# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 01:35:22 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(N)=[NH2+])[C@H](O)CCl
#
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
 0G6  0G6  D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide  peptide  65  31  .  2019-03-22  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_0G6
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
 0G6  N     N   NH2   0  -0.780  20.9914  10.7995  12.2567
 0G6  CA    C   CH1   0  -0.222  21.1669  10.8621  13.6902
 0G6  C     C   C     0   0.563  20.1196   9.9892  14.3645
 0G6  O     O   O     0  -0.495  19.7311   8.9517  13.8407
 0G6  CB    C   CH2   0  -0.532  22.5534  10.4003  14.2053
 0G6  CG    C   CR6   0   0.131  23.6488  11.3107  13.7345
 0G6  CD1   C   CR16  0  -0.302  23.9246  12.4874  14.4298
 0G6  CD2   C   CR16  0  -0.316  24.3790  11.0343  12.5810
 0G6  CE1   C   CR16  0  -0.238  24.9054  13.3633  13.9883
 0G6  CE2   C   CR16  0  -0.240  25.3629  11.9085  12.1350
 0G6  CZ    C   CR16  0  -0.268  25.6290  13.0758  12.8371
 0G6  N1    N   NT    0  -0.461  19.7015  10.3590  15.5866
 0G6  CA1   C   CH1   0  -0.220  18.8189   9.4916  16.3408
 0G6  C1    C   C     0   0.580  17.4275   9.4540  15.7178
 0G6  O1    O   O     0  -0.483  16.9244  10.4487  15.2201
 0G6  CB1   C   CH2   0  -0.473  18.7813  10.1487  17.7286
 0G6  CG1   C   CH2   0  -0.469  19.0123  11.6262  17.4368
 0G6  CD    C   CH2   0  -0.280  20.0047  11.6082  16.2813
 0G6  N2    N   NH1   0  -0.638  16.8036   8.2688  15.8250
 0G6  CA2   C   CH1   0  -0.114  15.4524   8.0193  15.3797
 0G6  C2    C   CH1   0   0.073  14.6015   7.4279  16.5117
 0G6  O2    O   OH1   0  -0.657  13.2704   7.4913  16.0586
 0G6  CB2   C   CH2   0  -0.416  15.4367   7.1265  14.1398
 0G6  CG2   C   CH2   0  -0.486  16.1455   7.7549  12.9479
 0G6  CD3   C   CH2   0  -0.270  16.0265   6.8674  11.7210
 0G6  NE    N   NH1   0  -0.635  16.7696   7.4398  10.6100
 0G6  CZ1   C   C     0   0.827  16.8912   6.8734   9.4170
 0G6  NH1   N   NH2   0  -0.816  16.2624   5.7382   9.1438
 0G6  NH2   N   NC2   1  -0.823  17.6562   7.4397   8.4904
 0G6  C3    C   CH2   0  -0.488  14.7194   8.2118  17.8222
 0G6  CL    CL  CL    0  -0.167  16.0944   7.6455  18.8361
 0G6  H     H   HNH2  0   0.354  21.6710  11.4009  11.8080
 0G6  H2    H   HNH2  0   0.341  21.1763   9.8607  11.9242
 0G6  HA    H   HCH1  0   0.268  21.0332  11.9044  13.9878
 0G6  HB2   H   HCH2  0   0.259  22.5514  10.3719  15.2985
 0G6  HB3   H   HCH2  0   0.258  22.7272   9.3776  13.8599
 0G6  HD1   H   HCR6  0   0.248  23.3679  12.7177  15.3319
 0G6  HD2   H   HCR6  0   0.248  24.1837  10.1206  12.0317
 0G6  HE1   H   HCR6  0   0.252  25.1090  14.2693  14.5450
 0G6  HE2   H   HCR6  0   0.252  25.9238  11.6739  11.2392
 0G6  HZ    H   HCR6  0   0.252  26.3974  13.7557  12.4924
 0G6  HA1   H   HCH1  0   0.280  19.2326   8.4819  16.3987
 0G6  HB21  H   HCH2  0   0.259  17.8531   9.9483  18.2618
 0G6  HB31  H   HCH2  0   0.257  19.5978   9.7466  18.3310
