# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:00:36 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)C[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
 TOY  TOY  '(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside'  ligand  69  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOY
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
 TOY  C11   C  CH1   0   0.310  -1.2379  -0.1423  -2.9612
 TOY  O11   O  O2    0  -0.533  -0.3073  -1.0202  -2.3896
 TOY  C21   C  CH1   0  -0.143  -1.9850  -0.9360  -4.0301
 TOY  N21   N  NH2   0  -0.793  -2.6034  -2.1077  -3.4369
 TOY  C31   C  CH2   0  -0.510  -1.0603  -1.2066  -5.2167
 TOY  C41   C  CH1   0   0.061  -0.4346   0.0866  -5.7272
 TOY  O41   O  OH1   0  -0.676   0.5253  -0.1419  -6.7354
 TOY  C51   C  CH1   0   0.019   0.2656   0.8085  -4.5807
 TOY  O51   O  O2    0  -0.517  -0.6482   0.9995  -3.5063
 TOY  C61   C  CH2   0  -0.300   0.7650   2.1904  -4.9597
 TOY  N61   N  NH2   0  -0.798   1.4737   2.8032  -3.8484
 TOY  C12   C  CH1   0  -0.109   2.2961  -1.0498   0.9659
 TOY  N12   N  NH2   0  -0.802   3.2816  -0.6378   1.9590
 TOY  C22   C  CH2   0  -0.471   2.8468  -1.1751  -0.4493
 TOY  C32   C  CH1   0  -0.103   1.7703  -1.5833  -1.4455
 TOY  N32   N  NH2   0  -0.798   2.3497  -1.6833  -2.7747
 TOY  C42   C  CH1   0   0.066   0.6392  -0.5544  -1.4473
 TOY  C52   C  CH1   0   0.025   0.0478  -0.4188  -0.0448
 TOY  O52   O  OH1   0  -0.671  -0.9453   0.5786  -0.0736
 TOY  C62   C  CH1   0   0.052   1.1389  -0.0596   0.9682
 TOY  O62   O  O2    0  -0.518   0.5872  -0.0407   2.2656
 TOY  C13   C  CH1   0   0.221   0.3754   1.1788   2.9058
 TOY  C23   C  CH1   0   0.026   0.9920   1.1111   4.3026
 TOY  O23   O  OH1   0  -0.708   2.3585   0.8064   4.2513
 TOY  C33   C  CH1   0  -0.156   0.2114   0.1606   5.2260
 TOY  N33   N  NH2   0  -0.786   0.6997   0.1714   6.5940
 TOY  C43   C  CH1   0   0.047  -1.2766   0.5064   5.1847
 TOY  O43   O  OH1   0  -0.666  -1.9864  -0.4608   5.9220
 TOY  C53   C  CH1   0  -0.027  -1.7481   0.5327   3.7260
 TOY  O53   O  O2    0  -0.502  -0.9862   1.4711   2.9806
 TOY  C63   C  CH2   0  -0.163  -3.1981   0.9246   3.5531
 TOY  O63   O  OH1   0  -0.667  -3.5198   0.7906   2.1873
 TOY  H11   H  HCH1  0   0.230  -1.9403   0.2294  -2.2126
 TOY  H21   H  HCH1  0   0.237  -2.7974  -0.2844  -4.3711
 TOY  HN21  H  HNH2  0   0.347  -3.1864  -2.5631  -4.1279
 TOY  HN22  H  HNH2  0   0.339  -1.8889  -2.7801  -3.1868
 TOY  H311  H  HCH2  0   0.227  -0.2669  -1.9038  -4.9264
 TOY  H312  H  HCH2  0   0.241  -1.6297  -1.6893  -6.0180
 TOY  H41   H  HCH1  0   0.192  -1.2406   0.7396  -6.1004
