# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 22:46:13 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (2S,3R,4R,5S,6R)-3-amino-4-({[(2S,3R,4R,5S,6R)-3-amino-2-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}methoxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](OCO[C@@H]3[C@@H](N)[C@@H](O)O[C@H](CO)[C@H]3O)[C@H]2N)[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
 N33  N33  '(2S,3R,4R,5S,6R)-3-amino-4-({[(2S,3R,4R,5S,6R)-3-amino-2-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}methoxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diol (non-preferred name)'  ligand  73  35  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N33
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
 N33  C11   C  CH1   0   0.309   1.5270   2.9689   1.2718
 N33  O11   O  O2    0  -0.518   2.3093   4.1032   1.3516
 N33  C21   C  CH1   0  -0.141   2.0818   1.9544   0.2834
 N33  N21   N  NH2   0  -0.794   2.3216   2.5617  -1.0097
 N33  C31   C  CH1   0  -0.041   1.1155   0.7463   0.2846
 N33  O31   O  O2    0  -0.498   1.2296   0.0567   1.5218
 N33  C41   C  CH1   0   0.025  -0.3668   1.1330   0.1222
 N33  O41   O  OH1   0  -0.664  -0.6916   1.3271  -1.2387
 N33  C51   C  CH1   0  -0.095  -0.7502   2.3542   0.9692
 N33  O51   O  O2    0  -0.507   0.2409   3.3653   0.8423
 N33  C61   C  CH2   0  -0.194  -1.0809   2.0462   2.4322
 N33  O61   O  OH1   0  -0.701  -1.4699   3.1928   3.1422
 N33  C12   C  CH1   0  -0.118   3.5119   6.7170   4.4920
 N33  N12   N  NH2   0  -0.784   3.8687   7.1841   5.8215
 N33  C22   C  CH2   0  -0.481   2.0344   6.3403   4.3543
 N33  C32   C  CH1   0  -0.077   1.6649   5.8507   2.9597
 N33  N32   N  NH2   0  -0.823   0.2466   5.5083   2.9087
 N33  C42   C  CH1   0   0.036   2.5340   4.6399   2.6472
 N33  C52   C  CH1   0  -0.002   4.0111   5.0139   2.7183
 N33  O52   O  OH1   0  -0.677   4.8346   3.9010   2.4541
 N33  C62   C  CH1   0   0.069   4.3885   5.5316   4.1034
 N33  O62   O  OH1   0  -0.671   5.7373   5.9257   4.1391
 N33  C13   C  CH1   0   0.299   2.0331  -4.9260   1.4425
 N33  O13   O  OH1   0  -0.658   2.4820  -5.9797   2.2227
 N33  C23   C  CH1   0  -0.179   1.1993  -3.9018   2.2183
 N33  N23   N  NH2   0  -0.827   0.0169  -4.5148   2.8160
 N33  C33   C  CH1   0  -0.028   0.7181  -2.8133   1.2468
 N33  O33   O  O2    0  -0.493   1.8121  -2.0573   0.7662
 N33  C43   C  CH1   0   0.024  -0.0087  -3.4463   0.0530
 N33  O43   O  OH1   0  -0.695  -1.2660  -3.9337   0.4651
 N33  C53   C  CH1   0  -0.064   0.8159  -4.5626  -0.5973
 N33  O53   O  O2    0  -0.505   1.3094  -5.4769   0.3691
 N33  C63   C  CH2   0  -0.188   1.9332  -4.0952  -1.5384
 N33  O63   O  OH1   0  -0.660   1.4278  -3.3286  -2.6065
 N33  C77   C  CH2   0   0.049   2.1771  -0.9646   1.5525
 N33  H11   H  HCH1  0   0.211   1.4735   2.4894   2.2584
 N33  H21   H  HCH1  0   0.245   3.0453   1.6010   0.6695
