# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:43:48 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)N[C@H]1CCSC1=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
 HT5  HT5  (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium  ligand  43  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HT5
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
 HT5  O1    O  O     0  -0.490  -1.6188   0.3338   1.7228
 HT5  C10   C  C     0   0.569  -1.5679   0.6060   0.5337
 HT5  N2    N  NH1   0  -0.637  -2.6724   0.7078  -0.2373
 HT5  SD    S  S2    0   0.030  -6.2516  -0.9389  -0.1793
 HT5  C11   C  CR15  0  -0.161  -3.9982   0.4963   0.2501
 HT5  C12   C  CR5   0   0.254  -4.4920  -0.9244  -0.0301
 HT5  O2    O  O     0  -0.370  -3.7992  -1.8974  -0.1345
 HT5  C13   C  CH2   0  -0.457  -5.0367   1.4386  -0.3374
 HT5  C14   C  CH2   0  -0.572  -6.3965   0.8669   0.0370
 HT5  C9    C  CH2   0  -0.586  -0.2708   0.9214  -0.1771
 HT5  C2    C  CH2   0  -0.415   0.9290   0.1710   0.3835
 HT5  C1    C  CH2   0  -0.416   2.2337   0.6054  -0.2726
 HT5  C50   C  CH2   0  -0.413   3.4471  -0.1334   0.2766
 HT5  C8    C  CH3   0  -0.662   9.8296  -0.1249  -0.3357
 HT5  C6    C  CH2   0  -0.420   8.5109  -0.6238   0.2384
 HT5  C3    C  CH2   0  -0.412   4.7635   0.3327  -0.3323
 HT5  C4    C  CH2   0  -0.412   5.9768  -0.3910   0.2380
 HT5  C5    C  CH2   0  -0.406   7.2987   0.0903  -0.3467
 HT5  H11   H  HCR5  0   0.310  -3.9911   0.6028   1.3405
 HT5  H141  H  HCH2  0   0.302  -7.1967   1.2325  -0.6019
 HT5  H142  H  HCH2  0   0.291  -6.6511   1.0798   1.0744
 HT5  H131  H  HCH2  0   0.283  -4.9210   2.4500   0.0503
 HT5  H132  H  HCH2  0   0.263  -4.9342   1.4762  -1.4250
 HT5  HA    H  HNH1  0   0.405  -2.5593   0.8602  -1.2273
 HT5  H9C1  H  HCH2  0   0.252  -0.3674   0.7352  -1.2497
 HT5  H9C2  H  HCH2  0   0.271  -0.1099   2.0007  -0.0739
 HT5  H2C1  H  HCH2  0   0.224   0.9948   0.3370   1.4611
 HT5  H2C2  H  HCH2  0   0.223   0.7903  -0.9052   0.2434
 HT5  H1C1  H  HCH2  0   0.212   2.1718   0.4521  -1.3554
 HT5  H1C2  H  HCH2  0   0.211   2.3670   1.6831  -0.1265
 HT5  H501  H  HCH2  0   0.208   3.4874  -0.0037   1.3639
 HT5  H502  H  HCH2  0   0.209   3.3280  -1.2090   0.1058
 HT5  H3C1  H  HCH2  0   0.207   4.7333   0.1933  -1.4186
 HT5  H3C2  H  HCH2  0   0.207   4.8742   1.4106  -0.1696
 HT5  H4C1  H  HCH2  0   0.206   5.9956  -0.2623   1.3260
 HT5  H4C2  H  HCH2  0   0.207   5.8732  -1.4678   0.0640
 HT5  H5C1  H  HCH2  0   0.205   7.3975   1.1687  -0.1788
 HT5  H5C2  H  HCH2  0   0.206   7.2880  -0.0449  -1.4341
 HT5  H6C1  H  HCH2  0   0.210   8.4171  -1.6998   0.0614
 HT5  H6C2  H  HCH2  0   0.210   8.5136  -0.4966   1.3256
 HT5  H8C1  H  HCH3  0   0.215   9.8716  -0.2730  -1.4165
 HT5  H8C2  H  HCH3  0   0.215   9.9623   0.9420  -0.1467
 HT5  H8C3  H  HCH3  0   0.225  10.6815  -0.6467   0.1018

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
 HT5  O2   C12   double  1.199  0.020  1.199
 HT5  C12  SD    single  1.766  0.020  1.766
