# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:00:43 2022
#   Inital geometry file: a 156 line input string
#   Ligand name: N-[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]-N'-[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]butanediamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](Cn2cc(CNC(=O)CCC(=O)N[C@@H]3O[C@@H](CO)[C@H](O)[C@H](O)[C@H]3O)nn2)[C@@H](O)[C@H](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
 S3W  S3W  'N-[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]-N'-[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]butanediamide (non-preferred name)'  ligand  70  37  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S3W
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
 S3W  N5    N  N     0  -0.317  64.5706  30.1587   2.0381
 S3W  N4    N  N     0  -0.108  64.4915  31.4239   1.8031
 S3W  N3    N  NR5   0  -0.251  65.6884  31.9481   1.9995
 S3W  N1    N  NH1   0  -0.690  65.4405  27.7268   8.8898
 S3W  N2    N  NH1   0  -0.640  67.1411  28.3879   3.8634
 S3W  C17   C  CR16  0   0.036  65.7822  35.5760   3.1252
 S3W  C16   C  CR16  0  -0.027  65.7866  36.1889   4.5208
 S3W  C18   C  CR16  0   0.015  65.7517  34.0556   3.2513
 S3W  C14   C  CR16  0   0.259  66.8833  34.0954   5.3513
 S3W  C15   C  CR16  0  -0.007  66.9512  35.6197   5.3287
 S3W  C12   C  CR5   0   0.149  65.8336  29.8491   2.3954
 S3W  C13   C  CR15  0  -0.067  66.5696  31.0064   2.3770
 S3W  C19   C  CH2   0  -0.322  65.8803  33.3783   1.8973
 S3W  C4    C  CH1   0  -0.002  61.9602  26.0993  10.5323
 S3W  C3    C  CH1   0   0.010  63.2482  25.8941  11.3236
 S3W  C5    C  CH1   0  -0.013  62.2817  26.0377   9.0440
 S3W  C1    C  CH1   0   0.209  64.4966  26.7672   9.3548
 S3W  C2    C  CH1   0  -0.026  64.3104  26.8867  10.8715
 S3W  C7    C  C     0   0.574  66.3218  27.5005   7.8843
 S3W  C8    C  CH2   0  -0.592  67.2290  28.6716   7.5773
 S3W  C9    C  CH2   0  -0.585  67.7945  28.6230   6.1737
 S3W  C10   C  C     0   0.578  66.7157  28.6473   5.1126
 S3W  O18   O  O     0  -0.503  66.8381  33.6056   4.0359
 S3W  O14   O  O2    0  -0.488  65.7890  33.7064   6.1056
 S3W  O15   O  OH1   0  -0.665  66.9658  36.0888   6.6526
 S3W  O16   O  OH1   0  -0.672  65.9005  37.5879   4.3703
 S3W  O17   O  OH1   0  -0.668  64.6574  35.9665   2.3813
 S3W  O5    O  O2    0  -0.485  63.2717  26.9830   8.6932
 S3W  O2    O  OH1   0  -0.663  65.4964  26.5790  11.5619
 S3W  O3    O  OH1   0  -0.668  62.9425  26.0265  12.6888
 S3W  O4    O  OH1   0  -0.667  61.3593  27.3371  10.8206
 S3W  O10   O  O     0  -0.485  65.5475  28.9013   5.3664
 S3W  O7    O  O     0  -0.477  66.4189  26.4297   7.3125
 S3W  HN1   H  HNH1  0   0.403  65.3643  28.6673   9.2493
 S3W  HN2   H  HNH1  0   0.406  68.1176  28.2021   3.7028
 S3W  HC17  H  HCR6  0   0.214  66.7167  35.8648   2.6159
 S3W  HC16  H  HCR6  0   0.226  64.8412  35.9265   5.0145
 S3W  HC18  H  HCR6  0   0.243  64.7920  33.7615   3.6987
 S3W  HC14  H  HCR6  0   0.236  67.8107  33.6788   5.7693
 S3W  HC15  H  HCR6  0   0.228  67.8851  35.8806   4.8109
