# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:47:36 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-(propylsulfonyl)-D-threonyl-N-(4-carbamimidoylbenzyl)-L-methioninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[S](=O)(=O)N[C@H]([C@H](C)O)C(=O)N[C@@H](CCSC)C(=O)NCc1ccc(cc1)C(N)=N
#
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
 PSM  PSM  N-(propylsulfonyl)-D-threonyl-N-(4-carbamimidoylbenzyl)-L-methioninamide  peptide  65  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PSM
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
 PSM  C15   C  C     0   0.545  -2.1519  -0.5835   0.1038
 PSM  O1    O  O     0  -0.480  -1.9922  -0.6609   1.3121
 PSM  C1    C  CH1   0   0.017  -4.0979  -1.8997  -0.7720
 PSM  O2    O  OH1   0  -0.659  -4.3496  -2.5851   0.4343
 PSM  N4    N  NC1   0  -0.731  -4.4681   0.2180   0.3612
 PSM  C5    C  CH1   0  -0.228  -3.5487  -0.4791  -0.5068
 PSM  S1    S  S     0   1.363  -4.2001   1.8094   0.7185
 PSM  O4    O  OS    0  -0.671  -4.4046   1.9987   2.1488
 PSM  O3    O  OS    0  -0.666  -2.9303   2.2097   0.1203
 PSM  C9    C  CH2   0  -0.582  -5.5130   2.6508  -0.1508
 PSM  C8    C  CH2   0  -0.444  -5.4470   4.1587   0.0499
 PSM  C7    C  CH3   0  -0.662  -6.5857   4.8517  -0.6859
 PSM  N17   N  NH1   0  -0.624  -1.1632  -0.6724  -0.7972
 PSM  C18   C  CH1   0  -0.229   0.2253  -0.8756  -0.4601
 PSM  C28   C  C     0   0.579   1.0557   0.1923  -1.1655
 PSM  O30   O  O     0  -0.489   0.8663   0.4484  -2.3451
 PSM  C19   C  CH2   0  -0.412   0.7187  -2.2614  -0.8929
 PSM  C20   C  CH2   0  -0.554  -0.0313  -3.3761  -0.1823
 PSM  S2    S  S2    0  -0.032   0.5973  -4.9842  -0.7362
 PSM  C6    C  CH3   0  -0.765  -0.4759  -6.0723   0.2249
 PSM  N31   N  NH1   0  -0.633   2.0014   0.7653  -0.4109
 PSM  C32   C  CH2   0  -0.329   2.9237   1.7664  -0.8967
 PSM  C25   C  CR6   0   0.079   4.3171   1.5516  -0.3700
 PSM  C16   C  CR16  0  -0.275   4.9028   0.2866  -0.3656
 PSM  C17   C  CR16  0  -0.259   6.1964   0.1092   0.0916
 PSM  C22   C  CR6   0   0.036   6.9480   1.1924   0.5453
 PSM  C26   C  C     0   0.334   8.3367   0.9679   1.0332
 PSM  N1    N  N     0  -0.651   8.6513  -0.1909   1.4705
 PSM  N2    N  NH2   0  -0.823   9.1481   2.0657   1.0116
 PSM  C23   C  CR16  0  -0.276   6.3622   2.4553   0.5442
 PSM  C24   C  CR16  0  -0.293   5.0599   2.6285   0.0965
 PSM  H1    H  HCH1  0   0.237  -3.3412  -2.4245  -1.3718
 PSM  HO2   H  HOH1  0   0.450  -3.5297  -2.7023   0.9257
 PSM  HN4   H  HNC1  0   0.410  -4.7716  -0.3122   1.1710
 PSM  H5    H  HCH1  0   0.295  -3.4964   0.0329  -1.4709
 PSM  H91   H  HCH2  0   0.289  -5.4159   2.3790  -1.2039
 PSM  H92   H  HCH2  0   0.293  -6.4496   2.2336   0.2231
 PSM  H81   H  HCH2  0   0.245  -5.5038   4.3905   1.1149
 PSM  H82   H  HCH2  0   0.246  -4.4897   4.5381  -0.3115
 PSM  H71   H  HCH3  0   0.228  -6.5386   4.6632  -1.7591
