# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:10:49 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,2S,3S,4R)-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=C[C@H](O)[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
 HMC  HMC  (1S,2S,3S,4R)-5-(hydroxymethyl)cyclohex-5-ene-1,2,3,4-tetrol  ligand  24  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 GRAND
;

data_comp_HMC
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
 HMC  C1   C  CH1   0  -0.047   1.5935  -0.1507  -0.6714
 HMC  O1   O  OH1   0  -0.664   2.0036   1.1392  -1.0893
 HMC  C2   C  CH1   0   0.036   0.3871  -0.5691  -1.5107
 HMC  O2   O  OH1   0  -0.668   0.5880  -0.3521  -2.8825
 HMC  C3   C  CH1   0   0.033  -0.8403   0.2065  -1.0662
 HMC  O3   O  OH1   0  -0.672  -1.9106  -0.0940  -1.9266
 HMC  C4   C  CH1   0  -0.061  -1.1785  -0.1795   0.3699
 HMC  O4   O  OH1   0  -0.672  -2.1998   0.6954   0.8173
 HMC  C5   C  C     0   0.033   0.0279  -0.1455   1.2767
 HMC  C6   C  C1    0  -0.314   1.2676  -0.1727   0.7946
 HMC  C7   C  CH2   0  -0.182  -0.2835  -0.1477   2.7436
 HMC  O7   O  OH1   0  -0.665   0.8795  -0.3488   3.5028
 HMC  H1   H  HCH1  0   0.221   2.4009  -0.8750  -0.8585
 HMC  HO1  H  HOH1  0   0.451   2.7309   1.4186  -0.5239
 HMC  H2   H  HCH1  0   0.213   0.2123  -1.6372  -1.3035
 HMC  HO2  H  HOH1  0   0.449   1.3520  -0.8675  -3.1603
 HMC  H3   H  HCH1  0   0.212  -0.6114   1.2829  -1.0886
 HMC  HO3  H  HOH1  0   0.446  -2.6789   0.3958  -1.6143
 HMC  H4   H  HCH1  0   0.241  -1.5549  -1.2131   0.3548
 HMC  HO4  H  HOH1  0   0.463  -2.8498   0.1938   1.3160
 HMC  H6   H  H     0   0.256   2.1130  -0.1826   1.4730
 HMC  H71  H  HCH2  0   0.209  -1.0329  -0.9308   2.9371
 HMC  H72  H  HCH2  0   0.222  -0.7683   0.8035   2.9982
 HMC  HO7  H  HOH1  0   0.461   0.6505  -0.2400   4.4299

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
 HMC  C1  O1   single  1.417  0.020  1.417
 HMC  C1  C2   single  1.528  0.020  1.528
 HMC  C1  C6   single  1.502  0.020  1.502
 HMC  C1  H1   single  0.970  0.020  1.090
 HMC  O1  HO1  single  0.850  0.020  0.980
 HMC  C2  O2   single  1.403  0.020  1.403
 HMC  C2  C3   single  1.518  0.020  1.518
 HMC  C2  H2   single  0.970  0.020  1.090
 HMC  O2  HO2  single  0.850  0.020  0.980
 HMC  C3  O3   single  1.406  0.020  1.406
 HMC  C3  C4   single  1.525  0.020  1.525
 HMC  C3  H3   single  0.970  0.020  1.090
 HMC  O3  HO3  single  0.850  0.020  0.980
 HMC  C4  O4   single  1.417  0.020  1.417
 HMC  C4  C5   single  1.510  0.020  1.510
 HMC  C4  H4   single  0.970  0.020  1.090
 HMC  O4  HO4  single  0.850  0.020  0.980
 HMC  C5  C6   double  1.330  0.020  1.330
 HMC  C5  C7   single  1.500  0.020  1.500
 HMC  C6  H6   single  0.930  0.020  1.080
 HMC  C7  O7   single  1.403  0.020  1.403
 HMC  C7  H71  single  0.970  0.020  1.090
 HMC  C7  H72  single  0.970  0.020  1.090
 HMC  O7  HO7  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
 HMC  H1   C1  C6   108.38  3.000
 HMC  H1   C1  C2   107.79  3.000
 HMC  C6   C1  C2   111.15  3.000
 HMC  H1   C1  O1   109.68  3.000
 HMC  C6   C1  O1   111.35  3.000
 HMC  C2   C1  O1   108.41  3.000
 HMC  HO1  O1  C1   108.05  3.000
 HMC  H2   C2  C3   108.17  3.000
 HMC  H2   C2  O2   110.88  3.000
 HMC  C3   C2  O2   108.84  3.000
 HMC  H2   C2  C1   106.70  3.000
 HMC  C3   C2  C1   109.73  3.000
 HMC  O2   C2  C1   112.43  3.000
 HMC  HO2  O2  C2   108.24  3.000
 HMC  H3   C3  C4   108.23  3.000
 HMC  H3   C3  O3   110.79  3.000
 HMC  C4   C3  O3   110.69  3.000
 HMC  H3   C3  C2   108.99  3.000
 HMC  C4   C3  C2   109.00  3.000
 HMC  O3   C3  C2   109.09  3.000
 HMC  HO3  O3  C3   107.47  3.000
 HMC  H4   C4  C5   107.63  3.000
 HMC  H4   C4  O4   109.75  3.000
 HMC  C5   C4  O4   111.86  3.000
 HMC  H4   C4  C3   107.50  3.000
 HMC  C5   C4  C3   112.50  3.000
 HMC  O4   C4  C3   107.50  3.000
 HMC  HO4  O4  C4   109.21  3.000
 HMC  C7   C5  C6   123.22  3.000
 HMC  C7   C5  C4   114.94  3.000
 HMC  C6   C5  C4   121.77  3.000
 HMC  H6   C6  C5   120.01  3.000
 HMC  H6   C6  C1   116.22  3.000
 HMC  C5   C6  C1   123.75  3.000
 HMC  H72  C7  H71  105.96  3.000
 HMC  H72  C7  O7   111.40  3.000
 HMC  H71  C7  O7   111.54  3.000
 HMC  H72  C7  C5   108.50  3.000
 HMC  H71  C7  C5   108.32  3.000
 HMC  O7   C7  C5   110.94  3.000
 HMC  HO7  O7  C7   107.95  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
 HMC  Var_01  C4  C5  C6  C1    4.05  30.0  1
 HMC  Var_02  O7  C7  C5  C4  169.74  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
 HMC  chir_01  C1  O1  C2  C6  positiv
 HMC  chir_02  C2  O2  C1  C3  negativ
 HMC  chir_03  C3  O3  C2  C4  positiv
 HMC  chir_04  C4  O4  C3  C5  negativ

