# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 07:46:14 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: a 3 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=O)N[C@@H]1[C@@H](O)C(=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)n2cc(nn2)c3ccccc3
#
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
 8LM  8LM  '2,6-anhydro-3,5-dideoxy-5-[(2-methylpropanoyl)amino]-3-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-D-galacto-non-2-enoni c acid'  D-saccharide  59  33  .  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_8LM
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
 8LM  C10   C  C     0   0.596   -2.2470  31.2063  -30.3056
 8LM  C13   C  CH3   0  -0.648    0.2013  30.7207  -30.4976
 8LM  C4    C  CH1   0   0.025   -5.7718  31.0572  -31.0524
 8LM  C3    C  C     0   0.161   -6.9701  31.9686  -31.1615
 8LM  C20   C  CR5   0   0.160   -9.9941  30.4639  -30.1438
 8LM  C21   C  CR6   0   0.065  -11.0712  29.9456  -29.3043
 8LM  C22   C  CR16  0  -0.335  -10.9620  29.9682  -27.9129
 8LM  C24   C  CR16  0  -0.267  -13.1346  28.9574  -27.6933
 8LM  C26   C  CR16  0  -0.292  -12.2295  29.4188  -29.8773
 8LM  C8    C  CH1   0   0.027   -3.2545  35.0942  -32.9072
 8LM  O8    O  OH1   0  -0.660   -4.2073  36.1005  -32.6873
 8LM  C7    C  CH1   0  -0.051   -3.3229  33.9329  -31.9055
 8LM  O7    O  OH1   0  -0.701   -3.1234  34.4878  -30.6267
 8LM  C6    C  CH1   0   0.045   -4.5732  33.0560  -31.9344
 8LM  C5    C  CH1   0  -0.173   -4.5187  31.9135  -30.9119
 8LM  N5    N  NH1   0  -0.638   -3.3497  31.0858  -31.0623
 8LM  C11   C  CH1   0  -0.383   -1.2018  30.1274  -30.4943
 8LM  C12   C  CH3   0  -0.648   -1.3653  29.0846  -29.3857
 8LM  O10   O  O     0  -0.513   -2.1026  32.1153  -29.4903
 8LM  O4    O  OH1   0  -0.644   -5.8832  30.2289  -29.9276
 8LM  N18   N  NR5   0  -0.349   -8.2211  31.3537  -30.9539
 8LM  C19   C  CR15  0  -0.083   -8.8283  31.0940  -29.7849
 8LM  C23   C  CR16  0  -0.235  -11.9845  29.4795  -27.1149
 8LM  C25   C  CR16  0  -0.239  -13.2508  28.9293  -29.0769
 8LM  N27   N  N     0  -0.320  -10.0061  30.3766  -31.4970
 8LM  N28   N  N     0  -0.086   -8.9433  30.9077  -31.9762
 8LM  C2    C  C     0   0.242   -6.8590  33.2809  -31.4004
 8LM  C1    C  C     0   0.522   -8.0261  34.2244  -31.3906
 8LM  O1B   O  OH1   0  -0.572   -7.6328  35.4754  -31.5152
 8LM  O1A   O  O     0  -0.410   -9.1705  33.8750  -31.2687
 8LM  O6    O  O2    0  -0.447   -5.6999  33.8815  -31.6473
 8LM  H1    H  HCH3  0   0.235    0.3239  31.4703  -31.2802
 8LM  H2    H  HCH3  0   0.228    0.4362  31.1863  -29.5407
 8LM  H3    H  HCH3  0   0.237    0.9347  29.9338  -30.6754
 8LM  H4    H  HCH1  0   0.268   -5.7030  30.4574  -31.9708
 8LM  H9    H  HCR6  0   0.249  -10.0719  30.3676  -27.4426
