# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:42:55 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCN=C1SC[C@@H]2[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)N12
#
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
 AMF  AMF  (3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol  ligand  50  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AMF
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
 AMF  O4    O  OH1   0  -0.670  -4.9827   1.5836   1.4177
 AMF  C4    C  CH1   0   0.051  -4.1710   0.4781   1.1260
 AMF  C5    C  CH1   0  -0.082  -2.9850   1.0005   0.3345
 AMF  C6    C  CH2   0  -0.564  -2.1122   1.9620   1.1230
 AMF  S1    S  S2    0   0.034  -0.5263   1.9526   0.2393
 AMF  C3    C  CH1   0  -0.002  -4.8957  -0.5711   0.2951
 AMF  O3    O  OH1   0  -0.671  -5.9947  -1.0187   1.0482
 AMF  C2    C  CH1   0  -0.005  -3.9379  -1.7072  -0.0296
 AMF  O2    O  OH1   0  -0.671  -4.6401  -2.6439  -0.8069
 AMF  C1    C  CH1   0   0.193  -2.6985  -1.2146  -0.7764
 AMF  O1    O  OH1   0  -0.680  -1.8231  -2.2860  -0.8616
 AMF  N1    N  NT    0  -0.523  -2.1014  -0.0937  -0.0435
 AMF  C7    C  C     0   0.381  -0.8675   0.3531  -0.4574
 AMF  N2    N  N     0  -0.498  -0.1107  -0.3010  -1.2354
 AMF  C8    C  CH2   0  -0.316   1.2124   0.1857  -1.5462
 AMF  C9    C  CH2   0  -0.426   2.2518  -0.3084  -0.5451
 AMF  C10   C  CH2   0  -0.418   3.6665   0.1233  -0.9086
 AMF  C11   C  CH2   0  -0.411   4.7030  -0.3359   0.1091
 AMF  C12   C  CH2   0  -0.411   6.1251   0.0791  -0.2476
 AMF  C13   C  CH2   0  -0.406   7.1533  -0.3575   0.7884
 AMF  C14   C  CH2   0  -0.418   8.5780   0.0550   0.4390
 AMF  C15   C  CH3   0  -0.662   9.5942  -0.3827   1.4849
 AMF  H4    H  HOH1  0   0.457  -5.7628   1.2730   1.8891
 AMF  HA    H  HCH1  0   0.220  -3.7979  -0.0008   2.0452
 AMF  H5    H  HCH1  0   0.265  -3.3616   1.5146  -0.5636
 AMF  H3    H  HCH1  0   0.216  -5.2255  -0.1011  -0.6457
 AMF  H61C  H  HCH2  0   0.303  -2.5130   2.9720   1.1314
 AMF  H62C  H  HCH2  0   0.291  -1.9604   1.6221   2.1478
 AMF  HB    H  HOH1  0   0.457  -6.5086  -1.6296   0.5103
 AMF  H2    H  HCH1  0   0.223  -3.5941  -2.1509   0.9170
 AMF  HC    H  HOH1  0   0.459  -4.1398  -3.4656  -0.8289
 AMF  H81C  H  HCH2  0   0.238   1.4765  -0.1724  -2.5439
 AMF  H82C  H  HCH2  0   0.210   1.2478   1.2835  -1.5978
 AMF  H91C  H  HCH2  0   0.217   1.9973   0.0671   0.4511
 AMF  H92C  H  HCH2  0   0.221   2.1992  -1.3998  -0.4891
 AMF  H101  H  HCH2  0   0.212   3.9262  -0.2707  -1.8970
 AMF  H102  H  HCH2  0   0.212   3.7060   1.2147  -0.9963
 AMF  H111  H  HCH2  0   0.208   4.4436   0.0680   1.0938
 AMF  H112  H  HCH2  0   0.208   4.6561  -1.4260   0.2075
 AMF  H121  H  HCH2  0   0.207   6.3927  -0.3392  -1.2241
 AMF  H122  H  HCH2  0   0.206   6.1681   1.1680  -0.3628
 AMF  H131  H  HCH2  0   0.206   6.8839   0.0625   1.7639
 AMF  H132  H  HCH2  0   0.205   7.1097  -1.4461   0.9066
 AMF  H141  H  HCH2  0   0.210   8.8490  -0.3670  -0.5336
 AMF  H142  H  HCH2  0   0.209   8.6216   1.1422   0.3196
 AMF  H151  H  HCH3  0   0.215   9.3571   0.0378   2.4642
 AMF  H152  H  HCH3  0   0.215   9.6091  -1.4691   1.5897
 AMF  H153  H  HCH3  0   0.225  10.6033  -0.0620   1.2235
 AMF  H154  H  HOH1  0   0.455  -1.0052  -1.9268  -1.2626
 AMF  H155  H  HCH1  0   0.206  -2.9974  -0.8550  -1.7772

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
 AMF  C10  C11   single  1.524  0.020  1.524
 AMF  C11  C12   single  1.524  0.020  1.524
