# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 14:40:10 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: L-arabinose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@H](O)[C@@H](O)C=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
 LAI  LAI  'L-arabinose              '  L-saccharide  20  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LAI
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
 LAI  O1    O  OH1   0  -0.670   3.6142   0.1754   0.2739
 LAI  C2    C  CH2   0  -0.160   2.4344   0.6964  -0.2910
 LAI  C4    C  CH1   0  -0.018   1.2729  -0.2077   0.0910
 LAI  C6    C  CH1   0  -0.037  -0.0593   0.3776  -0.4065
 LAI  C8    C  CH1   0  -0.075  -1.2417  -0.5550  -0.1200
 LAI  C10   C  C1    0   0.154  -2.4785   0.0550  -0.7196
 LAI  O14   O  OH1   0  -0.660   1.4535  -1.5226  -0.3801
 LAI  O16   O  OH1   0  -0.659  -0.3085   1.6537   0.1344
 LAI  O18   O  OH1   0  -0.668  -1.3865  -0.7625   1.2546
 LAI  O20   O  O     0  -0.377  -3.4672   0.2899  -0.0704
 LAI  HO1   H  HOH1  0   0.456   4.3334   0.7784   0.0669
 LAI  H2    H  HCH2  0   0.209   2.2308   1.7129   0.0611
 LAI  H2A   H  HCH2  0   0.191   2.4993   0.7476  -1.3893
 LAI  H4    H  HCH1  0   0.238   1.2362  -0.2840   1.1834
 LAI  H6    H  HCH1  0   0.251   0.0064   0.5137  -1.4929
 LAI  H8    H  HCH1  0   0.262  -1.0801  -1.5039  -0.6530
 LAI  H10   H  H     0   0.221  -2.4292   0.2629  -1.8004
 LAI  HO14  H  HOH1  0   0.447   1.6041  -1.4920  -1.3317
 LAI  HO16  H  HOH1  0   0.446  -0.4266   1.5584   1.0871
 LAI  HO18  H  HOH1  0   0.451  -2.2758  -0.4807   1.5083

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
 LAI  O1   C2    single  1.408  0.020  1.408
 LAI  C2   C4    single  1.521  0.020  1.521
 LAI  C4   C6    single  1.538  0.020  1.538
 LAI  C4   O14   single  1.408  0.020  1.408
 LAI  C6   C8    single  1.533  0.020  1.533
 LAI  C6   O16   single  1.408  0.020  1.408
 LAI  C8   C10   single  1.504  0.020  1.504
 LAI  C8   O18   single  1.398  0.020  1.398
 LAI  C10  O20   double  1.206  0.020  1.206
 LAI  O1   HO1   single  0.850  0.020  0.980
 LAI  C2   H2    single  0.970  0.020  1.090
 LAI  C2   H2A   single  0.970  0.020  1.090
 LAI  C4   H4    single  0.970  0.020  1.090
 LAI  C6   H6    single  0.970  0.020  1.090
 LAI  C8   H8    single  0.970  0.020  1.090
 LAI  C10  H10   single  0.930  0.020  1.080
 LAI  O14  HO14  single  0.850  0.020  0.980
 LAI  O16  HO16  single  0.850  0.020  0.980
 LAI  O18  HO18  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
 LAI  HO1   O1   C2   107.97  3.000
 LAI  H2A   C2   H2   106.76  3.000
 LAI  H2A   C2   C4   108.86  3.000
 LAI  H2    C2   C4   109.22  3.000
 LAI  H2A   C2   O1   111.58  3.000
 LAI  H2    C2   O1   111.74  3.000
 LAI  C4    C2   O1   108.62  3.000
 LAI  H4    C4   O14  105.83  3.000
 LAI  H4    C4   C6   108.67  3.000
 LAI  O14   C4   C6   110.99  3.000
 LAI  H4    C4   C2   108.51  3.000
 LAI  O14   C4   C2   111.91  3.000
 LAI  C6    C4   C2   110.74  3.000
 LAI  H6    C6   O16  106.17  3.000
 LAI  H6    C6   C8   107.86  3.000
 LAI  O16   C6   C8   110.06  3.000
 LAI  H6    C6   C4   108.41  3.000
 LAI  O16   C6   C4   111.96  3.000
 LAI  C8    C6   C4   112.10  3.000
 LAI  H8    C8   O18  111.32  3.000
 LAI  H8    C8   C10  106.11  3.000
 LAI  O18   C8   C10  111.54  3.000
 LAI  H8    C8   C6   108.72  3.000
 LAI  O18   C8   C6   110.73  3.000
 LAI  C10   C8   C6   108.25  3.000
 LAI  H10   C10  O20  121.87  3.000
 LAI  H10   C10  C8   115.52  3.000
 LAI  O20   C10  C8   122.60  3.000
 LAI  HO14  O14  C4   108.70  3.000
 LAI  HO16  O16  C6   108.15  3.000
 LAI  HO18  O18  C8   108.06  3.000

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
 LAI  chir_01  C4  C2   C6  O14  negativ
 LAI  chir_02  C6  O16  C4  C8   negativ
 LAI  chir_03  C8  O18  C6  C10  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
 LAI  plan-1  C8   0.020
 LAI  plan-1  C10  0.020
 LAI  plan-1  O20  0.020
 LAI  plan-1  H10  0.020