 0G6  HG2   H   HCH2  0   0.246  18.0843  12.1085  17.1301
 0G6  HG3   H   HCH2  0   0.256  19.4011  12.1701  18.2965
 0G6  HD21  H   HCH2  0   0.245  21.0355  11.6092  16.6472
 0G6  HD3   H   HCH2  0   0.259  19.8802  12.4700  15.6262
 0G6  H1    H   HNH1  0   0.396  17.3282   7.4850  16.1828
 0G6  HA2   H   HCH1  0   0.260  15.0211   8.9919  15.1298
 0G6  HB22  H   HCH2  0   0.231  15.9055   6.1673  14.3848
 0G6  HB32  H   HCH2  0   0.244  14.4001   6.9103  13.8747
 0G6  HG21  H   HCH2  0   0.243  15.7093   8.7340  12.7302
 0G6  HG31  H   HCH2  0   0.249  17.2018   7.9159  13.1762
 0G6  HD22  H   HCH2  0   0.256  16.4139   5.8697  11.9485
 0G6  HD31  H   HCH2  0   0.256  14.9727   6.7602  11.4479
 0G6  HE    H   HNH1  0   0.427  17.2705   8.3005  10.7723
 0G6  HH11  H   HNH2  0   0.434  16.3527   5.3014   8.2418
 0G6  HH12  H   HNH2  0   0.445  15.6460   5.2938   9.8027
 0G6  HH21  H   HNC2  0   0.431  17.7163   7.0625   7.5596
 0G6  HH22  H   HNC2  0   0.431  18.1344   8.3068   8.6674
 0G6  H11   H   HCH2  0   0.290  14.8530   9.2801  17.6551
 0G6  H21   H   HCH2  0   0.299  13.8262   8.0621  18.4266
 0G6  H33   H   HCH1  0   0.229  14.9083   6.3890  16.6954
 0G6  H34   H   HOH1  0   0.459  12.7289   6.9048  16.5967

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
 0G6  N    CA    single    1.458  0.019  1.458
 0G6  N    H     single    0.860  0.020  0.860
 0G6  N    H2    single    0.890  0.020  1.040
 0G6  CA   C     single    1.525  0.021  1.525
 0G6  CA   CB    single    1.521  0.033  1.521
 0G6  CA   HA    single    0.970  0.020  0.970
 0G6  C    O     double    1.231  0.020  1.231
 0G6  C    N1    single    1.344  0.020  1.344
 0G6  CB   CG    single    1.500  0.020  1.500
 0G6  CB   HB2   single    0.970  0.020  1.090
 0G6  CB   HB3   single    0.970  0.020  1.090
 0G6  CG   CD1   aromatic  1.394  0.020  1.394
 0G6  CG   CD2   aromatic  1.393  0.020  1.393
 0G6  CD1  CE1   aromatic  1.387  0.020  1.387
 0G6  CD1  HD1   single    0.930  0.020  1.080
 0G6  CD2  CE2   aromatic  1.390  0.020  1.390
 0G6  CD2  HD2   single    0.930  0.020  1.080
 0G6  CE1  CZ    aromatic  1.390  0.020  1.390
 0G6  CE1  HE1   single    0.930  0.020  1.080
 0G6  CE2  CZ    aromatic  1.388  0.020  1.388
 0G6  CE2  HE2   single    0.930  0.020  1.080
 0G6  CZ   HZ    single    0.930  0.020  1.080
 0G6  N1   CA1   single    1.449  0.020  1.449
 0G6  N1   CD    single    1.461  0.020  1.461
 0G6  CA1  C1    single    1.525  0.020  1.525
 0G6  CA1  CB1   single    1.536  0.020  1.536
 0G6  CA1  HA1   single    0.970  0.020  1.090
 0G6  C1   O1    double    1.221  0.020  1.221
 0G6  C1   N2    single    1.344  0.020  1.344
 0G6  CB1  CG1   single    1.524  0.020  1.524
 0G6  CB1  HB21  single    0.970  0.020  1.090
 0G6  CB1  HB31  single    0.970  0.020  1.090
 0G6  CG1  CD    single    1.523  0.020  1.523
 0G6  CG1  HG2   single    0.970  0.020  1.090
 0G6  CG1  HG3   single    0.970  0.020  1.090
