# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:05:12 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  31  17  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   0.263   2.4597   0.9318  -0.2396
 8VR  C2   C  CH1   0  -0.031   2.3501  -0.4662   0.3652
 8VR  C3   C  CH1   0   0.016   1.3918  -1.2998  -0.4774
 8VR  C4   C  CH1   0  -0.034   0.0611  -0.5887  -0.6411
 8VR  C5   C  CH1   0   0.012   0.2788   0.8423  -1.1254
 8VR  C6   C  CH2   0  -0.247  -1.0476   1.5686  -1.0721
 8VR  C7   C  CT    0   0.406  -1.7812   0.1501   0.6612
 8VR  C8   C  C     0   0.483  -2.8842  -0.5836  -0.1410
 8VR  C9   C  CH3   0  -0.692  -2.2205   0.2067   2.1156
 8VR  O1   O  OH1   0  -0.660   3.2663   1.6998   0.5733
 8VR  O2   O  OH1   0  -0.672   3.5914  -1.1285   0.3517
 8VR  O3   O  OH1   0  -0.666   1.1662  -2.5724   0.0647
 8VR  O4   O  O2    0  -0.487  -0.5988  -0.5794   0.6117
 8VR  O5   O  O2    0  -0.496   1.1864   1.5309  -0.2966
 8VR  O6   O  O2    0  -0.477  -1.6236   1.4601   0.2156
 8VR  O8A  O  OH1   0  -0.578  -3.8704   0.2306  -0.4739
 8VR  O8B  O  O     0  -0.418  -2.8725  -1.7648  -0.3645
 8VR  H1   H  HCH1  0   0.190   2.8723   0.8518  -1.2610
 8VR  H2   H  HCH1  0   0.228   1.9541  -0.3733   1.3865
 8VR  H3   H  HCH1  0   0.222   1.8227  -1.3748  -1.4897
 8VR  H4   H  HCH1  0   0.256  -0.5355  -1.1221  -1.3935
 8VR  H5   H  HCH1  0   0.248   0.6306   0.8176  -2.1675
 8VR  H6   H  HCH2  0   0.270  -0.9217   2.6323  -1.2748
 8VR  H7   H  HCH2  0   0.233  -1.7080   1.1623  -1.8487
 8VR  H8   H  HCH3  0   0.253  -3.1351   0.7875   2.2231
 8VR  H9   H  HCH3  0   0.253  -2.3997  -0.7949   2.5042
 8VR  H10  H  HCH3  0   0.263  -1.4381   0.6746   2.7132
 8VR  H11  H  HOH1  0   0.467   3.6259   2.4381   0.0703
 8VR  H12  H  HOH1  0   0.458   4.1690  -0.7144   1.0006
 8VR  H13  H  HOH1  0   0.452   2.0200  -3.0025   0.1798
 8VR  H14  H  HOH1  0   0.486  -4.5727  -0.2641  -0.9239

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  1.401  0.020  1.401
 8VR  C3   C4   single  1.518  0.020  1.518
 8VR  C3   C2   single  1.524  0.020  1.524
 8VR  O8B  C8   double  1.202  0.020  1.202
 8VR  O4   C4   single  1.416  0.020  1.416
 8VR  O4   C7   single  1.390  0.020  1.390
 8VR  O2   C2   single  1.407  0.020  1.407
 8VR  C4   C5   single  1.526  0.020  1.526
 8VR  C2   C1   single  1.527  0.020  1.527
 8VR  C8   C7   single  1.549  0.020  1.549
 8VR  C8   O8A  single  1.321  0.020  1.321
 8VR  C9   C7   single  1.520  0.020  1.520
 8VR  C7   O6   single  1.393  0.020  1.393
 8VR  C5   O5   single  1.409  0.020  1.409
 8VR  C5   C6   single  1.513  0.020  1.513
 8VR  C1   O5   single  1.408  0.020  1.408
 8VR  C1   O1   single  1.379  0.020  1.379
 8VR  O6   C6   single  1.415  0.020  1.415
 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
 8VR  O8A  H14  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   109.34  3.000
 8VR  H1   C1   O1   111.54  3.000
 8VR  O5   C1   O1   108.41  3.000
 8VR  H1   C1   C2   109.07  3.000
 8VR  O1   C1   C2   108.56  3.000
 8VR  O5   C1   C2   109.91  3.000
 8VR  H2   C2   O2   111.50  3.000
 8VR  H2   C2   C3   109.47  3.000
 8VR  O2   C2   C3   106.97  3.000
 8VR  H2   C2   C1   108.45  3.000
 8VR  O2   C2   C1   111.34  3.000
 8VR  C3   C2   C1   109.08  3.000
 8VR  H3   C3   O3   110.87  3.000
 8VR  H3   C3   C4   105.99  3.000
 8VR  O3   C3   C4   109.03  3.000
 8VR  H3   C3   C2   107.40  3.000
 8VR  C4   C3   C2   110.77  3.000
 8VR  O3   C3   C2   112.59  3.000
 8VR  H4   C4   O4   110.86  3.000
 8VR  H4   C4   C5   108.39  3.000
 8VR  O4   C4   C5   109.94  3.000
 8VR  H4   C4   C3   108.82  3.000
 8VR  C5   C4   C3   110.39  3.000
 8VR  O4   C4   C3   108.44  3.000
 8VR  H5   C5   O5   111.23  3.000
 8VR  H5   C5   C6   108.93  3.000
 8VR  O5   C5   C6   108.02  3.000
 8VR  H5   C5   C4   108.98  3.000
 8VR  C6   C5   C4   108.29  3.000
 8VR  O5   C5   C4   111.32  3.000
 8VR  H7   C6   H6   107.40  3.000
 8VR  H7   C6   O6   111.76  3.000
 8VR  H6   C6   O6   106.92  3.000
 8VR  H7   C6   C5   108.96  3.000
 8VR  H6   C6   C5   111.14  3.000
 8VR  O6   C6   C5   110.62  3.000
 8VR  O6   C7   O4   112.71  3.000
 8VR  O6   C7   C9   107.68  3.000
 8VR  O4   C7   C9   107.42  3.000
 8VR  O6   C7   C8   111.13  3.000
 8VR  C9   C7   C8   107.90  3.000
 8VR  O4   C7   C8   109.80  3.000
 8VR  O8B  C8   O8A  124.46  3.000
 8VR  O8A  C8   C7   111.72  3.000
 8VR  O8B  C8   C7   123.70  3.000
 8VR  H10  C9   H9   108.49  3.000
 8VR  H10  C9   H8   108.66  3.000
 8VR  H9   C9   H8   108.49  3.000
 8VR  H10  C9   C7   109.45  3.000
 8VR  H9   C9   C7   110.77  3.000
 8VR  H8   C9   C7   110.92  3.000
 8VR  H11  O1   C1   109.73  3.000
 8VR  H12  O2   C2   108.69  3.000
 8VR  H13  O3   C3   108.00  3.000
 8VR  C7   O4   C4   115.55  3.000
 8VR  C5   O5   C1   113.47  3.000
 8VR  C7   O6   C6   114.16  3.000
 8VR  H14  O8A  C8   110.06  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  CONST_01  H14  O8A  C8  C7   180.00   0.0  0
 8VR  Var_01    H6   C6   O6  C7  -176.52  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
 8VR  plan-1  H14  0.020