 N33  H211  H  HNH2  0   0.337   1.5228   3.0903  -1.3331
 N33  H212  H  HNH2  0   0.355   2.5065   1.8515  -1.7064
 N33  H31   H  HCH1  0   0.254   1.3710   0.0795  -0.5478
 N33  H41   H  HCH1  0   0.249  -0.9628   0.2735   0.4451
 N33  HO41  H  HOH1  0   0.441  -0.4084   2.2026  -1.5184
 N33  H51   H  HCH1  0   0.258  -1.6531   2.7910   0.5302
 N33  H611  H  HCH2  0   0.205  -0.2635   1.5148   2.9313
 N33  H612  H  HCH2  0   0.228  -1.9303   1.3577   2.4301
 N33  HO61  H  HOH1  0   0.451  -0.7452   3.8520   3.1518
 N33  H12   H  HCH1  0   0.228   3.7255   7.5330   3.7907
 N33  H121  H  HNH2  0   0.335   3.6039   6.4802   6.5027
 N33  H122  H  HNH2  0   0.346   3.3075   7.9970   6.0464
 N33  H221  H  HCH2  0   0.227   1.7874   5.5618   5.0865
 N33  H222  H  HCH2  0   0.250   1.4247   7.2120   4.6102
 N33  H32   H  HCH1  0   0.219   1.9060   6.6465   2.2388
 N33  H321  H  HNH2  0   0.362  -0.2880   6.2588   3.3320
 N33  H322  H  HNH2  0   0.367  -0.0549   5.4744   1.9427
 N33  H42   H  HCH1  0   0.222   2.3249   3.8702   3.4054
 N33  H52   H  HCH1  0   0.214   4.2010   5.8177   1.9889
 N33  HO52  H  HOH1  0   0.454   4.7355   3.6644   1.5267
 N33  H62   H  HCH1  0   0.195   4.2025   4.7193   4.8287
 N33  HO62  H  HOH1  0   0.445   6.2658   5.1870   3.8185
 N33  HO13  H  HOH1  0   0.448   1.7380  -6.5326   2.4889
 N33  H23   H  HCH1  0   0.247   1.8621  -3.4494   2.9701
 N33  H231  H  HNH2  0   0.365   0.2717  -5.2523   3.4615
 N33  H232  H  HNH2  0   0.376  -0.4593  -3.8246   3.3856
 N33  H33   H  HCH1  0   0.254   0.0028  -2.1617   1.7666
 N33  H43   H  HCH1  0   0.242  -0.1873  -2.6717  -0.6987
 N33  HO43  H  HOH1  0   0.445  -1.1014  -4.4310   1.2915
 N33  H53   H  HCH1  0   0.245   0.1183  -5.1501  -1.2055
 N33  H631  H  HCH2  0   0.212   2.4658  -4.9864  -1.8943
 N33  H632  H  HCH2  0   0.227   2.6612  -3.4683  -1.0266
 N33  HO63  H  HOH1  0   0.449   0.8786  -3.8977  -3.1550
 N33  H771  H  HCH2  0   0.224   2.2859  -1.2371   2.6072
 N33  H772  H  HCH2  0   0.223   3.1468  -0.6354   1.1661
 N33  H13   H  HCH1  0   0.218   2.9407  -4.4205   1.0905

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
 N33  C11  O11   single  1.380  0.020  1.380
 N33  C11  C21   single  1.521  0.020  1.521
 N33  C11  O51   single  1.413  0.020  1.413
 N33  C11  H11   single  0.970  0.020  1.090
 N33  O11  C42   single  1.420  0.020  1.420
 N33  C21  N21   single  1.449  0.020  1.449
 N33  C21  C31   single  1.547  0.020  1.547
 N33  C21  H21   single  0.970  0.020  1.090
 N33  N21  H211  single  0.890  0.020  1.040
 N33  N21  H212  single  0.890  0.020  1.040
 N33  C31  O31   single  1.421  0.020  1.421
 N33  C31  C41   single  1.540  0.020  1.540
 N33  C31  H31   single  0.970  0.020  1.090
 N33  O31  C77   single  1.393  0.020  1.393
 N33  C41  C51   single  1.535  0.020  1.535
 N33  C41  O41   single  1.413  0.020  1.413
