# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:44:28 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[(3,4-dihydro-2H-1lambda~4~-thiophen-5-yl)methyl]-4-(furan-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1=[SH]CCC1)N2CCN(CC2)C(=O)c3occc3
#
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
 Y1M  Y1M  N-[(3,4-dihydro-2H-1lambda~4~-thiophen-5-yl)methyl]-4-(furan-2-carbonyl)piperazine-1-carboxamide  ligand  43  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y1M
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
 Y1M  N1   N  NT    0  -0.510  -17.7504  15.6485  26.1130
 Y1M  C4   C  CH2   0  -0.425  -16.6059  22.2216  25.3376
 Y1M  C5   C  CH2   0  -0.558  -17.9833  21.7395  25.8274
 Y1M  C6   C  CH2   0  -0.278  -18.8770  15.2682  26.9463
 Y1M  C7   C  CH2   0  -0.323  -19.0205  13.7602  26.9940
 Y1M  C10  C  CR15  0  -0.315  -22.1569  11.1457  25.8973
 Y1M  C13  C  CH2   0  -0.305  -17.9266  13.5410  24.8713
 Y1M  N    N  NH1   0  -0.673  -16.2901  17.3374  25.4578
 Y1M  C    C  C     0   0.741  -17.0577  16.7900  26.4347
 Y1M  O    O  O     0  -0.545  -17.1025  17.2668  27.5666
 Y1M  C1   C  CH2   0  -0.303  -15.5395  18.5567  25.6942
 Y1M  C11  C  CR15  0  -0.335  -23.3131  11.5649  26.6109
 Y1M  C12  C  CR15  0   0.014  -23.0948  12.8610  26.9432
 Y1M  C14  C  CH2   0  -0.310  -17.7380  15.0498  24.7922
 Y1M  C2   C  CR5   0  -0.342  -16.3137  19.8192  25.4433
 Y1M  C3   C  CH2   0  -0.448  -15.5763  21.1207  25.6189
 Y1M  C9   C  CR5   0   0.210  -21.3181  12.2145  25.8678
 Y1M  N2   N  NT    0  -0.471  -19.1089  13.2252  25.6465
 Y1M  O1   O  O     0  -0.472  -19.8323  11.6639  24.1768
 Y1M  O2   O  O     0  -0.404  -21.8922  13.2632  26.4995
 Y1M  S    S  S3    0   0.193  -17.7681  19.9999  26.3401
 Y1M  H17  H  HCH2  0   0.242  -16.6570  22.4101  24.2662
 Y1M  H5   H  HCH2  0   0.283  -18.3631  22.2860  26.6889
 Y1M  H18  H  HCH2  0   0.297  -18.7395  21.7547  25.0462
 Y1M  H6   H  HCH2  0   0.266  -18.7233  15.6445  27.9537
 Y1M  H7   H  HCH2  0   0.231  -19.8062  15.7066  26.5612
 Y1M  H9   H  HCH2  0   0.253  -18.1386  13.3243  27.4758
 Y1M  H8   H  HCH2  0   0.279  -19.8795  13.4889  27.5972
 Y1M  H10  H  HCR5  0   0.271  -21.9689  10.1745  25.4692
 Y1M  H13  H  HCH2  0   0.248  -17.0480  13.0836  25.3378
 Y1M  H14  H  HCH2  0   0.275  -18.0199  13.1397  23.8660
 Y1M  H    H  HNH1  0   0.393  -16.5175  17.1596  24.4936
 Y1M  H1   H  HCH2  0   0.212  -15.1097  18.4893  26.7025
 Y1M  H2   H  HCH2  0   0.236  -14.6839  18.5486  25.0131
 Y1M  H11  H  HCR5  0   0.271  -24.1897  10.9819  26.8402