 0G6  CD   HD21  single    0.970  0.020  1.090
 0G6  CD   HD3   single    0.970  0.020  1.090
 0G6  N2   CA2   single    1.444  0.020  1.444
 0G6  N2   H1    single    0.860  0.020  1.020
 0G6  CA2  C2    single    1.535  0.020  1.535
 0G6  CA2  CB2   single    1.528  0.020  1.528
 0G6  CA2  HA2   single    0.970  0.020  1.090
 0G6  C2   O2    single    1.408  0.020  1.408
 0G6  C2   C3    single    1.532  0.020  1.532
 0G6  CB2  CG2   single    1.523  0.020  1.523
 0G6  CB2  HB22  single    0.970  0.020  1.090
 0G6  CB2  HB32  single    0.970  0.020  1.090
 0G6  CG2  CD3   single    1.519  0.020  1.519
 0G6  CG2  HG21  single    0.970  0.020  1.090
 0G6  CG2  HG31  single    0.970  0.020  1.090
 0G6  CD3  NE    single    1.454  0.020  1.454
 0G6  CD3  HD22  single    0.970  0.020  1.090
 0G6  CD3  HD31  single    0.970  0.020  1.090
 0G6  NE   CZ1   single    1.326  0.020  1.326
 0G6  NE   HE    single    0.860  0.020  1.020
 0G6  CZ1  NH1   single    1.326  0.020  1.326
 0G6  CZ1  NH2   double    1.328  0.020  1.328
 0G6  NH1  HH11  single    0.860  0.020  1.020
 0G6  NH1  HH12  single    0.860  0.020  1.020
 0G6  NH2  HH21  single    0.860  0.020  1.020
 0G6  NH2  HH22  single    0.860  0.020  1.020
 0G6  C3   H11   single    0.970  0.020  1.090
 0G6  C3   H21   single    0.970  0.020  1.090
 0G6  CL   C3    single    1.800  0.020  1.800
 0G6  C2   H33   single    0.970  0.020  1.090
 0G6  O2   H34   single    0.850  0.020  0.980

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
 0G6  H2    N    H     106.42  3.000
 0G6  H2    N    CA    110.08  3.000
 0G6  H     N    CA    114.00  3.000
 0G6  HA    CA   CB    109.00  3.000
 0G6  HA    CA   C     110.00  3.000
 0G6  CB    CA   C     110.50  1.500
 0G6  HA    CA   N     110.00  3.000
 0G6  CB    CA   N     110.40  1.500
 0G6  C     CA   N     111.00  2.800
 0G6  N1    C    O     121.55  3.000
 0G6  N1    C    CA    117.36  3.000
 0G6  O     C    CA    120.80  1.700
 0G6  HB3   CB   HB2   106.97  3.000
 0G6  HB3   CB   CG    110.63  3.000
 0G6  HB2   CB   CG    109.32  3.000
 0G6  HB3   CB   CA    108.42  3.000
 0G6  HB2   CB   CA    109.78  3.000
 0G6  CG    CB   CA    111.61  3.000
 0G6  CD2   CG   CD1   118.47  3.000
 0G6  CD2   CG   CB    121.48  3.000
 0G6  CD1   CG   CB    120.00  3.000
 0G6  HD1   CD1  CE1   119.57  3.000
 0G6  HD1   CD1  CG    119.49  3.000
 0G6  CE1   CD1  CG    120.93  3.000
 0G6  HD2   CD2  CE2   119.69  3.000
 0G6  HD2   CD2  CG    119.51  3.000
 0G6  CE2   CD2  CG    120.80  3.000
 0G6  HE1   CE1  CZ    120.07  3.000
 0G6  HE1   CE1  CD1   119.85  3.000
 0G6  CZ    CE1  CD1   120.08  3.000
 0G6  HE2   CE2  CZ    120.10  3.000
 0G6  HE2   CE2  CD2   119.74  3.000
 0G6  CZ    CE2  CD2   120.16  3.000
 0G6  HZ    CZ   CE2   120.22  3.000
 0G6  HZ    CZ   CE1   120.23  3.000
 0G6  CE2   CZ   CE1   119.55  3.000
 0G6  CD    N1   CA1   113.00  3.000
 0G6  CD    N1   C     127.10  3.000
 0G6  CA1   N1   C     119.88  3.000
 0G6  HA1   CA1  CB1   110.89  3.000
