# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:20:03 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=CC(=O)C(=CO1)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
 KOJ  KOJ  5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one  ligand  16  10  .  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_KOJ
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
 KOJ  C1    C  CR16  0  -0.083   1.4084   0.0289  -0.5576
 KOJ  C2    C  CR6   0   0.135   0.4959  -0.0517  -1.5437
 KOJ  C3    C  CR6   0   0.407  -0.9320  -0.0011  -1.2276
 KOJ  C4    C  CR16  0  -0.514  -1.1995   0.1179   0.1872
 KOJ  C5    C  CR6   0   0.380  -0.2079   0.1965   1.0959
 KOJ  C6    C  CH2   0  -0.221  -0.4026   0.3665   2.5686
 KOJ  O2    O  OH1   0  -0.608   0.7923  -0.1801  -2.8455
 KOJ  O3    O  OC    0  -0.460  -1.7957  -0.0617  -2.0938
 KOJ  O5    O  O     0  -0.399   1.0747   0.1570   0.7393
 KOJ  O6    O  OH1   0  -0.662   0.2863  -0.6591   3.2368
 KOJ  H1    H  HCR6  0   0.314   2.4795  -0.0032  -0.7078
 KOJ  H4    H  HCR6  0   0.288  -2.2269   0.1439   0.5244
 KOJ  H6C1  H  HCH2  0   0.233  -1.4784   0.3555   2.7743
 KOJ  H6C2  H  HCH2  0   0.246  -0.0336   1.3599   2.8513
 KOJ  H2    H  HOH1  0   0.478   1.7462  -0.2242  -2.9811
 KOJ  H6    H  HOH1  0   0.466   0.4617  -0.3665   4.1355

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
 KOJ  C1  C2    aromatic  1.346  0.020  1.346
 KOJ  C1  O5    aromatic  1.345  0.020  1.345
 KOJ  C1  H1    single    0.930  0.020  1.080
 KOJ  C2  C3    aromatic  1.463  0.020  1.463
 KOJ  C2  O2    single    1.341  0.020  1.341
 KOJ  C3  C4    aromatic  1.445  0.020  1.445
 KOJ  C3  O3    double    1.225  0.020  1.225
 KOJ  C4  C5    aromatic  1.347  0.020  1.347
 KOJ  C4  H4    single    0.930  0.020  1.080
 KOJ  C5  C6    single    1.495  0.020  1.495
 KOJ  C5  O5    aromatic  1.332  0.020  1.332
 KOJ  C6  O6    single    1.405  0.020  1.405
 KOJ  C6  H6C1  single    0.970  0.020  1.090
 KOJ  C6  H6C2  single    0.970  0.020  1.090
 KOJ  O2  H2    single    0.850  0.020  0.980
 KOJ  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
 KOJ  H1    C1  O5    112.47  3.000
 KOJ  H1    C1  C2    124.59  3.000
 KOJ  O5    C1  C2    122.94  3.000
 KOJ  O2    C2  C3    115.38  3.000
 KOJ  O2    C2  C1    124.54  3.000
 KOJ  C3    C2  C1    120.08  3.000
 KOJ  O3    C3  C4    124.48  3.000
 KOJ  O3    C3  C2    122.25  3.000
 KOJ  C4    C3  C2    113.27  3.000
 KOJ  H4    C4  C5    119.17  3.000
 KOJ  H4    C4  C3    118.89  3.000
 KOJ  C5    C4  C3    121.94  3.000
 KOJ  O5    C5  C6    113.11  3.000
 KOJ  O5    C5  C4    121.76  3.000
 KOJ  C6    C5  C4    125.11  3.000
 KOJ  H6C2  C6  H6C1  106.93  3.000
 KOJ  H6C2  C6  O6    111.94  3.000
 KOJ  H6C1  C6  O6    112.64  3.000
 KOJ  H6C2  C6  C5    108.25  3.000
 KOJ  H6C1  C6  C5    108.16  3.000
 KOJ  O6    C6  C5    108.76  3.000
 KOJ  H2    O2  C2    111.06  3.000
 KOJ  C5    O5  C1    119.99  3.000
 KOJ  H6    O6  C6    108.18  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
 KOJ  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 KOJ  CONST_02  C4  C5  O5  C1    0.00   0.0  0
 KOJ  CONST_03  C5  O5  C1  C2    0.00   0.0  0
 KOJ  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 KOJ  CONST_05  O5  C1  C2  C3    0.00   0.0  0
 KOJ  CONST_06  O5  C5  C4  C3    0.00   0.0  0
 KOJ  CONST_07  O3  C3  C2  C1  180.00   0.0  0
 KOJ  CONST_08  C6  C5  O5  C1  180.00   0.0  0
 KOJ  CONST_09  C6  C5  C4  C3  180.00   0.0  0
 KOJ  CONST_10  O2  C2  C3  C4  180.00   0.0  0
 KOJ  CONST_11  O3  C3  C4  C5  180.00   0.0  0
 KOJ  CONST_12  O5  C1  C2  O2  180.00   0.0  0
 KOJ  CONST_13  H4  C4  C3  C2  180.00   0.0  0
 KOJ  CONST_14  H1  C1  C2  C3  180.00   0.0  0
 KOJ  Var_01    O6  C6  C5  C4  125.90  30.0  2

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
 KOJ  plan-1  C2  0.020
 KOJ  plan-1  C3  0.020
 KOJ  plan-1  C4  0.020
 KOJ  plan-1  O3  0.020

