# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:03:29 2022
#   Inital geometry file: a 168 line input string
#   Ligand name: (2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2N)[C@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H]3O)[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
 B31  B31  (2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide  ligand  79  38  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B31
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
 B31  C01   C  CH1   0  -0.112  -2.6843  -0.0368  -0.4309
 B31  C02   C  CH2   0  -0.460  -2.2167  -1.4858  -0.4521
 B31  C03   C  CH1   0  -0.106  -0.8408  -1.6031  -1.0967
 B31  C04   C  CH1   0   0.071   0.1642  -0.7611  -0.3094
 B31  C05   C  CH1   0   0.014  -0.2873   0.7021  -0.3165
 B31  C06   C  CH1   0   0.065  -1.6728   0.8379   0.3127
 B31  N01   N  NH1   0  -0.642  -3.9928   0.0865   0.1729
 B31  N03   N  NH2   0  -0.792  -0.4294  -2.9951  -1.1179
 B31  O04   O  O2    0  -0.521   1.4239  -0.9170  -0.9284
 B31  O05   O  O2    0  -0.503   0.6369   1.4753   0.4098
 B31  O06   O  OH1   0  -0.660  -2.0304   2.1953   0.2791
 B31  C11   C  CH1   0   0.267   2.5737  -0.7699  -0.1431
 B31  C12   C  CH1   0  -0.153   3.7886  -0.8957  -1.0627
 B31  C13   C  CH1   0   0.043   3.9132  -2.3299  -1.5573
 B31  C14   C  CH1   0   0.002   3.9481  -3.2862  -0.3732
 B31  C15   C  CH1   0   0.005   2.7473  -3.0656   0.5487
 B31  C16   C  CH2   0  -0.303   2.8853  -3.8311   1.8522
 B31  N12   N  NH2   0  -0.814   3.6917   0.0258  -2.1785
 B31  N16   N  NH2   0  -0.796   1.6973  -3.6883   2.6764
 B31  O11   O  O2    0  -0.511   2.6479  -1.6929   0.9034
 B31  O13   O  OH1   0  -0.676   5.0948  -2.4260  -2.3216
 B31  O14   O  OH1   0  -0.677   3.9632  -4.6027  -0.8862
 B31  C21   C  CH1   0   0.302   0.8973   2.7694  -0.0351
 B31  C22   C  CH1   0  -0.076   0.9092   3.7397   1.1530
 B31  C23   C  CH1   0  -0.025   2.3694   3.6719   1.6005
 B31  C24   C  CH1   0   0.020   3.0800   3.5532   0.2561
 B31  C25   C  CH2   0  -0.172   4.4261   2.8668   0.3003
 B31  O21   O  O2    0  -0.510   2.1806   2.8503  -0.5982
 B31  O22   O  OH1   0  -0.673   0.6623   5.0606   0.7374
 B31  O23   O  OH1   0  -0.658   2.6343   2.5280   2.3697
 B31  O25   O  OH1   0  -0.671   4.9943   2.9407  -0.9895
 B31  C51   C  C     0   0.508  -5.0451   0.6915  -0.3969
 B31  C52   C  CH1   0  -0.084  -6.3460   0.6246   0.4008
 B31  C53   C  CH2   0  -0.455  -7.0621  -0.6892   0.0780
 B31  C54   C  CH2   0  -0.276  -8.3099  -0.9019   0.9219
 B31  N54   N  NH2   0  -0.801  -8.9430  -2.1682   0.5785
 B31  O51   O  O     0  -0.491  -5.0239   1.2300  -1.4945
 B31  O52   O  OH1   0  -0.658  -7.1307   1.7548   0.1341
 B31  H01   H  HCH1  0   0.259  -2.7721   0.3272  -1.4571
 B31  H02   H  HCH2  0   0.234  -2.1723  -1.8867   0.5664
 B31  H02A  H  HCH2  0   0.260  -2.9380  -2.0911  -1.0060
 B31  H03   H  HCH1  0   0.209  -0.9108  -1.1753  -2.1112
 B31  H04   H  HCH1  0   0.226   0.1902  -1.1363   0.7225
 B31  H05   H  HCH1  0   0.225  -0.3371   1.0418  -1.3624
 B31  H06   H  HCH1  0   0.211  -1.6052   0.4770   1.3515