 S3W  HC13  H  HCR5  0   0.303  67.6031  31.2176   2.5899
 S3W  H19A  H  HCH2  0   0.279  66.8632  33.5711   1.4659
 S3W  H19B  H  HCH2  0   0.295  65.1267  33.7593   1.2121
 S3W  HC4   H  HCH1  0   0.232  61.2786  25.2653  10.7585
 S3W  HC3   H  HCH1  0   0.213  63.6164  24.8801  11.0980
 S3W  HC5   H  HCH1  0   0.226  62.6489  25.0180   8.8414
 S3W  HC1   H  HCH1  0   0.225  64.8810  25.7644   9.1248
 S3W  HC2   H  HCH1  0   0.226  63.9644  27.9049  11.1012
 S3W  HC8B  H  HCH2  0   0.291  68.0559  28.6430   8.2935
 S3W  HC8A  H  HCH2  0   0.267  66.7105  29.6152   7.7555
 S3W  HC9B  H  HCH2  0   0.271  68.4291  27.7452   6.0371
 S3W  HC9A  H  HCH2  0   0.287  68.4442  29.4893   6.0188
 S3W  HO15  H  HOH1  0   0.454  67.3409  36.9743   6.6556
 S3W  HO16  H  HOH1  0   0.458  65.4716  38.0192   5.1146
 S3W  HO17  H  HOH1  0   0.453  64.6437  36.9290   2.3468
 S3W  HO2   H  HOH1  0   0.457  66.0969  27.3287  11.5023
 S3W  HO3   H  HOH1  0   0.453  63.7660  26.0304  13.1887
 S3W  HO4   H  HOH1  0   0.450  61.2508  27.3997  11.7757
 S3W  HO6   H  HOH1  0   0.454  60.6278  26.1922   6.2967
 S3W  C11   C  CH2   0  -0.368  66.2617  28.4551   2.7210
 S3W  C20   C  CH3   0  -0.411  65.6778  32.3099   6.2921
 S3W  C6    C  CH2   0  -0.155  61.0609  26.2810   8.1815
 S3W  O6    O  OH1   0  -0.666  61.3866  25.9768   6.8462
 S3W  H20B  H  HCH3  0   0.236  64.9437  32.1438   7.0788
 S3W  H20C  H  HCH3  0   0.219  65.3403  31.7935   5.3903
 S3W  H20A  H  HCH3  0   0.211  66.6291  31.8649   6.6057
 S3W  H11A  H  HCH2  0   0.263  65.3739  27.8410   2.8820
 S3W  H11B  H  HCH2  0   0.276  66.7974  28.0164   1.8787
 S3W  HC6B  H  HCH2  0   0.206  60.7304  27.3199   8.2930
 S3W  HC6A  H  HCH2  0   0.201  60.2504  25.6422   8.5569

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
 S3W  C19  N3    single    1.447  0.020  1.447
 S3W  C19  C18   single    1.519  0.020  1.519
 S3W  O18  C18   single    1.414  0.020  1.414
 S3W  O18  C14   single    1.404  0.020  1.404
 S3W  N3   N4    aromatic  1.321  0.020  1.321
 S3W  N3   C13   aromatic  1.344  0.020  1.344
 S3W  C17  C18   single    1.526  0.020  1.526
 S3W  C17  O17   single    1.404  0.020  1.404
 S3W  C17  C16   single    1.524  0.020  1.524
 S3W  N4   N5    aromatic  1.289  0.020  1.289
 S3W  C13  C12   aromatic  1.372  0.020  1.372
 S3W  C15  C14   single    1.526  0.020  1.526
 S3W  C15  C16   single    1.527  0.020  1.527
 S3W  C15  O15   single    1.405  0.020  1.405
 S3W  C14  O14   single    1.385  0.020  1.385
 S3W  O16  C16   single    1.412  0.020  1.412
 S3W  N5   C12   aromatic  1.349  0.020  1.349
 S3W  C12  C11   single    1.494  0.020  1.494
 S3W  C11  N2    single    1.443  0.020  1.443
 S3W  O14  C20   single    1.413  0.020  1.413
 S3W  N2   C10   single    1.345  0.020  1.345
 S3W  C10  O10   double    1.222  0.020  1.222
 S3W  C10  C9    single    1.513  0.020  1.513
 S3W  O6   C6    single    1.408  0.020  1.408
 S3W  C9   C8    single    1.514  0.020  1.514
 S3W  C6   C5    single    1.514  0.020  1.514
 S3W  O7   C7    double    1.218  0.020  1.218
 S3W  C8   C7    single    1.513  0.020  1.513
