# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:55:54 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-benzyl-2-[(morpholin-4-ylacetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN1CCOCC1)Nc2sc3CCCCc3c2C(=O)NCc4ccccc4
#
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
 4SH  4SH  N-benzyl-2-[(morpholin-4-ylacetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide  peptide  56  29  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4SH
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
 4SH  C8    C  C     0   0.511  -1.2113  -0.0858  -1.2829
 4SH  O2    O  O     0  -0.412  -1.9528   0.7497  -1.7628
 4SH  C9    C  CH2   0  -0.383  -1.4630  -1.5789  -1.3647
 4SH  N4    N  NT    0  -0.469  -2.8263  -1.8993  -1.0348
 4SH  O3    O  O2    0  -0.456  -4.8955  -3.3237   0.2759
 4SH  C14   C  CH2   0  -0.277  -3.1629  -3.2609  -1.4129
 4SH  C17   C  CH2   0  -0.310  -3.1164  -1.6842   0.3729
 4SH  C15   C  CH2   0  -0.181  -4.6183  -3.5384  -1.0905
 4SH  C16   C  CH2   0  -0.189  -4.5716  -2.0049   0.6543
 4SH  C1    C  CR5   0  -0.104   1.6122   1.8881   0.0997
 4SH  O1    O  O     0  -0.343   2.9223   1.0509   1.8859
 4SH  S1    S  S2    0   0.158  -0.4574   2.9191  -1.0254
 4SH  C2    C  C     0   0.429   2.5268   0.9095   0.7390
 4SH  N3    N  NH1   0  -0.633  -0.0586   0.2493  -0.6508
 4SH  C5    C  CR5   0   0.269   1.7933   3.3074   0.1574
 4SH  C6    C  CR5   0  -0.373   0.7654   3.9824  -0.4195
 4SH  C7    C  CR5   0   0.040   0.4338   1.5347  -0.5082
 4SH  C10   C  CH2   0  -0.450   2.9803   4.0132   0.7432
 4SH  C11   C  CH2   0  -0.480   3.0326   5.4706   0.2890
 4SH  C12   C  CH2   0  -0.448   1.6652   6.1385   0.3824
 4SH  C13   C  CH2   0  -0.428   0.6656   5.4678  -0.5584
 4SH  N2    N  NH1   0  -0.625   2.8423  -0.1497  -0.0368
 4SH  C3    C  CH2   0  -0.371   3.4363  -1.3786   0.4505
 4SH  C4    C  CR6   0   0.133   2.3896  -2.4631   0.5366
 4SH  C22   C  CR16  0  -0.309   1.4209  -2.4184   1.5404
 4SH  C21   C  CR16  0  -0.288   0.4171  -3.3741   1.5945
 4SH  C20   C  CR16  0  -0.193   0.3656  -4.3880   0.6454
 4SH  C19   C  CR16  0  -0.293   1.3235  -4.4384  -0.3572
 4SH  C18   C  CR16  0  -0.275   2.3286  -3.4792  -0.4108
 4SH  H9    H  HCH2  0   0.274  -0.7340  -2.1324  -0.7510
 4SH  H9A   H  HCH2  0   0.297  -1.2696  -1.8709  -2.4022
 4SH  H14   H  HCH2  0   0.181  -3.0063  -3.3881  -2.4869
 4SH  H14A  H  HCH2  0   0.264  -2.5250  -3.9999  -0.8994
 4SH  H17   H  HCH2  0   0.182  -2.4707  -2.3007   1.0208
 4SH  H17A  H  HCH2  0   0.283  -2.9374  -0.6394   0.6392
 4SH  H15   H  HCH2  0   0.229  -4.8588  -4.5783  -1.3152
 4SH  H15A  H  HCH2  0   0.215  -5.2568  -2.8999  -1.7172
 4SH  H16   H  HCH2  0   0.123  -5.2109  -1.2836   0.1258
