# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 03:52:45 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])NCCC[C@H](NC(=O)CN1CCC[C@H](N[S](=O)(=O)Cc2ccccc2)C1=O)C=O
#
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
 0IT  0IT  amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium  peptide  63  32  .  2022-08-09  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_0IT
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
 0IT  C3    C  CH2   0  -0.702   3.0396  -1.4387  -0.1099
 0IT  S     S  S     0   1.365   4.0981  -0.0451  -0.5354
 0IT  C11   C  CR6   0   0.117   3.8772  -2.6711   0.0279
 0IT  C6    C  CR16  0  -0.279   4.0974  -3.4990  -1.0695
 0IT  C5    C  CR16  0  -0.243   4.8835  -4.6354  -0.9456
 0IT  C4    C  CR16  0  -0.261   5.4648  -4.9501   0.2761
 0IT  C31   C  CR16  0  -0.242   5.2533  -4.1255   1.3735
 0IT  C21   C  CR16  0  -0.280   4.4657  -2.9899   1.2488
 0IT  O2S   O  OS    0  -0.666   4.7144  -0.3442  -1.8189
 0IT  O1S   O  OS    0  -0.666   4.9451   0.2323   0.6173
 0IT  N     N  NC1   0  -0.732   3.1611   1.2763  -0.7722
 0IT  CA    C  CH1   0  -0.201   2.6668   2.1171   0.2957
 0IT  CB    C  CH2   0  -0.439   2.9250   3.5850  -0.0108
 0IT  CG    C  CH2   0  -0.483   2.3206   4.4248   1.0979
 0IT  CD    C  CH2   0  -0.272   0.8223   4.2186   1.1549
 0IT  C     C  C     0   0.589   1.1973   1.8190   0.6025
 0IT  O     O  O     0  -0.484   0.7429   0.6996   0.4199
 0IT  N1    N  NT    0  -0.459   0.4541   2.8069   1.1408
 0IT  CA1   C  CH2   0  -0.454  -0.9327   2.5084   1.3798
 0IT  C1    C  C     0   0.564  -1.7265   2.4077   0.0828
 0IT  O1    O  O     0  -0.477  -1.2659   2.7378  -0.9943
 0IT  N2    N  NH1   0  -0.640  -2.9737   1.9265   0.2371
 0IT  CA2   C  CH1   0  -0.185  -3.9199   1.8963  -0.8424
 0IT  C2    C  C1    0   0.184  -4.4337   3.2749  -1.1952
 0IT  O2    O  O     0  -0.362  -4.1646   4.2789  -0.5922
 0IT  CB1   C  CH2   0  -0.473  -5.1086   0.9900  -0.5160
 0IT  CG1   C  CH2   0  -0.470  -4.7067  -0.4667  -0.3282
 0IT  CD1   C  CH2   0  -0.274  -5.9260  -1.3301  -0.0515
 0IT  NE    N  NH1   0  -0.637  -5.5205  -2.7111   0.1471
 0IT  CZ    C  C     0   0.830  -6.3571  -3.7058   0.4100
 0IT  NH1   N  NH2   0  -0.817  -7.6604  -3.4801   0.4946
 0IT  NH2   N  NC2   1  -0.823  -5.8877  -4.9354   0.5809
 0IT  H11   H  HCH2  0   0.314   2.2992  -1.5254  -0.9052
 0IT  H2A   H  HCH2  0   0.317   2.5251  -1.1747   0.8125
 0IT  H6    H  HCR6  0   0.256   3.6442  -3.2588  -2.0234
 0IT  H5    H  HCR6  0   0.259   5.0436  -5.2749  -1.8038
 0IT  H4    H  HCR6  0   0.259   6.0776  -5.8368   0.3734
 0IT  H3    H  HCR6  0   0.259   5.7024  -4.3667   2.3283
 0IT  H21   H  HCR6  0   0.256   4.3008  -2.3526   2.1088
 0IT  H     H  HNC1  0   0.418   2.6203   1.2540  -1.6285
 0IT  HA    H  HCH1  0   0.303   3.2180   1.8623   1.2062
 0IT  HB2   H  HCH2  0   0.262   3.9996   3.7481  -0.0958
 0IT  HB3   H  HCH2  0   0.240   2.4773   3.8491  -0.9736