 PSM  H72   H  HCH3  0   0.228  -7.5563   4.5067  -0.3279
 PSM  H73   H  HCH3  0   0.241  -6.5392   5.9297  -0.5349
 PSM  H17   H  HNH1  0   0.406  -1.3810  -0.5544  -1.7757
 PSM  H18   H  HCH1  0   0.286   0.3180  -0.7830   0.6229
 PSM  H191  H  HCH2  0   0.253   0.6070  -2.3631  -1.9753
 PSM  H192  H  HCH2  0   0.257   1.7863  -2.3353  -0.6702
 PSM  H201  H  HCH2  0   0.269   0.0885  -3.2924   0.8998
 PSM  H202  H  HCH2  0   0.249  -1.0984  -3.3246  -0.4088
 PSM  H61   H  HCH3  0   0.263  -0.3311  -5.9243   1.2941
 PSM  H62   H  HCH3  0   0.260  -1.5243  -5.9113  -0.0235
 PSM  H63   H  HCH3  0   0.276  -0.2144  -7.0990  -0.0236
 PSM  H31   H  HNH1  0   0.410   2.0236   0.5548   0.5748
 PSM  H321  H  HCH2  0   0.275   2.9269   1.7188  -1.9863
 PSM  H322  H  HCH2  0   0.265   2.5764   2.7674  -0.6267
 PSM  H16   H  HCR6  0   0.253   4.3458  -0.5711  -0.7235
 PSM  H2    H  HCR6  0   0.256   6.6375  -0.8784   0.0909
 PSM  HN1   H  H     0   0.323   9.6292  -0.2247   1.7456
 PSM  HN21  H  HNH2  0   0.395   8.9698   2.7819   0.3270
 PSM  HN22  H  HNH2  0   0.391  10.1281   1.9211   1.1969
 PSM  H23   H  HCR6  0   0.259   6.9025   3.3162   0.9162
 PSM  H24   H  HCR6  0   0.258   4.6192   3.6180   0.1174
 PSM  C3    C  CH3   0  -0.671  -5.3881  -1.8604  -1.5660
 PSM  H31A  H  HCH3  0   0.238  -6.1710  -1.3174  -1.0373
 PSM  H32   H  HCH3  0   0.237  -5.2224  -1.3717  -2.5257
 PSM  H33   H  HCH3  0   0.246  -5.7412  -2.8725  -1.7635

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
 PSM  C15  O1    double    1.221  0.020  1.221
 PSM  C15  N17   single    1.341  0.020  1.341
 PSM  C15  C5    single    1.528  0.020  1.528
 PSM  N17  C18   single    1.443  0.020  1.443
 PSM  N17  H17   single    0.860  0.020  1.020
 PSM  C18  C19   single    1.533  0.020  1.533
 PSM  C18  C28   single    1.526  0.020  1.526
 PSM  C18  H18   single    0.970  0.020  1.090
 PSM  C19  C20   single    1.520  0.020  1.520
 PSM  C19  H191  single    0.970  0.020  1.090
 PSM  C19  H192  single    0.970  0.020  1.090
 PSM  C20  S2    single    1.813  0.020  1.813
 PSM  C20  H201  single    0.970  0.020  1.090
 PSM  C20  H202  single    0.970  0.020  1.090
 PSM  C28  O30   double    1.222  0.020  1.222
 PSM  C28  N31   single    1.339  0.020  1.339
 PSM  N31  C32   single    1.445  0.020  1.445
 PSM  N31  H31   single    0.860  0.020  1.020
 PSM  C32  C25   single    1.505  0.020  1.505
 PSM  C32  H321  single    0.970  0.020  1.090
 PSM  C32  H322  single    0.970  0.020  1.090
 PSM  C16  C17   aromatic  1.384  0.020  1.384
 PSM  C16  C25   aromatic  1.394  0.020  1.394
 PSM  C16  H16   single    0.930  0.020  1.080
 PSM  C17  C22   aromatic  1.394  0.020  1.394
 PSM  C17  H2    single    0.930  0.020  1.080
 PSM  C22  C23   aromatic  1.392  0.020  1.392
 PSM  C22  C26   single    1.489  0.020  1.489
 PSM  C23  C24   aromatic  1.388  0.020  1.388