 TOY  H41O  H  HOH1  0   0.452   0.0967  -0.6146  -7.4555
 TOY  H51   H  HCH1  0   0.219   1.1248   0.2083  -4.2489
 TOY  H611  H  HCH2  0   0.190  -0.0864   2.7818  -5.3311
 TOY  H612  H  HCH2  0   0.228   1.4590   2.0841  -5.7947
 TOY  HN61  H  HNH2  0   0.347   1.8122   3.7148  -4.1272
 TOY  HN62  H  HNH2  0   0.341   0.8293   2.9677  -3.0865
 TOY  HN11  H  HNH2  0   0.368   3.9398  -1.3903   2.1226
 TOY  HN12  H  HNH2  0   0.355   3.8302   0.1334   1.5927
 TOY  H221  H  HCH2  0   0.250   3.6562  -1.9108  -0.4597
 TOY  H222  H  HCH2  0   0.225   3.2837  -0.2193  -0.7621
 TOY  H32   H  HCH1  0   0.203   1.3417  -2.5409  -1.1037
 TOY  HN1   H  HNH2  0   0.347   3.0852  -2.3796  -2.7635
 TOY  HN2   H  HNH2  0   0.350   1.6520  -2.0313  -3.4192
 TOY  H42   H  HCH1  0   0.223   1.0563   0.4138  -1.7591
 TOY  H52   H  HCH1  0   0.206  -0.3805  -1.3921   0.2425
 TOY  H52O  H  HOH1  0   0.447  -1.4484   0.5665   0.7490
 TOY  H62   H  HCH1  0   0.221   1.5326   0.9353   0.7063
 TOY  H13   H  HCH1  0   0.243   0.8282   1.9995   2.3362
 TOY  H23   H  HCH1  0   0.212   0.9051   2.1194   4.7307
 TOY  H23O  H  HOH1  0   0.458   2.5511   0.1658   3.5274
 TOY  H33   H  HCH1  0   0.229   0.3250  -0.8633   4.8471
 TOY  HN31  H  HNH2  0   0.344   1.6796  -0.0840   6.5900
 TOY  HN32  H  HNH2  0   0.333   0.6694   1.1196   6.9544
 TOY  H43   H  HCH1  0   0.210  -1.4171   1.5107   5.6140
 TOY  H43O  H  HOH1  0   0.453  -2.8085  -0.0734   6.2338
 TOY  H53   H  HCH1  0   0.224  -1.6216  -0.4794   3.3159
 TOY  H631  H  HCH2  0   0.201  -3.8207   0.2708   4.1740
 TOY  H632  H  HCH2  0   0.202  -3.3465   1.9528   3.9100
 TOY  H63O  H  HOH1  0   0.460  -4.4460   1.0184   2.0669
 TOY  H12   H  HCH1  0   0.241   1.9090  -2.0258   1.2795

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
 TOY  C11  O11   single  1.401  0.020  1.401
 TOY  C11  C21   single  1.527  0.020  1.527
 TOY  C11  O51   single  1.396  0.020  1.396
 TOY  C11  H11   single  0.970  0.020  1.090
 TOY  O11  C42   single  1.414  0.020  1.414
 TOY  C21  N21   single  1.452  0.020  1.452
 TOY  C21  C31   single  1.529  0.020  1.529
 TOY  C21  H21   single  0.970  0.020  1.090
 TOY  N21  HN21  single  0.890  0.020  1.040
 TOY  N21  HN22  single  0.890  0.020  1.040
 TOY  C31  C41   single  1.525  0.020  1.525
 TOY  C31  H311  single  0.970  0.020  1.090
 TOY  C31  H312  single  0.970  0.020  1.090
 TOY  C41  O41   single  1.411  0.020  1.411
 TOY  C41  C51   single  1.525  0.020  1.525
 TOY  C41  H41   single  0.970  0.020  1.090
 TOY  O41  H41O  single  0.850  0.020  0.980
 TOY  C51  O51   single  1.423  0.020  1.423
 TOY  C51  C61   single  1.517  0.020  1.517
 TOY  C51  H51   single  0.970  0.020  1.090
