# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 12:57:34 2019
#
#   Ligand name: 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[P](O)(O)=O)[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
Z9M        Z9M '2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose' saccharide 28 16 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_Z9M
#
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
Z9M         N1     N   NH2    0    .      -2.9862   -0.4422   -1.0575
Z9M         P1     P   P      0    .       1.2515   -1.3460    2.8187
Z9M         O6     O   OH1    0    .       2.8278    2.1010   -0.9320
Z9M         O1     O   OH1    0    .      -1.2873    0.6884   -3.0701
Z9M         O3     O   OH1    0    .      -1.4534   -1.6673    1.0504
Z9M         C1     C   CH1    0    .      -1.0001    0.8320   -1.7389
Z9M         O4     O   O2     0    .       0.6790   -0.0412    1.9886
Z9M         C2     C   CH1    0    .      -1.4986   -0.4059   -0.9867
Z9M         O5     O   O2     0    .       0.4715    1.0325   -1.5789
Z9M         C3     C   CH1    0    .      -1.0853   -0.3948    0.4430
Z9M         O9     O   O      0    .       1.7911   -0.8945    4.1503
Z9M         C4     C   CH1    0    .       0.3765   -0.1980    0.5980
Z9M         O7     O   OP    -1    .       0.1326   -2.3304    3.0375
Z9M         C5     C   CH1    0    .       0.8785    1.0483   -0.1662
Z9M         O8     O   OP    -1    .       2.3553   -2.0059    2.0242
Z9M         C6     C   CH2    0    .       2.3503    1.0907   -0.0944
Z9M        H11N    H   HNH2   0    .      -3.2738   -1.1346   -1.7284
Z9M        H12N    H   HNH2   0    .      -3.3644   -0.6769   -0.1426
Z9M         H1     H   HOH1   0    .      -1.4025    1.5478   -3.4646
Z9M         H3O    H   HOH1   0    .      -2.0678   -2.1262    0.4815
Z9M         H11    H   HCH1   0    .      -1.5112    1.6981   -1.3583
Z9M         H21    H   HCH1   0    .      -1.1003   -1.2804   -1.4559
Z9M         H31    H   HCH1   0    .      -1.6089    0.4145    0.9562
Z9M         H41    H   HCH1   0    .       0.8905   -1.0752    0.2157
Z9M         H51    H   HCH1   0    .       0.4659    1.9502    0.3127
Z9M         H61    H   HCH2   0    .       2.7574    0.1311   -0.4135
Z9M         H62    H   HCH2   0    .       2.6567    1.2930    0.9271
Z9M         H1O    H   HOH1   0    .       3.7554    2.1917   -0.8160
#
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
Z9M   C2      N1    single        1.490 0.020     1.490
Z9M   N1     H11N   single        0.890 0.020     1.040
Z9M   N1     H12N   single        0.890 0.020     1.040
Z9M   O9      P1    deloc         1.506 0.020     1.506
Z9M   P1      O7    deloc         1.506 0.020     1.506
Z9M   P1      O4    single        1.649 0.020     1.649
Z9M   P1      O8    deloc         1.512 0.020     1.512
Z9M   C6      O6    single        1.397 0.020     1.397
Z9M   C1      O1    single        1.369 0.020     1.369
Z9M   O1      H1    single        0.850 0.020     0.980
Z9M   C3      O3    single        1.457 0.020     1.457
Z9M   O3      H3O   single        0.850 0.020     0.980
Z9M   O5      C1    single        1.494 0.020     1.494
Z9M   C1      C2    single        1.532 0.020     1.532
Z9M   C1      H11   single        0.970 0.020     1.090
Z9M   O4      C4    single        1.432 0.020     1.432
Z9M   C3      C2    single        1.488 0.020     1.488
Z9M   C2      H21   single        0.970 0.020     1.090
Z9M   C5      O5    single        1.470 0.020     1.470
Z9M   C4      C3    single        1.483 0.020     1.483
Z9M   C3      H31   single        0.970 0.020     1.090
Z9M   C4      C5    single        1.546 0.020     1.546
Z9M   C4      H41   single        0.970 0.020     1.090
Z9M   C6      C5    single        1.474 0.020     1.474
Z9M   C5      H51   single        0.970 0.020     1.090
Z9M   C6      H61   single        0.970 0.020     1.090
Z9M   C6      H62   single        0.970 0.020     1.090
Z9M   O6      H1O   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
Z9M  H12N     N1     H11N         109.55 3.000
Z9M  H12N     N1      C2          109.52 3.000
Z9M  H11N     N1      C2          109.51 3.000
Z9M   O8      P1      O7          109.48 3.000
Z9M   O8      P1      O9          109.51 3.000
Z9M   O7      P1      O9          109.49 3.000
Z9M   O8      P1      O4          109.54 3.000
Z9M   O7      P1      O4          109.41 3.000
Z9M   O9      P1      O4          109.41 3.000
Z9M   H1O     O6      C6          109.48 3.000
Z9M   H1      O1      C1          109.47 3.000
Z9M   H3O     O3      C3          109.50 3.000
Z9M   H11     C1      O5          108.80 3.000
Z9M   H11     C1      C2          108.81 3.000
Z9M   O5      C1      C2          112.11 3.000
Z9M   H11     C1      O1          109.20 3.000
Z9M   C2      C1      O1          108.93 3.000
Z9M   O5      C1      O1          108.95 3.000
Z9M   C4      O4      P1          118.40 3.000
Z9M   H21     C2      C3          108.91 3.000
Z9M   H21     C2      C1          108.92 3.000
Z9M   C3      C2      C1          112.05 3.000
Z9M   H21     C2      N1          109.34 3.000
Z9M   C3      C2      N1          108.86 3.000
Z9M   C1      C2      N1          108.74 3.000
Z9M   C5      O5      C1          112.15 3.000
Z9M   H31     C3      C4          108.97 3.000
Z9M   H31     C3      C2          108.89 3.000
Z9M   C4      C3      C2          112.03 3.000
Z9M   H31     C3      O3          109.27 3.000
Z9M   C4      C3      O3          108.74 3.000
Z9M   C2      C3      O3          108.89 3.000
Z9M   H41     C4      C5          108.88 3.000
Z9M   H41     C4      C3          108.81 3.000
Z9M   C5      C4      C3          112.05 3.000
Z9M   H41     C4      O4          109.29 3.000
Z9M   C5      C4      O4          108.86 3.000
Z9M   C3      C4      O4          108.92 3.000
Z9M   H51     C5      C6          109.23 3.000
Z9M   H51     C5      C4          108.88 3.000
Z9M   C6      C5      C4          108.87 3.000
Z9M   H51     C5      O5          108.84 3.000
Z9M   C6      C5      O5          108.88 3.000
Z9M   C4      C5      O5          112.11 3.000
Z9M   H62     C6      H61         109.52 3.000
Z9M   H62     C6      C5          109.45 3.000
Z9M   H61     C6      C5          109.47 3.000
Z9M   H62     C6      O6          109.45 3.000
Z9M   H61     C6      O6          109.49 3.000
Z9M   C5      C6      O6          109.45 3.000
#
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
Z9M chir_01   C1      O1      O5      C2    positiv
Z9M chir_02   C2      N1      C3      C1    positiv
Z9M chir_03   C3      O3      C2      C4    positiv
Z9M chir_04   C4      O4      C3      C5    negativ
Z9M chir_05   C5      O5      C4      C6    negativ