 PSM  C23  H23   single    0.930  0.020  1.080
 PSM  C24  C25   aromatic  1.389  0.020  1.389
 PSM  C24  H24   single    0.930  0.020  1.080
 PSM  C26  N1    double    1.278  0.020  1.278
 PSM  C26  N2    single    1.365  0.020  1.365
 PSM  N1   HN1   single    0.890  0.020  1.040
 PSM  S2   C6    single    1.805  0.020  1.805
 PSM  C1   O2    single    1.410  0.020  1.410
 PSM  C1   C5    single    1.546  0.020  1.546
 PSM  C1   C3    single    1.515  0.020  1.515
 PSM  C1   H1    single    0.970  0.020  1.090
 PSM  O2   HO2   single    0.850  0.020  0.980
 PSM  N4   C5    single    1.444  0.020  1.444
 PSM  N4   S1    single    1.653  0.020  1.653
 PSM  N4   HN4   single    0.890  0.020  1.040
 PSM  C5   H5    single    0.970  0.020  1.090
 PSM  C3   H31A  single    0.970  0.020  1.090
 PSM  C3   H32   single    0.970  0.020  1.090
 PSM  C3   H33   single    0.970  0.020  1.090
 PSM  S1   O4    double    1.457  0.020  1.457
 PSM  S1   O3    double    1.460  0.020  1.460
 PSM  S1   C9    single    1.785  0.020  1.785
 PSM  C9   C8    single    1.523  0.020  1.523
 PSM  C9   H91   single    0.970  0.020  1.090
 PSM  C9   H92   single    0.970  0.020  1.090
 PSM  C8   C7    single    1.523  0.020  1.523
 PSM  C8   H81   single    0.970  0.020  1.090
 PSM  C8   H82   single    0.970  0.020  1.090
 PSM  N2   HN21  single    0.890  0.020  1.040
 PSM  N2   HN22  single    0.890  0.020  1.040
 PSM  C6   H61   single    0.970  0.020  1.090
 PSM  C6   H62   single    0.970  0.020  1.090
 PSM  C6   H63   single    0.970  0.020  1.090
 PSM  C7   H71   single    0.970  0.020  1.090
 PSM  C7   H72   single    0.970  0.020  1.090
 PSM  C7   H73   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
 PSM  N17   C15  C5    114.21  3.000
 PSM  C5    C15  O1    121.28  3.000
 PSM  N17   C15  O1    124.35  3.000
 PSM  H1    C1   C3    108.22  3.000
 PSM  H1    C1   C5    106.73  3.000
 PSM  C3    C1   C5    111.62  3.000
 PSM  H1    C1   O2    110.96  3.000
 PSM  C3    C1   O2    107.99  3.000
 PSM  C5    C1   O2    111.30  3.000
 PSM  HO2   O2   C1    110.10  3.000
 PSM  HN4   N4   S1    112.28  3.000
 PSM  HN4   N4   C5    114.72  3.000
 PSM  S1    N4   C5    119.44  3.000
 PSM  H5    C5   N4    109.55  3.000
 PSM  H5    C5   C1    107.23  3.000
 PSM  N4    C5   C1    108.70  3.000
 PSM  H5    C5   C15   109.93  3.000
 PSM  N4    C5   C15   112.01  3.000
 PSM  C1    C5   C15   109.30  3.000
 PSM  C9    S1   O3    108.11  3.000
 PSM  C9    S1   O4    108.28  3.000
 PSM  O3    S1   O4    119.26  3.000
 PSM  C9    S1   N4    103.25  3.000
 PSM  O3    S1   N4    108.45  3.000
 PSM  O4    S1   N4    108.33  3.000
 PSM  H92   C9   H91   108.16  3.000
 PSM  H92   C9   C8    111.75  3.000
 PSM  H91   C9   C8    111.70  3.000
 PSM  H92   C9   S1    106.50  3.000
 PSM  H91   C9   S1    106.68  3.000
 PSM  C8    C9   S1    111.76  3.000
 PSM  H82   C8   H81   107.15  3.000