 HT5  C12  C11   single  1.530  0.020  1.530
 HT5  SD   C14   single  1.824  0.020  1.824
 HT5  C14  C13   single  1.522  0.020  1.522
 HT5  C13  C11   single  1.520  0.020  1.520
 HT5  C11  N2    single  1.428  0.020  1.428
 HT5  N2   C10   single  1.351  0.020  1.351
 HT5  C10  O1    double  1.221  0.020  1.221
 HT5  C10  C9    single  1.512  0.020  1.512
 HT5  C9   C2    single  1.522  0.020  1.522
 HT5  C2   C1    single  1.524  0.020  1.524
 HT5  C1   C50   single  1.523  0.020  1.523
 HT5  C50  C3    single  1.523  0.020  1.523
 HT5  C3   C4    single  1.524  0.020  1.524
 HT5  C4   C5    single  1.523  0.020  1.523
 HT5  C5   C6    single  1.524  0.020  1.524
 HT5  C6   C8    single  1.522  0.020  1.522
 HT5  C11  H11   single  0.970  0.020  1.090
 HT5  C14  H141  single  0.970  0.020  1.090
 HT5  C14  H142  single  0.970  0.020  1.090
 HT5  C13  H131  single  0.970  0.020  1.090
 HT5  C13  H132  single  0.970  0.020  1.090
 HT5  N2   HA    single  0.860  0.020  1.020
 HT5  C9   H9C1  single  0.970  0.020  1.090
 HT5  C9   H9C2  single  0.970  0.020  1.090
 HT5  C2   H2C1  single  0.970  0.020  1.090
 HT5  C2   H2C2  single  0.970  0.020  1.090
 HT5  C1   H1C1  single  0.970  0.020  1.090
 HT5  C1   H1C2  single  0.970  0.020  1.090
 HT5  C50  H501  single  0.970  0.020  1.090
 HT5  C50  H502  single  0.970  0.020  1.090
 HT5  C3   H3C1  single  0.970  0.020  1.090
 HT5  C3   H3C2  single  0.970  0.020  1.090
 HT5  C4   H4C1  single  0.970  0.020  1.090
 HT5  C4   H4C2  single  0.970  0.020  1.090
 HT5  C5   H5C1  single  0.970  0.020  1.090
 HT5  C5   H5C2  single  0.970  0.020  1.090
 HT5  C6   H6C1  single  0.970  0.020  1.090
 HT5  C6   H6C2  single  0.970  0.020  1.090
 HT5  C8   H8C1  single  0.970  0.020  1.090
 HT5  C8   H8C2  single  0.970  0.020  1.090
 HT5  C8   H8C3  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
 HT5  C9    C10  N2    114.66  3.000
 HT5  C9    C10  O1    122.69  3.000
 HT5  N2    C10  O1    122.59  3.000
 HT5  HA    N2   C11   117.49  3.000
 HT5  HA    N2   C10   118.70  3.000
 HT5  C11   N2   C10   123.58  3.000
 HT5  C14   SD   C12    93.50  3.000
 HT5  H11   C11  C13   109.19  3.000
 HT5  H11   C11  C12   105.94  3.000
 HT5  C13   C11  C12   106.51  3.000
 HT5  H11   C11  N2    108.62  3.000
 HT5  C13   C11  N2    114.23  3.000
 HT5  C12   C11  N2    112.00  3.000
 HT5  O2    C12  C11   125.66  3.000
 HT5  C11   C12  SD    110.16  3.000
 HT5  O2    C12  SD    124.17  3.000
 HT5  H132  C13  H131  108.19  3.000
 HT5  H132  C13  C14   109.97  3.000
 HT5  H131  C13  C14   110.86  3.000
 HT5  H132  C13  C11   109.99  3.000
 HT5  H131  C13  C11   111.43  3.000
 HT5  C14   C13  C11   106.40  3.000
 HT5  H142  C14  H141  108.78  3.000
 HT5  H142  C14  C13   111.70  3.000
 HT5  H141  C14  C13   112.75  3.000
 HT5  H142  C14  SD    108.96  3.000
 HT5  H141  C14  SD    108.76  3.000
 HT5  C13   C14  SD    105.76  3.000
 HT5  H9C2  C9   H9C1  105.85  3.000
 HT5  H9C2  C9   C2    109.57  3.000
 HT5  H9C1  C9   C2    110.31  3.000
 HT5  H9C2  C9   C10   106.68  3.000