 N33  C41  H41   single  0.970  0.020  1.090
 N33  O41  HO41  single  0.850  0.020  0.980
 N33  C51  O51   single  1.422  0.020  1.422
 N33  C51  C61   single  1.531  0.020  1.531
 N33  C51  H51   single  0.970  0.020  1.090
 N33  C61  O61   single  1.404  0.020  1.404
 N33  C61  H611  single  0.970  0.020  1.090
 N33  C61  H612  single  0.970  0.020  1.090
 N33  O61  HO61  single  0.850  0.020  0.980
 N33  C12  N12   single  1.454  0.020  1.454
 N33  C12  C62   single  1.525  0.020  1.525
 N33  C12  C22   single  1.531  0.020  1.531
 N33  C12  H12   single  0.970  0.020  1.090
 N33  N12  H121  single  0.890  0.020  1.040
 N33  N12  H122  single  0.890  0.020  1.040
 N33  C22  C32   single  1.524  0.020  1.524
 N33  C22  H221  single  0.970  0.020  1.090
 N33  C22  H222  single  0.970  0.020  1.090
 N33  C32  C42   single  1.523  0.020  1.523
 N33  C32  N32   single  1.460  0.020  1.460
 N33  C32  H32   single  0.970  0.020  1.090
 N33  N32  H321  single  0.890  0.020  1.040
 N33  N32  H322  single  0.890  0.020  1.040
 N33  C42  C52   single  1.525  0.020  1.525
 N33  C42  H42   single  0.970  0.020  1.090
 N33  C52  C62   single  1.526  0.020  1.526
 N33  C52  O52   single  1.409  0.020  1.409
 N33  C52  H52   single  0.970  0.020  1.090
 N33  O52  HO52  single  0.850  0.020  0.980
 N33  C62  O62   single  1.406  0.020  1.406
 N33  C62  H62   single  0.970  0.020  1.090
 N33  O62  HO62  single  0.850  0.020  0.980
 N33  C13  C23   single  1.532  0.020  1.532
 N33  C13  O53   single  1.407  0.020  1.407
 N33  C13  O13   single  1.386  0.020  1.386
 N33  C13  H13   single  0.970  0.020  1.090
 N33  O13  HO13  single  0.850  0.020  0.980
 N33  C23  C33   single  1.536  0.020  1.536
 N33  C23  N23   single  1.460  0.020  1.460
 N33  C23  H23   single  0.970  0.020  1.090
 N33  N23  H231  single  0.890  0.020  1.040
 N33  N23  H232  single  0.890  0.020  1.040
 N33  C33  O33   single  1.414  0.020  1.414
 N33  C33  C43   single  1.534  0.020  1.534
 N33  C33  H33   single  0.970  0.020  1.090
 N33  O33  C77   single  1.395  0.020  1.395
 N33  C43  O43   single  1.410  0.020  1.410
 N33  C43  C53   single  1.533  0.020  1.533
 N33  C43  H43   single  0.970  0.020  1.090
 N33  O43  HO43  single  0.850  0.020  0.980
 N33  C53  C63   single  1.534  0.020  1.534
 N33  C53  O53   single  1.419  0.020  1.419
 N33  C53  H53   single  0.970  0.020  1.090
 N33  C63  O63   single  1.408  0.020  1.408
 N33  C63  H631  single  0.970  0.020  1.090
 N33  C63  H632  single  0.970  0.020  1.090
 N33  O63  HO63  single  0.850  0.020  0.980
 N33  C77  H771  single  0.970  0.020  1.090
 N33  C77  H772  single  0.970  0.020  1.090

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
 N33  H11   C11  O51   110.57  3.000
 N33  H11   C11  C21   108.08  3.000
 N33  O51   C11  C21   108.76  3.000
 N33  H11   C11  O11   109.54  3.000
