# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 22:55:20 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(2R,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
 Z8V  Z8V  N-[(2R,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 PERFECT
;

data_comp_Z8V
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
 Z8V  CAA  C  CH3   0  -0.778  -12.3027   9.9450  -10.1277
 Z8V  CAG  C  CH2   0  -0.178  -12.6371  17.9517   -8.9506
 Z8V  CAH  C  CH2   0  -0.134   -9.9137  13.9272   -9.0427
 Z8V  CAK  C  C     0   0.516  -12.4597  11.1785   -9.2720
 Z8V  CAL  C  CH1   0  -0.153  -12.5777  16.5356   -9.4967
 Z8V  CAM  C  CH1   0  -0.132  -11.1903  14.5487   -9.5840
 Z8V  CAN  C  CH1   0   0.039  -13.8450  15.7174   -9.1969
 Z8V  CAO  C  CH1   0   0.046  -13.7033  14.3166   -9.7868
 Z8V  CAP  C  CH1   0  -0.126  -12.4067  13.6480   -9.3039
 Z8V  NAI  N  NH1   0  -0.624  -12.2639  12.3466   -9.9119
 Z8V  NAJ  N  NH1   0  -0.580  -11.3728  15.8754   -9.0304
 Z8V  OAB  O  O     0  -0.497  -12.7233  11.0984   -8.0800
 Z8V  OAC  O  OH1   0  -0.670  -12.7757  17.8989   -7.5474
 Z8V  OAE  O  OH1   0  -0.671  -14.9947  16.3055   -9.7613
 Z8V  OAF  O  OH1   0  -0.654  -14.8258  13.5098   -9.5327
 Z8V  H1   H  HCH3  0   0.262  -13.1972   9.3286  -10.0428
 Z8V  H2   H  HCH3  0   0.247  -12.1284  10.1589  -11.1805
 Z8V  H3   H  HCH3  0   0.264  -11.4662   9.3533   -9.7549
 Z8V  H4   H  HCH2  0   0.213  -11.7164  18.4686   -9.2472
 Z8V  H5   H  HCH2  0   0.201  -13.4681  18.4924   -9.4202
 Z8V  H6   H  HCH2  0   0.187  -10.0045  13.8363   -7.9494
 Z8V  H7   H  HCH2  0   0.206   -9.8164  12.9098   -9.4369
 Z8V  H8   H  HCH1  0   0.236  -12.4983  16.6319  -10.5876
 Z8V  H9   H  HCH1  0   0.230  -11.0874  14.6535  -10.6734
 Z8V  H10  H  HCH1  0   0.206  -13.9494  15.6148   -8.1054
 Z8V  H11  H  HCH1  0   0.224  -13.6501  14.4120  -10.8795
 Z8V  H12  H  HCH1  0   0.250  -12.4730  13.4957   -8.2215
 Z8V  H13  H  HNH1  0   0.396  -12.0915  12.3221  -10.9053
 Z8V  H14  H  HNH1  0   0.339  -11.3797  15.8225   -8.0167
 Z8V  H16  H  HOH1  0   0.456  -12.7628  18.7968   -7.2048
 Z8V  H17  H  HOH1  0   0.451   -8.0141  14.2762   -9.1267
 Z8V  H18  H  HOH1  0   0.452  -15.2893  17.0196   -9.1893
 Z8V  H19  H  HOH1  0   0.440  -14.8956  13.3707   -8.5814
 Z8V  OAD  O  OH1   0  -0.663   -8.8145  14.7274   -9.4089

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
 Z8V  CAA  CAK  single  1.509  0.020  1.509
 Z8V  CAO  OAF  single  1.406  0.020  1.406
 Z8V  CAO  CAP  single  1.537  0.020  1.537
 Z8V  CAO  CAN  single  1.526  0.020  1.526
 Z8V  NAI  CAK  single  1.346  0.020  1.346
 Z8V  NAI  CAP  single  1.444  0.020  1.444
 Z8V  OAE  CAN  single  1.409  0.020  1.409
 Z8V  CAM  CAP  single  1.539  0.020  1.539
 Z8V  CAM  CAH  single  1.520  0.020  1.520
 Z8V  CAM  NAJ  single  1.449  0.020  1.449
 Z8V  OAD  CAH  single  1.408  0.020  1.408
 Z8V  CAL  CAN  single  1.538  0.020  1.538
 Z8V  CAL  NAJ  single  1.451  0.020  1.451
 Z8V  CAL  CAG  single  1.519  0.020  1.519
 Z8V  CAK  OAB  double  1.223  0.020  1.223
 Z8V  CAG  OAC  single  1.411  0.020  1.411
 Z8V  CAA  H1   single  0.970  0.020  1.090
 Z8V  CAA  H2   single  0.970  0.020  1.090
 Z8V  CAA  H3   single  0.970  0.020  1.090
 Z8V  CAG  H4   single  0.970  0.020  1.090
 Z8V  CAG  H5   single  0.970  0.020  1.090
 Z8V  CAH  H6   single  0.970  0.020  1.090
