# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:51:44 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2~{R},4~{a}~{R},6~{R},7~{R},8~{R},8~{a}~{R})-2-methyl-6,7,8-tris(oxidanyl)-4,4~{a},6,7,8,8~{a}-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(OC[C@H]2O[C@@H](O)[C@H](O)[C@@H](O)[C@H]2O1)C(O)=O
#
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
 8VR  8VR  '(2~{R},4~{a}~{R},6~{R},7~{R},8~{R},8~{a}~{R})-2-methyl-6,7,8-tris(oxidanyl)-4,4~{a},6,7,8,8~{a}-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid'  ligand  30  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8VR
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
 8VR  C1   C  CH1    0   0.264   2.4972   0.9290  -0.2795
 8VR  C2   C  CH1    0  -0.031   2.3727  -0.4622   0.3368
 8VR  C3   C  CH1    0   0.015   1.3843  -1.2821  -0.4829
 8VR  C4   C  CH1    0  -0.016   0.0606  -0.5507  -0.6201
 8VR  C5   C  CH1    0   0.012   0.2978   0.8719  -1.1259
 8VR  C6   C  CH2    0  -0.233  -1.0131   1.6277  -1.0496
 8VR  C7   C  CT     0   0.392  -1.7858   0.1996   0.6458
 8VR  C8   C  C      0   0.353  -2.8991  -0.4998  -0.2067
 8VR  C9   C  CH3    0  -0.702  -2.2466   0.2509   2.0911
 8VR  O1   O  OH1    0  -0.663   3.3346   1.6869   0.5150
 8VR  O2   O  OH1    0  -0.674   3.6037  -1.1457   0.3082
 8VR  O3   O  OH1    0  -0.668   1.1564  -2.5515   0.0688
 8VR  O4   O  O2     0  -0.501  -0.5742  -0.5136   0.6347
 8VR  O5   O  O2     0  -0.499   1.2387   1.5525  -0.3213
 8VR  O6   O  O2     0  -0.492  -1.5708   1.5266   0.2387
 8VR  O8A  O  OC    -1  -0.595  -3.7976   0.2437  -0.6377
 8VR  O8B  O  O      0  -0.590  -2.8214  -1.7357  -0.3083
 8VR  H1   H  HCH1   0   0.183   2.8945   0.8327  -1.3062
 8VR  H2   H  HCH1   0   0.224   1.9952  -0.3556   1.3638
 8VR  H3   H  HCH1   0   0.212   1.7957  -1.3685  -1.5029
 8VR  H4   H  HCH1   0   0.238  -0.5600  -1.0778  -1.3578
 8VR  H5   H  HCH1   0   0.231   0.6337   0.8341  -2.1734
 8VR  H6   H  HCH2   0   0.247  -0.8588   2.6885  -1.2569
 8VR  H7   H  HCH2   0   0.218  -1.6910   1.2372  -1.8176
 8VR  H8   H  HCH3   0   0.234  -3.1686   0.8253   2.1743
 8VR  H9   H  HCH3   0   0.234  -2.4390  -0.7545   2.4646
 8VR  H10  H  HCH3   0   0.235  -1.4890   0.7155   2.7249
 8VR  H11  H  HOH1   0   0.466   3.6891   2.4214   0.0033
 8VR  H12  H  HOH1   0   0.456   4.1999  -0.7318   0.9399
 8VR  H13  H  HOH1   0   0.449   2.0081  -2.9906   0.1624

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
 8VR  O3   C3   single  1.403  0.020  1.403
 8VR  C3   C4   single  1.519  0.020  1.519
 8VR  C3   C2   single  1.524  0.020  1.524
 8VR  O8B  C8   deloc   1.243  0.020  1.243
 8VR  O4   C4   single  1.407  0.020  1.407
 8VR  O4   C7   single  1.406  0.020  1.406
 8VR  O2   C2   single  1.408  0.020  1.408
 8VR  C4   C5   single  1.528  0.020  1.528
 8VR  C2   C1   single  1.527  0.020  1.527
 8VR  C8   C7   single  1.567  0.020  1.567
 8VR  C8   O8A  deloc   1.243  0.020  1.243
 8VR  C9   C7   single  1.518  0.020  1.518
 8VR  C7   O6   single  1.405  0.020  1.405
 8VR  C5   O5   single  1.413  0.020  1.413
 8VR  C5   C6   single  1.515  0.020  1.515
 8VR  C1   O5   single  1.405  0.020  1.405
