# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:49:25 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](OCC#Cc2cccnc2)[C@@H](O)[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
 FVQ  FVQ  '3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside'  D-saccharide  38  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_FVQ
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
 FVQ  O6    O  OH1   0  -0.669   2.1504   3.3598   0.5103
 FVQ  C6    C  CH2   0  -0.158   3.0234   2.3400   0.9362
 FVQ  C5    C  CH1   0  -0.017   2.4502   1.0073   0.5066
 FVQ  O5    O  O2    0  -0.497   2.4290   0.9974  -0.9127
 FVQ  C4    C  CH1   0   0.036   3.2648  -0.1762   1.0282
 FVQ  O4    O  OH1   0  -0.676   3.1808  -0.1693   2.4331
 FVQ  C3    C  CH1   0   0.000   2.6997  -1.4700   0.4506
 FVQ  O3    O  OH1   0  -0.673   3.5054  -2.5275   0.9139
 FVQ  C2    C  CH1   0  -0.030   2.6394  -1.4049  -1.0741
 FVQ  O2    O  OH1   0  -0.668   3.9525  -1.3619  -1.5706
 FVQ  C1    C  CH1   0   0.246   1.8790  -0.1432  -1.4948
 FVQ  O1    O  O2    0  -0.502   0.5365  -0.3267  -1.1478
 FVQ  C7    C  CH2   0  -0.336  -0.3142   0.7107  -1.5910
 FVQ  C8    C  CSP   0   0.013  -1.6628   0.4399  -1.1166
 FVQ  C9    C  CSP   0   0.188  -2.7810   0.2484  -0.7143
 FVQ  C10   C  CR6   0  -0.201  -4.0956   0.0187  -0.2204
 FVQ  C15   C  CR16  0  -0.185  -5.1635   0.8484  -0.5634
 FVQ  C14   C  CR16  0  -0.318  -6.4133   0.5762  -0.0367
 FVQ  C13   C  CR16  0  -0.064  -6.5564  -0.5121   0.8119
 FVQ  N12   N  N     0  -0.393  -5.5485  -1.3118   1.1441
 FVQ  C11   C  CR16  0  -0.092  -4.3530  -1.0518   0.6413
 FVQ  H6    H  HOH1  0   0.456   2.4777   4.1947   0.8563
 FVQ  H61C  H  HCH2  0   0.196   4.0288   2.4571   0.5079
 FVQ  H62C  H  HCH2  0   0.212   3.1354   2.3338   2.0254
 FVQ  H5    H  HCH1  0   0.227   1.4295   0.9254   0.9070
 FVQ  H4    H  HCH1  0   0.213   4.3081  -0.0599   0.6984
 FVQ  H1    H  HCH1  0   0.242   1.9745   0.0136  -2.5790
 FVQ  HA    H  HOH1  0   0.452   3.6091  -0.9684   2.7584
 FVQ  H3    H  HCH1  0   0.230   1.6704  -1.5783   0.8183
 FVQ  HB    H  HOH1  0   0.458   2.9978  -3.3436   0.8772
 FVQ  H2    H  HCH1  0   0.236   2.0976  -2.2822  -1.4536
 FVQ  HC    H  HOH1  0   0.457   3.9261  -1.5046  -2.5216
 FVQ  H71C  H  HCH2  0   0.261   0.0050   1.6874  -1.2104
 FVQ  H72C  H  HCH2  0   0.260  -0.3133   0.7773  -2.6867
 FVQ  H15   H  HCR6  0   0.277  -5.0114   1.6885  -1.2277
 FVQ  H11   H  HCR6  0   0.268  -3.5445  -1.7158   0.9271
 FVQ  H14   H  HCR6  0   0.280  -7.2652   1.1971  -0.2765
 FVQ  H13   H  HCR6  0   0.272  -7.5235  -0.7462   1.2417

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
 FVQ  O6   C6    single    1.408  0.020  1.408
 FVQ  C6   C5    single    1.513  0.020  1.513
