# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 12:48:10 2019
#
#   Ligand name: (2R,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H]1O[C@](O)(C[C@H](O)[C@H]1O)C(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
KDM        KDM '(2R,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid' d-saccharide 33 18 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_KDM
#
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
KDM         C1     C   CT     0    .      -0.0641   -0.0559   -2.2122
KDM         C10    C   C      0    .      -0.5581    0.1229   -3.6456
KDM         C2     C   CH2    0    .       1.4509   -0.1001   -2.2188
KDM         C3     C   CH1    0    .       2.0109   -0.1135   -0.8534
KDM         C4     C   CH1    0    .       1.4819    1.0136   -0.0171
KDM         C5     C   CH1    0    .      -0.0410    1.0586   -0.0149
KDM         C6     C   CH1    0    .      -0.5648   -0.1550    0.7135
KDM         C7     C   CH1    0    .      -1.1584    0.2738    2.0584
KDM         C9     C   CH2    0    .      -1.6708   -0.9548    2.8030
KDM         O4     O   OH1    0    .       1.9804    2.2504   -0.5392
KDM         O8     O   O      0    .      -0.2258   -0.7045   -4.5335
KDM         O9     O   OC    -1    .      -1.2975    1.0993   -3.9397
KDM         O3     O   OH1    0    .       1.6626   -1.3763   -0.2149
KDM         O5     O   O2     0    .      -0.5941    1.0735   -1.3712
KDM         O6     O   OH1    0    .      -1.5617   -0.7739   -0.0630
KDM         O7     O   OH1    0    .      -0.1725    0.9047    2.8231
KDM         O10    O   OH1    0    .      -1.8003   -0.6550    4.1655
KDM         O1     O   OH1    0    .      -0.5378   -1.2339   -1.7184
KDM        H21C    H   HCH2   0    .       1.7735   -0.9952   -2.7391
KDM        H22C    H   HCH2   0    .       1.8252    0.7731   -2.7430
KDM         H1     H   HOH1   0    .      -0.8541   -1.7693   -2.4299
KDM         H3     H   HCH1   0    .       3.0893   -0.0290   -0.9152
KDM         H4     H   HCH1   0    .       1.8308    0.8888    1.0012
KDM         HA     H   HOH1   0    .       2.4368   -1.9104   -0.1303
KDM         H5     H   HCH1   0    .      -0.3637    1.9528    0.5042
KDM         HB     H   HOH1   0    .       2.5122    2.6765    0.1144
KDM         H6     H   HCH1   0    .       0.2455   -0.8520    0.8826
KDM         H7     H   HCH1   0    .      -1.9781    0.9609    1.8886
KDM         HC     H   HOH1   0    .      -2.4128   -0.5443    0.2760
KDM        H91C    H   HCH2   0    .      -2.6372   -1.2433    2.4027
KDM        H92C    H   HCH2   0    .      -0.9688   -1.7724    2.6777
KDM         HD     H   HOH1   0    .      -0.5746    1.5442    3.3895
KDM         H10    H   HOH1   0    .      -2.2638   -1.3541    4.5990
#
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
KDM   C1      C10   single        1.527 0.020     1.527
KDM   C1      C2    single        1.516 0.020     1.516
KDM   C1      O5    single        1.505 0.020     1.505
KDM   C1      O1    single        1.362 0.020     1.362
KDM   C10     O9    deloc         1.260 0.020     1.260
KDM   C10     O8    deloc         1.258 0.020     1.258
KDM   C2      C3    single        1.476 0.020     1.476
KDM   C3      C4    single        1.500 0.020     1.500
KDM   C3      O3    single        1.457 0.020     1.457
KDM   C4      C5    single        1.524 0.020     1.524
KDM   C4      O4    single        1.432 0.020     1.432
KDM   C5      C6    single        1.509 0.020     1.509
KDM   C5      O5    single        1.465 0.020     1.465
KDM   C6      C7    single        1.531 0.020     1.531
KDM   C6      O6    single        1.407 0.020     1.407
KDM   C7      C9    single        1.525 0.020     1.525
KDM   C7      O7    single        1.398 0.020     1.398
KDM   C9      O10   single        1.401 0.020     1.401
KDM   C2     H21C   single        0.970 0.020     1.090
KDM   C2     H22C   single        0.970 0.020     1.090
KDM   O1      H1    single        0.850 0.020     0.980