 8VR  C1   O1   single  1.381  0.020  1.381
 8VR  O6   C6   single  1.407  0.020  1.407
 8VR  C1   H1   single  0.970  0.020  1.090
 8VR  C2   H2   single  0.970  0.020  1.090
 8VR  C3   H3   single  0.970  0.020  1.090
 8VR  C4   H4   single  0.970  0.020  1.090
 8VR  C5   H5   single  0.970  0.020  1.090
 8VR  C6   H6   single  0.970  0.020  1.090
 8VR  C6   H7   single  0.970  0.020  1.090
 8VR  C9   H8   single  0.970  0.020  1.090
 8VR  C9   H9   single  0.970  0.020  1.090
 8VR  C9   H10  single  0.970  0.020  1.090
 8VR  O1   H11  single  0.850  0.020  0.980
 8VR  O2   H12  single  0.850  0.020  0.980
 8VR  O3   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
 8VR  H1   C1  O5   109.45  3.000
 8VR  H1   C1  O1   111.37  3.000
 8VR  O5   C1  O1   108.47  3.000
 8VR  H1   C1  C2   108.96  3.000
 8VR  O1   C1  C2   108.50  3.000
 8VR  O5   C1  C2   110.08  3.000
 8VR  H2   C2  O2   111.48  3.000
 8VR  H2   C2  C3   109.39  3.000
 8VR  O2   C2  C3   107.15  3.000
 8VR  H2   C2  C1   108.47  3.000
 8VR  O2   C2  C1   111.27  3.000
 8VR  C3   C2  C1   109.03  3.000
 8VR  H3   C3  O3   110.69  3.000
 8VR  H3   C3  C4   106.21  3.000
 8VR  O3   C3  C4   109.25  3.000
 8VR  H3   C3  C2   107.32  3.000
 8VR  C4   C3  C2   110.79  3.000
 8VR  O3   C3  C2   112.38  3.000
 8VR  H4   C4  O4   110.89  3.000
 8VR  H4   C4  C5   108.18  3.000
 8VR  O4   C4  C5   109.92  3.000
 8VR  H4   C4  C3   108.78  3.000
 8VR  C5   C4  C3   110.05  3.000
 8VR  O4   C4  C3   108.99  3.000
 8VR  H5   C5  O5   110.81  3.000
 8VR  H5   C5  C6   109.22  3.000
 8VR  O5   C5  C6   107.89  3.000
 8VR  H5   C5  C4   109.29  3.000
 8VR  C6   C5  C4   108.26  3.000
 8VR  O5   C5  C4   111.30  3.000
 8VR  H7   C6  H6   107.48  3.000
 8VR  H7   C6  O6   111.76  3.000
 8VR  H6   C6  O6   107.43  3.000
 8VR  H7   C6  C5   108.79  3.000
 8VR  H6   C6  C5   110.66  3.000
 8VR  O6   C6  C5   110.68  3.000
 8VR  O6   C7  O4   110.19  3.000
 8VR  O6   C7  C9   106.89  3.000
 8VR  O4   C7  C9   106.63  3.000
 8VR  O6   C7  C8   111.89  3.000
 8VR  C9   C7  C8   108.51  3.000
 8VR  O4   C7  C8   112.43  3.000
 8VR  O8B  C8  O8A  127.71  3.000
 8VR  O8A  C8  C7   115.79  3.000
 8VR  O8B  C8  C7   116.36  3.000
 8VR  H10  C9  H9   108.44  3.000
 8VR  H10  C9  H8   108.58  3.000
 8VR  H9   C9  H8   108.11  3.000
 8VR  H10  C9  C7   110.89  3.000
 8VR  H9   C9  C7   110.41  3.000
 8VR  H8   C9  C7   110.33  3.000
 8VR  H11  O1  C1   109.65  3.000
 8VR  H12  O2  C2   108.63  3.000
 8VR  H13  O3  C3   107.89  3.000
 8VR  C7   O4  C4   114.16  3.000
 8VR  C5   O5  C1   113.56  3.000
 8VR  C7   O6  C6   113.19  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
 8VR  Var_01  H6  C6  O6  C7  -178.32  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
 8VR  chir_01  C1  C2  O5  O1  negativ
 8VR  chir_02  C2  O2  C1  C3  negativ
 8VR  chir_03  C3  O3  C2  C4  positiv
 8VR  chir_04  C4  O4  C5  C3  negativ
 8VR  chir_05  C5  O5  C4  C6  negativ
 8VR  chir_06  C7  O6  O4  C9  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
 8VR  plan-1  C7   0.020
 8VR  plan-1  C8   0.020
 8VR  plan-1  O8A  0.020
 8VR  plan-1  O8B  0.020

