# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 15:36:17 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1CN[C@H](CO)[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
 DJN  DJN  N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide  ligand  30  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DJN
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
 DJN  O7   O  O     0  -0.507  -3.2342  -0.0835   1.4313
 DJN  C7   C  C     0   0.521  -3.2314  -0.2246   0.2158
 DJN  C8   C  CH3   0  -0.781  -4.5167  -0.2813  -0.5736
 DJN  N2   N  NH1   0  -0.628  -2.1100  -0.3454  -0.5162
 DJN  C2   C  CH1   0  -0.087  -0.7689  -0.2466   0.0070
 DJN  C3   C  CH1   0   0.022  -0.1102   1.0622  -0.4209
 DJN  O3   O  OH1   0  -0.662  -0.8506   2.1313   0.1213
 DJN  C4   C  CH1   0   0.022   1.3501   1.1148   0.0373
 DJN  O4   O  OH1   0  -0.674   1.4397   1.1890   1.4397
 DJN  C5   C  CH1   0  -0.127   2.0917  -0.1204  -0.4579
 DJN  C6   C  CH2   0  -0.146   3.5465  -0.1100  -0.0257
 DJN  O6   O  OH1   0  -0.675   4.2020  -1.1927  -0.6535
 DJN  N5   N  NH1   0  -0.604   1.4232  -1.3125   0.0260
 DJN  C1   C  CH2   0  -0.288   0.0710  -1.4281  -0.4745
 DJN  H1   H  HCH3  0   0.266  -5.0170   0.6859  -0.5139
 DJN  H2   H  HCH3  0   0.246  -4.3756  -0.5257  -1.6248
 DJN  H3   H  HCH3  0   0.263  -5.1849  -1.0195  -0.1315
 DJN  H4   H  HNH1  0   0.394  -2.2059  -0.4316  -1.5160
 DJN  H5   H  HCH1  0   0.255  -0.8315  -0.2818   1.0951
 DJN  H6   H  HCH1  0   0.210  -0.1163   1.1018  -1.5210
 DJN  H7   H  HOH1  0   0.456  -0.6056   2.9380  -0.3436
 DJN  H8   H  HCH1  0   0.218   1.8177   1.9965  -0.4308
 DJN  H9   H  HOH1  0   0.445   0.8446   1.8901   1.7282
 DJN  H10  H  HCH1  0   0.210   2.0737  -0.0578  -1.5623
 DJN  H11  H  HCH2  0   0.196   3.9942   0.8504  -0.3145
 DJN  H12  H  HCH2  0   0.204   3.6064  -0.1869   1.0650
 DJN  H13  H  HOH1  0   0.457   5.0625  -1.3047  -0.2403
 DJN  H14  H  HNH1  0   0.355   1.9534  -2.1296  -0.2466
 DJN  H16  H  HCH2  0   0.249  -0.3708  -2.3531  -0.1002
 DJN  H17  H  HCH2  0   0.192   0.0233  -1.4742  -1.5769

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
 DJN  O4  C4   single  1.407  0.020  1.407
 DJN  O3  C3   single  1.409  0.020  1.409
 DJN  C4  C3   single  1.531  0.020  1.531
 DJN  C4  C5   single  1.523  0.020  1.523
 DJN  C6  C5   single  1.518  0.020  1.518
 DJN  C6  O6   single  1.413  0.020  1.413
 DJN  C3  C2   single  1.526  0.020  1.526
 DJN  C5  N5   single  1.450  0.020  1.450
 DJN  O7  C7   double  1.224  0.020  1.224
 DJN  C2  N2   single  1.443  0.020  1.443
 DJN  C2  C1   single  1.527  0.020  1.527
 DJN  N5  C1   single  1.446  0.020  1.446
 DJN  C7  N2   single  1.345  0.020  1.345
 DJN  C7  C8   single  1.509  0.020  1.509
 DJN  C8  H1   single  0.970  0.020  1.090
 DJN  C8  H2   single  0.970  0.020  1.090
 DJN  C8  H3   single  0.970  0.020  1.090
 DJN  N2  H4   single  0.860  0.020  1.020
 DJN  C2  H5   single  0.970  0.020  1.090
 DJN  C3  H6   single  0.970  0.020  1.090
