# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:44:09 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: S-[2-(acetylamino)ethyl] (2Z)-dec-2-enethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC\C=C/C(=O)SCCNC(C)=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
 DAC  DAC  'S-[2-(acetylamino)ethyl] (2Z)-dec-2-enethioate'  ligand  43  18  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DAC
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
 DAC  C1    C  C     0   0.221  -0.9351   0.0547    0.9167
 DAC  O1    O  O     0  -0.396   0.1855   0.3989    0.6229
 DAC  C2    C  C1    0  -0.324  -2.0352  -0.2032   -0.0166
 DAC  C3    C  C1    0  -0.132  -1.9259  -0.1714   -1.3509
 DAC  C4    C  CH2   0  -0.480  -0.7218   0.1162   -2.1884
 DAC  C5    C  CH2   0  -0.435  -0.9425  -0.2115   -3.6611
 DAC  C6    C  CH2   0  -0.415   0.2780   0.0994   -4.5159
 DAC  C7    C  CH2   0  -0.412   0.0779  -0.2297   -5.9894
 DAC  C8    C  CH2   0  -0.407   1.3014   0.0768   -6.8433
 DAC  C9    C  CH2   0  -0.419   1.1065  -0.2522   -8.3180
 DAC  C10   C  CH3   0  -0.662   2.3378   0.0526   -9.1598
 DAC  S     S  S2    0   0.006  -1.4357  -0.2014    2.6028
 DAC  C1'   C  CH2   0  -0.602   0.1026   0.1743    3.4796
 DAC  C2'   C  CH2   0  -0.240  -0.1209  -0.0546    4.9665
 DAC  N3'   N  NH1   0  -0.633   1.1065   0.2265    5.6779
 DAC  C4'   C  C     0   0.525   1.1677   0.2758    7.0185
 DAC  O4'   O  O     0  -0.508   0.1830   0.0995    7.7243
 DAC  C5'   C  CH3   0  -0.775   2.5264   0.5758    7.5991
 DAC  H2    H  H     0   0.272  -2.9979  -0.4418    0.4206
 DAC  H3    H  H     0   0.264  -2.8402  -0.3825   -1.8991
 DAC  H41   H  HCH2  0   0.252   0.1436  -0.4320   -1.8087
 DAC  H42   H  HCH2  0   0.255  -0.4610   1.1752   -2.0834
 DAC  H51   H  HCH2  0   0.221  -1.8047   0.3505   -4.0354
 DAC  H52   H  HCH2  0   0.223  -1.2001  -1.2706   -3.7644
 DAC  H61   H  HCH2  0   0.211   1.1407  -0.4576   -4.1331
 DAC  H62   H  HCH2  0   0.211   0.5337   1.1597   -4.4110
 DAC  H71   H  HCH2  0   0.208  -0.7830   0.3290   -6.3733
 DAC  H72   H  HCH2  0   0.208  -0.1803  -1.2896   -6.0921
 DAC  H81   H  HCH2  0   0.206   2.1622  -0.4816   -6.4585
 DAC  H82   H  HCH2  0   0.206   1.5602   1.1367   -6.7403
 DAC  H91   H  HCH2  0   0.210   0.2495   0.3091   -8.7037
 DAC  H92   H  HCH2  0   0.210   0.8452  -1.3101   -8.4205
 DAC  H101  H  HCH3  0   0.225   2.1801  -0.1989  -10.2093
 DAC  H102  H  HCH3  0   0.215   2.5981   1.1117   -9.1093
 DAC  H103  H  HCH3  0   0.215   3.2034  -0.5140   -8.8107
 DAC  H1'1  H  HCH2  0   0.291   0.8926  -0.4767    3.1032
 DAC  H1'2  H  HCH2  0   0.293   0.3830   1.2103    3.2882
 DAC  H2'1  H  HCH2  0   0.253  -0.9160   0.5984    5.3318
 DAC  H2'2  H  HCH2  0   0.249  -0.4407  -1.0852    5.1452
 DAC  HN'   H  HNH1  0   0.406   1.9535   0.3405    5.1455
 DAC  H5'1  H  HCH3  0   0.265   2.7878  -0.1937    8.3248
 DAC  H5'2  H  HCH3  0   0.249   3.3173   0.6317    6.8539
 DAC  H5'3  H  HCH3  0   0.268   2.4891   1.5258    8.1328

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