 S3W  O5   C5    single    1.413  0.020  1.413
 S3W  O5   C1    single    1.409  0.020  1.409
 S3W  C7   N1    single    1.356  0.020  1.356
 S3W  C5   C4    single    1.524  0.020  1.524
 S3W  N1   C1    single    1.424  0.020  1.424
 S3W  C1   C2    single    1.533  0.020  1.533
 S3W  C4   O4    single    1.406  0.020  1.406
 S3W  C4   C3    single    1.526  0.020  1.526
 S3W  C2   C3    single    1.523  0.020  1.523
 S3W  C2   O2    single    1.406  0.020  1.406
 S3W  C3   O3    single    1.405  0.020  1.405
 S3W  N1   HN1   single    0.860  0.020  1.020
 S3W  N2   HN2   single    0.860  0.020  1.020
 S3W  C17  HC17  single    0.970  0.020  1.090
 S3W  C16  HC16  single    0.970  0.020  1.090
 S3W  C18  HC18  single    0.970  0.020  1.090
 S3W  C14  HC14  single    0.970  0.020  1.090
 S3W  C15  HC15  single    0.970  0.020  1.090
 S3W  C20  H20B  single    0.970  0.020  1.090
 S3W  C20  H20C  single    0.970  0.020  1.090
 S3W  C20  H20A  single    0.970  0.020  1.090
 S3W  C11  H11A  single    0.970  0.020  1.090
 S3W  C11  H11B  single    0.970  0.020  1.090
 S3W  C13  HC13  single    0.930  0.020  1.080
 S3W  C19  H19A  single    0.970  0.020  1.090
 S3W  C19  H19B  single    0.970  0.020  1.090
 S3W  C4   HC4   single    0.970  0.020  1.090
 S3W  C3   HC3   single    0.970  0.020  1.090
 S3W  C5   HC5   single    0.970  0.020  1.090
 S3W  C1   HC1   single    0.970  0.020  1.090
 S3W  C2   HC2   single    0.970  0.020  1.090
 S3W  C6   HC6B  single    0.970  0.020  1.090
 S3W  C6   HC6A  single    0.970  0.020  1.090
 S3W  C8   HC8B  single    0.970  0.020  1.090
 S3W  C8   HC8A  single    0.970  0.020  1.090
 S3W  C9   HC9B  single    0.970  0.020  1.090
 S3W  C9   HC9A  single    0.970  0.020  1.090
 S3W  O15  HO15  single    0.850  0.020  0.980
 S3W  O16  HO16  single    0.850  0.020  0.980
 S3W  O17  HO17  single    0.850  0.020  0.980
 S3W  O2   HO2   single    0.850  0.020  0.980
 S3W  O3   HO3   single    0.850  0.020  0.980
 S3W  O4   HO4   single    0.850  0.020  0.980
 S3W  O6   HO6   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
 S3W  C12   N5   N4    109.33  3.000
 S3W  N3    N4   N5    107.86  3.000
 S3W  C19   N3   C13   128.73  3.000
 S3W  C13   N3   N4    110.96  3.000
 S3W  C19   N3   N4    120.13  3.000
 S3W  HN1   N1   C7    117.93  3.000
 S3W  HN1   N1   C1    117.48  3.000
 S3W  C7    N1   C1    124.09  3.000
 S3W  HN2   N2   C10   119.38  3.000
 S3W  HN2   N2   C11   118.24  3.000
 S3W  C10   N2   C11   122.24  3.000
 S3W  HC17  C17  O17   111.18  3.000
 S3W  HC17  C17  C18   108.42  3.000
 S3W  O17   C17  C18   107.76  3.000
 S3W  HC17  C17  C16   108.37  3.000
 S3W  O17   C17  C16   112.06  3.000
 S3W  C18   C17  C16   108.97  3.000
 S3W  HC16  C16  O16   110.75  3.000
 S3W  HC16  C16  C15   109.23  3.000
 S3W  O16   C16  C15   111.35  3.000
 S3W  HC16  C16  C17   108.24  3.000
 S3W  O16   C16  C17   107.53  3.000
 S3W  C15   C16  C17   109.67  3.000
 S3W  HC18  C18  O18   111.10  3.000
 S3W  HC18  C18  C19   108.50  3.000
 S3W  O18   C18  C19   106.72  3.000
