# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:59:57 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1cn(CCCCCCCCCN2C[C@H](O)[C@@H](O)[C@H](O)[C@H]2CO)nn1
#
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
 D0J  D0J  (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{9-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]nonyl}piperidine-3,4,5-triol  ligand  64  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0J
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
 D0J  C0A  C  CH2   0  -0.257  -4.1240   0.5635  -0.7756
 D0J  C1A  C  CH2   0  -0.327  -5.4944  -1.3989  -0.5592
 D0J  C2A  C  CH1   0   0.032  -6.5770  -2.0502   0.2896
 D0J  C3A  C  CH1   0   0.002  -7.8879  -1.3250   0.0689
 D0J  C4A  C  CH1   0   0.065  -7.7087   0.1655   0.3166
 D0J  C5A  C  CH1   0  -0.092  -6.5687   0.7338  -0.5409
 D0J  C6A  C  CH2   0  -0.211  -6.4549   2.2390  -0.3517
 D0J  CAA  C  CH3   0  -0.397  11.5186  -2.2334  -0.8673
 D0J  CCA  C  CR5   0   0.106   9.0532   0.0474   0.4950
 D0J  CDA  C  CR15  0  -0.089   8.0745   0.1530  -0.4593
 D0J  CEA  C  CH2   0  -0.287   5.9350   1.4772  -0.4830
 D0J  CFA  C  CH2   0  -0.432   4.7475   0.7163   0.0879
 D0J  CGA  C  CH2   0  -0.426   3.4385   1.2006  -0.5215
 D0J  CHA  C  CH2   0  -0.414   2.2197   0.4717   0.0296
 D0J  CIA  C  CH2   0  -0.413   0.9138   0.9554  -0.5879
 D0J  CJA  C  CH2   0  -0.413  -0.3153   0.2319  -0.0517
 D0J  CLA  C  CH2   0  -0.444  -2.8497   0.0067  -0.1497
 D0J  N1A  N  NT    0  -0.445  -5.3443   0.0028  -0.2163
 D0J  NXA  N  N     0  -0.326   8.7153   0.8483   1.5258
 D0J  NYA  N  N     0  -0.109   7.5949   1.4319   1.2581
 D0J  NZA  N  NR5   0  -0.251   7.2000   1.0284   0.0683
 D0J  O2A  O  OH1   0  -0.677  -6.7731  -3.4046  -0.0563
 D0J  O3A  O  OH1   0  -0.679  -8.9096  -1.7749   0.9314
 D0J  O4A  O  OH1   0  -0.680  -8.8941   0.8609   0.0042
 D0J  OLA  O  O2    0  -0.485  10.3544  -1.4572  -0.7342
 D0J  H1   H  HCH2  0   0.240  -4.1090   1.6361  -0.5903
 D0J  H2   H  HCH2  0   0.185  -4.0800   0.4383  -1.8715
 D0J  H3   H  HCH2  0   0.246  -4.5554  -1.9220  -0.3756
 D0J  H4   H  HCH2  0   0.196  -5.7323  -1.5371  -1.6298
 D0J  H5   H  HCH1  0   0.206  -6.2919  -1.9519   1.3466
 D0J  H6   H  HCH1  0   0.200  -8.1805  -1.4610  -0.9858
 D0J  H7   H  HCH1  0   0.204  -7.4375   0.3099   1.3723
 D0J  H8   H  HCH1  0   0.204  -6.8406   0.5908  -1.6051
 D0J  H9   H  HCH2  0   0.213  -5.7574   2.6538  -1.0893
 D0J  H10  H  HCH2  0   0.229  -7.4299   2.6782  -0.5855
 D0J  H11  H  HCH3  0   0.208  11.5989  -2.9933  -0.0814
 D0J  H12  H  HCH3  0   0.239  11.4748  -2.7380  -1.8314
 D0J  H13  H  HCH3  0   0.208  12.4268  -1.6201  -0.8384