 DAC  C1   O1    double  1.209  0.020  1.209
 DAC  C1   C2    single  1.466  0.020  1.466
 DAC  C1   S     single  1.777  0.020  1.777
 DAC  C2   C3    double  1.339  0.020  1.339
 DAC  C2   H2    single  0.930  0.020  1.080
 DAC  C3   C4    single  1.495  0.020  1.495
 DAC  C3   H3    single  0.930  0.020  1.080
 DAC  C4   C5    single  1.525  0.020  1.525
 DAC  C4   H41   single  0.970  0.020  1.090
 DAC  C4   H42   single  0.970  0.020  1.090
 DAC  C5   C6    single  1.522  0.020  1.522
 DAC  C5   H51   single  0.970  0.020  1.090
 DAC  C5   H52   single  0.970  0.020  1.090
 DAC  C6   C7    single  1.523  0.020  1.523
 DAC  C6   H61   single  0.970  0.020  1.090
 DAC  C6   H62   single  0.970  0.020  1.090
 DAC  C7   C8    single  1.523  0.020  1.523
 DAC  C7   H71   single  0.970  0.020  1.090
 DAC  C7   H72   single  0.970  0.020  1.090
 DAC  C8   C9    single  1.523  0.020  1.523
 DAC  C8   H81   single  0.970  0.020  1.090
 DAC  C8   H82   single  0.970  0.020  1.090
 DAC  C9   C10   single  1.522  0.020  1.522
 DAC  C9   H91   single  0.970  0.020  1.090
 DAC  C9   H92   single  0.970  0.020  1.090
 DAC  C10  H101  single  0.970  0.020  1.090
 DAC  C10  H102  single  0.970  0.020  1.090
 DAC  C10  H103  single  0.970  0.020  1.090
 DAC  S    C1'   single  1.810  0.020  1.810
 DAC  C1'  C2'   single  1.521  0.020  1.521
 DAC  C1'  H1'1  single  0.970  0.020  1.090
 DAC  C1'  H1'2  single  0.970  0.020  1.090
 DAC  C2'  N3'   single  1.446  0.020  1.446
 DAC  C2'  H2'1  single  0.970  0.020  1.090
 DAC  C2'  H2'2  single  0.970  0.020  1.090
 DAC  N3'  C4'   single  1.343  0.020  1.343
 DAC  N3'  HN'   single  0.860  0.020  1.020
 DAC  C4'  O4'   double  1.224  0.020  1.224
 DAC  C4'  C5'   single  1.508  0.020  1.508
 DAC  C5'  H5'1  single  0.970  0.020  1.090
 DAC  C5'  H5'2  single  0.970  0.020  1.090
 DAC  C5'  H5'3  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
 DAC  S     C1   C2    111.56  3.000
 DAC  S     C1   O1    122.19  3.000
 DAC  C2    C1   O1    126.25  3.000
 DAC  H2    C2   C3    118.66  3.000
 DAC  H2    C2   C1    116.65  3.000
 DAC  C3    C2   C1    124.69  3.000
 DAC  H3    C3   C4    115.62  3.000
 DAC  H3    C3   C2    115.43  3.000
 DAC  C4    C3   C2    128.95  3.000
 DAC  H42   C4   H41   105.26  3.000
 DAC  H42   C4   C5    109.56  3.000
 DAC  H41   C4   C5    110.03  3.000
 DAC  H42   C4   C3    108.90  3.000
 DAC  H41   C4   C3    110.29  3.000
 DAC  C5    C4   C3    112.53  3.000
 DAC  H52   C5   H51   106.20  3.000
 DAC  H52   C5   C6    109.47  3.000
 DAC  H51   C5   C6    109.55  3.000
 DAC  H52   C5   C4    109.45  3.000
 DAC  H51   C5   C4    109.50  3.000
 DAC  C6    C5   C4    112.48  3.000
 DAC  H62   C6   H61   105.95  3.000
 DAC  H62   C6   C7    109.41  3.000
 DAC  H61   C6   C7    109.36  3.000
 DAC  H62   C6   C5    109.33  3.000
 DAC  H61   C6   C5    109.35  3.000
 DAC  C7    C6   C5    113.19  3.000
 DAC  H72   C7   H71   105.98  3.000
 DAC  H72   C7   C8    109.35  3.000
 DAC  H71   C7   C8    109.39  3.000
