# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:12:07 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: L-alpha-glutamyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(O)=O)C(=O)NCC(=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
 0GJ  0GJ  L-alpha-glutamyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]glycinamide  peptide  54  26  .  2022-03-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0GJ
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
 0GJ  N     N   NH2   0  -0.776   5.4899  -0.1165   2.0913
 0GJ  CA    C   CH1   0  -0.227   4.4402  -0.1307   1.0987
 0GJ  C     C   C     0   0.539   3.0320  -0.1562   1.7004
 0GJ  O     O   O     0  -0.495   2.7976  -0.6635   2.7884
 0GJ  CB    C   CH2   0  -0.420   4.5972  -1.3401   0.1696
 0GJ  CG    C   CH2   0  -0.577   5.9123  -1.2897  -0.5884
 0GJ  CD    C   C     0   0.549   6.1263  -2.4669  -1.4960
 0GJ  OE1   O   O     0  -0.446   5.3771  -3.4049  -1.6131
 0GJ  OE2   O   OH1   0  -0.598   7.2624  -2.3597  -2.1798
 0GJ  N1    N   NH1   0  -0.640   2.0773   0.3900   0.9343
 0GJ  CA1   C   CH2   0  -0.370   0.6913   0.3953   1.3089
 0GJ  C1    C   C     0   0.522  -0.1579   0.8837   0.1485
 0GJ  O1    O   O     0  -0.480   0.2815   0.9539  -0.9886
 0GJ  N2    N   NH1   0  -0.641  -1.4144   1.2065   0.4910
 0GJ  CA2   C   CH1   0  -0.124  -2.4575   1.5701  -0.4474
 0GJ  C2    C   CH1   0   0.076  -2.7356   3.0884  -0.3957
 0GJ  O2    O   OH1   0  -0.660  -3.7417   3.4419  -1.3089
 0GJ  CB1   C   CH2   0  -0.449  -3.7169   0.7567  -0.1546
 0GJ  CG1   C   CH2   0  -0.469  -3.4973  -0.7426  -0.3022
 0GJ  CD1   C   CH2   0  -0.272  -4.7833  -1.5098  -0.0469
 0GJ  NE    N   NH1   0  -0.636  -4.5526  -2.9350  -0.2071
 0GJ  CZ    C   C     0   0.827  -5.4216  -3.8810   0.1216
 0GJ  NH1   N   NH2   0  -0.816  -6.6080  -3.5614   0.6188
 0GJ  NH2   N   NC2   1  -0.822  -5.0983  -5.1579  -0.0445
 0GJ  C3    C   CH2   0  -0.472  -1.4874   3.8676  -0.7610
 0GJ  CL    CL  CL    0  -0.168  -1.7870   5.6347  -0.6381
 0GJ  H     H   HNH2  0   0.354   5.4436   0.7359   2.6353
 0GJ  H2    H   HNH2  0   0.342   5.3461  -0.8760   2.7464
 0GJ  HA    H   HCH1  0   0.255   4.5368   0.7772   0.4937
 0GJ  HB2   H   HCH2  0   0.240   4.5364  -2.2567   0.7636
 0GJ  HB3   H   HCH2  0   0.246   3.7629  -1.3666  -0.5347
 0GJ  HG2   H   HCH2  0   0.276   5.9705  -0.3768  -1.1899
 0GJ  HG3   H   HCH2  0   0.286   6.7510  -1.2345   0.1101
 0GJ  HE2   H   HOH1  0   0.478   7.3767  -3.1320  -2.7533
 0GJ  H1    H   HNH1  0   0.402   2.3178   0.7846   0.0375
 0GJ  HA2   H   HCH2  0   0.284   0.3562  -0.6129   1.5740
 0GJ  HA3   H   HCH2  0   0.273   0.5172   1.0239   2.1870
 0GJ  H3    H   HNH1  0   0.407  -1.6708   1.1567   1.4664
 0GJ  HA1   H   HCH1  0   0.262  -2.1012   1.3196  -1.4499
 0GJ  HB21  H   HCH2  0   0.240  -4.0740   0.9851   0.8559
 0GJ  HB31  H   HCH2  0   0.249  -4.5072   1.0654  -0.8419