 Y1M  H12  H  HCR5  0   0.286  -23.6855  13.5935  27.4694
 Y1M  H16  H  HCH2  0   0.260  -16.7761  15.2199  24.3120
 Y1M  H15  H  HCH2  0   0.240  -18.5178  15.4811  24.1523
 Y1M  H3   H  HCH2  0   0.192  -15.1647  21.2541  26.6368
 Y1M  H19  H  HCH2  0   0.232  -14.7283  21.1949  24.9322
 Y1M  H20  H  HSH1  0   0.153  -17.5348  20.3243  27.6702
 Y1M  C8   C  C     0   0.496  -20.0203  12.3465  25.1755
 Y1M  H4   H  HCH2  0   0.242  -16.3433  23.1611  25.8249

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
 Y1M  O    C    double    1.229  0.020  1.229
 Y1M  N    C    single    1.358  0.020  1.358
 Y1M  C1   N    single    1.451  0.020  1.451
 Y1M  C2   C1   single    1.502  0.020  1.502
 Y1M  C2   C3   single    1.506  0.020  1.506
 Y1M  C3   C4   single    1.533  0.020  1.533
 Y1M  C4   C5   single    1.539  0.020  1.539
 Y1M  C5   S    single    1.826  0.020  1.826
 Y1M  S    C2   double    1.718  0.020  1.718
 Y1M  C    N1   single    1.373  0.020  1.373
 Y1M  N1   C6   single    1.452  0.020  1.452
 Y1M  C6   C7   single    1.516  0.020  1.516
 Y1M  C7   N2   single    1.453  0.020  1.453
 Y1M  N2   C8   single    1.351  0.020  1.351
 Y1M  C8   O1   double    1.224  0.020  1.224
 Y1M  C9   C8   single    1.477  0.020  1.477
 Y1M  C9   C10  aromatic  1.359  0.020  1.359
 Y1M  C10  C11  aromatic  1.422  0.020  1.422
 Y1M  C11  C12  aromatic  1.356  0.020  1.356
 Y1M  C12  O2   aromatic  1.343  0.020  1.343
 Y1M  O2   C9   aromatic  1.352  0.020  1.352
 Y1M  C13  N2   single    1.449  0.020  1.449
 Y1M  C14  C13  single    1.523  0.020  1.523
 Y1M  N1   C14  single    1.450  0.020  1.450
 Y1M  C4   H4   single    0.970  0.020  1.090
 Y1M  C4   H17  single    0.970  0.020  1.090
 Y1M  C5   H5   single    0.970  0.020  1.090
 Y1M  C5   H18  single    0.970  0.020  1.090
 Y1M  C6   H6   single    0.970  0.020  1.090
 Y1M  C6   H7   single    0.970  0.020  1.090
 Y1M  C7   H9   single    0.970  0.020  1.090
 Y1M  C7   H8   single    0.970  0.020  1.090
 Y1M  C10  H10  single    0.930  0.020  1.080
 Y1M  C13  H13  single    0.970  0.020  1.090
 Y1M  C13  H14  single    0.970  0.020  1.090
 Y1M  N    H    single    0.860  0.020  1.020
 Y1M  C1   H1   single    0.970  0.020  1.090
 Y1M  C1   H2   single    0.970  0.020  1.090
 Y1M  C11  H11  single    0.930  0.020  1.080
 Y1M  C12  H12  single    0.930  0.020  1.080
 Y1M  C14  H16  single    0.970  0.020  1.090
 Y1M  C14  H15  single    0.970  0.020  1.090
 Y1M  C3   H3   single    0.970  0.020  1.090
 Y1M  C3   H19  single    0.970  0.020  1.090
 Y1M  S    H20  single    1.200  0.020  1.300