 D0J  H14  H  HCH2  0   0.224  11.1751  -0.1027   0.5999
 D0J  H15  H  HCH2  0   0.225  10.3159  -1.4505   1.3370
 D0J  H17  H  HCH2  0   0.267   5.9915   1.3519  -1.5639
 D0J  H18  H  HCH2  0   0.272   5.8460   2.5446  -0.2810
 D0J  H19  H  HCH2  0   0.234   4.8737  -0.3531  -0.1031
 D0J  H20  H  HCH2  0   0.234   4.7235   0.8455   1.1734
 D0J  H21  H  HCH2  0   0.219   3.3300   2.2757  -0.3431
 D0J  H22  H  HCH2  0   0.219   3.4747   1.0749  -1.6089
 D0J  H23  H  HCH2  0   0.212   2.3283  -0.6042  -0.1446
 D0J  H24  H  HCH2  0   0.212   2.1793   0.6010   1.1166
 D0J  H25  H  HCH2  0   0.209   0.8072   2.0314  -0.4114
 D0J  H26  H  HCH2  0   0.209   0.9607   0.8311  -1.6755
 D0J  H27  H  HCH2  0   0.209  -0.2142  -0.8433  -0.2349
 D0J  H28  H  HCH2  0   0.209  -0.3629   0.3515   1.0362
 D0J  H31  H  HCH2  0   0.215  -2.9159   0.1191   0.9369
 D0J  H32  H  HCH2  0   0.220  -2.7372  -1.0632  -0.3467
 D0J  H34  H  HOH1  0   0.455  -6.0315  -3.9157   0.2808
 D0J  H35  H  HOH1  0   0.453  -9.1030  -2.6937   0.7207
 D0J  H36  H  HOH1  0   0.450  -9.6054   0.4776   0.5274
 D0J  O6A  O  OH1   0  -0.671  -6.0521   2.5294   0.9669
 D0J  CKA  C  CH2   0  -0.415  -1.6143   0.7312  -0.6714
 D0J  H16  H  HCR5  0   0.303   7.9357  -0.2966  -1.4269
 D0J  CBA  C  CH2   0  -0.172  10.3031  -0.7621   0.4793
 D0J  H29  H  HCH2  0   0.210  -1.7146   1.8056  -0.4822
 D0J  H30  H  HCH2  0   0.211  -1.5608   0.6202  -1.7601
 D0J  H37  H  HOH1  0   0.455  -6.1053   3.4811   1.0900

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
 D0J  CKA  CLA  single    1.524  0.020  1.524
 D0J  CKA  CJA  single    1.523  0.020  1.523
 D0J  CLA  C0A  single    1.525  0.020  1.525
 D0J  CIA  CJA  single    1.524  0.020  1.524
 D0J  CIA  CHA  single    1.523  0.020  1.523
 D0J  CGA  CHA  single    1.523  0.020  1.523
 D0J  CGA  CFA  single    1.523  0.020  1.523
 D0J  CEA  CFA  single    1.522  0.020  1.522
 D0J  CEA  NZA  single    1.451  0.020  1.451
 D0J  CDA  NZA  aromatic  1.345  0.020  1.345
 D0J  CDA  CCA  aromatic  1.371  0.020  1.371
 D0J  O2A  C2A  single    1.412  0.020  1.412
 D0J  C1A  C2A  single    1.522  0.020  1.522
 D0J  C1A  N1A  single    1.451  0.020  1.451
 D0J  C0A  N1A  single    1.455  0.020  1.455
 D0J  CAA  OLA  single    1.405  0.020  1.405
 D0J  OLA  CBA  single    1.399  0.020  1.399
 D0J  NZA  NYA  aromatic  1.317  0.020  1.317
 D0J  CBA  CCA  single    1.489  0.020  1.489
 D0J  C2A  C3A  single    1.514  0.020  1.514
 D0J  CCA  NXA  aromatic  1.348  0.020  1.348
 D0J  N1A  C5A  single    1.462  0.020  1.462
 D0J  NYA  NXA  aromatic  1.291  0.020  1.291
 D0J  C3A  O3A  single    1.411  0.020  1.411
