# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 01:32:08 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](CO)[C@H]1O[C@@](C[C@@H](O)[C@H]1O)(O\C=C\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
 KME  KME  '(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulopyranosidonic acid'  D-saccharide  39  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KME
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
 KME  C1    C  C      0   0.368   2.2469   0.6644  -1.6012
 KME  C2    C  CT     0   0.382   1.3195   0.6475  -0.3462
 KME  O2    O  O2     0  -0.495   1.9023  -0.0445   0.7405
 KME  C3    C  CH2    0  -0.523   1.0965   2.0787   0.1367
 KME  C4    C  CH1    0   0.032   0.0169   2.1396   1.2090
 KME  O4    O  OH1    0  -0.677  -0.3260   3.4685   1.5453
 KME  C5    C  CH1    0   0.025  -1.2551   1.4590   0.7108
 KME  O5    O  OH1    0  -0.675  -1.8157   2.1414  -0.3843
 KME  C6    C  CH1    0   0.001  -0.8974   0.0412   0.2848
 KME  O6    O  O2     0  -0.505   0.1124   0.0447  -0.7071
 KME  C7    C  CH1    0   0.001  -2.0769  -0.7442  -0.2964
 KME  O7    O  O2     0  -0.501  -3.1254  -0.7254   0.6482
 KME  C8    C  CH2    0  -0.142  -1.6786  -2.1841  -0.5772
 KME  O8    O  OH1    0  -0.671  -2.7813  -2.8518  -1.1474
 KME  C9    C  CH3    0  -0.405  -4.3545  -0.2415   0.1632
 KME  C10   C  C1     0   0.091   2.1276  -1.3689   0.5615
 KME  C11   C  C1     0  -0.341   2.2662  -2.2012   1.5880
 KME  C12   C  CH3    0  -0.703   2.5628  -3.6572   1.4260
 KME  O1A   O  O      0  -0.589   3.4607   0.5276  -1.3775
 KME  O1B   O  OC    -1  -0.589   1.6849   0.8757  -2.6863
 KME  H3    H  HCH2   0   0.252   2.0387   2.4921   0.5064
 KME  H3A   H  HCH2   0   0.246   0.7877   2.6809  -0.7204
 KME  H4    H  HCH1   0   0.212   0.3558   1.5940   2.0994
 KME  HO4   H  HOH1   0   0.455   0.4798   3.9549   1.7456
 KME  H5    H  HCH1   0   0.227  -1.9651   1.3971   1.5471
 KME  HO5   H  HOH1   0   0.448  -1.8921   3.0711  -0.1448
 KME  H6    H  HCH1   0   0.224  -0.5561  -0.4869   1.1884
 KME  H7    H  HCH1   0   0.222  -2.3901  -0.2731  -1.2372
 KME  H8    H  HCH2   0   0.205  -0.8115  -2.1953  -1.2450
 KME  H8A   H  HCH2   0   0.185  -1.3646  -2.6530   0.3668
 KME  HO8   H  HOH1   0   0.454  -2.5066  -3.7474  -1.3624
 KME  H9    H  HCH3   0   0.226  -5.0719  -0.2875   0.9825
 KME  H9A   H  HCH3   0   0.207  -4.2838   0.7972  -0.1736
 KME  H9B   H  HCH3   0   0.209  -4.7402  -0.8456  -0.6635
 KME  H10   H  H      0   0.227   2.2054  -1.7271  -0.4620
 KME  H11   H  H      0   0.229   2.1688  -1.8167   2.5992
 KME  H12   H  HCH3   0   0.229   1.7822  -4.2762   1.8741
 KME  H12A  H  HCH3   0   0.230   2.6432  -3.9371   0.3749
 KME  H12B  H  HCH3   0   0.228   3.4999  -3.9347   1.9141

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
 KME  O1A  C1    deloc   1.242  0.020  1.242
 KME  O1B  C1    deloc   1.240  0.020  1.240
 KME  C1   C2    single  1.561  0.020  1.561
 KME  O6   C2    single  1.397  0.020  1.397
 KME  C3   C2    single  1.527  0.020  1.527
 KME  C2   O2    single  1.414  0.020  1.414
 KME  O2   C10   single  1.355  0.020  1.355
 KME  C3   C4    single  1.523  0.020  1.523
 KME  C3   H3    single  0.970  0.020  1.090
 KME  C3   H3A   single  0.970  0.020  1.090
 KME  C5   C4    single  1.526  0.020  1.526
 KME  O4   C4    single  1.413  0.020  1.413
 KME  C4   H4    single  0.970  0.020  1.090
 KME  O4   HO4   single  0.850  0.020  0.980
 KME  O5   C5    single  1.407  0.020  1.407
 KME  C5   C6    single  1.523  0.020  1.523
 KME  C5   H5    single  0.970  0.020  1.090
 KME  O5   HO5   single  0.850  0.020  0.980
 KME  C7   C6    single  1.532  0.020  1.532
 KME  O6   C6    single  1.415  0.020  1.415
 KME  C6   H6    single  0.970  0.020  1.090
 KME  O7   C7    single  1.411  0.020  1.411
 KME  C7   C8    single  1.520  0.020  1.520
 KME  C7   H7    single  0.970  0.020  1.090
 KME  C9   O7    single  1.407  0.020  1.407
 KME  O8   C8    single  1.410  0.020  1.410
 KME  C8   H8    single  0.970  0.020  1.090
 KME  C8   H8A   single  0.970  0.020  1.090
 KME  O8   HO8   single  0.850  0.020  0.980
 KME  C9   H9    single  0.970  0.020  1.090
 KME  C9   H9A   single  0.970  0.020  1.090
 KME  C9   H9B   single  0.970  0.020  1.090
 KME  C10  C11   double  1.329  0.020  1.329
 KME  C10  H10   single  0.930  0.020  1.080
 KME  C11  C12   single  1.495  0.020  1.495
 KME  C11  H11   single  0.930  0.020  1.080
 KME  C12  H12   single  0.970  0.020  1.090
 KME  C12  H12A  single  0.970  0.020  1.090
 KME  C12  H12B  single  0.970  0.020  1.090

