# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:08:26 2019
#
#   Ligand name: 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose
#   Random seed: 3628800
#   SMILES string: C[C@@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)O[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
H2P        H2P '1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose' saccharide 30 17 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_H2P
#
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
H2P         C1     C   CT     0    .      -0.3488   -0.3992   -1.0020
H2P         C2     C   CH1    0    .       1.1740   -0.4003   -1.0476
H2P         C3     C   CH1    0    .       1.7720   -0.3732    0.3102
H2P         C4     C   CH1    0    .       1.2327    0.7513    1.1392
H2P         C5     C   CH1    0    .      -0.2976    0.7526    1.1805
H2P         C6     C   CH2    0    .      -0.7623    1.9857    1.8905
H2P         C7     C   CH3    0    .      -0.8846   -0.2597   -2.4252
H2P         O1     O   O2     0    .      -0.7744   -1.5782   -0.4774
H2P         O2     O   OH1    0    .       1.6180   -1.5902   -1.7276
H2P         O3     O   OH1    0    .       3.2125   -0.2151    0.1854
H2P         O4     O   OH1    0    .       1.7304    0.6216    2.4727
H2P         O5     O   O2     0    .      -0.8885    0.7275   -0.1680
H2P         O6     O   OH1    0    .      -2.1624    2.0227    1.8941
H2P         P      P   P      0    .      -2.3249   -2.0541   -0.7706
H2P         OP1    O   O      0    .      -2.7678   -3.0168    0.3052
H2P         OP2    O   OP    -1    .      -2.3964   -2.7355   -2.1162
H2P         OP3    O   OP    -1    .      -3.2310   -0.8462   -0.7693
H2P         H2     H   HCH1   0    .       1.5093    0.4715   -1.5963
H2P         H3     H   HCH1   0    .       1.5566   -1.3110    0.8077
H2P         H4     H   HCH1   0    .       1.5732    1.6906    0.7203
H2P         H5     H   HCH1   0    .      -0.6335   -0.1210    1.7260
H2P         H61    H   HCH2   0    .      -0.3787    2.8629    1.3805
H2P         H62    H   HCH2   0    .      -0.3983    1.9735    2.9123
H2P         H71    H   HCH3   0    .      -0.7754   -1.2059   -2.9475
H2P         H72    H   HCH3   0    .      -0.3248    0.5098   -2.9490
H2P         H73    H   HCH3   0    .      -1.9347    0.0161   -2.3913
H2P         HO2    H   HOH1   0    .       2.3513   -1.3797   -2.2840
H2P         HO3    H   HOH1   0    .       3.6471   -0.9166    0.6443
H2P         HO4    H   HOH1   0    .       2.3645    1.3011    2.6395
H2P         HO6    H   HOH1   0    .      -2.4575    2.7159    2.4636
#
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
H2P   C1      C2    single        1.523 0.020     1.523
H2P   C1      C7    single        1.527 0.020     1.527
H2P   C1      O1    single        1.359 0.020     1.359
H2P   C1      O5    single        1.502 0.020     1.502
H2P   C2      C3    single        1.484 0.020     1.484
H2P   C2      O2    single        1.441 0.020     1.441
H2P   C2      H2    single        0.970 0.020     1.090
H2P   C3      C4    single        1.497 0.020     1.497
H2P   C3      O3    single        1.454 0.020     1.454
H2P   C3      H3    single        0.970 0.020     1.090
H2P   C4      C5    single        1.531 0.020     1.531
H2P   C4      O4    single        1.429 0.020     1.429
H2P   C4      H4    single        0.970 0.020     1.090
H2P   C5      C6    single        1.497 0.020     1.497
H2P   C5      O5    single        1.473 0.020     1.473
H2P   C5      H5    single        0.970 0.020     1.090
H2P   C6      O6    single        1.401 0.020     1.401
H2P   C6      H61   single        0.970 0.020     1.090
