# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:44:36 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl 4,5-bis(acetylamino)-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](NC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CO)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
 6KL  6KL  'methyl 4,5-bis(acetylamino)-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  48  25  .  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_6KL
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
 6KL  C1   C  C      0   0.398  -0.4942   2.7811   1.0693
 6KL  O1   O  OC    -1  -0.590   0.3148   2.4295   1.9514
 6KL  O2   O  O2     0  -0.510  -0.6766   3.1942  -1.2567
 6KL  C2   C  CT     0   0.429  -0.2392   2.2188  -0.3692
 6KL  C3   C  CH2    0  -0.506   1.2243   1.8470  -0.6326
 6KL  C4   C  CH1    0  -0.084   1.6625   0.5507   0.0383
 6KL  O3   O  O      0  -0.588  -1.4985   3.4902   1.2131
 6KL  C11  C  CH3    0  -0.780   1.7802  -3.9967   0.8933
 6KL  C10  C  C      0   0.515   1.3817  -2.9155  -0.0812
 6KL  O10  O  O      0  -0.497   1.3781  -3.1071  -1.2885
 6KL  N5   N  NH1    0  -0.627   1.0057  -1.7533   0.4881
 6KL  C5   C  CH1    0  -0.083   0.6477  -0.5625  -0.2399
 6KL  N4   N  NH1    0  -0.625   2.9737   0.1579  -0.4267
 6KL  CA4  C  C      0   0.521   3.9387  -0.3500   0.3612
 6KL  OA4  O  O      0  -0.505   3.8400  -0.4390   1.5783
 6KL  CM4  C  CH3    0  -0.779   5.1789  -0.8132  -0.3637
 6KL  CM2  C  CH3    0  -0.421  -0.8346   2.8459  -2.6161
 6KL  O6   O  O2     0  -0.535  -1.0761   1.0920  -0.5640
 6KL  C6   C  CH1    0   0.043  -0.7612  -0.0920   0.1327
 6KL  C7   C  CH1    0  -0.027  -1.8367  -1.1033  -0.2614
 6KL  O7   O  OH1    0  -0.663  -1.8616  -1.3011  -1.6558
 6KL  C8   C  CH1    0  -0.014  -3.2249  -0.7071   0.2779
 6KL  O8   O  OH1    0  -0.659  -3.1862  -0.5038   1.6722
 6KL  C9   C  CH2    0  -0.160  -4.2684  -1.7442  -0.1081
 6KL  O9   O  OH1    0  -0.671  -5.5301  -1.3090   0.3432
 6KL  H2   H  HCH2   0   0.233   1.3768   1.7316  -1.7109
 6KL  H3   H  HCH2   0   0.252   1.8699   2.6659  -0.3095
 6KL  H4   H  HCH1   0   0.263   1.7279   0.7139   1.1117
 6KL  H5   H  HCH3   0   0.260   2.6118  -4.5696   0.4873
 6KL  H6   H  HCH3   0   0.247   2.0613  -3.6148   1.8734
 6KL  H7   H  HCH3   0   0.270   0.9433  -4.6840   1.0290
 6KL  H8   H  HNH1   0   0.394   1.1193  -1.6615   1.4853
 6KL  H9   H  HCH1   0   0.252   0.6706  -0.8050  -1.3042
 6KL  H10  H  HNH1   0   0.394   3.1210   0.1430  -1.4239
 6KL  H11  H  HCH3   0   0.248   5.1639  -0.6118  -1.4333
 6KL  H12  H  HCH3   0   0.264   6.0560  -0.3327   0.0684
 6KL  H13  H  HCH3   0   0.263   5.2956  -1.8879  -0.2196
 6KL  H14  H  HCH3   0   0.214  -1.6831   2.1783  -2.7830
 6KL  H15  H  HCH3   0   0.232  -1.0244   3.7749  -3.1523
 6KL  H16  H  HCH3   0   0.206   0.0525   2.3831  -3.0584
 6KL  H17  H  HCH1   0   0.227  -0.8061   0.0624   1.2184
 6KL  H18  H  HCH1   0   0.240  -1.5666  -2.0700   0.1790
 6KL  H19  H  HOH1   0   0.442  -1.9576  -0.4382  -2.0750
 6KL  H20  H  HCH1   0   0.232  -3.5103   0.2581  -0.1536
 6KL  H21  H  HOH1   0   0.442  -3.0013  -1.3472   2.1001
 6KL  H22  H  HCH2   0   0.206  -4.2540  -1.8833  -1.1936
 6KL  H23  H  HCH2   0   0.186  -3.9895  -2.7118   0.3396
