# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:37:17 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: N~6~-(4-aminobutyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNCCCC[C@H](N)C(O)=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
 5GG  5GG  N~6~-(4-aminobutyl)-L-lysine  L-peptide  37  15  .  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_5GG
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
 5GG  N    N  NH2    0  -0.784  37.0426  83.2191  40.6077
 5GG  CA   C  CH1    0  -0.213  37.8427  83.4748  39.4182
 5GG  C    C  C      0   0.381  39.3451  83.7716  39.6758
 5GG  O    O  O      0  -0.602  39.7122  83.9068  40.8600
 5GG  CB   C  CH2    0  -0.414  37.2230  84.6106  38.6011
 5GG  CG   C  CH2    0  -0.403  35.7817  84.3656  38.1725
 5GG  CD   C  CH2    0  -0.438  35.2477  85.4610  37.2579
 5GG  CE   C  CH2    0  -0.245  33.7926  85.2460  36.8722
 5GG  NZ   N  NH1    0  -0.599  33.3100  86.2943  35.9936
 5GG  CH   C  CH2    0  -0.443  31.4622  87.2130  34.6591
 5GG  CI   C  CH2    0  -0.426  30.0057  87.0552  34.2434
 5GG  CJ   C  CH2    0  -0.269  29.5472  88.1485  33.2908
 5GG  CF   C  CH2    0  -0.243  31.9255  86.1134  35.6014
 5GG  NY   N  NH2    0  -0.798  28.1466  87.9771  32.9300
 5GG  O1   O  OC    -1  -0.618  40.0642  83.8586  38.6576
 5GG  H1   H  HNH2   0   0.329  37.4502  82.4391  41.1095
 5GG  H2   H  HNH2   0   0.319  37.1596  84.0053  41.2378
 5GG  H4   H  HCH1   0   0.202  37.7970  82.5704  38.7973
 5GG  H5   H  HCH2   0   0.212  37.8395  84.7721  37.7142
 5GG  H6   H  HCH2   0   0.199  37.2728  85.5421  39.1800
 5GG  H7   H  HCH2   0   0.208  35.1406  84.2836  39.0533
 5GG  H8   H  HCH2   0   0.199  35.7174  83.3998  37.6583
 5GG  H9   H  HCH2   0   0.208  35.8617  85.5087  36.3512
 5GG  H10  H  HCH2   0   0.209  35.3459  86.4350  37.7476
 5GG  H11  H  HCH2   0   0.208  33.1766  85.2496  37.7778
 5GG  H12  H  HCH2   0   0.179  33.6778  84.2409  36.4321
 5GG  H13  H  HNH1   0   0.331  33.8849  86.3055  35.1581
 5GG  H15  H  HCH2   0   0.212  32.0976  87.2153  33.7662
 5GG  H16  H  HCH2   0   0.214  31.6067  88.1834  35.1437
 5GG  H17  H  HCH2   0   0.212  29.3631  87.0599  35.1292
 5GG  H18  H  HCH2   0   0.211  29.8669  86.0791  33.7653
 5GG  H19  H  HCH2   0   0.185  30.2244  88.1687  32.4240
 5GG  H20  H  HCH2   0   0.209  29.6554  89.1187  33.7838
 5GG  H21  H  HCH2   0   0.209  31.3093  86.1306  36.5066
 5GG  H22  H  HCH2   0   0.180  31.7445  85.1323  35.1308
 5GG  H23  H  HNH2   0   0.343  27.8633  88.7279  32.3132
 5GG  H24  H  HNH2   0   0.335  28.0454  87.1281  32.3866

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
 5GG  NY  CJ   single  1.456  0.020  1.456
 5GG  CJ  CI   single  1.521  0.020  1.521
 5GG  CI  CH   single  1.523  0.020  1.523
 5GG  CH  CF   single  1.520  0.020  1.520
 5GG  CF  NZ   single  1.450  0.020  1.450
 5GG  NZ  CE   single  1.450  0.020  1.450
 5GG  CE  CD   single  1.521  0.020  1.521
 5GG  CD  CG   single  1.524  0.020  1.524
 5GG  CG  CB   single  1.523  0.020  1.523
 5GG  CB  CA   single  1.530  0.020  1.530
 5GG  CA  C    single  1.525  0.021  1.525
 5GG  CA  N    single  1.458  0.019  1.458
 5GG  C   O    deloc   1.231  0.020  1.231
 5GG  C   O1   deloc   1.250  0.020  1.250
 5GG  N   H1   single  0.890  0.020  1.040
 5GG  N   H2   single  0.890  0.020  1.040
 5GG  CA  H4   single  0.970  0.020  1.090
 5GG  CB  H5   single  0.970  0.020  1.090
 5GG  CB  H6   single  0.970  0.020  1.090
 5GG  CG  H7   single  0.970  0.020  1.090
 5GG  CG  H8   single  0.970  0.020  1.090
 5GG  CD  H9   single  0.970  0.020  1.090