 D0J  C3A  C4A  single    1.521  0.020  1.521
 D0J  C5A  C4A  single    1.536  0.020  1.536
 D0J  C5A  C6A  single    1.521  0.020  1.521
 D0J  O6A  C6A  single    1.409  0.020  1.409
 D0J  C4A  O4A  single    1.409  0.020  1.409
 D0J  C0A  H1   single    0.970  0.020  1.090
 D0J  C0A  H2   single    0.970  0.020  1.090
 D0J  C1A  H3   single    0.970  0.020  1.090
 D0J  C1A  H4   single    0.970  0.020  1.090
 D0J  C2A  H5   single    0.970  0.020  1.090
 D0J  C3A  H6   single    0.970  0.020  1.090
 D0J  C4A  H7   single    0.970  0.020  1.090
 D0J  C5A  H8   single    0.970  0.020  1.090
 D0J  C6A  H9   single    0.970  0.020  1.090
 D0J  C6A  H10  single    0.970  0.020  1.090
 D0J  CAA  H11  single    0.970  0.020  1.090
 D0J  CAA  H12  single    0.970  0.020  1.090
 D0J  CAA  H13  single    0.970  0.020  1.090
 D0J  CBA  H14  single    0.970  0.020  1.090
 D0J  CBA  H15  single    0.970  0.020  1.090
 D0J  CDA  H16  single    0.930  0.020  1.080
 D0J  CEA  H17  single    0.970  0.020  1.090
 D0J  CEA  H18  single    0.970  0.020  1.090
 D0J  CFA  H19  single    0.970  0.020  1.090
 D0J  CFA  H20  single    0.970  0.020  1.090
 D0J  CGA  H21  single    0.970  0.020  1.090
 D0J  CGA  H22  single    0.970  0.020  1.090
 D0J  CHA  H23  single    0.970  0.020  1.090
 D0J  CHA  H24  single    0.970  0.020  1.090
 D0J  CIA  H25  single    0.970  0.020  1.090
 D0J  CIA  H26  single    0.970  0.020  1.090
 D0J  CJA  H27  single    0.970  0.020  1.090
 D0J  CJA  H28  single    0.970  0.020  1.090
 D0J  CKA  H29  single    0.970  0.020  1.090
 D0J  CKA  H30  single    0.970  0.020  1.090
 D0J  CLA  H31  single    0.970  0.020  1.090
 D0J  CLA  H32  single    0.970  0.020  1.090
 D0J  O2A  H34  single    0.850  0.020  0.980
 D0J  O3A  H35  single    0.850  0.020  0.980
 D0J  O4A  H36  single    0.850  0.020  0.980
 D0J  O6A  H37  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
 D0J  H2   C0A  H1   106.27  3.000
 D0J  H2   C0A  N1A  111.81  3.000
 D0J  H1   C0A  N1A  109.02  3.000
 D0J  H2   C0A  CLA  109.43  3.000
 D0J  H1   C0A  CLA  106.16  3.000
 D0J  N1A  C0A  CLA  113.73  3.000
 D0J  H4   C1A  H3   106.76  3.000
 D0J  H4   C1A  N1A  111.84  3.000
 D0J  H3   C1A  N1A  109.55  3.000
 D0J  H4   C1A  C2A  109.48  3.000
 D0J  H3   C1A  C2A  108.26  3.000
 D0J  N1A  C1A  C2A  110.81  3.000
 D0J  H5   C2A  O2A  110.95  3.000
 D0J  H5   C2A  C3A  108.77  3.000
 D0J  O2A  C2A  C3A  107.67  3.000
 D0J  H5   C2A  C1A  108.27  3.000
 D0J  C3A  C2A  C1A  109.24  3.000
 D0J  O2A  C2A  C1A  111.89  3.000
 D0J  H6   C3A  O3A  110.68  3.000
 D0J  H6   C3A  C4A  107.93  3.000
 D0J  O3A  C3A  C4A  107.35  3.000
