# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 30 23:18:52 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-(acetylamino)-4-O-{2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl}-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[C@@H]2O[C@@H]3CO[C@@](C)(O[C@H]3[C@H](O)[C@@H]2NC(C)=O)C(O)=O)[C@@H]1O
#
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
 KPM  KPM  2-(acetylamino)-4-O-{2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl}-2-deoxy-beta-D-glucopyranose  ligand  63  34  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KPM
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
 KPM  C1   C  CH3    0  -0.783   6.4125  -3.3892  -1.3335
 KPM  C2   C  C      0   0.524   5.5549  -2.7628  -0.2631
 KPM  O1   O  O      0  -0.494   5.4808  -3.2301   0.8623
 KPM  N1   N  NH1    0  -0.647   4.8887  -1.6529  -0.6503
 KPM  C3   C  CH1    0  -0.176   4.1154  -0.8190   0.2338
 KPM  C4   C  CH1    0   0.308   4.8525   0.4758   0.5702
 KPM  O2   O  OH1    0  -0.648   6.0066   0.1689   1.2524
 KPM  O3   O  O2     0  -0.494   4.0348   1.2653   1.3997
 KPM  C5   C  CH1    0  -0.009   2.8447   1.6884   0.7735
 KPM  C6   C  CH2    0  -0.164   2.1524   2.6631   1.7030
 KPM  O4   O  OH1    0  -0.666   2.9942   3.7712   1.8992
 KPM  C7   C  CH1    0   0.008   1.9727   0.4651   0.4585
 KPM  O5   O  O2     0  -0.500   0.8176   0.8928  -0.2415
 KPM  C8   C  CH1    0   0.300  -0.3981   0.6990   0.3737
 KPM  O6   O  O2     0  -0.483  -0.8704  -0.5865   0.0504
 KPM  C9   C  CH1    0   0.000  -2.0816  -0.8496   0.7180
 KPM  C10  C  CH2    0  -0.223  -2.5419  -2.2696   0.4476
 KPM  O7   O  O2     0  -0.496  -3.7868  -2.4623   1.0834
 KPM  C11  C  CT     0   0.379  -4.7881  -1.5555   0.6861
 KPM  C12  C  CH3    0  -0.703  -5.9867  -1.8059   1.5833
 KPM  O8   O  O2     0  -0.503  -4.3701  -0.2309   0.9304
 KPM  C13  C  CH1    0   0.012  -3.1841   0.0982   0.2522
 KPM  C14  C  CH1    0   0.050  -2.7661   1.5240   0.5431
 KPM  O9   O  OH1    0  -0.652  -3.7381   2.4026   0.0534
 KPM  C15  C  CH1    0  -0.224  -1.3851   1.7651  -0.1047
 KPM  N2   N  NH1    0  -0.613  -1.4546   1.7838  -1.5425
 KPM  C16  C  C      0   0.527  -1.5164   2.9147  -2.2683
 KPM  C17  C  CH3    0  -0.777  -1.5844   2.7144  -3.7612
 KPM  O10  O  O      0  -0.508  -1.5030   4.0324  -1.7701
 KPM  C18  C  C      0   0.358  -5.2247  -1.7726  -0.8026
 KPM  O11  O  OC    -1  -0.592  -5.0971  -2.9266  -1.2458
 KPM  O12  O  O      0  -0.589  -5.7281  -0.7897  -1.3712
 KPM  C19  C  CH1    0   0.036   2.7577  -0.5088  -0.4084
 KPM  O13  O  OH1    0  -0.648   1.9990  -1.6712  -0.5848
 KPM  H1   H  HCH3   0   0.265   6.3152  -4.4726  -1.2962
 KPM  H2   H  HCH3   0   0.251   6.1690  -3.0486  -2.3382
 KPM  H3   H  HCH3   0   0.272   7.4584  -3.1464  -1.1393
 KPM  H4   H  HNH1   0   0.403   5.0600  -1.3042  -1.5816
 KPM  H5   H  HCH1   0   0.275   3.9526  -1.3708   1.1633
 KPM  H6   H  HCH1   0   0.189   5.0664   1.0303  -0.3612
 KPM  H7   H  HOH1   0   0.466   6.6090   0.9194   1.2171
 KPM  H8   H  HCH1   0   0.229   3.0756   2.2023  -0.1744
 KPM  H9   H  HCH2   0   0.209   1.2016   2.9599   1.2470
 KPM  H10  H  HCH2   0   0.201   1.9142   2.1523   2.6465
 KPM  H11  H  HOH1   0   0.458   2.5277   4.4054   2.4507
