# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 10:41:40 2019
#
#   Ligand name: 2-deoxy-6-O-phosphono-alpha-D-arabino-hexopyranose
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@H](O)[C@H](O)[C@@H](CO[P](O)(O)=O)O1
#
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
D6G        D6G '2-deoxy-6-O-phosphono-alpha-D-arabino-hexopyranose' saccharide 26 15 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_D6G
#
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
D6G         C1     C   CH1    0    .      -0.2844   -1.1685   -1.8482
D6G         C2     C   CH2    0    .       1.2317   -1.1427   -1.8511
D6G         C3     C   CH1    0    .       1.7887   -1.1188   -0.4837
D6G         C4     C   CH1    0    .       1.2061   -0.0106    0.3418
D6G         C5     C   CH1    0    .      -0.3179   -0.0361    0.3404
D6G         C6     C   CH2    0    .      -0.8263    1.1886    1.0523
D6G         O1     O   OH1    0    .      -0.7043   -2.3628   -1.3455
D6G         O3     O   OH1    0    .       3.2319   -0.9341   -0.5672
D6G         O4     O   OH1    0    .       1.6695   -0.1452    1.6894
D6G         O5     O   O2     0    .      -0.8679   -0.0581   -1.0179
D6G         O6     O   O2     0    .      -2.2009    1.3206    0.8294
D6G         P      P   P      0    .      -3.0280    2.4681    1.6772
D6G         O1P    O   O      0    .      -2.9733    2.1422    3.1508
D6G         O2P    O   OP    -1    .      -2.4011    3.8207    1.4373
D6G         O3P    O   OP    -1    .      -4.4671    2.4921    1.2201
D6G         H1     H   HCH1   0    .      -0.6379   -1.0664   -2.8670
D6G         H21    H   HCH2   0    .       1.5968   -2.0267   -2.3634
D6G         H22    H   HCH2   0    .       1.5665   -0.2580   -2.3818
D6G         H3     H   HCH1   0    .       1.5762   -2.0653   -0.0013
D6G         H4     H   HCH1   0    .       1.5415    0.9385   -0.0585
D6G         H5     H   HCH1   0    .      -0.6535   -0.9208    0.8684
D6G         H61    H   HCH2   0    .      -0.3128    2.0659    0.6741
D6G         H62    H   HCH2   0    .      -0.6403    1.0915    2.1166
D6G         HO1    H   HOH1   0    .      -1.2145   -2.8169   -1.9976
D6G         HO3    H   HOH1   0    .       3.6642   -1.7604   -0.4185
D6G         HO4    H   HOH1   0    .       2.4571    0.3629    1.8038
#
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
D6G   C1      C2    single        1.516 0.020     1.516
D6G   C1      O1    single        1.362 0.020     1.362
D6G   C1      O5    single        1.504 0.020     1.504
D6G   C1      H1    single        0.970 0.020     1.090
D6G   C2      C3    single        1.477 0.020     1.477
D6G   C2      H21   single        0.970 0.020     1.090
D6G   C2      H22   single        0.970 0.020     1.090
D6G   C3      C4    single        1.500 0.020     1.500
D6G   C3      O3    single        1.457 0.020     1.457
D6G   C3      H3    single        0.970 0.020     1.090
D6G   C4      C5    single        1.524 0.020     1.524
D6G   C4      O4    single        1.431 0.020     1.431
D6G   C4      H4    single        0.970 0.020     1.090
D6G   C5      C6    single        1.505 0.020     1.505
D6G   C5      O5    single        1.466 0.020     1.466
D6G   C5      H5    single        0.970 0.020     1.090
D6G   C6      O6    single        1.399 0.020     1.399
D6G   C6      H61   single        0.970 0.020     1.090
D6G   C6      H62   single        0.970 0.020     1.090
D6G   O1      HO1   single        0.850 0.020     0.980
D6G   O3      HO3   single        0.850 0.020     0.980
D6G   O4      HO4   single        0.850 0.020     0.980
D6G   O6      P     single        1.649 0.020     1.649
D6G   P       O1P   deloc         1.510 0.020     1.510
D6G   P       O2P   deloc         1.510 0.020     1.510
D6G   P       O3P   deloc         1.510 0.020     1.510
#
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
D6G   H1      C1      O5          108.84 3.000
D6G   H1      C1      O1          109.22 3.000
D6G   O5      C1      O1          108.90 3.000
D6G   H1      C1      C2          108.84 3.000
D6G   O5      C1      C2          112.11 3.000
D6G   O1      C1      C2          108.90 3.000
D6G   H22     C2      H21         109.25 3.000
D6G   H22     C2      C3          108.87 3.000
D6G   H21     C2      C3          108.87 3.000
D6G   H22     C2      C1          108.87 3.000
D6G   H21     C2      C1          108.87 3.000
D6G   C3      C2      C1          112.06 3.000
D6G   H3      C3      O3          109.30 3.000
D6G   H3      C3      C4          108.92 3.000
D6G   O3      C3      C4          108.82 3.000
D6G   H3      C3      C2          108.92 3.000
D6G   O3      C3      C2          108.82 3.000
D6G   C4      C3      C2          112.03 3.000
D6G   H4      C4      O4          109.27 3.000
D6G   H4      C4      C5          108.90 3.000
D6G   O4      C4      C5          108.84 3.000
D6G   H4      C4      C3          108.90 3.000
D6G   O4      C4      C3          108.84 3.000
D6G   C5      C4      C3          112.06 3.000
D6G   H5      C5      O5          108.85 3.000
D6G   H5      C5      C6          109.23 3.000
D6G   O5      C5      C6          108.89 3.000
D6G   H5      C5      C4          108.84 3.000
D6G   O5      C5      C4          112.11 3.000
D6G   C6      C5      C4          108.89 3.000
D6G   H62     C6      H61         109.47 3.000
D6G   H62     C6      O6          109.47 3.000
D6G   H61     C6      O6          109.47 3.000
D6G   H62     C6      C5          109.47 3.000
D6G   H61     C6      C5          109.47 3.000
D6G   O6      C6      C5          109.47 3.000
D6G   HO1     O1      C1          109.47 3.000
D6G   HO3     O3      C3          109.47 3.000
D6G   HO4     O4      C4          109.47 3.000
D6G   C5      O5      C1          112.15 3.000
D6G   P       O6      C6          118.46 3.000
D6G   O3P     P       O2P         109.47 3.000
D6G   O3P     P       O1P         109.47 3.000
D6G   O2P     P       O1P         109.47 3.000
D6G   O3P     P       O6          109.47 3.000
D6G   O2P     P       O6          109.47 3.000
D6G   O1P     P       O6          109.47 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
D6G Var_01         O1P     P       O6      C6          -63.46  30.0 3
D6G Var_02         H61     C6      O6      P           -68.41  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
D6G chir_01   C1      C2      O1      O5    negativ
D6G chir_02   C3      O3      C4      C2    negativ
D6G chir_03   C4      O4      C3      C5    negativ
D6G chir_04   C5      O5      C4      C6    negativ