KDM   C3      H3    single        0.970 0.020     1.090
KDM   C4      H4    single        0.970 0.020     1.090
KDM   O3      HA    single        0.850 0.020     0.980
KDM   C5      H5    single        0.970 0.020     1.090
KDM   O4      HB    single        0.850 0.020     0.980
KDM   C6      H6    single        0.970 0.020     1.090
KDM   C7      H7    single        0.970 0.020     1.090
KDM   O6      HC    single        0.850 0.020     0.980
KDM   C9     H91C   single        0.970 0.020     1.090
KDM   C9     H92C   single        0.970 0.020     1.090
KDM   O7      HD    single        0.850 0.020     0.980
KDM   O10     H10   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
KDM   O1      C1      O5          108.90 3.000
KDM   O1      C1      C2          108.90 3.000
KDM   O5      C1      C2          112.11 3.000
KDM   O1      C1      C10         109.22 3.000
KDM   O5      C1      C10         108.84 3.000
KDM   C2      C1      C10         108.84 3.000
KDM   O9      C10     O8          120.00 3.000
KDM   O8      C10     C1          120.00 3.000
KDM   O9      C10     C1          120.00 3.000
KDM  H22C     C2     H21C         109.25 3.000
KDM  H22C     C2      C3          108.87 3.000
KDM  H21C     C2      C3          108.87 3.000
KDM  H22C     C2      C1          108.87 3.000
KDM  H21C     C2      C1          108.87 3.000
KDM   C3      C2      C1          112.06 3.000
KDM   H3      C3      O3          109.30 3.000
KDM   H3      C3      C4          108.92 3.000
KDM   O3      C3      C4          108.82 3.000
KDM   H3      C3      C2          108.92 3.000
KDM   O3      C3      C2          108.81 3.000
KDM   C4      C3      C2          112.03 3.000
KDM   H4      C4      O4          109.27 3.000
KDM   H4      C4      C5          108.89 3.000
KDM   O4      C4      C5          108.84 3.000
KDM   H4      C4      C3          108.89 3.000
KDM   O4      C4      C3          108.84 3.000
KDM   C5      C4      C3          112.06 3.000
KDM   H5      C5      O5          108.84 3.000
KDM   H5      C5      C6          109.22 3.000
KDM   O5      C5      C6          108.90 3.000
KDM   H5      C5      C4          108.84 3.000
KDM   O5      C5      C4          112.11 3.000
KDM   C6      C5      C4          108.90 3.000
KDM   H6      C6      O6          109.48 3.000
KDM   H6      C6      C7          109.47 3.000
KDM   O6      C6      C7          109.47 3.000
KDM   H6      C6      C5          109.48 3.000
KDM   O6      C6      C5          109.47 3.000
KDM   C7      C6      C5          109.46 3.000
KDM   H7      C7      O7          109.47 3.000
KDM   H7      C7      C9          109.47 3.000
KDM   O7      C7      C9          109.47 3.000
KDM   H7      C7      C6          109.47 3.000
KDM   O7      C7      C6          109.47 3.000
KDM   C9      C7      C6          109.47 3.000
KDM  H92C     C9     H91C         109.47 3.000
KDM  H92C     C9      O10         109.47 3.000
KDM  H91C     C9      O10         109.47 3.000
KDM  H92C     C9      C7          109.47 3.000
KDM  H91C     C9      C7          109.47 3.000
KDM   O10     C9      C7          109.47 3.000
KDM   HB      O4      C4          109.47 3.000
KDM   HA      O3      C3          109.47 3.000
KDM   C5      O5      C1          112.15 3.000
KDM   HC      O6      C6          109.47 3.000
KDM   HD      O7      C7          109.47 3.000
KDM   H10     O10     C9          109.47 3.000
KDM   H1      O1      C1          109.47 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
KDM chir_01   C1      C2      O5      O1    positiv
KDM chir_02   C3      O3      C2      C4    negativ
KDM chir_03   C4      O4      C3      C5    positiv
KDM chir_04   C5      O5      C6      C4    negativ
KDM chir_05   C6      O6      C5      C7    negativ
KDM chir_06   C7      O7      C6      C9    negativ
#
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
KDM plan-1     C1 0.020
KDM plan-1    C10 0.020
KDM plan-1     O8 0.020
KDM plan-1     O9 0.020