 0IT  HG2   H  HCH2  0   0.242   2.7738   4.1557   2.0559
 0IT  HG3   H  HCH2  0   0.263   2.5191   5.4846   0.9367
 0IT  HD1   H  HCH2  0   0.258   0.4206   4.6624   2.0673
 0IT  HD2   H  HCH2  0   0.244   0.3425   4.7230   0.3102
 0IT  HA2   H  HCH2  0   0.295  -1.0360   1.5868   1.9549
 0IT  HA3   H  HCH2  0   0.301  -1.3619   3.3056   1.9902
 0IT  HXT   H  H     0   0.208  -5.1012   3.2888  -2.0756
 0IT  H2    H  HNH1  0   0.408  -3.3191   1.7647   1.1710
 0IT  HA1   H  HCH1  0   0.288  -3.4348   1.5093  -1.7461
 0IT  HB21  H  HCH2  0   0.258  -5.6099   1.3625   0.3826
 0IT  HB31  H  HCH2  0   0.265  -5.8316   1.0680  -1.3318
 0IT  HG21  H  HCH2  0   0.255  -4.2033  -0.8276  -1.2290
 0IT  HG31  H  HCH2  0   0.254  -4.0003  -0.5643   0.5000
 0IT  HD21  H  HCH2  0   0.260  -6.4445  -0.9628   0.8387
 0IT  HD31  H  HCH2  0   0.261  -6.6202  -1.2633  -0.8935
 0IT  HE    H  HNH1  0   0.428  -4.5352  -2.9230   0.1203
 0IT  HH11  H  HNH2  0   0.448  -8.0538  -2.5655   0.3537
 0IT  HH12  H  HNH2  0   0.434  -8.3059  -4.2280   0.6834
 0IT  HH21  H  HNC2  0   0.431  -6.4957  -5.6961   0.8319
 0IT  HH22  H  HNC2  0   0.433  -4.8999  -5.1229   0.5628

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
 0IT  N    CA    single    1.458  0.019  1.458
 0IT  N    H     single    0.860  0.020  0.860
 0IT  CA   CB    single    1.521  0.033  1.521
 0IT  CA   C     single    1.525  0.021  1.525
 0IT  CA   HA    single    0.970  0.020  0.970
 0IT  CB   CG    single    1.517  0.020  1.517
 0IT  CB   HB2   single    0.970  0.020  1.090
 0IT  CB   HB3   single    0.970  0.020  1.090
 0IT  CG   CD    single    1.513  0.020  1.513
 0IT  CG   HG2   single    0.970  0.020  1.090
 0IT  CG   HG3   single    0.970  0.020  1.090
 0IT  CD   HD1   single    0.970  0.020  1.090
 0IT  CD   HD2   single    0.970  0.020  1.090
 0IT  C    O     double    1.231  0.020  1.231
 0IT  N1   CA1   single    1.439  0.020  1.439
 0IT  CD   N1    single    1.459  0.020  1.459
 0IT  CA1  C1    single    1.524  0.020  1.524
 0IT  CA1  HA2   single    0.970  0.020  1.090
 0IT  CA1  HA3   single    0.970  0.020  1.090
 0IT  C1   O1    double    1.217  0.020  1.217
 0IT  N2   CA2   single    1.436  0.020  1.436
 0IT  N2   H2    single    0.860  0.020  1.020
 0IT  CA2  C2    single    1.513  0.020  1.513
 0IT  CA2  CB1   single    1.530  0.020  1.530
 0IT  CA2  HA1   single    0.970  0.020  1.090
 0IT  C2   O2    double    1.202  0.020  1.202
 0IT  C2   HXT   single    0.930  0.020  1.080
 0IT  CB1  CG1   single    1.523  0.020  1.523
 0IT  CB1  HB21  single    0.970  0.020  1.090
 0IT  CB1  HB31  single    0.970  0.020  1.090
 0IT  CG1  CD1   single    1.520  0.020  1.520
 0IT  CG1  HG21  single    0.970  0.020  1.090
 0IT  CG1  HG31  single    0.970  0.020  1.090
 0IT  CD1  NE    single    1.453  0.020  1.453
 0IT  CD1  HD21  single    0.970  0.020  1.090
 0IT  CD1  HD31  single    0.970  0.020  1.090