 0G6  HA1   CA1  C1    110.14  3.000
 0G6  CB1   CA1  C1    110.94  3.000
 0G6  HA1   CA1  N1    110.49  3.000
 0G6  CB1   CA1  N1    103.24  3.000
 0G6  C1    CA1  N1    110.97  3.000
 0G6  N2    C1   O1    124.05  3.000
 0G6  N2    C1   CA1   114.39  3.000
 0G6  O1    C1   CA1   121.50  3.000
 0G6  HB31  CB1  HB21  107.43  3.000
 0G6  HB31  CB1  CG1   110.46  3.000
 0G6  HB21  CB1  CG1   113.67  3.000
 0G6  HB31  CB1  CA1   108.83  3.000
 0G6  HB21  CB1  CA1   112.62  3.000
 0G6  CG1   CB1  CA1   103.77  3.000
 0G6  HG3   CG1  HG2   107.77  3.000
 0G6  HG3   CG1  CD    111.85  3.000
 0G6  HG2   CG1  CD    110.27  3.000
 0G6  HG3   CG1  CB1   112.78  3.000
 0G6  HG2   CG1  CB1   110.73  3.000
 0G6  CD    CG1  CB1   103.45  3.000
 0G6  HD3   CD   HD21  107.94  3.000
 0G6  HD3   CD   CG1   111.86  3.000
 0G6  HD21  CD   CG1   111.11  3.000
 0G6  HD3   CD   N1    111.51  3.000
 0G6  HD21  CD   N1    110.81  3.000
 0G6  CG1   CD   N1    103.62  3.000
 0G6  H1    N2   CA2   117.49  3.000
 0G6  H1    N2   C1    118.17  3.000
 0G6  CA2   N2   C1    124.21  3.000
 0G6  HA2   CA2  CB2   109.29  3.000
 0G6  HA2   CA2  C2    107.02  3.000
 0G6  CB2   CA2  C2    111.57  3.000
 0G6  HA2   CA2  N2    106.61  3.000
 0G6  CB2   CA2  N2    111.15  3.000
 0G6  C2    CA2  N2    110.97  3.000
 0G6  H33   C2   C3    108.63  3.000
 0G6  H33   C2   O2    111.13  3.000
 0G6  C3    C2   O2    108.98  3.000
 0G6  H33   C2   CA2   109.44  3.000
 0G6  C3    C2   CA2   113.03  3.000
 0G6  O2    C2   CA2   105.64  3.000
 0G6  H34   O2   C2    108.94  3.000
 0G6  HB32  CB2  HB22  106.70  3.000
 0G6  HB32  CB2  CG2   109.49  3.000
 0G6  HB22  CB2  CG2   109.71  3.000
 0G6  HB32  CB2  CA2   108.82  3.000
 0G6  HB22  CB2  CA2   109.01  3.000
 0G6  CG2   CB2  CA2   112.91  3.000
 0G6  HG31  CG2  HG21  107.17  3.000
 0G6  HG31  CG2  CD3   109.31  3.000
 0G6  HG21  CG2  CD3   109.33  3.000
 0G6  HG31  CG2  CB2   110.33  3.000
 0G6  HG21  CG2  CB2   109.85  3.000
 0G6  CD3   CG2  CB2   110.77  3.000
 0G6  HD31  CD3  HD22  107.68  3.000
 0G6  HD31  CD3  NE    109.88  3.000
 0G6  HD22  CD3  NE    109.69  3.000
 0G6  HD31  CD3  CG2   109.54  3.000
 0G6  HD22  CD3  CG2   109.69  3.000
 0G6  NE    CD3  CG2   110.31  3.000
 0G6  HE    NE   CZ1   117.61  3.000
 0G6  HE    NE   CD3   117.82  3.000
 0G6  CZ1   NE   CD3   124.47  3.000
 0G6  NH2   CZ1  NH1   119.62  3.000
 0G6  NH2   CZ1  NE    119.88  3.000
 0G6  NH1   CZ1  NE    120.49  3.000
 0G6  HH12  NH1  HH11  116.78  3.000
 0G6  HH12  NH1  CZ1   122.27  3.000
 0G6  HH11  NH1  CZ1   120.90  3.000
 0G6  HH22  NH2  HH21  117.23  3.000
 0G6  HH22  NH2  CZ1   121.23  3.000
 0G6  HH21  NH2  CZ1   121.33  3.000
 0G6  H21   C3   H11   108.69  3.000
 0G6  H21   C3   CL    105.71  3.000
 0G6  H11   C3   CL    107.53  3.000
 0G6  CL    C3   C2    112.32  3.000
 0G6  H21   C3   C2    109.97  3.000
 0G6  H11   C3   C2    112.34  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