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
 Y1M  C14  N1   C    123.51  3.000
 Y1M  C14  N1   C6   114.91  3.000
 Y1M  C    N1   C6   118.33  3.000
 Y1M  H17  C4   H4   107.56  3.000
 Y1M  H17  C4   C3   109.65  3.000
 Y1M  H4   C4   C3   112.01  3.000
 Y1M  H17  C4   C5   108.98  3.000
 Y1M  H4   C4   C5   110.07  3.000
 Y1M  C3   C4   C5   108.52  3.000
 Y1M  H18  C5   H5   108.59  3.000
 Y1M  H18  C5   S    107.28  3.000
 Y1M  H5   C5   S    107.29  3.000
 Y1M  H18  C5   C4   112.91  3.000
 Y1M  H5   C5   C4   114.00  3.000
 Y1M  S    C5   C4   106.39  3.000
 Y1M  H7   C6   H6   107.88  3.000
 Y1M  H7   C6   C7   109.17  3.000
 Y1M  H6   C6   C7   109.20  3.000
 Y1M  H7   C6   N1   110.54  3.000
 Y1M  H6   C6   N1   109.37  3.000
 Y1M  C7   C6   N1   110.62  3.000
 Y1M  H8   C7   H9   107.07  3.000
 Y1M  H8   C7   N2   112.07  3.000
 Y1M  H9   C7   N2   108.09  3.000
 Y1M  H8   C7   C6   109.97  3.000
 Y1M  H9   C7   C6   109.48  3.000
 Y1M  N2   C7   C6   110.07  3.000
 Y1M  H10  C10  C9   126.33  3.000
 Y1M  H10  C10  C11  127.36  3.000
 Y1M  C9   C10  C11  106.31  3.000
 Y1M  H14  C13  H13  107.99  3.000
 Y1M  H14  C13  N2   110.15  3.000
 Y1M  H13  C13  N2   109.62  3.000
 Y1M  H14  C13  C14  109.18  3.000
 Y1M  H13  C13  C14  109.68  3.000
 Y1M  N2   C13  C14  110.18  3.000
 Y1M  H    N    C1   114.92  3.000
 Y1M  H    N    C    119.36  3.000
 Y1M  C1   N    C    120.93  3.000
 Y1M  O    C    N    121.79  3.000
 Y1M  N    C    N1   116.86  3.000
 Y1M  O    C    N1   121.31  3.000
 Y1M  H2   C1   H1   105.38  3.000
 Y1M  H2   C1   C2   107.78  3.000
 Y1M  H1   C1   C2   114.00  3.000
 Y1M  H2   C1   N    107.28  3.000
 Y1M  H1   C1   N    107.49  3.000
 Y1M  C2   C1   N    114.35  3.000
 Y1M  H11  C11  C12  126.60  3.000
 Y1M  H11  C11  C10  127.50  3.000
 Y1M  C12  C11  C10  105.90  3.000
 Y1M  H12  C12  O2   116.63  3.000
 Y1M  H12  C12  C11  132.92  3.000
 Y1M  O2   C12  C11  110.45  3.000
 Y1M  H15  C14  H16  108.03  3.000
 Y1M  H15  C14  C13  109.38  3.000
 Y1M  H16  C14  C13  106.69  3.000
 Y1M  H15  C14  N1   111.28  3.000
 Y1M  H16  C14  N1   110.17  3.000
 Y1M  C13  C14  N1   111.14  3.000
 Y1M  S    C2   C3   105.23  3.000
 Y1M  S    C2   C1   115.94  3.000
 Y1M  C3   C2   C1   117.03  3.000
 Y1M  H19  C3   H3   106.33  3.000
 Y1M  H19  C3   C2   111.40  3.000
 Y1M  H3   C3   C2   113.18  3.000
 Y1M  H19  C3   C4   110.90  3.000
 Y1M  H3   C3   C4   109.40  3.000
 Y1M  C2   C3   C4   105.68  3.000
 Y1M  O2   C9   C10  109.74  3.000
 Y1M  O2   C9   C8   121.52  3.000
 Y1M  C10  C9   C8   128.53  3.000
