# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:20:54 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (1R,4R,5S,6S,7R,10R,11S,12S)-1,7-bis(hydroxymethyl)-2,8,13,14-tetraoxatricyclo[8.2.1.1~4,7~]tetradecane-5,6,11,12-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]12OC[C@H]3O[C@@](CO)(OC[C@@H](O1)[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H]3O
#
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
 0U8  0U8  (1R,4R,5S,6S,7R,10R,11S,12S)-1,7-bis(hydroxymethyl)-2,8,13,14-tetraoxatricyclo[8.2.1.1~4,7~]tetradecane-5,6,11,12-tetrol  ligand  42  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0U8
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
 0U8  O1'  O  OH1   0  -0.668   2.7545   2.4285  -1.7341
 0U8  C1'  C  CH2   0  -0.175   3.2716   1.5357  -0.7841
 0U8  C2'  C  CT    0   0.482   2.1375   0.7470  -0.1404
 0U8  O6   O  O2    0  -0.499   1.2672   1.6938   0.3822
 0U8  C6   C  CH2   0  -0.195   0.0822   1.2912   1.0358
 0U8  C5   C  CR15  0  -0.050  -1.1596   1.4272   0.1607
 0U8  O5   O  O     0  -0.495  -1.2504   0.5058  -0.9122
 0U8  C2   C  CR5   0   0.510  -1.8436  -0.6876  -0.4965
 0U8  C1   C  CH2   0  -0.194  -2.7579  -1.1940  -1.6108
 0U8  O1   O  OH1   0  -0.660  -3.7459  -0.2311  -1.8701
 0U8  O2   O  O2    0  -0.504  -0.9049  -1.6700  -0.1719
 0U8  C6'  C  CH2   0  -0.212   0.1067  -2.0176  -1.0948
 0U8  C5'  C  CH1   0   0.033   1.4618  -1.4177  -0.7627
 0U8  O5'  O  O2    0  -0.501   1.5005  -0.0456  -1.1035
 0U8  C4'  C  CH1   0  -0.034   1.8783  -1.5192   0.7029
 0U8  O4'  O  OH1   0  -0.670   2.5815  -2.7208   0.9041
 0U8  C3'  C  CH1   0  -0.057   2.7130  -0.2527   0.8900
 0U8  O3'  O  OH1   0  -0.657   2.7115   0.3089   2.1712
 0U8  C3   C  CR15  0  -0.087  -2.6333  -0.3413   0.8063
 0U8  O3   O  OH1   0  -0.652  -2.1171  -1.0639   1.8910
 0U8  C4   C  CR15  0   0.027  -2.4308   1.1783   0.9643
 0U8  O4   O  OH1   0  -0.665  -3.4610   1.9404   0.3909
 0U8  H1   H  HOH1  0   0.457   3.4970   2.8456  -2.1797
 0U8  H2   H  HCH2  0   0.203   3.9602   0.8124  -1.2387
 0U8  H3   H  HCH2  0   0.203   3.8312   2.0519   0.0086
 0U8  H4   H  HCH2  0   0.230   0.1492   0.2948   1.4730
 0U8  H5   H  HCH2  0   0.234  -0.0460   1.9811   1.8754
 0U8  H6   H  HCR5  0   0.249  -1.1623   2.4307  -0.2757
 0U8  H7   H  HCH2  0   0.211  -2.1682  -1.4093  -2.5122
 0U8  H8   H  HCH2  0   0.213  -3.1864  -2.1464  -1.2761
 0U8  H9   H  HOH1  0   0.458  -4.4318  -0.6484  -2.3979
 0U8  H10  H  HCH2  0   0.237   0.2095  -3.1056  -1.0574
 0U8  H11  H  HCH2  0   0.235  -0.1474  -1.7617  -2.1279
 0U8  H12  H  HCH1  0   0.226   2.1993  -1.9622  -1.3705
 0U8  H13  H  HCH1  0   0.243   0.9984  -1.4810   1.3553
 0U8  H14  H  HOH1  0   0.456   2.5759  -2.9258   1.8433
 0U8  H15  H  HCH1  0   0.238   3.7382  -0.5004   0.5728
 0U8  H16  H  HOH1  0   0.458   3.2844  -0.2187   2.7356