 4SH  H16A  H  HCH2  0   0.270  -4.7723  -1.9116   1.7224
 4SH  HN3   H  HNH1  0   0.344   0.4733  -0.4925  -0.2159
 4SH  H10   H  HCH2  0   0.282   2.9352   3.9595   1.8346
 4SH  H10A  H  HCH2  0   0.240   3.9025   3.5025   0.4558
 4SH  H11   H  HCH2  0   0.219   3.7634   6.0129   0.8914
 4SH  H11A  H  HCH2  0   0.236   3.3829   5.5182  -0.7467
 4SH  H12   H  HCH2  0   0.256   1.2976   6.0798   1.4110
 4SH  H12A  H  HCH2  0   0.198   1.7420   7.1984   0.1342
 4SH  H13   H  HCH2  0   0.245   0.8755   5.7619  -1.5921
 4SH  H13A  H  HCH2  0   0.275  -0.3486   5.8116  -0.3414
 4SH  HN2   H  HNH1  0   0.370   2.6129  -0.1112  -1.0177
 4SH  H3    H  HCH2  0   0.236   4.2427  -1.6749  -0.2209
 4SH  H3A   H  HCH2  0   0.249   3.8796  -1.1839   1.4258
 4SH  H22   H  HCR6  0   0.259   1.4558  -1.6358   2.2899
 4SH  H21   H  HCR6  0   0.259  -0.3258  -3.3273   2.3801
 4SH  H20   H  HCR6  0   0.267  -0.4201  -5.1304   0.6853
 4SH  H19   H  HCR6  0   0.245   1.2870  -5.2210  -1.1028
 4SH  H18   H  HCR6  0   0.254   3.0688  -3.5240  -1.2008

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
 4SH  C5   C1    aromatic  1.432  0.020  1.432
 4SH  C7   C1    aromatic  1.372  0.020  1.372
 4SH  C1   C2    single    1.484  0.020  1.484
 4SH  O1   C2    double    1.221  0.020  1.221
 4SH  C6   S1    aromatic  1.730  0.020  1.730
 4SH  S1   C7    aromatic  1.726  0.020  1.726
 4SH  C2   N2    single    1.350  0.020  1.350
 4SH  N2   C3    single    1.449  0.020  1.449
 4SH  N2   HN2   single    0.860  0.020  1.020
 4SH  C8   O2    double    1.216  0.020  1.216
 4SH  C3   C4    single    1.510  0.020  1.510
 4SH  C3   H3    single    0.970  0.020  1.090
 4SH  C3   H3A   single    0.970  0.020  1.090
 4SH  C7   N3    single    1.384  0.020  1.384
 4SH  N3   C8    single    1.357  0.020  1.357
 4SH  N3   HN3   single    0.860  0.020  1.020
 4SH  C16  O3    single    1.410  0.020  1.410
 4SH  O3   C15   single    1.411  0.020  1.411
 4SH  C22  C4    aromatic  1.396  0.020  1.396
 4SH  C4   C18   aromatic  1.391  0.020  1.391
 4SH  C17  N4    single    1.453  0.020  1.453
 4SH  N4   C14   single    1.453  0.020  1.453
 4SH  N4   C9    single    1.439  0.020  1.439
 4SH  C6   C5    aromatic  1.358  0.020  1.358
 4SH  C10  C5    single    1.500  0.020  1.500
 4SH  C13  C6    single    1.495  0.020  1.495
 4SH  C8   C9    single    1.516  0.020  1.516
 4SH  C9   H9    single    0.970  0.020  1.090
 4SH  C9   H9A   single    0.970  0.020  1.090
 4SH  C11  C10   single    1.527  0.020  1.527
 4SH  C10  H10   single    0.970  0.020  1.090
 4SH  C10  H10A  single    0.970  0.020  1.090
 4SH  C12  C11   single    1.525  0.020  1.525
 4SH  C11  H11   single    0.970  0.020  1.090
