# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 05:36:42 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid
#   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)=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
 KDA  KDA  'prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid'  D-saccharide  37  19  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KDA
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
 KDA  C1    C  C     0   0.481   0.5305  -1.4169  -2.1096
 KDA  O1A   O  OH1   0  -0.584   0.9359  -0.9715  -3.2864
 KDA  O1B   O  O     0  -0.410   0.4829  -2.5747  -1.7958
 KDA  C2    C  CT    0   0.440   0.0665  -0.2517  -1.2177
 KDA  C3    C  CH2   0  -0.514  -1.2972   0.2421  -1.7079
 KDA  C4    C  CH1   0   0.029  -1.9130   1.1952  -0.6868
 KDA  O4    O  OH1   0  -0.672  -3.2387   1.5336  -1.0238
 KDA  C5    C  CH1   0   0.031  -1.9492   0.5419   0.6922
 KDA  O5    O  OH1   0  -0.673  -2.7935  -0.5811   0.7151
 KDA  C6    C  CH1   0  -0.042  -0.5381   0.0977   1.0499
 KDA  O6    O  O2    0  -0.506  -0.0195  -0.7826   0.0631
 KDA  C7    C  CH1   0  -0.011  -0.4419  -0.6397   2.3907
 KDA  O7    O  OH1   0  -0.659  -1.0617   0.1081   3.4086
 KDA  C8    C  CH2   0  -0.162   1.0083  -0.9608   2.7244
 KDA  O8    O  OH1   0  -0.668   1.0470  -1.6471   3.9522
 KDA  O2    O  O2    0  -0.498   0.9426   0.8289  -1.2906
 KDA  C9    C  CH2   0  -0.230   2.2627   0.6111  -0.8080
 KDA  C10   C  C1    0  -0.197   3.0490   1.8509  -1.0731
 KDA  C11   C  C2    0  -0.518   3.6539   2.5495  -0.1212
 KDA  H1A   H  HOH1  0   0.490   1.1865  -1.7135  -3.8582
 KDA  H31   H  HCH2  0   0.270  -1.1906   0.7314  -2.6785
 KDA  H32   H  HCH2  0   0.261  -1.9610  -0.6155  -1.8419
 KDA  H4    H  HCH1  0   0.222  -1.2921   2.0976  -0.6128
 KDA  HO4   H  HOH1  0   0.458  -3.2429   1.9547  -1.8894
 KDA  H5    H  HCH1  0   0.232  -2.2652   1.2984   1.4234
 KDA  HO5   H  HOH1  0   0.452  -3.6600  -0.3099   0.3948
 KDA  H6    H  HCH1  0   0.233   0.0834   1.0050   1.1102
 KDA  H7    H  HCH1  0   0.241  -1.0030  -1.5763   2.3220
 KDA  HO7   H  HOH1  0   0.446  -0.5497   0.9096   3.5642
 KDA  H81   H  HCH2  0   0.215   1.4418  -1.5580   1.9154
 KDA  H82   H  HCH2  0   0.182   1.5800  -0.0192   2.7689
 KDA  HO8   H  HOH1  0   0.456   1.9522  -1.9320   4.1041
 KDA  H91   H  HCH2  0   0.234   2.7308  -0.2401  -1.3200
 KDA  H92   H  HCH2  0   0.228   2.2669   0.3852   0.2630
 KDA  H10   H  H     0   0.257   3.1281   2.1619  -2.1102
 KDA  H111  H  H     0   0.248   4.2352   3.4330  -0.3491
 KDA  H112  H  H     0   0.242   3.5926   2.2635   0.9225

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
 KDA  C1   O1A   single  1.322  0.020  1.322
 KDA  C1   O1B   double  1.201  0.020  1.201
 KDA  C1   C2    single  1.539  0.020  1.539
 KDA  O1A  H1A   single  0.850  0.020  0.980
 KDA  C2   C3    single  1.531  0.020  1.531
 KDA  C2   O6    single  1.389  0.020  1.389
 KDA  C2   O2    single  1.393  0.020  1.393
 KDA  C3   C4    single  1.527  0.020  1.527
 KDA  C3   H31   single  0.970  0.020  1.090
 KDA  C3   H32   single  0.970  0.020  1.090
 KDA  C4   O4    single  1.409  0.020  1.409
 KDA  C4   C5    single  1.526  0.020  1.526
 KDA  C4   H4    single  0.970  0.020  1.090
 KDA  O4   HO4   single  0.850  0.020  0.980
 KDA  C5   O5    single  1.405  0.020  1.405
 KDA  C5   C6    single  1.522  0.020  1.522
 KDA  C5   H5    single  0.970  0.020  1.090
 KDA  O5   HO5   single  0.850  0.020  0.980
 KDA  C6   O6    single  1.420  0.020  1.420
 KDA  C6   C7    single  1.533  0.020  1.533
 KDA  C6   H6    single  0.970  0.020  1.090
 KDA  C7   O7    single  1.407  0.020  1.407
 KDA  C7   C8    single  1.522  0.020  1.522
 KDA  C7   H7    single  0.970  0.020  1.090
 KDA  O7   HO7   single  0.850  0.020  0.980
