# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:32:29 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: 6-O-octanoyl-beta-D-fructofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@H]1O[C@](O)(CO)[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
 TRV  TRV  6-O-octanoyl-beta-D-fructofuranose  D-saccharide  47  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TRV
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
 TRV  O2   O  OH1   0  -0.658  -17.3248  -19.5052  62.1391
 TRV  C1   C  CH2   0  -0.188  -16.4495  -18.4581  60.2630
 TRV  C2   C  CT    0   0.466  -16.2336  -18.7471  61.7422
 TRV  C3   C  CH1   0  -0.077  -16.0211  -17.4780  62.5917
 TRV  C4   C  CH1   0  -0.024  -14.9957  -17.9296  63.6266
 TRV  C5   C  CH1   0   0.002  -14.1326  -18.8526  62.7773
 TRV  C6   C  CH2   0  -0.179  -13.3851  -19.8666  63.6030
 TRV  O1   O  OH1   0  -0.665  -15.2970  -17.8401  59.7507
 TRV  O5   O  O2    0  -0.509  -15.0388  -19.4923  61.8996
 TRV  O3   O  OH1   0  -0.661  -17.2454  -17.0300  63.1003
 TRV  O4   O  OH1   0  -0.664  -14.2196  -16.9051  64.1843
 TRV  O6   O  O2    0  -0.455  -12.5647  -20.6362  62.7213
 TRV  C1N  C  C     0   0.587  -11.7407  -21.5258  63.2630
 TRV  C2N  C  CH2   0  -0.553  -10.9056  -22.2437  62.2391
 TRV  C3N  C  CH2   0  -0.427   -9.4176  -21.9336  62.4204
 TRV  C4N  C  CH2   0  -0.415   -8.5490  -22.6981  61.4302
 TRV  C5N  C  CH2   0  -0.413   -7.0677  -22.3706  61.5726
 TRV  C6N  C  CH2   0  -0.406   -6.1852  -23.1503  60.6058
 TRV  C7N  C  CH2   0  -0.419   -4.7039  -22.8201  60.7435
 TRV  C8N  C  CH3   0  -0.663   -3.8288  -23.6119  59.7817
 TRV  O1N  O  O     0  -0.459  -11.6648  -21.7155  64.4526
 TRV  H11  H  HCH2  0   0.215  -17.3362  -17.8207  60.1653
 TRV  H12  H  HCH2  0   0.213  -16.6696  -19.4032  59.7471
 TRV  H3   H  HCH1  0   0.240  -15.5399  -16.7138  61.9665
 TRV  H4   H  HCH1  0   0.227  -15.5010  -18.5144  64.4106
 TRV  H5   H  HCH1  0   0.234  -13.4136  -18.2450  62.2084
 TRV  H61  H  HCH2  0   0.240  -14.0823  -20.5176  64.1375
 TRV  H62  H  HCH2  0   0.248  -12.7681  -19.3449  64.3387
 TRV  HO1  H  HOH1  0   0.462  -15.5226  -17.4327  58.9103
 TRV  HO3  H  HOH1  0   0.461  -17.1095  -16.1695  63.5084
 TRV  HO4  H  HOH1  0   0.462  -14.6670  -16.5614  64.9626
 TRV  H22  H  HCH2  0   0.256  -11.2254  -21.9846  61.2294
 TRV  H23  H  HCH2  0   0.268  -11.0701  -23.3167  62.3707
 TRV  H24  H  HCH2  0   0.231   -9.2515  -20.8593  62.2968
 TRV  H25  H  HCH2  0   0.230   -9.1147  -22.1840  63.4401
 TRV  H26  H  HCH2  0   0.214   -8.8746  -22.4731  60.4091
 TRV  H27  H  HCH2  0   0.215   -8.7009  -23.7736  61.5710
 TRV  H28  H  HCH2  0   0.209   -6.7477  -22.5765  62.5999
 TRV  H29  H  HCH2  0   0.210   -6.9180  -21.2968  61.4162
 TRV  H30  H  HCH2  0   0.207   -6.5067  -22.9504  59.5774
 TRV  H31  H  HCH2  0   0.207   -6.3327  -24.2240  60.7667
 TRV  H32  H  HCH2  0   0.210   -4.3846  -23.0129  61.7725
 TRV  H33  H  HCH2  0   0.210   -4.5553  -21.7488  60.5758
 TRV  H34  H  HCH3  0   0.226   -2.7719  -23.3776  59.9141
 TRV  H35  H  HCH3  0   0.215   -3.9493  -24.6865  59.9319