 AMF  C12  C13   single  1.524  0.020  1.524
 AMF  C13  C14   single  1.524  0.020  1.524
 AMF  C14  C15   single  1.522  0.020  1.522
 AMF  O4   H4    single  0.850  0.020  0.980
 AMF  C4   HA    single  0.970  0.020  1.090
 AMF  C5   H5    single  0.970  0.020  1.090
 AMF  C3   H3    single  0.970  0.020  1.090
 AMF  C6   H61C  single  0.970  0.020  1.090
 AMF  C6   H62C  single  0.970  0.020  1.090
 AMF  O3   HB    single  0.850  0.020  0.980
 AMF  C2   H2    single  0.970  0.020  1.090
 AMF  O2   HC    single  0.850  0.020  0.980
 AMF  C8   H81C  single  0.970  0.020  1.090
 AMF  C8   H82C  single  0.970  0.020  1.090
 AMF  C9   H91C  single  0.970  0.020  1.090
 AMF  C9   H92C  single  0.970  0.020  1.090
 AMF  C10  H101  single  0.970  0.020  1.090
 AMF  C10  H102  single  0.970  0.020  1.090
 AMF  C11  H111  single  0.970  0.020  1.090
 AMF  C11  H112  single  0.970  0.020  1.090
 AMF  C12  H121  single  0.970  0.020  1.090
 AMF  C12  H122  single  0.970  0.020  1.090
 AMF  C13  H131  single  0.970  0.020  1.090
 AMF  C13  H132  single  0.970  0.020  1.090
 AMF  C14  H141  single  0.970  0.020  1.090
 AMF  C14  H142  single  0.970  0.020  1.090
 AMF  C15  H151  single  0.970  0.020  1.090
 AMF  C15  H152  single  0.970  0.020  1.090
 AMF  C15  H153  single  0.970  0.020  1.090
 AMF  O1   H154  single  0.850  0.020  0.980
 AMF  C1   H155  single  0.970  0.020  1.090
 AMF  O4   C4    single  1.402  0.020  1.402
 AMF  C4   C5    single  1.519  0.020  1.519
 AMF  C5   C6    single  1.519  0.020  1.519
 AMF  C6   S1    single  1.816  0.020  1.816
 AMF  C4   C3    single  1.522  0.020  1.522
 AMF  C3   O3    single  1.405  0.020  1.405
 AMF  C3   C2    single  1.521  0.020  1.521
 AMF  C2   O2    single  1.405  0.020  1.405
 AMF  C2   C1    single  1.528  0.020  1.528
 AMF  C1   O1    single  1.386  0.020  1.386
 AMF  C5   N1    single  1.456  0.020  1.456
 AMF  C1   N1    single  1.466  0.020  1.466
 AMF  S1   C7    single  1.778  0.020  1.778
 AMF  N1   C7    single  1.376  0.020  1.376
 AMF  C7   N2    double  1.267  0.020  1.267
 AMF  N2   C8    single  1.444  0.020  1.444
 AMF  C8   C9    single  1.525  0.020  1.525
 AMF  C9   C10   single  1.523  0.020  1.523

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
 AMF  H4    O4   C4    108.45  3.000
 AMF  HA    C4   C3    108.49  3.000
 AMF  C3    C4   C5    108.94  3.000
 AMF  HA    C4   C5    108.66  3.000
 AMF  C3    C4   O4    112.42  3.000
 AMF  C5    C4   O4    106.82  3.000
 AMF  HA    C4   O4    111.42  3.000
 AMF  H5    C5   N1    110.28  3.000
 AMF  N1    C5   C6    105.17  3.000
 AMF  H5    C5   C6    108.92  3.000
 AMF  N1    C5   C4    110.53  3.000
 AMF  C6    C5   C4    113.32  3.000
 AMF  H5    C5   C4    108.58  3.000
 AMF  H62C  C6   H61C  109.50  3.000
 AMF  H62C  C6   S1    109.53  3.000
 AMF  H61C  C6   S1    109.31  3.000
 AMF  S1    C6   C5    104.24  3.000
 AMF  H62C  C6   C5    111.75  3.000
 AMF  H61C  C6   C5    112.36  3.000
 AMF  C7    S1   C6     91.59  3.000
 AMF  H3    C3   C2    108.94  3.000
 AMF  C2    C3   O3    111.65  3.000
 AMF  H3    C3   O3    111.05  3.000
 AMF  C2    C3   C4    109.37  3.000
 AMF  O3    C3   C4    107.42  3.000
 AMF  H3    C3   C4    108.33  3.000
 AMF  HB    O3   C3    108.67  3.000
 AMF  H2    C2   C1    107.27  3.000
 AMF  C1    C2   O2    110.48  3.000
 AMF  H2    C2   O2    111.29  3.000
 AMF  C1    C2   C3    111.97  3.000
 AMF  O2    C2   C3    107.54  3.000
 AMF  H2    C2   C3    108.31  3.000
 AMF  HC    O2   C2    108.79  3.000