 FVQ  C5   O5    single    1.419  0.020  1.419
 FVQ  C5   C4    single    1.528  0.020  1.528
 FVQ  O5   C1    single    1.394  0.020  1.394
 FVQ  C4   O4    single    1.407  0.020  1.407
 FVQ  C4   C3    single    1.525  0.020  1.525
 FVQ  C3   O3    single    1.408  0.020  1.408
 FVQ  C3   C2    single    1.527  0.020  1.527
 FVQ  C2   O2    single    1.404  0.020  1.404
 FVQ  C2   C1    single    1.532  0.020  1.532
 FVQ  C1   O1    single    1.399  0.020  1.399
 FVQ  O1   C7    single    1.413  0.020  1.413
 FVQ  C7   C8    single    1.455  0.020  1.455
 FVQ  C8   C9    triple    1.204  0.020  1.204
 FVQ  C9   C10   single    1.423  0.020  1.423
 FVQ  C10  C15   aromatic  1.395  0.020  1.395
 FVQ  C10  C11   aromatic  1.398  0.020  1.398
 FVQ  C15  C14   aromatic  1.383  0.020  1.383
 FVQ  C14  C13   aromatic  1.387  0.020  1.387
 FVQ  C13  N12   aromatic  1.329  0.020  1.329
 FVQ  C11  N12   aromatic  1.323  0.020  1.323
 FVQ  O6   H6    single    0.850  0.020  0.980
 FVQ  C6   H61C  single    0.970  0.020  1.090
 FVQ  C6   H62C  single    0.970  0.020  1.090
 FVQ  C5   H5    single    0.970  0.020  1.090
 FVQ  C4   H4    single    0.970  0.020  1.090
 FVQ  C1   H1    single    0.970  0.020  1.090
 FVQ  O4   HA    single    0.850  0.020  0.980
 FVQ  C3   H3    single    0.970  0.020  1.090
 FVQ  O3   HB    single    0.850  0.020  0.980
 FVQ  C2   H2    single    0.970  0.020  1.090
 FVQ  O2   HC    single    0.850  0.020  0.980
 FVQ  C7   H71C  single    0.970  0.020  1.090
 FVQ  C7   H72C  single    0.970  0.020  1.090
 FVQ  C15  H15   single    0.930  0.020  1.080
 FVQ  C11  H11   single    0.930  0.020  1.080
 FVQ  C14  H14   single    0.930  0.020  1.080
 FVQ  C13  H13   single    0.930  0.020  1.080

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
 FVQ  H6    O6   C6    108.00  3.000
 FVQ  H62C  C6   H61C  107.13  3.000
 FVQ  H62C  C6   C5    108.44  3.000
 FVQ  H61C  C6   C5    109.26  3.000
 FVQ  H62C  C6   O6    111.61  3.000
 FVQ  H61C  C6   O6    111.84  3.000
 FVQ  C5    C6   O6    108.49  3.000
 FVQ  H5    C5   C4    108.23  3.000
 FVQ  H5    C5   O5    110.47  3.000
 FVQ  C4    C5   O5    110.11  3.000
 FVQ  H5    C5   C6    108.29  3.000
 FVQ  C4    C5   C6    112.54  3.000
 FVQ  O5    C5   C6    107.20  3.000
 FVQ  C1    O5   C5    115.42  3.000
 FVQ  H4    C4   C3    109.11  3.000
 FVQ  H4    C4   O4    110.81  3.000
 FVQ  C3    C4   O4    111.10  3.000
 FVQ  H4    C4   C5    108.74  3.000
 FVQ  C3    C4   C5    109.28  3.000
 FVQ  O4    C4   C5    107.76  3.000
 FVQ  HA    O4   C4    107.85  3.000
 FVQ  H3    C3   C2    107.54  3.000
 FVQ  H3    C3   O3    110.62  3.000
 FVQ  C2    C3   O3    112.53  3.000
 FVQ  H3    C3   C4    107.70  3.000
 FVQ  C2    C3   C4    110.88  3.000
 FVQ  O3    C3   C4    107.49  3.000
