# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:27:41 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2S,4S,5R,6R)-5-(acetylamino)-2,4-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(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
 SLM  SLM  '(2S,4S,5R,6R)-5-(acetylamino)-2,4-dihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxamide (non-preferred name)'  D-saccharide  41  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_SLM
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
 SLM  C1    C  C     0   0.454   1.2261   3.1271   0.6387
 SLM  C2    C  CT    0   0.408   0.3556   2.1434  -0.1754
 SLM  C3    C  CH2   0  -0.516  -1.1097   2.3665   0.1888
 SLM  C4    C  CH1   0   0.071  -1.9921   1.2503  -0.3614
 SLM  C5    C  CH1   0  -0.115  -1.4472  -0.1006   0.0918
 SLM  C6    C  CH1   0   0.027   0.0369  -0.2228  -0.2852
 SLM  C7    C  CH1   0  -0.032   0.6907  -1.4629   0.3210
 SLM  C8    C  CH1   0  -0.012   2.1312  -1.6678  -0.1895
 SLM  C9    C  CH2   0  -0.163   2.7090  -2.9686   0.3448
 SLM  C11   C  CH3   0  -0.782  -3.7186  -3.0362  -0.6817
 SLM  N5    N  NH1   0  -0.635  -2.1894  -1.1820  -0.5045
 SLM  O1A   O  O     0  -0.471   1.5637   2.8690   1.7806
 SLM  O2    O  OH1   0  -0.663   0.4779   2.3324  -1.5525
 SLM  O4    O  OH1   0  -0.661  -3.3137   1.3583   0.1068
 SLM  O6    O  O2    0  -0.516   0.7812   0.8755   0.2119
 SLM  O7    O  OH1   0  -0.661   0.6479  -1.4235   1.7274
 SLM  O8    O  OH1   0  -0.660   2.1915  -1.6107  -1.5967
 SLM  O9    O  OH1   0  -0.671   4.0569  -3.0628  -0.0540
 SLM  N1    N  NH2   0  -0.793   1.5039   4.2712   0.0081
 SLM  O10   O  O     0  -0.499  -3.1572  -1.9764   1.3819
 SLM  H11N  H  HNH2  0   0.410   1.2047   4.4464  -0.9356
 SLM  H12N  H  HNH2  0   0.408   2.0223   4.9963   0.4769
 SLM  H31C  H  HCH2  0   0.261  -1.2010   2.3891   1.2781
 SLM  H32C  H  HCH2  0   0.267  -1.4419   3.3382  -0.1860
 SLM  H2    H  HOH1  0   0.459   1.3803   2.1291  -1.8311
 SLM  H4    H  HCH1  0   0.214  -1.9691   1.2815  -1.4598
 SLM  H5    H  HCH1  0   0.266  -1.5514  -0.1787   1.1758
 SLM  HA    H  HOH1  0   0.454  -3.7244   2.1181  -0.3176
 SLM  H6    H  HCH1  0   0.234   0.1157  -0.2820  -1.3778
 SLM  HB    H  HNH1  0   0.397  -2.1618  -1.2600  -1.5094
 SLM  H7    H  HCH1  0   0.245   0.0965  -2.3331   0.0192
 SLM  H8    H  HCH1  0   0.233   2.7534  -0.8399   0.1680
 SLM  HC    H  HOH1  0   0.444   1.0666  -0.6033   2.0147
 SLM  H91C  H  HCH2  0   0.208   2.6078  -2.9859   1.4347
 SLM  H92C  H  HCH2  0   0.188   2.1131  -3.8098  -0.0442
 SLM  HD    H  HOH1  0   0.444   1.7377  -2.3807  -1.9576
 SLM  H9    H  HOH1  0   0.455   4.4291  -3.8544   0.3442
 SLM  H111  H  HCH3  0   0.248  -3.5221  -2.9363  -1.7475
 SLM  H112  H  HCH3  0   0.267  -3.4192  -4.0368  -0.3699
 SLM  H113  H  HCH3  0   0.265  -4.7930  -2.9548  -0.5187