 PSM  H82   C8   C7    109.74  3.000
 PSM  H81   C8   C7    109.63  3.000
 PSM  H82   C8   C9    109.79  3.000
 PSM  H81   C8   C9    109.68  3.000
 PSM  C7    C8   C9    110.77  3.000
 PSM  H73   C7   H72   107.79  3.000
 PSM  H73   C7   H71   107.79  3.000
 PSM  H72   C7   H71   107.86  3.000
 PSM  H73   C7   C8    110.58  3.000
 PSM  H72   C7   C8    111.28  3.000
 PSM  H71   C7   C8    111.38  3.000
 PSM  H17   N17  C18   116.77  3.000
 PSM  H17   N17  C15   118.99  3.000
 PSM  C18   N17  C15   124.19  3.000
 PSM  H18   C18  C19   109.24  3.000
 PSM  H18   C18  C28   110.69  3.000
 PSM  C19   C18  C28   109.08  3.000
 PSM  H18   C18  N17   107.56  3.000
 PSM  C28   C18  N17   108.49  3.000
 PSM  C19   C18  N17   111.77  3.000
 PSM  N31   C28  O30   124.34  3.000
 PSM  N31   C28  C18   115.05  3.000
 PSM  O30   C28  C18   120.58  3.000
 PSM  H192  C19  H191  107.18  3.000
 PSM  H192  C19  C20   109.70  3.000
 PSM  H191  C19  C20   110.15  3.000
 PSM  H192  C19  C18   108.53  3.000
 PSM  H191  C19  C18   109.32  3.000
 PSM  C20   C19  C18   111.85  3.000
 PSM  H202  C20  H201  108.01  3.000
 PSM  H202  C20  S2    108.49  3.000
 PSM  H201  C20  S2    109.43  3.000
 PSM  H202  C20  C19   110.53  3.000
 PSM  H201  C20  C19   110.67  3.000
 PSM  S2    C20  C19   109.67  3.000
 PSM  C6    S2   C20    99.55  3.000
 PSM  H63   C6   H62   108.58  3.000
 PSM  H63   C6   H61   108.69  3.000
 PSM  H62   C6   H61   109.37  3.000
 PSM  H63   C6   S2    107.71  3.000
 PSM  H62   C6   S2    111.20  3.000
 PSM  H61   C6   S2    111.20  3.000
 PSM  H31   N31  C32   117.34  3.000
 PSM  H31   N31  C28   118.51  3.000
 PSM  C32   N31  C28   123.90  3.000
 PSM  H322  C32  H321  106.72  3.000
 PSM  H322  C32  C25   109.77  3.000
 PSM  H321  C32  C25   109.91  3.000
 PSM  H322  C32  N31   110.40  3.000
 PSM  H321  C32  N31   107.90  3.000
 PSM  C25   C32  N31   111.98  3.000
 PSM  C24   C25  C16   118.55  3.000
 PSM  C24   C25  C32   120.14  3.000
 PSM  C16   C25  C32   121.30  3.000
 PSM  H16   C16  C17   119.23  3.000
 PSM  H16   C16  C25   120.09  3.000
 PSM  C17   C16  C25   120.68  3.000
 PSM  H2    C17  C22   119.32  3.000
 PSM  H2    C17  C16   119.88  3.000
 PSM  C22   C17  C16   120.79  3.000
 PSM  C23   C22  C26   121.98  3.000
 PSM  C26   C22  C17   119.49  3.000
 PSM  C23   C22  C17   118.53  3.000
 PSM  N2    C26  N1    126.04  3.000
 PSM  N2    C26  C22   115.33  3.000
 PSM  N1    C26  C22   118.58  3.000
 PSM  HN1   N1   C26   111.07  3.000
 PSM  HN22  N2   HN21  113.54  3.000
 PSM  HN22  N2   C26   117.36  3.000
 PSM  HN21  N2   C26   118.53  3.000
 PSM  H23   C23  C24   118.68  3.000
 PSM  H23   C23  C22   120.74  3.000
 PSM  C24   C23  C22   120.56  3.000
 PSM  H24   C24  C23   119.31  3.000
 PSM  H24   C24  C25   119.81  3.000
 PSM  C23   C24  C25   120.89  3.000
 PSM  H33   C3   H32   107.83  3.000
 PSM  H33   C3   H31A  108.53  3.000
