# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 20:01:03 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN[C@H]1C[C@](O)(CO)[C@@H](O)[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
 VND  VND  "(1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol"
  ligand  40  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VND
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
 VND  N1   N  NH1   0  -0.608  -11.3973  22.9659  -13.4213
 VND  C4   C  CH1   0   0.013   -8.8874  21.6144  -12.2347
 VND  C5   C  CH1   0  -0.001   -8.8906  22.0924  -10.7860
 VND  C6   C  CT    0   0.156  -10.1109  22.9709  -10.4656
 VND  C7   C  CH2   0  -0.168  -10.0352  23.5417   -9.0441
 VND  C8   C  CH2   0  -0.273  -12.5414  23.8426  -13.5869
 VND  C10  C  CH2   0  -0.430  -14.3133  22.0413  -13.1942
 VND  C1   C  CH2   0  -0.460  -10.2116  24.0999  -11.4893
 VND  C11  C  CH3   0  -0.656  -15.5787  21.3924  -13.7363
 VND  C2   C  CH1   0  -0.134  -10.1985  23.6430  -12.9571
 VND  C3   C  CH1   0   0.071   -8.9419  22.8035  -13.1874
 VND  C9   C  CH2   0  -0.423  -13.7490  23.0981  -14.1388
 VND  O1   O  OH1   0  -0.678  -11.2972  22.1977  -10.5409
 VND  O2   O  OH1   0  -0.666   -8.8473  24.2783   -8.8805
 VND  O3   O  OH1   0  -0.678   -8.8724  20.9349   -9.9698
 VND  O4   O  OH1   0  -0.677   -7.7011  20.9061  -12.5249
 VND  O5   O  OH1   0  -0.669   -8.8817  22.3986  -14.5307
 VND  H1   H  HNH1  0   0.354  -11.6377  22.2344  -12.7655
 VND  H3   H  HCH1  0   0.204   -9.7614  20.9688  -12.4076
 VND  H4   H  HCH1  0   0.224   -7.9829  22.6894  -10.6347
 VND  H5   H  HCH2  0   0.209  -10.9253  24.1657   -8.8857
 VND  H6   H  HCH2  0   0.202  -10.0972  22.7151   -8.3219
 VND  H7   H  HCH2  0   0.218  -12.2621  24.6357  -14.2874
 VND  H8   H  HCH2  0   0.184  -12.8422  24.3510  -12.6562
 VND  H9   H  HCH2  0   0.213  -13.5668  21.2633  -13.0103
 VND  H10  H  HCH2  0   0.211  -14.5222  22.5010  -12.2229
 VND  H11  H  HCH2  0   0.243   -9.3712  24.7804  -11.3300
 VND  H12  H  HCH2  0   0.249  -11.1116  24.6879  -11.2875
 VND  H13  H  HCH3  0   0.225  -15.9688  20.6387  -13.0516
 VND  H14  H  HCH3  0   0.215  -16.3643  22.1334  -13.8949
 VND  H15  H  HCH3  0   0.216  -15.3907  20.9030  -14.6936
 VND  H16  H  HCH1  0   0.240  -10.0939  24.5455  -13.5705
 VND  H17  H  HCH1  0   0.199   -8.0833  23.4531  -12.9455
 VND  H18  H  HCH2  0   0.214  -14.5312  23.8315  -14.3571
 VND  H19  H  HCH2  0   0.209  -13.4817  22.6337  -15.0932
 VND  H20  H  HOH1  0   0.442  -11.1479  21.3831  -10.0447
 VND  H21  H  HOH1  0   0.458   -8.8148  24.6037   -7.9766
 VND  H22  H  HOH1  0   0.460   -8.4199  21.1351   -9.1451
 VND  H23  H  HOH1  0   0.449   -7.6795  20.1174  -11.9736
 VND  H24  H  HOH1  0   0.442   -8.0840  21.8709  -14.6398

