# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 22:47:58 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   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
 KDN  KDN  '3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid'  D-saccharide  34  18  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDN
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
 KDN  C1    C  CT    0   0.411  -1.5981   0.8386  -0.2280
 KDN  C10   C  C     0   0.507  -1.9785   2.1067   0.5611
 KDN  C2    C  CH2   0  -0.530  -2.5568  -0.2907   0.1512
 KDN  C3    C  CH1   0  -0.003  -2.0318  -1.6323  -0.3498
 KDN  C4    C  CH1   0   0.068  -0.6160  -1.8436   0.1554
 KDN  C5    C  CH1   0   0.013   0.2587  -0.6712  -0.2805
 KDN  C6    C  CH1   0  -0.029   1.6664  -0.7388   0.3168
 KDN  C7    C  CH1   0  -0.072   2.6178   0.2856  -0.3243
 KDN  C9    C  CH2   0  -0.117   4.0209   0.1837   0.2771
 KDN  O4    O  OH1   0  -0.634  -0.0299  -3.0042  -0.3791
 KDN  O9    O  O     0  -0.479  -1.3961   2.4947   1.5391
 KDN  O8    O  OH1   0  -0.546  -3.0907   2.6396   0.0912
 KDN  O3    O  OH1   0  -0.680  -2.8070  -2.7087   0.1303
 KDN  O5    O  O2    0  -0.481  -0.2948   0.5563   0.1683
 KDN  O6    O  OH1   0  -0.653   1.6267  -0.6136   1.7201
 KDN  O7    O  OH1   0  -0.746   2.6398   0.1238  -1.7225
 KDN  O10   O  OH1   0  -0.534   4.8426   1.1943  -0.2724
 KDN  O1    O  OH1   0  -0.620  -1.6872   1.0330  -1.6020
 KDN  H21C  H  HCH2  0   0.248  -2.6534  -0.3301   1.2401
 KDN  H22C  H  HCH2  0   0.279  -3.5480  -0.0898  -0.2627
 KDN  H1    H  HOH1  0   0.475  -1.0835   1.7335  -1.8788
 KDN  H3    H  HCH1  0   0.174  -2.0062  -1.6347  -1.4496
 KDN  H4    H  HCH1  0   0.165  -0.6484  -1.8800   1.2542
 KDN  HA    H  HOH1  0   0.449  -3.6497  -2.7092  -0.3331
 KDN  H5    H  HCH1  0   0.238   0.3334  -0.6813  -1.3747
 KDN  HB    H  HOH1  0   0.462  -0.5525  -3.7638  -0.1002
 KDN  H6    H  HCH1  0   0.276   2.0632  -1.7390   0.1108
 KDN  H7    H  HCH1  0   0.251   2.2326   1.2968  -0.1499
 KDN  HC    H  HOH1  0   0.425   1.1451   0.1960   1.9287
 KDN  HD    H  HOH1  0   0.434   3.0283  -0.7336  -1.9296
 KDN  H91C  H  HCH2  0   0.114   3.9485   0.2750   1.3652
 KDN  H92C  H  HCH2  0   0.152   4.4249  -0.8203   0.0731
 KDN  H8    H  HOH1  0   0.518  -3.3638   3.3814   0.6486
 KDN  H10   H  HOH1  0   0.461   5.7314   1.0838   0.0765

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
 KDN  C1   C2    single  1.529  0.020  1.529
 KDN  C1   O1    single  1.391  0.020  1.391
 KDN  C1   O5    single  1.391  0.020  1.391
 KDN  C1   C10   single  1.541  0.020  1.541
 KDN  C2   C3    single  1.525  0.020  1.525
 KDN  C3   C4    single  1.518  0.020  1.518
 KDN  C3   O3    single  1.411  0.020  1.411
 KDN  C4   C5    single  1.526  0.020  1.526
 KDN  C4   O4    single  1.406  0.020  1.406
 KDN  C5   C6    single  1.531  0.020  1.531
 KDN  C5   O5    single  1.419  0.020  1.419
 KDN  C6   C7    single  1.538  0.020  1.538
 KDN  C6   O6    single  1.409  0.020  1.409
 KDN  C7   O7    single  1.408  0.020  1.408
 KDN  C7   C9    single  1.530  0.020  1.530
 KDN  O8   C10   single  1.320  0.020  1.320
 KDN  O9   C10   double  1.203  0.020  1.203
 KDN  O10  C9    single  1.414  0.020  1.414
 KDN  C2   H21C  single  0.970  0.020  1.090
 KDN  C2   H22C  single  0.970  0.020  1.090
 KDN  O1   H1    single  0.850  0.020  0.980