 PSM  H32   C3   H31A  108.24  3.000
 PSM  H33   C3   C1    110.28  3.000
 PSM  H32   C3   C1    110.10  3.000
 PSM  H31A  C3   C1    111.74  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
 PSM  CONST_01  C22   C17  C16  C25     0.00   0.0  0
 PSM  CONST_02  C22   C23  C24  C25     0.00   0.0  0
 PSM  CONST_03  C23   C22  C17  C16     0.00   0.0  0
 PSM  CONST_04  C23   C24  C25  C16     0.00   0.0  0
 PSM  CONST_05  C24   C25  C16  C17     0.00   0.0  0
 PSM  CONST_06  C24   C23  C22  C17     0.00   0.0  0
 PSM  CONST_07  C17   C16  C25  C32   180.00   0.0  0
 PSM  CONST_08  C23   C24  C25  C32   180.00   0.0  0
 PSM  CONST_09  C26   C22  C17  C16   180.00   0.0  0
 PSM  CONST_10  C24   C23  C22  C26   180.00   0.0  0
 PSM  CONST_11  H2    C17  C16  C25   180.00   0.0  0
 PSM  CONST_12  H23   C23  C24  C25   180.00   0.0  0
 PSM  CONST_13  H24   C24  C25  C16   180.00   0.0  0
 PSM  CONST_14  H16   C16  C17  C22   180.00   0.0  0
 PSM  CONST_15  HN1   N1   C26  C22   180.00   0.0  0
 PSM  CONST_17  HN22  N2   C26  C22   180.00   0.0  0
 PSM  CONST_18  C18   N17  C15  O1      0.00   0.0  0
 PSM  CONST_19  C18   N17  C15  C5    180.00   0.0  0
 PSM  CONST_20  C32   N31  C28  C18   180.00   0.0  0
 PSM  CONST_21  C32   N31  C28  O30     0.00   0.0  0
 PSM  CONST_22  H17   N17  C15  O1    180.00   0.0  0
 PSM  CONST_23  H31   N31  C28  C18     0.00   0.0  0
 PSM  Var_01    C16   C25  C32  N31    45.42  30.0  2
 PSM  Var_02    N1    C26  C22  C17   -24.42  30.0  2
 PSM  Var_03    C25   C32  N31  C28  -139.06  30.0  3
 PSM  Var_04    C8    C9   S1   N4   -179.96  30.0  3
 PSM  Var_05    O4    S1   N4   C5   -135.30  30.0  3
 PSM  Var_06    C7    C8   C9   S1   -179.29  30.0  3
 PSM  Var_07    S2    C20  C19  C18  -179.99  30.0  3
 PSM  Var_08    H71   C7   C8   C9    -60.53  30.0  3
 PSM  Var_09    H61   C6   S2   C20   -61.82  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
 PSM  chir_01  C1   O2   C5   C3   positiv
 PSM  chir_02  C5   N4   C1   C15  positiv
 PSM  chir_03  C18  N17  C28  C19  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
 PSM  plan-1  C32   0.020
 PSM  plan-1  C25   0.020
 PSM  plan-1  C16   0.020
 PSM  plan-1  C17   0.020
 PSM  plan-1  C22   0.020
 PSM  plan-1  C26   0.020
 PSM  plan-1  C23   0.020
 PSM  plan-1  C24   0.020
 PSM  plan-1  H16   0.020
 PSM  plan-1  H2    0.020
 PSM  plan-1  H23   0.020
 PSM  plan-1  H24   0.020
 PSM  plan-2  C15   0.020
 PSM  plan-2  O1    0.020
 PSM  plan-2  C5    0.020
 PSM  plan-2  N17   0.020
 PSM  plan-2  C18   0.020
 PSM  plan-2  H17   0.020
 PSM  plan-3  C18   0.020
 PSM  plan-3  C28   0.020
 PSM  plan-3  O30   0.020
 PSM  plan-3  N31   0.020
 PSM  plan-3  C32   0.020
 PSM  plan-3  H31   0.020
 PSM  plan-4  C22   0.020
 PSM  plan-4  C26   0.020
 PSM  plan-4  N1    0.020
 PSM  plan-4  N2    0.020
 PSM  plan-4  HN1   0.020
 PSM  plan-4  HN21  0.020
 PSM  plan-4  HN22  0.020