 D0J  H6   C3A  C2A  108.05  3.000
 D0J  C4A  C3A  C2A  110.09  3.000
 D0J  O3A  C3A  C2A  112.65  3.000
 D0J  H7   C4A  O4A  110.82  3.000
 D0J  H7   C4A  C5A  107.73  3.000
 D0J  O4A  C4A  C5A  108.54  3.000
 D0J  H7   C4A  C3A  108.30  3.000
 D0J  O4A  C4A  C3A  110.38  3.000
 D0J  C5A  C4A  C3A  111.04  3.000
 D0J  H8   C5A  N1A  110.75  3.000
 D0J  H8   C5A  C6A  105.40  3.000
 D0J  N1A  C5A  C6A  113.85  3.000
 D0J  H8   C5A  C4A  107.85  3.000
 D0J  C6A  C5A  C4A  110.62  3.000
 D0J  N1A  C5A  C4A  108.22  3.000
 D0J  H10  C6A  H9   105.73  3.000
 D0J  H10  C6A  O6A  111.83  3.000
 D0J  H9   C6A  O6A  111.70  3.000
 D0J  H10  C6A  C5A  107.68  3.000
 D0J  H9   C6A  C5A  109.76  3.000
 D0J  O6A  C6A  C5A  109.98  3.000
 D0J  H13  CAA  H12  108.41  3.000
 D0J  H13  CAA  H11  107.95  3.000
 D0J  H12  CAA  H11  108.45  3.000
 D0J  H13  CAA  OLA  112.01  3.000
 D0J  H12  CAA  OLA  107.85  3.000
 D0J  H11  CAA  OLA  112.06  3.000
 D0J  NXA  CCA  CDA  107.91  3.000
 D0J  NXA  CCA  CBA  122.77  3.000
 D0J  CDA  CCA  CBA  129.32  3.000
 D0J  H16  CDA  NZA  122.73  3.000
 D0J  H16  CDA  CCA  133.31  3.000
 D0J  NZA  CDA  CCA  103.96  3.000
 D0J  H18  CEA  H17  107.50  3.000
 D0J  H18  CEA  NZA  107.68  3.000
 D0J  H17  CEA  NZA  107.23  3.000
 D0J  H18  CEA  CFA  110.88  3.000
 D0J  H17  CEA  CFA  110.80  3.000
 D0J  NZA  CEA  CFA  112.53  3.000
 D0J  H20  CFA  H19  106.95  3.000
 D0J  H20  CFA  CGA  109.92  3.000
 D0J  H19  CFA  CGA  109.89  3.000
 D0J  H20  CFA  CEA  109.30  3.000
 D0J  H19  CFA  CEA  109.48  3.000
 D0J  CGA  CFA  CEA  111.20  3.000
 D0J  H22  CGA  H21  106.12  3.000
 D0J  H22  CGA  CHA  109.32  3.000
 D0J  H21  CGA  CHA  109.36  3.000
 D0J  H22  CGA  CFA  109.41  3.000
 D0J  H21  CGA  CFA  109.39  3.000
 D0J  CHA  CGA  CFA  113.00  3.000
 D0J  H24  CHA  H23  106.11  3.000
 D0J  H24  CHA  CIA  109.46  3.000
 D0J  H23  CHA  CIA  109.42  3.000
 D0J  H24  CHA  CGA  109.39  3.000
 D0J  H23  CHA  CGA  109.46  3.000
 D0J  CIA  CHA  CGA  112.78  3.000
 D0J  H26  CIA  H25  105.99  3.000
 D0J  H26  CIA  CJA  109.27  3.000
 D0J  H25  CIA  CJA  109.34  3.000
 D0J  H26  CIA  CHA  109.25  3.000
 D0J  H25  CIA  CHA  109.27  3.000
 D0J  CJA  CIA  CHA  113.46  3.000
 D0J  H28  CJA  H27  106.10  3.000
 D0J  H28  CJA  CKA  109.34  3.000
 D0J  H27  CJA  CKA  109.41  3.000
 D0J  H28  CJA  CIA  109.43  3.000
 D0J  H27  CJA  CIA  109.44  3.000
 D0J  CKA  CJA  CIA  112.90  3.000
 D0J  H32  CLA  H31  106.59  3.000
 D0J  H32  CLA  CKA  108.66  3.000
 D0J  H31  CLA  CKA  109.88  3.000
 D0J  H32  CLA  C0A  111.67  3.000
 D0J  H31  CLA  C0A  108.63  3.000
 D0J  CKA  CLA  C0A  111.30  3.000