 0IT  NE   CZ    single    1.326  0.020  1.326
 0IT  NE   HE    single    0.860  0.020  1.020
 0IT  CZ   NH1   single    1.325  0.020  1.325
 0IT  CZ   NH2   double    1.327  0.020  1.327
 0IT  NH1  HH11  single    0.860  0.020  1.020
 0IT  NH1  HH12  single    0.860  0.020  1.020
 0IT  NH2  HH21  single    0.860  0.020  1.020
 0IT  NH2  HH22  single    0.860  0.020  1.020
 0IT  C3   C11   single    1.497  0.020  1.497
 0IT  C3   S     single    1.801  0.020  1.801
 0IT  C3   H11   single    0.970  0.020  1.090
 0IT  C3   H2A   single    0.970  0.020  1.090
 0IT  C11  C21   aromatic  1.392  0.020  1.392
 0IT  C11  C6    aromatic  1.392  0.020  1.392
 0IT  C21  C31   aromatic  1.388  0.020  1.388
 0IT  C21  H21   single    0.930  0.020  1.080
 0IT  C31  C4    aromatic  1.389  0.020  1.389
 0IT  C31  H3    single    0.930  0.020  1.080
 0IT  C4   C5    aromatic  1.389  0.020  1.389
 0IT  C4   H4    single    0.930  0.020  1.080
 0IT  C5   C6    aromatic  1.387  0.020  1.387
 0IT  C5   H5    single    0.930  0.020  1.080
 0IT  C6   H6    single    0.930  0.020  1.080
 0IT  S    O1S   double    1.457  0.020  1.457
 0IT  S    O2S   double    1.455  0.020  1.455
 0IT  N    S     single    1.637  0.020  1.637
 0IT  C    N1    single    1.348  0.020  1.348
 0IT  C1   N2    single    1.346  0.020  1.346

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
 0IT  H2A   C3   H11   108.45  3.000
 0IT  H2A   C3   C11   112.72  3.000
 0IT  H11   C3   C11   112.45  3.000
 0IT  H2A   C3   S     106.88  3.000
 0IT  H11   C3   S     106.76  3.000
 0IT  C11   C3   S     109.27  3.000
 0IT  N     S    O1S   107.07  3.000
 0IT  N     S    O2S   106.30  3.000
 0IT  O1S   S    O2S   119.39  3.000
 0IT  N     S    C3    108.81  3.000
 0IT  O2S   S    C3    107.36  3.000
 0IT  O1S   S    C3    107.58  3.000
 0IT  C21   C11  C6    119.22  3.000
 0IT  C6    C11  C3    120.38  3.000
 0IT  C21   C11  C3    120.39  3.000
 0IT  H6    C6   C5    119.83  3.000
 0IT  H6    C6   C11   119.75  3.000
 0IT  C5    C6   C11   120.41  3.000
 0IT  H5    C5   C4    120.12  3.000
 0IT  H5    C5   C6    119.80  3.000
 0IT  C4    C5   C6    120.08  3.000
 0IT  H4    C4   C31   120.11  3.000
 0IT  H4    C4   C5    120.11  3.000
 0IT  C31   C4   C5    119.79  3.000
 0IT  H3    C31  C21   119.82  3.000
 0IT  H3    C31  C4    120.10  3.000
 0IT  C21   C31  C4    120.09  3.000
 0IT  H21   C21  C31   119.78  3.000
 0IT  H21   C21  C11   119.82  3.000
 0IT  C31   C21  C11   120.40  3.000
 0IT  H     N    CA    114.00  3.000
 0IT  H     N    S     114.21  3.000
 0IT  CA    N    S     123.92  3.000
 0IT  HA    CA   C     110.00  3.000
 0IT  HA    CA   CB    109.00  3.000
 0IT  C     CA   CB    110.50  1.500
 0IT  HA    CA   N     110.00  3.000
 0IT  C     CA   N     111.00  2.800
 0IT  CB    CA   N     110.40  1.500
 0IT  HB3   CB   HB2   107.38  3.000
 0IT  HB3   CB   CG    110.28  3.000
 0IT  HB2   CB   CG    111.52  3.000
