# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 18:52:51 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)OC(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
 PKM  PKM  '4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid'  D-saccharide  45  24  .  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_PKM
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
 PKM  C1    C  C     0   0.522  -0.4110  -2.9257  -0.6333
 PKM  C10   C  C     0   0.528   1.2423   3.0252  -0.1422
 PKM  C11   C  CH3   0  -0.782   1.4518   4.0681  -1.2117
 PKM  O1B   O  O     0  -0.433  -1.1802  -3.8519  -0.6389
 PKM  C2    C  CT    0   0.417  -0.0873  -2.1461   0.6590
 PKM  C3    C  CH2   0  -0.549   1.3567  -1.6647   0.7843
 PKM  C4    C  CH1   0   0.050   1.6662  -0.4012  -0.0045
 PKM  O4    O  O2    0  -0.459   2.9040   0.1511   0.4503
 PKM  C5    C  CH1   0  -0.121   0.6078   0.6687   0.2333
 PKM  C6    C  CH1   0   0.024  -0.7769   0.0816  -0.0643
 PKM  C7    C  CH1   0  -0.027  -1.9065   1.0530   0.2758
 PKM  C8    C  CH1   0  -0.014  -3.2851   0.5062  -0.1427
 PKM  C9    C  CH2   0  -0.164  -4.3581   1.5649   0.0597
 PKM  O10   O  O     0  -0.494   1.3900   3.2796   1.0427
 PKM  N5    N  NH1   0  -0.638   0.8556   1.8158  -0.5997
 PKM  C     C  C     0   0.569   4.0433  -0.2468  -0.1133
 PKM  O     O  O     0  -0.451   4.1019  -1.0699  -0.9916
 PKM  CH3   C  CH3   0  -0.774   5.2259   0.4328   0.5085
 PKM  O1    O  OH1   0  -0.575   0.1930  -2.4486  -1.7011
 PKM  O6    O  O2    0  -0.512  -1.0032  -1.0734   0.7235
 PKM  O7    O  OH1   0  -0.659  -1.8876   1.4212   1.6332
 PKM  O8    O  OH1   0  -0.658  -3.2679   0.0271  -1.4677
 PKM  O9    O  OH1   0  -0.671  -5.6136   1.0008  -0.2374
 PKM  H113  H  HCH3  0   0.270   0.6595   4.8143  -1.1420
 PKM  H112  H  HCH3  0   0.265   2.3977   4.5801  -1.0426
 PKM  H111  H  HCH3  0   0.249   1.4510   3.6643  -2.2225
 PKM  H32   H  HCH2  0   0.279   1.5202  -1.4507   1.8445
 PKM  H31   H  HCH2  0   0.283   2.0405  -2.4704   0.5084
 PKM  H4    H  HCH1  0   0.259   1.7363  -0.6096  -1.0734
 PKM  H5    H  HCH1  0   0.276   0.6447   0.9912   1.2753
 PKM  H6    H  HCH1  0   0.242  -0.8420  -0.1461  -1.1353
 PKM  H7    H  HCH1  0   0.247  -1.7199   1.9745  -0.2875
 PKM  H8    H  HCH1  0   0.235  -3.5284  -0.3605   0.4823
 PKM  H92   H  HCH2  0   0.209  -4.3122   1.9302   1.0908
 PKM  H91   H  HCH2  0   0.190  -4.1340   2.4238  -0.5928
 PKM  HN5   H  HNH1  0   0.401   0.7893   1.6867  -1.5976
 PKM  H14   H  HCH3  0   0.280   5.5028  -0.0999   1.4206
 PKM  H16   H  HCH3  0   0.265   6.0756   0.4063  -0.1685
 PKM  H15   H  HCH3  0   0.265   5.0059   1.4623   0.7829
 PKM  HOB1  H  HOH1  0   0.495  -0.0796  -2.9328  -2.4974
 PKM  HO7   H  HOH1  0   0.446  -2.0089   0.6280   2.1674
 PKM  HO8   H  HOH1  0   0.445  -3.1931   0.7769  -2.0688
 PKM  HO9   H  HOH1  0   0.455  -6.2871   1.6616  -0.0540
 PKM  O2    O  OH1   0  -0.648  -0.3385  -2.9637   1.7321
 PKM  H1    H  HOH1  0   0.460  -1.0921  -3.5379   1.5359

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
