# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:23:14 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  35  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_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  OC    -1  -0.592   0.2252  -4.1232  -0.4995
 HTM  C1    C  C      0   0.376  -0.9034  -3.7685  -0.1244
 HTM  C2    C  C      0   0.176  -1.0972  -2.2715   0.0999
 HTM  C3    C  C1     0  -0.412  -2.2406  -1.7319   0.5237
 HTM  C4    C  CH1    0   0.066  -2.4504  -0.2561   0.6892
 HTM  C5    C  CH1    0  -0.190  -1.3143   0.4990   0.0107
 HTM  C6    C  CH1    0   0.335   0.0015  -0.2085   0.3374
 HTM  C8    C  CH2    0  -0.495   3.2835   1.2563  -0.1648
 HTM  C9    C  CH2    0  -0.144   4.7048   0.9387   0.2596
 HTM  C11   C  CH3    0  -0.781  -1.0596   4.2678   0.2405
 HTM  N5    N  NH1    0  -0.629  -1.2817   1.8751   0.4223
 HTM  O1B   O  O      0  -0.590  -1.8989  -4.4834   0.0900
 HTM  O4    O  OH1    0  -0.664  -3.6597   0.1820   0.1092
 HTM  O6    O  O2     0  -0.482   0.0011  -1.5269  -0.1782
 HTM  O7    O  O2     0  -0.481   1.0357   0.4810  -0.2363
 HTM  O9    O  OH1    0  -0.673   5.5391   2.0101  -0.1239
 HTM  O10   O  O      0  -0.503  -1.1395   2.7975  -1.6387
 HTM  H3    H  H      0   0.253  -3.0629  -2.3953   0.7560
 HTM  H4    H  HCH1   0   0.219  -2.4420  -0.0078   1.7621
 HTM  H5    H  HCH1   0   0.277  -1.4612   0.4672  -1.0719
 HTM  H6    H  HCH1   0   0.196   0.1237  -0.2720   1.4346
 HTM  H71   H  HCH2   0   0.207   2.3246   0.0152   1.3157
 HTM  H72   H  HCH2   0   0.215   2.6629  -0.8079  -0.2090
 HTM  H81   H  HCH2   0   0.234   3.2509   1.4004  -1.2483
 HTM  H82   H  HCH2   0   0.232   2.9590   2.1906   0.3014
 HTM  H91   H  HCH2   0   0.193   4.7359   0.7773   1.3456
 HTM  H92   H  HCH2   0   0.194   5.0230  -0.0025  -0.2081
 HTM  H111  H  HCH3   0   0.264  -1.8103   4.9362  -0.1798
 HTM  H112  H  HCH3   0   0.248  -1.1863   4.2395   1.3212
 HTM  H113  H  HCH3   0   0.266  -0.0825   4.6996   0.0215
 HTM  HN5   H  HNH1   0   0.399  -1.2686   2.0604   1.4129
 HTM  HO4   H  HOH1   0   0.455  -4.3860  -0.1446   0.6490
 HTM  HO9   H  HOH1   0   0.453   6.4383   1.7970   0.1405
 HTM  C7    C  CH2    0  -0.148   2.3329   0.1424   0.2252
 HTM  C10   C  C      0   0.526  -1.1612   2.9165  -0.4222

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    deloc   1.241  0.020  1.241
 HTM  C1   C2    single  1.526  0.020  1.526
 HTM  C1   O1B   deloc   1.244  0.020  1.244
 HTM  C2   C3    double  1.333  0.020  1.333
 HTM  C2   O6    single  1.356  0.020  1.356
 HTM  C3   C4    single  1.500  0.020  1.500
 HTM  C3   H3    single  0.930  0.020  1.080
 HTM  C4   C5    single  1.524  0.020  1.524
 HTM  C4   O4    single  1.411  0.020  1.411
 HTM  C4   H4    single  0.970  0.020  1.090
 HTM  C5   C6    single  1.529  0.020  1.529
 HTM  C5   N5    single  1.437  0.020  1.437
 HTM  C5   H5    single  0.970  0.020  1.090
 HTM  C6   O6    single  1.416  0.020  1.416
 HTM  C6   O7    single  1.369  0.020  1.369
 HTM  C6   H6    single  0.970  0.020  1.090
