# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 04:42:41 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: prop-2-en-1-yl 3-deoxy-alpha-D-manno-octos-2-ulopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1O[C@@](C[C@@H](O)[C@H]1O)(OCC=C)C=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
 KDR  KDR  'prop-2-en-1-yl 3-deoxy-alpha-D-manno-octos-2-ulopyranoside'  D-saccharide  36  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDR
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
 KDR  C11   C  C2    0  -0.522   3.3883   2.7509  -2.0312
 KDR  C10   C  C1    0  -0.189   3.2242   1.9049  -1.0226
 KDR  C9    C  CH2   0  -0.231   1.8937   1.5455  -0.4503
 KDR  O2    O  O2    0  -0.500   1.7199   0.1370  -0.5846
 KDR  C2    C  CT    0   0.405   1.0969  -0.5330   0.4553
 KDR  C1    C  C1    0   0.151   1.9342  -0.5248   1.7348
 KDR  O1A   O  O     0  -0.350   3.1113  -0.2903   1.7488
 KDR  C3    C  CH2   0  -0.523   0.9302  -1.9929   0.0254
 KDR  O6    O  O2    0  -0.516  -0.1256   0.0331   0.8238
 KDR  C6    C  CH1   0  -0.034  -1.1613  -0.0323  -0.1472
 KDR  C7    C  CH1   0  -0.015  -2.3713   0.6995   0.4480
 KDR  O7    O  OH1   0  -0.659  -3.4908   0.5584  -0.3923
 KDR  C8    C  CH2   0  -0.162  -2.0422   2.1616   0.7127
 KDR  O8    O  OH1   0  -0.669  -3.1670   2.7771   1.2938
 KDR  C5    C  CH1   0   0.030  -1.4521  -1.4751  -0.5362
 KDR  O5    O  OH1   0  -0.674  -1.9641  -2.1506   0.5843
 KDR  C4    C  CH1   0   0.029  -0.1572  -2.1090  -1.0383
 KDR  O4    O  OH1   0  -0.671  -0.4443  -3.4522  -1.3508
 KDR  H11   H  H     0   0.245   4.3715   3.0023  -2.4064
 KDR  H11A  H  H     0   0.241   2.5447   3.2237  -2.5206
 KDR  H10   H  H     0   0.251   4.0853   1.4406  -0.5522
 KDR  H9    H  HCH2  0   0.232   1.8451   1.8628   0.5962
 KDR  H9A   H  HCH2  0   0.235   1.0934   2.0721  -0.9809
 KDR  H1    H  H     0   0.218   1.3788  -0.8058   2.6464
 KDR  H3    H  HCH2  0   0.272   1.8847  -2.3744  -0.3448
 KDR  H3A   H  HCH2  0   0.260   0.6487  -2.5950   0.8937
 KDR  H6    H  HCH1  0   0.234  -0.8556   0.4958  -1.0638
 KDR  H7    H  HCH1  0   0.241  -2.6408   0.2220   1.3943
 KDR  HO7   H  HOH1  0   0.446  -3.3335   1.0522  -1.2050
 KDR  H8    H  HCH2  0   0.213  -1.1674   2.2222   1.3679
 KDR  H8A   H  HCH2  0   0.188  -1.7637   2.6418  -0.2390
 KDR  HO8   H  HOH1  0   0.456  -2.9244   3.6771   1.5279
 KDR  H5    H  HCH1  0   0.234  -2.1726  -1.4658  -1.3652
 KDR  HO5   H  HOH1  0   0.452  -2.0365  -3.0852   0.3635
 KDR  H4    H  HCH1  0   0.222   0.1566  -1.5585  -1.9348
 KDR  HO4   H  HOH1  0   0.458   0.3695  -3.8923  -1.6166

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
 KDR  C11  C10   double  1.327  0.020  1.327
 KDR  C10  C9    single  1.492  0.020  1.492
 KDR  C9   O2    single  1.425  0.020  1.425
 KDR  O2   C2    single  1.385  0.020  1.385
 KDR  C2   C1    single  1.529  0.020  1.529
 KDR  C2   C3    single  1.531  0.020  1.531
 KDR  C2   O6    single  1.397  0.020  1.397
 KDR  C1   O1A   double  1.200  0.020  1.200
 KDR  C3   C4    single  1.526  0.020  1.526
 KDR  O6   C6    single  1.421  0.020  1.421
 KDR  C6   C7    single  1.534  0.020  1.534
 KDR  C6   C5    single  1.522  0.020  1.522
 KDR  C7   O7    single  1.407  0.020  1.407
 KDR  C7   C8    single  1.522  0.020  1.522
 KDR  C8   O8    single  1.408  0.020  1.408
 KDR  C5   O5    single  1.405  0.020  1.405
 KDR  C5   C4    single  1.527  0.020  1.527
 KDR  C4   O4    single  1.409  0.020  1.409
 KDR  C11  H11   single  0.930  0.020  1.080
 KDR  C11  H11A  single  0.930  0.020  1.080
 KDR  C10  H10   single  0.930  0.020  1.080
 KDR  C9   H9    single  0.970  0.020  1.090
