# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:00:53 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-O-prop-2-yn-1-yl-beta-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](OCC#C)[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
 TVV  TVV  3-O-prop-2-yn-1-yl-beta-D-galactopyranose  D-saccharide  29  15  .  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_TVV
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
 TVV  C1   C  CH1   0   0.258  -1.2919  28.9222  17.3934
 TVV  C2   C  CH1   0  -0.007  -1.7493  27.6703  16.6433
 TVV  O2   O  OH1   0  -0.665  -3.1331  27.4797  16.7844
 TVV  O5   O  O2    0  -0.492   0.1043  29.0523  17.3294
 TVV  C5   C  CH1   0  -0.001   0.7749  27.9842  17.9610
 TVV  C6   C  CH2   0  -0.167   2.2557  28.2939  17.9834
 TVV  O6   O  OH1   0  -0.669   2.4728  29.4140  18.8066
 TVV  C4   C  CH1   0  -0.040   0.4737  26.6614  17.2513
 TVV  O4   O  OH1   0  -0.668   0.9468  26.6335  15.9269
 TVV  C3   C  CH1   0   0.023  -1.0429  26.4559  17.2286
 TVV  O3   O  O2    0  -0.476  -1.4433  25.3395  16.4728
 TVV  CAQ  C  CH2   0  -0.315  -0.9771  24.0912  16.9155
 TVV  CAD  C  CSP   0   0.197  -1.4070  23.7589  18.2761
 TVV  CAC  C  CSP1  0  -0.490  -1.7581  23.4853  19.3927
 TVV  H1   H  HCH1  0   0.188  -1.6039  28.8381  18.4501
 TVV  H2   H  HCH1  0   0.224  -1.4628  27.7828  15.5869
 TVV  HO2  H  HOH1  0   0.452  -3.5797  28.2392  16.3961
 TVV  H5   H  HCH1  0   0.222   0.4292  27.8802  19.0033
 TVV  H61  H  HCH2  0   0.206   2.7815  27.4052  18.3578
 TVV  H62  H  HCH2  0   0.203   2.6073  28.4723  16.9598
 TVV  HO6  H  HOH1  0   0.457   3.4030  29.6495  18.7508
 TVV  H4   H  HCH1  0   0.246   0.9324  25.8641  17.8525
 TVV  HO4  H  HOH1  0   0.459   1.8674  26.3573  15.9294
 TVV  H3   H  HCH1  0   0.229  -1.3668  26.3420  18.2758
 TVV  H65  H  HCH2  0   0.285  -1.3796  23.3497  16.2224
 TVV  HAQ  H  HCH2  0   0.251   0.1143  24.0074  16.8585
 TVV  HAD  H  H     0   0.285  -2.0683  23.2400  20.3828
 TVV  O1   O  OH1   0  -0.662  -1.8668  30.0193  16.7841
 TVV  HO1  H  HOH1  0   0.468  -1.8964  30.7558  17.4035

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
 TVV  O4   C4   single  1.407  0.020  1.407
 TVV  O3   CAQ  single  1.404  0.020  1.404
 TVV  O3   C3   single  1.406  0.020  1.406
 TVV  C2   O2   single  1.404  0.020  1.404
 TVV  C2   C3   single  1.522  0.020  1.522
 TVV  C2   C1   single  1.529  0.020  1.529
 TVV  CAQ  CAD  single  1.465  0.020  1.465
 TVV  C4   C3   single  1.531  0.020  1.531
 TVV  C4   C5   single  1.531  0.020  1.531
 TVV  O5   C1   single  1.404  0.020  1.404
 TVV  O5   C5   single  1.410  0.020  1.410
 TVV  C6   C5   single  1.513  0.020  1.513
 TVV  C6   O6   single  1.407  0.020  1.407
 TVV  CAD  CAC  triple  1.202  0.020  1.202
 TVV  C1   H1   single  0.939  0.020  1.096
 TVV  C2   H2   single  0.939  0.020  1.096
 TVV  O2   HO2  single  0.832  0.020  0.971
 TVV  C5   H5   single  0.939  0.020  1.096
 TVV  C6   H61  single  0.939  0.020  1.096
 TVV  C6   H62  single  0.939  0.020  1.096
 TVV  O6   HO6  single  0.832  0.020  0.971
 TVV  C4   H4   single  0.939  0.020  1.096
 TVV  O4   HO4  single  0.832  0.020  0.971
 TVV  C3   H3   single  0.939  0.020  1.096
 TVV  CAQ  H65  single  0.939  0.020  1.096
 TVV  CAQ  HAQ  single  0.939  0.020  1.096
 TVV  CAC  HAD  single  0.913  0.020  1.066
 TVV  C1   O1   single  1.380  0.020  1.380
 TVV  O1   HO1  single  0.832  0.020  0.971

