# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:47:37 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-[(3S,4R,5R,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
 NOK  NOK  N-[(3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide  ligand  30  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NOK
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
 NOK  C8    C  CH3   0  -0.779   4.5640  -0.1175  -0.5441
 NOK  C7    C  C     0   0.517   3.2919   0.0261   0.2538
 NOK  O7    O  O     0  -0.503   3.3079   0.0971   1.4750
 NOK  N2    N  NH1   0  -0.638   2.1596   0.0598  -0.4753
 NOK  C2    C  CH1   0  -0.123   0.8287   0.1773   0.0736
 NOK  C1    C  CH2   0  -0.312   0.1009   1.4065  -0.4779
 NOK  N5    N  NH1   0  -0.574  -1.2605   1.5190  -0.0001
 NOK  C5    C  CH1   0  -0.161  -2.0654   0.3337  -0.2405
 NOK  C6    C  CH2   0  -0.142  -3.4559   0.5245   0.3420
 NOK  O6    O  OH1   0  -0.669  -4.0798   1.6194  -0.2873
 NOK  C4    C  CH1   0   0.060  -1.4077  -0.9333   0.3223
 NOK  O4    O  OH1   0  -0.677  -2.1922  -2.0509  -0.0212
 NOK  C3    C  CH1   0   0.025   0.0087  -1.0763  -0.2236
 NOK  O3    O  OH1   0  -0.673   0.5708  -2.2298   0.3602
 NOK  H8C1  H  HCH3  0   0.265   5.2508   0.6864  -0.2809
 NOK  H8C2  H  HCH3  0   0.267   5.0489  -1.0572  -0.2787
 NOK  H8C3  H  HCH3  0   0.248   4.4110  -0.1037  -1.6213
 NOK  H2    H  HNH1  0   0.398   2.2421   0.0091  -1.4791
 NOK  HA    H  HCH1  0   0.255   0.9315   0.2851   1.1558
 NOK  H1C1  H  HCH2  0   0.254   0.6486   2.3098  -0.2040
 NOK  H1C2  H  HCH2  0   0.224   0.0891   1.3628  -1.5730
 NOK  H3    H  HCH1  0   0.209  -0.0627  -1.1944  -1.3171
 NOK  H5    H  HNH1  0   0.343  -1.2572   1.7361   0.9907
 NOK  HB    H  HCH1  0   0.232  -2.1585   0.2071  -1.3280
 NOK  H6C1  H  HCH2  0   0.213  -4.0332  -0.3952   0.2060
 NOK  H6C2  H  HCH2  0   0.185  -3.3613   0.6836   1.4274
 NOK  H4    H  HCH1  0   0.195  -1.3410  -0.8250   1.4191
 NOK  H6    H  HOH1  0   0.453  -4.9895   1.6551   0.0208
 NOK  HC    H  HOH1  0   0.449  -1.7009  -2.8419   0.2257
 NOK  HD    H  HOH1  0   0.456   1.3290  -2.5035  -0.1647

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
 NOK  C8  C7    single  1.508  0.020  1.508
 NOK  C7  O7    double  1.223  0.020  1.223
 NOK  C7  N2    single  1.347  0.020  1.347
 NOK  N2  C2    single  1.444  0.020  1.444
 NOK  C2  C1    single  1.531  0.020  1.531
 NOK  C2  C3    single  1.527  0.020  1.527
 NOK  C1  N5    single  1.447  0.020  1.447
 NOK  N5  C5    single  1.453  0.020  1.453
 NOK  C5  C6    single  1.520  0.020  1.520
 NOK  C5  C4    single  1.534  0.020  1.534
 NOK  C6  O6    single  1.408  0.020  1.408
 NOK  C4  O4    single  1.408  0.020  1.408
 NOK  C4  C3    single  1.525  0.020  1.525
 NOK  C3  O3    single  1.410  0.020  1.410
 NOK  C8  H8C1  single  0.970  0.020  1.090
 NOK  C8  H8C2  single  0.970  0.020  1.090
 NOK  C8  H8C3  single  0.970  0.020  1.090
 NOK  N2  H2    single  0.860  0.020  1.020
 NOK  C2  HA    single  0.970  0.020  1.090
 NOK  C1  H1C1  single  0.970  0.020  1.090
 NOK  C1  H1C2  single  0.970  0.020  1.090