 KDR  C9   H9A   single  0.970  0.020  1.090
 KDR  C1   H1    single  0.930  0.020  1.080
 KDR  C3   H3    single  0.970  0.020  1.090
 KDR  C3   H3A   single  0.970  0.020  1.090
 KDR  C6   H6    single  0.970  0.020  1.090
 KDR  C7   H7    single  0.970  0.020  1.090
 KDR  O7   HO7   single  0.850  0.020  0.980
 KDR  C8   H8    single  0.970  0.020  1.090
 KDR  C8   H8A   single  0.970  0.020  1.090
 KDR  O8   HO8   single  0.850  0.020  0.980
 KDR  C5   H5    single  0.970  0.020  1.090
 KDR  O5   HO5   single  0.850  0.020  0.980
 KDR  C4   H4    single  0.970  0.020  1.090
 KDR  O4   HO4   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
 KDR  H11A  C11  H11  116.70  3.000
 KDR  H11A  C11  C10  121.68  3.000
 KDR  H11   C11  C10  121.62  3.000
 KDR  H10   C10  C9   115.98  3.000
 KDR  H10   C10  C11  120.27  3.000
 KDR  C9    C10  C11  123.74  3.000
 KDR  H9A   C9   H9   106.94  3.000
 KDR  H9A   C9   O2   109.90  3.000
 KDR  H9    C9   O2   111.78  3.000
 KDR  H9A   C9   C10  110.49  3.000
 KDR  H9    C9   C10  109.65  3.000
 KDR  O2    C9   C10  108.10  3.000
 KDR  C2    O2   C9   117.52  3.000
 KDR  O6    C2   C3   111.43  3.000
 KDR  O6    C2   C1   104.85  3.000
 KDR  C3    C2   C1   107.44  3.000
 KDR  O6    C2   O2   113.31  3.000
 KDR  C3    C2   O2   107.43  3.000
 KDR  C1    C2   O2   112.29  3.000
 KDR  H1    C1   O1A  122.25  3.000
 KDR  H1    C1   C2   114.47  3.000
 KDR  O1A   C1   C2   123.21  3.000
 KDR  H3A   C3   H3   107.56  3.000
 KDR  H3A   C3   C4   109.16  3.000
 KDR  H3    C3   C4   111.09  3.000
 KDR  H3A   C3   C2   109.28  3.000
 KDR  H3    C3   C2   109.46  3.000
 KDR  C4    C3   C2   110.24  3.000
 KDR  C6    O6   C2   116.04  3.000
 KDR  H6    C6   C5   107.15  3.000
 KDR  H6    C6   C7   108.25  3.000
 KDR  C5    C6   C7   113.62  3.000
 KDR  H6    C6   O6   110.14  3.000
 KDR  C5    C6   O6   110.94  3.000
 KDR  C7    C6   O6   106.72  3.000
 KDR  H7    C7   C8   108.80  3.000
 KDR  H7    C7   O7   106.08  3.000
 KDR  C8    C7   O7   111.86  3.000
 KDR  H7    C7   C6   108.77  3.000
 KDR  C8    C7   C6   110.81  3.000
 KDR  O7    C7   C6   110.37  3.000
 KDR  HO7   O7   C7   108.81  3.000
 KDR  H8A   C8   H8   106.91  3.000
 KDR  H8A   C8   O8   111.60  3.000
 KDR  H8    C8   O8   111.55  3.000
 KDR  H8A   C8   C7   108.85  3.000
 KDR  H8    C8   C7   109.28  3.000
 KDR  O8    C8   C7   108.61  3.000
 KDR  HO8   O8   C8   107.95  3.000
 KDR  H5    C5   C4   108.16  3.000
 KDR  H5    C5   O5   111.53  3.000
 KDR  C4    C5   O5   111.82  3.000
 KDR  H5    C5   C6   108.07  3.000
 KDR  C4    C5   C6   108.40  3.000
 KDR  O5    C5   C6   108.75  3.000
 KDR  HO5   O5   C5   108.13  3.000
 KDR  H4    C4   O4   110.81  3.000
 KDR  H4    C4   C5   107.63  3.000
 KDR  O4    C4   C5   107.22  3.000
 KDR  H4    C4   C3   109.11  3.000
 KDR  O4    C4   C3   111.87  3.000
 KDR  C5    C4   C3   110.10  3.000
 KDR  HO4   O4   C4   108.97  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
 KDR  Var_01  H9   C9   O2   C2    20.97  30.0  1
 KDR  Var_02  O2   C9   C10  C11  120.49  30.0  3
 KDR  Var_03  H11  C11  C10  C9   178.75   0.0  2

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
 KDR  chir_01  C2  C1  C3  O6  negativ
 KDR  chir_02  C6  O6  C7  C5  positiv
 KDR  chir_03  C7  O7  C6  C8  negativ
 KDR  chir_04  C5  O5  C6  C4  negativ
 KDR  chir_05  C4  O4  C5  C3  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
 KDR  plan-1  C11   0.020
 KDR  plan-1  C10   0.020
 KDR  plan-1  C9    0.020
 KDR  plan-1  H11   0.020
 KDR  plan-1  H11A  0.020
 KDR  plan-1  H10   0.020
 KDR  plan-2  C2    0.020
 KDR  plan-2  C1    0.020
 KDR  plan-2  O1A   0.020
 KDR  plan-2  H1    0.020