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
 KME  O1B   C1   O1A   128.27  3.000
 KME  O1B   C1   C2    115.86  3.000
 KME  O1A   C1   C2    115.78  3.000
 KME  O6    C2   C3    111.11  3.000
 KME  C3    C2   O2    106.01  3.000
 KME  O6    C2   O2    110.10  3.000
 KME  O2    C2   C1    112.23  3.000
 KME  C3    C2   C1    109.33  3.000
 KME  O6    C2   C1    108.09  3.000
 KME  C10   O2   C2    116.43  3.000
 KME  H3A   C3   H3    107.49  3.000
 KME  H3A   C3   C4    109.27  3.000
 KME  H3    C3   C4    110.96  3.000
 KME  H3A   C3   C2    108.06  3.000
 KME  H3    C3   C2    109.60  3.000
 KME  C4    C3   C2    111.33  3.000
 KME  H4    C4   C5    107.48  3.000
 KME  H4    C4   O4    110.44  3.000
 KME  C5    C4   O4    107.15  3.000
 KME  H4    C4   C3    109.41  3.000
 KME  O4    C4   C3    112.17  3.000
 KME  C5    C4   C3    110.07  3.000
 KME  HO4   O4   C4    108.76  3.000
 KME  H5    C5   C6    108.19  3.000
 KME  H5    C5   O5    111.24  3.000
 KME  C6    C5   O5    109.11  3.000
 KME  H5    C5   C4    108.38  3.000
 KME  C6    C5   C4    108.10  3.000
 KME  O5    C5   C4    111.71  3.000
 KME  HO5   O5   C5    107.83  3.000
 KME  H6    C6   C7    107.71  3.000
 KME  H6    C6   O6    110.81  3.000
 KME  C7    C6   O6    106.54  3.000
 KME  H6    C6   C5    106.85  3.000
 KME  O6    C6   C5    111.18  3.000
 KME  C7    C6   C5    113.74  3.000
 KME  C6    O6   C2    115.88  3.000
 KME  H7    C7   C8    108.84  3.000
 KME  H7    C7   O7    110.85  3.000
 KME  C8    C7   O7    109.32  3.000
 KME  H7    C7   C6    108.96  3.000
 KME  C8    C7   C6    110.73  3.000
 KME  O7    C7   C6    108.14  3.000
 KME  C9    O7   C7    115.01  3.000
 KME  H8A   C8   H8    107.05  3.000
 KME  H8A   C8   O8    111.63  3.000
 KME  H8    C8   O8    111.59  3.000
 KME  H8A   C8   C7    108.67  3.000
 KME  H8    C8   C7    109.27  3.000
 KME  O8    C8   C7    108.57  3.000
 KME  HO8   O8   C8    107.96  3.000
 KME  H9B   C9   H9A   108.32  3.000
 KME  H9B   C9   H9    108.22  3.000
 KME  H9A   C9   H9    108.30  3.000
 KME  H9B   C9   O7    112.24  3.000
 KME  H9A   C9   O7    112.09  3.000
 KME  H9    C9   O7    107.54  3.000
 KME  H10   C10  C11   120.89  3.000
 KME  H10   C10  O2    117.27  3.000
 KME  C11   C10  O2    121.83  3.000
 KME  H11   C11  C12   117.62  3.000
 KME  H11   C11  C10   119.22  3.000
 KME  C12   C11  C10   123.17  3.000
 KME  H12B  C12  H12A  107.59  3.000
 KME  H12B  C12  H12   106.61  3.000
 KME  H12A  C12  H12   107.61  3.000
 KME  H12B  C12  C11   111.67  3.000
 KME  H12A  C12  C11   111.66  3.000
 KME  H12   C12  C11   111.45  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
 KME  Var_01  C11  C10  O2   C2   -158.62  30.0  3
 KME  Var_02  C12  C11  C10  O2   -177.78   0.0  2
 KME  Var_03  H9   C9   O7   C7    179.56  30.0  3
 KME  Var_04  H12  C12  C11  C10  -120.65  30.0  3

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
 KME  chir_01  C2  O6  C3  O2  negativ
 KME  chir_02  C4  O4  C3  C5  positiv
 KME  chir_03  C5  O5  C4  C6  positiv
 KME  chir_04  C6  O6  C7  C5  positiv
 KME  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
 KME  plan-1  C1   0.020
 KME  plan-1  C2   0.020
 KME  plan-1  O1A  0.020
 KME  plan-1  O1B  0.020
 KME  plan-2  O2   0.020
 KME  plan-2  C10  0.020
 KME  plan-2  C11  0.020
 KME  plan-2  C12  0.020
 KME  plan-2  H10  0.020
 KME  plan-2  H11  0.020

