# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:29:33 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1OC[C@H](O)CO)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
 DYM  DYM  '(2R)-2,3-dihydroxypropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid'  L-saccharide  36  20  .  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_DYM
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
 DYM  C1    C  C      0   0.376  -1.4520  -3.6933  -0.2006
 DYM  C2    C  CR6    0   0.176  -1.5088  -2.1927   0.0705
 DYM  C3    C  CR16   0  -0.413  -2.6076  -1.5553   0.4764
 DYM  C4    C  CR16   0   0.067  -2.6787  -0.0704   0.6775
 DYM  C5    C  CR16   0  -0.188  -1.4509   0.5880   0.0592
 DYM  C6    C  CR16   0   0.337  -0.2251  -0.2555   0.4073
 DYM  C8    C  CH1    0  -0.043   3.2358   0.7907  -0.0473
 DYM  C9    C  CH2    0  -0.166   4.5331   0.4247   0.6567
 DYM  C11   C  CH3    0  -0.782  -0.8333   4.3033   0.4215
 DYM  N5    N  NH1    0  -0.629  -1.2972   1.9416   0.5150
 DYM  O1A   O  OC    -1  -0.592  -0.3642  -4.1337  -0.6043
 DYM  O1B   O  O      0  -0.589  -2.5045  -4.3239   0.0053
 DYM  O4    O  OH1    0  -0.664  -3.8180   0.4993   0.0711
 DYM  O6    O  O      0  -0.481  -0.3355  -1.5504  -0.1519
 DYM  O7    O  O2     0  -0.478   0.8973   0.3388  -0.1075
 DYM  O8    O  OH1    0  -0.657   3.3603   0.7769  -1.4494
 DYM  O9    O  OH1    0  -0.668   5.5356   1.3305   0.2651
 DYM  O10   O  O      0  -0.502  -1.0083   2.9095  -1.5101
 DYM  H3    H  HCR6   0   0.254  -3.4972  -2.1409   0.6672
 DYM  H4    H  HCR6   0   0.218  -2.6844   0.1467   1.7572
 DYM  H5    H  HCR6   0   0.277  -1.5638   0.6019  -1.0277
 DYM  H6    H  HCR6   0   0.195  -0.1519  -0.3614   1.5057
 DYM  H71   H  HCH2   0   0.215   2.0752  -0.0942   1.5346
 DYM  H72   H  HCH2   0   0.217   2.3221  -1.1550   0.1429
 DYM  H8    H  HCH1   0   0.232   2.9774   1.8216   0.2178
 DYM  H91   H  HCH2   0   0.202   4.3631   0.4508   1.7406
 DYM  H92   H  HCH2   0   0.195   4.8020  -0.6117   0.4034
 DYM  H111  H  HCH3   0   0.264  -1.4650   5.0709  -0.0235
 DYM  H112  H  HCH3   0   0.248  -1.0375   4.2607   1.4897
 DYM  H113  H  HCH3   0   0.266   0.2028   4.6158   0.2848
 DYM  HN5   H  HNH1   0   0.399  -1.2915   2.0951   1.5112
 DYM  HO4   H  HOH1   0   0.454  -4.5931   0.2172   0.5664
 DYM  HO8   H  HOH1   0   0.443   3.6499  -0.1002  -1.7246
 DYM  HO9   H  HOH1   0   0.456   6.3486   1.0840   0.7145
 DYM  C7    C  CH2    0  -0.166   2.1190  -0.1176   0.4381
 DYM  C10   C  C      0   0.526  -1.0519   2.9917  -0.2912

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
 DYM  C1   C2    single  1.526  0.020  1.526
 DYM  C1   O1A   deloc   1.241  0.020  1.241
 DYM  C1   O1B   deloc   1.244  0.020  1.244
 DYM  C2   C3    double  1.334  0.020  1.334
 DYM  C2   O6    single  1.356  0.020  1.356
 DYM  C3   C4    single  1.500  0.020  1.500
 DYM  C3   H3    single  0.930  0.020  1.080
 DYM  C4   C5    single  1.524  0.020  1.524
 DYM  C4   O4    single  1.411  0.020  1.411
 DYM  C4   H4    single  0.970  0.020  1.090
 DYM  C5   C6    single  1.528  0.020  1.528
 DYM  C5   N5    single  1.437  0.020  1.437
 DYM  C5   H5    single  0.970  0.020  1.090
 DYM  C6   O6    single  1.415  0.020  1.415
 DYM  C6   O7    single  1.370  0.020  1.370
 DYM  C6   H6    single  0.970  0.020  1.090
 DYM  C7   C8    single  1.519  0.020  1.519
 DYM  C7   O7    single  1.414  0.020  1.414
 DYM  C7   H71   single  0.970  0.020  1.090
 DYM  C7   H72   single  0.970  0.020  1.090
 DYM  C8   C9    single  1.521  0.020  1.521
 DYM  C8   O8    single  1.408  0.020  1.408
 DYM  C8   H8    single  0.970  0.020  1.090
 DYM  C9   O9    single  1.407  0.020  1.407
 DYM  C9   H91   single  0.970  0.020  1.090