 8LM  H10   H  HCR6  0   0.258  -13.9335  28.5754  -27.0713
 8LM  H23   H  HCR6  0   0.254  -12.3339  29.3930  -30.9541
 8LM  HO9   H  HOH1  0   0.456   -4.5365  33.8470  -35.6055
 8LM  H8    H  HCH1  0   0.215   -2.2344  35.4927  -32.7756
 8LM  HO8   H  HOH1  0   0.447   -4.2480  36.2835  -31.7437
 8LM  H7    H  HCH1  0   0.228   -2.4911  33.2725  -32.1871
 8LM  HO7   H  HOH1  0   0.462   -2.7873  33.7849  -30.0446
 8LM  H6    H  HCH1  0   0.269   -4.6951  32.6354  -32.9384
 8LM  H5    H  HCH1  0   0.291   -4.5156  32.3335  -29.9021
 8LM  HN5   H  HNH1  0   0.409   -3.3810  30.3448  -31.7459
 8LM  H11   H  HCH1  0   0.259   -1.3751  29.6336  -31.4550
 8LM  H20   H  HCH3  0   0.243   -0.6422  28.2809  -29.5246
 8LM  H21   H  HCH3  0   0.231   -1.1931  29.5265  -28.4035
 8LM  H22   H  HCH3  0   0.238   -2.3617  28.6416  -29.3908
 8LM  HO4   H  HOH1  0   0.470   -6.2270  29.3723  -30.1963
 8LM  H24   H  HCR5  0   0.311   -8.4101  31.3877  -28.8383
 8LM  H25   H  HCR6  0   0.260  -11.8808  29.5057  -26.0380
 8LM  H26   H  HCR6  0   0.259  -14.1425  28.5243  -29.5374
 8LM  HO1B  H  HOH1  0   0.493   -8.4040  36.0627  -31.4890
 8LM  C9    C  CH2   0  -0.186   -3.3111  34.6754  -34.3630
 8LM  H91   H  HCH2  0   0.204   -2.5337  33.9168  -34.5209
 8LM  O9    O  OH1   0  -0.658   -4.5904  34.2046  -34.7148
 8LM  H92   H  HCH2  0   0.216   -3.0272  35.5425  -34.9745

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
 8LM  O9   C9    single    1.408  0.020  1.408
 8LM  C9   C8    single    1.516  0.020  1.516
 8LM  C8   O8    single    1.403  0.020  1.403
 8LM  C8   C7    single    1.535  0.020  1.535
 8LM  C7   C6    single    1.527  0.020  1.527
 8LM  C7   O7    single    1.408  0.020  1.408
 8LM  O1A  C1    double    1.203  0.020  1.203
 8LM  N28  N27   aromatic  1.281  0.020  1.281
 8LM  N28  N18   aromatic  1.329  0.020  1.329
 8LM  C6   O6    single    1.426  0.020  1.426
 8LM  C6   C5    single    1.534  0.020  1.534
 8LM  N27  C20   aromatic  1.356  0.020  1.356
 8LM  O6   C2    single    1.329  0.020  1.329
 8LM  C1   C2    single    1.501  0.020  1.501
 8LM  C1   O1B   single    1.317  0.020  1.317
 8LM  C3   C2    double    1.339  0.020  1.339
 8LM  C3   C4    single    1.509  0.020  1.509
 8LM  C3   N18   single    1.409  0.020  1.409
 8LM  N5   C5    single    1.440  0.020  1.440
 8LM  N5   C10   single    1.343  0.020  1.343
 8LM  C4   C5    single    1.524  0.020  1.524
 8LM  C4   O4    single    1.401  0.020  1.401
 8LM  N18  C19   aromatic  1.343  0.020  1.343
 8LM  C12  C11   single    1.531  0.020  1.531
 8LM  C20  C19   aromatic  1.373  0.020  1.373
 8LM  C20  C21   single    1.461  0.020  1.461
 8LM  C11  C10   single    1.514  0.020  1.514
 8LM  C11  C13   single    1.523  0.020  1.523
 8LM  C10  O10   double    1.230  0.020  1.230