H2P   C6      H62   single        0.970 0.020     1.090
H2P   C7      H71   single        0.970 0.020     1.090
H2P   C7      H72   single        0.970 0.020     1.090
H2P   C7      H73   single        0.970 0.020     1.090
H2P   O1      P     single        1.648 0.020     1.648
H2P   O2      HO2   single        0.850 0.020     0.980
H2P   O3      HO3   single        0.850 0.020     0.980
H2P   O4      HO4   single        0.850 0.020     0.980
H2P   O6      HO6   single        0.850 0.020     0.980
H2P   P       OP1   deloc         1.510 0.020     1.510
H2P   P       OP2   deloc         1.510 0.020     1.510
H2P   P       OP3   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
H2P   O5      C1      O1          108.91 3.000
H2P   O5      C1      C7          108.84 3.000
H2P   O1      C1      C7          109.22 3.000
H2P   O5      C1      C2          112.11 3.000
H2P   O1      C1      C2          108.91 3.000
H2P   C7      C1      C2          108.84 3.000
H2P   H2      C2      O2          109.28 3.000
H2P   H2      C2      C3          108.90 3.000
H2P   O2      C2      C3          108.83 3.000
H2P   H2      C2      C1          108.90 3.000
H2P   O2      C2      C1          108.83 3.000
H2P   C3      C2      C1          112.05 3.000
H2P   H3      C3      O3          109.30 3.000
H2P   H3      C3      C4          108.92 3.000
H2P   O3      C3      C4          108.82 3.000
H2P   H3      C3      C2          108.92 3.000
H2P   O3      C3      C2          108.82 3.000
H2P   C4      C3      C2          112.03 3.000
H2P   H4      C4      O4          109.27 3.000
H2P   H4      C4      C5          108.89 3.000
H2P   O4      C4      C5          108.84 3.000
H2P   H4      C4      C3          108.89 3.000
H2P   O4      C4      C3          108.84 3.000
H2P   C5      C4      C3          112.06 3.000
H2P   H5      C5      O5          108.84 3.000
H2P   H5      C5      C6          109.22 3.000
H2P   O5      C5      C6          108.90 3.000
H2P   H5      C5      C4          108.84 3.000
H2P   O5      C5      C4          112.11 3.000
H2P   C6      C5      C4          108.90 3.000
H2P   H62     C6      H61         109.47 3.000
H2P   H62     C6      O6          109.47 3.000
H2P   H61     C6      O6          109.47 3.000
H2P   H62     C6      C5          109.47 3.000
H2P   H61     C6      C5          109.47 3.000
H2P   O6      C6      C5          109.47 3.000
H2P   H73     C7      H72         109.47 3.000
H2P   H73     C7      H71         109.47 3.000
H2P   H72     C7      H71         109.47 3.000
H2P   H73     C7      C1          109.47 3.000
H2P   H72     C7      C1          109.47 3.000
H2P   H71     C7      C1          109.47 3.000
H2P   P       O1      C1          118.46 3.000
H2P   HO2     O2      C2          109.47 3.000
H2P   HO3     O3      C3          109.47 3.000
H2P   HO4     O4      C4          109.47 3.000
H2P   C5      O5      C1          112.15 3.000
H2P   HO6     O6      C6          109.47 3.000
H2P   OP3     P       OP2         109.47 3.000
H2P   OP3     P       OP1         109.47 3.000
H2P   OP2     P       OP1         109.47 3.000
H2P   OP3     P       O1          109.47 3.000
H2P   OP2     P       O1          109.47 3.000
H2P   OP1     P       O1          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
H2P Var_01         OP1     P       O1      C1         -156.69  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
H2P chir_01   C1      C2      O1      O5    negativ
H2P chir_02   C2      O2      C1      C3    negativ
H2P chir_03   C3      O3      C2      C4    positiv
H2P chir_04   C4      O4      C5      C3    positiv
H2P chir_05   C5      O5      C4      C6    negativ
