# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:49:58 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: (1S)-2-amino-1-phenylethyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)c2ccccc2
#
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
 TVY  TVY  '(1S)-2-amino-1-phenylethyl alpha-D-mannopyranoside'  D-saccharide  42  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_TVY
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
 TVY  C7   C  CR16  0  -0.247  16.2410  20.9124  15.7497
 TVY  C8   C  CR16  0  -0.301  15.6131  20.0916  14.8206
 TVY  C9   C  CR6   0   0.103  15.4156  18.7404  15.0823
 TVY  C10  C  CR16  0  -0.290  15.8524  18.2205  16.2986
 TVY  C11  C  CR16  0  -0.244  16.4774  19.0375  17.2305
 TVY  C12  C  CR16  0  -0.269  16.6760  20.3857  16.9586
 TVY  C13  C  CH1   0  -0.013  14.7802  17.8505  14.0423
 TVY  C15  C  CH2   0  -0.309  15.8265  17.1168  13.2031
 TVY  N17  N  NH2   0  -0.790  16.6429  18.0589  12.4627
 TVY  O1   O  O2    0  -0.508  13.9760  16.8423  14.6244
 TVY  C1   C  CR16  0   0.336  12.7894  17.2734  15.2192
 TVY  O5   O  O     0  -0.497  11.8901  17.7805  14.2804
 TVY  C5   C  CR16  0  -0.007  11.0999  16.8029  13.6365
 TVY  C4   C  CR16  0  -0.002  10.0966  16.2140  14.6357
 TVY  C2   C  CR16  0  -0.089  12.2104  16.0776  15.9789
 TVY  C3   C  CR16  0  -0.010  10.6925  16.1964  16.0536
 TVY  C6   C  CH2   0  -0.166  10.3981  17.4559  12.4691
 TVY  O6   O  OH1   0  -0.665  11.3503  17.8314  11.5044
 TVY  O2   O  OH1   0  -0.664  12.8091  16.0674  17.2540
 TVY  O3   O  OH1   0  -0.671  10.3022  17.3742  16.7195
 TVY  O4   O  OH1   0  -0.669   9.7869  14.9208  14.1752
 TVY  H11  H  HCR6  0   0.253  16.3870  21.9624  15.5302
 TVY  H12  H  HCR6  0   0.241  15.2703  20.5105  13.8819
 TVY  H13  H  HCR6  0   0.247  15.6910  17.1743  16.5273
 TVY  H14  H  HCR6  0   0.252  16.8097  18.6214  18.1731
 TVY  H15  H  HCR6  0   0.253  17.1620  21.0216  17.6875
 TVY  H6   H  HCH1  0   0.231  14.1762  18.4694  13.3644
 TVY  H7   H  HCH2  0   0.212  15.2981  16.3912  12.5692
 TVY  H8   H  HCH2  0   0.225  16.4746  16.5424  13.8708
 TVY  H9   H  HNH2  0   0.353  17.3840  17.5571  11.9917
 TVY  H10  H  HNH2  0   0.340  16.0901  18.4836  11.7285
 TVY  H1   H  HCR6  0   0.222  12.9760  18.0991  15.9168
 TVY  H5   H  HCR6  0   0.228  11.7276  15.9833  13.2573
 TVY  H4   H  HCR6  0   0.228   9.1988  16.8480  14.6681
 TVY  H2   H  HCR6  0   0.233  12.4490  15.1571  15.4271
 TVY  H3   H  HCR6  0   0.234  10.2979  15.3097  16.5746
 TVY  H61  H  HCH2  0   0.200   9.8279  18.3197  12.8390
 TVY  H62  H  HCH2  0   0.206   9.6690  16.7403  12.0684
 TVY  HO2  H  HOH1  0   0.458  12.6626  15.2035  17.6517
 TVY  HO3  H  HOH1  0   0.449  10.7490  17.3899  17.5729
 TVY  HO4  H  HOH1  0   0.456   9.0258  14.5960  14.6662
 TVY  HO6  H  HOH1  0   0.455  10.8873  18.2747  10.7879

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
 TVY  O6   C6   single    1.406  0.020  1.406
 TVY  C6   C5   single    1.511  0.020  1.511