 S3W  HC18  C18  C17   108.52  3.000
 S3W  O18   C18  C17   110.35  3.000
 S3W  C19   C18  C17   111.64  3.000
 S3W  HC14  C14  O14   110.68  3.000
 S3W  HC14  C14  O18   104.55  3.000
 S3W  O14   C14  O18   112.75  3.000
 S3W  HC14  C14  C15   110.28  3.000
 S3W  O14   C14  C15   108.89  3.000
 S3W  O18   C14  C15   109.63  3.000
 S3W  HC15  C15  O15   110.85  3.000
 S3W  HC15  C15  C14   106.37  3.000
 S3W  O15   C15  C14   108.67  3.000
 S3W  HC15  C15  C16   108.07  3.000
 S3W  O15   C15  C16   112.46  3.000
 S3W  C14   C15  C16   110.25  3.000
 S3W  C13   C12  C11   129.52  3.000
 S3W  C11   C12  N5    122.70  3.000
 S3W  C13   C12  N5    107.77  3.000
 S3W  HC13  C13  C12   132.70  3.000
 S3W  HC13  C13  N3    123.22  3.000
 S3W  C12   C13  N3    104.07  3.000
 S3W  H19B  C19  H19A  108.26  3.000
 S3W  H19B  C19  C18   110.28  3.000
 S3W  H19A  C19  C18   110.49  3.000
 S3W  H19B  C19  N3    107.40  3.000
 S3W  H19A  C19  N3    108.80  3.000
 S3W  C18   C19  N3    111.50  3.000
 S3W  HC4   C4   O4    111.12  3.000
 S3W  HC4   C4   C5    107.51  3.000
 S3W  O4    C4   C5    109.03  3.000
 S3W  HC4   C4   C3    108.32  3.000
 S3W  O4    C4   C3    111.89  3.000
 S3W  C5    C4   C3    108.85  3.000
 S3W  HC3   C3   O3    111.00  3.000
 S3W  HC3   C3   C2    107.81  3.000
 S3W  O3    C3   C2    112.26  3.000
 S3W  HC3   C3   C4    107.43  3.000
 S3W  O3    C3   C4    107.91  3.000
 S3W  C2    C3   C4    110.32  3.000
 S3W  HC5   C5   O5    109.86  3.000
 S3W  HC5   C5   C6    108.20  3.000
 S3W  O5    C5   C6    108.42  3.000
 S3W  HC5   C5   C4    106.68  3.000
 S3W  O5    C5   C4    111.30  3.000
 S3W  C6    C5   C4    112.31  3.000
 S3W  HC1   C1   O5    110.23  3.000
 S3W  HC1   C1   C2    108.72  3.000
 S3W  O5    C1   C2    110.31  3.000
 S3W  HC1   C1   N1    108.35  3.000
 S3W  C2    C1   N1    110.56  3.000
 S3W  O5    C1   N1    108.65  3.000
 S3W  HC2   C2   O2    111.43  3.000
 S3W  HC2   C2   C1    108.49  3.000
 S3W  O2    C2   C1    111.48  3.000
 S3W  HC2   C2   C3    108.79  3.000
 S3W  O2    C2   C3    107.45  3.000
 S3W  C1    C2   C3    109.13  3.000
 S3W  O7    C7   C8    122.51  3.000
 S3W  C8    C7   N1    114.27  3.000
 S3W  O7    C7   N1    123.15  3.000
 S3W  HC8A  C8   HC8B  105.95  3.000
 S3W  HC8A  C8   C9    110.89  3.000
 S3W  HC8B  C8   C9    108.89  3.000
 S3W  HC8A  C8   C7    110.56  3.000
 S3W  HC8B  C8   C7    107.46  3.000
 S3W  C9    C8   C7    112.78  3.000
 S3W  HC9A  C9   HC9B  105.89  3.000
 S3W  HC9A  C9   C10   108.15  3.000
 S3W  HC9B  C9   C10   109.85  3.000
 S3W  HC9A  C9   C8    109.13  3.000
 S3W  HC9B  C9   C8    111.03  3.000
 S3W  C10   C9   C8    112.53  3.000
 S3W  O10   C10  C9    122.63  3.000
 S3W  C9    C10  N2    115.00  3.000
 S3W  O10   C10  N2    122.36  3.000
 S3W  C14   O18  C18   115.70  3.000
 S3W  C20   O14  C14   114.31  3.000
 S3W  HO15  O15  C15   108.34  3.000
 S3W  HO16  O16  C16   109.03  3.000
 S3W  HO17  O17  C17   107.96  3.000
 S3W  C1    O5   C5    112.96  3.000
 S3W  HO2   O2   C2    108.98  3.000
 S3W  HO3   O3   C3    108.57  3.000