 AMF  H155  C1   N1    108.30  3.000
 AMF  N1    C1   O1    111.37  3.000
 AMF  H155  C1   O1    111.52  3.000
 AMF  N1    C1   C2    109.42  3.000
 AMF  O1    C1   C2    107.04  3.000
 AMF  H155  C1   C2    109.16  3.000
 AMF  H154  O1   C1    105.61  3.000
 AMF  C7    N1   C1    117.59  3.000
 AMF  C7    N1   C5    112.22  3.000
 AMF  C1    N1   C5    117.19  3.000
 AMF  N2    C7   N1    123.54  3.000
 AMF  N2    C7   S1    126.19  3.000
 AMF  N1    C7   S1    110.26  3.000
 AMF  C8    N2   C7    120.36  3.000
 AMF  H82C  C8   H81C  106.06  3.000
 AMF  H82C  C8   C9    109.40  3.000
 AMF  H81C  C8   C9    109.18  3.000
 AMF  C9    C8   N2    111.96  3.000
 AMF  H82C  C8   N2    112.10  3.000
 AMF  H81C  C8   N2    107.92  3.000
 AMF  H92C  C9   H91C  106.52  3.000
 AMF  H92C  C9   C10   109.86  3.000
 AMF  H91C  C9   C10   109.63  3.000
 AMF  C10   C9   C8    112.61  3.000
 AMF  H92C  C9   C8    108.90  3.000
 AMF  H91C  C9   C8    109.13  3.000
 AMF  H102  C10  H101  106.12  3.000
 AMF  H102  C10  C11   109.22  3.000
 AMF  H101  C10  C11   109.46  3.000
 AMF  H102  C10  C9    109.57  3.000
 AMF  H101  C10  C9    109.49  3.000
 AMF  C11   C10  C9    112.77  3.000
 AMF  H112  C11  H111  106.02  3.000
 AMF  H112  C11  C12   109.39  3.000
 AMF  H111  C11  C12   109.33  3.000
 AMF  H112  C11  C10   109.32  3.000
 AMF  H111  C11  C10   109.16  3.000
 AMF  C12   C11  C10   113.36  3.000
 AMF  H122  C12  H121  106.03  3.000
 AMF  H122  C12  C13   109.26  3.000
 AMF  H121  C12  C13   109.38  3.000
 AMF  H122  C12  C11   109.39  3.000
 AMF  H121  C12  C11   109.43  3.000
 AMF  C13   C12  C11   113.12  3.000
 AMF  H132  C13  H131  105.96  3.000
 AMF  H132  C13  C14   109.32  3.000
 AMF  H131  C13  C14   109.28  3.000
 AMF  H132  C13  C12   109.34  3.000
 AMF  H131  C13  C12   109.25  3.000
 AMF  C14   C13  C12   113.42  3.000
 AMF  H142  C14  H141  106.03  3.000
 AMF  H142  C14  C15   109.51  3.000
 AMF  H141  C14  C15   109.54  3.000
 AMF  H142  C14  C13   109.34  3.000
 AMF  H141  C14  C13   109.32  3.000
 AMF  C15   C14  C13   112.87  3.000
 AMF  H153  C15  H152  107.63  3.000
 AMF  H153  C15  H151  107.62  3.000
 AMF  H152  C15  H151  107.47  3.000
 AMF  H153  C15  C14   111.62  3.000
 AMF  H152  C15  C14   111.18  3.000
 AMF  H151  C15  C14   111.13  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
 AMF  CONST_04  N2    C7   N1   C1      0.00   0.0  0
 AMF  CONST_05  C8    N2   C7   S1      0.00   0.0  0
 AMF  CONST_06  C8    N2   C7   N1    180.00   0.0  0
 AMF  Var_01    N1    C7   S1   C6      0.78  30.0  1
 AMF  Var_02    H61C  C6   S1   C7   -143.61  30.0  1
 AMF  Var_03    C9    C8   N2   C7     88.72  30.0  3
 AMF  Var_04    C10   C9   C8   N2    176.36  30.0  3
 AMF  Var_05    C11   C10  C9   C8    178.43  30.0  3
 AMF  Var_06    C12   C11  C10  C9    179.52  30.0  3
 AMF  Var_07    C13   C12  C11  C10   178.79  30.0  3
 AMF  Var_08    C14   C13  C12  C11  -179.96  30.0  3
 AMF  Var_09    C15   C14  C13  C12   179.77  30.0  3
 AMF  Var_10    H151  C15  C14  C13   -58.85  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
 AMF  chir_01  C4  O4  C5  C3  positiv
 AMF  chir_02  C5  N1  C6  C4  positiv
 AMF  chir_03  C3  O3  C4  C2  negativ
 AMF  chir_04  C2  O2  C3  C1  positiv
 AMF  chir_05  C1  O1  N1  C2  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
 AMF  plan-1  C5  0.020
 AMF  plan-1  S1  0.020
 AMF  plan-1  C1  0.020
 AMF  plan-1  N1  0.020
 AMF  plan-1  C7  0.020
 AMF  plan-1  N2  0.020
 AMF  plan-1  C8  0.020