 B31  HN01  H  HNH1  0   0.401  -4.1181  -0.3193   1.0887
 B31  HN03  H  HNH2  0   0.348  -1.1265  -3.5367  -1.6150
 B31  HN0A  H  HNH2  0   0.348   0.4196  -3.0847  -1.6608
 B31  HO06  H  HOH1  0   0.455  -2.7642   2.3363   0.8846
 B31  H11   H  HCH1  0   0.254   2.5847   0.2010   0.3562
 B31  H12   H  HCH1  0   0.216   4.6599  -0.6938  -0.4170
 B31  H13   H  HCH1  0   0.205   3.0361  -2.5638  -2.1795
 B31  H14   H  HCH1  0   0.210   4.8671  -3.0813   0.1964
 B31  H15   H  HCH1  0   0.228   1.8295  -3.3967   0.0491
 B31  H16   H  HCH2  0   0.218   3.0093  -4.8909   1.6173
 B31  H16A  H  HCH2  0   0.194   3.8145  -3.5085   2.3467
 B31  HN12  H  HNH2  0   0.348   3.5675   0.9698  -1.8318
 B31  HN1A  H  HNH2  0   0.343   4.5731   0.0325  -2.6751
 B31  HN16  H  HNH2  0   0.347   1.8316  -4.2008   3.5384
 B31  HN1B  H  HNH2  0   0.341   1.5920  -2.7197   2.9492
 B31  HO13  H  HOH1  0   0.449   5.1495  -3.3217  -2.6699
 B31  HO14  H  HOH1  0   0.457   4.4161  -5.1762  -0.2623
 B31  H21   H  HCH1  0   0.225   0.1693   3.0641  -0.7999
 B31  H22   H  HCH1  0   0.246   0.2094   3.4216   1.9350
 B31  H23   H  HCH1  0   0.240   2.6680   4.5909   2.1203
 B31  H24   H  HCH1  0   0.233   3.2287   4.5655  -0.1413
 B31  H25   H  HCH2  0   0.213   5.0506   3.3803   1.0436
 B31  H25A  H  HCH2  0   0.211   4.3133   1.8291   0.6304
 B31  HO22  H  HOH1  0   0.456  -0.2336   5.1096   0.3895
 B31  HO23  H  HOH1  0   0.454   2.0958   2.5628   3.1665
 B31  HO25  H  HOH1  0   0.456   5.7918   2.4043  -0.9968
 B31  H52   H  HCH1  0   0.248  -6.1201   0.6481   1.4725
 B31  H53   H  HCH2  0   0.231  -7.3214  -0.7030  -0.9870
 B31  H53A  H  HCH2  0   0.234  -6.3771  -1.5260   0.2420
 B31  H54   H  HCH2  0   0.216  -8.0187  -0.9408   1.9754
 B31  H54A  H  HCH2  0   0.201  -8.9754  -0.0367   0.8144
 B31  HN54  H  HNH2  0   0.348  -9.7300  -2.3262   1.1948
 B31  HN5A  H  HNH2  0   0.338  -9.3393  -2.1002  -0.3513
 B31  HO52  H  HOH1  0   0.441  -7.1301   1.8934  -0.8211

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
 B31  C06  C01   single  1.530  0.020  1.530
 B31  N01  C01   single  1.446  0.020  1.446
 B31  C01  C02   single  1.523  0.020  1.523
 B31  C01  H01   single  0.970  0.020  1.090
 B31  C02  C03   single  1.524  0.020  1.524
 B31  C02  H02   single  0.970  0.020  1.090
 B31  C02  H02A  single  0.970  0.020  1.090
 B31  C04  C03   single  1.529  0.020  1.529
 B31  C03  N03   single  1.452  0.020  1.452
 B31  C03  H03   single  0.970  0.020  1.090
 B31  C05  C04   single  1.531  0.020  1.531
 B31  C04  O04   single  1.412  0.020  1.412
 B31  C04  H04   single  0.970  0.020  1.090
 B31  O05  C05   single  1.407  0.020  1.407
 B31  C06  C05   single  1.528  0.020  1.528
 B31  C05  H05   single  0.970  0.020  1.090
 B31  O06  C06   single  1.404  0.020  1.404
 B31  C06  H06   single  0.970  0.020  1.090
 B31  C51  N01   single  1.341  0.020  1.341
 B31  N01  HN01  single  0.860  0.020  1.020
 B31  N03  HN03  single  0.890  0.020  1.040
 B31  N03  HN0A  single  0.890  0.020  1.040
 B31  C11  O04   single  1.400  0.020  1.400
 B31  C21  O05   single  1.393  0.020  1.393
