# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:47:05 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: 3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CO[C@@H]2[C@@H](O)[C@H](O)O[C@H](CO)[C@@H]2O)c1
#
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
 TVM  TVM  3-O-[(3-methoxyphenyl)methyl]-beta-D-galactopyranose  D-saccharide  41  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 PERFECT
;

data_comp_TVM
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
 TVM  C4   C  CH1   0  -0.024  18.4698   -6.6777  -0.7857
 TVM  C3   C  CH1   0   0.016  17.8896   -8.0528  -1.1209
 TVM  C2   C  CH1   0  -0.011  18.6716   -9.1624  -0.4314
 TVM  C1   C  CH1   0   0.261  20.1566   -9.0029  -0.7642
 TVM  O2   O  OH1   0  -0.658  18.1816  -10.3922  -0.9020
 TVM  O4   O  OH1   0  -0.670  18.2137   -6.4090   0.5715
 TVM  C5   C  CH1   0  -0.002  19.9650   -6.6902  -1.1084
 TVM  C6   C  CH2   0  -0.169  20.6374   -5.3796  -0.7639
 TVM  O5   O  O2    0  -0.495  20.6107   -7.7246  -0.3979
 TVM  O3   O  O2    0  -0.490  16.5464   -8.1770  -0.7493
 TVM  C24  C  CH2   0  -0.192  15.6126   -7.5592  -1.5960
 TVM  C25  C  CR6   0   0.077  14.3554   -8.3863  -1.6572
 TVM  C26  C  CR16  0  -0.336  13.1303   -7.7740  -1.8815
 TVM  C27  C  CR16  0  -0.228  11.9821   -8.5506  -1.9941
 TVM  C28  C  CR16  0  -0.353  12.0444   -9.9268  -1.8751
 TVM  C29  C  CR6   0   0.402  13.2757  -10.5440  -1.6427
 TVM  C30  C  CR16  0  -0.442  14.4292   -9.7734  -1.5351
 TVM  O31  O  O2    0  -0.473  13.2560  -11.8880  -1.5359
 TVM  C32  C  CH3   0  -0.438  14.4726  -12.5657  -1.2959
 TVM  H4   H  HCH1  0   0.243  17.9926   -5.9290  -1.4338
 TVM  H3   H  HCH1  0   0.228  17.9972   -8.1909  -2.2096
 TVM  H2   H  HCH1  0   0.226  18.5528   -9.0706   0.6583
 TVM  H1   H  HCH1  0   0.186  20.2933   -9.1409  -1.8520
 TVM  HO6  H  HOH1  0   0.457  22.3968   -4.6004  -0.9538
 TVM  HO2  H  HOH1  0   0.453  18.5647  -11.0948  -0.3678
 TVM  HO4  H  HOH1  0   0.458  18.2159   -5.4576   0.7079
 TVM  H5   H  HCH1  0   0.220  20.0646   -6.8533  -2.1950
 TVM  H61  H  HCH2  0   0.205  20.0503   -4.5690  -1.2161
 TVM  H62  H  HCH2  0   0.203  20.6133   -5.2307   0.3228
 TVM  H28  H  HCH2  0   0.228  16.0179   -7.4564  -2.6126
 TVM  H29  H  HCH2  0   0.230  15.3753   -6.5446  -1.2531
 TVM  H30  H  HCR6  0   0.246  13.0660   -6.6959  -1.9639
 TVM  H31  H  HCR6  0   0.256  11.0254   -8.0757  -2.1700
 TVM  H32  H  HCR6  0   0.259  11.1489  -10.5304  -1.9563
 TVM  H33  H  HCR6  0   0.279  15.3924  -10.2301  -1.3494
 TVM  H34  H  HCH3  0   0.260  14.2324  -13.6250  -1.2493
 TVM  H35  H  HCH3  0   0.227  15.1980  -12.4043  -2.0976
 TVM  H36  H  HCH3  0   0.226  14.9282  -12.2670  -0.3479
 TVM  O1   O  OH1   0  -0.661  20.8637   -9.9432  -0.0427
 TVM  HO1  H  HOH1  0   0.466  21.7175  -10.0955  -0.4611
 TVM  O6   O  OH1   0  -0.669  21.9568   -5.4009  -1.2530

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
 TVM  C26  C27  aromatic  1.391  0.020  1.391
 TVM  C26  C25  aromatic  1.388  0.020  1.388
