# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:42:17 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: prop-2-en-1-yl 3-deoxy-beta-L-gulo-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
 KDE  KDE  'prop-2-en-1-yl 3-deoxy-beta-L-gulo-oct-2-ulopyranosidonic acid'  D-saccharide  36  19  .  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_KDE
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
 KDE  O1A   O  O      0  -0.606  -3.0196   0.9097   1.5150
 KDE  C1    C  C      0   0.354  -1.8128   0.6434   1.6605
 KDE  O1B   O  OC    -1  -0.577  -1.1836   0.5057   2.7199
 KDE  C2    C  CT     0   0.424  -1.0193   0.5234   0.3231
 KDE  O2    O  O2     0  -0.513  -1.6711  -0.3027  -0.6064
 KDE  C9    C  CH2    0  -0.211  -1.9484  -1.6207  -0.1752
 KDE  C10   C  C1     0  -0.199  -2.6447  -2.3327  -1.2877
 KDE  C11   C  C2     0  -0.526  -2.2412  -3.4904  -1.7953
 KDE  C3    C  CH2    0  -0.522  -0.9124   1.9019  -0.3314
 KDE  C4    C  CH1    0   0.025   0.0677   1.8965  -1.4967
 KDE  O4    O  OH1    0  -0.678   0.2869   3.1912  -2.0184
 KDE  C5    C  CH1    0   0.022   1.4195   1.3582  -1.0367
 KDE  O5    O  OH1    0  -0.669   2.0221   2.2106  -0.0964
 KDE  C6    C  CH1    0  -0.025   1.1871  -0.0210  -0.4371
 KDE  O6    O  O2     0  -0.518   0.2510   0.0130   0.6197
 KDE  C7    C  CH1    0  -0.010   2.4372  -0.6923   0.1410
 KDE  O7    O  OH1    0  -0.669   2.7805  -0.1737   1.4012
 KDE  C8    C  CH2    0  -0.155   2.2396  -2.2025   0.1936
 KDE  O8    O  OH1    0  -0.672   3.4399  -2.8002   0.6226
 KDE  H9    H  HCH2   0   0.215  -1.0364  -2.1604   0.1035
 KDE  H9A   H  HCH2   0   0.220  -2.6008  -1.6088   0.7077
 KDE  H10   H  H      0   0.249  -3.5495  -1.8635  -1.6636
 KDE  H11   H  H      0   0.238  -1.3444  -3.9874  -1.4429
 KDE  H11A  H  H      0   0.242  -2.7952  -3.9901  -2.5790
 KDE  H3    H  HCH2   0   0.250  -1.9040   2.2190  -0.6607
 KDE  H3A   H  HCH2   0   0.241  -0.5757   2.6204   0.4204
 KDE  H4    H  HCH1   0   0.211  -0.3067   1.2269  -2.2827
 KDE  HO4   H  HOH1   0   0.455  -0.5645   3.6133  -2.1700
 KDE  H5    H  HCH1   0   0.221   2.0653   1.2239  -1.9193
 KDE  HO5   H  HOH1   0   0.445   1.9736   3.1067  -0.4474
 KDE  H6    H  HCH1   0   0.227   0.8252  -0.6464  -1.2664
 KDE  H7    H  HCH1   0   0.231   3.2749  -0.4888  -0.5368
 KDE  HO7   H  HOH1   0   0.441   1.9532  -0.0183   1.8737
 KDE  H8    H  HCH2   0   0.196   1.4062  -2.4409   0.8690
 KDE  H8A   H  HCH2   0   0.191   1.9525  -2.5510  -0.8078
 KDE  HO8   H  HOH1   0   0.454   3.2974  -3.7490   0.6764

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
 KDE  O1A  C1    deloc   1.244  0.020  1.244
 KDE  C1   O1B   deloc   1.240  0.020  1.240
 KDE  C1   C2    single  1.560  0.020  1.560
 KDE  C2   O2    single  1.404  0.020  1.404
 KDE  C2   C3    single  1.530  0.020  1.530
 KDE  C2   O6    single  1.401  0.020  1.401
 KDE  O2   C9    single  1.414  0.020  1.414
 KDE  C9   C10   single  1.493  0.020  1.493
 KDE  C9   H9    single  0.970  0.020  1.090
 KDE  C9   H9A   single  0.970  0.020  1.090
 KDE  C10  C11   double  1.327  0.020  1.327
 KDE  C10  H10   single  0.930  0.020  1.080
 KDE  C11  H11   single  0.930  0.020  1.080
 KDE  C11  H11A  single  0.930  0.020  1.080
 KDE  C3   C4    single  1.523  0.020  1.523
 KDE  C3   H3    single  0.970  0.020  1.090
 KDE  C3   H3A   single  0.970  0.020  1.090
 KDE  C4   O4    single  1.413  0.020  1.413
 KDE  C4   C5    single  1.526  0.020  1.526
 KDE  C4   H4    single  0.970  0.020  1.090
 KDE  O4   HO4   single  0.850  0.020  0.980
 KDE  C5   O5    single  1.405  0.020  1.405
 KDE  C5   C6    single  1.522  0.020  1.522