 KPM  H12  H  HCH1   0   0.245   1.6980  -0.0334   1.3987
 KPM  H13  H  HCH1   0   0.214  -0.3089   0.7835   1.4718
 KPM  H14  H  HCH1   0   0.223  -1.9497  -0.7237   1.8055
 KPM  H15  H  HCH2   0   0.215  -2.6032  -2.4442  -0.6337
 KPM  H16  H  HCH2   0   0.248  -1.8464  -2.9979   0.8689
 KPM  H17  H  HCH3   0   0.236  -6.3552  -2.8226   1.4509
 KPM  H18  H  HCH3   0   0.236  -5.7246  -1.6664   2.6338
 KPM  H19  H  HCH3   0   0.237  -6.7948  -1.1193   1.3338
 KPM  H20  H  HCH1   0   0.221  -3.3212  -0.0132  -0.8341
 KPM  H21  H  HCH1   0   0.217  -2.6379   1.6341   1.6317
 KPM  H22  H  HOH1   0   0.451  -3.4604   3.3043   0.2446
 KPM  H23  H  HCH1   0   0.284  -1.0158   2.7389   0.2271
 KPM  H24  H  HNH1   0   0.400  -1.4815   0.9030  -2.0310
 KPM  H25  H  HCH3   0   0.265  -2.4494   3.2448  -4.1581
 KPM  H26  H  HCH3   0   0.267  -0.6973   3.1480  -4.2236
 KPM  H27  H  HCH3   0   0.248  -1.6519   1.6700  -4.0604
 KPM  H29  H  HCH1   0   0.213   2.9465  -0.0094  -1.3745
 KPM  H30  H  HOH1   0   0.450   2.4986  -2.2704  -1.1501

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
 KPM  O4   C6   single  1.405  0.020  1.405
 KPM  C6   C5   single  1.514  0.020  1.514
 KPM  O3   C5   single  1.410  0.020  1.410
 KPM  O3   C4   single  1.407  0.020  1.407
 KPM  O10  C16  double  1.224  0.020  1.224
 KPM  C5   C7   single  1.535  0.020  1.535
 KPM  O2   C4   single  1.375  0.020  1.375
 KPM  C4   C3   single  1.527  0.020  1.527
 KPM  C16  C17  single  1.508  0.020  1.508
 KPM  C16  N2   single  1.345  0.020  1.345
 KPM  C7   O5   single  1.417  0.020  1.417
 KPM  C7   C19  single  1.522  0.020  1.522
 KPM  O5   C8   single  1.376  0.020  1.376
 KPM  C3   C19  single  1.534  0.020  1.534
 KPM  C3   N1   single  1.441  0.020  1.441
 KPM  C15  N2   single  1.440  0.020  1.440
 KPM  C15  C8   single  1.530  0.020  1.530
 KPM  C15  C14  single  1.544  0.020  1.544
 KPM  O9   C14  single  1.399  0.020  1.399
 KPM  C19  O13  single  1.399  0.020  1.399
 KPM  C8   O6   single  1.407  0.020  1.407
 KPM  C14  C13  single  1.514  0.020  1.514
 KPM  N1   C2   single  1.351  0.020  1.351
 KPM  O1   C2   double  1.221  0.020  1.221
 KPM  C2   C1   single  1.508  0.020  1.508
 KPM  O6   C9   single  1.408  0.020  1.408
 KPM  C13  C9   single  1.527  0.020  1.527
 KPM  C13  O8   single  1.405  0.020  1.405
 KPM  C9   C10  single  1.517  0.020  1.517
 KPM  O8   C11  single  1.410  0.020  1.410
 KPM  O12  C18  deloc   1.242  0.020  1.242
 KPM  C10  O7   single  1.411  0.020  1.411
 KPM  C11  C18  single  1.566  0.020  1.566
 KPM  C11  O7   single  1.408  0.020  1.408
 KPM  C11  C12  single  1.518  0.020  1.518
 KPM  C18  O11  deloc   1.243  0.020  1.243
 KPM  C1   H1   single  0.970  0.020  1.090
 KPM  C1   H2   single  0.970  0.020  1.090
 KPM  C1   H3   single  0.970  0.020  1.090
 KPM  N1   H4   single  0.860  0.020  1.020
 KPM  C3   H5   single  0.970  0.020  1.090
 KPM  C4   H6   single  0.970  0.020  1.090
 KPM  O2   H7   single  0.850  0.020  0.980
 KPM  C5   H8   single  0.970  0.020  1.090
 KPM  C6   H9   single  0.970  0.020  1.090
 KPM  C6   H10  single  0.970  0.020  1.090
 KPM  O4   H11  single  0.850  0.020  0.980
 KPM  C7   H12  single  0.970  0.020  1.090