 B31  O06  HO06  single  0.850  0.020  0.980
 B31  C12  C11   single  1.529  0.020  1.529
 B31  C11  O11   single  1.397  0.020  1.397
 B31  C11  H11   single  0.970  0.020  1.090
 B31  N12  C12   single  1.450  0.020  1.450
 B31  C12  C13   single  1.522  0.020  1.522
 B31  C12  H12   single  0.970  0.020  1.090
 B31  O13  C13   single  1.410  0.020  1.410
 B31  C13  C14   single  1.522  0.020  1.522
 B31  C13  H13   single  0.970  0.020  1.090
 B31  C14  C15   single  1.530  0.020  1.530
 B31  C14  O14   single  1.413  0.020  1.413
 B31  C14  H14   single  0.970  0.020  1.090
 B31  O11  C15   single  1.421  0.020  1.421
 B31  C15  C16   single  1.518  0.020  1.518
 B31  C15  H15   single  0.970  0.020  1.090
 B31  C16  N16   single  1.453  0.020  1.453
 B31  C16  H16   single  0.970  0.020  1.090
 B31  C16  H16A  single  0.970  0.020  1.090
 B31  N12  HN12  single  0.890  0.020  1.040
 B31  N12  HN1A  single  0.890  0.020  1.040
 B31  N16  HN16  single  0.890  0.020  1.040
 B31  N16  HN1B  single  0.890  0.020  1.040
 B31  O13  HO13  single  0.850  0.020  0.980
 B31  O14  HO14  single  0.850  0.020  0.980
 B31  C22  C21   single  1.534  0.020  1.534
 B31  O21  C21   single  1.404  0.020  1.404
 B31  C21  H21   single  0.970  0.020  1.090
 B31  O22  C22   single  1.407  0.020  1.407
 B31  C23  C22   single  1.529  0.020  1.529
 B31  C22  H22   single  0.970  0.020  1.090
 B31  C23  C24   single  1.525  0.020  1.525
 B31  C23  O23   single  1.404  0.020  1.404
 B31  C23  H23   single  0.970  0.020  1.090
 B31  C24  C25   single  1.512  0.020  1.512
 B31  C24  O21   single  1.426  0.020  1.426
 B31  C24  H24   single  0.970  0.020  1.090
 B31  C25  O25   single  1.411  0.020  1.411
 B31  C25  H25   single  0.970  0.020  1.090
 B31  C25  H25A  single  0.970  0.020  1.090
 B31  O22  HO22  single  0.850  0.020  0.980
 B31  O23  HO23  single  0.850  0.020  0.980
 B31  O25  HO25  single  0.850  0.020  0.980
 B31  O51  C51   double  1.223  0.020  1.223
 B31  C51  C52   single  1.527  0.020  1.527
 B31  C53  C52   single  1.531  0.020  1.531
 B31  C52  O52   single  1.402  0.020  1.402
 B31  C52  H52   single  0.970  0.020  1.090
 B31  C54  C53   single  1.521  0.020  1.521
 B31  C53  H53   single  0.970  0.020  1.090
 B31  C53  H53A  single  0.970  0.020  1.090
 B31  N54  C54   single  1.457  0.020  1.457
 B31  C54  H54   single  0.970  0.020  1.090
 B31  C54  H54A  single  0.970  0.020  1.090
 B31  N54  HN54  single  0.890  0.020  1.040
 B31  N54  HN5A  single  0.890  0.020  1.040
 B31  O52  HO52  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
 B31  H01   C01  N01   106.92  3.000
 B31  H01   C01  C06   108.61  3.000
 B31  N01   C01  C06   110.27  3.000
 B31  H01   C01  C02   109.20  3.000
 B31  N01   C01  C02   111.39  3.000
 B31  C06   C01  C02   110.35  3.000
 B31  H02A  C02  H02   107.18  3.000
 B31  H02A  C02  C03   109.82  3.000
 B31  H02   C02  C03   109.18  3.000
 B31  H02A  C02  C01   109.36  3.000
 B31  H02   C02  C01   110.35  3.000
 B31  C03   C02  C01   110.88  3.000
 B31  H03   C03  N03   112.11  3.000
 B31  H03   C03  C04   107.55  3.000
 B31  N03   C03  C04   110.44  3.000
