# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:52:49 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: methyl 3-[(thiophen-2-ylacetyl)amino]thiophene-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1sccc1NC(=O)Cc2sccc2
#
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
 SYY  SYY  'methyl 3-[(thiophen-2-ylacetyl)amino]thiophene-2-carboxylate'  ligand  29  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SYY
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
 SYY  S     S  S2    0   0.277  -3.7984   1.5858  -0.1640
 SYY  C1    C  CR15  0  -0.195  -1.3080   2.1970  -0.0898
 SYY  N1    N  NH1   0  -0.756  -0.2743  -0.0772   0.0741
 SYY  O1    O  O     0  -0.474  -2.3134  -2.0281   0.0939
 SYY  C2    C  CR5   0   0.446  -1.3547   0.7755  -0.0169
 SYY  O2    O  O2    0  -0.464  -4.3931  -1.2064  -0.0438
 SYY  S2    S  S2    0   0.227   4.2530  -0.0029  -1.0395
 SYY  C3    C  CR5   0  -0.458  -2.6555   0.3006  -0.0473
 SYY  O3    O  O     0  -0.428   1.4728   1.3833   0.0710
 SYY  C5    C  CR15  0  -0.416  -2.5530   2.7431  -0.1717
 SYY  C6    C  C     0   0.649  -3.0767  -1.0862   0.0089
 SYY  C9    C  CH3   0  -0.376  -4.9442  -2.5241   0.0011
 SYY  C11   C  C     0   0.576   1.0489   0.2498   0.1140
 SYY  C12   C  CH2   0  -0.682   1.9424  -0.9756   0.2175
 SYY  C14   C  CR5   0  -0.100   3.3919  -0.6533   0.3021
 SYY  C15   C  CR15  0  -0.213   4.2205  -0.8198   1.3711
 SYY  C16   C  CR15  0  -0.152   5.5603  -0.4222   1.1071
 SYY  C17   C  CR15  0  -0.450   5.7247   0.0399  -0.1620
 SYY  H1    H  HCR5  0   0.281  -0.4077   2.7861  -0.0827
 SYY  HN1   H  HNH1  0   0.414  -0.5141  -1.0607   0.1153
 SYY  H5    H  HCR5  0   0.284  -2.7886   3.7944  -0.2365
 SYY  H9    H  HCH3  0   0.235  -4.6003  -3.1257  -0.8394
 SYY  H9A   H  HCH3  0   0.226  -4.6911  -3.0262   0.9340
 SYY  H9B   H  HCH3  0   0.245  -6.0206  -2.3967  -0.0609
 SYY  H12   H  HCH2  0   0.286   1.6537  -1.5421   1.1069
 SYY  H12A  H  HCH2  0   0.287   1.7329  -1.6314  -0.6340
 SYY  H15   H  HCR5  0   0.232   3.8824  -1.2196   2.3175
 SYY  H16   H  HCR5  0   0.237   6.3622  -0.4816   1.8286
 SYY  H17   H  HCR5  0   0.262   6.6277   0.4032  -0.6276

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
 SYY  S    C3    aromatic  1.724  0.020  1.724
 SYY  S    C5    aromatic  1.700  0.020  1.700
 SYY  C1   C2    aromatic  1.424  0.020  1.424
 SYY  C1   C5    aromatic  1.362  0.020  1.362
 SYY  N1   C2    single    1.379  0.020  1.379
 SYY  N1   C11   single    1.364  0.020  1.364
 SYY  O1   C6    double    1.215  0.020  1.215
 SYY  C2   C3    aromatic  1.385  0.020  1.385
 SYY  O2   C6    single    1.323  0.020  1.323
 SYY  O2   C9    single    1.429  0.020  1.429
 SYY  S2   C14   aromatic  1.722  0.020  1.722
 SYY  S2   C17   aromatic  1.714  0.020  1.714
 SYY  C3   C6    single    1.450  0.020  1.450
 SYY  O3   C11   double    1.211  0.020  1.211
 SYY  C11  C12   single    1.520  0.020  1.520
 SYY  C12  C14   single    1.487  0.020  1.487
 SYY  C14  C15   aromatic  1.363  0.020  1.363
 SYY  C15  C16   aromatic  1.422  0.020  1.422
 SYY  C16  C17   aromatic  1.361  0.020  1.361
 SYY  C1   H1    single    0.930  0.020  1.080
 SYY  N1   HN1   single    0.860  0.020  1.020
 SYY  C5   H5    single    0.930  0.020  1.080
 SYY  C9   H9    single    0.970  0.020  1.090
 SYY  C9   H9A   single    0.970  0.020  1.090
 SYY  C9   H9B   single    0.970  0.020  1.090
 SYY  C12  H12   single    0.970  0.020  1.090
 SYY  C12  H12A  single    0.970  0.020  1.090
 SYY  C15  H15   single    0.930  0.020  1.080
 SYY  C16  H16   single    0.930  0.020  1.080
 SYY  C17  H17   single    0.930  0.020  1.080

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
 SYY  C5    S    C3    91.27  3.000
 SYY  H1    C1   C5   123.08  3.000
 SYY  H1    C1   C2   125.00  3.000
 SYY  C5    C1   C2   111.92  3.000
 SYY  HN1   N1   C11  117.47  3.000
 SYY  HN1   N1   C2   114.67  3.000
