# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:12:27 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (3S,4R,5R)-3-amino-4,5-dihydroxycyclohex-1-ene-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C=C(C[C@@H](O)[C@@H]1O)C([O-])=O
#
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
 DHS  DHS  (3S,4R,5R)-3-amino-4,5-dihydroxycyclohex-1-ene-1-carboxylate  ligand  22  12  .  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_DHS
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
 DHS  N    N  NH2    0  -0.814  -1.4626   2.5136   0.3727
 DHS  C1   C  C      0  -0.106   1.0959   0.0110  -0.0133
 DHS  C3   C  CH1    0  -0.135  -1.0305   1.3062  -0.3293
 DHS  C4   C  CH1    0   0.050  -1.7422   0.0834   0.2493
 DHS  C5   C  CH1    0   0.053  -1.1105  -1.1749  -0.3204
 DHS  C6   C  CH2    0  -0.536   0.3402  -1.2765   0.1380
 DHS  C7   C  C      0   0.392   2.6135  -0.0306   0.1025
 DHS  C2   C  C1     0  -0.261   0.4579   1.1634  -0.2145
 DHS  O2   O  OH1    0  -0.677  -3.1180   0.0880  -0.0643
 DHS  O3   O  OH1    0  -0.673  -1.8663  -2.2893   0.0990
 DHS  O4   O  OC    -1  -0.598   3.1127  -1.1506   0.3336
 DHS  O5   O  O      0  -0.599   3.2349   1.0422  -0.0330
 DHS  HN1  H  HNH2   0   0.349  -0.9041   3.2980   0.0575
 DHS  HN2  H  HNH2   0   0.342  -2.4088   2.7456   0.0956
 DHS  H3   H  HCH1   0   0.215  -1.2823   1.3520  -1.4033
 DHS  H4   H  HCH1   0   0.200  -1.5924   0.0904   1.3401
 DHS  H5   H  HCH1   0   0.195  -1.1253  -1.0954  -1.4197
 DHS  H61  H  HCH2   0   0.241   0.8437  -2.0728  -0.4164
 DHS  H62  H  HCH2   0   0.232   0.3587  -1.5909   1.1881
 DHS  H2   H  H      0   0.236   1.0434   2.0712  -0.3253
 DHS  HO2  H  HOH1   0   0.448  -3.5564   0.7319   0.4990
 DHS  HO3  H  HOH1   0   0.447  -1.4495  -3.0787  -0.2605

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
 DHS  N   C3   single  1.462  0.020  1.462
 DHS  N   HN1  single  0.890  0.020  1.040
 DHS  N   HN2  single  0.890  0.020  1.040
 DHS  C1  C6   single  1.501  0.020  1.501
 DHS  C1  C7   single  1.523  0.020  1.523
 DHS  C1  C2   double  1.333  0.020  1.333
 DHS  C3  C4   single  1.528  0.020  1.528
 DHS  C3  C2   single  1.500  0.020  1.500
 DHS  C3  H3   single  0.970  0.020  1.090
 DHS  C4  C5   single  1.519  0.020  1.519
 DHS  C4  O2   single  1.411  0.020  1.411
 DHS  C4  H4   single  0.970  0.020  1.090
 DHS  C5  C6   single  1.525  0.020  1.525
 DHS  C5  O3   single  1.410  0.020  1.410
 DHS  C5  H5   single  0.970  0.020  1.090
 DHS  C6  H61  single  0.970  0.020  1.090
 DHS  C6  H62  single  0.970  0.020  1.090
 DHS  C7  O4   deloc   1.248  0.020  1.248
 DHS  C7  O5   deloc   1.247  0.020  1.247
 DHS  C2  H2   single  0.930  0.020  1.080
 DHS  O2  HO2  single  0.850  0.020  0.980
 DHS  O3  HO3  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
 DHS  HN2  N   HN1  104.63  3.000
 DHS  HN2  N   C3   109.51  3.000
 DHS  HN1  N   C3   109.09  3.000
 DHS  C2   C1  C7   120.82  3.000
 DHS  C2   C1  C6   121.07  3.000
 DHS  C7   C1  C6   118.09  3.000
 DHS  H3   C3  C2   107.74  3.000
 DHS  H3   C3  C4   107.17  3.000
 DHS  C2   C3  C4   110.92  3.000
 DHS  H3   C3  N    111.43  3.000
 DHS  C2   C3  N    109.58  3.000
 DHS  C4   C3  N    109.96  3.000
 DHS  H4   C4  O2   110.66  3.000
 DHS  H4   C4  C5   108.68  3.000
 DHS  O2   C4  C5   108.95  3.000
 DHS  H4   C4  C3   107.85  3.000
 DHS  O2   C4  C3   111.55  3.000
 DHS  C5   C4  C3   109.09  3.000
 DHS  H5   C5  O3   110.27  3.000
 DHS  H5   C5  C6   108.50  3.000
 DHS  O3   C5  C6   111.58  3.000
 DHS  H5   C5  C4   107.98  3.000
 DHS  O3   C5  C4   108.68  3.000
 DHS  C6   C5  C4   109.76  3.000
 DHS  H62  C6  H61  105.61  3.000
 DHS  H62  C6  C5   108.85  3.000
 DHS  H61  C6  C5   109.53  3.000
 DHS  H62  C6  C1   109.52  3.000
 DHS  H61  C6  C1   109.99  3.000
 DHS  C5   C6  C1   113.06  3.000
 DHS  O5   C7  O4   126.37  3.000
 DHS  O5   C7  C1   117.70  3.000
 DHS  O4   C7  C1   115.93  3.000
 DHS  H2   C2  C3   116.61  3.000
 DHS  H2   C2  C1   118.70  3.000
 DHS  C3   C2  C1   124.69  3.000
 DHS  HO2  O2  C4   108.46  3.000
 DHS  HO3  O3  C5   107.76  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
 DHS  Var_01  C6  C1  C2  C3  -0.88  30.0  1
 DHS  Var_02  C2  C1  C6  C5  15.14  30.0  1
 DHS  Var_03  O4  C7  C1  C6  -0.82  30.0  2

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
 DHS  chir_01  C3  N   C4  C2  positiv
 DHS  chir_02  C4  O2  C3  C5  positiv
 DHS  chir_03  C5  O3  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
 DHS  plan-1  C1  0.020
 DHS  plan-1  C7  0.020
 DHS  plan-1  O4  0.020
 DHS  plan-1  O5  0.020

