# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:19:12 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: octyl alpha-D-arabinofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[C@H]1O[C@H](CO)[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
 AFO  AFO  'octyl alpha-D-arabinofuranoside'  D-saccharide  44  18  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFO
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
 AFO  C1    C  CH1   0   0.283  92.8768   9.9158   1.5629
 AFO  O1    O  O2    0  -0.497  93.8704  10.1508   2.5065
 AFO  C2    C  CH1   0  -0.012  93.2231   8.6401   0.8031
 AFO  O2    O  OH1   0  -0.665  92.0229   8.1585   0.2531
 AFO  C3    C  CH1   0  -0.054  94.1761   9.1588  -0.2790
 AFO  O3    O  OH1   0  -0.665  95.4922   9.0880   0.2071
 AFO  C4    C  CH1   0   0.003  93.6791  10.6004  -0.5058
 AFO  O4    O  O2    0  -0.507  92.8127  10.9111   0.5827
 AFO  C5    C  CH2   0  -0.163  92.9279  10.7496  -1.8102
 AFO  O5    O  OH1   0  -0.666  92.5127  12.0866  -1.9521
 AFO  C1'   C  CH2   0  -0.132  93.6467  11.2749   3.3354
 AFO  C2'   C  CH2   0  -0.467  94.7759  11.3794   4.3410
 AFO  C3'   C  CH2   0  -0.440  94.5974  12.5818   5.2609
 AFO  C4'   C  CH2   0  -0.426  95.8109  12.8673   6.1430
 AFO  C5'   C  CH2   0  -0.429  96.2415  11.7212   7.0558
 AFO  C6'   C  CH2   0  -0.410  95.1685  11.2639   8.0358
 AFO  C7'   C  CH2   0  -0.414  95.6591  10.1859   8.9949
 AFO  C8'   C  CH3   0  -0.659  94.5871   9.7330   9.9763
 AFO  H1    H  HCH1  0   0.224  91.8902   9.8697   2.0456
 AFO  H2    H  HCH1  0   0.239  93.7118   7.8977   1.4449
 AFO  HO2   H  HOH1  0   0.456  92.2231   7.3937  -0.2962
 AFO  H3    H  HCH1  0   0.237  94.0725   8.5621  -1.1968
 AFO  HO3   H  HOH1  0   0.451  96.0842   9.4421  -0.4637
 AFO  H4    H  HCH1  0   0.235  94.5329  11.2908  -0.5045
 AFO  H51   H  HCH2  0   0.197  93.6027  10.4460  -2.6219
 AFO  H52   H  HCH2  0   0.196  92.0802  10.0519  -1.8193
 AFO  HO5   H  HOH1  0   0.453  92.0313  12.1643  -2.7806
 AFO  H1'   H  HCH2  0   0.201  93.5988  12.1966   2.7440
 AFO  H1'A  H  HCH2  0   0.196  92.6834  11.1776   3.8570
 AFO  H2'   H  HCH2  0   0.225  94.8259  10.4580   4.9278
 AFO  H2'A  H  HCH2  0   0.220  95.7267  11.4663   3.8050
 AFO  H3'   H  HCH2  0   0.223  94.3983  13.4711   4.6544
 AFO  H3'A  H  HCH2  0   0.218  93.7066  12.4398   5.8802
 AFO  H4'   H  HCH2  0   0.217  96.6545  13.1440   5.5028
 AFO  H4'A  H  HCH2  0   0.217  95.5978  13.7480   6.7568
 AFO  H5'   H  HCH2  0   0.212  96.5714  10.8665   6.4566
 AFO  H5'A  H  HCH2  0   0.217  97.1232  12.0426   7.6194
 AFO  H6'   H  HCH2  0   0.204  94.8092  12.1255   8.6102
 AFO  H6'A  H  HCH2  0   0.211  94.3002  10.8821   7.4891
 AFO  H7'   H  HCH2  0   0.208  96.0164   9.3269   8.4184
 AFO  H7'A  H  HCH2  0   0.209  96.5265  10.5603   9.5472
 AFO  H8'   H  HCH3  0   0.224  94.9541   8.9483  10.6386
 AFO  H8'A  H  HCH3  0   0.214  94.2500  10.5622  10.6009
