# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:49:24 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-methylpropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CO[C@@H]1OC(=C[C@H](O)[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
 IEM  IEM  '2-methylpropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid'  L-saccharide  37  19  .  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_IEM
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
 IEM  C1    C  C      0   0.375   1.1846  -3.7225  -0.0523
 IEM  C2    C  C      0   0.176   0.2923  -2.4998   0.1448
 IEM  C3    C  C1     0  -0.416  -0.9882  -2.5743   0.5103
 IEM  C4    C  CH1    0   0.066  -1.8852  -1.3802   0.6481
 IEM  C5    C  CH1    0  -0.185  -1.2145  -0.1675   0.0168
 IEM  C6    C  CH1    0   0.336   0.2637  -0.1676   0.4107
 IEM  O7    O  O2     0  -0.480   0.8613   0.9393  -0.1221
 IEM  C7    C  CH2    0  -0.127   2.1192   1.3064   0.4156
 IEM  C8    C  CH1    0  -0.272   2.3541   2.7880   0.1696
 IEM  C9    C  CH3    0  -0.663   3.7097   3.1860   0.7439
 IEM  C10   C  CH3    0  -0.656   2.2619   3.1412  -1.3114
 IEM  C12   C  CH3    0  -0.782  -2.6518   3.3218   0.2753
 IEM  N5    N  NH1    0  -0.631  -1.8558   1.0535   0.4207
 IEM  O1A   O  OC    -1  -0.592   2.3609  -3.4931  -0.3743
 IEM  O1B   O  O      0  -0.589   0.6420  -4.8278   0.1269
 IEM  O4    O  OH1    0  -0.664  -3.1272  -1.5652   0.0045
 IEM  O6    O  O2     0  -0.483   0.9161  -1.3201  -0.0929
 IEM  O11   O  O      0  -0.501  -1.8874   2.0627  -1.6054
 IEM  H3    H  H      0   0.254  -1.4027  -3.5519   0.7171
 IEM  H4    H  HCH1   0   0.218  -2.0465  -1.1728   1.7180
 IEM  H5    H  HCH1   0   0.274  -1.2819  -0.2502  -1.0709
 IEM  H6    H  HCH1   0   0.195   0.3522  -0.1818   1.5127
 IEM  H71   H  HCH2   0   0.204   2.9228   0.7208  -0.0496
 IEM  H72   H  HCH2   0   0.213   2.1450   1.0983   1.4935
 IEM  H8    H  HCH1   0   0.222   1.5763   3.3415   0.7075
 IEM  H91   H  HCH3   0   0.233   3.8818   4.2561   0.6229
 IEM  H92   H  HCH3   0   0.228   3.7818   2.9599   1.8094
 IEM  H93   H  HCH3   0   0.218   4.5229   2.6621   0.2362
 IEM  H101  H  HCH3   0   0.236   1.2719   2.9347  -1.7175
 IEM  H102  H  HCH3   0   0.224   2.4695   4.2009  -1.4673
 IEM  H103  H  HCH3   0   0.211   2.9924   2.5742  -1.8942
 IEM  H121  H  HCH3   0   0.248  -2.9724   3.1492   1.3012
 IEM  H122  H  HCH3   0   0.266  -1.8875   4.1001   0.2851
 IEM  H123  H  HCH3   0   0.263  -3.4971   3.7027  -0.2954
 IEM  HN5   H  HNH1   0   0.398  -2.0298   1.1787   1.4055
 IEM  HO4   H  HOH1   0   0.454  -3.6143  -2.2447   0.4810
 IEM  C11   C  C      0   0.530  -2.0951   2.0934  -0.4015

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
 IEM  C1   C2    single  1.527  0.020  1.527
 IEM  C1   O1A   deloc   1.241  0.020  1.241
 IEM  C1   O1B   deloc   1.244  0.020  1.244
 IEM  C2   C3    double  1.334  0.020  1.334
 IEM  C2   O6    single  1.356  0.020  1.356
 IEM  C3   C4    single  1.500  0.020  1.500
 IEM  C3   H3    single  0.930  0.020  1.080
 IEM  C4   C5    single  1.523  0.020  1.523
 IEM  C4   O4    single  1.411  0.020  1.411
 IEM  C4   H4    single  0.970  0.020  1.090
 IEM  C5   C6    single  1.530  0.020  1.530
 IEM  C5   N5    single  1.437  0.020  1.437
 IEM  C5   H5    single  0.970  0.020  1.090
 IEM  C6   O7    single  1.366  0.020  1.366
 IEM  C6   O6    single  1.417  0.020  1.417
 IEM  C6   H6    single  0.970  0.020  1.090
 IEM  O7   C7    single  1.416  0.020  1.416
 IEM  C7   C8    single  1.520  0.020  1.520
 IEM  C7   H71   single  0.970  0.020  1.090
 IEM  C7   H72   single  0.970  0.020  1.090
 IEM  C8   C9    single  1.525  0.020  1.525
 IEM  C8   C10   single  1.525  0.020  1.525
 IEM  C8   H8    single  0.970  0.020  1.090
 IEM  C9   H91   single  0.970  0.020  1.090
 IEM  C9   H92   single  0.970  0.020  1.090
 IEM  C9   H93   single  0.970  0.020  1.090
 IEM  C10  H101  single  0.970  0.020  1.090
