114.42  3.000
 0YR  OAA  CAI  NAH  124.61  3.000
 0YR  H4   CAJ  OAD  105.16  3.000
 0YR  H4   CAJ  CAL  107.36  3.000
 0YR  OAD  CAJ  CAL  113.70  3.000
 0YR  H4   CAJ  CAG  108.60  3.000
 0YR  OAD  CAJ  CAG  111.94  3.000
 0YR  CAL  CAJ  CAG  109.76  3.000
 0YR  H5   CAK  OAE  106.78  3.000
 0YR  H5   CAK  CAL  109.74  3.000
 0YR  OAE  CAK  CAL  112.35  3.000
 0YR  H5   CAK  CAI  110.65  3.000
 0YR  CAL  CAK  CAI  108.27  3.000
 0YR  OAE  CAK  CAI  109.06  3.000
 0YR  H6   CAL  OAF  105.45  3.000
 0YR  H6   CAL  CAK  107.02  3.000
 0YR  OAF  CAL  CAK  111.32  3.000
 0YR  H6   CAL  CAJ  109.41  3.000
 0YR  OAF  CAL  CAJ  110.33  3.000
 0YR  CAK  CAL  CAJ  112.96  3.000
 0YR  H7   OAB  CAG  108.10  3.000
 0YR  H8   OAD  CAJ  109.03  3.000
 0YR  H9   OAF  CAL  109.12  3.000
 0YR  H10  OAE  CAK  108.07  3.000
 0YR  H11  OAC  NAH  106.32  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
 0YR  CONST_01  OAC  NAH  CAI  CAK  180.00  0.0  0
 0YR  CONST_02  OAC  NAH  CAI  OAA    0.00  0.0  0
 0YR  CONST_03  H3   NAH  CAI  CAK    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
 0YR  chir_01  CAJ  CAL  OAD  CAG  positiv
 0YR  chir_02  CAK  OAE  CAL  CAI  positiv
 0YR  chir_03  CAL  OAF  CAJ  CAK  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
 0YR  plan-1  NAH  0.020
 0YR  plan-1  CAI  0.020
 0YR  plan-1  CAK  0.020
 0YR  plan-1  OAC  0.020
 0YR  plan-1  H3   0.020
 0YR  plan-1  OAA  0.020