 TVM  C27  C28  aromatic  1.383  0.020  1.383
 TVM  O2   C2   single    1.405  0.020  1.405
 TVM  C24  C25  single    1.506  0.020  1.506
 TVM  C24  O3   single    1.404  0.020  1.404
 TVM  C25  C30  aromatic  1.394  0.020  1.394
 TVM  C28  C29  aromatic  1.397  0.020  1.397
 TVM  C3   O3   single    1.399  0.020  1.399
 TVM  C3   C2   single    1.522  0.020  1.522
 TVM  C3   C4   single    1.530  0.020  1.530
 TVM  C30  C29  aromatic  1.391  0.020  1.391
 TVM  C29  O31  single    1.348  0.020  1.348
 TVM  C1   C2   single    1.530  0.020  1.530
 TVM  C1   O5   single    1.405  0.020  1.405
 TVM  C5   C4   single    1.530  0.020  1.530
 TVM  C5   O5   single    1.411  0.020  1.411
 TVM  C5   C6   single    1.513  0.020  1.513
 TVM  C4   O4   single    1.407  0.020  1.407
 TVM  O31  C32  single    1.413  0.020  1.413
 TVM  O6   C6   single    1.407  0.020  1.407
 TVM  C4   H4   single    0.970  0.020  1.090
 TVM  C3   H3   single    0.970  0.020  1.090
 TVM  C2   H2   single    0.970  0.020  1.090
 TVM  C1   H1   single    0.970  0.020  1.090
 TVM  O6   HO6  single    0.850  0.020  0.980
 TVM  O2   HO2  single    0.850  0.020  0.980
 TVM  O4   HO4  single    0.850  0.020  0.980
 TVM  C5   H5   single    0.970  0.020  1.090
 TVM  C6   H61  single    0.970  0.020  1.090
 TVM  C6   H62  single    0.970  0.020  1.090
 TVM  C24  H28  single    0.970  0.020  1.090
 TVM  C24  H29  single    0.970  0.020  1.090
 TVM  C26  H30  single    0.930  0.020  1.080
 TVM  C27  H31  single    0.930  0.020  1.080
 TVM  C28  H32  single    0.930  0.020  1.080
 TVM  C30  H33  single    0.930  0.020  1.080
 TVM  C32  H34  single    0.970  0.020  1.090
 TVM  C32  H35  single    0.970  0.020  1.090
 TVM  C32  H36  single    0.970  0.020  1.090
 TVM  C1   O1   single    1.380  0.020  1.380
 TVM  O1   HO1  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
 TVM  H4   C4   C5   107.78  3.000
 TVM  H4   C4   O4   111.07  3.000
 TVM  C5   C4   O4   112.52  3.000
 TVM  H4   C4   C3   108.57  3.000
 TVM  O4   C4   C3   108.30  3.000
 TVM  C5   C4   C3   108.49  3.000
 TVM  H3   C3   O3   110.17  3.000
 TVM  H3   C3   C2   107.80  3.000
 TVM  O3   C3   C2   107.94  3.000
 TVM  H3   C3   C4   106.98  3.000
 TVM  C2   C3   C4   111.17  3.000
 TVM  O3   C3   C4   112.69  3.000
 TVM  H2   C2   O2   111.54  3.000
 TVM  H2   C2   C1   108.15  3.000
 TVM  O2   C2   C1   110.90  3.000
 TVM  H2   C2   C3   109.41  3.000
 TVM  C1   C2   C3   108.91  3.000
 TVM  O2   C2   C3   107.89  3.000
 TVM  O1   C1   H1   111.48  3.000
 TVM  O1   C1   O5   108.54  3.000
 TVM  H1   C1   O5   109.28  3.000
 TVM  O1   C1   C2   108.21  3.000
 TVM  H1   C1   C2   108.73  3.000
 TVM  O5   C1   C2   110.60  3.000
 TVM  HO2  O2   C2   108.33  3.000
 TVM  HO4  O4   C4   109.00  3.000
 TVM  H5   C5   O5   110.25  3.000
 TVM  H5   C5   C6   108.20  3.000
 TVM  O5   C5   C6   108.48  3.000
 TVM  H5   C5   C4   107.29  3.000
 TVM  C6   C5   C4   112.29  3.000
 TVM  O5   C5   C4   110.30  3.000