 IEM  C10  H102  single  0.970  0.020  1.090
 IEM  C10  H103  single  0.970  0.020  1.090
 IEM  C11  C12   single  1.509  0.020  1.509
 IEM  C11  N5    single  1.347  0.020  1.347
 IEM  C11  O11   double  1.222  0.020  1.222
 IEM  C12  H121  single  0.970  0.020  1.090
 IEM  C12  H122  single  0.970  0.020  1.090
 IEM  C12  H123  single  0.970  0.020  1.090
 IEM  N5   HN5   single  0.860  0.020  1.020
 IEM  O4   HO4   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
 IEM  O1B   C1   O1A   127.95  3.000
 IEM  O1B   C1   C2    115.98  3.000
 IEM  O1A   C1   C2    116.07  3.000
 IEM  O6    C2   C3    122.59  3.000
 IEM  O6    C2   C1    113.92  3.000
 IEM  C3    C2   C1    123.49  3.000
 IEM  H3    C3   C4    118.21  3.000
 IEM  H3    C3   C2    118.08  3.000
 IEM  C4    C3   C2    123.71  3.000
 IEM  H4    C4   O4    109.81  3.000
 IEM  H4    C4   C5    108.49  3.000
 IEM  O4    C4   C5    107.64  3.000
 IEM  H4    C4   C3    109.07  3.000
 IEM  O4    C4   C3    112.34  3.000
 IEM  C5    C4   C3    109.42  3.000
 IEM  H5    C5   N5    108.45  3.000
 IEM  H5    C5   C6    108.41  3.000
 IEM  N5    C5   C6    111.03  3.000
 IEM  H5    C5   C4    108.98  3.000
 IEM  N5    C5   C4    111.32  3.000
 IEM  C6    C5   C4    108.59  3.000
 IEM  H6    C6   O6    107.88  3.000
 IEM  H6    C6   O7    111.36  3.000
 IEM  O6    C6   O7    108.60  3.000
 IEM  H6    C6   C5    109.51  3.000
 IEM  O6    C6   C5    110.70  3.000
 IEM  O7    C6   C5    108.80  3.000
 IEM  C7    O7   C6    116.77  3.000
 IEM  H72   C7   H71   107.32  3.000
 IEM  H72   C7   C8    109.87  3.000
 IEM  H71   C7   C8    109.77  3.000
 IEM  H72   C7   O7    110.14  3.000
 IEM  H71   C7   O7    110.54  3.000
 IEM  C8    C7   O7    109.18  3.000
 IEM  H8    C8   C10   108.46  3.000
 IEM  H8    C8   C9    108.32  3.000
 IEM  C10   C8   C9    111.03  3.000
 IEM  H8    C8   C7    107.65  3.000
 IEM  C10   C8   C7    111.93  3.000
 IEM  C9    C8   C7    109.32  3.000
 IEM  H93   C9   H92   107.76  3.000
 IEM  H93   C9   H91   107.55  3.000
 IEM  H92   C9   H91   107.52  3.000
 IEM  H93   C9   C8    111.19  3.000
 IEM  H92   C9   C8    111.85  3.000
 IEM  H91   C9   C8    110.77  3.000
 IEM  H103  C10  H102  107.48  3.000
 IEM  H103  C10  H101  108.07  3.000
 IEM  H102  C10  H101  107.68  3.000
 IEM  H103  C10  C8    110.93  3.000
 IEM  H102  C10  C8    110.62  3.000
 IEM  H101  C10  C8    111.89  3.000
 IEM  H123  C12  H122  107.40  3.000
 IEM  H123  C12  H121  108.71  3.000
 IEM  H122  C12  H121  108.12  3.000
 IEM  H123  C12  C11   109.64  3.000
 IEM  H122  C12  C11   109.05  3.000
 IEM  H121  C12  C11   113.72  3.000
 IEM  HN5   N5   C11   118.02  3.000
 IEM  HN5   N5   C5    117.21  3.000
 IEM  C11   N5   C5    124.31  3.000
 IEM  HO4   O4   C4    108.19  3.000
 IEM  C6    O6   C2    115.70  3.000
 IEM  O11   C11  N5    123.48  3.000
 IEM  O11   C11  C12   121.67  3.000
 IEM  N5    C11  C12   114.85  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
 IEM  CONST_01  C12   C11  N5   C5    180.00   0.0  0
 IEM  CONST_02  O11   C11  N5   C5      0.00   0.0  0
 IEM  CONST_03  HN5   N5   C11  C12     0.00   0.0  0
 IEM  Var_01    O6    C2   C3   C4      2.35  30.0  1
 IEM  Var_02    O1A   C1   C2   C3   -178.96  30.0  2
 IEM  Var_03    C8    C7   O7   C6   -156.36  30.0  3
 IEM  Var_04    C9    C8   C7   O7   -179.84  30.0  3
 IEM  Var_05    H91   C9   C8   C7   -177.27  30.0  3
 IEM  Var_06    H101  C10  C8   C7     62.01  30.0  3
 IEM  Var_07    H121  C12  C11  N5    -11.43  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
 IEM  chir_01  C4  C3  C5  O4  negativ
 IEM  chir_02  C5  N5  C4  C6  positiv
 IEM  chir_03  C6  O7  O6  C5  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
 IEM  plan-1  C5   0.020
 IEM  plan-1  C12  0.020
 IEM  plan-1  N5   0.020
 IEM  plan-1  O11  0.020
 IEM  plan-1  HN5  0.020
 IEM  plan-1  C11  0.020
 IEM  plan-2  C1   0.020
 IEM  plan-2  C2   0.020
 IEM  plan-2  O1A  0.020
 IEM  plan-2  O1B  0.020

