# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:38:31 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,6-anhydro-3-deoxy-L-xylo-hexonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[C@@H](C[C@@H]1O)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
 GCT  GCT  '2,6-anhydro-3-deoxy-L-xylo-hexonic acid'  D-saccharide  20  11  .  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_GCT
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
 GCT  C1    C  CH2    0  -0.214   1.5843  -0.3295   0.9203
 GCT  C2    C  CH1    0   0.002   0.5241   0.2321   1.8672
 GCT  O2    O  OH1    0  -0.676   0.7085  -0.2483   3.1819
 GCT  C3    C  CH1    0   0.045  -0.8518  -0.2047   1.3926
 GCT  O3    O  OH1    0  -0.674  -1.8907   0.3860   2.1404
 GCT  C4    C  CH2    0  -0.486  -1.0245   0.1718  -0.0696
 GCT  C5    C  CH1    0  -0.081   0.1309  -0.3717  -0.9078
 GCT  C6    C  C      0   0.383  -0.0174   0.0123  -2.3928
 GCT  O6A   O  O      0  -0.594   0.9008   0.6561  -2.9243
 GCT  O6B   O  OC    -1  -0.619  -1.0756  -0.3803  -2.9244
 GCT  O5    O  O2     0  -0.483   1.3695   0.0833  -0.4041
 GCT  HC11  H  HCH2   0   0.234   2.5762   0.0222   1.2160
 GCT  HC12  H  HCH2   0   0.193   1.5866  -1.4284   1.0010
 GCT  HC2   H  HCH1   0   0.207   0.5686   1.3309   1.8379
 GCT  HO2   H  HOH1   0   0.456   1.4567   0.2096   3.5766
 GCT  HC3   H  HCH1   0   0.192  -0.8949  -1.3046   1.4727
 GCT  HO3   H  HOH1   0   0.445  -1.7557   0.1600   3.0665
 GCT  HC41  H  HCH2   0   0.226  -1.0695   1.2626  -0.1650
 GCT  HC42  H  HCH2   0   0.245  -1.9644  -0.2286  -0.4507
 GCT  HC5   H  HCH1   0   0.201   0.1014  -1.4737  -0.8461

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
 GCT  C1  C2    single  1.528  0.020  1.528
 GCT  C1  O5    single  1.404  0.020  1.404
 GCT  C1  HC11  single  0.970  0.020  1.090
 GCT  C1  HC12  single  0.970  0.020  1.090
 GCT  C2  O2    single  1.412  0.020  1.412
 GCT  C2  C3    single  1.520  0.020  1.520
 GCT  C2  HC2   single  0.970  0.020  1.090
 GCT  O2  HO2   single  0.850  0.020  0.980
 GCT  C3  O3    single  1.410  0.020  1.410
 GCT  C3  C4    single  1.520  0.020  1.520
 GCT  C3  HC3   single  0.970  0.020  1.090
 GCT  O3  HO3   single  0.850  0.020  0.980
 GCT  C4  C5    single  1.527  0.020  1.527
 GCT  C4  HC41  single  0.970  0.020  1.090
 GCT  C4  HC42  single  0.970  0.020  1.090
 GCT  C5  C6    single  1.541  0.020  1.541
 GCT  C5  O5    single  1.412  0.020  1.412
 GCT  C5  HC5   single  0.970  0.020  1.090
 GCT  C6  O6A   deloc   1.241  0.020  1.241
 GCT  C6  O6B   deloc   1.248  0.020  1.248

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
 GCT  HC12  C1  HC11  107.40  3.000
 GCT  HC12  C1  O5    111.27  3.000
 GCT  HC11  C1  O5    107.42  3.000
 GCT  HC12  C1  C2    108.82  3.000
 GCT  HC11  C1  C2    110.10  3.000
 GCT  O5    C1  C2    111.74  3.000
 GCT  HC2   C2  C3    108.39  3.000
 GCT  HC2   C2  O2    111.06  3.000
 GCT  C3    C2  O2    108.14  3.000
 GCT  HC2   C2  C1    108.81  3.000
 GCT  C3    C2  C1    109.20  3.000
 GCT  O2    C2  C1    111.18  3.000
 GCT  HO2   O2  C2    108.77  3.000
 GCT  HC3   C3  C4    108.20  3.000
 GCT  HC3   C3  O3    110.51  3.000
 GCT  C4    C3  O3    108.83  3.000
 GCT  HC3   C3  C2    107.40  3.000
 GCT  C4    C3  C2    109.40  3.000
 GCT  O3    C3  C2    112.40  3.000
 GCT  HO3   O3  C3    107.97  3.000
 GCT  HC42  C4  HC41  107.43  3.000
 GCT  HC42  C4  C5    109.24  3.000
 GCT  HC41  C4  C5    109.72  3.000
 GCT  HC42  C4  C3    110.08  3.000
 GCT  HC41  C4  C3    109.58  3.000
 GCT  C5    C4  C3    110.72  3.000
 GCT  HC5   C5  O5    108.97  3.000
 GCT  HC5   C5  C6    107.45  3.000
 GCT  O5    C5  C6    110.35  3.000
 GCT  HC5   C5  C4    107.71  3.000
 GCT  O5    C5  C4    110.68  3.000
 GCT  C6    C5  C4    111.55  3.000
 GCT  O6B   C6  O6A   127.47  3.000
 GCT  O6B   C6  C5    114.45  3.000
 GCT  O6A   C6  C5    118.08  3.000
 GCT  C5    O5  C1    112.08  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
 GCT  Var_01  HC11  C1  O5  C5  177.46  30.0  1

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
 GCT  chir_01  C2  C1  O2  C3  positiv
 GCT  chir_02  C3  O3  C2  C4  positiv
 GCT  chir_03  C5  O5  C4  C6  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
 GCT  plan-1  C5   0.020
 GCT  plan-1  C6   0.020
 GCT  plan-1  O6A  0.020
 GCT  plan-1  O6B  0.020

