# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:33:32 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-hydroxypropyl 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]1OCCCO)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
 HTM  HTM  '3-hydroxypropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid'  L-saccharide  36  19  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HTM
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
 HTM  O1A   O  OH1   0  -0.583   0.3460  -4.0521  -0.4908
 HTM  C1    C  C     0   0.506  -0.8820  -3.7382  -0.1215
 HTM  C2    C  C     0   0.235  -1.0545  -2.2734   0.0820
 HTM  C3    C  C1    0  -0.362  -2.2080  -1.7707   0.5184
 HTM  C4    C  CH1   0   0.057  -2.4232  -0.2975   0.7075
 HTM  C5    C  CH1   0  -0.192  -1.3003   0.4787   0.0258
 HTM  C6    C  CH1   0   0.331   0.0328  -0.2105   0.3251
 HTM  C8    C  CH2   0  -0.496   3.2891   1.2800  -0.2544
 HTM  C9    C  CH2   0  -0.144   4.7200   0.9819   0.1524
 HTM  C11   C  CH3   0  -0.781  -1.0971   4.2449   0.2996
 HTM  N5    N  NH1   0  -0.631  -1.2811   1.8469   0.4573
 HTM  O1B   O  O     0  -0.430  -1.7716  -4.5372   0.0353
 HTM  O4    O  OH1   0  -0.657  -3.6433   0.1296   0.1560
 HTM  O6    O  O2    0  -0.487   0.0332  -1.5331  -0.2095
 HTM  O7    O  O2    0  -0.476   1.0449   0.4867  -0.2639
 HTM  O9    O  OH1   0  -0.672   5.5398   2.0484  -0.2730
 HTM  O10   O  O     0  -0.498  -1.1855   2.7932  -1.5949
 HTM  H1A   H  HOH1  0   0.490   0.4179  -5.0113  -0.6107
 HTM  H3    H  H     0   0.284  -3.0209  -2.4445   0.7542
 HTM  H4    H  HCH1  0   0.241  -2.3941  -0.0820   1.7861
 HTM  H5    H  HCH1  0   0.288  -1.4595   0.4612  -1.0555
 HTM  H6    H  HCH1  0   0.212   0.1758  -0.2950   1.4171
 HTM  H71   H  HCH2  0   0.212   2.3705   0.0604   1.2697
 HTM  H72   H  HCH2  0   0.219   2.6830  -0.7884  -0.2475
 HTM  H81   H  HCH2  0   0.236   3.2368   1.3996  -1.3401
 HTM  H82   H  HCH2  0   0.234   2.9654   2.2216   0.1973
 HTM  H91   H  HCH2  0   0.194   4.7709   0.8482   1.2414
 HTM  H92   H  HCH2  0   0.194   5.0360   0.0313  -0.2970
 HTM  H111  H  HCH3  0   0.268  -0.1186   4.6796   0.0923
 HTM  H112  H  HCH3  0   0.266  -1.8457   4.9167  -0.1188
 HTM  H113  H  HCH3  0   0.249  -1.2299   4.2038   1.3790
 HTM  HN5   H  HNH1  0   0.402  -1.2610   2.0205   1.4499
 HTM  HO4   H  HOH1  0   0.461  -4.3536  -0.1205   0.7552
 HTM  HO9   H  HOH1  0   0.454   6.4445   1.8493  -0.0164
 HTM  C7    C  CH2   0  -0.151   2.3568   0.1669   0.1775
 HTM  C10   C  C     0   0.527  -1.1911   2.9009  -0.3780

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
 HTM  O1A  C1    single  1.320  0.020  1.320
 HTM  O1A  H1A   single  0.850  0.020  0.980
 HTM  C1   C2    single  1.489  0.020  1.489
 HTM  C1   O1B   double  1.206  0.020  1.206
 HTM  C2   C3    double  1.332  0.020  1.332
 HTM  C2   O6    single  1.348  0.020  1.348
 HTM  C3   C4    single  1.501  0.020  1.501
 HTM  C3   H3    single  0.930  0.020  1.080
 HTM  C4   C5    single  1.526  0.020  1.526
 HTM  C4   O4    single  1.405  0.020  1.405
 HTM  C4   H4    single  0.970  0.020  1.090
 HTM  C5   C6    single  1.530  0.020  1.530
 HTM  C5   N5    single  1.435  0.020  1.435
 HTM  C5   H5    single  0.970  0.020  1.090
 HTM  C6   O6    single  1.426  0.020  1.426
 HTM  C6   O7    single  1.363  0.020  1.363
 HTM  C6   H6    single  0.970  0.020  1.090
 HTM  C7   C8    single  1.515  0.020  1.515
 HTM  C7   O7    single  1.421  0.020  1.421
 HTM  C7   H71   single  0.970  0.020  1.090
 HTM  C7   H72   single  0.970  0.020  1.090
 HTM  C8   C9    single  1.517  0.020  1.517
 HTM  C8   H81   single  0.970  0.020  1.090
 HTM  C8   H82   single  0.970  0.020  1.090
 HTM  C9   O9    single  1.411  0.020  1.411
 HTM  C9   H91   single  0.970  0.020  1.090
