# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 20:23:34 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(2S,3S,4R,5R,6R)-4,5-dihydroxy-2,6-bis(hydroxymethyl)piperidin-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)N[C@@H]1CO
#
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
 Z7S  Z7S  N-[(2S,3S,4R,5R,6R)-4,5-dihydroxy-2,6-bis(hydroxymethyl)piperidin-3-yl]acetamide  ligand  34  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Z7S
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
 Z7S  CAA  C  CH3   0  -0.777  -12.3906   9.9090   -9.9528
 Z7S  CAG  C  CH2   0  -0.189  -11.9216  17.8737   -8.7144
 Z7S  CAH  C  CH2   0  -0.152  -10.3559  14.2353  -10.5855
 Z7S  CAK  C  C     0   0.523  -12.3881  11.1710   -9.1257
 Z7S  CAL  C  CH1   0  -0.131  -12.0154  16.4840   -9.3235
 Z7S  CAM  C  CH1   0  -0.142  -11.0417  14.2498   -9.2177
 Z7S  CAN  C  CH1   0   0.062  -13.4463  15.9315   -9.3100
 Z7S  CAO  C  CH1   0   0.029  -13.4770  14.5394   -9.9240
 Z7S  CAP  C  CH1   0  -0.100  -12.4477  13.6359   -9.2348
 Z7S  NAI  N  NH1   0  -0.655  -12.4810  12.3189   -9.8310
 Z7S  NAJ  N  NH1   0  -0.607  -11.1524  15.5607   -8.6064
 Z7S  OAB  O  O     0  -0.489  -12.3116  11.1417   -7.9070
 Z7S  OAC  O  OH1   0  -0.665  -12.4213  17.8670   -7.3978
 Z7S  OAE  O  OH1   0  -0.672  -14.3184  16.7504  -10.0545
 Z7S  OAF  O  OH1   0  -0.662  -14.7765  14.0208   -9.7756
 Z7S  H1   H  HCH3  0   0.265  -13.2074   9.2654   -9.6270
 Z7S  H2   H  HCH3  0   0.248  -12.4945  10.0846  -11.0220
 Z7S  H3   H  HCH3  0   0.265  -11.4620   9.3646   -9.7815
 Z7S  H4   H  HCH2  0   0.210  -10.8693  18.1911   -8.7463
 Z7S  H5   H  HCH2  0   0.207  -12.4706  18.5738   -9.3556
 Z7S  H6   H  HCH2  0   0.195  -10.9607  14.7556  -11.3391
 Z7S  H7   H  HCH2  0   0.202  -10.2552  13.1967  -10.9237
 Z7S  H8   H  HCH1  0   0.214  -11.7221  16.6145  -10.3792
 Z7S  H9   H  HCH1  0   0.247  -10.4319  13.6329   -8.5484
 Z7S  H10  H  HCH1  0   0.212  -13.7759  15.8428   -8.2663
 Z7S  H11  H  HCH1  0   0.203  -13.2183  14.6335  -10.9920
 Z7S  H12  H  HCH1  0   0.266  -12.7576  13.5257   -8.1935
 Z7S  H13  H  HNH1  0   0.403  -12.4729  12.2533  -10.8375
 Z7S  H14  H  HNH1  0   0.352  -10.2296  15.9631   -8.5001
 Z7S  H16  H  HOH1  0   0.454  -12.4440  18.7739   -7.0808
 Z7S  H17  H  HOH1  0   0.454   -8.6705  14.8872  -11.2939
 Z7S  H18  H  HOH1  0   0.453  -14.6030  17.4812   -9.4987
 Z7S  H19  H  HOH1  0   0.446  -14.7932  13.1391  -10.1624
 Z7S  OAD  O  OH1   0  -0.667   -9.0960  14.8502  -10.4327

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
 Z7S  CAH  OAD  single  1.410  0.020  1.410
 Z7S  CAH  CAM  single  1.530  0.020  1.530
 Z7S  OAE  CAN  single  1.409  0.020  1.409
 Z7S  OAF  CAO  single  1.407  0.020  1.407
 Z7S  CAO  CAN  single  1.522  0.020  1.522
 Z7S  CAO  CAP  single  1.533  0.020  1.533
 Z7S  NAI  CAP  single  1.446  0.020  1.446
 Z7S  NAI  CAK  single  1.350  0.020  1.350
 Z7S  CAA  CAK  single  1.509  0.020  1.509
 Z7S  CAN  CAL  single  1.534  0.020  1.534
 Z7S  CAL  CAG  single  1.520  0.020  1.520
 Z7S  CAL  NAJ  single  1.453  0.020  1.453
 Z7S  CAP  CAM  single  1.534  0.020  1.534
 Z7S  CAM  NAJ  single  1.451  0.020  1.451
 Z7S  CAK  OAB  double  1.222  0.020  1.222
 Z7S  CAG  OAC  single  1.408  0.020  1.408
 Z7S  CAA  H1   single  0.970  0.020  1.090
 Z7S  CAA  H2   single  0.970  0.020  1.090
 Z7S  CAA  H3   single  0.970  0.020  1.090
 Z7S  CAG  H4   single  0.970  0.020  1.090