 KPM  C8   H13  single  0.970  0.020  1.090
 KPM  C9   H14  single  0.970  0.020  1.090
 KPM  C10  H15  single  0.970  0.020  1.090
 KPM  C10  H16  single  0.970  0.020  1.090
 KPM  C12  H17  single  0.970  0.020  1.090
 KPM  C12  H18  single  0.970  0.020  1.090
 KPM  C12  H19  single  0.970  0.020  1.090
 KPM  C13  H20  single  0.970  0.020  1.090
 KPM  C14  H21  single  0.970  0.020  1.090
 KPM  O9   H22  single  0.850  0.020  0.980
 KPM  C15  H23  single  0.970  0.020  1.090
 KPM  N2   H24  single  0.860  0.020  1.020
 KPM  C17  H25  single  0.970  0.020  1.090
 KPM  C17  H26  single  0.970  0.020  1.090
 KPM  C17  H27  single  0.970  0.020  1.090
 KPM  C19  H29  single  0.970  0.020  1.090
 KPM  O13  H30  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
 KPM  H3   C1   H2   108.00  3.000
 KPM  H3   C1   H1   107.52  3.000
 KPM  H2   C1   H1   108.85  3.000
 KPM  H3   C1   C2   109.05  3.000
 KPM  H2   C1   C2   113.46  3.000
 KPM  H1   C1   C2   109.78  3.000
 KPM  N1   C2   O1   123.27  3.000
 KPM  O1   C2   C1   122.00  3.000
 KPM  N1   C2   C1   114.73  3.000
 KPM  H4   N1   C3   117.22  3.000
 KPM  H4   N1   C2   117.69  3.000
 KPM  C3   N1   C2   124.36  3.000
 KPM  H5   C3   C19  109.05  3.000
 KPM  H5   C3   C4   108.21  3.000
 KPM  C19  C3   C4   110.36  3.000
 KPM  H5   C3   N1   108.03  3.000
 KPM  C19  C3   N1   109.59  3.000
 KPM  C4   C3   N1   111.52  3.000
 KPM  H6   C4   O3   109.13  3.000
 KPM  H6   C4   O2   111.57  3.000
 KPM  O3   C4   O2   108.69  3.000
 KPM  H6   C4   C3   109.46  3.000
 KPM  O2   C4   C3   108.97  3.000
 KPM  O3   C4   C3   108.97  3.000
 KPM  H7   O2   C4   109.44  3.000
 KPM  C5   O3   C4   113.40  3.000
 KPM  H8   C5   C7   108.30  3.000
 KPM  H8   C5   C6   108.87  3.000
 KPM  C7   C5   C6   112.28  3.000
 KPM  H8   C5   O3   110.18  3.000
 KPM  C7   C5   O3   109.36  3.000
 KPM  C6   C5   O3   107.85  3.000
 KPM  H10  C6   H9   107.17  3.000
 KPM  H10  C6   O4   112.11  3.000
 KPM  H9   C6   O4   111.37  3.000
 KPM  H10  C6   C5   109.08  3.000
 KPM  H9   C6   C5   108.40  3.000
 KPM  O4   C6   C5   108.62  3.000
 KPM  H11  O4   C6   108.04  3.000
 KPM  H12  C7   C19  109.03  3.000
 KPM  H12  C7   O5   110.84  3.000
 KPM  C19  C7   O5   109.41  3.000
 KPM  H12  C7   C5   109.14  3.000
 KPM  C19  C7   C5   109.50  3.000
 KPM  O5   C7   C5   108.90  3.000
 KPM  C8   O5   C7   117.19  3.000
 KPM  H13  C8   C15  108.04  3.000
 KPM  H13  C8   O6   108.98  3.000
 KPM  C15  C8   O6   110.38  3.000
 KPM  H13  C8   O5   111.23  3.000
 KPM  O6   C8   O5   108.81  3.000
 KPM  C15  C8   O5   109.39  3.000
 KPM  C9   O6   C8   110.52  3.000
 KPM  H14  C9   C13  108.45  3.000
 KPM  H14  C9   C10  108.61  3.000
 KPM  C13  C9   C10  107.91  3.000
 KPM  H14  C9   O6   110.09  3.000
 KPM  C10  C9   O6   110.57  3.000
 KPM  C13  C9   O6   111.13  3.000
 KPM  H16  C10  H15  108.05  3.000
 KPM  H16  C10  O7   107.28  3.000
 KPM  H15  C10  O7   111.91  3.000
 KPM  H16  C10  C9   111.24  3.000
 KPM  H15  C10  C9   109.98  3.000
 KPM  O7   C10  C9   108.37  3.000
 KPM  C11  O7   C10  114.35  3.000
 KPM  C18  C11  O8   112.17  3.000
 KPM  C18  C11  C12  108.59  3.000
 KPM  O8   C11  C12  106.65  3.000
 KPM  C12  C11  O7   106.77  3.000