 DAC  H72   C7   C6    109.31  3.000
 DAC  H71   C7   C6    109.39  3.000
 DAC  C8    C7   C6    113.16  3.000
 DAC  H82   C8   H81   105.92  3.000
 DAC  H82   C8   C9    109.28  3.000
 DAC  H81   C8   C9    109.29  3.000
 DAC  H82   C8   C7    109.37  3.000
 DAC  H81   C8   C7    109.36  3.000
 DAC  C9    C8   C7    113.36  3.000
 DAC  H92   C9   H91   106.00  3.000
 DAC  H92   C9   C10   109.56  3.000
 DAC  H91   C9   C10   109.62  3.000
 DAC  H92   C9   C8    109.26  3.000
 DAC  H91   C9   C8    109.30  3.000
 DAC  C10   C9   C8    112.86  3.000
 DAC  H103  C10  H102  107.43  3.000
 DAC  H103  C10  H101  107.62  3.000
 DAC  H102  C10  H101  107.61  3.000
 DAC  H103  C10  C9    111.13  3.000
 DAC  H102  C10  C9    111.19  3.000
 DAC  H101  C10  C9    111.65  3.000
 DAC  C1'   S    C1    100.97  3.000
 DAC  H1'2  C1'  H1'1  108.69  3.000
 DAC  H1'2  C1'  C2'   110.64  3.000
 DAC  H1'1  C1'  C2'   110.73  3.000
 DAC  H1'2  C1'  S     109.31  3.000
 DAC  H1'1  C1'  S     108.93  3.000
 DAC  C2'   C1'  S     108.51  3.000
 DAC  H2'2  C2'  H2'1  107.22  3.000
 DAC  H2'2  C2'  N3'   110.55  3.000
 DAC  H2'1  C2'  N3'   109.71  3.000
 DAC  H2'2  C2'  C1'   110.15  3.000
 DAC  H2'1  C2'  C1'   110.12  3.000
 DAC  N3'   C2'  C1'   109.08  3.000
 DAC  HN'   N3'  C4'   119.04  3.000
 DAC  HN'   N3'  C2'   118.41  3.000
 DAC  C4'   N3'  C2'   122.47  3.000
 DAC  C5'   C4'  O4'   122.10  3.000
 DAC  C5'   C4'  N3'   115.65  3.000
 DAC  O4'   C4'  N3'   122.25  3.000
 DAC  H5'3  C5'  H5'2  108.39  3.000
 DAC  H5'3  C5'  H5'1  107.31  3.000
 DAC  H5'2  C5'  H5'1  108.54  3.000
 DAC  H5'3  C5'  C4'   109.33  3.000
 DAC  H5'2  C5'  C4'   113.67  3.000
 DAC  H5'1  C5'  C4'   109.40  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
 DAC  CONST_01  O4'   C4'  N3'  C2'     0.00   0.0  0
 DAC  CONST_02  C5'   C4'  N3'  C2'   180.00   0.0  0
 DAC  CONST_03  HN'   N3'  C4'  O4'   180.00   0.0  0
 DAC  Var_01    C4    C3   C2   C1      0.14   0.0  2
 DAC  Var_02    C2'   C1'  S    C1   -177.53  30.0  3
 DAC  Var_03    C3    C2   C1   O1      4.35  30.0  2
 DAC  Var_04    C5    C4   C3   C2    168.75  30.0  3
 DAC  Var_05    C6    C5   C4   C3    179.23  30.0  3
 DAC  Var_06    C7    C6   C5   C4    179.66  30.0  3
 DAC  Var_07    C8    C7   C6   C5   -179.79  30.0  3
 DAC  Var_08    C9    C8   C7   C6    179.94  30.0  3
 DAC  Var_09    C10   C9   C8   C7   -179.74  30.0  3
 DAC  Var_10    N3'   C2'  C1'  S     179.31  30.0  3
 DAC  Var_11    C4'   N3'  C2'  C1'   171.34  30.0  3
 DAC  Var_12    H101  C10  C9   C8    179.46  30.0  3
 DAC  Var_13    H5'1  C5'  C4'  N3'  -126.53  30.0  3

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
 DAC  plan-1  C2'  0.020
 DAC  plan-1  N3'  0.020
 DAC  plan-1  C4'  0.020
 DAC  plan-1  O4'  0.020
 DAC  plan-1  C5'  0.020
 DAC  plan-1  HN'  0.020
 DAC  plan-2  C1   0.020
 DAC  plan-2  O1   0.020
 DAC  plan-2  C2   0.020
 DAC  plan-2  S    0.020
 DAC  plan-3  C1   0.020
 DAC  plan-3  C2   0.020
 DAC  plan-3  C3   0.020
 DAC  plan-3  C4   0.020
 DAC  plan-3  H2   0.020
 DAC  plan-3  H3   0.020