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
 VND  O5   C3   single  1.404  0.020  1.404
 VND  C9   C8   single  1.522  0.020  1.522
 VND  C9   C10  single  1.526  0.020  1.526
 VND  C8   N1   single  1.451  0.020  1.451
 VND  N1   C2   single  1.453  0.020  1.453
 VND  C11  C10  single  1.522  0.020  1.522
 VND  C3   C2   single  1.529  0.020  1.529
 VND  C3   C4   single  1.525  0.020  1.525
 VND  C2   C1   single  1.537  0.020  1.537
 VND  O4   C4   single  1.412  0.020  1.412
 VND  C4   C5   single  1.526  0.020  1.526
 VND  C1   C6   single  1.527  0.020  1.527
 VND  O1   C6   single  1.418  0.020  1.418
 VND  C5   C6   single  1.537  0.020  1.537
 VND  C5   O3   single  1.416  0.020  1.416
 VND  C6   C7   single  1.534  0.020  1.534
 VND  C7   O2   single  1.407  0.020  1.407
 VND  N1   H1   single  0.890  0.020  1.040
 VND  C4   H3   single  0.970  0.020  1.090
 VND  C5   H4   single  0.970  0.020  1.090
 VND  C7   H5   single  0.970  0.020  1.090
 VND  C7   H6   single  0.970  0.020  1.090
 VND  C8   H7   single  0.970  0.020  1.090
 VND  C8   H8   single  0.970  0.020  1.090
 VND  C10  H9   single  0.970  0.020  1.090
 VND  C10  H10  single  0.970  0.020  1.090
 VND  C1   H11  single  0.970  0.020  1.090
 VND  C1   H12  single  0.970  0.020  1.090
 VND  C11  H13  single  0.970  0.020  1.090
 VND  C11  H14  single  0.970  0.020  1.090
 VND  C11  H15  single  0.970  0.020  1.090
 VND  C2   H16  single  0.970  0.020  1.090
 VND  C3   H17  single  0.970  0.020  1.090
 VND  C9   H18  single  0.970  0.020  1.090
 VND  C9   H19  single  0.970  0.020  1.090
 VND  O1   H20  single  0.850  0.020  0.980
 VND  O2   H21  single  0.850  0.020  0.980
 VND  O3   H22  single  0.850  0.020  0.980
 VND  O4   H23  single  0.850  0.020  0.980
 VND  O5   H24  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
 VND  H1   N1   C2   109.02  3.000
 VND  H1   N1   C8   108.88  3.000
 VND  C2   N1   C8   113.92  3.000
 VND  H3   C4   O4   109.92  3.000
 VND  H3   C4   C3   109.33  3.000
 VND  O4   C4   C3   107.03  3.000
 VND  H3   C4   C5   109.35  3.000
 VND  O4   C4   C5   110.74  3.000
 VND  C3   C4   C5   110.42  3.000
 VND  H4   C5   O3   110.77  3.000
 VND  H4   C5   C6   108.49  3.000
 VND  O3   C5   C6   110.92  3.000
 VND  H4   C5   C4   107.44  3.000
 VND  O3   C5   C4   106.93  3.000
 VND  C6   C5   C4   112.25  3.000
 VND  O1   C6   C1   108.20  3.000
 VND  O1   C6   C7   107.06  3.000
 VND  C1   C6   C7   110.45  3.000
 VND  C7   C6   C5   111.51  3.000
 VND  O1   C6   C5   109.96  3.000
 VND  C1   C6   C5   109.58  3.000
 VND  H6   C7   H5   106.66  3.000
 VND  H6   C7   O2   111.40  3.000
 VND  H5   C7   O2   111.71  3.000
 VND  H6   C7   C6   109.04  3.000
 VND  H5   C7   C6   107.76  3.000
 VND  O2   C7   C6   110.13  3.000
 VND  H8   C8   H7   106.01  3.000