 FVQ  HB    O3   C3    108.82  3.000
 FVQ  H2    C2   C1    108.54  3.000
 FVQ  H2    C2   O2    111.31  3.000
 FVQ  C1    C2   O2    109.98  3.000
 FVQ  H2    C2   C3    109.28  3.000
 FVQ  C1    C2   C3    109.20  3.000
 FVQ  O2    C2   C3    108.50  3.000
 FVQ  HC    O2   C2    108.62  3.000
 FVQ  H1    C1   O1    110.28  3.000
 FVQ  H1    C1   C2    110.19  3.000
 FVQ  O1    C1   C2    107.47  3.000
 FVQ  H1    C1   O5    105.12  3.000
 FVQ  O1    C1   O5    112.49  3.000
 FVQ  C2    C1   O5    111.31  3.000
 FVQ  C7    O1   C1    113.82  3.000
 FVQ  H72C  C7   H71C  107.00  3.000
 FVQ  H72C  C7   C8    109.73  3.000
 FVQ  H71C  C7   C8    108.82  3.000
 FVQ  H72C  C7   O1    110.92  3.000
 FVQ  H71C  C7   O1    111.72  3.000
 FVQ  C8    C7   O1    108.61  3.000
 FVQ  C9    C8   C7    180.00  3.000
 FVQ  C10   C9   C8    180.00  3.000
 FVQ  C11   C10  C15   117.77  3.000
 FVQ  C11   C10  C9    120.50  3.000
 FVQ  C15   C10  C9    121.72  3.000
 FVQ  H15   C15  C14   120.91  3.000
 FVQ  H15   C15  C10   120.35  3.000
 FVQ  C14   C15  C10   118.75  3.000
 FVQ  H14   C14  C13   120.32  3.000
 FVQ  H14   C14  C15   120.97  3.000
 FVQ  C13   C14  C15   118.71  3.000
 FVQ  H13   C13  N12   116.59  3.000
 FVQ  H13   C13  C14   120.27  3.000
 FVQ  N12   C13  C14   123.14  3.000
 FVQ  C11   N12  C13   118.18  3.000
 FVQ  H11   C11  N12   116.96  3.000
 FVQ  H11   C11  C10   119.60  3.000
 FVQ  N12   C11  C10   123.45  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
 FVQ  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 FVQ  CONST_02  C13  N12  C11  C10     0.00   0.0  0
 FVQ  CONST_03  N12  C11  C10  C15     0.00   0.0  0
 FVQ  CONST_04  N12  C13  C14  C15     0.00   0.0  0
 FVQ  CONST_05  C11  C10  C15  C14     0.00   0.0  0
 FVQ  CONST_06  C11  N12  C13  C14     0.00   0.0  0
 FVQ  CONST_07  C14  C15  C10  C9    180.00   0.0  0
 FVQ  CONST_08  N12  C11  C10  C9    180.00   0.0  0
 FVQ  CONST_09  H14  C14  C15  C10   180.00   0.0  0
 FVQ  CONST_10  H11  C11  C10  C15   180.00   0.0  0
 FVQ  CONST_11  H13  C13  C14  C15   180.00   0.0  0
 FVQ  CONST_12  H15  C15  C14  C13   180.00   0.0  0
 FVQ  Var_01    C8   C7   O1   C1   -177.29  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
 FVQ  chir_01  C5  C6  O5  C4  negativ
 FVQ  chir_02  C4  O4  C5  C3  positiv
 FVQ  chir_03  C3  O3  C2  C4  positiv
 FVQ  chir_04  C2  O2  C3  C1  negativ
 FVQ  chir_05  C1  O1  O5  C2  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
 FVQ  plan-1  C8   0.020
 FVQ  plan-1  C9   0.020
 FVQ  plan-1  C10  0.020
 FVQ  plan-1  C15  0.020
 FVQ  plan-1  C14  0.020
 FVQ  plan-1  C13  0.020
 FVQ  plan-1  N12  0.020
 FVQ  plan-1  C11  0.020
 FVQ  plan-1  H15  0.020
 FVQ  plan-1  H11  0.020
 FVQ  plan-1  H14  0.020
 FVQ  plan-1  H13  0.020