 TOY  C61  N61   single  1.454  0.020  1.454
 TOY  C61  H611  single  0.970  0.020  1.090
 TOY  C61  H612  single  0.970  0.020  1.090
 TOY  N61  HN61  single  0.890  0.020  1.040
 TOY  N61  HN62  single  0.890  0.020  1.040
 TOY  C12  N12   single  1.459  0.020  1.459
 TOY  C12  C22   single  1.524  0.020  1.524
 TOY  C12  C62   single  1.523  0.020  1.523
 TOY  C12  H12   single  0.970  0.020  1.090
 TOY  N12  HN11  single  0.890  0.020  1.040
 TOY  N12  HN12  single  0.890  0.020  1.040
 TOY  C22  C32   single  1.522  0.020  1.522
 TOY  C22  H221  single  0.970  0.020  1.090
 TOY  C22  H222  single  0.970  0.020  1.090
 TOY  C32  N32   single  1.453  0.020  1.453
 TOY  C32  C42   single  1.529  0.020  1.529
 TOY  C32  H32   single  0.970  0.020  1.090
 TOY  N32  HN1   single  0.890  0.020  1.040
 TOY  N32  HN2   single  0.890  0.020  1.040
 TOY  C42  C52   single  1.528  0.020  1.528
 TOY  C42  H42   single  0.970  0.020  1.090
 TOY  C52  O52   single  1.408  0.020  1.408
 TOY  C52  C62   single  1.531  0.020  1.531
 TOY  C52  H52   single  0.970  0.020  1.090
 TOY  O52  H52O  single  0.850  0.020  0.980
 TOY  C62  O62   single  1.410  0.020  1.410
 TOY  C62  H62   single  0.970  0.020  1.090
 TOY  O62  C13   single  1.394  0.020  1.394
 TOY  C13  C23   single  1.528  0.020  1.528
 TOY  C13  O53   single  1.395  0.020  1.395
 TOY  C13  H13   single  0.970  0.020  1.090
 TOY  C23  O23   single  1.401  0.020  1.401
 TOY  C23  C33   single  1.538  0.020  1.538
 TOY  C23  H23   single  0.970  0.020  1.090
 TOY  O23  H23O  single  0.850  0.020  0.980
 TOY  C33  N33   single  1.453  0.020  1.453
 TOY  C33  C43   single  1.528  0.020  1.528
 TOY  C33  H33   single  0.970  0.020  1.090
 TOY  N33  HN31  single  0.890  0.020  1.040
 TOY  N33  HN32  single  0.890  0.020  1.040
 TOY  C43  O43   single  1.408  0.020  1.408
 TOY  C43  C53   single  1.533  0.020  1.533
 TOY  C43  H43   single  0.970  0.020  1.090
 TOY  O43  H43O  single  0.850  0.020  0.980
 TOY  C53  O53   single  1.420  0.020  1.420
 TOY  C53  C63   single  1.512  0.020  1.512
 TOY  C53  H53   single  0.970  0.020  1.090
 TOY  C63  O63   single  1.410  0.020  1.410
 TOY  C63  H631  single  0.970  0.020  1.090
 TOY  C63  H632  single  0.970  0.020  1.090
 TOY  O63  H63O  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
 TOY  H11   C11  O51   105.13  3.000
 TOY  H11   C11  C21   110.01  3.000
 TOY  O51   C11  C21   111.01  3.000
 TOY  H11   C11  O11   111.15  3.000
 TOY  O51   C11  O11   113.03  3.000
 TOY  C21   C11  O11   106.55  3.000
 TOY  C42   O11  C11   120.65  3.000
 TOY  H21   C21  C31   108.19  3.000
 TOY  H21   C21  N21   106.94  3.000