 HTM  C7   C8    single  1.515  0.020  1.515
 HTM  C7   O7    single  1.418  0.020  1.418
 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  1.509  0.020  1.509
 HTM  C10  N5    single  1.346  0.020  1.346
 HTM  C10  O10   double  1.223  0.020  1.223
 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  O1B   C1   C2    115.89  3.000
 HTM  O1B   C1   O1A   127.98  3.000
 HTM  C2    C1   O1A   116.13  3.000
 HTM  O6    C2   C3    122.52  3.000
 HTM  O6    C2   C1    113.93  3.000
 HTM  C3    C2   C1    123.54  3.000
 HTM  H3    C3   C4    118.25  3.000
 HTM  H3    C3   C2    118.16  3.000
 HTM  C4    C3   C2    123.59  3.000
 HTM  H4    C4   O4    109.69  3.000
 HTM  H4    C4   C5    108.45  3.000
 HTM  O4    C4   C5    107.59  3.000
 HTM  H4    C4   C3    109.17  3.000
 HTM  O4    C4   C3    112.34  3.000
 HTM  C5    C4   C3    109.53  3.000
 HTM  H5    C5   N5    108.34  3.000
 HTM  H5    C5   C6    108.29  3.000
 HTM  N5    C5   C6    111.25  3.000
 HTM  H5    C5   C4    109.05  3.000
 HTM  N5    C5   C4    111.35  3.000
 HTM  C6    C5   C4    108.49  3.000
 HTM  H6    C6   O7    111.18  3.000
 HTM  H6    C6   O6    107.94  3.000
 HTM  O7    C6   O6    108.46  3.000
 HTM  H6    C6   C5    109.49  3.000
 HTM  O7    C6   C5    109.11  3.000
 HTM  O6    C6   C5    110.66  3.000
 HTM  H82   C8   H81   107.51  3.000
 HTM  H82   C8   C9    109.73  3.000
 HTM  H81   C8   C9    109.43  3.000
 HTM  H82   C8   C7    109.40  3.000
 HTM  H81   C8   C7    109.46  3.000
 HTM  C9    C8   C7    111.22  3.000
 HTM  H92   C9   H91   106.67  3.000
 HTM  H92   C9   O9    111.33  3.000
 HTM  H91   C9   O9    111.32  3.000
 HTM  H92   C9   C8    109.38  3.000
 HTM  H91   C9   C8    109.50  3.000
 HTM  O9    C9   C8    108.60  3.000
 HTM  H113  C11  H112  108.31  3.000
 HTM  H113  C11  H111  107.28  3.000
 HTM  H112  C11  H111  108.59  3.000
 HTM  H113  C11  C10   109.08  3.000
 HTM  H112  C11  C10   113.89  3.000
 HTM  H111  C11  C10   109.49  3.000
 HTM  HN5   N5   C10   118.24  3.000
 HTM  HN5   N5   C5    117.25  3.000
 HTM  C10   N5   C5    124.28  3.000
 HTM  HO4   O4   C4    108.12  3.000
 HTM  C6    O6   C2    115.91  3.000
 HTM  C7    O7   C6    115.75  3.000
 HTM  HO9   O9   C9    108.06  3.000
 HTM  H72   C7   H71   107.19  3.000
 HTM  H72   C7   O7    110.71  3.000
 HTM  H71   C7   O7    110.13  3.000
 HTM  H72   C7   C8    110.28  3.000
 HTM  H71   C7   C8    110.21  3.000
 HTM  O7    C7   C8    108.34  3.000
 HTM  O10   C10  N5    123.41  3.000
 HTM  O10   C10  C11   121.54  3.000
 HTM  N5    C10  C11   115.05  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  HN5   N5   C10  C11     0.00   0.0  0
 HTM  Var_01    O6    C2   C3   C4      2.30  30.0  1
 HTM  Var_02    C3    C2   C1   O1A  -178.83  30.0  2
 HTM  Var_03    C8    C7   O7   C6   -162.48  30.0  1
 HTM  Var_04    O9    C9   C8   C7   -179.76  30.0  3
 HTM  Var_05    O7    C7   C8   C9   -178.15  30.0  1
 HTM  Var_06    H111  C11  C10  N5   -126.98  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