 8LM  C26  C21   aromatic  1.396  0.020  1.396
 8LM  C26  C25   aromatic  1.387  0.020  1.387
 8LM  C21  C22   aromatic  1.396  0.020  1.396
 8LM  C25  C24   aromatic  1.389  0.020  1.389
 8LM  C22  C23   aromatic  1.386  0.020  1.386
 8LM  C24  C23   aromatic  1.389  0.020  1.389
 8LM  C13  H1    single    0.970  0.020  1.090
 8LM  C13  H2    single    0.970  0.020  1.090
 8LM  C13  H3    single    0.970  0.020  1.090
 8LM  C4   H4    single    0.970  0.020  1.090
 8LM  C22  H9    single    0.930  0.020  1.080
 8LM  C24  H10   single    0.930  0.020  1.080
 8LM  C26  H23   single    0.930  0.020  1.080
 8LM  O9   HO9   single    0.850  0.020  0.980
 8LM  C9   H91   single    0.970  0.020  1.090
 8LM  C9   H92   single    0.970  0.020  1.090
 8LM  C8   H8    single    0.970  0.020  1.090
 8LM  O8   HO8   single    0.850  0.020  0.980
 8LM  C7   H7    single    0.970  0.020  1.090
 8LM  O7   HO7   single    0.850  0.020  0.980
 8LM  C6   H6    single    0.970  0.020  1.090
 8LM  C5   H5    single    0.970  0.020  1.090
 8LM  N5   HN5   single    0.860  0.020  1.020
 8LM  C11  H11   single    0.970  0.020  1.090
 8LM  C12  H20   single    0.970  0.020  1.090
 8LM  C12  H21   single    0.970  0.020  1.090
 8LM  C12  H22   single    0.970  0.020  1.090
 8LM  O4   HO4   single    0.850  0.020  0.980
 8LM  C19  H24   single    0.930  0.020  1.080
 8LM  C23  H25   single    0.930  0.020  1.080
 8LM  C25  H26   single    0.930  0.020  1.080
 8LM  O1B  HO1B  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
 8LM  O10   C10  C11  121.90  3.000
 8LM  O10   C10  N5   122.44  3.000
 8LM  C11   C10  N5   115.64  3.000
 8LM  H3    C13  H2   107.85  3.000
 8LM  H3    C13  H1   107.66  3.000
 8LM  H2    C13  H1   108.19  3.000
 8LM  H3    C13  C11  109.81  3.000
 8LM  H2    C13  C11  111.29  3.000
 8LM  H1    C13  C11  111.89  3.000
 8LM  H4    C4   O4   110.68  3.000
 8LM  H4    C4   C5   109.40  3.000
 8LM  O4    C4   C5   108.87  3.000
 8LM  H4    C4   C3   108.59  3.000
 8LM  O4    C4   C3   110.60  3.000
 8LM  C5    C4   C3   108.67  3.000
 8LM  C2    C3   N18  121.86  3.000
 8LM  N18   C3   C4   115.50  3.000
 8LM  C2    C3   C4   122.61  3.000
 8LM  N27   C20  C19  107.33  3.000
 8LM  C19   C20  C21  129.70  3.000
 8LM  N27   C20  C21  122.96  3.000
 8LM  C26   C21  C22  118.71  3.000
 8LM  C22   C21  C20  120.63  3.000
 8LM  C26   C21  C20  120.66  3.000
 8LM  H9    C22  C23  119.10  3.000
 8LM  H9    C22  C21  120.21  3.000
 8LM  C23   C22  C21  120.69  3.000
 8LM  H10   C24  C25  120.25  3.000
 8LM  H10   C24  C23  120.30  3.000
 8LM  C25   C24  C23  119.45  3.000
 8LM  H23   C26  C25  119.66  3.000
 8LM  H23   C26  C21  119.85  3.000
 8LM  C25   C26  C21  120.50  3.000
 8LM  H8    C8   C7   103.69  3.000
 8LM  H8    C8   O8   110.50  3.000
