# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 10:50:51 2019
#
#   Ligand name: 4-O-phosphono-D-glycero-beta-D-manno-heptopyranose
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[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
GPH        GPH '4-O-phosphono-D-glycero-beta-D-manno-heptopyranose' d-saccharide 31 18 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_GPH
#
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
GPH         C1     C   CH1    0    .      -0.7188    0.4786   -1.9323
GPH         C2     C   CH1    0    .       0.8003    0.5420   -1.9799
GPH         C3     C   CH1    0    .       1.4017    0.5452   -0.6205
GPH         C4     C   CH1    0    .       0.9129   -0.5926    0.2099
GPH         C5     C   CH1    0    .      -0.6170   -0.6579    0.2531
GPH         C6     C   CH1    0    .      -1.1388    0.5366    1.0117
GPH         C7     C   CH2    0    .      -2.6091    0.2734    1.4456
GPH         O2     O   OH1    0    .       1.1968    1.7477   -2.6660
GPH         O3     O   OH1    0    .       1.0536    1.8053    0.0522
GPH         O4     O   O2     0    .       1.4224   -1.8376   -0.3467
GPH         P1     P   P      0    .       2.4183   -2.8038    0.6159
GPH         O8     O   O      0    .       3.5933   -1.9862    1.1086
GPH         O9     O   OP    -1    .       1.6316   -3.3170    1.7990
GPH         O10    O   OP    -1    .       2.9272   -3.9801   -0.2030
GPH         O5     O   O2     0    .      -1.2095   -0.6637   -1.0935
GPH         O6     O   OH1    0    .      -0.3497    0.7516    2.1425
GPH         O7     O   OH1    0    .      -2.6295   -0.2557    2.7753
GPH        O101    O   OH1    0    .      -1.1957    1.6449   -1.4153
GPH         H1     H   HCH1   0    .      -1.1011    0.3557   -2.9574
GPH         H2     H   HCH1   0    .       1.1738   -0.3273   -2.5309
GPH         H3     H   HCH1   0    .       2.4791    0.4750   -0.7132
GPH         H4     H   HCH1   0    .       1.2848   -0.4751    1.2149
GPH         H5     H   HCH1   0    .      -0.9123   -1.5622    0.7667
GPH         H6     H   HCH1   0    .      -1.1027    1.4116    0.3763
GPH         H7     H   HCH2   0    .      -3.1674    1.2095    1.4184
GPH         H7A    H   HCH2   0    .      -3.0599   -0.4314    0.7749
GPH         HO2    H   HOH1   0    .       1.6183    1.5284   -3.4540
GPH         HO3    H   HOH1   0    .       1.8487    2.2775    0.2736
GPH         HO6    H   HOH1   0    .      -0.7223    1.4462    2.6576
GPH         HO7    H   HOH1   0    .      -3.5251   -0.2502    3.1070
GPH         H15    H   HOH1   0    .      -1.7038    2.1119   -2.0907
#
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
GPH   C1      C2    single        1.521 0.020     1.521
GPH   C1      O5    single        1.500 0.020     1.500
GPH   C1     O101   single        1.362 0.020     1.362
GPH   C1      H1    single        0.970 0.020     1.090
GPH   C2      C3    single        1.487 0.020     1.487
GPH   C2      O2    single        1.443 0.020     1.443
GPH   C2      H2    single        0.970 0.020     1.090
GPH   C3      C4    single        1.491 0.020     1.491
GPH   C3      O3    single        1.470 0.020     1.470
GPH   C3      H3    single        0.970 0.020     1.090
GPH   C4      C5    single        1.532 0.020     1.532
GPH   C4      O4    single        1.456 0.020     1.456
GPH   C4      H4    single        0.970 0.020     1.090
GPH   C5      C6    single        1.508 0.020     1.508
GPH   C5      O5    single        1.471 0.020     1.471
GPH   C5      H5    single        0.970 0.020     1.090
GPH   C6      C7    single        1.555 0.020     1.555
GPH   C6      O6    single        1.396 0.020     1.396
GPH   C6      H6    single        0.970 0.020     1.090