 AFO  H8'B  H  HCH3  0   0.214  93.7137   9.3413   9.4514

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
 AFO  C1   O1    single  1.390  0.020  1.390
 AFO  C1   C2    single  1.525  0.020  1.525
 AFO  C1   O4    single  1.398  0.020  1.398
 AFO  O1   C1'   single  1.415  0.020  1.415
 AFO  C2   O2    single  1.405  0.020  1.405
 AFO  C2   C3    single  1.532  0.020  1.532
 AFO  C3   O3    single  1.405  0.020  1.405
 AFO  C3   C4    single  1.542  0.020  1.542
 AFO  C4   O4    single  1.425  0.020  1.425
 AFO  C4   C5    single  1.513  0.020  1.513
 AFO  C5   O5    single  1.407  0.020  1.407
 AFO  C1'  C2'   single  1.516  0.020  1.516
 AFO  C2'  C3'   single  1.524  0.020  1.524
 AFO  C3'  C4'   single  1.527  0.020  1.527
 AFO  C4'  C5'   single  1.527  0.020  1.527
 AFO  C5'  C6'   single  1.523  0.020  1.523
 AFO  C6'  C7'   single  1.524  0.020  1.524
 AFO  C7'  C8'   single  1.522  0.020  1.522
 AFO  C1   H1    single  0.970  0.020  1.090
 AFO  C2   H2    single  0.970  0.020  1.090
 AFO  O2   HO2   single  0.850  0.020  0.980
 AFO  C3   H3    single  0.970  0.020  1.090
 AFO  O3   HO3   single  0.850  0.020  0.980
 AFO  C4   H4    single  0.970  0.020  1.090
 AFO  C5   H51   single  0.970  0.020  1.090
 AFO  C5   H52   single  0.970  0.020  1.090
 AFO  O5   HO5   single  0.850  0.020  0.980
 AFO  C1'  H1'   single  0.970  0.020  1.090
 AFO  C1'  H1'A  single  0.970  0.020  1.090
 AFO  C2'  H2'   single  0.970  0.020  1.090
 AFO  C2'  H2'A  single  0.970  0.020  1.090
 AFO  C3'  H3'   single  0.970  0.020  1.090
 AFO  C3'  H3'A  single  0.970  0.020  1.090
 AFO  C4'  H4'   single  0.970  0.020  1.090
 AFO  C4'  H4'A  single  0.970  0.020  1.090
 AFO  C5'  H5'   single  0.970  0.020  1.090
 AFO  C5'  H5'A  single  0.970  0.020  1.090
 AFO  C6'  H6'   single  0.970  0.020  1.090
 AFO  C6'  H6'A  single  0.970  0.020  1.090
 AFO  C7'  H7'   single  0.970  0.020  1.090
 AFO  C7'  H7'A  single  0.970  0.020  1.090
 AFO  C8'  H8'   single  0.970  0.020  1.090
 AFO  C8'  H8'A  single  0.970  0.020  1.090
 AFO  C8'  H8'B  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
 AFO  H1    C1   O4    107.25  3.000
 AFO  H1    C1   C2    112.80  3.000
 AFO  O4    C1   C2    104.87  3.000
 AFO  H1    C1   O1    110.52  3.000
 AFO  O4    C1   O1    112.85  3.000
 AFO  C2    C1   O1    108.50  3.000
 AFO  C1'   O1   C1    114.77  3.000
 AFO  H2    C2   C3    111.43  3.000
 AFO  H2    C2   O2    112.20  3.000
 AFO  C3    C2   O2    111.76  3.000
 AFO  H2    C2   C1    112.10  3.000
 AFO  C3    C2   C1    102.12  3.000
 AFO  O2    C2   C1    106.73  3.000
 AFO  HO2   O2   C2    108.54  3.000
 AFO  H3    C3   C4    110.75  3.000
 AFO  H3    C3   O3    110.47  3.000
 AFO  C4    C3   O3    113.58  3.000
 AFO  H3    C3   C2    110.31  3.000
 AFO  C4    C3   C2    102.70  3.000
 AFO  O3    C3   C2    108.73  3.000
 AFO  HO3   O3   C3    108.45  3.000
 AFO  H4    C4   C5    108.97  3.000