 5GG  CD  H10  single  0.970  0.020  1.090
 5GG  CE  H11  single  0.970  0.020  1.090
 5GG  CE  H12  single  0.970  0.020  1.090
 5GG  NZ  H13  single  0.890  0.020  1.040
 5GG  CH  H15  single  0.970  0.020  1.090
 5GG  CH  H16  single  0.970  0.020  1.090
 5GG  CI  H17  single  0.970  0.020  1.090
 5GG  CI  H18  single  0.970  0.020  1.090
 5GG  CJ  H19  single  0.970  0.020  1.090
 5GG  CJ  H20  single  0.970  0.020  1.090
 5GG  CF  H21  single  0.970  0.020  1.090
 5GG  CF  H22  single  0.970  0.020  1.090
 5GG  NY  H23  single  0.890  0.020  1.040
 5GG  NY  H24  single  0.890  0.020  1.040

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
 5GG  H2   N   H1   104.04  3.000
 5GG  H2   N   CA   107.94  3.000
 5GG  H1   N   CA   108.58  3.000
 5GG  H4   CA  CB   107.01  3.000
 5GG  H4   CA  C    106.95  3.000
 5GG  CB   CA  C    110.10  1.900
 5GG  H4   CA  N    107.12  3.000
 5GG  C    CA  N    111.00  2.800
 5GG  CB   CA  N    110.50  1.700
 5GG  O1   C   O    126.63  3.000
 5GG  O1   C   CA   115.78  3.000
 5GG  O    C   CA   120.80  1.700
 5GG  H6   CB  H5   106.09  3.000
 5GG  H6   CB  CG   109.13  3.000
 5GG  H5   CB  CG   109.23  3.000
 5GG  H6   CB  CA   109.26  3.000
 5GG  H5   CB  CA   108.34  3.000
 5GG  CG   CB  CA   114.46  3.000
 5GG  H8   CG  H7   106.12  3.000
 5GG  H8   CG  CD   109.35  3.000
 5GG  H7   CG  CD   109.40  3.000
 5GG  H8   CG  CB   109.22  3.000
 5GG  H7   CG  CB   109.90  3.000
 5GG  CD   CG  CB   112.64  3.000
 5GG  H10  CD  H9   106.33  3.000
 5GG  H10  CD  CE   108.98  3.000
 5GG  H9   CD  CE   109.42  3.000
 5GG  H10  CD  CG   109.86  3.000
 5GG  H9   CD  CG   109.35  3.000
 5GG  CE   CD  CG   112.70  3.000
 5GG  H12  CE  H11  105.92  3.000
 5GG  H12  CE  NZ   112.47  3.000
 5GG  H11  CE  NZ   108.13  3.000
 5GG  H12  CE  CD   109.25  3.000
 5GG  H11  CE  CD   109.15  3.000
 5GG  NZ   CE  CD   111.71  3.000
 5GG  H13  NZ  CF   108.65  3.000
 5GG  H13  NZ  CE   108.56  3.000
 5GG  CF   NZ  CE   113.04  3.000
 5GG  H16  CH  H15  106.40  3.000
 5GG  H16  CH  CF   109.07  3.000
 5GG  H15  CH  CF   109.25  3.000
 5GG  H16  CH  CI   109.82  3.000
 5GG  H15  CH  CI   109.41  3.000
 5GG  CF   CH  CI   112.69  3.000
 5GG  H18  CI  H17  106.41  3.000
 5GG  H18  CI  CJ   109.20  3.000
 5GG  H17  CI  CJ   109.08  3.000
 5GG  H18  CI  CH   109.43  3.000
 5GG  H17  CI  CH   109.89  3.000
 5GG  CJ   CI  CH   112.64  3.000
 5GG  H20  CJ  H19  106.14  3.000
 5GG  H20  CJ  NY   108.13  3.000
 5GG  H19  CJ  NY   113.51  3.000
 5GG  H20  CJ  CI   109.00  3.000
 5GG  H19  CJ  CI   108.73  3.000
 5GG  NY   CJ  CI   111.13  3.000
 5GG  H22  CF  H21  105.92  3.000
 5GG  H22  CF  CH   109.20  3.000
 5GG  H21  CF  CH   109.24  3.000
 5GG  H22  CF  NZ   112.51  3.000
 5GG  H21  CF  NZ   108.16  3.000
 5GG  CH   CF  NZ   111.61  3.000
 5GG  H24  NY  H23  105.47  3.000
 5GG  H24  NY  CJ   109.12  3.000
 5GG  H23  NY  CJ   109.44  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
 5GG  Var_01  CD   CG  CB  CA  -174.81  30.0  1
 5GG  Var_02  CE   CD  CG  CB  -177.80  30.0  1
 5GG  Var_03  NZ   CE  CD  CG  -179.54  30.0  1
 5GG  Var_04  CF   NZ  CE  CD   179.68  30.0  1
 5GG  Var_05  CH   CF  NZ  CE  -178.82  30.0  1
 5GG  Var_06  CI   CH  CF  NZ  -179.38  30.0  1
 5GG  Var_07  NY   CJ  CI  CH  -179.18  30.0  1
 5GG  Var_08  CF   CH  CI  CJ  -179.47  30.0  3
 5GG  Var_09  H23  NY  CJ  CI   178.76  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
 5GG  chir_01  CA  CB  C  N  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
 5GG  plan-1  CA  0.020
 5GG  plan-1  C   0.020
 5GG  plan-1  O   0.020
 5GG  plan-1  O1  0.020