 0GJ  HG21  H   HCH2  0   0.247  -3.1368  -0.9584  -1.3125
 0GJ  HG31  H   HCH2  0   0.248  -2.7298  -1.0893   0.3936
 0GJ  HD2   H   HCH2  0   0.258  -5.1297  -1.3104   0.9706
 0GJ  HD3   H   HCH2  0   0.258  -5.5632  -1.1719  -0.7361
 0GJ  HE    H   HNH1  0   0.426  -3.7059  -3.2245  -0.6712
 0GJ  HH11  H   HNH2  0   0.446  -6.9292  -2.6096   0.6609
 0GJ  HH12  H   HNH2  0   0.434  -7.2590  -4.2727   0.9053
 0GJ  HH21  H   HNC2  0   0.432  -4.1673  -5.4294  -0.3115
 0GJ  HH22  H   HNC2  0   0.431  -5.7436  -5.8940   0.1855
 0GJ  H27   H   HCH1  0   0.230  -3.0191   3.3502   0.6327
 0GJ  H28   H   HOH1  0   0.463  -4.5996   3.3322  -0.8901
 0GJ  H11   H   HCH2  0   0.291  -0.6670   3.6442  -0.0856
 0GJ  H21   H   HCH2  0   0.284  -1.1737   3.6632  -1.7841

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
 0GJ  N    CA    single  1.458  0.019  1.458
 0GJ  N    H     single  0.860  0.020  0.860
 0GJ  N    H2    single  0.890  0.020  1.040
 0GJ  CA   C     single  1.525  0.021  1.525
 0GJ  CA   CB    single  1.521  0.033  1.521
 0GJ  CA   HA    single  0.970  0.020  0.970
 0GJ  C    O     double  1.231  0.020  1.231
 0GJ  C    N1    single  1.340  0.020  1.340
 0GJ  CB   CG    single  1.519  0.020  1.519
 0GJ  CB   HB2   single  0.970  0.020  1.090
 0GJ  CB   HB3   single  0.970  0.020  1.090
 0GJ  CG   CD    single  1.502  0.020  1.502
 0GJ  CG   HG2   single  0.970  0.020  1.090
 0GJ  CG   HG3   single  0.970  0.020  1.090
 0GJ  CD   OE1   double  1.206  0.020  1.206
 0GJ  CD   OE2   single  1.330  0.020  1.330
 0GJ  OE2  HE2   single  0.850  0.020  0.980
 0GJ  N1   CA1   single  1.436  0.020  1.436
 0GJ  N1   H1    single  0.860  0.020  1.020
 0GJ  CA1  C1    single  1.519  0.020  1.519
 0GJ  CA1  HA2   single  0.970  0.020  1.090
 0GJ  CA1  HA3   single  0.970  0.020  1.090
 0GJ  C1   O1    double  1.221  0.020  1.221
 0GJ  C1   N2    single  1.342  0.020  1.342
 0GJ  N2   CA2   single  1.449  0.020  1.449
 0GJ  N2   H3    single  0.860  0.020  1.020
 0GJ  CA2  C2    single  1.544  0.020  1.544
 0GJ  CA2  CB1   single  1.528  0.020  1.528
 0GJ  CA2  HA1   single  0.970  0.020  1.090
 0GJ  C2   O2    single  1.404  0.020  1.404
 0GJ  C2   C3    single  1.516  0.020  1.516
 0GJ  CB1  CG1   single  1.522  0.020  1.522
 0GJ  CB1  HB21  single  0.970  0.020  1.090
 0GJ  CB1  HB31  single  0.970  0.020  1.090
 0GJ  CG1  CD1   single  1.519  0.020  1.519
 0GJ  CG1  HG21  single  0.970  0.020  1.090
 0GJ  CG1  HG31  single  0.970  0.020  1.090
 0GJ  CD1  NE    single  1.453  0.020  1.453
 0GJ  CD1  HD2   single  0.970  0.020  1.090
 0GJ  CD1  HD3   single  0.970  0.020  1.090
 0GJ  NE   CZ    single  1.326  0.020  1.326
 0GJ  NE   HE    single  0.860  0.020  1.020
 0GJ  CZ   NH1   single  1.325  0.020  1.325
 0GJ  CZ   NH2   double  1.328  0.020  1.328
 0GJ  NH1  HH11  single  0.860  0.020  1.020
 0GJ  NH1  HH12  single  0.860  0.020  1.020