 KDE  C5   H5    single  0.970  0.020  1.090
 KDE  O5   HO5   single  0.850  0.020  0.980
 KDE  C6   O6    single  1.412  0.020  1.412
 KDE  C6   C7    single  1.532  0.020  1.532
 KDE  C6   H6    single  0.970  0.020  1.090
 KDE  C7   O7    single  1.405  0.020  1.405
 KDE  C7   C8    single  1.524  0.020  1.524
 KDE  C7   H7    single  0.970  0.020  1.090
 KDE  O7   HO7   single  0.850  0.020  0.980
 KDE  C8   O8    single  1.408  0.020  1.408
 KDE  C8   H8    single  0.970  0.020  1.090
 KDE  C8   H8A   single  0.970  0.020  1.090
 KDE  O8   HO8   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
 KDE  C2    C1   O1B  117.78  3.000
 KDE  C2    C1   O1A  114.18  3.000
 KDE  O1B   C1   O1A  128.01  3.000
 KDE  O6    C2   C3   110.83  3.000
 KDE  O6    C2   O2   110.29  3.000
 KDE  C3    C2   O2   106.23  3.000
 KDE  O6    C2   C1   107.93  3.000
 KDE  C3    C2   C1   109.45  3.000
 KDE  O2    C2   C1   112.14  3.000
 KDE  C9    O2   C2   115.94  3.000
 KDE  H9A   C9   H9   107.18  3.000
 KDE  H9A   C9   C10  109.10  3.000
 KDE  H9    C9   C10  110.05  3.000
 KDE  H9A   C9   O2   110.59  3.000
 KDE  H9    C9   O2   111.93  3.000
 KDE  C10   C9   O2   107.98  3.000
 KDE  H10   C10  C11  119.85  3.000
 KDE  H10   C10  C9   116.12  3.000
 KDE  C11   C10  C9   124.00  3.000
 KDE  H11A  C11  H11  116.56  3.000
 KDE  H11A  C11  C10  121.62  3.000
 KDE  H11   C11  C10  121.81  3.000
 KDE  H3A   C3   H3   107.23  3.000
 KDE  H3A   C3   C4   109.29  3.000
 KDE  H3    C3   C4   110.78  3.000
 KDE  H3A   C3   C2   108.64  3.000
 KDE  H3    C3   C2   109.11  3.000
 KDE  C4    C3   C2   111.67  3.000
 KDE  H4    C4   C5   107.62  3.000
 KDE  H4    C4   O4   110.32  3.000
 KDE  C5    C4   O4   107.28  3.000
 KDE  H4    C4   C3   109.29  3.000
 KDE  C5    C4   C3   109.92  3.000
 KDE  O4    C4   C3   112.28  3.000
 KDE  HO4   O4   C4   108.84  3.000
 KDE  H5    C5   C6   107.13  3.000
 KDE  H5    C5   O5   111.02  3.000
 KDE  C6    C5   O5   110.59  3.000
 KDE  H5    C5   C4   108.71  3.000
 KDE  C6    C5   C4   107.65  3.000
 KDE  O5    C5   C4   111.58  3.000
 KDE  HO5   O5   C5   107.38  3.000
 KDE  H6    C6   C7   107.68  3.000
 KDE  H6    C6   O6   111.09  3.000
 KDE  C7    C6   O6   105.60  3.000
 KDE  H6    C6   C5   105.58  3.000
 KDE  C7    C6   C5   114.91  3.000
 KDE  O6    C6   C5   111.98  3.000
 KDE  C6    O6   C2   116.84  3.000
 KDE  H7    C7   C8   107.71  3.000
 KDE  H7    C7   O7   107.41  3.000
 KDE  C8    C7   O7   111.49  3.000
 KDE  H7    C7   C6   107.98  3.000
 KDE  C8    C7   C6   109.97  3.000
 KDE  O7    C7   C6   112.09  3.000
 KDE  HO7   O7   C7   106.80  3.000
 KDE  H8A   C8   H8   107.05  3.000
 KDE  H8A   C8   O8   111.47  3.000
 KDE  H8    C8   O8   111.54  3.000
 KDE  H8A   C8   C7   108.47  3.000
 KDE  H8    C8   C7   109.54  3.000
 KDE  O8    C8   C7   108.71  3.000
 KDE  HO8   O8   C8   108.05  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
 KDE  Var_01  C10  C9   O2   C2  179.63  30.0  3
 KDE  Var_02  C11  C10  C9   O2  126.07  30.0  3
 KDE  Var_03  H11  C11  C10  C9   -1.78   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
 KDE  chir_01  C2  O2  C3  O6  positiv
 KDE  chir_02  C4  O4  C5  C3  negativ
 KDE  chir_03  C5  O5  C4  C6  positiv
 KDE  chir_04  C6  O6  C7  C5  positiv
 KDE  chir_05  C7  O7  C6  C8  positiv

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
 KDE  plan-1  O1A   0.020
 KDE  plan-1  C1    0.020
 KDE  plan-1  O1B   0.020
 KDE  plan-1  C2    0.020
 KDE  plan-2  C9    0.020
 KDE  plan-2  C10   0.020
 KDE  plan-2  C11   0.020
 KDE  plan-2  H10   0.020
 KDE  plan-2  H11   0.020
 KDE  plan-2  H11A  0.020