 0U8  H17  H  HCR5  0   0.246  -3.6988  -0.5616   0.6636
 0U8  H18  H  HOH1  0   0.455  -2.6699  -0.8683   2.6541
 0U8  H19  H  HCR5  0   0.227  -2.2991   1.4279   2.0267
 0U8  H20  H  HOH1  0   0.449  -4.3006   1.6493   0.7600

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
 0U8  O4'  C4'  single  1.407  0.020  1.407
 0U8  O3'  C3'  single  1.399  0.020  1.399
 0U8  C3'  C4'  single  1.528  0.020  1.528
 0U8  C3'  C2'  single  1.547  0.020  1.547
 0U8  C4'  C5'  single  1.527  0.020  1.527
 0U8  C5'  C6'  single  1.519  0.020  1.519
 0U8  C5'  O5'  single  1.414  0.020  1.414
 0U8  O1'  C1'  single  1.403  0.020  1.403
 0U8  C1'  C2'  single  1.524  0.020  1.524
 0U8  C2'  O5'  single  1.401  0.020  1.401
 0U8  C2'  O6   single  1.388  0.020  1.388
 0U8  C6'  O2   single  1.413  0.020  1.413
 0U8  O2   C2   single  1.397  0.020  1.397
 0U8  O6   C6   single  1.412  0.020  1.412
 0U8  O3   C3   single  1.402  0.020  1.402
 0U8  C2   O5   single  1.396  0.020  1.396
 0U8  C2   C3   single  1.562  0.020  1.562
 0U8  C2   C1   single  1.528  0.020  1.528
 0U8  C6   C5   single  1.525  0.020  1.525
 0U8  C4   C3   single  1.541  0.020  1.541
 0U8  C4   C5   single  1.524  0.020  1.524
 0U8  C4   O4   single  1.404  0.020  1.404
 0U8  O1   C1   single  1.404  0.020  1.404
 0U8  O5   C5   single  1.417  0.020  1.417
 0U8  O1'  H1   single  0.850  0.020  0.980
 0U8  C1'  H2   single  0.970  0.020  1.090
 0U8  C1'  H3   single  0.970  0.020  1.090
 0U8  C6   H4   single  0.970  0.020  1.090
 0U8  C6   H5   single  0.970  0.020  1.090
 0U8  C5   H6   single  0.970  0.020  1.090
 0U8  C1   H7   single  0.970  0.020  1.090
 0U8  C1   H8   single  0.970  0.020  1.090
 0U8  O1   H9   single  0.850  0.020  0.980
 0U8  C6'  H10  single  0.970  0.020  1.090
 0U8  C6'  H11  single  0.970  0.020  1.090
 0U8  C5'  H12  single  0.970  0.020  1.090
 0U8  C4'  H13  single  0.970  0.020  1.090
 0U8  O4'  H14  single  0.850  0.020  0.980
 0U8  C3'  H15  single  0.970  0.020  1.090
 0U8  O3'  H16  single  0.850  0.020  0.980
 0U8  C3   H17  single  0.970  0.020  1.090
 0U8  O3   H18  single  0.850  0.020  0.980
 0U8  C4   H19  single  0.970  0.020  1.090
 0U8  O4   H20  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
 0U8  H1   O1'  C1'  107.78  3.000
 0U8  H3   C1'  H2   106.80  3.000
 0U8  H3   C1'  C2'  108.50  3.000
 0U8  H2   C1'  C2'  107.50  3.000
 0U8  H3   C1'  O1'  112.17  3.000
 0U8  H2   C1'  O1'  111.74  3.000
 0U8  C2'  C1'  O1'  109.95  3.000
 0U8  C3'  C2'  O5'  105.16  3.000
 0U8  O5'  C2'  O6   111.08  3.000
 0U8  C3'  C2'  O6   115.04  3.000
 0U8  O6   C2'  C1'  105.82  3.000
 0U8  O5'  C2'  C1'  109.93  3.000
 0U8  C3'  C2'  C1'  109.82  3.000
 0U8  C6   O6   C2'  120.40  3.000
 0U8  H5   C6   H4   106.01  3.000
 0U8  H5   C6   C5   106.78  3.000
 0U8  H4   C6   C5   111.20  3.000