 SLM  C10   C  C     0   0.526  -3.0052  -2.0154   0.1699

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
 SLM  C1   C2    single  1.545  0.020  1.545
 SLM  C1   O1A   double  1.218  0.020  1.218
 SLM  C1   N1    single  1.336  0.020  1.336
 SLM  C2   C3    single  1.526  0.020  1.526
 SLM  C2   O2    single  1.395  0.020  1.395
 SLM  C2   O6    single  1.392  0.020  1.392
 SLM  C3   C4    single  1.526  0.020  1.526
 SLM  C4   C5    single  1.526  0.020  1.526
 SLM  C4   O4    single  1.406  0.020  1.406
 SLM  C5   C6    single  1.536  0.020  1.536
 SLM  C5   N5    single  1.441  0.020  1.441
 SLM  C6   C7    single  1.527  0.020  1.527
 SLM  C6   O6    single  1.417  0.020  1.417
 SLM  C7   C8    single  1.542  0.020  1.542
 SLM  C7   O7    single  1.408  0.020  1.408
 SLM  C8   C9    single  1.520  0.020  1.520
 SLM  C8   O8    single  1.410  0.020  1.410
 SLM  C9   O9    single  1.409  0.020  1.409
 SLM  C10  C11   single  1.509  0.020  1.509
 SLM  C10  N5    single  1.347  0.020  1.347
 SLM  C10  O10   double  1.222  0.020  1.222
 SLM  N1   H11N  single  0.860  0.020  1.020
 SLM  N1   H12N  single  0.860  0.020  1.020
 SLM  C3   H31C  single  0.970  0.020  1.090
 SLM  C3   H32C  single  0.970  0.020  1.090
 SLM  O2   H2    single  0.850  0.020  0.980
 SLM  C4   H4    single  0.970  0.020  1.090
 SLM  C5   H5    single  0.970  0.020  1.090
 SLM  O4   HA    single  0.850  0.020  0.980
 SLM  C6   H6    single  0.970  0.020  1.090
 SLM  N5   HB    single  0.860  0.020  1.020
 SLM  C7   H7    single  0.970  0.020  1.090
 SLM  C8   H8    single  0.970  0.020  1.090
 SLM  O7   HC    single  0.850  0.020  0.980
 SLM  C9   H91C  single  0.970  0.020  1.090
 SLM  C9   H92C  single  0.970  0.020  1.090
 SLM  O8   HD    single  0.850  0.020  0.980
 SLM  O9   H9    single  0.850  0.020  0.980
 SLM  C11  H111  single  0.970  0.020  1.090
 SLM  C11  H112  single  0.970  0.020  1.090
 SLM  C11  H113  single  0.970  0.020  1.090

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
 SLM  N1    C1   O1A   124.49  3.000
 SLM  N1    C1   C2    114.44  3.000
 SLM  O1A   C1   C2    120.99  3.000
 SLM  O6    C2   O2    111.78  3.000
 SLM  O6    C2   C3    111.11  3.000
 SLM  O2    C2   C3    107.45  3.000
 SLM  O6    C2   C1    105.13  3.000
 SLM  O2    C2   C1    112.60  3.000
 SLM  C3    C2   C1    108.79  3.000
 SLM  H32C  C3   H31C  107.32  3.000
 SLM  H32C  C3   C4    110.54  3.000
 SLM  H31C  C3   C4    109.03  3.000
 SLM  H32C  C3   C2    109.87  3.000
 SLM  H31C  C3   C2    108.72  3.000
 SLM  C4    C3   C2    111.25  3.000
 SLM  H4    C4   O4    110.50  3.000
 SLM  H4    C4   C5    108.33  3.000
 SLM  O4    C4   C5    107.74  3.000
 SLM  H4    C4   C3    109.12  3.000
 SLM  O4    C4   C3    111.55  3.000
 SLM  C5    C4   C3    109.52  3.000
 SLM  H5    C5   N5    107.94  3.000