 Z8V  CAH  H7   single  0.970  0.020  1.090
 Z8V  CAL  H8   single  0.970  0.020  1.090
 Z8V  CAM  H9   single  0.970  0.020  1.090
 Z8V  CAN  H10  single  0.970  0.020  1.090
 Z8V  CAO  H11  single  0.970  0.020  1.090
 Z8V  CAP  H12  single  0.970  0.020  1.090
 Z8V  NAI  H13  single  0.860  0.020  1.020
 Z8V  NAJ  H14  single  0.890  0.020  1.040
 Z8V  OAC  H16  single  0.850  0.020  0.980
 Z8V  OAD  H17  single  0.850  0.020  0.980
 Z8V  OAE  H18  single  0.850  0.020  0.980
 Z8V  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
 Z8V  H3   CAA  H2   108.33  3.000
 Z8V  H3   CAA  H1   107.23  3.000
 Z8V  H2   CAA  H1   108.54  3.000
 Z8V  H3   CAA  CAK  109.23  3.000
 Z8V  H2   CAA  CAK  113.86  3.000
 Z8V  H1   CAA  CAK  109.44  3.000
 Z8V  H5   CAG  H4   106.73  3.000
 Z8V  H5   CAG  OAC  111.70  3.000
 Z8V  H4   CAG  OAC  111.65  3.000
 Z8V  H5   CAG  CAL  109.59  3.000
 Z8V  H4   CAG  CAL  108.02  3.000
 Z8V  OAC  CAG  CAL  109.06  3.000
 Z8V  H7   CAH  H6   106.74  3.000
 Z8V  H7   CAH  OAD  111.40  3.000
 Z8V  H6   CAH  OAD  111.70  3.000
 Z8V  H7   CAH  CAM  109.04  3.000
 Z8V  H6   CAH  CAM  108.55  3.000
 Z8V  OAD  CAH  CAM  109.31  3.000
 Z8V  OAB  CAK  NAI  123.46  3.000
 Z8V  OAB  CAK  CAA  121.42  3.000
 Z8V  NAI  CAK  CAA  115.11  3.000
 Z8V  H8   CAL  NAJ  107.41  3.000
 Z8V  H8   CAL  CAN  107.45  3.000
 Z8V  NAJ  CAL  CAN  112.31  3.000
 Z8V  H8   CAL  CAG  106.16  3.000
 Z8V  NAJ  CAL  CAG  109.95  3.000
 Z8V  CAN  CAL  CAG  113.18  3.000
 Z8V  H9   CAM  NAJ  107.64  3.000
 Z8V  H9   CAM  CAP  108.06  3.000
 Z8V  NAJ  CAM  CAP  111.51  3.000
 Z8V  H9   CAM  CAH  108.26  3.000
 Z8V  NAJ  CAM  CAH  110.13  3.000
 Z8V  CAP  CAM  CAH  111.09  3.000
 Z8V  H10  CAN  OAE  111.01  3.000
 Z8V  H10  CAN  CAO  107.84  3.000
 Z8V  OAE  CAN  CAO  107.69  3.000
 Z8V  H10  CAN  CAL  108.72  3.000
 Z8V  OAE  CAN  CAL  111.85  3.000
 Z8V  CAO  CAN  CAL  109.65  3.000
 Z8V  H11  CAO  OAF  105.57  3.000
 Z8V  H11  CAO  CAP  108.03  3.000
 Z8V  OAF  CAO  CAP  111.55  3.000
 Z8V  H11  CAO  CAN  108.02  3.000
 Z8V  CAP  CAO  CAN  110.87  3.000
 Z8V  OAF  CAO  CAN  112.51  3.000
 Z8V  H12  CAP  NAI  107.27  3.000
 Z8V  H12  CAP  CAO  108.67  3.000
 Z8V  NAI  CAP  CAO  110.08  3.000
 Z8V  H12  CAP  CAM  108.00  3.000
 Z8V  NAI  CAP  CAM  111.89  3.000
 Z8V  CAO  CAP  CAM  110.79  3.000
 Z8V  H13  NAI  CAP  116.98  3.000
 Z8V  H13  NAI  CAK  118.17  3.000
 Z8V  CAP  NAI  CAK  124.59  3.000
 Z8V  H14  NAJ  CAM  109.55  3.000
 Z8V  H14  NAJ  CAL  109.81  3.000
 Z8V  CAM  NAJ  CAL  113.48  3.000
 Z8V  H16  OAC  CAG  108.56  3.000
 Z8V  H18  OAE  CAN  108.77  3.000
 Z8V  H19  OAF  CAO  108.60  3.000
 Z8V  H17  OAD  CAH  107.87  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
 Z8V  CONST_01  CAP  NAI  CAK  CAA   180.00   0.0  0
 Z8V  CONST_02  OAB  CAK  NAI  CAP     0.00   0.0  0
 Z8V  CONST_03  H13  NAI  CAK  CAA     0.00   0.0  0
 Z8V  Var_01    H1   CAA  CAK  NAI  -126.34  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
 Z8V  chir_01  CAL  CAN  NAJ  CAG  positiv
 Z8V  chir_02  CAM  NAJ  CAH  CAP  negativ
 Z8V  chir_03  CAN  OAE  CAL  CAO  positiv
 Z8V  chir_04  CAO  OAF  CAN  CAP  negativ
 Z8V  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
 Z8V  plan-1  CAA  0.020
 Z8V  plan-1  CAK  0.020
 Z8V  plan-1  CAP  0.020
 Z8V  plan-1  NAI  0.020
 Z8V  plan-1  OAB  0.020
 Z8V  plan-1  H13  0.020