 B31  H03   C03  C02   107.57  3.000
 B31  N03   C03  C02   109.63  3.000
 B31  C04   C03  C02   109.47  3.000
 B31  H04   C04  O04   110.67  3.000
 B31  H04   C04  C05   109.74  3.000
 B31  O04   C04  C05   111.49  3.000
 B31  H04   C04  C03   108.13  3.000
 B31  O04   C04  C03   107.45  3.000
 B31  C05   C04  C03   109.26  3.000
 B31  H05   C05  O05   110.53  3.000
 B31  H05   C05  C06   108.84  3.000
 B31  O05   C05  C06   109.53  3.000
 B31  H05   C05  C04   108.22  3.000
 B31  C06   C05  C04   110.51  3.000
 B31  O05   C05  C04   109.21  3.000
 B31  H06   C06  O06   110.78  3.000
 B31  H06   C06  C05   107.67  3.000
 B31  O06   C06  C05   107.88  3.000
 B31  H06   C06  C01   108.15  3.000
 B31  O06   C06  C01   111.88  3.000
 B31  C05   C06  C01   110.40  3.000
 B31  HN01  N01  C51   118.00  3.000
 B31  HN01  N01  C01   117.17  3.000
 B31  C51   N01  C01   124.82  3.000
 B31  HN0A  N03  HN03  105.47  3.000
 B31  HN0A  N03  C03   109.30  3.000
 B31  HN03  N03  C03   108.95  3.000
 B31  C11   O04  C04   118.36  3.000
 B31  C21   O05  C05   117.93  3.000
 B31  HO06  O06  C06   108.72  3.000
 B31  H11   C11  O11   104.15  3.000
 B31  H11   C11  C12   109.89  3.000
 B31  O11   C11  C12   110.72  3.000
 B31  H11   C11  O04   110.99  3.000
 B31  O11   C11  O04   113.22  3.000
 B31  C12   C11  O04   107.85  3.000
 B31  H12   C12  N12   112.75  3.000
 B31  H12   C12  C13   107.34  3.000
 B31  N12   C12  C13   110.74  3.000
 B31  H12   C12  C11   105.10  3.000
 B31  C13   C12  C11   109.76  3.000
 B31  N12   C12  C11   110.94  3.000
 B31  H13   C13  O13   110.29  3.000
 B31  H13   C13  C14   108.94  3.000
 B31  O13   C13  C14   111.07  3.000
 B31  H13   C13  C12   108.58  3.000
 B31  C14   C13  C12   109.94  3.000
 B31  O13   C13  C12   107.99  3.000
 B31  H14   C14  O14   110.64  3.000
 B31  H14   C14  C15   108.47  3.000
 B31  O14   C14  C15   111.19  3.000
 B31  H14   C14  C13   107.74  3.000
 B31  O14   C14  C13   107.64  3.000
 B31  C15   C14  C13   111.11  3.000
 B31  H15   C15  O11   110.30  3.000
 B31  H15   C15  C16   108.37  3.000
 B31  O11   C15  C16   106.21  3.000
 B31  H15   C15  C14   109.82  3.000
 B31  C16   C15  C14   111.93  3.000
 B31  O11   C15  C14   110.15  3.000
 B31  H16A  C16  H16   106.55  3.000
 B31  H16A  C16  N16   113.99  3.000
 B31  H16   C16  N16   108.07  3.000
 B31  H16A  C16  C15   108.34  3.000
 B31  H16   C16  C15   108.35  3.000
 B31  N16   C16  C15   111.30  3.000
 B31  HN1A  N12  HN12  105.58  3.000
 B31  HN1A  N12  C12   108.88  3.000
 B31  HN12  N12  C12   109.69  3.000
 B31  HN1B  N16  HN16  105.61  3.000
 B31  HN1B  N16  C16   109.39  3.000
 B31  HN16  N16  C16   108.96  3.000
 B31  C15   O11  C11   117.05  3.000
 B31  HO13  O13  C13   107.88  3.000
 B31  HO14  O14  C14   108.99  3.000
 B31  H21   C21  O21   108.16  3.000
 B31  H21   C21  C22   112.05  3.000
 B31  O21   C21  C22   105.49  3.000
 B31  H21   C21  O05   110.39  3.000
 B31  O21   C21  O05   110.65  3.000
 B31  C22   C21  O05   109.98  3.000
 B31  H22   C22  O22   111.78  3.000
 B31  H22   C22  C23   112.83  3.000
 B31  O22   C22  C23   107.21  3.000