 S3W  HO4   O4   C4    107.98  3.000
 S3W  H11B  C11  H11A  106.69  3.000
 S3W  H11B  C11  C12   110.36  3.000
 S3W  H11A  C11  C12   108.91  3.000
 S3W  H11B  C11  N2    107.06  3.000
 S3W  H11A  C11  N2    110.65  3.000
 S3W  C12   C11  N2    112.99  3.000
 S3W  H20A  C20  H20C  108.20  3.000
 S3W  H20A  C20  H20B  108.45  3.000
 S3W  H20C  C20  H20B  108.42  3.000
 S3W  H20A  C20  O14   111.75  3.000
 S3W  H20C  C20  O14   112.48  3.000
 S3W  H20B  C20  O14   107.41  3.000
 S3W  HC6A  C6   HC6B  107.11  3.000
 S3W  HC6A  C6   O6    111.67  3.000
 S3W  HC6B  C6   O6    111.78  3.000
 S3W  HC6A  C6   C5    107.87  3.000
 S3W  HC6B  C6   C5    109.72  3.000
 S3W  O6    C6   C5    108.60  3.000
 S3W  HO6   O6   C6    108.13  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
 S3W  CONST_01  C13   N3   N4   N5      0.00   0.0  0
 S3W  CONST_02  N3    C13  C12  N5      0.00   0.0  0
 S3W  CONST_03  C12   C13  N3   N4      0.00   0.0  0
 S3W  CONST_04  C13   C12  N5   N4      0.00   0.0  0
 S3W  CONST_05  C12   N5   N4   N3      0.00   0.0  0
 S3W  CONST_06  C19   N3   N4   N5    180.00   0.0  0
 S3W  CONST_07  C11   C12  N5   N4    180.00   0.0  0
 S3W  CONST_08  C11   C12  C13  N3    180.00   0.0  0
 S3W  CONST_09  C19   N3   C13  C12   180.00   0.0  0
 S3W  CONST_10  HC13  C13  C12  N5    180.00   0.0  0
 S3W  CONST_11  O7    C7   N1   C1      0.00   0.0  0
 S3W  CONST_12  C8    C7   N1   C1    180.00   0.0  0
 S3W  CONST_13  O10   C10  N2   C11     0.00   0.0  0
 S3W  CONST_14  C9    C10  N2   C11   180.00   0.0  0
 S3W  CONST_15  HN1   N1   C7   C8      0.00   0.0  0
 S3W  CONST_16  HN2   N2   C10  C9      0.00   0.0  0
 S3W  Var_01    C18   C19  N3   N4     93.47  30.0  1
 S3W  Var_02    N2    C11  C12  N5   -138.49  30.0  2
 S3W  Var_03    C10   N2   C11  C12    69.20  30.0  3
 S3W  Var_04    H20B  C20  O14  C14   166.64  30.0  3
 S3W  Var_05    C9    C8   C7   N1   -157.46  30.0  2
 S3W  Var_06    C8    C9   C10  N2   -169.64  30.0  3
 S3W  Var_07    C10   C9   C8   C7     60.36  30.0  1

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
 S3W  chir_01  C17  C18  O17  C16  negativ
 S3W  chir_02  C16  O16  C15  C17  positiv
 S3W  chir_03  C18  O18  C19  C17  positiv
 S3W  chir_04  C14  O18  O14  C15  positiv
 S3W  chir_05  C15  O15  C14  C16  negativ
 S3W  chir_06  C4   C5   O4   C3   positiv
 S3W  chir_07  C3   O3   C2   C4   positiv
 S3W  chir_08  C5   O5   C4   C6   negativ
 S3W  chir_09  C1   O5   N1   C2   negativ
 S3W  chir_10  C2   O2   C1   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
 S3W  plan-1  N5    0.020
 S3W  plan-1  N4    0.020
 S3W  plan-1  N3    0.020
 S3W  plan-1  C12   0.020
 S3W  plan-1  C13   0.020
 S3W  plan-1  C19   0.020
 S3W  plan-1  HC13  0.020
 S3W  plan-1  C11   0.020
 S3W  plan-2  N1    0.020
 S3W  plan-2  C1    0.020
 S3W  plan-2  C7    0.020
 S3W  plan-2  C8    0.020
 S3W  plan-2  O7    0.020
 S3W  plan-2  HN1   0.020
 S3W  plan-3  N2    0.020
 S3W  plan-3  C9    0.020
 S3W  plan-3  C10   0.020
 S3W  plan-3  O10   0.020
 S3W  plan-3  HN2   0.020
 S3W  plan-3  C11   0.020