 0U8  H5   C6   O6   105.89  3.000
 0U8  H4   C6   O6   113.24  3.000
 0U8  C5   C6   O6   113.10  3.000
 0U8  H6   C5   C4   110.97  3.000
 0U8  H6   C5   O5   107.10  3.000
 0U8  C4   C5   O5   103.86  3.000
 0U8  H6   C5   C6   108.22  3.000
 0U8  O5   C5   C6   115.38  3.000
 0U8  C4   C5   C6   111.22  3.000
 0U8  C2   O5   C5   110.95  3.000
 0U8  C3   C2   O2   107.56  3.000
 0U8  C3   C2   C1   112.29  3.000
 0U8  O2   C2   C1   109.79  3.000
 0U8  C1   C2   O5   108.69  3.000
 0U8  C3   C2   O5   105.88  3.000
 0U8  O2   C2   O5   112.63  3.000
 0U8  H8   C1   H7   106.86  3.000
 0U8  H8   C1   O1   112.15  3.000
 0U8  H7   C1   O1   111.14  3.000
 0U8  H8   C1   C2   107.40  3.000
 0U8  H7   C1   C2   110.01  3.000
 0U8  O1   C1   C2   109.18  3.000
 0U8  H9   O1   C1   107.82  3.000
 0U8  C6'  O2   C2   120.15  3.000
 0U8  H11  C6'  H10  106.66  3.000
 0U8  H11  C6'  C5'  108.74  3.000
 0U8  H10  C6'  C5'  107.56  3.000
 0U8  H11  C6'  O2   113.13  3.000
 0U8  H10  C6'  O2   106.84  3.000
 0U8  C5'  C6'  O2   113.51  3.000
 0U8  H12  C5'  C4'  108.34  3.000
 0U8  H12  C5'  O5'  109.20  3.000
 0U8  C4'  C5'  O5'  106.76  3.000
 0U8  H12  C5'  C6'  106.37  3.000
 0U8  O5'  C5'  C6'  110.79  3.000
 0U8  C4'  C5'  C6'  115.27  3.000
 0U8  C5'  O5'  C2'  113.31  3.000
 0U8  H13  C4'  C3'  109.68  3.000
 0U8  H13  C4'  O4'  110.24  3.000
 0U8  C3'  C4'  O4'  114.67  3.000
 0U8  H13  C4'  C5'  110.49  3.000
 0U8  C3'  C4'  C5'  102.20  3.000
 0U8  O4'  C4'  C5'  109.29  3.000
 0U8  H14  O4'  C4'  108.60  3.000
 0U8  H15  C3'  O3'  110.80  3.000
 0U8  H15  C3'  C4'  106.67  3.000
 0U8  O3'  C3'  C4'  116.37  3.000
 0U8  H15  C3'  C2'  107.45  3.000
 0U8  C4'  C3'  C2'  104.53  3.000
 0U8  O3'  C3'  C2'  110.50  3.000
 0U8  H16  O3'  C3'  108.46  3.000
 0U8  H17  C3   C4   109.81  3.000
 0U8  H17  C3   O3   110.78  3.000
 0U8  C4   C3   O3   112.37  3.000
 0U8  H17  C3   C2   109.74  3.000
 0U8  C4   C3   C2   103.75  3.000
 0U8  O3   C3   C2   110.17  3.000
 0U8  H18  O3   C3   107.29  3.000
 0U8  H19  C4   O4   111.07  3.000
 0U8  H19  C4   C3   109.80  3.000
 0U8  O4   C4   C3   113.39  3.000
 0U8  H19  C4   C5   111.87  3.000
 0U8  O4   C4   C5   107.94  3.000
 0U8  C3   C4   C5   102.50  3.000
 0U8  H20  O4   C4   108.63  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
 0U8  Var_01  C5   C6   O6  C2'  -101.39  30.0  1
 0U8  Var_02  C5'  C6'  O2  C2    102.54  30.0  1

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
 0U8  chir_01  C2'  C3'  O5'  O6   negativ
 0U8  chir_02  C5   O5   C4   C6   negativ
 0U8  chir_03  C2   O2   O5   C3   positiv
 0U8  chir_04  C5'  O5'  C4'  C6'  negativ
 0U8  chir_05  C4'  O4'  C5'  C3'  positiv
 0U8  chir_06  C3'  O3'  C4'  C2'  negativ
 0U8  chir_07  C3   O3   C2   C4   positiv
 0U8  chir_08  C4   O4   C3   C5   negativ