 HT5  H9C1  C9   C10   110.49  3.000
 HT5  C2    C9   C10   113.59  3.000
 HT5  H2C2  C2   H2C1  106.47  3.000
 HT5  H2C2  C2   C1    109.50  3.000
 HT5  H2C1  C2   C1    109.26  3.000
 HT5  H2C2  C2   C9    109.74  3.000
 HT5  H2C1  C2   C9    109.63  3.000
 HT5  C1    C2   C9    112.08  3.000
 HT5  H1C2  C1   H1C1  106.04  3.000
 HT5  H1C2  C1   C50   109.40  3.000
 HT5  H1C1  C1   C50   109.49  3.000
 HT5  H1C2  C1   C2    109.09  3.000
 HT5  H1C1  C1   C2    109.72  3.000
 HT5  C50   C1   C2    112.87  3.000
 HT5  H502  C50  H501  105.96  3.000
 HT5  H502  C50  C3    109.39  3.000
 HT5  H501  C50  C3    109.18  3.000
 HT5  H502  C50  C1    109.47  3.000
 HT5  H501  C50  C1    109.25  3.000
 HT5  C3    C50  C1    113.32  3.000
 HT5  H8C3  C8   H8C2  107.65  3.000
 HT5  H8C3  C8   H8C1  107.59  3.000
 HT5  H8C2  C8   H8C1  107.41  3.000
 HT5  H8C3  C8   C6    111.63  3.000
 HT5  H8C2  C8   C6    111.12  3.000
 HT5  H8C1  C8   C6    111.24  3.000
 HT5  H6C2  C6   H6C1  105.96  3.000
 HT5  H6C2  C6   C5    109.20  3.000
 HT5  H6C1  C6   C5    109.30  3.000
 HT5  H6C2  C6   C8    109.53  3.000
 HT5  H6C1  C6   C8    109.60  3.000
 HT5  C5    C6   C8    113.00  3.000
 HT5  H3C2  C3   H3C1  105.97  3.000
 HT5  H3C2  C3   C4    109.34  3.000
 HT5  H3C1  C3   C4    109.43  3.000
 HT5  H3C2  C3   C50   109.21  3.000
 HT5  H3C1  C3   C50   109.48  3.000
 HT5  C4    C3   C50   113.16  3.000
 HT5  H4C2  C4   H4C1  105.94  3.000
 HT5  H4C2  C4   C5    109.37  3.000
 HT5  H4C1  C4   C5    109.22  3.000
 HT5  H4C2  C4   C3    109.39  3.000
 HT5  H4C1  C4   C3    109.24  3.000
 HT5  C5    C4   C3    113.41  3.000
 HT5  H5C2  C5   H5C1  105.92  3.000
 HT5  H5C2  C5   C4    109.48  3.000
 HT5  H5C1  C5   C4    109.29  3.000
 HT5  H5C2  C5   C6    109.33  3.000
 HT5  H5C1  C5   C6    109.31  3.000
 HT5  C4    C5   C6    113.26  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
 HT5  CONST_01  C11   N2   C10  O1      0.00   0.0  0
 HT5  CONST_02  C9    C10  N2   C11   180.00   0.0  0
 HT5  CONST_03  HA    N2   C10  O1    180.00   0.0  0
 HT5  Var_01    C11   C13  C14  SD    -40.83  30.0  1
 HT5  Var_02    C13   C14  SD   C12    22.24  30.0  1
 HT5  Var_03    C2    C9   C10  O1     32.32  30.0  3
 HT5  Var_04    C1    C2   C9   C10  -174.90  30.0  3
 HT5  Var_05    C50   C1   C2   C9    179.93  30.0  3
 HT5  Var_06    C3    C50  C1   C2   -177.67  30.0  3
 HT5  Var_07    C4    C3   C50  C1    178.95  30.0  3
 HT5  Var_08    C5    C4   C3   C50  -178.84  30.0  3
 HT5  Var_09    C4    C5   C6   C8   -179.20  30.0  1
 HT5  Var_10    C3    C4   C5   C6    179.29  30.0  1
 HT5  Var_11    H8C1  C8   C6   C5    -60.11  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
 HT5  chir_01  C11  C12  C13  N2  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
 HT5  plan-1  O1   0.020
 HT5  plan-1  C10  0.020
 HT5  plan-1  N2   0.020
 HT5  plan-1  C11  0.020
 HT5  plan-1  C9   0.020
 HT5  plan-1  HA   0.020
 HT5  plan-2  SD   0.020
 HT5  plan-2  C11  0.020
 HT5  plan-2  C12  0.020
 HT5  plan-2  O2   0.020