 TVM  H62  C6   H61  107.21  3.000
 TVM  H62  C6   C5   109.48  3.000
 TVM  H61  C6   C5   107.94  3.000
 TVM  H62  C6   O6   111.53  3.000
 TVM  H61  C6   O6   111.67  3.000
 TVM  C5   C6   O6   108.93  3.000
 TVM  C5   O5   C1   112.81  3.000
 TVM  C24  O3   C3   116.06  3.000
 TVM  H29  C24  H28  106.40  3.000
 TVM  H29  C24  C25  109.88  3.000
 TVM  H28  C24  C25  108.76  3.000
 TVM  H29  C24  O3   111.25  3.000
 TVM  H28  C24  O3   110.71  3.000
 TVM  C25  C24  O3   109.76  3.000
 TVM  C30  C25  C26  119.98  3.000
 TVM  C30  C25  C24  119.90  3.000
 TVM  C26  C25  C24  120.08  3.000
 TVM  H30  C26  C27  120.04  3.000
 TVM  H30  C26  C25  120.25  3.000
 TVM  C27  C26  C25  119.71  3.000
 TVM  H31  C27  C28  119.37  3.000
 TVM  H31  C27  C26  119.85  3.000
 TVM  C28  C27  C26  120.77  3.000
 TVM  H32  C28  C29  119.68  3.000
 TVM  H32  C28  C27  120.74  3.000
 TVM  C29  C28  C27  119.59  3.000
 TVM  O31  C29  C30  123.92  3.000
 TVM  O31  C29  C28  116.15  3.000
 TVM  C30  C29  C28  119.93  3.000
 TVM  H33  C30  C29  121.16  3.000
 TVM  H33  C30  C25  118.82  3.000
 TVM  C29  C30  C25  120.02  3.000
 TVM  C32  O31  C29  118.61  3.000
 TVM  H36  C32  H35  108.61  3.000
 TVM  H36  C32  H34  108.73  3.000
 TVM  H35  C32  H34  108.78  3.000
 TVM  H36  C32  O31  112.02  3.000
 TVM  H35  C32  O31  112.08  3.000
 TVM  H34  C32  O31  106.52  3.000
 TVM  HO1  O1   C1   109.57  3.000
 TVM  HO6  O6   C6   107.97  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
 TVM  CONST_01  C28  C27  C26  C25     0.00   0.0  0
 TVM  CONST_02  C28  C29  C30  C25     0.00   0.0  0
 TVM  CONST_03  C29  C28  C27  C26     0.00   0.0  0
 TVM  CONST_04  C29  C30  C25  C26     0.00   0.0  0
 TVM  CONST_05  C30  C25  C26  C27     0.00   0.0  0
 TVM  CONST_06  C30  C29  C28  C27     0.00   0.0  0
 TVM  CONST_07  C27  C26  C25  C24   180.00   0.0  0
 TVM  CONST_08  C29  C30  C25  C24   180.00   0.0  0
 TVM  CONST_09  O31  C29  C30  C25   180.00   0.0  0
 TVM  CONST_10  O31  C29  C28  C27   180.00   0.0  0
 TVM  CONST_11  H31  C27  C26  C25   180.00   0.0  0
 TVM  CONST_12  H32  C28  C27  C26   180.00   0.0  0
 TVM  CONST_13  H33  C30  C25  C26   180.00   0.0  0
 TVM  CONST_14  H30  C26  C27  C28   180.00   0.0  0
 TVM  Var_01    C25  C24  O3   C3    144.79  30.0  3
 TVM  Var_02    C26  C25  C24  O3    150.58  30.0  2
 TVM  Var_03    H34  C32  O31  C29  -179.81  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
 TVM  chir_01  C4  C3  C5  O4  positiv
 TVM  chir_02  C3  O3  C2  C4  positiv
 TVM  chir_03  C2  O2  C3  C1  positiv
 TVM  chir_04  C1  O5  O1  C2  negativ
 TVM  chir_05  C5  O5  C6  C4  positiv

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
 TVM  plan-1  C24  0.020
 TVM  plan-1  C25  0.020
 TVM  plan-1  C26  0.020
 TVM  plan-1  C27  0.020
 TVM  plan-1  C28  0.020
 TVM  plan-1  C29  0.020
 TVM  plan-1  C30  0.020
 TVM  plan-1  O31  0.020
 TVM  plan-1  H30  0.020
 TVM  plan-1  H31  0.020
 TVM  plan-1  H32  0.020
 TVM  plan-1  H33  0.020