 Y1M  C13  N2   C8   120.39  3.000
 Y1M  C13  N2   C7   111.50  3.000
 Y1M  C8   N2   C7   127.17  3.000
 Y1M  C9   O2   C12  107.59  3.000
 Y1M  H20  S    C2   112.47  3.000
 Y1M  H20  S    C5    93.79  3.000
 Y1M  C2   S    C5    93.06  3.000
 Y1M  O1   C8   N2   122.93  3.000
 Y1M  O1   C8   C9   117.87  3.000
 Y1M  N2   C8   C9   119.19  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
 Y1M  CONST_01  C12  O2   C9   C10     0.00   0.0  0
 Y1M  CONST_02  O2   C12  C11  C10     0.00   0.0  0
 Y1M  CONST_03  O2   C9   C10  C11     0.00   0.0  0
 Y1M  CONST_04  C9   O2   C12  C11     0.00   0.0  0
 Y1M  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 Y1M  CONST_06  C11  C10  C9   C8    180.00   0.0  0
 Y1M  CONST_07  C12  O2   C9   C8    180.00   0.0  0
 Y1M  CONST_09  C9   C8   N2   C13   180.00   0.0  0
 Y1M  CONST_10  H12  C12  C11  C10   180.00   0.0  0
 Y1M  CONST_11  H10  C10  C11  C12   180.00   0.0  0
 Y1M  CONST_12  H11  C11  C10  C9    180.00   0.0  0
 Y1M  CONST_15  O1   C8   N2   C13     0.00   0.0  0
 Y1M  CONST_16  C14  N1   C    O     180.00   0.0  0
 Y1M  CONST_18  C14  N1   C    N       0.00   0.0  0
 Y1M  CONST_19  C1   N    C    N1    180.00   0.0  0
 Y1M  CONST_21  C1   N    C    O       0.00   0.0  0
 Y1M  Var_01    N2   C7   C6   N1    -54.58  30.0  1
 Y1M  Var_02    N2   C13  C14  N1     52.85  30.0  1
 Y1M  Var_03    S    C2   C3   C4    -48.21  30.0  1
 Y1M  Var_04    C2   S    C5   C4    -19.03  30.0  1
 Y1M  Var_05    C2   C3   C4   C5     33.94  30.0  1
 Y1M  Var_06    C3   C2   S    C5     39.20  30.0  1
 Y1M  Var_07    C13  C14  N1   C6    -50.56  30.0  1
 Y1M  Var_08    C13  N2   C7   C6     60.01  30.0  1
 Y1M  Var_09    C14  N1   C6   C7     51.40  30.0  1
 Y1M  Var_10    C14  C13  N2   C7    -58.93  30.0  1
 Y1M  Var_11    S    C5   C4   C3     -6.33  30.0  1
 Y1M  Var_12    N2   C8   C9   C10  -154.56  30.0  2
 Y1M  Var_13    C2   C1   N    C     -86.75  30.0  1

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
 Y1M  plan-1  C10  0.020
 Y1M  plan-1  C11  0.020
 Y1M  plan-1  C12  0.020
 Y1M  plan-1  C9   0.020
 Y1M  plan-1  O2   0.020
 Y1M  plan-1  H10  0.020
 Y1M  plan-1  H11  0.020
 Y1M  plan-1  H12  0.020
 Y1M  plan-1  C8   0.020
 Y1M  plan-2  N1   0.020
 Y1M  plan-2  C6   0.020
 Y1M  plan-2  N    0.020
 Y1M  plan-2  C    0.020
 Y1M  plan-2  O    0.020
 Y1M  plan-2  C1   0.020
 Y1M  plan-2  C14  0.020
 Y1M  plan-2  H    0.020
 Y1M  plan-3  C7   0.020
 Y1M  plan-3  C13  0.020
 Y1M  plan-3  C9   0.020
 Y1M  plan-3  N2   0.020
 Y1M  plan-3  O1   0.020
 Y1M  plan-3  C8   0.020