 8LM  C7    C8   O8   114.21  3.000
 8LM  H8    C8   C9   104.41  3.000
 8LM  C7    C8   C9   114.58  3.000
 8LM  O8    C8   C9   108.86  3.000
 8LM  HO8   O8   C8   108.60  3.000
 8LM  H7    C7   C6   105.65  3.000
 8LM  H7    C7   O7   111.25  3.000
 8LM  C6    C7   O7   111.06  3.000
 8LM  H7    C7   C8   104.70  3.000
 8LM  O7    C7   C8   106.75  3.000
 8LM  C6    C7   C8   117.28  3.000
 8LM  HO7   O7   C7   107.92  3.000
 8LM  H6    C6   O6   108.60  3.000
 8LM  H6    C6   C5   109.20  3.000
 8LM  O6    C6   C5   108.96  3.000
 8LM  H6    C6   C7   109.20  3.000
 8LM  C5    C6   C7   112.70  3.000
 8LM  O6    C6   C7   108.10  3.000
 8LM  H5    C5   N5   108.35  3.000
 8LM  H5    C5   C6   109.24  3.000
 8LM  N5    C5   C6   112.78  3.000
 8LM  H5    C5   C4   107.65  3.000
 8LM  N5    C5   C4   109.56  3.000
 8LM  C6    C5   C4   109.13  3.000
 8LM  HN5   N5   C5   117.90  3.000
 8LM  HN5   N5   C10  118.25  3.000
 8LM  C5    N5   C10  123.79  3.000
 8LM  H11   C11  C12  108.15  3.000
 8LM  H11   C11  C13  108.65  3.000
 8LM  C12   C11  C13  111.42  3.000
 8LM  H11   C11  C10  108.77  3.000
 8LM  C13   C11  C10  111.02  3.000
 8LM  C12   C11  C10  108.75  3.000
 8LM  H22   C12  H21  108.25  3.000
 8LM  H22   C12  H20  107.82  3.000
 8LM  H21   C12  H20  107.98  3.000
 8LM  H22   C12  C11  111.77  3.000
 8LM  H21   C12  C11  111.06  3.000
 8LM  H20   C12  C11  109.82  3.000
 8LM  HO4   O4   C4   109.32  3.000
 8LM  N28   N18  C19  111.05  3.000
 8LM  C19   N18  C3   127.88  3.000
 8LM  N28   N18  C3   121.04  3.000
 8LM  H24   C19  N18  122.52  3.000
 8LM  H24   C19  C20  133.27  3.000
 8LM  N18   C19  C20  104.19  3.000
 8LM  H25   C23  C24  120.18  3.000
 8LM  H25   C23  C22  119.58  3.000
 8LM  C24   C23  C22  120.24  3.000
 8LM  H26   C25  C26  119.56  3.000
 8LM  H26   C25  C24  120.03  3.000
 8LM  C26   C25  C24  120.41  3.000
 8LM  N28   N27  C20  109.83  3.000
 8LM  N27   N28  N18  107.59  3.000
 8LM  O6    C2   C1   113.30  3.000
 8LM  C1    C2   C3   123.41  3.000
 8LM  O6    C2   C3   123.29  3.000
 8LM  O1A   C1   O1B  124.72  3.000
 8LM  O1B   C1   C2   111.36  3.000
 8LM  O1A   C1   C2   123.91  3.000
 8LM  HO1B  O1B  C1   109.58  3.000
 8LM  C2    O6   C6   117.71  3.000
 8LM  H92   C9   H91  106.40  3.000
 8LM  H92   C9   C8   107.87  3.000
 8LM  H91   C9   C8   107.62  3.000
 8LM  H92   C9   O9   111.09  3.000
 8LM  H91   C9   O9   112.12  3.000
 8LM  C8    C9   O9   111.49  3.000
 8LM  HO9   O9   C9   107.76  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
 8LM  CONST_01  N18   N28  N27  C20    0.00   0.0  0
 8LM  CONST_02  N28   N18  C19  C20    0.00   0.0  0
 8LM  CONST_03  C25   C26  C21  C20  180.00   0.0  0
 8LM  CONST_04  C23   C22  C21  C20  180.00   0.0  0
 8LM  CONST_05  N28   N27  C20  C21  180.00   0.0  0
