# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:15:41 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2R,4S,5R,6R)-5-(acetylamino)-4-amino-6-(diethylcarbamoyl)tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(=O)[C@@H]1O[C@H](C[C@H](N)[C@H]1NC(C)=O)C(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
 G28  G28  '(2R,4S,5R,6R)-5-(acetylamino)-4-amino-6-(diethylcarbamoyl)tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  L-saccharide  43  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 OK
;

data_comp_G28
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
 G28  C1    C  C      0   0.383   3.6937  -0.3664  -0.7532
 G28  O1A   O  OC    -1  -0.624   4.5899   0.4807  -0.9499
 G28  O1B   O  O      0  -0.597   3.8018  -1.6013  -0.8244
 G28  C2    C  CH1    0  -0.074   2.3273   0.2334  -0.3770
 G28  C3    C  CH2    0  -0.482   1.8325   1.1949  -1.4483
 G28  C4    C  CH1    0  -0.084   0.4343   1.7097  -1.1343
 G28  C5    C  CH1    0  -0.101  -0.5029   0.5220  -0.8884
 G28  N5    N  NH1    0  -0.637  -0.7617  -0.1955  -2.1193
 G28  C10   C  C      0   0.526  -1.7820   0.0956  -2.9453
 G28  O10   O  O      0  -0.509  -2.6006   0.9739  -2.7051
 G28  C11   C  CH3    0  -0.778  -1.8632  -0.7437  -4.1952
 G28  C6    C  CH1    0  -0.109   0.0808  -0.4676   0.1368
 G28  O6    O  O2     0  -0.491   1.3953  -0.8236  -0.1764
 G28  C7    C  C      0   0.558  -0.0652  -0.0208   1.5993
 G28  O7    O  O      0  -0.485   0.9161   0.1955   2.2908
 G28  N8    N  NT     0  -0.457  -1.3262   0.0896   2.0900
 G28  C81   C  CH2    0  -0.305  -1.4883   0.6539   3.4242
 G28  C82   C  CH3    0  -0.668  -1.3706  -0.3397   4.5722
 G28  C9    C  CH2    0  -0.341  -2.4852  -0.5714   1.4998
 G28  C91   C  CH3    0  -0.658  -2.5841  -2.0655   1.7857
 G28  N4    N  NH2    0  -0.786   0.4471   2.5377   0.0568
 G28  H2    H  HCH1   0   0.222   2.4546   0.7936   0.5531
 G28  H31   H  HCH2   0   0.241   2.5297   2.0300  -1.5313
 G28  H32   H  HCH2   0   0.227   1.8187   0.7026  -2.4261
 G28  H4    H  HCH1   0   0.226   0.0531   2.2412  -2.0184
 G28  H5    H  HCH1   0   0.267  -1.4580   0.9125  -0.5343
 G28  HN5   H  HNH1   0   0.400  -0.1030  -0.9064  -2.3960
 G28  H111  H  HCH3   0   0.266  -1.7986  -0.0959  -5.0696
 G28  H112  H  HCH3   0   0.248  -1.0827  -1.4986  -4.2676
 G28  H113  H  HCH3   0   0.266  -2.8314  -1.2428  -4.2331
 G28  H6    H  HCH1   0   0.270  -0.4903  -1.3975   0.0320
 G28  H811  H  HCH2   0   0.240  -2.4682   1.1339   3.4535
 G28  H812  H  HCH2   0   0.245  -0.7516   1.4456   3.5496
 G28  H821  H  HCH3   0   0.232  -1.4289   0.1912   5.5233
 G28  H822  H  HCH3   0   0.227  -2.1733  -1.0757   4.5596
 G28  H823  H  HCH3   0   0.231  -0.4195  -0.8700   4.5436
 G28  H91   H  HCH2   0   0.261  -3.3724  -0.0678   1.8847
 G28  H92   H  HCH2   0   0.254  -2.5136  -0.4118   0.4232
 G28  H911  H  HCH3   0   0.237  -3.4484  -2.4778   1.2641
 G28  H912  H  HCH3   0   0.229  -1.7016  -2.6057   1.4399
 G28  H913  H  HCH3   0   0.237  -2.7074  -2.2712   2.8473
 G28  HN41  H  HNH2   0   0.349   1.1259   3.2807  -0.0516
 G28  HN42  H  HNH2   0   0.347  -0.4516   2.9899   0.1703