 NOK  C3  H3    single  0.970  0.020  1.090
 NOK  N5  H5    single  0.890  0.020  1.040
 NOK  C5  HB    single  0.970  0.020  1.090
 NOK  C6  H6C1  single  0.970  0.020  1.090
 NOK  C6  H6C2  single  0.970  0.020  1.090
 NOK  C4  H4    single  0.970  0.020  1.090
 NOK  O6  H6    single  0.850  0.020  0.980
 NOK  O4  HC    single  0.850  0.020  0.980
 NOK  O3  HD    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
 NOK  H8C3  C8  H8C2  108.32  3.000
 NOK  H8C3  C8  H8C1  108.57  3.000
 NOK  H8C2  C8  H8C1  107.26  3.000
 NOK  H8C3  C8  C7    113.82  3.000
 NOK  H8C2  C8  C7    109.17  3.000
 NOK  H8C1  C8  C7    109.49  3.000
 NOK  N2    C7  O7    123.35  3.000
 NOK  N2    C7  C8    115.14  3.000
 NOK  O7    C7  C8    121.50  3.000
 NOK  H2    N2  C2    117.24  3.000
 NOK  H2    N2  C7    117.95  3.000
 NOK  C2    N2  C7    124.81  3.000
 NOK  HA    C2  C3    108.93  3.000
 NOK  HA    C2  C1    108.80  3.000
 NOK  C3    C2  C1    109.49  3.000
 NOK  HA    C2  N2    107.32  3.000
 NOK  C3    C2  N2    110.73  3.000
 NOK  C1    C2  N2    111.49  3.000
 NOK  H1C2  C1  H1C1  106.80  3.000
 NOK  H1C2  C1  N5    108.83  3.000
 NOK  H1C1  C1  N5    108.97  3.000
 NOK  H1C2  C1  C2    109.45  3.000
 NOK  H1C1  C1  C2    109.60  3.000
 NOK  N5    C1  C2    112.99  3.000
 NOK  H5    N5  C5    109.76  3.000
 NOK  H5    N5  C1    109.64  3.000
 NOK  C5    N5  C1    113.78  3.000
 NOK  HB    C5  C4    107.71  3.000
 NOK  HB    C5  C6    108.44  3.000
 NOK  C4    C5  C6    110.81  3.000
 NOK  HB    C5  N5    107.74  3.000
 NOK  C4    C5  N5    112.06  3.000
 NOK  C6    C5  N5    109.95  3.000
 NOK  H6C2  C6  H6C1  106.81  3.000
 NOK  H6C2  C6  O6    111.48  3.000
 NOK  H6C1  C6  O6    111.35  3.000
 NOK  H6C2  C6  C5    108.50  3.000
 NOK  H6C1  C6  C5    109.24  3.000
 NOK  O6    C6  C5    109.37  3.000
 NOK  H6    O6  C6    107.75  3.000
 NOK  H4    C4  C3    107.98  3.000
 NOK  H4    C4  O4    110.73  3.000
 NOK  C3    C4  O4    110.84  3.000
 NOK  H4    C4  C5    108.01  3.000
 NOK  C3    C4  C5    110.14  3.000
 NOK  O4    C4  C5    109.09  3.000
 NOK  HC    O4  C4    107.76  3.000
 NOK  H3    C3  O3    110.43  3.000
 NOK  H3    C3  C4    107.76  3.000
 NOK  O3    C3  C4    107.39  3.000
 NOK  H3    C3  C2    108.41  3.000
 NOK  O3    C3  C2    112.15  3.000
 NOK  C4    C3  C2    110.62  3.000
 NOK  HD    O3  C3    108.73  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
 NOK  CONST_01  C2    N2  C7  C8  180.00   0.0  0
 NOK  CONST_02  C2    N2  C7  O7    0.00   0.0  0
 NOK  CONST_03  H2    N2  C7  C8    0.00   0.0  0
 NOK  Var_01    C5    N5  C1  C2  -54.47  30.0  1
 NOK  Var_02    H8C1  C8  C7  O7  -54.53  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
 NOK  chir_01  C2  N2  C1  C3  negativ
 NOK  chir_02  C5  N5  C4  C6  negativ
 NOK  chir_03  C4  O4  C5  C3  positiv
 NOK  chir_04  C3  O3  C4  C2  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
 NOK  plan-1  C8  0.020
 NOK  plan-1  C7  0.020
 NOK  plan-1  O7  0.020
 NOK  plan-1  N2  0.020
 NOK  plan-1  C2  0.020
 NOK  plan-1  H2  0.020

