# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 10:05:42 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-O-acetyl-2,6-dideoxy-3-C-methyl-alpha-L-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)C[C@](C)(O)[C@H]1OC(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
 ERI  ERI  4-O-acetyl-2,6-dideoxy-3-C-methyl-alpha-L-arabino-hexopyranose  L-saccharide  30  14  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ERI
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
 ERI  O1   O  OH1   0  -0.659  7.2748   8.3444  -3.6295
 ERI  C1   C  CH1   0   0.248  5.9259   8.1118  -3.3653
 ERI  C2   C  CH2   0  -0.491  5.1728   9.4338  -3.3711
 ERI  C3   C  CT    0   0.189  4.9290  10.0189  -4.7649
 ERI  O3   O  OH1   0  -0.670  3.9494  11.0290  -4.5884
 ERI  CC3  C  CH3   0  -0.689  6.1863  10.6323  -5.3779
 ERI  C4   C  CH1   0   0.026  4.3424   8.8822  -5.6149
 ERI  O4   O  O2    0  -0.475  4.2026   9.3413  -6.9593
 ERI  CME  C  CH3   0  -0.773  3.0937   9.9443  -8.9231
 ERI  CO4  C  C     0   0.560  3.0061   9.3410  -7.5531
 ERI  OC4  O  O     0  -0.438  2.0016   8.9113  -7.0491
 ERI  C5   C  CH1   0   0.018  5.2149   7.6245  -5.6022
 ERI  O5   O  O2    0  -0.497  5.3587   7.1891  -4.2598
 ERI  C6   C  CH3   0  -0.690  4.5961   6.4779  -6.3781
 ERI  HO1  H  HOH1  0   0.455  7.7655   7.5277  -3.4857
 ERI  H1   H  HCH1  0   0.227  5.8040   7.6391  -2.3840
 ERI  H21  H  HCH2  0   0.253  4.1996   9.2514  -2.9066
 ERI  H22  H  HCH2  0   0.255  5.6923  10.1586  -2.7401
 ERI  HO3  H  HOH1  0   0.447  3.9298  11.5817  -5.3770
 ERI  H31  H  HCH3  0   0.232  5.9550  11.1484  -6.3116
 ERI  H32  H  HCH3  0   0.239  6.6114  11.3637  -4.6894
 ERI  H33  H  HCH3  0   0.241  6.9569   9.8957  -5.5899
 ERI  H4   H  HCH1  0   0.256  3.3618   8.6252  -5.2027
 ERI  H41  H  HCH3  0   0.261  2.1229   9.9258  -9.4100
 ERI  H42  H  HCH3  0   0.272  3.4419  10.9758  -8.8608
 ERI  H43  H  HCH3  0   0.271  3.8114   9.3985  -9.5363
 ERI  H5   H  HCH1  0   0.222  6.1958   7.8518  -6.0398
 ERI  H61  H  HCH3  0   0.245  5.2134   5.5840  -6.2856
 ERI  H62  H  HCH3  0   0.229  3.5947   6.2444  -6.0138
 ERI  H63  H  HCH3  0   0.236  4.5299   6.7149  -7.4390

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
 ERI  O1   C1   single  1.394  0.020  1.394
 ERI  O1   HO1  single  0.850  0.020  0.980
 ERI  C1   C2   single  1.521  0.020  1.521
 ERI  C1   O5   single  1.405  0.020  1.405
 ERI  C1   H1   single  0.970  0.020  1.090
 ERI  C2   C3   single  1.531  0.020  1.531
 ERI  C2   H21  single  0.970  0.020  1.090
 ERI  C2   H22  single  0.970  0.020  1.090
 ERI  C3   O3   single  1.418  0.020  1.418
 ERI  C3   CC3  single  1.527  0.020  1.527
 ERI  C3   C4   single  1.536  0.020  1.536
 ERI  O3   HO3  single  0.850  0.020  0.980
 ERI  CC3  H31  single  0.970  0.020  1.090
 ERI  CC3  H32  single  0.970  0.020  1.090
 ERI  CC3  H33  single  0.970  0.020  1.090
 ERI  C4   O4   single  1.428  0.020  1.428
 ERI  C4   C5   single  1.531  0.020  1.531
 ERI  C4   H4   single  0.970  0.020  1.090