 SLM  H5    C5   C6    109.28  3.000
 SLM  N5    C5   C6    109.66  3.000
 SLM  H5    C5   C4    108.92  3.000
 SLM  N5    C5   C4    110.96  3.000
 SLM  C6    C5   C4    110.04  3.000
 SLM  H6    C6   O6    110.70  3.000
 SLM  H6    C6   C7    108.70  3.000
 SLM  O6    C6   C7    105.38  3.000
 SLM  H6    C6   C5    108.55  3.000
 SLM  O6    C6   C5    111.09  3.000
 SLM  C7    C6   C5    112.38  3.000
 SLM  H7    C7   O7    106.31  3.000
 SLM  H7    C7   C8    108.04  3.000
 SLM  O7    C7   C8    111.27  3.000
 SLM  H7    C7   C6    107.65  3.000
 SLM  O7    C7   C6    111.15  3.000
 SLM  C8    C7   C6    112.11  3.000
 SLM  H8    C8   O8    105.71  3.000
 SLM  H8    C8   C9    108.43  3.000
 SLM  O8    C8   C9    111.67  3.000
 SLM  H8    C8   C7    108.79  3.000
 SLM  O8    C8   C7    111.41  3.000
 SLM  C9    C8   C7    110.64  3.000
 SLM  H92C  C9   H91C  106.83  3.000
 SLM  H92C  C9   O9    111.50  3.000
 SLM  H91C  C9   O9    111.67  3.000
 SLM  H92C  C9   C8    108.88  3.000
 SLM  H91C  C9   C8    109.16  3.000
 SLM  O9    C9   C8    108.74  3.000
 SLM  H113  C11  H112  107.26  3.000
 SLM  H113  C11  H111  108.52  3.000
 SLM  H112  C11  H111  108.35  3.000
 SLM  H113  C11  C10   109.34  3.000
 SLM  H112  C11  C10   109.25  3.000
 SLM  H111  C11  C10   113.91  3.000
 SLM  HB    N5   C10   117.88  3.000
 SLM  HB    N5   C5    117.16  3.000
 SLM  C10   N5   C5    124.68  3.000
 SLM  H2    O2   C2    109.75  3.000
 SLM  HA    O4   C4    108.35  3.000
 SLM  C6    O6   C2    116.60  3.000
 SLM  HC    O7   C7    107.95  3.000
 SLM  HD    O8   C8    108.74  3.000
 SLM  H9    O9   C9    107.96  3.000
 SLM  H12N  N1   H11N  117.69  3.000
 SLM  H12N  N1   C1    120.27  3.000
 SLM  H11N  N1   C1    122.04  3.000
 SLM  O10   C10  N5    123.51  3.000
 SLM  O10   C10  C11   121.51  3.000
 SLM  N5    C10  C11   114.98  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
 SLM  CONST_01  C11   C10  N5   C5   180.00   0.0  0
 SLM  CONST_02  O10   C10  N5   C5     0.00   0.0  0
 SLM  CONST_03  H11N  N1   C1   C2     0.00   0.0  0
 SLM  CONST_04  H12N  N1   C1   C2   180.00   0.0  0
 SLM  CONST_05  HB    N5   C10  C11    0.00   0.0  0
 SLM  Var_01    H111  C11  C10  N5    -3.03  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
 SLM  chir_01  C2  C3  O2  O6  positiv
 SLM  chir_02  C4  O4  C5  C3  positiv
 SLM  chir_03  C5  N5  C6  C4  negativ
 SLM  chir_04  C6  O6  C7  C5  negativ
 SLM  chir_05  C7  O7  C6  C8  negativ
 SLM  chir_06  C8  O8  C7  C9  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
 SLM  plan-1  C1    0.020
 SLM  plan-1  C2    0.020
 SLM  plan-1  O1A   0.020
 SLM  plan-1  N1    0.020
 SLM  plan-1  H11N  0.020
 SLM  plan-1  H12N  0.020
 SLM  plan-2  C5    0.020
 SLM  plan-2  C11   0.020
 SLM  plan-2  N5    0.020
 SLM  plan-2  O10   0.020
 SLM  plan-2  HB    0.020
 SLM  plan-2  C10   0.020

