# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:20:42 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,2S,4S)-4-ethenylcyclohexane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CC[C@@H](C[C@@H]1O)C=C
#
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
 8MD  8MD  (1S,2S,4S)-4-ethenylcyclohexane-1,2-diol  ligand  24  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8MD
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
 8MD  C1   C  CH1   0   0.043   1.5650  -0.5175  -0.2288
 8MD  C2   C  CH2   0  -0.480   0.6435  -1.6524   0.1979
 8MD  C3   C  CH2   0  -0.426  -0.7829  -1.4165  -0.2844
 8MD  C4   C  CH1   0  -0.322  -1.3277  -0.0715   0.2060
 8MD  C5   C  CH2   0  -0.452  -0.3770   1.0606  -0.1953
 8MD  C6   C  CH1   0   0.058   1.0425   0.8146   0.2920
 8MD  C7   C  C1    0  -0.117  -2.6997   0.1734  -0.3409
 8MD  C8   C  C2    0  -0.549  -3.8043   0.2986   0.3850
 8MD  O2   O  OH1   0  -0.679   1.8431   1.8957  -0.1337
 8MD  H1   H  HCH1  0   0.196   1.5781  -0.4693  -1.3293
 8MD  H3   H  HCH2  0   0.239   1.0203  -2.6004  -0.1958
 8MD  H4   H  HCH2  0   0.221   0.6575  -1.7375   1.2899
 8MD  H5   H  HCH2  0   0.218  -0.8108  -1.4391  -1.3800
 8MD  H6   H  HCH2  0   0.241  -1.4307  -2.2256   0.0595
 8MD  H7   H  HCH1  0   0.232  -1.3900  -0.1027   1.3006
 8MD  H8   H  HCH2  0   0.221  -0.3716   1.1614  -1.2871
 8MD  H9   H  HCH2  0   0.246  -0.7411   2.0094   0.2073
 8MD  H10  H  HCH1  0   0.189   1.0280   0.7572   1.3937
 8MD  H11  H  H     0   0.238  -2.7692   0.2420  -1.4249
 8MD  H12  H  H     0   0.232  -3.7840   0.2377   1.4672
 8MD  H13  H  H     0   0.234  -4.7698   0.4658  -0.0749
 8MD  H14  H  HOH1  0   0.444   2.7536   1.7033   0.1136
 8MD  O1   O  OH1   0  -0.684   2.8787  -0.6725   0.2732
 8MD  H2   H  HOH1  0   0.453   3.2946  -1.4124  -0.1794

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
 8MD  O2  C6   single  1.411  0.020  1.411
 8MD  C6  C5   single  1.521  0.020  1.521
 8MD  C6  C1   single  1.523  0.020  1.523
 8MD  C5  C4   single  1.532  0.020  1.532
 8MD  C1  C2   single  1.523  0.020  1.523
 8MD  C4  C7   single  1.497  0.020  1.497
 8MD  C4  C3   single  1.532  0.020  1.532
 8MD  C7  C8   double  1.328  0.020  1.328
 8MD  C2  C3   single  1.524  0.020  1.524
 8MD  C1  H1   single  0.970  0.020  1.090
 8MD  C2  H3   single  0.970  0.020  1.090
 8MD  C2  H4   single  0.970  0.020  1.090
 8MD  C3  H5   single  0.970  0.020  1.090
 8MD  C3  H6   single  0.970  0.020  1.090
 8MD  C4  H7   single  0.970  0.020  1.090
 8MD  C5  H8   single  0.970  0.020  1.090
 8MD  C5  H9   single  0.970  0.020  1.090
 8MD  C6  H10  single  0.970  0.020  1.090
 8MD  C7  H11  single  0.930  0.020  1.080
 8MD  C8  H12  single  0.930  0.020  1.080
 8MD  C8  H13  single  0.930  0.020  1.080
 8MD  O2  H14  single  0.850  0.020  0.980
 8MD  C1  O1   single  1.415  0.020  1.415
 8MD  O1  H2   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
 8MD  O1   C1  H1   110.38  3.000
 8MD  O1   C1  C6   107.04  3.000
 8MD  H1   C1  C6   107.91  3.000
 8MD  O1   C1  C2   112.38  3.000
 8MD  H1   C1  C2   108.64  3.000
 8MD  C6   C1  C2   110.39  3.000
 8MD  H4   C2  H3   106.69  3.000
 8MD  H4   C2  C3   109.85  3.000
 8MD  H3   C2  C3   110.05  3.000
 8MD  H4   C2  C1   109.23  3.000
 8MD  H3   C2  C1   109.67  3.000
 8MD  C3   C2  C1   111.24  3.000
 8MD  H6   C3  H5   106.52  3.000
 8MD  H6   C3  C4   109.80  3.000
 8MD  H5   C3  C4   109.21  3.000
 8MD  H6   C3  C2   109.93  3.000
 8MD  H5   C3  C2   109.69  3.000
 8MD  C4   C3  C2   111.56  3.000
 8MD  H7   C4  C7   108.49  3.000
 8MD  H7   C4  C5   108.52  3.000
 8MD  C7   C4  C5   110.62  3.000
 8MD  H7   C4  C3   108.34  3.000
 8MD  C7   C4  C3   110.65  3.000
 8MD  C5   C4  C3   110.14  3.000
 8MD  H9   C5  H8   106.77  3.000
 8MD  H9   C5  C6   109.47  3.000
 8MD  H8   C5  C6   109.23  3.000
 8MD  H9   C5  C4   109.78  3.000
 8MD  H8   C5  C4   109.38  3.000
 8MD  C6   C5  C4   112.08  3.000
 8MD  H10  C6  O2   110.40  3.000
 8MD  H10  C6  C5   108.42  3.000
 8MD  O2   C6  C5   108.00  3.000
 8MD  H10  C6  C1   107.49  3.000
 8MD  C5   C6  C1   110.62  3.000
 8MD  O2   C6  C1   111.87  3.000
 8MD  H11  C7  C8   119.05  3.000
 8MD  H11  C7  C4   115.63  3.000
 8MD  C8   C7  C4   125.32  3.000
 8MD  H13  C8  H12  116.71  3.000
 8MD  H13  C8  C7   121.63  3.000
 8MD  H12  C8  C7   121.66  3.000
 8MD  H14  O2  C6   107.81  3.000
 8MD  H2   O1  C1   108.58  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
 8MD  Var_01  C4   C3  C2  C1  -56.17  30.0  1
 8MD  Var_02  H12  C8  C7  C4    0.55   0.0  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
 8MD  chir_01  C1  C6  C2  O1  positiv
 8MD  chir_02  C4  C5  C7  C3  negativ
 8MD  chir_03  C6  O2  C5  C1  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
 8MD  plan-1  C4   0.020
 8MD  plan-1  C7   0.020
 8MD  plan-1  C8   0.020
 8MD  plan-1  H11  0.020
 8MD  plan-1  H12  0.020
 8MD  plan-1  H13  0.020