 0IT  HB3   CB   CA    109.92  3.000
 0IT  HB2   CB   CA    109.11  3.000
 0IT  CG    CB   CA    108.62  3.000
 0IT  HG3   CG   HG2   107.06  3.000
 0IT  HG3   CG   CD    108.55  3.000
 0IT  HG2   CG   CD    110.11  3.000
 0IT  HG3   CG   CB    110.96  3.000
 0IT  HG2   CG   CB    109.82  3.000
 0IT  CD    CG   CB    110.28  3.000
 0IT  HD2   CD   HD1   107.25  3.000
 0IT  HD2   CD   N1    109.13  3.000
 0IT  HD1   CD   N1    107.98  3.000
 0IT  N1    CD   CG    112.41  3.000
 0IT  HD2   CD   CG    110.00  3.000
 0IT  HD1   CD   CG    109.91  3.000
 0IT  N1    C    O     121.73  3.000
 0IT  N1    C    CA    117.81  3.000
 0IT  O     C    CA    120.80  1.700
 0IT  CA1   N1   C     116.46  3.000
 0IT  C     N1   CD    125.01  3.000
 0IT  CA1   N1   CD    116.26  3.000
 0IT  HA3   CA1  HA2   106.54  3.000
 0IT  HA3   CA1  C1    108.62  3.000
 0IT  HA2   CA1  C1    110.08  3.000
 0IT  HA3   CA1  N1    108.68  3.000
 0IT  HA2   CA1  N1    110.74  3.000
 0IT  C1    CA1  N1    111.99  3.000
 0IT  N2    C1   O1    123.32  3.000
 0IT  N2    C1   CA1   114.13  3.000
 0IT  O1    C1   CA1   122.56  3.000
 0IT  H2    N2   CA2   117.84  3.000
 0IT  H2    N2   C1    118.74  3.000
 0IT  CA2   N2   C1    122.15  3.000
 0IT  HA1   CA2  CB1   108.09  3.000
 0IT  HA1   CA2  C2    106.24  3.000
 0IT  CB1   CA2  C2    109.00  3.000
 0IT  HA1   CA2  N2    109.61  3.000
 0IT  CB1   CA2  N2    111.35  3.000
 0IT  C2    CA2  N2    112.33  3.000
 0IT  HXT   C2   O2    121.65  3.000
 0IT  HXT   C2   CA2   113.73  3.000
 0IT  O2    C2   CA2   124.62  3.000
 0IT  HB31  CB1  HB21  106.60  3.000
 0IT  HB31  CB1  CG1   109.57  3.000
 0IT  HB21  CB1  CG1   110.20  3.000
 0IT  HB31  CB1  CA2   108.21  3.000
 0IT  HB21  CB1  CA2   109.24  3.000
 0IT  CG1   CB1  CA2   112.82  3.000
 0IT  HG31  CG1  HG21  107.30  3.000
 0IT  HG31  CG1  CD1   109.26  3.000
 0IT  HG21  CG1  CD1   109.39  3.000
 0IT  HG31  CG1  CB1   110.46  3.000
 0IT  HG21  CG1  CB1   109.62  3.000
 0IT  CD1   CG1  CB1   110.75  3.000
 0IT  HD31  CD1  HD21  107.77  3.000
 0IT  HD31  CD1  NE    109.91  3.000
 0IT  HD21  CD1  NE    109.89  3.000
 0IT  HD31  CD1  CG1   109.54  3.000
 0IT  HD21  CD1  CG1   109.74  3.000
 0IT  NE    CD1  CG1   109.94  3.000
 0IT  HE    NE   CZ    117.66  3.000
 0IT  HE    NE   CD1   117.96  3.000
 0IT  CZ    NE   CD1   124.33  3.000
 0IT  NH2   CZ   NH1   119.82  3.000
 0IT  NH2   CZ   NE    119.82  3.000
 0IT  NH1   CZ   NE    120.35  3.000
 0IT  HH12  NH1  HH11  116.84  3.000
 0IT  HH12  NH1  CZ    121.09  3.000
 0IT  HH11  NH1  CZ    122.05  3.000
 0IT  HH22  NH2  HH21  117.22  3.000
 0IT  HH22  NH2  CZ    121.18  3.000
 0IT  HH21  NH2  CZ    121.27  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
 0IT  CONST_01  C4    C31  C21  C11     0.00   0.0  0
 0IT  CONST_02  C4    C5   C6   C11     0.00   0.0  0
 0IT  CONST_03  C31   C21  C11  C6      0.00   0.0  0
 0IT  CONST_04  C31   C4   C5   C6      0.00   0.0  0