 HTM  C9   H92   single  0.970  0.020  1.090
 HTM  C10  C11   single  1.508  0.020  1.508
 HTM  C10  N5    single  1.348  0.020  1.348
 HTM  C10  O10   double  1.222  0.020  1.222
 HTM  C11  H111  single  0.970  0.020  1.090
 HTM  C11  H112  single  0.970  0.020  1.090
 HTM  C11  H113  single  0.970  0.020  1.090
 HTM  N5   HN5   single  0.860  0.020  1.020
 HTM  O4   HO4   single  0.850  0.020  0.980
 HTM  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
 HTM  H1A   O1A  C1    109.81  3.000
 HTM  O1B   C1   C2    123.27  3.000
 HTM  O1B   C1   O1A   124.40  3.000
 HTM  C2    C1   O1A   112.33  3.000
 HTM  O6    C2   C3    124.23  3.000
 HTM  O6    C2   C1    114.67  3.000
 HTM  C3    C2   C1    121.10  3.000
 HTM  H3    C3   C4    118.43  3.000
 HTM  H3    C3   C2    119.15  3.000
 HTM  C4    C3   C2    122.41  3.000
 HTM  H4    C4   O4    110.37  3.000
 HTM  H4    C4   C5    108.60  3.000
 HTM  O4    C4   C5    107.99  3.000
 HTM  H4    C4   C3    108.18  3.000
 HTM  O4    C4   C3    111.92  3.000
 HTM  C5    C4   C3    109.73  3.000
 HTM  H5    C5   N5    108.35  3.000
 HTM  H5    C5   C6    108.25  3.000
 HTM  N5    C5   C6    111.04  3.000
 HTM  H5    C5   C4    109.06  3.000
 HTM  N5    C5   C4    111.13  3.000
 HTM  C6    C5   C4    108.94  3.000
 HTM  H6    C6   O7    111.73  3.000
 HTM  H6    C6   O6    107.43  3.000
 HTM  O7    C6   O6    108.19  3.000
 HTM  H6    C6   C5    109.91  3.000
 HTM  O7    C6   C5    109.39  3.000
 HTM  O6    C6   C5    110.15  3.000
 HTM  H82   C8   H81   107.56  3.000
 HTM  H82   C8   C9    109.73  3.000
 HTM  H81   C8   C9    109.44  3.000
 HTM  H82   C8   C7    109.44  3.000
 HTM  H81   C8   C7    109.51  3.000
 HTM  C9    C8   C7    111.08  3.000
 HTM  H92   C9   H91   106.68  3.000
 HTM  H92   C9   O9    111.33  3.000
 HTM  H91   C9   O9    111.35  3.000
 HTM  H92   C9   C8    109.38  3.000
 HTM  H91   C9   C8    109.48  3.000
 HTM  O9    C9   C8    108.58  3.000
 HTM  H113  C11  H112  108.68  3.000
 HTM  H113  C11  H111  108.24  3.000
 HTM  H112  C11  H111  107.33  3.000
 HTM  H113  C11  C10   113.85  3.000
 HTM  H112  C11  C10   109.53  3.000
 HTM  H111  C11  C10   109.01  3.000
 HTM  HN5   N5   C10   118.32  3.000
 HTM  HN5   N5   C5    117.43  3.000
 HTM  C10   N5   C5    124.07  3.000
 HTM  HO4   O4   C4    108.50  3.000
 HTM  C6    O6   C2    115.35  3.000
 HTM  C7    O7   C6    115.87  3.000
 HTM  HO9   O9   C9    108.05  3.000
 HTM  H72   C7   H71   107.32  3.000
 HTM  H72   C7   O7    110.53  3.000
 HTM  H71   C7   O7    110.04  3.000
 HTM  H72   C7   C8    110.30  3.000
 HTM  H71   C7   C8    110.33  3.000
 HTM  O7    C7   C8    108.32  3.000
 HTM  O10   C10  N5    123.28  3.000
 HTM  O10   C10  C11   121.72  3.000
 HTM  N5    C10  C11   115.00  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
 HTM  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 HTM  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 HTM  CONST_03  H1A   O1A  C1   C2    180.00   0.0  0
 HTM  CONST_04  HN5   N5   C10  C11     0.00   0.0  0
 HTM  Var_01    O6    C2   C3   C4      1.23  30.0  1
 HTM  Var_02    C3    C2   C1   O1A  -176.75  30.0  2
 HTM  Var_03    C8    C7   O7   C6   -163.50  30.0  1
 HTM  Var_04    O9    C9   C8   C7   -179.96  30.0  3
 HTM  Var_05    O7    C7   C8   C9   -178.38  30.0  2
 HTM  Var_06    H111  C11  C10  N5    114.23  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
 HTM  chir_01  C4  C3  C5  O4  negativ
 HTM  chir_02  C5  N5  C4  C6  positiv
 HTM  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
 HTM  plan-1  C5   0.020
 HTM  plan-1  C11  0.020
 HTM  plan-1  N5   0.020
 HTM  plan-1  O10  0.020
 HTM  plan-1  HN5  0.020
 HTM  plan-1  C10  0.020
 HTM  plan-2  O1A  0.020
 HTM  plan-2  C1   0.020
 HTM  plan-2  C2   0.020
 HTM  plan-2  O1B  0.020
 HTM  plan-2  H1A  0.020