 4SH  C11  H11A  single    0.970  0.020  1.090
 4SH  C12  C13   single    1.528  0.020  1.528
 4SH  C12  H12   single    0.970  0.020  1.090
 4SH  C12  H12A  single    0.970  0.020  1.090
 4SH  C13  H13   single    0.970  0.020  1.090
 4SH  C13  H13A  single    0.970  0.020  1.090
 4SH  C15  C14   single    1.516  0.020  1.516
 4SH  C14  H14   single    0.970  0.020  1.090
 4SH  C14  H14A  single    0.970  0.020  1.090
 4SH  C15  H15   single    0.970  0.020  1.090
 4SH  C15  H15A  single    0.970  0.020  1.090
 4SH  C16  C17   single    1.516  0.020  1.516
 4SH  C16  H16   single    0.970  0.020  1.090
 4SH  C16  H16A  single    0.970  0.020  1.090
 4SH  C17  H17   single    0.970  0.020  1.090
 4SH  C17  H17A  single    0.970  0.020  1.090
 4SH  C18  C19   aromatic  1.390  0.020  1.390
 4SH  C18  H18   single    0.930  0.020  1.080
 4SH  C20  C19   aromatic  1.388  0.020  1.388
 4SH  C19  H19   single    0.930  0.020  1.080
 4SH  C21  C20   aromatic  1.390  0.020  1.390
 4SH  C20  H20   single    0.930  0.020  1.080
 4SH  C22  C21   aromatic  1.387  0.020  1.387
 4SH  C21  H21   single    0.930  0.020  1.080
 4SH  C22  H22   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
 4SH  N3    C8   C9   114.16  3.000
 4SH  C9    C8   O2   123.65  3.000
 4SH  N3    C8   O2   122.16  3.000
 4SH  H9A   C9   H9   106.07  3.000
 4SH  H9A   C9   N4   108.98  3.000
 4SH  H9    C9   N4   112.78  3.000
 4SH  H9A   C9   C8   106.53  3.000
 4SH  H9    C9   C8   110.78  3.000
 4SH  N4    C9   C8   111.36  3.000
 4SH  C17   N4   C14  110.15  3.000
 4SH  C14   N4   C9   111.63  3.000
 4SH  C17   N4   C9   112.23  3.000
 4SH  C16   O3   C15  110.93  3.000
 4SH  H14A  C14  H14  107.25  3.000
 4SH  H14A  C14  C15  109.48  3.000
 4SH  H14   C14  C15  108.98  3.000
 4SH  H14A  C14  N4   111.88  3.000
 4SH  H14   C14  N4   109.37  3.000
 4SH  C15   C14  N4   109.80  3.000
 4SH  H17A  C17  H17  107.17  3.000
 4SH  H17A  C17  C16  108.31  3.000
 4SH  H17   C17  C16  109.54  3.000
 4SH  H17A  C17  N4   110.17  3.000
 4SH  H17   C17  N4   111.68  3.000
 4SH  C16   C17  N4   109.88  3.000
 4SH  H15A  C15  H15  107.96  3.000
 4SH  H15A  C15  C14  109.27  3.000
 4SH  H15   C15  C14  110.02  3.000
 4SH  H15A  C15  O3   110.47  3.000
 4SH  H15   C15  O3   107.54  3.000
 4SH  C14   C15  O3   111.51  3.000
 4SH  H16A  C16  H16  107.91  3.000
 4SH  H16A  C16  C17  109.89  3.000
 4SH  H16   C16  C17  109.27  3.000
 4SH  H16A  C16  O3   107.50  3.000
 4SH  H16   C16  O3   110.57  3.000
 4SH  C17   C16  O3   111.62  3.000
 4SH  C7    C1   C5   112.44  3.000
 4SH  C7    C1   C2   123.38  3.000
 4SH  C5    C1   C2   123.94  3.000
 4SH  C7    S1   C6    91.32  3.000
 4SH  N2    C2   O1   123.69  3.000
