# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:21:51 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: methyl beta-D-arabinopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 ARW  ARW  'methyl beta-D-arabinopyranoside'  D-saccharide  23  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 GRAND
;

data_comp_ARW
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
 ARW  C1    C  CH1   0   0.308   0.0969  -0.3177   1.0374
 ARW  C2    C  CH1   0  -0.026  -1.1785  -0.0423   0.2383
 ARW  C3    C  CH1   0  -0.031  -0.9023  -0.2254  -1.2531
 ARW  C4    C  CH1   0   0.014   0.3261   0.5871  -1.6599
 ARW  C5    C  CH2   0  -0.220   1.5003   0.2687  -0.7370
 ARW  O1    O  O2    0  -0.503  -0.1655  -0.0423   2.3626
 ARW  O2    O  OH1   0  -0.672  -1.6370   1.2736   0.4179
 ARW  O3    O  OH1   0  -0.672  -0.7091  -1.6045  -1.4645
 ARW  O4    O  OH1   0  -0.674   0.6182   0.2632  -2.9996
 ARW  O5    O  O2    0  -0.497   1.1505   0.5084   0.6088
 ARW  CM    C  CH3   0  -0.405   0.8378  -0.4528   3.2713
 ARW  H1    H  HCH1  0   0.191   0.3855  -1.3764   0.9054
 ARW  HA    H  HCH1  0   0.233  -1.9378  -0.7767   0.5454
 ARW  H3    H  HCH1  0   0.238  -1.7730   0.1377  -1.8188
 ARW  H4    H  HCH1  0   0.220   0.0777   1.6506  -1.5538
 ARW  H5C1  H  HCH2  0   0.247   2.3525   0.9123  -0.9660
 ARW  H5C2  H  HCH2  0   0.210   1.8214  -0.7719  -0.8841
 ARW  H2    H  HOH1  0   0.453  -1.7069   1.4490   1.3622
 ARW  HB    H  HOH1  0   0.454  -0.4337  -1.7340  -2.3782
 ARW  HC    H  HOH1  0   0.459   1.3591   0.8003  -3.2971
 ARW  HMC1  H  HCH3  0   0.238   0.4121  -0.3966   4.2715
 ARW  HMC2  H  HCH3  0   0.212   1.1482  -1.4858   3.0837
 ARW  HMC3  H  HCH3  0   0.220   1.7217   0.1875   3.2329

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
 ARW  C1  C2    single  1.530  0.020  1.530
 ARW  C1  O1    single  1.379  0.020  1.379
 ARW  C1  O5    single  1.406  0.020  1.406
 ARW  C1  H1    single  0.970  0.020  1.090
 ARW  C2  C3    single  1.528  0.020  1.528
 ARW  C2  O2    single  1.405  0.020  1.405
 ARW  C2  HA    single  0.970  0.020  1.090
 ARW  C3  C4    single  1.528  0.020  1.528
 ARW  C3  O3    single  1.409  0.020  1.409
 ARW  C3  H3    single  0.970  0.020  1.090
 ARW  C4  C5    single  1.527  0.020  1.527
 ARW  C4  O4    single  1.409  0.020  1.409
 ARW  C4  H4    single  0.970  0.020  1.090
 ARW  C5  O5    single  1.411  0.020  1.411
 ARW  C5  H5C1  single  0.970  0.020  1.090
 ARW  C5  H5C2  single  0.970  0.020  1.090
 ARW  O1  CM    single  1.414  0.020  1.414
 ARW  O2  H2    single  0.850  0.020  0.980
 ARW  O3  HB    single  0.850  0.020  0.980
 ARW  O4  HC    single  0.850  0.020  0.980
 ARW  CM  HMC1  single  0.970  0.020  1.090
 ARW  CM  HMC2  single  0.970  0.020  1.090
 ARW  CM  HMC3  single  0.970  0.020  1.090

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
 ARW  H1    C1  O5    109.32  3.000
 ARW  H1    C1  O1    110.85  3.000
 ARW  O5    C1  O1    108.56  3.000
 ARW  H1    C1  C2    109.13  3.000
 ARW  O5    C1  C2    111.08  3.000
 ARW  O1    C1  C2    107.90  3.000
 ARW  HA    C2  O2    111.36  3.000
 ARW  HA    C2  C3    108.50  3.000
 ARW  O2    C2  C3    107.22  3.000
 ARW  HA    C2  C1    108.02  3.000
 ARW  O2    C2  C1    111.95  3.000
 ARW  C3    C2  C1    109.73  3.000
 ARW  H3    C3  O3    110.77  3.000
 ARW  H3    C3  C4    108.90  3.000
 ARW  O3    C3  C4    111.74  3.000
 ARW  H3    C3  C2    108.62  3.000
 ARW  O3    C3  C2    106.78  3.000
 ARW  C4    C3  C2    109.97  3.000
 ARW  H4    C4  O4    111.21  3.000
 ARW  H4    C4  C5    108.52  3.000
 ARW  O4    C4  C5    111.55  3.000
 ARW  H4    C4  C3    107.92  3.000
 ARW  O4    C4  C3    107.31  3.000
 ARW  C5    C4  C3    110.27  3.000
 ARW  H5C2  C5  H5C1  107.57  3.000
 ARW  H5C2  C5  O5    111.16  3.000
 ARW  H5C1  C5  O5    107.06  3.000
 ARW  H5C2  C5  C4    109.95  3.000
 ARW  H5C1  C5  C4    110.51  3.000
 ARW  O5    C5  C4    110.51  3.000
 ARW  CM    O1  C1    115.12  3.000
 ARW  H2    O2  C2    108.64  3.000
 ARW  HB    O3  C3    108.25  3.000
 ARW  HC    O4  C4    108.98  3.000
 ARW  C5    O5  C1    112.13  3.000
 ARW  HMC3  CM  HMC2  108.52  3.000
 ARW  HMC3  CM  HMC1  108.57  3.000
 ARW  HMC2  CM  HMC1  108.48  3.000
 ARW  HMC3  CM  O1    112.42  3.000
 ARW  HMC2  CM  O1    111.40  3.000
 ARW  HMC1  CM  O1    107.33  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
 ARW  Var_01  C4    C5  O5  C1    62.44  30.0  1
 ARW  Var_02  HMC1  CM  O1  C1  -166.81  30.0  3

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
 ARW  chir_01  C1  C2  O1  O5  positiv
 ARW  chir_02  C2  O2  C1  C3  positiv
 ARW  chir_03  C3  O3  C2  C4  negativ
 ARW  chir_04  C4  O4  C3  C5  negativ

