# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:52:42 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C=C(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
 HSD  HSD  (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol  ligand  25  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HSD
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
 HSD  N1   N  NH2   0  -0.800   1.1214   2.7350   0.2217
 HSD  C1   C  CH1   0  -0.165   0.6884   1.4674  -0.3521
 HSD  C2   C  C1    0  -0.295  -0.7807   1.1752  -0.2266
 HSD  C3   C  C     0   0.020  -1.2758  -0.0343   0.0250
 HSD  C4   C  CH2   0  -0.182  -2.7427  -0.3071   0.1754
 HSD  O1   O  OH1   0  -0.665  -3.4797   0.8868   0.1378
 HSD  C5   C  CH1   0  -0.057  -0.3786  -1.2312   0.2446
 HSD  O2   O  OH1   0  -0.672  -0.8587  -2.3826  -0.4297
 HSD  C6   C  CH1   0   0.037   1.0461  -0.9830  -0.2437
 HSD  O3   O  OH1   0  -0.672   1.9176  -1.9909   0.2033
 HSD  C7   C  CH1   0   0.060   1.5243   0.3570   0.2768
 HSD  O4   O  OH1   0  -0.677   2.8856   0.5360  -0.0159
 HSD  H1   H  HNH2  0   0.360   0.7734   3.5083  -0.3300
 HSD  H2   H  HNH2  0   0.346   0.7331   2.8490   1.1511
 HSD  H3   H  HCH1  0   0.247   0.9445   1.5122  -1.4183
 HSD  H4   H  H     0   0.248  -1.4476   2.0201  -0.3577
 HSD  H5   H  HCH2  0   0.219  -3.0590  -0.9982  -0.6168
 HSD  H6   H  HCH2  0   0.206  -2.8973  -0.8447   1.1248
 HSD  H7   H  HOH1  0   0.460  -4.4132   0.6595   0.1197
 HSD  H8   H  HCH1  0   0.236  -0.3328  -1.4288   1.3256
 HSD  H9   H  HOH1  0   0.462  -1.3938  -2.9031   0.1754
 HSD  H10  H  HCH1  0   0.205   1.0286  -0.9431  -1.3458
 HSD  H11  H  HOH1  0   0.447   1.5813  -2.8329  -0.1219
 HSD  H12  H  HCH1  0   0.193   1.3576   0.3856   1.3686
 HSD  H13  H  HOH1  0   0.441   3.0504   1.4799   0.1150

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
 HSD  N1  C1   single  1.457  0.020  1.457
 HSD  C1  C2   single  1.503  0.020  1.503
 HSD  C2  C3   double  1.331  0.020  1.331
 HSD  C3  C4   single  1.500  0.020  1.500
 HSD  C4  O1   single  1.404  0.020  1.404
 HSD  C3  C5   single  1.512  0.020  1.512
 HSD  C5  O2   single  1.418  0.020  1.418
 HSD  C5  C6   single  1.526  0.020  1.526
 HSD  C6  O3   single  1.405  0.020  1.405
 HSD  C6  C7   single  1.515  0.020  1.515
 HSD  C1  C7   single  1.525  0.020  1.525
 HSD  C7  O4   single  1.404  0.020  1.404
 HSD  N1  H1   single  0.890  0.020  1.040
 HSD  N1  H2   single  0.890  0.020  1.040
 HSD  C1  H3   single  0.970  0.020  1.090
 HSD  C2  H4   single  0.930  0.020  1.080
 HSD  C4  H5   single  0.970  0.020  1.090
 HSD  C4  H6   single  0.970  0.020  1.090
 HSD  O1  H7   single  0.850  0.020  0.980
 HSD  C5  H8   single  0.970  0.020  1.090
 HSD  O2  H9   single  0.850  0.020  0.980
 HSD  C6  H10  single  0.970  0.020  1.090
 HSD  O3  H11  single  0.850  0.020  0.980
 HSD  C7  H12  single  0.970  0.020  1.090
 HSD  O4  H13  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
 HSD  H2   N1  H1  106.40  3.000
 HSD  H2   N1  C1  110.19  3.000
 HSD  H1   N1  C1  110.37  3.000
 HSD  H3   C1  C7  107.60  3.000
 HSD  H3   C1  C2  108.49  3.000
 HSD  C7   C1  C2  111.08  3.000
 HSD  H3   C1  N1  106.13  3.000
 HSD  C7   C1  N1  107.94  3.000
 HSD  C2   C1  N1  115.25  3.000
 HSD  H4   C2  C3  120.14  3.000
 HSD  H4   C2  C1  116.08  3.000
 HSD  C3   C2  C1  123.78  3.000
 HSD  C5   C3  C4  114.95  3.000
 HSD  C5   C3  C2  121.75  3.000
 HSD  C4   C3  C2  123.24  3.000
 HSD  H6   C4  H5  105.92  3.000
 HSD  H6   C4  O1  111.37  3.000
 HSD  H5   C4  O1  111.40  3.000
 HSD  H6   C4  C3  108.20  3.000
 HSD  H5   C4  C3  108.90  3.000
 HSD  O1   C4  C3  110.86  3.000
 HSD  H7   O1  C4  108.02  3.000
 HSD  H8   C5  C6  107.75  3.000
 HSD  H8   C5  O2  109.61  3.000
 HSD  C6   C5  O2  107.21  3.000
 HSD  H8   C5  C3  108.04  3.000
 HSD  C6   C5  C3  112.25  3.000
 HSD  O2   C5  C3  111.89  3.000
 HSD  H9   O2  C5  109.21  3.000
 HSD  H10  C6  C7  108.44  3.000
 HSD  H10  C6  O3  110.71  3.000
 HSD  C7   C6  O3  109.23  3.000
 HSD  H10  C6  C5  108.11  3.000
 HSD  C7   C6  C5  109.18  3.000
 HSD  O3   C6  C5  111.13  3.000
 HSD  H11  O3  C6  107.64  3.000
 HSD  H12  C7  O4  110.43  3.000
 HSD  H12  C7  C6  108.35  3.000
 HSD  O4   C7  C6  110.31  3.000
 HSD  H12  C7  C1  107.82  3.000
 HSD  O4   C7  C1  110.64  3.000
 HSD  C6   C7  C1  109.22  3.000
 HSD  H13  O4  C7  105.15  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
 HSD  Var_01  C5  C3  C2  C1   1.63  30.0  1
 HSD  Var_02  O1  C4  C3  C2  -5.42  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
 HSD  chir_01  C1  N1  C2  C7  positiv
 HSD  chir_02  C5  O2  C3  C6  positiv
 HSD  chir_03  C6  O3  C5  C7  negativ
 HSD  chir_04  C7  O4  C6  C1  positiv

