# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 04:48:21 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-deoxy-6-O-phosphono-D-arabino-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(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
 DG6  DG6  2-deoxy-6-O-phosphono-D-arabino-hexitol  ligand  28  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DG6
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
 DG6  C1    C  CH2    0  -0.135   5.1981   0.3639   0.2095
 DG6  O1    O  OH1    0  -0.676   6.2523  -0.4688   0.6486
 DG6  C2    C  CH2    0  -0.489   3.9021  -0.4209   0.2871
 DG6  C3    C  CH1    0   0.022   2.6898   0.4033  -0.1347
 DG6  O3    O  OH1    0  -0.673   2.7925   0.8459  -1.4764
 DG6  C4    C  CH1    0  -0.020   1.3815  -0.3577   0.1122
 DG6  O4    O  OH1    0  -0.668   1.3731  -1.6070  -0.5520
 DG6  C5    C  CH1    0  -0.030   0.1331   0.4619  -0.2563
 DG6  O5    O  OH1    0  -0.665   0.2003   1.7702   0.2686
 DG6  C6    C  CH2    0  -0.126  -1.1448  -0.2470   0.1717
 DG6  O6    O  O2     0  -0.658  -2.2508   0.4079  -0.3685
 DG6  P     P  P      0   1.219  -3.7774   0.0270   0.2898
 DG6  O1P   O  OP    -1  -0.900  -4.6858   0.8577  -0.6074
 DG6  O2P   O  OP    -1  -0.908  -3.9092  -1.4842   0.1252
 DG6  O3P   O  O      0  -0.905  -3.7104   0.4905   1.7413
 DG6  HC11  H  HCH2   0   0.187   5.1152   1.2640   0.8348
 DG6  HC12  H  HCH2   0   0.192   5.3672   0.7062  -0.8180
 DG6  HO1   H  HOH1   0   0.452   7.0747   0.0210   0.5608
 DG6  HC21  H  HCH2   0   0.227   3.9763  -1.3197  -0.3333
 DG6  HC22  H  HCH2   0   0.231   3.7526  -0.7609   1.3165
 DG6  HC3   H  HCH1   0   0.226   2.6623   1.3098   0.4763
 DG6  HO3   H  HOH1   0   0.440   3.0298   0.0953  -2.0314
 DG6  HC4   H  HCH1   0   0.221   1.3418  -0.5915   1.1838
 DG6  HO4   H  HOH1   0   0.442   1.1970  -1.4604  -1.4877
 DG6  HC5   H  HCH1   0   0.210   0.1181   0.5825  -1.3466
 DG6  HO5   H  HOH1   0   0.441   0.0331   1.7229   1.2160
 DG6  HC61  H  HCH2   0   0.179  -1.0998  -1.2968  -0.1425
 DG6  HC62  H  HCH2   0   0.164  -1.1767  -0.2588   1.2743

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
 DG6  C1  O1    single  1.413  0.020  1.413
 DG6  C1  C2    single  1.517  0.020  1.517
 DG6  C1  HC11  single  0.970  0.020  1.090
 DG6  C1  HC12  single  0.970  0.020  1.090
 DG6  O1  HO1   single  0.850  0.020  0.980
 DG6  C2  C3    single  1.525  0.020  1.525
 DG6  C2  HC21  single  0.970  0.020  1.090
 DG6  C2  HC22  single  0.970  0.020  1.090
 DG6  C3  O3    single  1.417  0.020  1.417
 DG6  C3  C4    single  1.534  0.020  1.534
 DG6  C3  HC3   single  0.970  0.020  1.090
 DG6  O3  HO3   single  0.850  0.020  0.980
 DG6  C4  O4    single  1.415  0.020  1.415
 DG6  C4  C5    single  1.538  0.020  1.538
 DG6  C4  HC4   single  0.970  0.020  1.090
 DG6  O4  HO4   single  0.850  0.020  0.980
 DG6  C5  O5    single  1.411  0.020  1.411
 DG6  C5  C6    single  1.523  0.020  1.523
 DG6  C5  HC5   single  0.970  0.020  1.090
 DG6  O5  HO5   single  0.850  0.020  0.980
 DG6  C6  O6    single  1.394  0.020  1.394
 DG6  C6  HC61  single  0.970  0.020  1.090
 DG6  C6  HC62  single  0.970  0.020  1.090
 DG6  O6  P     single  1.705  0.020  1.705
 DG6  P   O1P   deloc   1.523  0.020  1.523
 DG6  P   O2P   deloc   1.526  0.020  1.526
 DG6  P   O3P   deloc   1.525  0.020  1.525

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
 DG6  HC12  C1  HC11  106.81  3.000
 DG6  HC12  C1  C2    109.95  3.000
 DG6  HC11  C1  C2    109.27  3.000
 DG6  HC12  C1  O1    111.11  3.000
 DG6  HC11  C1  O1    111.23  3.000
 DG6  C2    C1  O1    108.46  3.000
 DG6  HO1   O1  C1    108.03  3.000
 DG6  HC22  C2  HC21  106.70  3.000
 DG6  HC22  C2  C3    108.63  3.000
 DG6  HC21  C2  C3    109.93  3.000
 DG6  HC22  C2  C1    108.99  3.000
 DG6  HC21  C2  C1    109.75  3.000
 DG6  C3    C2  C1    112.66  3.000
 DG6  HC3   C3  C4    107.45  3.000
 DG6  HC3   C3  O3    105.78  3.000
 DG6  C4    C3  O3    111.67  3.000
 DG6  HC3   C3  C2    108.27  3.000
 DG6  C4    C3  C2    111.43  3.000
 DG6  O3    C3  C2    111.91  3.000
 DG6  HO3   O3  C3    108.67  3.000
 DG6  HC4   C4  C5    108.55  3.000
 DG6  HC4   C4  O4    105.66  3.000
 DG6  C5    C4  O4    110.68  3.000
 DG6  HC4   C4  C3    107.08  3.000
 DG6  C5    C4  C3    112.92  3.000
 DG6  O4    C4  C3    111.57  3.000
 DG6  HO4   O4  C4    108.82  3.000
 DG6  HC5   C5  C6    108.61  3.000
 DG6  HC5   C5  O5    105.57  3.000
 DG6  C6    C5  O5    111.53  3.000
 DG6  HC5   C5  C4    107.92  3.000
 DG6  C6    C5  C4    111.45  3.000
 DG6  O5    C5  C4    111.48  3.000
 DG6  HO5   O5  C5    108.18  3.000
 DG6  HC62  C6  HC61  106.10  3.000
 DG6  HC62  C6  O6    111.68  3.000
 DG6  HC61  C6  O6    111.78  3.000
 DG6  HC62  C6  C5    108.07  3.000
 DG6  HC61  C6  C5    109.31  3.000
 DG6  O6    C6  C5    109.77  3.000
 DG6  P     O6  C6    117.10  3.000
 DG6  O3P   P   O2P   114.05  3.000
 DG6  O3P   P   O1P   114.90  3.000
 DG6  O2P   P   O1P   115.16  3.000
 DG6  O3P   P   O6    105.08  3.000
 DG6  O2P   P   O6    104.89  3.000
 DG6  O1P   P   O6    100.64  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
 DG6  Var_01  C3   C2  C1  O1   178.56  30.0  3
 DG6  Var_02  O1P  P   O6  C6  -176.57  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
 DG6  chir_01  C3  C2  O3  C4  negativ
 DG6  chir_02  C4  O4  C3  C5  negativ
 DG6  chir_03  C5  O5  C4  C6  negativ