GPH   C7      O7    single        1.431 0.020     1.431
GPH   C7      H7    single        0.970 0.020     1.090
GPH   C7      H7A   single        0.970 0.020     1.090
GPH   O2      HO2   single        0.850 0.020     0.980
GPH   O3      HO3   single        0.850 0.020     0.980
GPH   O4      P1    single        1.689 0.020     1.689
GPH   P1      O8    deloc         1.514 0.020     1.514
GPH   P1      O9    deloc         1.511 0.020     1.511
GPH   P1      O10   deloc         1.521 0.020     1.521
GPH   O6      HO6   single        0.850 0.020     0.980
GPH   O7      HO7   single        0.850 0.020     0.980
GPH  O101     H15   single        0.850 0.020     0.980
#
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
GPH   H1      C1     O101         109.11 3.000
GPH   H1      C1      O5          108.79 3.000
GPH  O101     C1      O5          108.98 3.000
GPH   H1      C1      C2          108.80 3.000
GPH  O101     C1      C2          109.02 3.000
GPH   O5      C1      C2          112.09 3.000
GPH   H2      C2      O2          109.30 3.000
GPH   H2      C2      C3          108.90 3.000
GPH   O2      C2      C3          108.78 3.000
GPH   H2      C2      C1          108.86 3.000
GPH   O2      C2      C1          108.91 3.000
GPH   C3      C2      C1          112.05 3.000
GPH   H3      C3      O3          109.27 3.000
GPH   H3      C3      C4          108.92 3.000
GPH   O3      C3      C4          108.76 3.000
GPH   H3      C3      C2          108.89 3.000
GPH   O3      C3      C2          108.93 3.000
GPH   C4      C3      C2          112.03 3.000
GPH   H4      C4      O4          109.20 3.000
GPH   H4      C4      C5          108.84 3.000
GPH   O4      C4      C5          108.89 3.000
GPH   H4      C4      C3          108.84 3.000
GPH   O4      C4      C3          108.96 3.000
GPH   C5      C4      C3          112.07 3.000
GPH   H5      C5      O5          108.75 3.000
GPH   H5      C5      C6          109.21 3.000
GPH   O5      C5      C6          108.91 3.000
GPH   H5      C5      C4          108.78 3.000
GPH   O5      C5      C4          112.12 3.000
GPH   C6      C5      C4          109.02 3.000
GPH   H6      C6      O6          109.41 3.000
GPH   H6      C6      C7          109.40 3.000
GPH   O6      C6      C7          109.54 3.000
GPH   H6      C6      C5          109.49 3.000
GPH   O6      C6      C5          109.51 3.000
GPH   C7      C6      C5          109.47 3.000
GPH   H7A     C7      H7          109.48 3.000
GPH   H7A     C7      O7          109.40 3.000
GPH   H7      C7      O7          109.47 3.000
GPH   H7A     C7      C6          109.52 3.000
GPH   H7      C7      C6          109.38 3.000
GPH   O7      C7      C6          109.59 3.000
GPH   HO2     O2      C2          109.51 3.000
GPH   HO3     O3      C3          109.52 3.000
GPH   P1      O4      C4          118.54 3.000
GPH   O10     P1      O9          109.46 3.000
GPH   O10     P1      O8          109.46 3.000
GPH   O9      P1      O8          109.44 3.000
GPH   O10     P1      O4          109.44 3.000
GPH   O9      P1      O4          109.49 3.000
GPH   O8      P1      O4          109.53 3.000
GPH   C5      O5      C1          112.16 3.000
GPH   HO6     O6      C6          109.46 3.000
GPH   HO7     O7      C7          109.51 3.000
GPH   H15    O101     C1          109.44 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
GPH Var_01         O8      P1      O4      C4          -55.05  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
GPH chir_01   C1      C2      O5     O101   negativ
GPH chir_02   C2      O2      C1      C3    positiv
GPH chir_03   C3      O3      C2      C4    positiv
GPH chir_04   C4      O4      C3      C5    negativ
GPH chir_05   C5      O5      C6      C4    positiv
GPH chir_06   C6      O6      C5      C7    negativ