 TRV  H36  H  HCH3  0   0.216   -4.0866  -23.3948  58.7435
 TRV  HO2  H  HOH1  0   0.455  -17.4694  -19.4360  63.0893

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
 TRV  O1   C1   single  1.405  0.020  1.405
 TRV  C8N  C7N  single  1.522  0.020  1.522
 TRV  C1   C2   single  1.523  0.020  1.523
 TRV  C7N  C6N  single  1.524  0.020  1.524
 TRV  C6N  C5N  single  1.524  0.020  1.524
 TRV  C5N  C4N  single  1.524  0.020  1.524
 TRV  C2N  C3N  single  1.531  0.020  1.531
 TRV  C2N  C1N  single  1.504  0.020  1.504
 TRV  O5   C2   single  1.417  0.020  1.417
 TRV  O5   C5   single  1.415  0.020  1.415
 TRV  C4N  C3N  single  1.523  0.020  1.523
 TRV  C2   O2   single  1.387  0.020  1.387
 TRV  C2   C3   single  1.542  0.020  1.542
 TRV  O6   C1N  single  1.328  0.020  1.328
 TRV  O6   C6   single  1.429  0.020  1.429
 TRV  C1N  O1N  double  1.207  0.020  1.207
 TRV  C5   C6   single  1.506  0.020  1.506
 TRV  C5   C4   single  1.523  0.020  1.523
 TRV  C3   O3   single  1.399  0.020  1.399
 TRV  C3   C4   single  1.525  0.020  1.525
 TRV  C4   O4   single  1.401  0.020  1.401
 TRV  C1   H11  single  0.970  0.020  1.090
 TRV  C1   H12  single  0.970  0.020  1.090
 TRV  C3   H3   single  0.970  0.020  1.090
 TRV  C4   H4   single  0.970  0.020  1.090
 TRV  C5   H5   single  0.970  0.020  1.090
 TRV  C6   H61  single  0.970  0.020  1.090
 TRV  C6   H62  single  0.970  0.020  1.090
 TRV  O1   HO1  single  0.850  0.020  0.980
 TRV  O3   HO3  single  0.850  0.020  0.980
 TRV  O4   HO4  single  0.850  0.020  0.980
 TRV  C2N  H22  single  0.970  0.020  1.090
 TRV  C2N  H23  single  0.970  0.020  1.090
 TRV  C3N  H24  single  0.970  0.020  1.090
 TRV  C3N  H25  single  0.970  0.020  1.090
 TRV  C4N  H26  single  0.970  0.020  1.090
 TRV  C4N  H27  single  0.970  0.020  1.090
 TRV  C5N  H28  single  0.970  0.020  1.090
 TRV  C5N  H29  single  0.970  0.020  1.090
 TRV  C6N  H30  single  0.970  0.020  1.090
 TRV  C6N  H31  single  0.970  0.020  1.090
 TRV  C7N  H32  single  0.970  0.020  1.090
 TRV  C7N  H33  single  0.970  0.020  1.090
 TRV  C8N  H34  single  0.970  0.020  1.090
 TRV  C8N  H35  single  0.970  0.020  1.090
 TRV  C8N  H36  single  0.970  0.020  1.090
 TRV  O2   HO2  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
 TRV  HO2  O2   C2   111.16  3.000
 TRV  H12  C1   H11  107.22  3.000
 TRV  H12  C1   O1   111.81  3.000
 TRV  H11  C1   O1   112.04  3.000
 TRV  H12  C1   C2   108.74  3.000
 TRV  H11  C1   C2   108.16  3.000
 TRV  O1   C1   C2   108.76  3.000
 TRV  O5   C2   C3   104.80  3.000
 TRV  C3   C2   C1   113.49  3.000
 TRV  O5   C2   C1   109.10  3.000
 TRV  C3   C2   O2   113.63  3.000
 TRV  O5   C2   O2   110.14  3.000
 TRV  C1   C2   O2   105.68  3.000
 TRV  H3   C3   O3   111.55  3.000
 TRV  H3   C3   C4   107.32  3.000
 TRV  O3   C3   C4   115.87  3.000
 TRV  H3   C3   C2   108.63  3.000
 TRV  C4   C3   C2   102.87  3.000
 TRV  O3   C3   C2   110.07  3.000
 TRV  H4   C4   O4   111.06  3.000
 TRV  H4   C4   C5   109.60  3.000
 TRV  O4   C4   C5   110.57  3.000
 TRV  H4   C4   C3   109.39  3.000