 Z7S  CAG  H5   single  0.970  0.020  1.090
 Z7S  CAH  H6   single  0.970  0.020  1.090
 Z7S  CAH  H7   single  0.970  0.020  1.090
 Z7S  CAL  H8   single  0.970  0.020  1.090
 Z7S  CAM  H9   single  0.970  0.020  1.090
 Z7S  CAN  H10  single  0.970  0.020  1.090
 Z7S  CAO  H11  single  0.970  0.020  1.090
 Z7S  CAP  H12  single  0.970  0.020  1.090
 Z7S  NAI  H13  single  0.860  0.020  1.020
 Z7S  NAJ  H14  single  0.890  0.020  1.040
 Z7S  OAC  H16  single  0.850  0.020  0.980
 Z7S  OAD  H17  single  0.850  0.020  0.980
 Z7S  OAE  H18  single  0.850  0.020  0.980
 Z7S  OAF  H19  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
 Z7S  H3   CAA  H2   108.43  3.000
 Z7S  H3   CAA  H1   107.25  3.000
 Z7S  H2   CAA  H1   108.50  3.000
 Z7S  H3   CAA  CAK  109.28  3.000
 Z7S  H2   CAA  CAK  113.81  3.000
 Z7S  H1   CAA  CAK  109.36  3.000
 Z7S  H5   CAG  H4   106.13  3.000
 Z7S  H5   CAG  OAC  111.85  3.000
 Z7S  H4   CAG  OAC  111.59  3.000
 Z7S  H5   CAG  CAL  108.57  3.000
 Z7S  H4   CAG  CAL  108.13  3.000
 Z7S  OAC  CAG  CAL  110.39  3.000
 Z7S  H7   CAH  H6   106.72  3.000
 Z7S  H7   CAH  OAD  111.36  3.000
 Z7S  H6   CAH  OAD  111.11  3.000
 Z7S  H7   CAH  CAM  109.01  3.000
 Z7S  H6   CAH  CAM  111.24  3.000
 Z7S  OAD  CAH  CAM  107.43  3.000
 Z7S  OAB  CAK  NAI  123.07  3.000
 Z7S  OAB  CAK  CAA  121.80  3.000
 Z7S  NAI  CAK  CAA  115.12  3.000
 Z7S  H8   CAL  NAJ  112.92  3.000
 Z7S  H8   CAL  CAN  107.39  3.000
 Z7S  NAJ  CAL  CAN  108.71  3.000
 Z7S  H8   CAL  CAG  105.00  3.000
 Z7S  NAJ  CAL  CAG  110.28  3.000
 Z7S  CAN  CAL  CAG  112.53  3.000
 Z7S  H9   CAM  NAJ  107.09  3.000
 Z7S  H9   CAM  CAP  106.95  3.000
 Z7S  NAJ  CAM  CAP  107.24  3.000
 Z7S  H9   CAM  CAH  106.94  3.000
 Z7S  NAJ  CAM  CAH  114.80  3.000
 Z7S  CAP  CAM  CAH  113.39  3.000
 Z7S  H10  CAN  OAE  111.31  3.000
 Z7S  H10  CAN  CAO  107.67  3.000
 Z7S  OAE  CAN  CAO  107.81  3.000
 Z7S  H10  CAN  CAL  108.51  3.000
 Z7S  CAO  CAN  CAL  110.17  3.000
 Z7S  OAE  CAN  CAL  111.31  3.000
 Z7S  H11  CAO  OAF  110.50  3.000
 Z7S  H11  CAO  CAP  109.15  3.000
 Z7S  OAF  CAO  CAP  110.82  3.000
 Z7S  H11  CAO  CAN  107.94  3.000
 Z7S  CAP  CAO  CAN  110.13  3.000
 Z7S  OAF  CAO  CAN  108.25  3.000
 Z7S  H12  CAP  NAI  107.14  3.000
 Z7S  H12  CAP  CAO  107.31  3.000
 Z7S  NAI  CAP  CAO  109.62  3.000
 Z7S  H12  CAP  CAM  106.85  3.000
 Z7S  NAI  CAP  CAM  112.96  3.000
 Z7S  CAO  CAP  CAM  112.61  3.000
 Z7S  H13  NAI  CAP  118.06  3.000
 Z7S  H13  NAI  CAK  117.73  3.000
 Z7S  CAP  NAI  CAK  123.87  3.000
 Z7S  H14  NAJ  CAM  109.51  3.000
 Z7S  H14  NAJ  CAL  109.92  3.000
 Z7S  CAM  NAJ  CAL  114.31  3.000
 Z7S  H16  OAC  CAG  108.20  3.000
 Z7S  H18  OAE  CAN  108.64  3.000
 Z7S  H19  OAF  CAO  108.13  3.000
 Z7S  H17  OAD  CAH  108.37  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
 Z7S  CONST_01  CAP  NAI  CAK  CAA   180.00   0.0  0
 Z7S  CONST_02  OAB  CAK  NAI  CAP     0.00   0.0  0
 Z7S  CONST_03  H13  NAI  CAK  CAA     0.00   0.0  0
 Z7S  Var_01    H1   CAA  CAK  NAI  -123.05  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
 Z7S  chir_01  CAL  CAN  CAG  NAJ  negativ
 Z7S  chir_02  CAM  NAJ  CAH  CAP  positiv
 Z7S  chir_03  CAN  OAE  CAO  CAL  negativ
 Z7S  chir_04  CAO  OAF  CAN  CAP  negativ
 Z7S  chir_05  CAP  NAI  CAM  CAO  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
 Z7S  plan-1  CAA  0.020
 Z7S  plan-1  CAK  0.020
 Z7S  plan-1  CAP  0.020
 Z7S  plan-1  NAI  0.020
 Z7S  plan-1  OAB  0.020
 Z7S  plan-1  H13  0.020