 TVY  N17  C15  single    1.450  0.020  1.450
 TVY  C15  C13  single    1.529  0.020  1.529
 TVY  C5   O5   single    1.412  0.020  1.412
 TVY  C5   C4   single    1.534  0.020  1.534
 TVY  O4   C4   single    1.407  0.020  1.407
 TVY  O5   C1   single    1.395  0.020  1.395
 TVY  C4   C3   single    1.538  0.020  1.538
 TVY  C13  C9   single    1.509  0.020  1.509
 TVY  C13  O1   single    1.415  0.020  1.415
 TVY  C8   C9   aromatic  1.390  0.020  1.390
 TVY  C8   C7   aromatic  1.390  0.020  1.390
 TVY  C1   O1   single    1.396  0.020  1.396
 TVY  C1   C2   single    1.530  0.020  1.530
 TVY  C9   C10  aromatic  1.393  0.020  1.393
 TVY  C7   C12  aromatic  1.389  0.020  1.389
 TVY  C3   C2   single    1.524  0.020  1.524
 TVY  C3   O3   single    1.408  0.020  1.408
 TVY  C2   O2   single    1.409  0.020  1.409
 TVY  C10  C11  aromatic  1.388  0.020  1.388
 TVY  C12  C11  aromatic  1.390  0.020  1.390
 TVY  C7   H11  single    0.930  0.020  1.080
 TVY  C8   H12  single    0.930  0.020  1.080
 TVY  C10  H13  single    0.930  0.020  1.080
 TVY  C11  H14  single    0.930  0.020  1.080
 TVY  C12  H15  single    0.930  0.020  1.080
 TVY  C13  H6   single    0.970  0.020  1.090
 TVY  C15  H7   single    0.970  0.020  1.090
 TVY  C15  H8   single    0.970  0.020  1.090
 TVY  N17  H9   single    0.890  0.020  1.040
 TVY  N17  H10  single    0.890  0.020  1.040
 TVY  C1   H1   single    0.970  0.020  1.090
 TVY  C5   H5   single    0.970  0.020  1.090
 TVY  C4   H4   single    0.970  0.020  1.090
 TVY  C2   H2   single    0.970  0.020  1.090
 TVY  C3   H3   single    0.970  0.020  1.090
 TVY  C6   H61  single    0.970  0.020  1.090
 TVY  C6   H62  single    0.970  0.020  1.090
 TVY  O2   HO2  single    0.850  0.020  0.980
 TVY  O3   HO3  single    0.850  0.020  0.980
 TVY  O4   HO4  single    0.850  0.020  0.980
 TVY  O6   HO6  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
 TVY  H11  C7   C12  120.15  3.000
 TVY  H11  C7   C8   119.89  3.000
 TVY  C12  C7   C8   119.97  3.000
 TVY  H12  C8   C9   119.59  3.000
 TVY  H12  C8   C7   119.59  3.000
 TVY  C9   C8   C7   120.82  3.000
 TVY  C13  C9   C10  120.91  3.000
 TVY  C10  C9   C8   118.85  3.000
 TVY  C13  C9   C8   120.21  3.000
 TVY  H13  C10  C11  119.60  3.000
 TVY  H13  C10  C9   119.88  3.000
 TVY  C11  C10  C9   120.51  3.000
 TVY  H14  C11  C12  119.96  3.000
 TVY  H14  C11  C10  119.77  3.000
 TVY  C12  C11  C10  120.27  3.000
 TVY  H15  C12  C11  120.15  3.000
 TVY  H15  C12  C7   120.27  3.000
 TVY  C11  C12  C7   119.58  3.000
 TVY  H6   C13  O1   110.05  3.000
 TVY  H6   C13  C15  107.93  3.000
 TVY  O1   C13  C15  105.83  3.000
 TVY  H6   C13  C9   108.93  3.000
 TVY  O1   C13  C9   112.09  3.000
 TVY  C15  C13  C9   111.91  3.000
 TVY  H8   C15  H7   106.88  3.000
 TVY  H8   C15  N17  108.63  3.000
 TVY  H7   C15  N17  113.91  3.000
 TVY  H8   C15  C13  108.81  3.000
 TVY  H7   C15  C13  107.73  3.000
 TVY  N17  C15  C13  110.72  3.000
 TVY  H10  N17  H9   105.70  3.000