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
 TVV  O1   C1   H1   111.41  3.000
 TVV  O1   C1   O5   108.69  3.000
 TVV  H1   C1   O5   109.36  3.000
 TVV  O1   C1   C2   108.03  3.000
 TVV  H1   C1   C2   108.80  3.000
 TVV  O5   C1   C2   110.55  3.000
 TVV  H2   C2   C3   109.27  3.000
 TVV  H2   C2   O2   111.53  3.000
 TVV  C3   C2   O2   108.09  3.000
 TVV  H2   C2   C1   108.02  3.000
 TVV  C3   C2   C1   109.01  3.000
 TVV  O2   C2   C1   110.89  3.000
 TVV  HO2  O2   C2   108.04  3.000
 TVV  C5   O5   C1   112.48  3.000
 TVV  H5   C5   C4   107.15  3.000
 TVV  H5   C5   C6   108.18  3.000
 TVV  C4   C5   C6   112.11  3.000
 TVV  H5   C5   O5   110.21  3.000
 TVV  C6   C5   O5   108.48  3.000
 TVV  C4   C5   O5   110.68  3.000
 TVV  H62  C6   H61  107.23  3.000
 TVV  H62  C6   O6   111.53  3.000
 TVV  H61  C6   O6   111.77  3.000
 TVV  H62  C6   C5   109.46  3.000
 TVV  H61  C6   C5   107.94  3.000
 TVV  O6   C6   C5   108.83  3.000
 TVV  HO6  O6   C6   108.09  3.000
 TVV  H4   C4   C3   108.93  3.000
 TVV  H4   C4   O4   111.12  3.000
 TVV  C3   C4   O4   108.46  3.000
 TVV  H4   C4   C5   106.92  3.000
 TVV  C3   C4   C5   108.53  3.000
 TVV  O4   C4   C5   112.79  3.000
 TVV  HO4  O4   C4   108.99  3.000
 TVV  H3   C3   O3   110.18  3.000
 TVV  H3   C3   C4   106.92  3.000
 TVV  O3   C3   C4   113.37  3.000
 TVV  H3   C3   C2   108.15  3.000
 TVV  C4   C3   C2   111.01  3.000
 TVV  O3   C3   C2   107.13  3.000
 TVV  CAQ  O3   C3   116.22  3.000
 TVV  HAQ  CAQ  H65  106.39  3.000
 TVV  HAQ  CAQ  CAD  108.85  3.000
 TVV  H65  CAQ  CAD  109.10  3.000
 TVV  HAQ  CAQ  O3   112.47  3.000
 TVV  H65  CAQ  O3   106.34  3.000
 TVV  CAD  CAQ  O3   113.39  3.000
 TVV  CAC  CAD  CAQ  180.00  3.000
 TVV  HAD  CAC  CAD  180.00  3.000
 TVV  HO1  O1   C1   109.68  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
 TVV  Var_01  CAD  CAQ  O3   C3   60.07  30.0  3
 TVV  Var_02  H65  CAQ  CAD  CAC  94.92  30.0  2

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
 TVV  chir_01  C1  C2  O5  O1  negativ
 TVV  chir_02  C2  O2  C1  C3  negativ
 TVV  chir_03  C5  O5  C4  C6  negativ
 TVV  chir_04  C4  O4  C5  C3  negativ
 TVV  chir_05  C3  O3  C2  C4  positiv