 8LM  CONST_06  N18   C19  C20  C21  180.00   0.0  0
 8LM  CONST_07  C24   C25  C26  C21    0.00   0.0  0
 8LM  CONST_08  C24   C23  C22  C21    0.00   0.0  0
 8LM  CONST_09  N27   C20  C21  C22  180.00   0.0  0
 8LM  CONST_10  C19   C20  C21  C22    0.00   0.0  0
 8LM  CONST_11  C25   C26  C21  C22    0.00   0.0  0
 8LM  CONST_12  C25   C24  C23  C22    0.00   0.0  0
 8LM  CONST_13  N27   C20  C21  C26    0.00   0.0  0
 8LM  CONST_14  C19   C20  C21  C26  180.00   0.0  0
 8LM  CONST_15  C23   C22  C21  C26    0.00   0.0  0
 8LM  CONST_16  C23   C24  C25  C26    0.00   0.0  0
 8LM  CONST_17  N27   C20  C19  N18    0.00   0.0  0
 8LM  CONST_18  N27   N28  N18  C19    0.00   0.0  0
 8LM  CONST_19  N28   N27  C20  C19    0.00   0.0  0
 8LM  CONST_20  N27   N28  N18  C3   180.00   0.0  0
 8LM  CONST_21  C20   C19  N18  C3   180.00   0.0  0
 8LM  CONST_22  H24   C19  N18  C3     0.00   0.0  0
 8LM  CONST_23  H23   C26  C21  C20    0.00   0.0  0
 8LM  CONST_24  H9    C22  C21  C20    0.00   0.0  0
 8LM  CONST_25  H26   C25  C26  C21  180.00   0.0  0
 8LM  CONST_26  H25   C23  C22  C21  180.00   0.0  0
 8LM  CONST_27  H10   C24  C23  C22  180.00   0.0  0
 8LM  CONST_28  C11   C10  N5   C5   180.00   0.0  0
 8LM  CONST_29  O10   C10  N5   C5     0.00   0.0  0
 8LM  CONST_30  HO1B  O1B  C1   C2   180.00   0.0  0
 8LM  CONST_31  HN5   N5   C10  C11    0.00   0.0  0
 8LM  Var_01    O6    C2   C3   C4     4.48  30.0  1
 8LM  Var_02    N28   N18  C3   C4   -94.63  30.0  2
 8LM  Var_03    O1A   C1   C2   C3    -5.84  30.0  3
 8LM  Var_04    N5    C10  C11  C13  138.97  30.0  3
 8LM  Var_05    H20   C12  C11  C10  178.08  30.0  3
 8LM  Var_06    H1    C13  C11  C10  -58.20  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
 8LM  chir_01  C4  C3  C5  O4  negativ
 8LM  chir_02  C8  O8  C7  C9  negativ
 8LM  chir_03  C7  O7  C8  C6  positiv
 8LM  chir_04  C6  O6  C5  C7  positiv
 8LM  chir_05  C5  N5  C4  C6  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
 8LM  plan-1  C3    0.020
 8LM  plan-1  C20   0.020
 8LM  plan-1  C21   0.020
 8LM  plan-1  N18   0.020
 8LM  plan-1  C19   0.020
 8LM  plan-1  N27   0.020
 8LM  plan-1  N28   0.020
 8LM  plan-1  H24   0.020
 8LM  plan-2  C20   0.020
 8LM  plan-2  C21   0.020
 8LM  plan-2  C22   0.020
 8LM  plan-2  C24   0.020
 8LM  plan-2  C26   0.020
 8LM  plan-2  C23   0.020
 8LM  plan-2  C25   0.020
 8LM  plan-2  H9    0.020
 8LM  plan-2  H10   0.020
 8LM  plan-2  H23   0.020
 8LM  plan-2  H25   0.020
 8LM  plan-2  H26   0.020
 8LM  plan-3  C10   0.020
 8LM  plan-3  C5    0.020
 8LM  plan-3  N5    0.020
 8LM  plan-3  C11   0.020
 8LM  plan-3  O10   0.020
 8LM  plan-3  HN5   0.020
 8LM  plan-4  C2    0.020
 8LM  plan-4  C1    0.020
 8LM  plan-4  O1B   0.020
 8LM  plan-4  O1A   0.020
 8LM  plan-4  HO1B  0.020