 N33  O51   C11  O11   107.63  3.000
 N33  C21   C11  O11   112.27  3.000
 N33  C42   O11  C11   116.93  3.000
 N33  H21   C21  C31   107.27  3.000
 N33  H21   C21  N21   107.70  3.000
 N33  C31   C21  N21   115.56  3.000
 N33  H21   C21  C11   107.86  3.000
 N33  C31   C21  C11   107.00  3.000
 N33  N21   C21  C11   111.15  3.000
 N33  H212  N21  H211  106.92  3.000
 N33  H212  N21  C21   110.52  3.000
 N33  H211  N21  C21   111.96  3.000
 N33  H31   C31  C41   107.27  3.000
 N33  H31   C31  O31   110.30  3.000
 N33  C41   C31  O31   106.91  3.000
 N33  H31   C31  C21   109.19  3.000
 N33  C41   C31  C21   113.89  3.000
 N33  O31   C31  C21   109.24  3.000
 N33  C77   O31  C31   115.44  3.000
 N33  H41   C41  C51   109.02  3.000
 N33  H41   C41  O41   105.48  3.000
 N33  C51   C41  O41   111.40  3.000
 N33  H41   C41  C31   107.20  3.000
 N33  O41   C41  C31   110.94  3.000
 N33  C51   C41  C31   112.45  3.000
 N33  HO41  O41  C41   109.73  3.000
 N33  H51   C51  C61   106.58  3.000
 N33  H51   C51  O51   104.80  3.000
 N33  C61   C51  O51   112.27  3.000
 N33  H51   C51  C41   107.58  3.000
 N33  C61   C51  C41   114.91  3.000
 N33  O51   C51  C41   110.03  3.000
 N33  C51   O51  C11   114.08  3.000
 N33  H612  C61  H611  105.97  3.000
 N33  H612  C61  O61   107.46  3.000
 N33  H611  C61  O61   111.88  3.000
 N33  H612  C61  C51   107.01  3.000
 N33  H611  C61  C51   111.83  3.000
 N33  O61   C61  C51   112.26  3.000
 N33  HO61  O61  C61   110.46  3.000
 N33  H12   C12  C62   107.67  3.000
 N33  H12   C12  C22   108.27  3.000
 N33  C62   C12  C22   109.91  3.000
 N33  H12   C12  N12   107.33  3.000
 N33  C22   C12  N12   113.46  3.000
 N33  C62   C12  N12   109.99  3.000
 N33  H122  N12  H121  105.25  3.000
 N33  H122  N12  C12   108.96  3.000
 N33  H121  N12  C12   109.09  3.000
 N33  H222  C22  H221  106.49  3.000
 N33  H222  C22  C32   109.57  3.000
 N33  H221  C22  C32   109.16  3.000
 N33  H222  C22  C12   108.71  3.000
 N33  H221  C22  C12   109.39  3.000
 N33  C32   C22  C12   113.29  3.000
 N33  H32   C32  C42   108.40  3.000
 N33  H32   C32  N32   111.07  3.000
 N33  C42   C32  N32   111.15  3.000
 N33  H32   C32  C22   108.31  3.000
 N33  N32   C32  C22   110.06  3.000
 N33  C42   C32  C22   107.75  3.000
 N33  H322  N32  H321  105.43  3.000
 N33  H322  N32  C32   109.30  3.000
 N33  H321  N32  C32   108.91  3.000
 N33  H42   C42  C52   108.87  3.000
 N33  H42   C42  C32   107.84  3.000
 N33  C52   C42  C32   110.37  3.000
 N33  H42   C42  O11   109.52  3.000
 N33  C52   C42  O11   106.76  3.000
 N33  C32   C42  O11   113.41  3.000
 N33  H52   C52  C62   108.10  3.000
 N33  H52   C52  O52   110.56  3.000
 N33  C62   C52  O52   107.07  3.000
 N33  H52   C52  C42   108.36  3.000
 N33  O52   C52  C42   111.31  3.000
 N33  C62   C52  C42   111.41  3.000
 N33  HO52  O52  C52   108.34  3.000
 N33  H62   C62  O62   110.55  3.000