 DJN  O3  H7   single  0.850  0.020  0.980
 DJN  C4  H8   single  0.970  0.020  1.090
 DJN  O4  H9   single  0.850  0.020  0.980
 DJN  C5  H10  single  0.970  0.020  1.090
 DJN  C6  H11  single  0.970  0.020  1.090
 DJN  C6  H12  single  0.970  0.020  1.090
 DJN  O6  H13  single  0.850  0.020  0.980
 DJN  N5  H14  single  0.890  0.020  1.040
 DJN  C1  H16  single  0.970  0.020  1.090
 DJN  C1  H17  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
 DJN  N2   C7  C8   114.97  3.000
 DJN  C8   C7  O7   121.46  3.000
 DJN  N2   C7  O7   123.57  3.000
 DJN  H3   C8  H2   108.62  3.000
 DJN  H3   C8  H1   107.30  3.000
 DJN  H2   C8  H1   108.15  3.000
 DJN  H3   C8  C7   109.60  3.000
 DJN  H2   C8  C7   113.78  3.000
 DJN  H1   C8  C7   109.19  3.000
 DJN  H4   N2  C2   116.99  3.000
 DJN  H4   N2  C7   117.92  3.000
 DJN  C2   N2  C7   124.86  3.000
 DJN  H5   C2  C1   108.73  3.000
 DJN  H5   C2  C3   109.40  3.000
 DJN  C1   C2  C3   109.73  3.000
 DJN  H5   C2  N2   107.83  3.000
 DJN  C1   C2  N2   110.11  3.000
 DJN  C3   C2  N2   110.99  3.000
 DJN  H6   C3  C4   107.64  3.000
 DJN  H6   C3  O3   110.76  3.000
 DJN  C4   C3  O3   111.09  3.000
 DJN  H6   C3  C2   107.97  3.000
 DJN  C4   C3  C2   110.92  3.000
 DJN  O3   C3  C2   108.42  3.000
 DJN  H7   O3  C3   108.44  3.000
 DJN  H8   C4  C5   107.70  3.000
 DJN  H8   C4  O4   110.74  3.000
 DJN  C5   C4  O4   109.62  3.000
 DJN  H8   C4  C3   107.75  3.000
 DJN  C5   C4  C3   109.82  3.000
 DJN  O4   C4  C3   111.14  3.000
 DJN  H9   O4  C4   107.30  3.000
 DJN  H10  C5  N5   111.85  3.000
 DJN  H10  C5  C6   107.43  3.000
 DJN  N5   C5  C6   110.64  3.000
 DJN  H10  C5  C4   105.70  3.000
 DJN  N5   C5  C4   109.49  3.000
 DJN  C6   C5  C4   111.63  3.000
 DJN  H12  C6  H11  107.52  3.000
 DJN  H12  C6  O6   111.30  3.000
 DJN  H11  C6  O6   111.35  3.000
 DJN  H12  C6  C5   109.61  3.000
 DJN  H11  C6  C5   108.77  3.000
 DJN  O6   C6  C5   108.24  3.000
 DJN  H13  O6  C6   108.28  3.000
 DJN  H14  N5  C1   109.40  3.000
 DJN  H14  N5  C5   109.43  3.000
 DJN  C1   N5  C5   112.41  3.000
 DJN  H17  C1  H16  106.82  3.000
 DJN  H17  C1  N5   112.90  3.000
 DJN  H16  C1  N5   109.12  3.000
 DJN  H17  C1  C2   108.86  3.000
 DJN  H16  C1  C2   108.96  3.000
 DJN  N5   C1  C2   110.07  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
 DJN  CONST_01  C2  N2  C7  O7    0.00   0.0  0
 DJN  CONST_02  C2  N2  C7  C8  180.00   0.0  0
 DJN  CONST_03  H4  N2  C7  O7  180.00   0.0  0
 DJN  Var_01    C5  N5  C1  C2  -61.97  30.0  1
 DJN  Var_02    H1  C8  C7  O7   65.88  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
 DJN  chir_01  C2  C3  N2  C1  negativ
 DJN  chir_02  C3  O3  C2  C4  positiv
 DJN  chir_03  C4  O4  C3  C5  positiv
 DJN  chir_04  C5  N5  C4  C6  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
 DJN  plan-1  O7  0.020
 DJN  plan-1  C7  0.020
 DJN  plan-1  C8  0.020
 DJN  plan-1  N2  0.020
 DJN  plan-1  C2  0.020
 DJN  plan-1  H4  0.020