 0GJ  NH2  HH21  single  0.860  0.020  1.020
 0GJ  NH2  HH22  single  0.860  0.020  1.020
 0GJ  C3   H11   single  0.970  0.020  1.090
 0GJ  C3   H21   single  0.970  0.020  1.090
 0GJ  CL   C3    single  1.797  0.020  1.797
 0GJ  C2   H27   single  0.970  0.020  1.090
 0GJ  O2   H28   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
 0GJ  H2    N    H     106.10  3.000
 0GJ  H2    N    CA    109.50  3.000
 0GJ  H     N    CA    114.00  3.000
 0GJ  HA    CA   CB    109.00  3.000
 0GJ  HA    CA   C     110.00  3.000
 0GJ  CB    CA   C     110.50  1.500
 0GJ  HA    CA   N     110.00  3.000
 0GJ  CB    CA   N     110.40  1.500
 0GJ  C     CA   N     111.00  2.800
 0GJ  N1    C    O     122.74  3.000
 0GJ  N1    C    CA    115.06  3.000
 0GJ  O     C    CA    120.80  1.700
 0GJ  HB3   CB   HB2   106.70  3.000
 0GJ  HB3   CB   CG    109.90  3.000
 0GJ  HB2   CB   CG    110.30  3.000
 0GJ  HB3   CB   CA    109.37  3.000
 0GJ  HB2   CB   CA    109.04  3.000
 0GJ  CG    CB   CA    111.40  3.000
 0GJ  HG3   CG   HG2   105.56  3.000
 0GJ  HG3   CG   CD    108.45  3.000
 0GJ  HG2   CG   CD    108.29  3.000
 0GJ  HG3   CG   CB    110.32  3.000
 0GJ  HG2   CG   CB    110.36  3.000
 0GJ  CD    CG   CB    113.52  3.000
 0GJ  OE2   CD   OE1   122.90  3.000
 0GJ  OE2   CD   CG    111.67  3.000
 0GJ  OE1   CD   CG    125.43  3.000
 0GJ  HE2   OE2  CD    109.93  3.000
 0GJ  H1    N1   CA1   117.43  3.000
 0GJ  H1    N1   C     119.84  3.000
 0GJ  CA1   N1   C     122.68  3.000
 0GJ  HA3   CA1  HA2   106.62  3.000
 0GJ  HA3   CA1  C1    109.85  3.000
 0GJ  HA2   CA1  C1    108.06  3.000
 0GJ  HA3   CA1  N1    111.42  3.000
 0GJ  HA2   CA1  N1    110.81  3.000
 0GJ  C1    CA1  N1    109.98  3.000
 0GJ  N2    C1   O1    124.12  3.000
 0GJ  N2    C1   CA1   113.95  3.000
 0GJ  O1    C1   CA1   121.92  3.000
 0GJ  H3    N2   CA2   117.07  3.000
 0GJ  H3    N2   C1    118.20  3.000
 0GJ  CA2   N2   C1    124.68  3.000
 0GJ  HA1   CA2  CB1   108.82  3.000
 0GJ  HA1   CA2  C2    108.34  3.000
 0GJ  CB1   CA2  C2    111.63  3.000
 0GJ  HA1   CA2  N2    107.56  3.000
 0GJ  CB1   CA2  N2    109.61  3.000
 0GJ  C2    CA2  N2    110.76  3.000
 0GJ  H27   C2   C3    108.40  3.000
 0GJ  H27   C2   O2    111.34  3.000
 0GJ  C3    C2   O2    107.69  3.000
 0GJ  H27   C2   CA2   108.20  3.000
 0GJ  C3    C2   CA2   110.42  3.000
 0GJ  O2    C2   CA2   110.78  3.000
 0GJ  H28   O2   C2    109.12  3.000
 0GJ  HB31  CB1  HB21  106.61  3.000
 0GJ  HB31  CB1  CG1   108.77  3.000
 0GJ  HB21  CB1  CG1   109.98  3.000
 0GJ  HB31  CB1  CA2   109.00  3.000
 0GJ  HB21  CB1  CA2   109.54  3.000
 0GJ  CG1   CB1  CA2   112.76  3.000
 0GJ  HG31  CG1  HG21  107.10  3.000
 0GJ  HG31  CG1  CD1   109.11  3.000
 0GJ  HG21  CG1  CD1   109.54  3.000
 0GJ  HG31  CG1  CB1   110.62  3.000
 0GJ  HG21  CG1  CB1   109.35  3.000
 0GJ  CD1   CG1  CB1   111.03  3.000
 0GJ  HD3   CD1  HD2   107.70  3.000
 0GJ  HD3   CD1  NE    110.29  3.000