 TOY  C31   C21  N21   115.60  3.000
 TOY  H21   C21  C11   105.76  3.000
 TOY  C31   C21  C11   109.84  3.000
 TOY  N21   C21  C11   110.00  3.000
 TOY  HN22  N21  HN21  106.03  3.000
 TOY  HN22  N21  C21   109.66  3.000
 TOY  HN21  N21  C21   109.24  3.000
 TOY  H312  C31  H311  106.86  3.000
 TOY  H312  C31  C41   110.02  3.000
 TOY  H311  C31  C41   109.35  3.000
 TOY  H312  C31  C21   109.36  3.000
 TOY  H311  C31  C21   110.19  3.000
 TOY  C41   C31  C21   110.98  3.000
 TOY  H41   C41  C51   108.05  3.000
 TOY  H41   C41  O41   110.57  3.000
 TOY  C51   C41  O41   107.55  3.000
 TOY  H41   C41  C31   108.41  3.000
 TOY  C51   C41  C31   109.77  3.000
 TOY  O41   C41  C31   112.40  3.000
 TOY  H41O  O41  C41   108.14  3.000
 TOY  H51   C51  C61   108.38  3.000
 TOY  H51   C51  O51   110.32  3.000
 TOY  C61   C51  O51   106.12  3.000
 TOY  H51   C51  C41   109.10  3.000
 TOY  C61   C51  C41   113.23  3.000
 TOY  O51   C51  C41   109.65  3.000
 TOY  C51   O51  C11   117.14  3.000
 TOY  H612  C61  H611  106.62  3.000
 TOY  H612  C61  N61   108.43  3.000
 TOY  H611  C61  N61   114.11  3.000
 TOY  H612  C61  C51   108.17  3.000
 TOY  H611  C61  C51   108.59  3.000
 TOY  N61   C61  C51   110.70  3.000
 TOY  HN62  N61  HN61  105.91  3.000
 TOY  HN62  N61  C61   109.51  3.000
 TOY  HN61  N61  C61   109.41  3.000
 TOY  H12   C12  C62   108.07  3.000
 TOY  H12   C12  C22   108.68  3.000
 TOY  C62   C12  C22   109.24  3.000
 TOY  H12   C12  N12   107.18  3.000
 TOY  C62   C12  N12   109.19  3.000
 TOY  C22   C12  N12   114.30  3.000
 TOY  HN12  N12  HN11  105.75  3.000
 TOY  HN12  N12  C12   109.52  3.000
 TOY  HN11  N12  C12   109.82  3.000
 TOY  H222  C22  H221  106.78  3.000
 TOY  H222  C22  C32   109.19  3.000
 TOY  H221  C22  C32   109.67  3.000
 TOY  H222  C22  C12   109.71  3.000
 TOY  H221  C22  C12   109.36  3.000
 TOY  C32   C22  C12   111.98  3.000
 TOY  H32   C32  C42   107.27  3.000
 TOY  H32   C32  N32   112.24  3.000
 TOY  C42   C32  N32   109.89  3.000
 TOY  H32   C32  C22   107.74  3.000
 TOY  C42   C32  C22   110.09  3.000
 TOY  N32   C32  C22   109.57  3.000
 TOY  HN2   N32  HN1   105.74  3.000
 TOY  HN2   N32  C32   109.35  3.000
 TOY  HN1   N32  C32   109.07  3.000
 TOY  H42   C42  C52   109.21  3.000
 TOY  H42   C42  C32   108.19  3.000
 TOY  C52   C42  C32   110.18  3.000
 TOY  H42   C42  O11   110.79  3.000
 TOY  C52   C42  O11   112.44  3.000
 TOY  C32   C42  O11   105.91  3.000
 TOY  H52   C52  C62   108.16  3.000
 TOY  H52   C52  O52   110.92  3.000
 TOY  C62   C52  O52   110.49  3.000
 TOY  H52   C52  C42   108.14  3.000
 TOY  C62   C52  C42   110.62  3.000