 4SH  N2    C2   C1   114.44  3.000
 4SH  O1    C2   C1   121.84  3.000
 4SH  HN3   N3   C7   116.74  3.000
 4SH  HN3   N3   C8   117.79  3.000
 4SH  C7    N3   C8   125.44  3.000
 4SH  C10   C5   C6   122.06  3.000
 4SH  C10   C5   C1   125.60  3.000
 4SH  C6    C5   C1   112.32  3.000
 4SH  C13   C6   C5   125.71  3.000
 4SH  C13   C6   S1   122.06  3.000
 4SH  C5    C6   S1   112.22  3.000
 4SH  N3    C7   S1   122.04  3.000
 4SH  N3    C7   C1   126.19  3.000
 4SH  S1    C7   C1   111.69  3.000
 4SH  H10A  C10  H10  105.92  3.000
 4SH  H10A  C10  C11  109.81  3.000
 4SH  H10   C10  C11  110.18  3.000
 4SH  H10A  C10  C5   110.19  3.000
 4SH  H10   C10  C5   109.51  3.000
 4SH  C11   C10  C5   111.10  3.000
 4SH  H11A  C11  H11  106.64  3.000
 4SH  H11A  C11  C12  109.02  3.000
 4SH  H11   C11  C12  110.43  3.000
 4SH  H11A  C11  C10  109.50  3.000
 4SH  H11   C11  C10  109.45  3.000
 4SH  C12   C11  C10  111.66  3.000
 4SH  H12A  C12  H12  106.83  3.000
 4SH  H12A  C12  C13  109.42  3.000
 4SH  H12   C12  C13  109.61  3.000
 4SH  H12A  C12  C11  110.39  3.000
 4SH  H12   C12  C11  109.60  3.000
 4SH  C13   C12  C11  110.90  3.000
 4SH  H13A  C13  H13  106.31  3.000
 4SH  H13A  C13  C12  110.30  3.000
 4SH  H13   C13  C12  109.75  3.000
 4SH  H13A  C13  C6   110.86  3.000
 4SH  H13   C13  C6   109.98  3.000
 4SH  C12   C13  C6   109.59  3.000
 4SH  HN2   N2   C3   116.92  3.000
 4SH  HN2   N2   C2   118.42  3.000
 4SH  C3    N2   C2   124.59  3.000
 4SH  H3A   C3   H3   107.40  3.000
 4SH  H3A   C3   C4   111.08  3.000
 4SH  H3    C3   C4   110.65  3.000
 4SH  H3A   C3   N2   108.44  3.000
 4SH  H3    C3   N2   109.05  3.000
 4SH  C4    C3   N2   110.12  3.000
 4SH  C18   C4   C22  118.88  3.000
 4SH  C18   C4   C3   121.09  3.000
 4SH  C22   C4   C3   119.95  3.000
 4SH  H22   C22  C21  119.58  3.000
 4SH  H22   C22  C4   119.87  3.000
 4SH  C21   C22  C4   120.55  3.000
 4SH  H21   C21  C20  120.12  3.000
 4SH  H21   C21  C22  119.69  3.000
 4SH  C20   C21  C22  120.19  3.000
 4SH  H20   C20  C19  120.21  3.000
 4SH  H20   C20  C21  120.16  3.000
 4SH  C19   C20  C21  119.63  3.000
 4SH  H19   C19  C18  119.80  3.000
 4SH  H19   C19  C20  120.08  3.000
 4SH  C18   C19  C20  120.12  3.000
 4SH  H18   C18  C19  119.57  3.000
 4SH  H18   C18  C4   119.80  3.000
 4SH  C19   C18  C4   120.63  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
 4SH  CONST_01  S1   C6   C5   C1     0.00   0.0  0
 4SH  CONST_02  C6   S1   C7   C1     0.00   0.0  0
 4SH  CONST_03  C5   C1   C7   S1     0.00   0.0  0
 4SH  CONST_04  C7   S1   C6   C5     0.00   0.0  0
 4SH  CONST_05  C7   C1   C5   C6     0.00   0.0  0
 4SH  CONST_06  C20  C21  C22  C4     0.00   0.0  0
 4SH  CONST_07  C20  C19  C18  C4     0.00   0.0  0