 KDA  C8   O8    single  1.407  0.020  1.407
 KDA  C8   H81   single  0.970  0.020  1.090
 KDA  C8   H82   single  0.970  0.020  1.090
 KDA  O8   HO8   single  0.850  0.020  0.980
 KDA  O2   C9    single  1.422  0.020  1.422
 KDA  C9   C10   single  1.492  0.020  1.492
 KDA  C9   H91   single  0.970  0.020  1.090
 KDA  C9   H92   single  0.970  0.020  1.090
 KDA  C10  C11   double  1.327  0.020  1.327
 KDA  C10  H10   single  0.930  0.020  1.080
 KDA  C11  H111  single  0.930  0.020  1.080
 KDA  C11  H112  single  0.930  0.020  1.080

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
 KDA  C2    C1   O1B   124.52  3.000
 KDA  C2    C1   O1A   110.69  3.000
 KDA  O1B   C1   O1A   124.73  3.000
 KDA  H1A   O1A  C1    110.27  3.000
 KDA  O2    C2   O6    112.56  3.000
 KDA  O2    C2   C3    107.05  3.000
 KDA  O6    C2   C3    111.31  3.000
 KDA  O2    C2   C1    111.55  3.000
 KDA  O6    C2   C1    105.29  3.000
 KDA  C3    C2   C1    109.10  3.000
 KDA  H32   C3   H31   107.57  3.000
 KDA  H32   C3   C4    109.09  3.000
 KDA  H31   C3   C4    110.74  3.000
 KDA  H32   C3   C2    109.10  3.000
 KDA  H31   C3   C2    110.01  3.000
 KDA  C4    C3   C2    110.28  3.000
 KDA  H4    C4   C5    107.72  3.000
 KDA  H4    C4   O4    110.53  3.000
 KDA  C5    C4   O4    107.25  3.000
 KDA  H4    C4   C3    109.28  3.000
 KDA  C5    C4   C3    110.29  3.000
 KDA  O4    C4   C3    111.68  3.000
 KDA  HO4   O4   C4    108.92  3.000
 KDA  H5    C5   C6    108.13  3.000
 KDA  H5    C5   O5    111.52  3.000
 KDA  C6    C5   O5    108.66  3.000
 KDA  H5    C5   C4    108.26  3.000
 KDA  C6    C5   C4    108.37  3.000
 KDA  O5    C5   C4    111.78  3.000
 KDA  HO5   O5   C5    108.07  3.000
 KDA  H6    C6   C7    108.24  3.000
 KDA  H6    C6   O6    110.03  3.000
 KDA  C7    C6   O6    106.65  3.000
 KDA  H6    C6   C5    107.19  3.000
 KDA  C7    C6   C5    113.83  3.000
 KDA  O6    C6   C5    110.86  3.000
 KDA  C6    O6   C2    115.23  3.000
 KDA  H7    C7   C8    108.77  3.000
 KDA  H7    C7   O7    105.94  3.000
 KDA  C8    C7   O7    111.91  3.000
 KDA  H7    C7   C6    108.95  3.000
 KDA  C8    C7   C6    110.66  3.000
 KDA  O7    C7   C6    110.45  3.000
 KDA  HO7   O7   C7    108.96  3.000
 KDA  H82   C8   H81   106.87  3.000
 KDA  H82   C8   O8    111.54  3.000
 KDA  H81   C8   O8    111.58  3.000
 KDA  H82   C8   C7    108.83  3.000
 KDA  H81   C8   C7    109.28  3.000
 KDA  O8    C8   C7    108.68  3.000
 KDA  HO8   O8   C8    107.96  3.000
 KDA  C9    O2   C2    116.56  3.000
 KDA  H92   C9   H91   107.13  3.000
 KDA  H92   C9   C10   110.08  3.000
 KDA  H91   C9   C10   109.68  3.000
 KDA  H92   C9   O2    111.54  3.000
 KDA  H91   C9   O2    110.86  3.000
 KDA  C10   C9   O2    107.56  3.000
 KDA  H10   C10  C11   120.08  3.000
 KDA  H10   C10  C9    116.50  3.000
 KDA  C11   C10  C9    123.40  3.000
 KDA  H112  C11  H111  116.66  3.000
 KDA  H112  C11  C10   121.74  3.000
 KDA  H111  C11  C10   121.60  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
 KDA  CONST_01  H1A   O1A  C1   C2  180.00   0.0  0
 KDA  Var_01    C10   C9   O2   C2  175.84  30.0  3
 KDA  Var_02    C11   C10  C9   O2  121.84  30.0  3
 KDA  Var_03    H111  C11  C10  C9  178.63   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
 KDA  chir_01  C2  C3  O6  O2  positiv
 KDA  chir_02  C4  O4  C5  C3  negativ
 KDA  chir_03  C5  O5  C4  C6  positiv
 KDA  chir_04  C6  O6  C7  C5  positiv
 KDA  chir_05  C7  O7  C6  C8  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
 KDA  plan-1  C1    0.020
 KDA  plan-1  O1A   0.020
 KDA  plan-1  O1B   0.020
 KDA  plan-1  C2    0.020
 KDA  plan-1  H1A   0.020
 KDA  plan-2  C9    0.020
 KDA  plan-2  C10   0.020
 KDA  plan-2  C11   0.020
 KDA  plan-2  H10   0.020
 KDA  plan-2  H111  0.020
 KDA  plan-2  H112  0.020

