# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:30:38 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1,5-anhydro-2-deoxy-3-O-(2-deoxy-alpha-D-arabino-hexopyranosyl)-D-arabino-hex-1-enitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC=C[C@@H](O[C@@H]2C[C@@H](O)[C@H](O)[C@@H](CO)O2)[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
 XD3  XD3  1,5-anhydro-2-deoxy-3-O-(2-deoxy-alpha-D-arabino-hexopyranosyl)-D-arabino-hex-1-enitol  ligand  40  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XD3
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
 XD3  O7   O  OH1   0  -0.676   3.8823   2.3137  -0.8605
 XD3  C11  C  CH1   0   0.015   2.8397   1.4096  -0.5584
 XD3  C    C  CH1   0   0.043   3.4784   0.0469  -0.3276
 XD3  O    O  OH1   0  -0.676   4.1043  -0.4416  -1.4891
 XD3  C10  C  CH2   0  -0.516   2.0655   1.8216   0.6869
 XD3  C3   C  CH1   0   0.256   1.0726   0.7466   1.0961
 XD3  O2   O  O2    0  -0.502   1.7075  -0.4971   1.2325
 XD3  C1   C  CH1   0  -0.011   2.4043  -0.9600   0.0878
 XD3  C2   C  CH2   0  -0.160   3.0007  -2.3069   0.4403
 XD3  O1   O  OH1   0  -0.666   1.9584  -3.2004   0.7573
 XD3  O3   O  O2    0  -0.507   0.0469   0.7181   0.1532
 XD3  C4   C  CH1   0   0.047  -1.1515   0.0647   0.5344
 XD3  C9   C  CH1   0  -0.018  -2.3092   0.8879  -0.0142
 XD3  O6   O  OH1   0  -0.667  -2.4244   2.0530   0.7634
 XD3  C7   C  CH1   0  -0.020  -3.5951   0.0543   0.0312
 XD3  C8   C  CH2   0  -0.167  -4.7942   0.8193  -0.4827
 XD3  O5   O  OH1   0  -0.669  -5.9369   0.0070  -0.3653
 XD3  O4   O  O2    0  -0.465  -3.4628  -1.1157  -0.7711
 XD3  C6   C  C1    0   0.047  -2.3122  -1.7979  -0.6104
 XD3  C5   C  C1    0  -0.400  -1.2270  -1.3355   0.0027
 XD3  H1   H  HOH1  0   0.457   3.4999   3.1011  -1.2595
 XD3  H2   H  HCH1  0   0.215   2.1517   1.3225  -1.4104
 XD3  H3   H  HCH1  0   0.204   4.2015   0.1460   0.4997
 XD3  H4   H  HOH1  0   0.452   4.7289   0.2271  -1.7893
 XD3  H5   H  HCH2  0   0.244   2.7673   1.9695   1.5126
 XD3  H6   H  HCH2  0   0.252   1.5442   2.7689   0.5316
 XD3  H7   H  HCH1  0   0.236   0.6671   0.9627   2.0925
 XD3  H8   H  HCH1  0   0.221   1.7087  -1.0950  -0.7535
 XD3  H9   H  HCH2  0   0.214   3.5850  -2.6596  -0.4151
 XD3  H10  H  HCH2  0   0.193   3.6982  -2.1819   1.2806
 XD3  H11  H  HOH1  0   0.457   2.3320  -4.0841   0.8168
 XD3  H12  H  HCH1  0   0.230  -1.2277   0.0550   1.6322
 XD3  H13  H  HCH1  0   0.234  -2.0917   1.1264  -1.0651
 XD3  H14  H  HOH1  0   0.461  -2.7560   2.7686   0.2144
 XD3  H15  H  HCH1  0   0.237  -3.7787  -0.2563   1.0708
 XD3  H16  H  HCH2  0   0.210  -4.8943   1.7365   0.1067
 XD3  H17  H  HCH2  0   0.201  -4.6088   1.1192  -1.5238
 XD3  H18  H  HOH1  0   0.458  -6.7033   0.5410  -0.5918
 XD3  H19  H  H     0   0.270  -2.3630  -2.7927  -1.0377
 XD3  H20  H  H     0   0.266  -0.3781  -1.9954   0.1124

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
 XD3  O7   C11  single  1.413  0.020  1.413
 XD3  C11  C10  single  1.523  0.020  1.523
 XD3  C11  C    single  1.522  0.020  1.522
 XD3  O    C    single  1.407  0.020  1.407
 XD3  C10  C3   single  1.520  0.020  1.520
 XD3  C    C1   single  1.530  0.020  1.530
 XD3  O1   C2   single  1.409  0.020  1.409
 XD3  C3   O2   single  1.403  0.020  1.403
 XD3  C3   O3   single  1.394  0.020  1.394
 XD3  C1   O2   single  1.418  0.020  1.418
 XD3  C1   C2   single  1.515  0.020  1.515
 XD3  O3   C4   single  1.417  0.020  1.417
 XD3  O6   C9   single  1.405  0.020  1.405
 XD3  C4   C9   single  1.523  0.020  1.523
 XD3  C4   C5   single  1.500  0.020  1.500
 XD3  C9   C7   single  1.533  0.020  1.533
 XD3  C5   C6   double  1.329  0.020  1.329
 XD3  C7   C8   single  1.512  0.020  1.512
 XD3  C7   O4   single  1.425  0.020  1.425
 XD3  C8   O5   single  1.407  0.020  1.407
 XD3  C6   O4   single  1.347  0.020  1.347
 XD3  O7   H1   single  0.850  0.020  0.980
 XD3  C11  H2   single  0.970  0.020  1.090