 4SH  CONST_08  C19  C18  C4   C22    0.00   0.0  0
 4SH  CONST_09  C19  C20  C21  C22    0.00   0.0  0
 4SH  CONST_10  C18  C19  C20  C21    0.00   0.0  0
 4SH  CONST_11  C18  C4   C22  C21    0.00   0.0  0
 4SH  CONST_12  C2   C1   C7   S1   180.00   0.0  0
 4SH  CONST_13  C6   C5   C1   C2   180.00   0.0  0
 4SH  CONST_14  C10  C5   C1   C2     0.00   0.0  0
 4SH  CONST_15  C5   C1   C7   N3   180.00   0.0  0
 4SH  CONST_16  C6   S1   C7   N3   180.00   0.0  0
 4SH  CONST_17  C21  C22  C4   C3   180.00   0.0  0
 4SH  CONST_18  C19  C18  C4   C3   180.00   0.0  0
 4SH  CONST_19  H21  C21  C22  C4   180.00   0.0  0
 4SH  CONST_20  H19  C19  C18  C4   180.00   0.0  0
 4SH  CONST_21  H18  C18  C4   C22  180.00   0.0  0
 4SH  CONST_22  H20  C20  C21  C22  180.00   0.0  0
 4SH  CONST_23  H22  C22  C21  C20  180.00   0.0  0
 4SH  CONST_25  C1   C7   N3   C8   180.00   0.0  0
 4SH  CONST_26  S1   C7   N3   C8     0.00   0.0  0
 4SH  CONST_27  HN3  N3   C7   C1     0.00   0.0  0
 4SH  CONST_28  C7   N3   C8   O2     0.00   0.0  0
 4SH  CONST_29  C7   N3   C8   C9   180.00   0.0  0
 4SH  CONST_31  HN2  N2   C2   C1     0.00   0.0  0
 4SH  CONST_32  C3   N2   C2   O1     0.00   0.0  0
 4SH  Var_01    O3   C16  C17  N4    56.86  30.0  1
 4SH  Var_02    O3   C15  C14  N4   -57.26  30.0  1
 4SH  Var_03    C16  C17  N4   C14  -56.33  30.0  1
 4SH  Var_04    C15  C14  N4   C17   56.53  30.0  1
 4SH  Var_05    C11  C10  C5   C1   163.82  30.0  1
 4SH  Var_06    C12  C13  C6   S1   164.66  30.0  1
 4SH  Var_07    C12  C11  C10  C5    45.06  30.0  1
 4SH  Var_08    C11  C12  C13  C6    46.22  30.0  1
 4SH  Var_09    C13  C12  C11  C10  -63.32  30.0  1
 4SH  Var_10    C17  N4   C9   C8   -69.45  30.0  2
 4SH  Var_11    C22  C4   C3   N2   -72.73  30.0  2
 4SH  Var_12    N4   C9   C8   O2   -46.25  30.0  3
 4SH  Var_13    C4   C3   N2   C2   102.96  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
 4SH  plan-1  C3   0.020
 4SH  plan-1  C4   0.020
 4SH  plan-1  C22  0.020
 4SH  plan-1  C21  0.020
 4SH  plan-1  C20  0.020
 4SH  plan-1  C19  0.020
 4SH  plan-1  C18  0.020
 4SH  plan-1  H22  0.020
 4SH  plan-1  H21  0.020
 4SH  plan-1  H20  0.020
 4SH  plan-1  H19  0.020
 4SH  plan-1  H18  0.020
 4SH  plan-2  C8   0.020
 4SH  plan-2  O2   0.020
 4SH  plan-2  C9   0.020
 4SH  plan-2  N3   0.020
 4SH  plan-2  C7   0.020
 4SH  plan-2  HN3  0.020
 4SH  plan-3  C1   0.020
 4SH  plan-3  O1   0.020
 4SH  plan-3  S1   0.020
 4SH  plan-3  C2   0.020
 4SH  plan-3  N3   0.020
 4SH  plan-3  C5   0.020
 4SH  plan-3  C6   0.020
 4SH  plan-3  C7   0.020
 4SH  plan-3  C10  0.020
 4SH  plan-3  C13  0.020
 4SH  plan-3  N2   0.020
 4SH  plan-3  C3   0.020
 4SH  plan-3  HN2  0.020

