# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 08:16:47 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R,2S,3S,4S,5R,6R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[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
 YLL  YLL  (1R,2S,3S,4S,5R,6R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol  ligand  27  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YLL
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
 YLL  O5    O  OH1   0  -0.674   1.8888   0.2639  -0.1909
 YLL  C7    C  CH1   0   0.074   0.6673   0.7702   0.2963
 YLL  C5    C  CH1   0  -0.375   0.4060   2.1230  -0.3615
 YLL  C6    C  CH2   0  -0.147   0.3874   1.9799  -1.8809
 YLL  O6    O  OH1   0  -0.673   0.0072   3.2110  -2.4556
 YLL  C4    C  CH1   0   0.013  -0.8913   2.7427   0.1793
 YLL  O4    O  OH1   0  -0.674  -2.0284   1.9811  -0.1684
 YLL  C3    C  CH1   0  -0.037  -0.8762   2.8312   1.7069
 YLL  O3    O  OH1   0  -0.668   0.0381   3.8071   2.1675
 YLL  C2    C  CH1   0   0.001  -0.6033   1.4720   2.3568
 YLL  O2    O  OH1   0  -0.665  -0.6142   1.5637   3.7599
 YLL  C1    C  CH1   0  -0.027   0.6973   0.8695   1.8237
 YLL  OXT   O  OH1   0  -0.663   0.9787  -0.3893   2.3954
 YLL  H5    H  HOH1  0   0.447   2.0676  -0.5613   0.2734
 YLL  H7    H  HCH1  0   0.199  -0.1604   0.0935   0.0250
 YLL  HA    H  HCH1  0   0.235   1.2342   2.8009  -0.1091
 YLL  H6C1  H  HCH2  0   0.193  -0.3062   1.1751  -2.1625
 YLL  H6C2  H  HCH2  0   0.224   1.3793   1.6729  -2.2257
 YLL  H4    H  HCH1  0   0.244  -0.9820   3.7667  -0.2003
 YLL  H6    H  HOH1  0   0.458   0.0134   3.1086  -3.4113
 YLL  HB    H  HOH1  0   0.460  -2.2081   2.1092  -1.1048
 YLL  H3    H  HCH1  0   0.259  -1.8598   3.1803   2.0353
 YLL  HC    H  HOH1  0   0.449   0.9152   3.6346   1.8103
 YLL  H2    H  HCH1  0   0.239  -1.4271   0.7981   2.0930
 YLL  HD    H  HOH1  0   0.440  -0.0144   2.2743   4.0151
 YLL  HXT   H  HOH1  0   0.446   0.2098  -0.9604   2.2830
 YLL  H1    H  HCH1  0   0.222   1.5463   1.5034   2.1150

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
 YLL  O5   C7    single  1.409  0.020  1.409
 YLL  O5   H5    single  0.850  0.020  0.980
 YLL  C7   C5    single  1.527  0.020  1.527
 YLL  C7   C1    single  1.531  0.020  1.531
 YLL  C7   H7    single  0.970  0.020  1.090
 YLL  C5   C6    single  1.526  0.020  1.526
 YLL  C5   C4    single  1.536  0.020  1.536
 YLL  C5   HA    single  0.970  0.020  1.090
 YLL  C6   O6    single  1.411  0.020  1.411
 YLL  C6   H6C1  single  0.970  0.020  1.090
 YLL  C6   H6C2  single  0.970  0.020  1.090
 YLL  O6   H6    single  0.850  0.020  0.980
 YLL  C4   O4    single  1.412  0.020  1.412
 YLL  C4   C3    single  1.530  0.020  1.530
 YLL  C4   H4    single  0.970  0.020  1.090
 YLL  O4   HB    single  0.850  0.020  0.980
 YLL  C3   O3    single  1.414  0.020  1.414
 YLL  C3   C2    single  1.531  0.020  1.531
 YLL  C3   H3    single  0.970  0.020  1.090
 YLL  O3   HC    single  0.850  0.020  0.980
 YLL  C2   O2    single  1.406  0.020  1.406
 YLL  C2   C1    single  1.529  0.020  1.529
 YLL  C2   H2    single  0.970  0.020  1.090
 YLL  O2   HD    single  0.850  0.020  0.980
 YLL  C1   H1    single  0.970  0.020  1.090
 YLL  C1   OXT   single  1.411  0.020  1.411
 YLL  OXT  HXT   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
 YLL  H5    O5   C7    107.58  3.000
 YLL  H7    C7   C1    107.45  3.000
 YLL  H7    C7   C5    108.01  3.000
 YLL  C1    C7   C5    112.07  3.000
 YLL  H7    C7   O5    110.18  3.000
 YLL  C1    C7   O5    110.57  3.000
 YLL  C5    C7   O5    108.53  3.000
 YLL  HA    C5   C4    107.85  3.000
 YLL  HA    C5   C6    107.19  3.000
 YLL  C4    C5   C6    112.21  3.000
 YLL  HA    C5   C7    108.57  3.000
 YLL  C4    C5   C7    110.51  3.000
 YLL  C6    C5   C7    110.36  3.000
 YLL  H6C2  C6   H6C1  106.62  3.000
 YLL  H6C2  C6   O6    111.15  3.000
 YLL  H6C1  C6   O6    111.38  3.000
 YLL  H6C2  C6   C5    109.21  3.000
 YLL  H6C1  C6   C5    109.35  3.000
 YLL  O6    C6   C5    109.09  3.000
 YLL  H6    O6   C6    108.08  3.000
 YLL  H4    C4   C3    107.01  3.000
 YLL  H4    C4   O4    110.62  3.000
 YLL  C3    C4   O4    106.56  3.000
 YLL  H4    C4   C5    108.96  3.000
 YLL  C3    C4   C5    111.49  3.000
 YLL  O4    C4   C5    112.07  3.000
 YLL  HB    O4   C4    108.56  3.000
 YLL  H3    C3   C2    108.42  3.000
 YLL  H3    C3   O3    105.26  3.000
 YLL  C2    C3   O3    111.04  3.000
 YLL  H3    C3   C4    108.01  3.000
 YLL  C2    C3   C4    111.97  3.000
 YLL  O3    C3   C4    111.80  3.000
 YLL  HC    O3   C3    110.15  3.000
 YLL  H2    C2   C1    108.24  3.000
 YLL  H2    C2   O2    105.92  3.000
 YLL  C1    C2   O2    112.34  3.000
 YLL  H2    C2   C3    108.03  3.000
 YLL  C1    C2   C3    110.69  3.000
 YLL  O2    C2   C3    111.36  3.000
 YLL  HD    O2   C2    107.90  3.000
 YLL  H1    C1   OXT   104.67  3.000
 YLL  OXT   C1   C2    112.33  3.000
 YLL  H1    C1   C2    109.72  3.000
 YLL  OXT   C1   C7    110.51  3.000
 YLL  H1    C1   C7    108.48  3.000
 YLL  C2    C1   C7    110.89  3.000
 YLL  HXT   OXT  C1    108.79  3.000

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
 YLL  chir_01  C7  O5   C5  C1  positiv
 YLL  chir_02  C5  C7   C6  C4  negativ
 YLL  chir_03  C4  O4   C5  C3  positiv
 YLL  chir_04  C3  O3   C4  C2  negativ
 YLL  chir_05  C2  O2   C3  C1  negativ
 YLL  chir_06  C1  OXT  C2  C7  positiv

