# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:42:26 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-2-(hydroxyimino)-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\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
 LOG  LOG  'N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-2-(hydroxyimino)-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)'  D-saccharide  30  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LOG
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
 LOG  C2    C  CH1   0  -0.183   0.7719   0.3652  -0.1693
 LOG  C3    C  CH1   0   0.049  -0.1116   1.4862   0.3701
 LOG  C4    C  CH1   0  -0.022  -1.5192   1.3326  -0.1931
 LOG  C5    C  CH1   0  -0.022  -2.0748  -0.0383   0.1920
 LOG  C6    C  CH2   0  -0.159  -3.4266  -0.3096  -0.4268
 LOG  C8    C  CH3   0  -0.782   4.4861   0.2308   0.4863
 LOG  N2    N  NH1   0  -0.622   2.0854   0.4164   0.3990
 LOG  O1    O  OH1   0  -0.558   0.0932  -3.1336   0.4852
 LOG  O3    O  OH1   0  -0.661   0.4709   2.7026  -0.0012
 LOG  O4    O  OH1   0  -0.667  -2.3044   2.3644   0.3552
 LOG  O5    O  O2    0  -0.467  -1.1979  -1.0795  -0.2517
 LOG  O6    O  OH1   0  -0.666  -3.9124  -1.5364   0.0570
 LOG  C1    C  C     0   0.455   0.1050  -0.9757   0.0417
 LOG  O7    O  O     0  -0.498   3.2154   0.1234  -1.5352
 LOG  N1    N  N     0  -0.189   0.8097  -1.9716   0.3770
 LOG  H2    H  HCH1  0   0.296   0.8696   0.5114  -1.2503
 LOG  H3    H  HCH1  0   0.224  -0.1731   1.3926   1.4677
 LOG  HA    H  HNH1  0   0.402   2.1545   0.4358   1.4043
 LOG  H4    H  HCH1  0   0.241  -1.4692   1.4083  -1.2888
 LOG  HB    H  HOH1  0   0.454  -0.1153   3.4107   0.2876
 LOG  H5    H  HCH1  0   0.247  -2.1609  -0.0897   1.2859
 LOG  HC    H  HOH1  0   0.468  -2.9586   2.6429  -0.2916
 LOG  H61C  H  HCH2  0   0.212  -4.0924   0.5197  -0.1628
 LOG  H62C  H  HCH2  0   0.205  -3.3249  -0.3089  -1.5209
 LOG  H6    H  HOH1  0   0.459  -4.8102  -1.6502  -0.2676
 LOG  H81C  H  HCH3  0   0.250   4.3480   0.5171   1.5271
 LOG  H82C  H  HCH3  0   0.270   4.9053  -0.7760   0.4630
 LOG  H83C  H  HCH3  0   0.266   5.2174   0.8984   0.0332
 LOG  H1    H  HOH1  0   0.473   0.7566  -3.7802   0.7459
 LOG  C7    C  C     0   0.527   3.2132   0.2508  -0.3196

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
 LOG  C2  C3    single  1.526  0.020  1.526
 LOG  C2  N2    single  1.432  0.020  1.432
 LOG  C2  C1    single  1.512  0.020  1.512
 LOG  C3  C4    single  1.524  0.020  1.524
 LOG  C3  O3    single  1.399  0.020  1.399
 LOG  C4  C5    single  1.529  0.020  1.529
 LOG  C4  O4    single  1.408  0.020  1.408
 LOG  C5  C6    single  1.511  0.020  1.511
 LOG  C5  O5    single  1.432  0.020  1.432
 LOG  C6  O6    single  1.405  0.020  1.405
 LOG  C7  C8    single  1.507  0.020  1.507
 LOG  C7  N2    single  1.347  0.020  1.347
 LOG  C7  O7    double  1.222  0.020  1.222
 LOG  O1  N1    single  1.370  0.020  1.370
 LOG  O5  C1    single  1.340  0.020  1.340
 LOG  C1  N1    double  1.265  0.020  1.265
 LOG  C2  H2    single  0.970  0.020  1.090
 LOG  C3  H3    single  0.970  0.020  1.090