 TVY  H10  N17  C15  109.60  3.000
 TVY  H9   N17  C15  109.15  3.000
 TVY  C1   O1   C13  116.01  3.000
 TVY  H1   C1   C2   109.69  3.000
 TVY  H1   C1   O5   105.30  3.000
 TVY  C2   C1   O5   111.97  3.000
 TVY  H1   C1   O1   111.03  3.000
 TVY  C2   C1   O1   106.97  3.000
 TVY  O5   C1   O1   111.93  3.000
 TVY  C5   O5   C1   114.56  3.000
 TVY  H5   C5   C6   108.71  3.000
 TVY  H5   C5   C4   108.17  3.000
 TVY  C6   C5   C4   111.44  3.000
 TVY  H5   C5   O5   110.72  3.000
 TVY  C4   C5   O5   109.56  3.000
 TVY  C6   C5   O5   108.24  3.000
 TVY  H4   C4   O4   111.09  3.000
 TVY  H4   C4   C3   107.20  3.000
 TVY  O4   C4   C3   112.11  3.000
 TVY  H4   C4   C5   109.39  3.000
 TVY  C3   C4   C5   110.58  3.000
 TVY  O4   C4   C5   106.48  3.000
 TVY  H2   C2   O2   110.86  3.000
 TVY  H2   C2   C3   107.82  3.000
 TVY  O2   C2   C3   112.30  3.000
 TVY  H2   C2   C1   108.84  3.000
 TVY  O2   C2   C1   107.11  3.000
 TVY  C3   C2   C1   109.88  3.000
 TVY  H3   C3   O3   110.51  3.000
 TVY  H3   C3   C2   108.49  3.000
 TVY  O3   C3   C2   111.37  3.000
 TVY  H3   C3   C4   107.85  3.000
 TVY  O3   C3   C4   108.60  3.000
 TVY  C2   C3   C4   109.96  3.000
 TVY  H62  C6   H61  106.90  3.000
 TVY  H62  C6   O6   111.93  3.000
 TVY  H61  C6   O6   111.85  3.000
 TVY  H62  C6   C5   107.99  3.000
 TVY  H61  C6   C5   108.70  3.000
 TVY  O6   C6   C5   109.33  3.000
 TVY  HO6  O6   C6   107.96  3.000
 TVY  HO2  O2   C2   108.41  3.000
 TVY  HO3  O3   C3   107.70  3.000
 TVY  HO4  O4   C4   108.50  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
 TVY  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 TVY  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 TVY  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 TVY  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 TVY  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 TVY  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 TVY  CONST_07  C13  C9   C8   C7   180.00   0.0  0
 TVY  CONST_08  C13  C9   C10  C11  180.00   0.0  0
 TVY  CONST_09  H14  C11  C12  C7   180.00   0.0  0
 TVY  CONST_10  H13  C10  C9   C8   180.00   0.0  0
 TVY  CONST_11  H15  C12  C7   C8   180.00   0.0  0
 TVY  CONST_12  H11  C7   C8   C9   180.00   0.0  0
 TVY  CONST_13  H12  C8   C9   C10  180.00   0.0  0
 TVY  Var_01    H9   N17  C15  C13  174.29  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
 TVY  chir_01  C13  C15  C9  O1  positiv
 TVY  chir_02  C1   O5   O1  C2  positiv
 TVY  chir_03  C5   O5   C6  C4  positiv
 TVY  chir_04  C4   O4   C5  C3  positiv
 TVY  chir_05  C2   O2   C3  C1  negativ
 TVY  chir_06  C3   O3   C2  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
 TVY  plan-1  C7   0.020
 TVY  plan-1  C8   0.020
 TVY  plan-1  C9   0.020
 TVY  plan-1  C10  0.020
 TVY  plan-1  C11  0.020
 TVY  plan-1  C12  0.020
 TVY  plan-1  C13  0.020
 TVY  plan-1  H11  0.020
 TVY  plan-1  H12  0.020
 TVY  plan-1  H13  0.020
 TVY  plan-1  H14  0.020
 TVY  plan-1  H15  0.020