 B31  H22   C22  C21   111.34  3.000
 B31  C23   C22  C21   101.89  3.000
 B31  O22   C22  C21   111.34  3.000
 B31  H23   C23  O23   111.81  3.000
 B31  H23   C23  C24   110.86  3.000
 B31  O23   C23  C24   109.37  3.000
 B31  H23   C23  C22   111.19  3.000
 B31  O23   C23  C22   112.13  3.000
 B31  C24   C23  C22   100.98  3.000
 B31  H24   C24  O21   108.86  3.000
 B31  H24   C24  C25   107.98  3.000
 B31  O21   C24  C25   110.82  3.000
 B31  H24   C24  C23   108.08  3.000
 B31  O21   C24  C23   105.82  3.000
 B31  C25   C24  C23   115.11  3.000
 B31  H25A  C25  H25   107.32  3.000
 B31  H25A  C25  O25   111.51  3.000
 B31  H25   C25  O25   111.41  3.000
 B31  H25A  C25  C24   110.33  3.000
 B31  H25   C25  C24   108.29  3.000
 B31  O25   C25  C24   107.94  3.000
 B31  C24   O21  C21   111.40  3.000
 B31  HO22  O22  C22   108.54  3.000
 B31  HO23  O23  C23   108.58  3.000
 B31  HO25  O25  C25   108.17  3.000
 B31  O51   C51  C52   120.19  3.000
 B31  C52   C51  N01   115.25  3.000
 B31  O51   C51  N01   124.51  3.000
 B31  H52   C52  O52   106.52  3.000
 B31  H52   C52  C53   108.74  3.000
 B31  O52   C52  C53   112.96  3.000
 B31  H52   C52  C51   109.53  3.000
 B31  O52   C52  C51   110.01  3.000
 B31  C53   C52  C51   109.02  3.000
 B31  H53A  C53  H53   106.51  3.000
 B31  H53A  C53  C54   108.87  3.000
 B31  H53   C53  C54   110.07  3.000
 B31  H53A  C53  C52   109.39  3.000
 B31  H53   C53  C52   109.05  3.000
 B31  C54   C53  C52   112.75  3.000
 B31  H54A  C54  H54   106.50  3.000
 B31  H54A  C54  N54   113.51  3.000
 B31  H54   C54  N54   108.17  3.000
 B31  H54A  C54  C53   109.45  3.000
 B31  H54   C54  C53   108.72  3.000
 B31  N54   C54  C53   110.32  3.000
 B31  HN5A  N54  HN54  105.37  3.000
 B31  HN5A  N54  C54   109.15  3.000
 B31  HN54  N54  C54   109.28  3.000
 B31  HO52  O52  C52   107.69  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
 B31  CONST_01  O51   C51  N01  C01     0.00   0.0  0
 B31  CONST_02  C52   C51  N01  C01   180.00   0.0  0
 B31  CONST_03  HN01  N01  C51  C52     0.00   0.0  0
 B31  Var_01    HN16  N16  C16  C15  -179.28  30.0  3
 B31  Var_02    N54   C54  C53  C52  -179.63  30.0  2
 B31  Var_03    HN54  N54  C54  C53   175.83  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
 B31  chir_01  C01  C06  N01  C02  positiv
 B31  chir_02  C03  N03  C04  C02  positiv
 B31  chir_03  C04  O04  C05  C03  negativ
 B31  chir_04  C05  O05  C06  C04  positiv
 B31  chir_05  C06  O06  C05  C01  positiv
 B31  chir_06  C11  O04  O11  C12  negativ
 B31  chir_07  C12  N12  C13  C11  positiv
 B31  chir_08  C13  O13  C12  C14  positiv
 B31  chir_09  C14  O14  C15  C13  positiv
 B31  chir_10  C15  O11  C14  C16  negativ
 B31  chir_11  C21  O05  C22  O21  negativ
 B31  chir_12  C22  O22  C23  C21  positiv
 B31  chir_13  C23  O23  C22  C24  positiv
 B31  chir_14  C24  O21  C23  C25  negativ
 B31  chir_15  C52  C51  C53  O52  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
 B31  plan-1  C01   0.020
 B31  plan-1  N01   0.020
 B31  plan-1  C51   0.020
 B31  plan-1  C52   0.020
 B31  plan-1  O51   0.020
 B31  plan-1  HN01  0.020