 LOG  N2  HA    single  0.860  0.020  1.020
 LOG  C4  H4    single  0.970  0.020  1.090
 LOG  O3  HB    single  0.850  0.020  0.980
 LOG  C5  H5    single  0.970  0.020  1.090
 LOG  O4  HC    single  0.850  0.020  0.980
 LOG  C6  H61C  single  0.970  0.020  1.090
 LOG  C6  H62C  single  0.970  0.020  1.090
 LOG  O6  H6    single  0.850  0.020  0.980
 LOG  C8  H81C  single  0.970  0.020  1.090
 LOG  C8  H82C  single  0.970  0.020  1.090
 LOG  C8  H83C  single  0.970  0.020  1.090
 LOG  O1  H1    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
 LOG  H2    C2  C1    107.18  3.000
 LOG  H2    C2  N2    107.76  3.000
 LOG  C1    C2  N2    112.38  3.000
 LOG  H2    C2  C3    107.61  3.000
 LOG  C1    C2  C3    110.29  3.000
 LOG  N2    C2  C3    111.38  3.000
 LOG  H3    C3  O3    111.16  3.000
 LOG  H3    C3  C4    107.91  3.000
 LOG  O3    C3  C4    111.97  3.000
 LOG  H3    C3  C2    108.76  3.000
 LOG  O3    C3  C2    107.69  3.000
 LOG  C4    C3  C2    109.28  3.000
 LOG  H4    C4  O4    111.29  3.000
 LOG  H4    C4  C5    109.23  3.000
 LOG  O4    C4  C5    110.88  3.000
 LOG  H4    C4  C3    108.62  3.000
 LOG  O4    C4  C3    107.30  3.000
 LOG  C5    C4  C3    109.45  3.000
 LOG  H5    C5  O5    108.82  3.000
 LOG  H5    C5  C6    109.23  3.000
 LOG  O5    C5  C6    106.88  3.000
 LOG  H5    C5  C4    108.74  3.000
 LOG  O5    C5  C4    110.58  3.000
 LOG  C6    C5  C4    112.52  3.000
 LOG  H62C  C6  H61C  107.20  3.000
 LOG  H62C  C6  O6    112.05  3.000
 LOG  H61C  C6  O6    111.57  3.000
 LOG  H62C  C6  C5    108.95  3.000
 LOG  H61C  C6  C5    108.00  3.000
 LOG  O6    C6  C5    108.96  3.000
 LOG  H83C  C8  H82C  107.39  3.000
 LOG  H83C  C8  H81C  108.77  3.000
 LOG  H82C  C8  H81C  108.18  3.000
 LOG  H83C  C8  C7    109.67  3.000
 LOG  H82C  C8  C7    109.00  3.000
 LOG  H81C  C8  C7    113.63  3.000
 LOG  HA    N2  C7    118.49  3.000
 LOG  HA    N2  C2    117.34  3.000
 LOG  C7    N2  C2    123.48  3.000
 LOG  H1    O1  N1    103.34  3.000
 LOG  HB    O3  C3    107.83  3.000
 LOG  HC    O4  C4    109.26  3.000
 LOG  C1    O5  C5    118.13  3.000
 LOG  H6    O6  C6    108.05  3.000
 LOG  N1    C1  O5    122.60  3.000
 LOG  N1    C1  C2    119.29  3.000
 LOG  O5    C1  C2    117.84  3.000
 LOG  C1    N1  O1    113.41  3.000
 LOG  O7    C7  N2    123.01  3.000
 LOG  O7    C7  C8    121.94  3.000
 LOG  N2    C7  C8    115.05  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
 LOG  CONST_01  C8    C7  N2  C2  180.00   0.0  0
 LOG  CONST_02  O7    C7  N2  C2    0.00   0.0  0
 LOG  CONST_03  HA    N2  C7  C8    0.00   0.0  0
 LOG  Var_01    N1    C1  O5  C5  141.00  30.0  1
 LOG  Var_02    O5    C1  N1  O1   -3.68  30.0  2
 LOG  Var_03    H81C  C8  C7  N2   -9.60  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
 LOG  chir_01  C2  C3  N2  C1  negativ
 LOG  chir_02  C3  O3  C2  C4  positiv
 LOG  chir_03  C4  O4  C5  C3  positiv
 LOG  chir_04  C5  O5  C4  C6  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
 LOG  plan-1  C2  0.020
 LOG  plan-1  C8  0.020
 LOG  plan-1  N2  0.020
 LOG  plan-1  O7  0.020
 LOG  plan-1  HA  0.020
 LOG  plan-1  C7  0.020