 TRV  O4   C4   C3   115.21  3.000
 TRV  C5   C4   C3   100.49  3.000
 TRV  H5   C5   O5   110.35  3.000
 TRV  H5   C5   C6   109.33  3.000
 TRV  O5   C5   C6   110.71  3.000
 TRV  H5   C5   C4   108.92  3.000
 TRV  C6   C5   C4   112.56  3.000
 TRV  O5   C5   C4   104.90  3.000
 TRV  H62  C6   H61  108.37  3.000
 TRV  H62  C6   O6   110.39  3.000
 TRV  H61  C6   O6   110.30  3.000
 TRV  H62  C6   C5   109.14  3.000
 TRV  H61  C6   C5   110.63  3.000
 TRV  O6   C6   C5   108.01  3.000
 TRV  HO1  O1   C1   108.24  3.000
 TRV  C5   O5   C2   111.79  3.000
 TRV  HO3  O3   C3   108.48  3.000
 TRV  HO4  O4   C4   109.02  3.000
 TRV  C1N  O6   C6   117.72  3.000
 TRV  O1N  C1N  C2N  124.13  3.000
 TRV  O1N  C1N  O6   123.11  3.000
 TRV  C2N  C1N  O6   112.74  3.000
 TRV  H23  C2N  H22  107.49  3.000
 TRV  H23  C2N  C3N  109.32  3.000
 TRV  H22  C2N  C3N  110.28  3.000
 TRV  H23  C2N  C1N  107.64  3.000
 TRV  H22  C2N  C1N  110.74  3.000
 TRV  C3N  C2N  C1N  111.25  3.000
 TRV  H25  C3N  H24  106.75  3.000
 TRV  H25  C3N  C4N  109.48  3.000
 TRV  H24  C3N  C4N  109.45  3.000
 TRV  H25  C3N  C2N  109.48  3.000
 TRV  H24  C3N  C2N  109.46  3.000
 TRV  C4N  C3N  C2N  112.07  3.000
 TRV  H27  C4N  H26  106.28  3.000
 TRV  H27  C4N  C5N  109.51  3.000
 TRV  H26  C4N  C5N  109.39  3.000
 TRV  H27  C4N  C3N  109.28  3.000
 TRV  H26  C4N  C3N  109.48  3.000
 TRV  C5N  C4N  C3N  112.70  3.000
 TRV  H29  C5N  H28  106.15  3.000
 TRV  H29  C5N  C6N  109.38  3.000
 TRV  H28  C5N  C6N  109.25  3.000
 TRV  H29  C5N  C4N  109.28  3.000
 TRV  H28  C5N  C4N  109.34  3.000
 TRV  C6N  C5N  C4N  113.19  3.000
 TRV  H31  C6N  H30  106.09  3.000
 TRV  H31  C6N  C7N  109.26  3.000
 TRV  H30  C6N  C7N  109.30  3.000
 TRV  H31  C6N  C5N  109.29  3.000
 TRV  H30  C6N  C5N  109.40  3.000
 TRV  C7N  C6N  C5N  113.25  3.000
 TRV  H33  C7N  H32  106.08  3.000
 TRV  H33  C7N  C8N  109.52  3.000
 TRV  H32  C7N  C8N  109.55  3.000
 TRV  H33  C7N  C6N  109.28  3.000
 TRV  H32  C7N  C6N  109.29  3.000
 TRV  C8N  C7N  C6N  112.89  3.000
 TRV  H36  C8N  H35  107.49  3.000
 TRV  H36  C8N  H34  107.56  3.000
 TRV  H35  C8N  H34  107.56  3.000
 TRV  H36  C8N  C7N  111.20  3.000
 TRV  H35  C8N  C7N  111.19  3.000
 TRV  H34  C8N  C7N  111.63  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
 TRV  Var_01  C2N  C1N  O6   C6   -178.41  30.0  3
 TRV  Var_02  C3N  C2N  C1N  O6    115.91  30.0  2
 TRV  Var_03  C4N  C3N  C2N  C1N   177.56  30.0  3
 TRV  Var_04  C5N  C4N  C3N  C2N   178.41  30.0  2
 TRV  Var_05  C6N  C5N  C4N  C3N   178.85  30.0  1
 TRV  Var_06  C7N  C6N  C5N  C4N   179.79  30.0  1
 TRV  Var_07  C8N  C7N  C6N  C5N   179.53  30.0  1
 TRV  Var_08  H61  C6   O6   C1N   -64.00  30.0  3
 TRV  Var_09  H34  C8N  C7N  C6N  -178.63  30.0  3

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
 TRV  chir_01  C2  O5  O2  C3  negativ
 TRV  chir_02  C3  O3  C2  C4  positiv
 TRV  chir_03  C4  O4  C3  C5  negativ
 TRV  chir_04  C5  O5  C4  C6  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
 TRV  plan-1  O6   0.020
 TRV  plan-1  C1N  0.020
 TRV  plan-1  C2N  0.020
 TRV  plan-1  O1N  0.020