 SYY  C11   N1   C2   127.86  3.000
 SYY  C3    C2   N1   121.68  3.000
 SYY  C3    C2   C1   111.83  3.000
 SYY  N1    C2   C1   126.49  3.000
 SYY  C9    O2   C6   117.79  3.000
 SYY  C17   S2   C14   92.29  3.000
 SYY  C6    C3   C2   126.85  3.000
 SYY  C6    C3   S    121.53  3.000
 SYY  C2    C3   S    111.63  3.000
 SYY  H5    C5   C1   126.42  3.000
 SYY  H5    C5   S    120.23  3.000
 SYY  C1    C5   S    113.35  3.000
 SYY  C3    C6   O2   111.98  3.000
 SYY  C3    C6   O1   124.15  3.000
 SYY  O2    C6   O1   123.87  3.000
 SYY  H9B   C9   H9A  109.48  3.000
 SYY  H9B   C9   H9   109.50  3.000
 SYY  H9A   C9   H9   109.45  3.000
 SYY  H9B   C9   O2   105.80  3.000
 SYY  H9A   C9   O2   111.24  3.000
 SYY  H9    C9   O2   111.30  3.000
 SYY  C12   C11  O3   123.45  3.000
 SYY  C12   C11  N1   112.28  3.000
 SYY  O3    C11  N1   124.27  3.000
 SYY  H12A  C12  H12  105.77  3.000
 SYY  H12A  C12  C14  111.13  3.000
 SYY  H12   C12  C14  108.87  3.000
 SYY  H12A  C12  C11  108.50  3.000
 SYY  H12   C12  C11  108.53  3.000
 SYY  C14   C12  C11  113.71  3.000
 SYY  C15   C14  C12  127.64  3.000
 SYY  C15   C14  S2   110.69  3.000
 SYY  C12   C14  S2   121.67  3.000
 SYY  H15   C15  C16  124.07  3.000
 SYY  H15   C15  C14  122.79  3.000
 SYY  C16   C15  C14  113.14  3.000
 SYY  H16   C16  C17  123.50  3.000
 SYY  H16   C16  C15  124.05  3.000
 SYY  C17   C16  C15  112.45  3.000
 SYY  H17   C17  C16  128.16  3.000
 SYY  H17   C17  S2   120.41  3.000
 SYY  C16   C17  S2   111.43  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
 SYY  CONST_01  C1   C2   C3   S       0.00   0.0  0
 SYY  CONST_02  C2   C1   C5   S       0.00   0.0  0
 SYY  CONST_03  C3   S    C5   C1      0.00   0.0  0
 SYY  CONST_04  C5   S    C3   C2      0.00   0.0  0
 SYY  CONST_05  C16  C15  C14  S2      0.00   0.0  0
 SYY  CONST_06  C15  C16  C17  S2      0.00   0.0  0
 SYY  CONST_07  C5   C1   C2   C3      0.00   0.0  0
 SYY  CONST_08  C16  C17  S2   C14     0.00   0.0  0
 SYY  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 SYY  CONST_10  C17  S2   C14  C15     0.00   0.0  0
 SYY  CONST_11  N1   C2   C3   S     180.00   0.0  0
 SYY  CONST_12  C6   C3   C2   C1    180.00   0.0  0
 SYY  CONST_13  C5   C1   C2   N1    180.00   0.0  0
 SYY  CONST_14  C6   C3   S    C5    180.00   0.0  0
 SYY  CONST_15  C17  S2   C14  C12   180.00   0.0  0
 SYY  CONST_16  C16  C15  C14  C12   180.00   0.0  0
 SYY  CONST_17  H1   C1   C5   S     180.00   0.0  0
 SYY  CONST_18  H5   C5   C1   C2    180.00   0.0  0
 SYY  CONST_19  H15  C15  C14  S2    180.00   0.0  0
 SYY  CONST_20  H16  C16  C17  S2    180.00   0.0  0
 SYY  CONST_21  H17  C17  S2   C14   180.00   0.0  0
 SYY  CONST_22  C11  N1   C2   C1      0.00   0.0  0
 SYY  CONST_23  C11  N1   C2   C3    180.00   0.0  0
 SYY  CONST_24  HN1  N1   C2   C1    180.00   0.0  0
 SYY  CONST_25  O3   C11  N1   C2      0.00   0.0  0
 SYY  CONST_26  C12  C11  N1   C2    180.00   0.0  0
 SYY  Var_01    O1   C6   C3   S    -179.86  30.0  2
 SYY  Var_02    C11  C12  C14  S2    -69.36  30.0  1
 SYY  Var_03    C14  C12  C11  N1   -178.36  30.0  3
 SYY  Var_04    H9   C9   O2   C6    -60.76  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
 SYY  plan-1  S    0.020
 SYY  plan-1  C1   0.020
 SYY  plan-1  N1   0.020
 SYY  plan-1  C2   0.020
 SYY  plan-1  C3   0.020
 SYY  plan-1  C5   0.020
 SYY  plan-1  C6   0.020
 SYY  plan-1  H1   0.020
 SYY  plan-1  H5   0.020
 SYY  plan-2  S2   0.020
 SYY  plan-2  C12  0.020
 SYY  plan-2  C14  0.020
 SYY  plan-2  C15  0.020
 SYY  plan-2  C16  0.020
 SYY  plan-2  C17  0.020
 SYY  plan-2  H15  0.020
 SYY  plan-2  H16  0.020
 SYY  plan-2  H17  0.020
 SYY  plan-3  N1   0.020
 SYY  plan-3  C2   0.020
 SYY  plan-3  O3   0.020
 SYY  plan-3  C11  0.020
 SYY  plan-3  C12  0.020
 SYY  plan-3  HN1  0.020
 SYY  plan-4  O1   0.020
 SYY  plan-4  O2   0.020
 SYY  plan-4  C3   0.020
 SYY  plan-4  C6   0.020