 0GJ  HD2   CD1  NE    109.39  3.000
 0GJ  HD3   CD1  CG1   109.97  3.000
 0GJ  HD2   CD1  CG1   109.42  3.000
 0GJ  NE    CD1  CG1   110.03  3.000
 0GJ  HE    NE   CZ    117.37  3.000
 0GJ  HE    NE   CD1   117.77  3.000
 0GJ  CZ    NE   CD1   124.65  3.000
 0GJ  NH2   CZ   NH1   119.79  3.000
 0GJ  NH2   CZ   NE    119.71  3.000
 0GJ  NH1   CZ   NE    120.50  3.000
 0GJ  HH12  NH1  HH11  116.79  3.000
 0GJ  HH12  NH1  CZ    121.03  3.000
 0GJ  HH11  NH1  CZ    122.01  3.000
 0GJ  HH22  NH2  HH21  117.20  3.000
 0GJ  HH22  NH2  CZ    121.27  3.000
 0GJ  HH21  NH2  CZ    121.22  3.000
 0GJ  H21   C3   H11   109.15  3.000
 0GJ  H21   C3   CL    107.27  3.000
 0GJ  H11   C3   CL    106.61  3.000
 0GJ  CL    C3   C2    110.59  3.000
 0GJ  H21   C3   C2    111.53  3.000
 0GJ  H11   C3   C2    111.49  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
 0GJ  CONST_01  CA1   N1   C    CA    180.00   0.0  0
 0GJ  CONST_02  CA1   N1   C    O       0.00   0.0  0
 0GJ  CONST_03  CA2   N2   C1   CA1   180.00   0.0  0
 0GJ  CONST_04  CA2   N2   C1   O1      0.00   0.0  0
 0GJ  CONST_05  NH1   CZ   NE   CD1     0.00   0.0  0
 0GJ  CONST_06  NH2   CZ   NE   CD1   180.00   0.0  0
 0GJ  CONST_07  H1    N1   C    CA      0.00   0.0  0
 0GJ  CONST_08  H3    N2   C1   CA1     0.00   0.0  0
 0GJ  CONST_09  HE2   OE2  CD   CG    180.00   0.0  0
 0GJ  CONST_10  HH11  NH1  CZ   NE      0.00   0.0  0
 0GJ  CONST_11  HH12  NH1  CZ   NE    180.00   0.0  0
 0GJ  CONST_12  HH21  NH2  CZ   NE      0.00   0.0  0
 0GJ  CONST_13  HH22  NH2  CZ   NE    180.00   0.0  0
 0GJ  CONST_14  HE    NE   CZ   NH1   180.00   0.0  0
 0GJ  Var_01    CD    CG   CB   CA    178.97  30.0  3
 0GJ  Var_02    C1    CA1  N1   C    -171.13  30.0  3
 0GJ  Var_03    OE1   CD   CG   CB     -2.29  30.0  3
 0GJ  Var_04    O1    C1   CA1  N1     14.90  30.0  3
 0GJ  Var_05    CD1   CG1  CB1  CA2  -178.15  30.0  3
 0GJ  Var_06    NE    CD1  CG1  CB1   179.40  30.0  3
 0GJ  Var_07    CZ    NE   CD1  CG1   170.41  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
 0GJ  chir_01  CA   N   C    CB   positiv
 0GJ  chir_02  CA2  N2  C2   CB1  positiv
 0GJ  chir_03  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
 0GJ  plan-1  CA    0.020
 0GJ  plan-1  C     0.020
 0GJ  plan-1  O     0.020
 0GJ  plan-1  N1    0.020
 0GJ  plan-1  CA1   0.020
 0GJ  plan-1  H1    0.020
 0GJ  plan-2  CA1   0.020
 0GJ  plan-2  C1    0.020
 0GJ  plan-2  O1    0.020
 0GJ  plan-2  N2    0.020
 0GJ  plan-2  CA2   0.020
 0GJ  plan-2  H3    0.020
 0GJ  plan-3  CD1   0.020
 0GJ  plan-3  NE    0.020
 0GJ  plan-3  CZ    0.020
 0GJ  plan-3  NH1   0.020
 0GJ  plan-3  NH2   0.020
 0GJ  plan-3  HE    0.020
 0GJ  plan-3  HH11  0.020
 0GJ  plan-3  HH12  0.020
 0GJ  plan-3  HH21  0.020
 0GJ  plan-3  HH22  0.020
 0GJ  plan-4  CG    0.020
 0GJ  plan-4  CD    0.020
 0GJ  plan-4  OE1   0.020
 0GJ  plan-4  OE2   0.020
 0GJ  plan-4  HE2   0.020

