# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:42:19 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)O[C@@H](C)[C@H](O)[C@H]1OC
#
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
 7CV  7CV  6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose  L-saccharide  29  13  .  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_7CV
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
 7CV  C1   C  CH1   0   0.232   1.2127   1.1131   0.6672
 7CV  C2   C  CH1   0  -0.011   1.1416  -0.3755   0.3181
 7CV  C3   C  CH1   0   0.034  -0.3024  -0.8660   0.3873
 7CV  C4   C  CH1   0   0.028  -1.1940   0.0110  -0.4845
 7CV  C5   C  CH1   0   0.014  -1.0183   1.4844  -0.0896
 7CV  C6   C  CH3   0  -0.700  -1.7778   2.4249  -1.0035
 7CV  O2   O  O2    0  -0.492   1.6167  -0.5867  -0.9872
 7CV  O3   O  O2    0  -0.497  -0.3280  -2.2145  -0.0088
 7CV  O4   O  OH1   0  -0.669  -2.5315  -0.3932  -0.3003
 7CV  O5   O  O2    0  -0.500   0.3519   1.8585  -0.1466
 7CV  C24  C  CH3   0  -0.407   3.0118  -0.7433  -1.0754
 7CV  C27  C  CH3   0  -0.406  -1.1778  -3.0495   0.7420
 7CV  O1   O  OH1   0  -0.668   0.9245   1.2372   2.0249
 7CV  H1   H  HCH1  0   0.234   2.2118   1.5061   0.4422
 7CV  H2   H  HCH1  0   0.235   1.7447  -0.9400   1.0443
 7CV  H3   H  HCH1  0   0.226  -0.6356  -0.7663   1.4310
 7CV  H4   H  HCH1  0   0.214  -0.8914  -0.1102  -1.5340
 7CV  H5   H  HCH1  0   0.213  -1.3991   1.6081   0.9333
 7CV  H6   H  HCH3  0   0.232  -2.8517   2.2576  -0.9246
 7CV  H7   H  HCH3  0   0.246  -1.5958   3.4634  -0.7259
 7CV  H8   H  HCH3  0   0.229  -1.4867   2.2930  -2.0474
 7CV  H9   H  HOH1  0   0.455  -3.0465  -0.1064  -1.0596
 7CV  H10  H  HCH3  0   0.208   3.5630   0.1535  -0.7721
 7CV  H11  H  HCH3  0   0.210   3.3654  -1.5781  -0.4596
 7CV  H12  H  HCH3  0   0.237   3.2556  -0.9534  -2.1159
 7CV  H13  H  HCH3  0   0.205  -1.0047  -2.9470   1.8194
 7CV  H14  H  HCH3  0   0.211  -2.2361  -2.8602   0.5486
 7CV  H15  H  HCH3  0   0.227  -0.9558  -4.0794   0.4624
 7CV  H16  H  HOH1  0   0.462   1.1140   2.1390   2.3056

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
 7CV  O4   C4   single  1.409  0.020  1.409
 7CV  C27  O3   single  1.408  0.020  1.408
 7CV  O3   C3   single  1.406  0.020  1.406
 7CV  C4   C3   single  1.525  0.020  1.525
 7CV  C4   C5   single  1.535  0.020  1.535
 7CV  C3   C2   single  1.527  0.020  1.527
 7CV  C6   C5   single  1.516  0.020  1.516
 7CV  C5   O5   single  1.421  0.020  1.421
 7CV  C2   O2   single  1.405  0.020  1.405
 7CV  C2   C1   single  1.531  0.020  1.531
 7CV  O2   C24  single  1.407  0.020  1.407
 7CV  O5   C1   single  1.400  0.020  1.400
 7CV  C1   O1   single  1.393  0.020  1.393
 7CV  C1   H1   single  0.970  0.020  1.090
 7CV  C2   H2   single  0.970  0.020  1.090
 7CV  C3   H3   single  0.970  0.020  1.090