 XD3  C    H3   single  0.970  0.020  1.090
 XD3  O    H4   single  0.850  0.020  0.980
 XD3  C10  H5   single  0.970  0.020  1.090
 XD3  C10  H6   single  0.970  0.020  1.090
 XD3  C3   H7   single  0.970  0.020  1.090
 XD3  C1   H8   single  0.970  0.020  1.090
 XD3  C2   H9   single  0.970  0.020  1.090
 XD3  C2   H10  single  0.970  0.020  1.090
 XD3  O1   H11  single  0.850  0.020  0.980
 XD3  C4   H12  single  0.970  0.020  1.090
 XD3  C9   H13  single  0.970  0.020  1.090
 XD3  O6   H14  single  0.850  0.020  0.980
 XD3  C7   H15  single  0.970  0.020  1.090
 XD3  C8   H16  single  0.970  0.020  1.090
 XD3  C8   H17  single  0.970  0.020  1.090
 XD3  O5   H18  single  0.850  0.020  0.980
 XD3  C6   H19  single  0.930  0.020  1.080
 XD3  C5   H20  single  0.930  0.020  1.080

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
 XD3  H1   O7   C11  108.62  3.000
 XD3  H2   C11  C10  109.71  3.000
 XD3  H2   C11  C    108.02  3.000
 XD3  C10  C11  C    109.36  3.000
 XD3  H2   C11  O7   110.31  3.000
 XD3  C    C11  O7   107.19  3.000
 XD3  C10  C11  O7   112.14  3.000
 XD3  H3   C    C1   108.40  3.000
 XD3  H3   C    O    111.02  3.000
 XD3  C1   C    O    107.94  3.000
 XD3  H3   C    C11  107.96  3.000
 XD3  C1   C    C11  109.62  3.000
 XD3  O    C    C11  111.85  3.000
 XD3  H4   O    C    107.75  3.000
 XD3  H6   C10  H5   107.24  3.000
 XD3  H6   C10  C3   109.87  3.000
 XD3  H5   C10  C3   108.16  3.000
 XD3  H6   C10  C11  111.16  3.000
 XD3  H5   C10  C11  109.13  3.000
 XD3  C3   C10  C11  111.16  3.000
 XD3  H7   C3   O3   110.27  3.000
 XD3  H7   C3   O2   104.68  3.000
 XD3  O3   C3   O2   112.38  3.000
 XD3  H7   C3   C10  110.28  3.000
 XD3  O3   C3   C10  108.25  3.000
 XD3  O2   C3   C10  110.95  3.000
 XD3  C1   O2   C3   115.68  3.000
 XD3  H8   C1   C2   108.53  3.000
 XD3  H8   C1   O2   110.29  3.000
 XD3  C2   C1   O2   107.21  3.000
 XD3  H8   C1   C    108.49  3.000
 XD3  C2   C1   C    111.84  3.000
 XD3  O2   C1   C    110.45  3.000
 XD3  H10  C2   H9   107.19  3.000
 XD3  H10  C2   O1   111.69  3.000
 XD3  H9   C2   O1   111.50  3.000
 XD3  H10  C2   C1   109.07  3.000
 XD3  H9   C2   C1   108.35  3.000
 XD3  O1   C2   C1   108.96  3.000
 XD3  H11  O1   C2   108.02  3.000
 XD3  C4   O3   C3   116.73  3.000
 XD3  H12  C4   C5   110.00  3.000
 XD3  H12  C4   C9   108.15  3.000
 XD3  C5   C4   C9   109.80  3.000
 XD3  H12  C4   O3   109.33  3.000
 XD3  C5   C4   O3   112.19  3.000
 XD3  C9   C4   O3   107.26  3.000
 XD3  H13  C9   C7   108.19  3.000
 XD3  H13  C9   O6   111.43  3.000
 XD3  C7   C9   O6   111.45  3.000
 XD3  H13  C9   C4   108.13  3.000
 XD3  C7   C9   C4   109.45  3.000
 XD3  O6   C9   C4   108.12  3.000
 XD3  H14  O6   C9   109.24  3.000
 XD3  H15  C7   O4   108.40  3.000
 XD3  H15  C7   C8   109.36  3.000
 XD3  O4   C7   C8   107.32  3.000
 XD3  H15  C7   C9   108.75  3.000
 XD3  O4   C7   C9   110.60  3.000
 XD3  C8   C7   C9   112.33  3.000
 XD3  H17  C8   H16  107.26  3.000
 XD3  H17  C8   O5   111.93  3.000
 XD3  H16  C8   O5   111.38  3.000
 XD3  H17  C8   C7   109.04  3.000
 XD3  H16  C8   C7   108.26  3.000
 XD3  O5   C8   C7   108.88  3.000
 XD3  H18  O5   C8   107.89  3.000
 XD3  C6   O4   C7   115.34  3.000
 XD3  H19  C6   C5   122.64  3.000
 XD3  H19  C6   O4   112.19  3.000
 XD3  C5   C6   O4   125.17  3.000
 XD3  H20  C5   C6   118.39  3.000
 XD3  H20  C5   C4   119.64  3.000
 XD3  C6   C5   C4   121.96  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
 XD3  Var_01  O4  C6  C5  C4   -3.19  30.0  1
 XD3  Var_02  C5  C6  O4  C7  -14.28  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
 XD3  chir_01  C11  O7  C10  C    positiv
 XD3  chir_02  C    O   C1   C11  positiv
 XD3  chir_03  C3   O3  O2   C10  negativ
 XD3  chir_04  C1   O2  C2   C    positiv
 XD3  chir_05  C4   O3  C5   C9   positiv
 XD3  chir_06  C9   O6  C7   C4   positiv
 XD3  chir_07  C7   O4  C9   C8   negativ