 KDN  C3   H3    single  0.970  0.020  1.090
 KDN  C4   H4    single  0.970  0.020  1.090
 KDN  O3   HA    single  0.850  0.020  0.980
 KDN  C5   H5    single  0.970  0.020  1.090
 KDN  O4   HB    single  0.850  0.020  0.980
 KDN  C6   H6    single  0.970  0.020  1.090
 KDN  C7   H7    single  0.970  0.020  1.090
 KDN  O6   HC    single  0.850  0.020  0.980
 KDN  O7   HD    single  0.850  0.020  0.980
 KDN  C9   H91C  single  0.970  0.020  1.090
 KDN  C9   H92C  single  0.970  0.020  1.090
 KDN  O8   H8    single  0.850  0.020  0.980
 KDN  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
 KDN  O1    C1   O5    111.71  3.000
 KDN  O5    C1   C2    111.53  3.000
 KDN  O1    C1   C2    107.94  3.000
 KDN  O5    C1   C10   104.62  3.000
 KDN  O1    C1   C10   112.03  3.000
 KDN  C2    C1   C10   109.02  3.000
 KDN  O8    C10  O9    124.57  3.000
 KDN  O9    C10  C1    124.21  3.000
 KDN  O8    C10  C1    110.97  3.000
 KDN  H22C  C2   H21C  107.67  3.000
 KDN  H22C  C2   C3    110.46  3.000
 KDN  H21C  C2   C3    109.01  3.000
 KDN  H22C  C2   C1    109.81  3.000
 KDN  H21C  C2   C1    109.20  3.000
 KDN  C3    C2   C1    110.63  3.000
 KDN  H3    C3   O3    110.57  3.000
 KDN  H3    C3   C4    108.10  3.000
 KDN  O3    C3   C4    107.04  3.000
 KDN  H3    C3   C2    109.77  3.000
 KDN  O3    C3   C2    111.73  3.000
 KDN  C4    C3   C2    109.52  3.000
 KDN  H4    C4   O4    111.39  3.000
 KDN  H4    C4   C5    109.12  3.000
 KDN  O4    C4   C5    106.66  3.000
 KDN  H4    C4   C3    108.04  3.000
 KDN  O4    C4   C3    112.16  3.000
 KDN  C5    C4   C3    109.42  3.000
 KDN  H5    C5   O5    110.48  3.000
 KDN  H5    C5   C6    109.04  3.000
 KDN  O5    C5   C6    105.87  3.000
 KDN  H5    C5   C4    108.47  3.000
 KDN  O5    C5   C4    110.52  3.000
 KDN  C6    C5   C4    112.44  3.000
 KDN  H6    C6   O6    106.17  3.000
 KDN  H6    C6   C7    107.80  3.000
 KDN  O6    C6   C7    111.91  3.000
 KDN  H6    C6   C5    107.46  3.000
 KDN  O6    C6   C5    111.02  3.000
 KDN  C7    C6   C5    112.14  3.000
 KDN  H7    C7   O7    105.64  3.000
 KDN  H7    C7   C9    108.74  3.000
 KDN  O7    C7   C9    111.62  3.000
 KDN  H7    C7   C6    109.32  3.000
 KDN  C9    C7   C6    111.05  3.000
 KDN  O7    C7   C6    110.31  3.000
 KDN  H92C  C9   H91C  106.53  3.000
 KDN  H92C  C9   O10   111.49  3.000
 KDN  H91C  C9   O10   111.43  3.000
 KDN  H92C  C9   C7    108.93  3.000
 KDN  H91C  C9   C7    108.94  3.000
 KDN  O10   C9   C7    109.43  3.000
 KDN  HB    O4   C4    108.35  3.000
 KDN  H8    O8   C10   110.02  3.000
 KDN  HA    O3   C3    108.53  3.000
 KDN  C5    O5   C1    116.79  3.000
 KDN  HC    O6   C6    107.69  3.000
 KDN  HD    O7   C7    108.78  3.000
 KDN  H10   O10  C9    108.32  3.000
 KDN  H1    O1   C1    110.16  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
 KDN  CONST_01  H8  O8  C10  C1  180.00  0.0  0

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
 KDN  chir_01  C1  C2  O5  C10  positiv
 KDN  chir_02  C3  O3  C2  C4   negativ
 KDN  chir_03  C4  O4  C3  C5   positiv
 KDN  chir_04  C5  O5  C6  C4   negativ
 KDN  chir_05  C6  O6  C5  C7   negativ
 KDN  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
 KDN  plan-1  C1   0.020
 KDN  plan-1  C10  0.020
 KDN  plan-1  O9   0.020
 KDN  plan-1  O8   0.020
 KDN  plan-1  H8   0.020