 VND  H8   C8   C9   108.37  3.000
 VND  H7   C8   C9   108.96  3.000
 VND  H8   C8   N1   113.42  3.000
 VND  H7   C8   N1   108.05  3.000
 VND  C9   C8   N1   111.81  3.000
 VND  H10  C10  H9   106.24  3.000
 VND  H10  C10  C9   109.21  3.000
 VND  H9   C10  C9   110.15  3.000
 VND  H10  C10  C11  109.66  3.000
 VND  H9   C10  C11  108.91  3.000
 VND  C9   C10  C11  112.48  3.000
 VND  H12  C1   H11  105.73  3.000
 VND  H12  C1   C2   110.06  3.000
 VND  H11  C1   C2   108.52  3.000
 VND  H12  C1   C6   109.15  3.000
 VND  H11  C1   C6   108.17  3.000
 VND  C2   C1   C6   114.81  3.000
 VND  H15  C11  H14  107.52  3.000
 VND  H15  C11  H13  107.61  3.000
 VND  H14  C11  H13  107.64  3.000
 VND  H15  C11  C10  111.12  3.000
 VND  H14  C11  C10  111.14  3.000
 VND  H13  C11  C10  111.62  3.000
 VND  H16  C2   C3   106.82  3.000
 VND  H16  C2   C1   106.88  3.000
 VND  C3   C2   C1   108.31  3.000
 VND  H16  C2   N1   106.47  3.000
 VND  C1   C2   N1   115.88  3.000
 VND  C3   C2   N1   111.97  3.000
 VND  H17  C3   O5   110.24  3.000
 VND  H17  C3   C2   106.46  3.000
 VND  O5   C3   C2   109.74  3.000
 VND  H17  C3   C4   107.12  3.000
 VND  C2   C3   C4   111.32  3.000
 VND  O5   C3   C4   111.80  3.000
 VND  H19  C9   H18  106.56  3.000
 VND  H19  C9   C10  109.65  3.000
 VND  H18  C9   C10  108.87  3.000
 VND  H19  C9   C8   109.26  3.000
 VND  H18  C9   C8   108.15  3.000
 VND  C10  C9   C8   114.06  3.000
 VND  H20  O1   C6   107.66  3.000
 VND  H21  O2   C7   108.36  3.000
 VND  H22  O3   C5   109.27  3.000
 VND  H23  O4   C4   108.19  3.000
 VND  H24  O5   C3   107.58  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
 VND  Var_01  C9   C8   N1   C2    177.20  30.0  1
 VND  Var_02  H7   C8   N1   C2     57.31  30.0  1
 VND  Var_03  H8   C8   N1   C2    -59.90  30.0  1
 VND  Var_04  C10  C9   C8   N1     65.69  30.0  1
 VND  Var_05  C11  C10  C9   C8    175.74  30.0  3
 VND  Var_06  H18  C9   C8   N1   -173.03  30.0  1
 VND  Var_07  H19  C9   C8   N1    -57.42  30.0  1
 VND  Var_08  H9   C10  C9   C8    -62.57  30.0  3
 VND  Var_09  H10  C10  C9   C8     53.75  30.0  3
 VND  Var_10  H7   C8   C9   C10  -174.96  30.0  3
 VND  Var_11  H8   C8   C9   C10   -60.04  30.0  3
 VND  Var_12  H18  C9   C10  C11    54.86  30.0  1
 VND  Var_13  H19  C9   C10  C11   -61.37  30.0  1
 VND  Var_14  H1   N1   C8   C9    -60.89  30.0  3
 VND  Var_15  H13  C11  C10  C9    179.90  30.0  3
 VND  Var_16  H14  C11  C10  C9    -59.92  30.0  3
 VND  Var_17  H15  C11  C10  C9     59.77  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
 VND  chir_01  C4  C3  O4  C5  negativ
 VND  chir_02  C5  O3  C4  C6  negativ
 VND  chir_03  C6  C7  C5  C1  positiv
 VND  chir_04  C2  N1  C3  C1  positiv
 VND  chir_05  C3  O5  C2  C4  negativ