 PKM  C11  C10   single  1.508  0.020  1.508
 PKM  O10  C10   double  1.221  0.020  1.221
 PKM  C10  N5    single  1.350  0.020  1.350
 PKM  O7   C7    single  1.406  0.020  1.406
 PKM  N5   C5    single  1.439  0.020  1.439
 PKM  CH3  C     single  1.499  0.020  1.499
 PKM  C5   C4    single  1.524  0.020  1.524
 PKM  C5   C6    single  1.533  0.020  1.533
 PKM  O4   C     single  1.332  0.020  1.332
 PKM  O4   C4    single  1.430  0.020  1.430
 PKM  C    O     double  1.205  0.020  1.205
 PKM  C7   C6    single  1.528  0.020  1.528
 PKM  C7   C8    single  1.541  0.020  1.541
 PKM  C9   C8    single  1.521  0.020  1.521
 PKM  C9   O9    single  1.408  0.020  1.408
 PKM  C4   C3    single  1.521  0.020  1.521
 PKM  C6   O6    single  1.416  0.020  1.416
 PKM  C8   O8    single  1.409  0.020  1.409
 PKM  O6   C2    single  1.412  0.020  1.412
 PKM  C3   C2    single  1.527  0.020  1.527
 PKM  C2   C1    single  1.544  0.020  1.544
 PKM  C1   O1B   double  1.204  0.020  1.204
 PKM  C1   O1    single  1.316  0.020  1.316
 PKM  C11  H113  single  0.970  0.020  1.090
 PKM  C11  H112  single  0.970  0.020  1.090
 PKM  C11  H111  single  0.970  0.020  1.090
 PKM  C3   H32   single  0.970  0.020  1.090
 PKM  C3   H31   single  0.970  0.020  1.090
 PKM  C4   H4    single  0.970  0.020  1.090
 PKM  C5   H5    single  0.970  0.020  1.090
 PKM  C6   H6    single  0.970  0.020  1.090
 PKM  C7   H7    single  0.970  0.020  1.090
 PKM  C8   H8    single  0.970  0.020  1.090
 PKM  C9   H92   single  0.970  0.020  1.090
 PKM  C9   H91   single  0.970  0.020  1.090
 PKM  N5   HN5   single  0.860  0.020  1.020
 PKM  CH3  H14   single  0.970  0.020  1.090
 PKM  CH3  H16   single  0.970  0.020  1.090
 PKM  CH3  H15   single  0.970  0.020  1.090
 PKM  O1   HOB1  single  0.850  0.020  0.980
 PKM  O7   HO7   single  0.850  0.020  0.980
 PKM  O8   HO8   single  0.850  0.020  0.980
 PKM  O9   HO9   single  0.850  0.020  0.980
 PKM  C2   O2    single  1.372  0.020  1.372
 PKM  O2   H1    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
 PKM  O1    C1   C2    113.57  3.000
 PKM  O1    C1   O1B   124.62  3.000
 PKM  C2    C1   O1B   121.76  3.000
 PKM  N5    C10  O10   123.39  3.000
 PKM  N5    C10  C11   114.77  3.000
 PKM  O10   C10  C11   121.82  3.000
 PKM  H111  C11  H112  108.62  3.000
 PKM  H111  C11  H113  108.22  3.000
 PKM  H112  C11  H113  107.42  3.000
 PKM  H111  C11  C10   113.70  3.000
 PKM  H112  C11  C10   109.61  3.000
 PKM  H113  C11  C10   109.08  3.000
 PKM  O2    C2   O6    107.35  3.000
 PKM  O2    C2   C3    107.26  3.000
 PKM  O6    C2   C3    111.72  3.000
 PKM  O2    C2   C1    108.39  3.000
 PKM  C3    C2   C1    115.22  3.000
 PKM  O6    C2   C1    106.62  3.000
 PKM  H31   C3   H32   107.19  3.000
 PKM  H31   C3   C4    110.75  3.000
 PKM  H32   C3   C4    108.04  3.000
 PKM  H31   C3   C2    109.80  3.000
 PKM  H32   C3   C2    106.41  3.000
 PKM  C4    C3   C2    114.30  3.000
 PKM  H4    C4   C5    109.37  3.000
 PKM  H4    C4   O4    109.25  3.000
 PKM  C5    C4   O4    106.29  3.000