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
 G28  C1   O1A   deloc   1.249  0.020  1.249
 G28  C1   O1B   deloc   1.242  0.020  1.242
 G28  C1   C2    single  1.539  0.020  1.539
 G28  C2   C3    single  1.522  0.020  1.522
 G28  C2   O6    single  1.423  0.020  1.423
 G28  C2   H2    single  0.970  0.020  1.090
 G28  C3   C4    single  1.523  0.020  1.523
 G28  C3   H31   single  0.970  0.020  1.090
 G28  C3   H32   single  0.970  0.020  1.090
 G28  C4   C5    single  1.533  0.020  1.533
 G28  C4   N4    single  1.451  0.020  1.451
 G28  C4   H4    single  0.970  0.020  1.090
 G28  C5   N5    single  1.448  0.020  1.448
 G28  C5   C6    single  1.540  0.020  1.540
 G28  C5   H5    single  0.970  0.020  1.090
 G28  N5   C10   single  1.345  0.020  1.345
 G28  N5   HN5   single  0.860  0.020  1.020
 G28  C10  O10   double  1.224  0.020  1.224
 G28  C10  C11   single  1.508  0.020  1.508
 G28  C11  H111  single  0.970  0.020  1.090
 G28  C11  H112  single  0.970  0.020  1.090
 G28  C11  H113  single  0.970  0.020  1.090
 G28  C6   O6    single  1.397  0.020  1.397
 G28  C6   C7    single  1.536  0.020  1.536
 G28  C6   H6    single  0.970  0.020  1.090
 G28  C7   O7    double  1.220  0.020  1.220
 G28  C7   N8    single  1.358  0.020  1.358
 G28  N8   C81   single  1.458  0.020  1.458
 G28  N8   C9    single  1.459  0.020  1.459
 G28  C81  C82   single  1.523  0.020  1.523
 G28  C81  H811  single  0.970  0.020  1.090
 G28  C81  H812  single  0.970  0.020  1.090
 G28  C82  H821  single  0.970  0.020  1.090
 G28  C82  H822  single  0.970  0.020  1.090
 G28  C82  H823  single  0.970  0.020  1.090
 G28  C9   C91   single  1.524  0.020  1.524
 G28  C9   H91   single  0.970  0.020  1.090
 G28  C9   H92   single  0.970  0.020  1.090
 G28  C91  H911  single  0.970  0.020  1.090
 G28  C91  H912  single  0.970  0.020  1.090
 G28  C91  H913  single  0.970  0.020  1.090
 G28  N4   HN41  single  0.890  0.020  1.040
 G28  N4   HN42  single  0.890  0.020  1.040

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
 G28  C2    C1   O1B   118.62  3.000
 G28  C2    C1   O1A   114.29  3.000
 G28  O1B   C1   O1A   127.09  3.000
 G28  H2    C2   O6    109.68  3.000
 G28  H2    C2   C3    108.24  3.000
 G28  O6    C2   C3    110.82  3.000
 G28  H2    C2   C1    107.72  3.000
 G28  O6    C2   C1    109.05  3.000
 G28  C3    C2   C1    111.27  3.000
 G28  H32   C3   H31   106.51  3.000
 G28  H32   C3   C4    108.95  3.000
 G28  H31   C3   C4    110.10  3.000
 G28  H32   C3   C2    110.41  3.000
 G28  H31   C3   C2    109.22  3.000
 G28  C4    C3   C2    111.52  3.000
 G28  H4    C4   N4    112.78  3.000
 G28  H4    C4   C5    106.95  3.000
 G28  N4    C4   C5    108.42  3.000
 G28  H4    C4   C3    108.41  3.000
 G28  N4    C4   C3    110.75  3.000
 G28  C5    C4   C3    109.42  3.000
 G28  H5    C5   C6    110.23  3.000
 G28  H5    C5   N5    107.27  3.000
 G28  C6    C5   N5    108.37  3.000
 G28  H5    C5   C4    108.06  3.000
 G28  C6    C5   C4    111.90  3.000
 G28  N5    C5   C4    110.91  3.000
 G28  HN5   N5   C10   118.69  3.000
 G28  HN5   N5   C5    117.78  3.000