 DYM  C9   H92   single  0.970  0.020  1.090
 DYM  C10  C11   single  1.509  0.020  1.509
 DYM  C10  N5    single  1.346  0.020  1.346
 DYM  C10  O10   double  1.222  0.020  1.222
 DYM  C11  H111  single  0.970  0.020  1.090
 DYM  C11  H112  single  0.970  0.020  1.090
 DYM  C11  H113  single  0.970  0.020  1.090
 DYM  N5   HN5   single  0.860  0.020  1.020
 DYM  O4   HO4   single  0.850  0.020  0.980
 DYM  O8   HO8   single  0.850  0.020  0.980
 DYM  O9   HO9   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
 DYM  O1B   C1   O1A   127.98  3.000
 DYM  O1B   C1   C2    115.95  3.000
 DYM  O1A   C1   C2    116.07  3.000
 DYM  O6    C2   C3    122.45  3.000
 DYM  O6    C2   C1    113.86  3.000
 DYM  C3    C2   C1    123.69  3.000
 DYM  H3    C3   C4    118.24  3.000
 DYM  H3    C3   C2    118.19  3.000
 DYM  C4    C3   C2    123.57  3.000
 DYM  H4    C4   O4    109.73  3.000
 DYM  H4    C4   C5    108.46  3.000
 DYM  O4    C4   C5    107.56  3.000
 DYM  H4    C4   C3    109.07  3.000
 DYM  O4    C4   C3    112.36  3.000
 DYM  C5    C4   C3    109.57  3.000
 DYM  H5    C5   N5    108.34  3.000
 DYM  H5    C5   C6    108.44  3.000
 DYM  N5    C5   C6    111.22  3.000
 DYM  H5    C5   C4    109.01  3.000
 DYM  N5    C5   C4    111.38  3.000
 DYM  C6    C5   C4    108.38  3.000
 DYM  H6    C6   O7    111.13  3.000
 DYM  H6    C6   O6    108.06  3.000
 DYM  O7    C6   O6    108.20  3.000
 DYM  H6    C6   C5    109.40  3.000
 DYM  O7    C6   C5    109.39  3.000
 DYM  O6    C6   C5    110.64  3.000
 DYM  H8    C8   O8    105.74  3.000
 DYM  H8    C8   C9    108.40  3.000
 DYM  O8    C8   C9    112.53  3.000
 DYM  H8    C8   C7    108.18  3.000
 DYM  O8    C8   C7    112.18  3.000
 DYM  C9    C8   C7    109.59  3.000
 DYM  H92   C9   H91   106.72  3.000
 DYM  H92   C9   O9    111.61  3.000
 DYM  H91   C9   O9    111.71  3.000
 DYM  H92   C9   C8    109.19  3.000
 DYM  H91   C9   C8    108.62  3.000
 DYM  O9    C9   C8    108.91  3.000
 DYM  H113  C11  H112  108.20  3.000
 DYM  H113  C11  H111  107.33  3.000
 DYM  H112  C11  H111  108.65  3.000
 DYM  H113  C11  C10   109.12  3.000
 DYM  H112  C11  C10   113.74  3.000
 DYM  H111  C11  C10   109.61  3.000
 DYM  HN5   N5   C10   118.17  3.000
 DYM  HN5   N5   C5    117.23  3.000
 DYM  C10   N5   C5    124.36  3.000
 DYM  HO4   O4   C4    108.11  3.000
 DYM  C6    O6   C2    115.86  3.000
 DYM  C7    O7   C6    115.01  3.000
 DYM  HO8   O8   C8    108.66  3.000
 DYM  HO9   O9   C9    107.91  3.000
 DYM  H72   C7   H71   107.23  3.000
 DYM  H72   C7   O7    111.17  3.000
 DYM  H71   C7   O7    110.13  3.000
 DYM  H72   C7   C8    110.07  3.000
 DYM  H71   C7   C8    109.62  3.000
 DYM  O7    C7   C8    108.60  3.000
 DYM  O10   C10  N5    123.45  3.000
 DYM  O10   C10  C11   121.62  3.000
 DYM  N5    C10  C11   114.93  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
 DYM  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 DYM  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 DYM  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 DYM  Var_01    O6    C2   C3   C4      2.42  30.0  1
 DYM  Var_02    O1A   C1   C2   C3    178.32  30.0  2
 DYM  Var_03    C8    C7   O7   C6   -170.28  30.0  1
 DYM  Var_04    H111  C11  C10  N5   -129.83  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
 DYM  chir_01  C4  C3  C5  O4  negativ
 DYM  chir_02  C5  N5  C4  C6  positiv
 DYM  chir_03  C6  O7  O6  C5  positiv
 DYM  chir_04  C8  O8  C9  C7  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
 DYM  plan-1  C5   0.020
 DYM  plan-1  C11  0.020
 DYM  plan-1  N5   0.020
 DYM  plan-1  O10  0.020
 DYM  plan-1  HN5  0.020
 DYM  plan-1  C10  0.020
 DYM  plan-2  C1   0.020
 DYM  plan-2  C2   0.020
 DYM  plan-2  O1A  0.020
 DYM  plan-2  O1B  0.020