 D0J  C5A  N1A  C1A  110.11  3.000
 D0J  C5A  N1A  C0A  115.11  3.000
 D0J  C1A  N1A  C0A  111.61  3.000
 D0J  NYA  NXA  CCA  109.11  3.000
 D0J  NZA  NYA  NXA  108.00  3.000
 D0J  NYA  NZA  CEA  120.66  3.000
 D0J  NYA  NZA  CDA  111.02  3.000
 D0J  CEA  NZA  CDA  128.25  3.000
 D0J  H34  O2A  C2A  108.48  3.000
 D0J  H35  O3A  C3A  108.43  3.000
 D0J  H36  O4A  C4A  107.73  3.000
 D0J  CBA  OLA  CAA  112.76  3.000
 D0J  H37  O6A  C6A  107.94  3.000
 D0J  H30  CKA  H29  105.99  3.000
 D0J  H30  CKA  CLA  109.36  3.000
 D0J  H29  CKA  CLA  109.44  3.000
 D0J  H30  CKA  CJA  109.23  3.000
 D0J  H29  CKA  CJA  109.22  3.000
 D0J  CLA  CKA  CJA  113.34  3.000
 D0J  H15  CBA  H14  106.29  3.000
 D0J  H15  CBA  OLA  111.40  3.000
 D0J  H14  CBA  OLA  111.33  3.000
 D0J  H15  CBA  CCA  109.99  3.000
 D0J  H14  CBA  CCA  109.77  3.000
 D0J  OLA  CBA  CCA  108.05  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
 D0J  CONST_01  NYA  NZA  CDA  CCA     0.00   0.0  0
 D0J  CONST_02  NZA  NYA  NXA  CCA     0.00   0.0  0
 D0J  CONST_03  NXA  NYA  NZA  CDA     0.00   0.0  0
 D0J  CONST_04  NYA  NXA  CCA  CDA     0.00   0.0  0
 D0J  CONST_05  NZA  CDA  CCA  NXA     0.00   0.0  0
 D0J  CONST_06  NZA  CDA  CCA  CBA   180.00   0.0  0
 D0J  CONST_07  NYA  NXA  CCA  CBA   180.00   0.0  0
 D0J  CONST_08  CEA  NZA  CDA  CCA   180.00   0.0  0
 D0J  CONST_09  NXA  NYA  NZA  CEA   180.00   0.0  0
 D0J  CONST_10  H16  CDA  CCA  NXA   180.00   0.0  0
 D0J  Var_01    C5A  N1A  C1A  C2A   -64.35  30.0  1
 D0J  Var_02    CLA  C0A  N1A  C1A   -68.09  30.0  2
 D0J  Var_03    CFA  CEA  NZA  CDA    97.28  30.0  1
 D0J  Var_04    OLA  CBA  CCA  CDA     0.03  30.0  2
 D0J  Var_05    CCA  CBA  OLA  CAA   178.56  30.0  3
 D0J  Var_06    NZA  CEA  CFA  CGA  -179.39  30.0  1
 D0J  Var_07    N1A  C0A  CLA  CKA  -174.15  30.0  3
 D0J  Var_08    CJA  CKA  CLA  C0A   178.70  30.0  2
 D0J  Var_09    CHA  CGA  CFA  CEA  -179.58  30.0  1
 D0J  Var_10    CIA  CHA  CGA  CFA  -179.73  30.0  3
 D0J  Var_11    CJA  CIA  CHA  CGA   179.75  30.0  1
 D0J  Var_12    CKA  CJA  CIA  CHA   179.65  30.0  3
 D0J  Var_13    CLA  CKA  CJA  CIA   179.56  30.0  1
 D0J  Var_14    H11  CAA  OLA  CBA    60.56  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
 D0J  chir_01  C2A  O2A  C1A  C3A  negativ
 D0J  chir_02  C3A  O3A  C2A  C4A  positiv
 D0J  chir_03  C4A  O4A  C3A  C5A  negativ
 D0J  chir_04  C5A  N1A  C4A  C6A  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
 D0J  plan-1  CCA  0.020
 D0J  plan-1  CDA  0.020
 D0J  plan-1  CEA  0.020
 D0J  plan-1  NXA  0.020
 D0J  plan-1  NYA  0.020
 D0J  plan-1  NZA  0.020
 D0J  plan-1  H16  0.020
 D0J  plan-1  CBA  0.020