 N33  H62   C62  C52   107.74  3.000
 N33  O62   C62  C52   110.82  3.000
 N33  H62   C62  C12   107.91  3.000
 N33  O62   C62  C12   109.10  3.000
 N33  C52   C62  C12   110.66  3.000
 N33  HO62  O62  C62   107.64  3.000
 N33  H13   C13  O53   111.17  3.000
 N33  H13   C13  C23   107.75  3.000
 N33  O53   C13  C23   111.61  3.000
 N33  H13   C13  O13   105.25  3.000
 N33  O53   C13  O13   107.36  3.000
 N33  C23   C13  O13   113.56  3.000
 N33  HO13  O13  C13   109.97  3.000
 N33  H23   C23  C33   109.25  3.000
 N33  H23   C23  N23   112.40  3.000
 N33  C33   C23  N23   107.62  3.000
 N33  H23   C23  C13   107.06  3.000
 N33  N23   C23  C13   111.56  3.000
 N33  C33   C23  C13   108.91  3.000
 N33  H232  N23  H231  104.82  3.000
 N33  H232  N23  C23   108.95  3.000
 N33  H231  N23  C23   111.28  3.000
 N33  H33   C33  C43   107.73  3.000
 N33  H33   C33  O33   110.34  3.000
 N33  C43   C33  O33   108.82  3.000
 N33  H33   C33  C23   108.97  3.000
 N33  C43   C33  C23   110.37  3.000
 N33  O33   C33  C23   110.57  3.000
 N33  C77   O33  C33   115.45  3.000
 N33  H43   C43  C53   108.18  3.000
 N33  H43   C43  O43   107.46  3.000
 N33  C53   C43  O43   110.61  3.000
 N33  H43   C43  C33   108.65  3.000
 N33  C53   C43  C33   112.07  3.000
 N33  O43   C43  C33   109.73  3.000
 N33  HO43  O43  C43   105.82  3.000
 N33  H53   C53  C63   106.65  3.000
 N33  H53   C53  O53   104.70  3.000
 N33  C63   C53  O53   111.16  3.000
 N33  H53   C53  C43   106.46  3.000
 N33  O53   C53  C43   111.56  3.000
 N33  C63   C53  C43   115.49  3.000
 N33  C53   O53  C13   116.50  3.000
 N33  H632  C63  H631  107.19  3.000
 N33  H632  C63  O63   106.44  3.000
 N33  H631  C63  O63   111.73  3.000
 N33  H632  C63  C53   111.97  3.000
 N33  H631  C63  C53   107.76  3.000
 N33  O63   C63  C53   111.70  3.000
 N33  HO63  O63  C63   108.37  3.000
 N33  H772  C77  H771  109.08  3.000
 N33  H772  C77  O33   105.57  3.000
 N33  H771  C77  O33   111.97  3.000
 N33  H772  C77  O31   111.98  3.000
 N33  H771  C77  O31   105.74  3.000
 N33  O33   C77  O31   112.57  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
 N33  Var_01  O33  C77  O31  C31  -69.17  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
 N33  chir_01  C11  O11  C21  O51  positiv
 N33  chir_02  C21  N21  C31  C11  positiv
 N33  chir_03  C31  O31  C41  C21  negativ
 N33  chir_04  C41  O41  C31  C51  negativ
 N33  chir_05  C51  O51  C41  C61  negativ
 N33  chir_06  C12  N12  C62  C22  negativ
 N33  chir_07  C32  N32  C42  C22  positiv
 N33  chir_08  C42  O11  C52  C32  negativ
 N33  chir_09  C52  O52  C42  C62  negativ
 N33  chir_10  C62  O62  C52  C12  positiv
 N33  chir_11  C13  C23  O53  O13  positiv
 N33  chir_12  C23  N23  C33  C13  positiv
 N33  chir_13  C33  O33  C43  C23  negativ
 N33  chir_14  C43  O43  C33  C53  negativ
 N33  chir_15  C53  O53  C43  C63  negativ