 6KL  H24  H  HOH1   0   0.454  -6.1841  -1.9539   0.0607

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
 6KL  OA4  CA4  double  1.224  0.020  1.224
 6KL  CA4  CM4  single  1.509  0.020  1.509
 6KL  CA4  N4   single  1.345  0.020  1.345
 6KL  O3   C1   deloc   1.238  0.020  1.238
 6KL  C11  C10  single  1.509  0.020  1.509
 6KL  N4   C4   single  1.446  0.020  1.446
 6KL  C4   C5   single  1.532  0.020  1.532
 6KL  C4   C3   single  1.524  0.020  1.524
 6KL  N5   C10  single  1.348  0.020  1.348
 6KL  N5   C5   single  1.441  0.020  1.441
 6KL  O8   C8   single  1.410  0.020  1.410
 6KL  C1   O1   deloc   1.247  0.020  1.247
 6KL  C1   C2   single  1.565  0.020  1.565
 6KL  C10  O10  double  1.222  0.020  1.222
 6KL  C5   C6   single  1.531  0.020  1.531
 6KL  C3   C2   single  1.533  0.020  1.533
 6KL  C6   C7   single  1.528  0.020  1.528
 6KL  C6   O6   single  1.409  0.020  1.409
 6KL  C2   O6   single  1.417  0.020  1.417
 6KL  C2   O2   single  1.389  0.020  1.389
 6KL  C7   C8   single  1.541  0.020  1.541
 6KL  C7   O7   single  1.409  0.020  1.409
 6KL  C8   C9   single  1.521  0.020  1.521
 6KL  C9   O9   single  1.409  0.020  1.409
 6KL  O2   CM2  single  1.412  0.020  1.412
 6KL  C3   H2   single  0.970  0.020  1.090
 6KL  C3   H3   single  0.970  0.020  1.090
 6KL  C4   H4   single  0.970  0.020  1.090
 6KL  C11  H5   single  0.970  0.020  1.090
 6KL  C11  H6   single  0.970  0.020  1.090
 6KL  C11  H7   single  0.970  0.020  1.090
 6KL  N5   H8   single  0.860  0.020  1.020
 6KL  C5   H9   single  0.970  0.020  1.090
 6KL  N4   H10  single  0.860  0.020  1.020
 6KL  CM4  H11  single  0.970  0.020  1.090
 6KL  CM4  H12  single  0.970  0.020  1.090
 6KL  CM4  H13  single  0.970  0.020  1.090
 6KL  CM2  H14  single  0.970  0.020  1.090
 6KL  CM2  H15  single  0.970  0.020  1.090
 6KL  CM2  H16  single  0.970  0.020  1.090
 6KL  C6   H17  single  0.970  0.020  1.090
 6KL  C7   H18  single  0.970  0.020  1.090
 6KL  O7   H19  single  0.850  0.020  0.980
 6KL  C8   H20  single  0.970  0.020  1.090
 6KL  O8   H21  single  0.850  0.020  0.980
 6KL  C9   H22  single  0.970  0.020  1.090
 6KL  C9   H23  single  0.970  0.020  1.090
 6KL  O9   H24  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
 6KL  O3   C1   C2   116.40  3.000
 6KL  C2   C1   O1   116.29  3.000
 6KL  O3   C1   O1   127.27  3.000
 6KL  CM2  O2   C2   118.48  3.000
 6KL  O6   C2   C3   110.33  3.000
 6KL  O6   C2   O2   106.53  3.000
 6KL  C3   C2   O2   111.17  3.000
 6KL  O2   C2   C1   106.47  3.000
 6KL  O6   C2   C1   108.41  3.000
 6KL  C3   C2   C1   113.61  3.000
 6KL  H3   C3   H2   106.75  3.000
 6KL  H3   C3   C4   109.74  3.000
 6KL  H2   C3   C4   107.69  3.000
 6KL  H3   C3   C2   109.38  3.000
 6KL  H2   C3   C2   109.13  3.000
 6KL  C4   C3   C2   113.90  3.000
 6KL  H4   C4   N4   107.68  3.000
 6KL  H4   C4   C5   109.16  3.000
 6KL  N4   C4   C5   110.18  3.000
 6KL  H4   C4   C3   108.91  3.000
 6KL  C5   C4   C3   110.35  3.000
 6KL  N4   C4   C3   110.50  3.000
 6KL  H7   C11  H6   107.88  3.000
 6KL  H7   C11  H5   107.51  3.000
 6KL  H6   C11  H5   108.85  3.000
 6KL  H7   C11  C10  109.20  3.000
 6KL  H6   C11  C10  113.46  3.000
 6KL  H5   C11  C10  109.76  3.000
