# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:57:46 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2R,4S,6S)-4-amino-4,6-dimethyldihydro-2H-pyran-2,5,5(6H)-triol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)C[C@](C)(N)C1(O)O
#
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
 DVC  DVC  '(2R,4S,6S)-4-amino-4,6-dimethyldihydro-2H-pyran-2,5,5(6H)-triol (non-preferred name)'  L-saccharide  27  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DVC
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
 DVC  C1    C  CH1   0   0.276  38.3553  -1.3314  19.3395
 DVC  O1    O  OH1   0  -0.665  37.3432  -0.7390  20.1145
 DVC  C2    C  CH2   0  -0.508  38.2197  -2.8429  19.1985
 DVC  C3    C  CT    0   0.038  37.1014  -3.3131  18.2594
 DVC  N3    N  NH2   0  -0.792  37.2835  -4.7456  18.0640
 DVC  C4    C  CT    0   0.494  37.2308  -2.4975  16.9395
 DVC  O4    O  OH1   0  -0.674  38.4148  -2.9260  16.3317
 DVC  C5    C  CH1   0  -0.016  37.2812  -0.9831  17.2476
 DVC  O5    O  O2    0  -0.489  38.3728  -0.6924  18.1027
 DVC  C6    C  CH3   0  -0.716  37.4392  -0.0892  16.0281
 DVC  C3M   C  CH3   0  -0.658  35.7195  -3.1372  18.8955
 DVC  O41   O  OH1   0  -0.670  36.1108  -2.8011  16.1576
 DVC  H1    H  HCH1  0   0.211  39.3354  -1.1092  19.7815
 DVC  HO1   H  HOH1  0   0.454  37.0777  -1.3456  20.8130
 DVC  H2    H  HCH2  0   0.246  39.1765  -3.2163  18.8245
 DVC  H2A   H  HCH2  0   0.247  38.0854  -3.2989  20.1841
 DVC  HN3   H  HNH2  0   0.338  36.5662  -5.1022  17.4433
 DVC  HN3A  H  HNH2  0   0.341  38.1687  -4.9293  17.6076
 DVC  HO4   H  HOH1  0   0.451  38.6963  -2.3031  15.6525
 DVC  H5    H  HCH1  0   0.229  36.3344  -0.7115  17.7275
 DVC  H6    H  HCH3  0   0.259  37.4183   0.9555  16.3378
 DVC  H6A   H  HCH3  0   0.229  38.3813  -0.2475  15.4994
 DVC  H6B   H  HCH3  0   0.237  36.6203  -0.2235  15.3220
 DVC  H3M   H  HCH3  0   0.231  34.9511  -3.6345  18.3036
 DVC  H3MA  H  HCH3  0   0.230  35.7212  -3.5961  19.8849
 DVC  H3MB  H  HCH3  0   0.230  35.4216  -2.0986  19.0143
 DVC  HO41  H  HOH1  0   0.447  36.1771  -2.3687  15.2988

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
 DVC  O5   C1    single  1.392  0.020  1.392
 DVC  C2   C1    single  1.524  0.020  1.524
 DVC  C1   O1    single  1.406  0.020  1.406
 DVC  C1   H1    single  0.970  0.020  1.090
 DVC  O1   HO1   single  0.850  0.020  0.980
 DVC  C3   C2    single  1.534  0.020  1.534
 DVC  C2   H2    single  0.970  0.020  1.090
 DVC  C2   H2A   single  0.970  0.020  1.090
 DVC  C4   C3    single  1.557  0.020  1.557
 DVC  N3   C3    single  1.457  0.020  1.457
 DVC  C3   C3M   single  1.531  0.020  1.531
 DVC  N3   HN3   single  0.890  0.020  1.040
 DVC  N3   HN3A  single  0.890  0.020  1.040
 DVC  O41  C4    single  1.399  0.020  1.399
 DVC  O4   C4    single  1.398  0.020  1.398
 DVC  C4   C5    single  1.546  0.020  1.546
 DVC  O4   HO4   single  0.850  0.020  0.980
 DVC  C6   C5    single  1.520  0.020  1.520
 DVC  C5   O5    single  1.417  0.020  1.417
 DVC  C5   H5    single  0.970  0.020  1.090
 DVC  C6   H6    single  0.970  0.020  1.090
 DVC  C6   H6A   single  0.970  0.020  1.090
 DVC  C6   H6B   single  0.970  0.020  1.090
 DVC  C3M  H3M   single  0.970  0.020  1.090
 DVC  C3M  H3MA  single  0.970  0.020  1.090
 DVC  C3M  H3MB  single  0.970  0.020  1.090
 DVC  O41  HO41  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
 DVC  H1    C1   O5    104.69  3.000
 DVC  H1    C1   C2    108.51  3.000
 DVC  O5    C1   C2    111.97  3.000
 DVC  H1    C1   O1    109.60  3.000
 DVC  C2    C1   O1    113.88  3.000
 DVC  O5    C1   O1    107.78  3.000
 DVC  HO1   O1   C1    109.46  3.000
 DVC  H2A   C2   H2    105.86  3.000
 DVC  H2A   C2   C3    109.53  3.000
 DVC  H2    C2   C3    108.90  3.000
 DVC  H2A   C2   C1    109.93  3.000
 DVC  H2    C2   C1    107.01  3.000
 DVC  C3    C2   C1    115.17  3.000
 DVC  C3M   C3   C4    111.53  3.000
 DVC  C3M   C3   N3    106.34  3.000
 DVC  C4    C3   N3    113.01  3.000
 DVC  C3M   C3   C2    111.61  3.000
 DVC  N3    C3   C2    106.99  3.000
 DVC  C4    C3   C2    107.33  3.000
 DVC  HN3A  N3   HN3   106.19  3.000
 DVC  HN3A  N3   C3    110.36  3.000
 DVC  HN3   N3   C3    109.85  3.000
 DVC  O41   C4   C5    110.48  3.000
 DVC  C5    C4   O4    111.05  3.000
 DVC  O41   C4   O4    111.61  3.000
 DVC  C5    C4   C3    110.30  3.000
 DVC  O4    C4   C3    106.16  3.000
 DVC  O41   C4   C3    107.07  3.000
 DVC  HO4   O4   C4    110.83  3.000
 DVC  H5    C5   C6    107.18  3.000
 DVC  H5    C5   O5    110.53  3.000
 DVC  C6    C5   O5    106.46  3.000
 DVC  H5    C5   C4    107.57  3.000
 DVC  O5    C5   C4    110.26  3.000
 DVC  C6    C5   C4    114.80  3.000
 DVC  C5    O5   C1    115.61  3.000
 DVC  H6B   C6   H6A   108.46  3.000
 DVC  H6B   C6   H6    106.73  3.000
 DVC  H6A   C6   H6    107.04  3.000
 DVC  H6B   C6   C5    111.67  3.000
 DVC  H6A   C6   C5    113.14  3.000
 DVC  H6    C6   C5    109.49  3.000
 DVC  H3MB  C3M  H3MA  107.66  3.000
 DVC  H3MB  C3M  H3M   107.58  3.000
 DVC  H3MA  C3M  H3M   107.57  3.000
 DVC  H3MB  C3M  C3    113.73  3.000
 DVC  H3MA  C3M  C3    109.09  3.000
 DVC  H3M   C3M  C3    110.99  3.000
 DVC  HO41  O41  C4    110.22  3.000

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
 DVC  chir_01  C1  O5   C2  O1  positiv
 DVC  chir_02  C3  C3M  C4  C2  negativ
 DVC  chir_03  C5  O5   C6  C4  negativ