 KPM  C18  C11  O7   112.16  3.000
 KPM  O8   C11  O7   110.19  3.000
 KPM  H19  C12  H18  108.55  3.000
 KPM  H19  C12  H17  108.03  3.000
 KPM  H18  C12  H17  108.51  3.000
 KPM  H19  C12  C11  110.26  3.000
 KPM  H18  C12  C11  110.98  3.000
 KPM  H17  C12  C11  110.43  3.000
 KPM  C13  O8   C11  112.74  3.000
 KPM  H20  C13  C14  108.62  3.000
 KPM  H20  C13  O8   110.34  3.000
 KPM  C14  C13  O8   111.15  3.000
 KPM  H20  C13  C9   109.17  3.000
 KPM  O8   C13  C9   108.47  3.000
 KPM  C14  C13  C9   109.06  3.000
 KPM  H21  C14  C15  107.15  3.000
 KPM  H21  C14  O9   111.35  3.000
 KPM  C15  C14  O9   112.12  3.000
 KPM  H21  C14  C13  108.43  3.000
 KPM  O9   C14  C13  109.42  3.000
 KPM  C15  C14  C13  108.26  3.000
 KPM  H22  O9   C14  108.57  3.000
 KPM  H23  C15  N2   107.94  3.000
 KPM  H23  C15  C14  108.29  3.000
 KPM  N2   C15  C14  112.20  3.000
 KPM  H23  C15  C8   107.93  3.000
 KPM  C14  C15  C8   109.69  3.000
 KPM  N2   C15  C8   110.64  3.000
 KPM  H24  N2   C16  118.17  3.000
 KPM  H24  N2   C15  118.31  3.000
 KPM  C16  N2   C15  123.51  3.000
 KPM  O10  C16  C17  121.66  3.000
 KPM  C17  C16  N2   115.13  3.000
 KPM  O10  C16  N2   123.21  3.000
 KPM  H27  C17  H26  108.39  3.000
 KPM  H27  C17  H25  108.53  3.000
 KPM  H26  C17  H25  107.33  3.000
 KPM  H27  C17  C16  113.73  3.000
 KPM  H26  C17  C16  109.29  3.000
 KPM  H25  C17  C16  109.38  3.000
 KPM  O12  C18  O11  127.82  3.000
 KPM  O11  C18  C11  116.04  3.000
 KPM  O12  C18  C11  116.00  3.000
 KPM  H29  C19  O13  110.99  3.000
 KPM  H29  C19  C7   107.30  3.000
 KPM  O13  C19  C7   108.89  3.000
 KPM  H29  C19  C3   107.85  3.000
 KPM  O13  C19  C3   111.39  3.000
 KPM  C7   C19  C3   110.34  3.000
 KPM  H30  O13  C19  108.03  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
 KPM  CONST_01  C3   N1   C2   C1   180.00   0.0  0
 KPM  CONST_02  C3   N1   C2   O1     0.00   0.0  0
 KPM  CONST_03  O10  C16  N2   C15    0.00   0.0  0
 KPM  CONST_04  C17  C16  N2   C15  180.00   0.0  0
 KPM  CONST_05  H4   N1   C2   C1     0.00   0.0  0
 KPM  CONST_06  H24  N2   C16  C17    0.00   0.0  0
 KPM  Var_01    H15  C10  O7   C11  -64.10  30.0  1
 KPM  Var_02    H1   C1   C2   O1    41.54  30.0  3
 KPM  Var_03    H25  C17  C16  N2   125.95  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
 KPM  chir_01  C3   C4   C19  N1   negativ
 KPM  chir_02  C4   O2   O3   C3   positiv
 KPM  chir_03  C5   O3   C6   C7   positiv
 KPM  chir_04  C7   O5   C19  C5   negativ
 KPM  chir_05  C8   O5   O6   C15  positiv
 KPM  chir_06  C9   O6   C13  C10  negativ
 KPM  chir_07  C11  O7   O8   C12  positiv
 KPM  chir_08  C13  O8   C14  C9   negativ
 KPM  chir_09  C14  O9   C15  C13  positiv
 KPM  chir_10  C15  N2   C14  C8   negativ
 KPM  chir_11  C19  O13  C7   C3   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
 KPM  plan-1  C1   0.020
 KPM  plan-1  C2   0.020
 KPM  plan-1  O1   0.020
 KPM  plan-1  N1   0.020
 KPM  plan-1  C3   0.020
 KPM  plan-1  H4   0.020
 KPM  plan-2  C15  0.020
 KPM  plan-2  N2   0.020
 KPM  plan-2  C16  0.020
 KPM  plan-2  C17  0.020
 KPM  plan-2  O10  0.020
 KPM  plan-2  H24  0.020
 KPM  plan-3  C11  0.020
 KPM  plan-3  C18  0.020
 KPM  plan-3  O11  0.020
 KPM  plan-3  O12  0.020