 ERI  O4   CO4  single  1.336  0.020  1.336
 ERI  CME  CO4  single  1.500  0.020  1.500
 ERI  CME  H41  single  0.970  0.020  1.090
 ERI  CME  H42  single  0.970  0.020  1.090
 ERI  CME  H43  single  0.970  0.020  1.090
 ERI  CO4  OC4  double  1.203  0.020  1.203
 ERI  C5   O5   single  1.419  0.020  1.419
 ERI  C5   C6   single  1.516  0.020  1.516
 ERI  C5   H5   single  0.970  0.020  1.090
 ERI  C6   H61  single  0.970  0.020  1.090
 ERI  C6   H62  single  0.970  0.020  1.090
 ERI  C6   H63  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
 ERI  HO1  O1   C1   108.84  3.000
 ERI  H1   C1   O5   104.00  3.000
 ERI  H1   C1   C2   108.85  3.000
 ERI  O5   C1   C2   111.62  3.000
 ERI  H1   C1   O1   110.44  3.000
 ERI  O5   C1   O1   112.31  3.000
 ERI  C2   C1   O1   109.47  3.000
 ERI  H22  C2   H21  106.77  3.000
 ERI  H22  C2   C3   110.36  3.000
 ERI  H21  C2   C3   107.98  3.000
 ERI  H22  C2   C1   109.81  3.000
 ERI  H21  C2   C1   107.09  3.000
 ERI  C3   C2   C1   114.47  3.000
 ERI  C4   C3   CC3  112.93  3.000
 ERI  C4   C3   O3   109.40  3.000
 ERI  CC3  C3   O3   109.42  3.000
 ERI  C4   C3   C2   106.36  3.000
 ERI  CC3  C3   C2   112.82  3.000
 ERI  O3   C3   C2   105.59  3.000
 ERI  HO3  O3   C3   108.72  3.000
 ERI  H33  CC3  H32  107.54  3.000
 ERI  H33  CC3  H31  107.69  3.000
 ERI  H32  CC3  H31  107.79  3.000
 ERI  H33  CC3  C3   112.93  3.000
 ERI  H32  CC3  C3   109.67  3.000
 ERI  H31  CC3  C3   111.02  3.000
 ERI  H4   C4   C5   108.34  3.000
 ERI  H4   C4   O4   110.03  3.000
 ERI  C5   C4   O4   109.14  3.000
 ERI  H4   C4   C3   107.92  3.000
 ERI  C5   C4   C3   112.69  3.000
 ERI  O4   C4   C3   108.70  3.000
 ERI  CO4  O4   C4   120.42  3.000
 ERI  H43  CME  H42  107.18  3.000
 ERI  H43  CME  H41  109.13  3.000
 ERI  H42  CME  H41  109.09  3.000
 ERI  H43  CME  CO4  110.54  3.000
 ERI  H42  CME  CO4  110.30  3.000
 ERI  H41  CME  CO4  110.51  3.000
 ERI  OC4  CO4  CME  125.12  3.000
 ERI  OC4  CO4  O4   124.17  3.000
 ERI  CME  CO4  O4   110.71  3.000
 ERI  H5   C5   C6   108.49  3.000
 ERI  H5   C5   O5   110.50  3.000
 ERI  C6   C5   O5   107.06  3.000
 ERI  H5   C5   C4   109.63  3.000
 ERI  C6   C5   C4   112.61  3.000
 ERI  O5   C5   C4   108.53  3.000
 ERI  C5   O5   C1   116.22  3.000
 ERI  H63  C6   H62  108.43  3.000
 ERI  H63  C6   H61  107.18  3.000
 ERI  H62  C6   H61  108.42  3.000
 ERI  H63  C6   C5   111.02  3.000
 ERI  H62  C6   C5   111.44  3.000
 ERI  H61  C6   C5   110.21  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
 ERI  Var_01  CME  CO4  O4   C4  176.42  30.0  3
 ERI  Var_02  H41  CME  CO4  O4  178.96  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
 ERI  chir_01  C1  O1  C2   O5  negativ
 ERI  chir_02  C3  C2  CC3  C4  negativ
 ERI  chir_03  C4  O4  C5   C3  negativ
 ERI  chir_04  C5  O5  C4   C6  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
 ERI  plan-1  O4   0.020
 ERI  plan-1  CME  0.020
 ERI  plan-1  CO4  0.020
 ERI  plan-1  OC4  0.020