 0IT  CONST_05  C21   C31  C4   C5      0.00   0.0  0
 0IT  CONST_06  C21   C11  C6   C5      0.00   0.0  0
 0IT  CONST_08  C31   C21  C11  C3    180.00   0.0  0
 0IT  CONST_09  C5    C6   C11  C3    180.00   0.0  0
 0IT  CONST_10  CA1   N1   C    CA    180.00   0.0  0
 0IT  CONST_11  O     C    N1   CD    180.00   0.0  0
 0IT  CONST_12  H3    C31  C21  C11   180.00   0.0  0
 0IT  CONST_13  H5    C5   C6   C11   180.00   0.0  0
 0IT  CONST_14  H21   C21  C11  C6    180.00   0.0  0
 0IT  CONST_15  H4    C4   C5   C6    180.00   0.0  0
 0IT  CONST_16  H6    C6   C5   C4    180.00   0.0  0
 0IT  CONST_17  CA1   N1   C    O       0.00   0.0  0
 0IT  CONST_18  CA2   N2   C1   CA1   180.00   0.0  0
 0IT  CONST_19  CA2   N2   C1   O1      0.00   0.0  0
 0IT  CONST_20  NH1   CZ   NE   CD1     0.00   0.0  0
 0IT  CONST_21  NH2   CZ   NE   CD1   180.00   0.0  0
 0IT  CONST_22  H2    N2   C1   CA1     0.00   0.0  0
 0IT  CONST_23  HH11  NH1  CZ   NE      0.00   0.0  0
 0IT  CONST_24  HH12  NH1  CZ   NE    180.00   0.0  0
 0IT  CONST_25  HH21  NH2  CZ   NE    180.00   0.0  0
 0IT  CONST_26  HH22  NH2  CZ   NE      0.00   0.0  0
 0IT  CONST_27  HE    NE   CZ   NH1   180.00   0.0  0
 0IT  Var_01    CD    CG   CB   CA    -61.97  30.0  1
 0IT  Var_02    N1    CD   CG   CB     48.51  30.0  1
 0IT  Var_03    C     N1   CD   CG    -26.16  30.0  1
 0IT  Var_04    C21   C11  C3   S      87.82  30.0  2
 0IT  Var_05    C1    CA1  N1   CD     92.62  30.0  3
 0IT  Var_06    CA    N    S    C3     82.29  30.0  1
 0IT  Var_07    O1S   S    C3   C11   -67.72  30.0  3
 0IT  Var_08    O1    C1   CA1  N1    -10.00  30.0  3
 0IT  Var_09    CD1   CG1  CB1  CA2  -178.15  30.0  3
 0IT  Var_10    NE    CD1  CG1  CB1  -179.04  30.0  3
 0IT  Var_11    CZ    NE   CD1  CG1   179.84  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
 0IT  chir_01  CA   N   CB  C    negativ
 0IT  chir_02  CA2  N2  C2  CB1  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
 0IT  plan-1  C3    0.020
 0IT  plan-1  C11   0.020
 0IT  plan-1  C6    0.020
 0IT  plan-1  C5    0.020
 0IT  plan-1  C4    0.020
 0IT  plan-1  C31   0.020
 0IT  plan-1  C21   0.020
 0IT  plan-1  H6    0.020
 0IT  plan-1  H5    0.020
 0IT  plan-1  H4    0.020
 0IT  plan-1  H3    0.020
 0IT  plan-1  H21   0.020
 0IT  plan-2  CA1   0.020
 0IT  plan-2  C1    0.020
 0IT  plan-2  O1    0.020
 0IT  plan-2  N2    0.020
 0IT  plan-2  CA2   0.020
 0IT  plan-2  H2    0.020
 0IT  plan-3  CD1   0.020
 0IT  plan-3  NE    0.020
 0IT  plan-3  CZ    0.020
 0IT  plan-3  NH1   0.020
 0IT  plan-3  NH2   0.020
 0IT  plan-3  HE    0.020
 0IT  plan-3  HH11  0.020
 0IT  plan-3  HH12  0.020
 0IT  plan-3  HH21  0.020
 0IT  plan-3  HH22  0.020
 0IT  plan-4  CA    0.020
 0IT  plan-4  CD    0.020
 0IT  plan-4  C     0.020
 0IT  plan-4  O     0.020
 0IT  plan-4  N1    0.020
 0IT  plan-4  CA1   0.020
 0IT  plan-5  CA2   0.020
 0IT  plan-5  C2    0.020
 0IT  plan-5  O2    0.020
 0IT  plan-5  HXT   0.020