 PKM  H4    C4   C3    111.25  3.000
 PKM  O4    C4   C3    109.39  3.000
 PKM  C5    C4   C3    111.16  3.000
 PKM  C     O4   C4    119.38  3.000
 PKM  H5    C5   N5    108.14  3.000
 PKM  H5    C5   C6    109.21  3.000
 PKM  N5    C5   C6    110.39  3.000
 PKM  H5    C5   C4    109.45  3.000
 PKM  C6    C5   C4    109.16  3.000
 PKM  N5    C5   C4    110.47  3.000
 PKM  H6    C6   O6    111.36  3.000
 PKM  H6    C6   C7    107.79  3.000
 PKM  O6    C6   C7    106.05  3.000
 PKM  H6    C6   C5    108.83  3.000
 PKM  O6    C6   C5    110.40  3.000
 PKM  C7    C6   C5    112.39  3.000
 PKM  H7    C7   O7    105.88  3.000
 PKM  H7    C7   C8    108.12  3.000
 PKM  O7    C7   C8    111.53  3.000
 PKM  H7    C7   C6    107.11  3.000
 PKM  C8    C7   C6    112.04  3.000
 PKM  O7    C7   C6    111.79  3.000
 PKM  H8    C8   O8    105.67  3.000
 PKM  H8    C8   C9    108.54  3.000
 PKM  O8    C8   C9    111.74  3.000
 PKM  H8    C8   C7    108.93  3.000
 PKM  O8    C8   C7    111.42  3.000
 PKM  C9    C8   C7    110.36  3.000
 PKM  H91   C9   H92   106.81  3.000
 PKM  H91   C9   O9    111.64  3.000
 PKM  H92   C9   O9    111.69  3.000
 PKM  H91   C9   C8    108.69  3.000
 PKM  H92   C9   C8    109.15  3.000
 PKM  O9    C9   C8    108.79  3.000
 PKM  HN5   N5   C5    117.35  3.000
 PKM  HN5   N5   C10   117.97  3.000
 PKM  C5    N5   C10   124.57  3.000
 PKM  CH3   C    O     125.00  3.000
 PKM  O     C    O4    123.65  3.000
 PKM  CH3   C    O4    111.34  3.000
 PKM  H15   CH3  H16   109.77  3.000
 PKM  H15   CH3  H14   107.59  3.000
 PKM  H16   CH3  H14   108.07  3.000
 PKM  H15   CH3  C     111.97  3.000
 PKM  H16   CH3  C     110.33  3.000
 PKM  H14   CH3  C     108.99  3.000
 PKM  HOB1  O1   C1    110.84  3.000
 PKM  C6    O6   C2    119.37  3.000
 PKM  HO7   O7   C7    108.52  3.000
 PKM  HO8   O8   C8    108.84  3.000
 PKM  HO9   O9   C9    108.00  3.000
 PKM  H1    O2   C2    109.72  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
 PKM  CONST_01  C5    N5   C10  C11   180.00   0.0  0
 PKM  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 PKM  CONST_03  HOB1  O1   C1   C2    180.00   0.0  0
 PKM  CONST_04  HN5   N5   C10  C11     0.00   0.0  0
 PKM  Var_01    CH3   C    O4   C4   -179.37  30.0  3
 PKM  Var_02    H14   CH3  C    O4     82.88  30.0  3
 PKM  Var_03    H113  C11  C10  O10   -68.90  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
 PKM  chir_01  C2  C3  O6  O2  positiv
 PKM  chir_02  C4  O4  C5  C3  positiv
 PKM  chir_03  C5  N5  C6  C4  negativ
 PKM  chir_04  C6  O6  C7  C5  negativ
 PKM  chir_05  C7  O7  C6  C8  negativ
 PKM  chir_06  C8  O8  C7  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
 PKM  plan-1  C10   0.020
 PKM  plan-1  C11   0.020
 PKM  plan-1  C5    0.020
 PKM  plan-1  O10   0.020
 PKM  plan-1  N5    0.020
 PKM  plan-1  HN5   0.020
 PKM  plan-2  C1    0.020
 PKM  plan-2  O1B   0.020
 PKM  plan-2  C2    0.020
 PKM  plan-2  O1    0.020
 PKM  plan-2  HOB1  0.020
 PKM  plan-3  O4    0.020
 PKM  plan-3  C     0.020
 PKM  plan-3  O     0.020
 PKM  plan-3  CH3   0.020