 TOY  O52   C52  C42   108.49  3.000
 TOY  H52O  O52  C52   109.98  3.000
 TOY  H62   C62  O62   110.27  3.000
 TOY  H62   C62  C52   108.01  3.000
 TOY  O62   C62  C52   109.45  3.000
 TOY  H62   C62  C12   108.38  3.000
 TOY  O62   C62  C12   107.91  3.000
 TOY  C52   C62  C12   112.82  3.000
 TOY  C13   O62  C62   119.60  3.000
 TOY  H13   C13  O53   105.91  3.000
 TOY  H13   C13  C23   109.95  3.000
 TOY  O53   C13  C23   110.74  3.000
 TOY  H13   C13  O62   110.70  3.000
 TOY  O53   C13  O62   110.88  3.000
 TOY  C23   C13  O62   108.65  3.000
 TOY  H23   C23  C33   107.04  3.000
 TOY  H23   C23  O23   106.91  3.000
 TOY  C33   C23  O23   112.49  3.000
 TOY  H23   C23  C13   106.47  3.000
 TOY  C33   C23  C13   111.80  3.000
 TOY  O23   C23  C13   111.70  3.000
 TOY  H23O  O23  C23   111.03  3.000
 TOY  H33   C33  C43   107.61  3.000
 TOY  H33   C33  N33   107.29  3.000
 TOY  C43   C33  N33   110.55  3.000
 TOY  H33   C33  C23   108.47  3.000
 TOY  C43   C33  C23   109.76  3.000
 TOY  N33   C33  C23   112.97  3.000
 TOY  HN32  N33  HN31  105.43  3.000
 TOY  HN32  N33  C33   109.35  3.000
 TOY  HN31  N33  C33   108.64  3.000
 TOY  H43   C43  C53   108.42  3.000
 TOY  H43   C43  O43   110.97  3.000
 TOY  C53   C43  O43   110.79  3.000
 TOY  H43   C43  C33   108.66  3.000
 TOY  C53   C43  C33   109.21  3.000
 TOY  O43   C43  C33   108.74  3.000
 TOY  H43O  O43  C43   108.92  3.000
 TOY  H53   C53  C63   107.84  3.000
 TOY  H53   C53  O53   110.54  3.000
 TOY  C63   C53  O53   106.45  3.000
 TOY  H53   C53  C43   107.68  3.000
 TOY  C63   C53  C43   114.09  3.000
 TOY  O53   C53  C43   110.23  3.000
 TOY  C53   O53  C13   114.42  3.000
 TOY  H632  C63  H631  107.32  3.000
 TOY  H632  C63  O63   111.90  3.000
 TOY  H631  C63  O63   111.26  3.000
 TOY  H632  C63  C53   109.58  3.000
 TOY  H631  C63  C53   108.99  3.000
 TOY  O63   C63  C53   107.76  3.000
 TOY  H63O  O63  C63   108.58  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
 TOY  Var_01  HN61  N61  C61  C51  178.97  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
 TOY  chir_01  C11  O11  C21  O51  positiv
 TOY  chir_02  C21  N21  C31  C11  positiv
 TOY  chir_03  C41  O41  C51  C31  positiv
 TOY  chir_04  C51  O51  C41  C61  negativ
 TOY  chir_05  C12  N12  C22  C62  positiv
 TOY  chir_06  C32  N32  C42  C22  positiv
 TOY  chir_07  C42  O11  C52  C32  negativ
 TOY  chir_08  C52  O52  C42  C62  negativ
 TOY  chir_09  C62  O62  C12  C52  negativ
 TOY  chir_10  C13  O62  O53  C23  negativ
 TOY  chir_11  C23  O23  C13  C33  negativ
 TOY  chir_12  C33  N33  C43  C23  negativ
 TOY  chir_13  C43  O43  C53  C33  positiv
 TOY  chir_14  C53  O53  C43  C63  negativ