 G28  C10   N5   C5    123.40  3.000
 G28  C11   C10  O10   121.73  3.000
 G28  C11   C10  N5    115.44  3.000
 G28  O10   C10  N5    122.83  3.000
 G28  H113  C11  H112  108.50  3.000
 G28  H113  C11  H111  107.27  3.000
 G28  H112  C11  H111  108.44  3.000
 G28  H113  C11  C10   109.36  3.000
 G28  H112  C11  C10   113.75  3.000
 G28  H111  C11  C10   109.32  3.000
 G28  H6    C6   C7    106.75  3.000
 G28  H6    C6   O6    104.63  3.000
 G28  C7    C6   O6    112.14  3.000
 G28  H6    C6   C5    106.50  3.000
 G28  C7    C6   C5    114.26  3.000
 G28  O6    C6   C5    111.78  3.000
 G28  C6    O6   C2    117.28  3.000
 G28  N8    C7   O7    121.87  3.000
 G28  N8    C7   C6    117.13  3.000
 G28  O7    C7   C6    120.99  3.000
 G28  C9    N8   C81   117.21  3.000
 G28  C9    N8   C7    123.70  3.000
 G28  C81   N8   C7    117.75  3.000
 G28  H812  C81  H811  106.54  3.000
 G28  H812  C81  C82   109.59  3.000
 G28  H811  C81  C82   109.64  3.000
 G28  H812  C81  N8    108.16  3.000
 G28  H811  C81  N8    107.14  3.000
 G28  C82   C81  N8    115.39  3.000
 G28  H823  C82  H822  108.32  3.000
 G28  H823  C82  H821  107.85  3.000
 G28  H822  C82  H821  107.43  3.000
 G28  H823  C82  C81   111.42  3.000
 G28  H822  C82  C81   112.04  3.000
 G28  H821  C82  C81   109.61  3.000
 G28  H92   C9   H91   105.08  3.000
 G28  H92   C9   C91   109.11  3.000
 G28  H91   C9   C91   109.49  3.000
 G28  H92   C9   N8    110.75  3.000
 G28  H91   C9   N8    107.12  3.000
 G28  C91   C9   N8    114.82  3.000
 G28  H913  C91  H912  107.90  3.000
 G28  H913  C91  H911  107.78  3.000
 G28  H912  C91  H911  107.60  3.000
 G28  H913  C91  C9    112.05  3.000
 G28  H912  C91  C9    111.92  3.000
 G28  H911  C91  C9    109.41  3.000
 G28  HN42  N4   HN41  106.23  3.000
 G28  HN42  N4   C4    109.83  3.000
 G28  HN41  N4   C4    109.69  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
 G28  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 G28  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 G28  CONST_03  C81   N8   C7   C6    180.00   0.0  0
 G28  CONST_05  C81   N8   C7   O7      0.00   0.0  0
 G28  CONST_07  HN5   N5   C10  O10   180.00   0.0  0
 G28  Var_01    C82   C81  N8   C7    -86.27  30.0  3
 G28  Var_02    C91   C9   N8   C7     75.86  30.0  3
 G28  Var_03    H111  C11  C10  N5   -120.64  30.0  3
 G28  Var_04    H821  C82  C81  N8    175.63  30.0  3
 G28  Var_05    H911  C91  C9   N8   -177.12  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
 G28  chir_01  C2  C1  C3  O6  negativ
 G28  chir_02  C4  N4  C5  C3  positiv
 G28  chir_03  C5  N5  C6  C4  negativ
 G28  chir_04  C6  O6  C7  C5  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
 G28  plan-1  C5   0.020
 G28  plan-1  N5   0.020
 G28  plan-1  C10  0.020
 G28  plan-1  O10  0.020
 G28  plan-1  C11  0.020
 G28  plan-1  HN5  0.020
 G28  plan-2  C6   0.020
 G28  plan-2  C7   0.020
 G28  plan-2  O7   0.020
 G28  plan-2  N8   0.020
 G28  plan-2  C81  0.020
 G28  plan-2  C9   0.020
 G28  plan-3  C1   0.020
 G28  plan-3  O1A  0.020
 G28  plan-3  O1B  0.020
 G28  plan-3  C2   0.020