 0G6  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 0G6  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 0G6  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 0G6  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 0G6  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 0G6  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 0G6  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 0G6  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 0G6  CONST_09  HE1   CE1  CD1  CG    180.00   0.0  0
 0G6  CONST_10  HE2   CE2  CD2  CG    180.00   0.0  0
 0G6  CONST_11  HD2   CD2  CG   CD1   180.00   0.0  0
 0G6  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 0G6  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 0G6  CONST_14  CA1   N1   C    CA    180.00   0.0  0
 0G6  CONST_15  CD    N1   C    CA      0.00   0.0  0
 0G6  CONST_16  CA1   N1   C    O       0.00   0.0  0
 0G6  CONST_17  CD    N1   C    O     180.00   0.0  0
 0G6  CONST_18  CA2   N2   C1   CA1   180.00   0.0  0
 0G6  CONST_19  H1    N2   C1   CA1     0.00   0.0  0
 0G6  CONST_20  CA2   N2   C1   O1      0.00   0.0  0
 0G6  CONST_21  NH1   CZ1  NE   CD3     0.00   0.0  0
 0G6  CONST_22  NH2   CZ1  NE   CD3   180.00   0.0  0
 0G6  CONST_23  HH11  NH1  CZ1  NE    180.00   0.0  0
 0G6  CONST_24  HH12  NH1  CZ1  NE      0.00   0.0  0
 0G6  CONST_25  HH21  NH2  CZ1  NE    180.00   0.0  0
 0G6  CONST_26  HH22  NH2  CZ1  NE      0.00   0.0  0
 0G6  CONST_27  HE    NE   CZ1  NH1   180.00   0.0  0
 0G6  Var_01    CB1   CG1  CD   N1     29.31  30.0  1
 0G6  Var_02    CG1   CD   N1   CA1   -11.55  30.0  1
 0G6  Var_03    CD    CG1  CB1  CA1   -36.25  30.0  1
 0G6  Var_04    CD1   CG   CB   CA     83.38  30.0  2
 0G6  Var_05    CD3   CG2  CB2  CA2  -176.47  30.0  3
 0G6  Var_06    NE    CD3  CG2  CB2  -176.81  30.0  3
 0G6  Var_07    CZ1   NE   CD3  CG2   177.69  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
 0G6  chir_01  CA   N   C    CB   negativ
 0G6  chir_02  CA1  N1  C1   CB1  positiv
 0G6  chir_03  CA2  N2  C2   CB2  positiv
 0G6  chir_04  C2   O2  CA2  C3   negativ

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
 0G6  plan-1  CB    0.020
 0G6  plan-1  CG    0.020
 0G6  plan-1  CD1   0.020
 0G6  plan-1  CD2   0.020
 0G6  plan-1  CE1   0.020
 0G6  plan-1  CE2   0.020
 0G6  plan-1  CZ    0.020
 0G6  plan-1  HD1   0.020
 0G6  plan-1  HD2   0.020
 0G6  plan-1  HE1   0.020
 0G6  plan-1  HE2   0.020
 0G6  plan-1  HZ    0.020
 0G6  plan-2  CA1   0.020
 0G6  plan-2  C1    0.020
 0G6  plan-2  O1    0.020
 0G6  plan-2  N2    0.020
 0G6  plan-2  CA2   0.020
 0G6  plan-2  H1    0.020
 0G6  plan-3  CA    0.020
 0G6  plan-3  C     0.020
 0G6  plan-3  O     0.020
 0G6  plan-3  N1    0.020
 0G6  plan-3  CA1   0.020
 0G6  plan-3  CD    0.020
 0G6  plan-4  CD3   0.020
 0G6  plan-4  NE    0.020
 0G6  plan-4  CZ1   0.020
 0G6  plan-4  NH1   0.020
 0G6  plan-4  NH2   0.020
 0G6  plan-4  HE    0.020
 0G6  plan-4  HH11  0.020
 0G6  plan-4  HH12  0.020
 0G6  plan-4  HH21  0.020
 0G6  plan-4  HH22  0.020