 AFO  H4    C4   O4    109.55  3.000
 AFO  C5    C4   O4    109.58  3.000
 AFO  H4    C4   C3    109.70  3.000
 AFO  C5    C4   C3    112.28  3.000
 AFO  O4    C4   C3    106.70  3.000
 AFO  C4    O4   C1    110.63  3.000
 AFO  H52   C5   H51   107.01  3.000
 AFO  H52   C5   O5    112.03  3.000
 AFO  H51   C5   O5    111.68  3.000
 AFO  H52   C5   C4    109.14  3.000
 AFO  H51   C5   C4    107.76  3.000
 AFO  O5    C5   C4    109.10  3.000
 AFO  HO5   O5   C5    108.14  3.000
 AFO  H1'A  C1'  H1'   106.98  3.000
 AFO  H1'A  C1'  C2'   110.12  3.000
 AFO  H1'   C1'  C2'   109.42  3.000
 AFO  H1'A  C1'  O1    110.25  3.000
 AFO  H1'   C1'  O1    111.04  3.000
 AFO  C2'   C1'  O1    109.01  3.000
 AFO  H2'A  C2'  H2'   106.85  3.000
 AFO  H2'A  C2'  C3'   109.54  3.000
 AFO  H2'   C2'  C3'   110.25  3.000
 AFO  H2'A  C2'  C1'   109.13  3.000
 AFO  H2'   C2'  C1'   109.39  3.000
 AFO  C3'   C2'  C1'   111.56  3.000
 AFO  H3'A  C3'  H3'   105.72  3.000
 AFO  H3'A  C3'  C4'   110.14  3.000
 AFO  H3'   C3'  C4'   108.22  3.000
 AFO  H3'A  C3'  C2'   109.54  3.000
 AFO  H3'   C3'  C2'   109.13  3.000
 AFO  C4'   C3'  C2'   113.77  3.000
 AFO  H4'A  C4'  H4'   105.94  3.000
 AFO  H4'A  C4'  C5'   108.88  3.000
 AFO  H4'   C4'  C5'   108.78  3.000
 AFO  H4'A  C4'  C3'   108.65  3.000
 AFO  H4'   C4'  C3'   108.78  3.000
 AFO  C5'   C4'  C3'   115.40  3.000
 AFO  H5'A  C5'  H5'   105.57  3.000
 AFO  H5'A  C5'  C6'   108.92  3.000
 AFO  H5'   C5'  C6'   109.27  3.000
 AFO  H5'A  C5'  C4'   108.33  3.000
 AFO  H5'   C5'  C4'   110.10  3.000
 AFO  C6'   C5'  C4'   114.28  3.000
 AFO  H6'A  C6'  H6'   106.01  3.000
 AFO  H6'A  C6'  C7'   108.84  3.000
 AFO  H6'   C6'  C7'   109.38  3.000
 AFO  H6'A  C6'  C5'   110.00  3.000
 AFO  H6'   C6'  C5'   109.39  3.000
 AFO  C7'   C6'  C5'   112.98  3.000
 AFO  H7'A  C7'  H7'   106.01  3.000
 AFO  H7'A  C7'  C8'   109.55  3.000
 AFO  H7'   C7'  C8'   109.63  3.000
 AFO  H7'A  C7'  C6'   109.31  3.000
 AFO  H7'   C7'  C6'   109.19  3.000
 AFO  C8'   C7'  C6'   112.92  3.000
 AFO  H8'B  C8'  H8'A  107.50  3.000
 AFO  H8'B  C8'  H8'   107.65  3.000
 AFO  H8'A  C8'  H8'   107.64  3.000
 AFO  H8'B  C8'  C7'   111.11  3.000
 AFO  H8'A  C8'  C7'   111.13  3.000
 AFO  H8'   C8'  C7'   111.63  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
 AFO  Var_01  C2'  C1'  O1   C1    177.98  30.0  3
 AFO  Var_02  C3'  C2'  C1'  O1    179.59  30.0  3
 AFO  Var_03  C4'  C3'  C2'  C1'  -170.72  30.0  3
 AFO  Var_04  C5'  C4'  C3'  C2'   -58.08  30.0  3
 AFO  Var_05  C6'  C5'  C4'  C3'   -59.28  30.0  3
 AFO  Var_06  C7'  C6'  C5'  C4'  -176.07  30.0  3
 AFO  Var_07  C8'  C7'  C6'  C5'   179.83  30.0  3
 AFO  Var_08  H8'  C8'  C7'  C6'   178.86  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
 AFO  chir_01  C1  O1  C2  O4  positiv
 AFO  chir_02  C2  O2  C3  C1  negativ
 AFO  chir_03  C3  O3  C4  C2  positiv
 AFO  chir_04  C4  O4  C3  C5  negativ