 7CV  C4   H4   single  0.970  0.020  1.090
 7CV  C5   H5   single  0.970  0.020  1.090
 7CV  C6   H6   single  0.970  0.020  1.090
 7CV  C6   H7   single  0.970  0.020  1.090
 7CV  C6   H8   single  0.970  0.020  1.090
 7CV  O4   H9   single  0.850  0.020  0.980
 7CV  C24  H10  single  0.970  0.020  1.090
 7CV  C24  H11  single  0.970  0.020  1.090
 7CV  C24  H12  single  0.970  0.020  1.090
 7CV  C27  H13  single  0.970  0.020  1.090
 7CV  C27  H14  single  0.970  0.020  1.090
 7CV  C27  H15  single  0.970  0.020  1.090
 7CV  O1   H16  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
 7CV  H1   C1   O1   110.87  3.000
 7CV  H1   C1   O5   104.49  3.000
 7CV  O1   C1   O5   113.07  3.000
 7CV  H1   C1   C2   110.11  3.000
 7CV  O1   C1   C2   107.41  3.000
 7CV  O5   C1   C2   110.90  3.000
 7CV  H2   C2   O2   110.54  3.000
 7CV  H2   C2   C3   108.89  3.000
 7CV  O2   C2   C3   108.28  3.000
 7CV  H2   C2   C1   108.85  3.000
 7CV  O2   C2   C1   110.02  3.000
 7CV  C3   C2   C1   110.24  3.000
 7CV  H3   C3   O3   110.41  3.000
 7CV  H3   C3   C4   108.26  3.000
 7CV  O3   C3   C4   112.34  3.000
 7CV  H3   C3   C2   107.48  3.000
 7CV  C4   C3   C2   110.02  3.000
 7CV  O3   C3   C2   108.22  3.000
 7CV  H4   C4   O4   110.76  3.000
 7CV  H4   C4   C5   108.66  3.000
 7CV  O4   C4   C5   110.50  3.000
 7CV  H4   C4   C3   108.76  3.000
 7CV  C5   C4   C3   109.75  3.000
 7CV  O4   C4   C3   108.37  3.000
 7CV  H5   C5   O5   109.99  3.000
 7CV  H5   C5   C6   108.54  3.000
 7CV  O5   C5   C6   107.19  3.000
 7CV  H5   C5   C4   107.93  3.000
 7CV  O5   C5   C4   110.65  3.000
 7CV  C6   C5   C4   112.52  3.000
 7CV  H8   C6   H7   108.30  3.000
 7CV  H8   C6   H6   108.27  3.000
 7CV  H7   C6   H6   107.00  3.000
 7CV  H8   C6   C5   111.60  3.000
 7CV  H7   C6   C5   110.73  3.000
 7CV  H6   C6   C5   110.79  3.000
 7CV  C24  O2   C2   114.23  3.000
 7CV  C27  O3   C3   115.44  3.000
 7CV  H9   O4   C4   108.64  3.000
 7CV  C5   O5   C1   115.42  3.000
 7CV  H12  C24  H11  108.51  3.000
 7CV  H12  C24  H10  108.05  3.000
 7CV  H11  C24  H10  107.80  3.000
 7CV  H12  C24  O2   107.67  3.000
 7CV  H11  C24  O2   111.69  3.000
 7CV  H10  C24  O2   112.99  3.000
 7CV  H15  C27  H14  108.40  3.000
 7CV  H15  C27  H13  107.96  3.000
 7CV  H14  C27  H13  108.11  3.000
 7CV  H15  C27  O3   107.50  3.000
 7CV  H14  C27  O3   112.80  3.000
 7CV  H13  C27  O3   111.92  3.000
 7CV  H16  O1   C1   109.07  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
 7CV  Var_01  H10  C24  O2  C2  -63.82  30.0  3
 7CV  Var_02  H13  C27  O3  C3  -50.76  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
 7CV  chir_01  C1  C2  O5  O1  negativ
 7CV  chir_02  C2  O2  C3  C1  positiv
 7CV  chir_03  C3  O3  C4  C2  positiv
 7CV  chir_04  C4  O4  C5  C3  negativ
 7CV  chir_05  C5  O5  C4  C6  positiv