 6KL  N5   C10  O10  123.47  3.000
 6KL  O10  C10  C11  121.75  3.000
 6KL  N5   C10  C11  114.76  3.000
 6KL  H8   N5   C5   116.91  3.000
 6KL  H8   N5   C10  117.71  3.000
 6KL  C5   N5   C10  124.65  3.000
 6KL  H9   C5   C6   108.95  3.000
 6KL  H9   C5   N5   107.68  3.000
 6KL  C6   C5   N5   111.07  3.000
 6KL  H9   C5   C4   108.94  3.000
 6KL  C6   C5   C4   110.00  3.000
 6KL  N5   C5   C4   110.13  3.000
 6KL  H10  N4   CA4  117.96  3.000
 6KL  H10  N4   C4   117.05  3.000
 6KL  CA4  N4   C4   124.38  3.000
 6KL  CM4  CA4  OA4  121.42  3.000
 6KL  CM4  CA4  N4   115.08  3.000
 6KL  OA4  CA4  N4   123.49  3.000
 6KL  H13  CM4  H12  107.23  3.000
 6KL  H13  CM4  H11  108.28  3.000
 6KL  H12  CM4  H11  108.62  3.000
 6KL  H13  CM4  CA4  109.08  3.000
 6KL  H12  CM4  CA4  109.61  3.000
 6KL  H11  CM4  CA4  113.82  3.000
 6KL  H16  CM2  H15  107.64  3.000
 6KL  H16  CM2  H14  108.03  3.000
 6KL  H15  CM2  H14  108.09  3.000
 6KL  H16  CM2  O2   113.75  3.000
 6KL  H15  CM2  O2   106.44  3.000
 6KL  H14  CM2  O2   112.62  3.000
 6KL  C6   O6   C2   117.91  3.000
 6KL  H17  C6   C7   108.63  3.000
 6KL  H17  C6   O6   111.21  3.000
 6KL  C7   C6   O6   105.74  3.000
 6KL  H17  C6   C5   108.75  3.000
 6KL  O6   C6   C5   110.08  3.000
 6KL  C7   C6   C5   112.42  3.000
 6KL  H18  C7   C8   107.95  3.000
 6KL  H18  C7   O7   106.16  3.000
 6KL  C8   C7   O7   111.50  3.000
 6KL  H18  C7   C6   107.86  3.000
 6KL  O7   C7   C6   111.14  3.000
 6KL  C8   C7   C6   111.94  3.000
 6KL  H19  O7   C7   107.85  3.000
 6KL  H20  C8   C9   108.80  3.000
 6KL  H20  C8   O8   105.65  3.000
 6KL  C9   C8   O8   111.61  3.000
 6KL  H20  C8   C7   108.87  3.000
 6KL  C9   C8   C7   110.72  3.000
 6KL  O8   C8   C7   111.00  3.000
 6KL  H21  O8   C8   108.56  3.000
 6KL  H23  C9   H22  106.75  3.000
 6KL  H23  C9   O9   111.57  3.000
 6KL  H22  C9   O9   111.64  3.000
 6KL  H23  C9   C8   108.79  3.000
 6KL  H22  C9   C8   109.23  3.000
 6KL  O9   C9   C8   108.81  3.000
 6KL  H24  O9   C9   107.94  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
 6KL  CONST_01  OA4  CA4  N4   C4     0.00   0.0  0
 6KL  CONST_02  CM4  CA4  N4   C4   180.00   0.0  0
 6KL  CONST_03  C5   N5   C10  C11  180.00   0.0  0
 6KL  CONST_04  C5   N5   C10  O10    0.00   0.0  0
 6KL  CONST_05  H8   N5   C10  C11    0.00   0.0  0
 6KL  CONST_06  H10  N4   CA4  OA4  180.00   0.0  0
 6KL  Var_01    H14  CM2  O2   C2    70.53  30.0  3
 6KL  Var_02    H5   C11  C10  O10   38.47  30.0  3
 6KL  Var_03    H11  CM4  CA4  N4     4.10  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
 6KL  chir_01  C2  C3  O6  O2  positiv
 6KL  chir_02  C4  N4  C5  C3  positiv
 6KL  chir_03  C5  N5  C6  C4  negativ
 6KL  chir_04  C6  O6  C7  C5  negativ
 6KL  chir_05  C7  O7  C6  C8  negativ
 6KL  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
 6KL  plan-1  C11  0.020
 6KL  plan-1  C10  0.020
 6KL  plan-1  O10  0.020
 6KL  plan-1  N5   0.020
 6KL  plan-1  C5   0.020
 6KL  plan-1  H8   0.020
 6KL  plan-2  C4   0.020
 6KL  plan-2  N4   0.020
 6KL  plan-2  CA4  0.020
 6KL  plan-2  OA4  0.020
 6KL  plan-2  CM4  0.020
 6KL  plan-2  H10  0.020
 6KL  plan-3  C1   0.020
 6KL  plan-3  O1   0.020
 6KL  plan-3  C2   0.020
 6KL  plan-3  O3   0.020

