# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:30:00 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N~5~-[N-(2-carboxyethyl)carbamimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCCC(O)=O)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
 C67  C67  N~5~-[N-(2-carboxyethyl)carbamimidoyl]-L-ornithine  ligand  35  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C67
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
 C67  N    N  NH2   0  -0.776   4.5893   1.8408  -0.6026
 C67  CA   C  CH1   0  -0.206   4.6444   0.6777   0.2494
 C67  C    C  C     0   0.521   5.9428  -0.1085   0.1214
 C67  O    O  O     0  -0.441   6.7152  -0.0107  -0.7994
 C67  CB   C  CH2   0  -0.432   3.4615  -0.2594  -0.0324
 C67  CG   C  CH2   0  -0.457   2.1145   0.3973   0.2359
 C67  CD   C  CH2   0  -0.222   0.9644  -0.5429  -0.0891
 C67  NE   N  NH1   0  -0.670  -0.2987   0.0781   0.2379
 C67  CZ   C  C     0   0.617  -1.4763  -0.5802  -0.0008
 C67  NH1  N  N     0  -0.731  -1.4581  -1.8169  -0.3432
 C67  NH2  N  NH1   0  -0.678  -2.5921   0.1905   0.2393
 C67  C01  C  CH2   0  -0.610  -4.9486   0.6955   0.3981
 C67  C02  C  CH2   0  -0.263  -3.9039  -0.2374  -0.1881
 C67  C03  C  C     0   0.555  -6.3509   0.3011   0.0296
 C67  O02  O  OH1   0  -0.594  -7.2433   1.1637   0.5016
 C67  O03  O  O     0  -0.443  -6.6494  -0.6767  -0.6093
 C67  H1   H  HNH2  0   0.354   5.3277   2.4903  -0.3642
 C67  H2   H  HNH2  0   0.343   4.7439   1.5752  -1.5675
 C67  H4   H  HCH1  0   0.266   4.5692   1.0116   1.2895
 C67  H6   H  HCH2  0   0.232   3.5130  -0.5936  -1.0745
 C67  H7   H  HCH2  0   0.243   3.5522  -1.1553   0.5859
 C67  H8   H  HCH2  0   0.226   2.0574   0.6947   1.2876
 C67  H9   H  HCH2  0   0.233   2.0260   1.3101  -0.3577
 C67  H10  H  HCH2  0   0.207   1.0117  -0.8324  -1.1465
 C67  H11  H  HCH2  0   0.219   1.0640  -1.4649   0.4880
 C67  H12  H  HNH1  0   0.378  -0.3187   1.0820   0.1476
 C67  H13  H  H     0   0.325  -2.3908  -2.1940  -0.4483
 C67  H14  H  HNH1  0   0.382  -2.4479   1.1891   0.2154
 C67  H15  H  HCH2  0   0.292  -4.8685   0.7104   1.4889
 C67  H16  H  HCH2  0   0.286  -4.7810   1.7259   0.0701
 C67  H17  H  HCH2  0   0.236  -3.9931  -0.2693  -1.2797
 C67  H18  H  HCH2  0   0.240  -4.0894  -1.2478   0.1798
 C67  H19  H  HOH1  0   0.481  -8.1380   0.8820   0.2587
 C67  O1   O  OH1   0  -0.594   6.1277  -0.9377   1.1427
 C67  H3   H  HOH1  0   0.481   6.9459  -1.4426   1.0218

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
 C67  N    CA   single  1.443  0.020  1.443
 C67  O03  C03  double  1.206  0.020  1.206
 C67  C03  O02  single  1.328  0.020  1.328
 C67  C03  C01  single  1.503  0.020  1.503
 C67  C01  C02  single  1.518  0.020  1.518
 C67  CA   C    single  1.523  0.020  1.523
 C67  CA   CB   single  1.535  0.020  1.535
 C67  CG   CB   single  1.522  0.020  1.522
 C67  CG   CD   single  1.521  0.020  1.521
 C67  C02  NH2  single  1.445  0.020  1.445
 C67  C    O    double  1.206  0.020  1.206
 C67  NE   CD   single  1.445  0.020  1.445
 C67  NE   CZ   single  1.370  0.020  1.370
 C67  NH2  CZ   single  1.377  0.020  1.377
 C67  CZ   NH1  double  1.283  0.020  1.283
 C67  N    H1   single  0.890  0.020  1.040
 C67  N    H2   single  0.890  0.020  1.040
 C67  CA   H4   single  0.970  0.020  1.090
 C67  CB   H6   single  0.970  0.020  1.090
 C67  CB   H7   single  0.970  0.020  1.090
 C67  CG   H8   single  0.970  0.020  1.090
 C67  CG   H9   single  0.970  0.020  1.090
 C67  CD   H10  single  0.970  0.020  1.090
 C67  CD   H11  single  0.970  0.020  1.090
 C67  NE   H12  single  0.890  0.020  1.040
 C67  NH1  H13  single  0.890  0.020  1.040
 C67  NH2  H14  single  0.890  0.020  1.040
 C67  C01  H15  single  0.970  0.020  1.090
 C67  C01  H16  single  0.970  0.020  1.090
 C67  C02  H17  single  0.970  0.020  1.090
 C67  C02  H18  single  0.970  0.020  1.090
 C67  O02  H19  single  0.850  0.020  0.980
 C67  C    O1   single  1.328  0.020  1.328
 C67  O1   H3   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
 C67  H2   N    H1   106.35  3.000
 C67  H2   N    CA   110.21  3.000
 C67  H1   N    CA   110.51  3.000
 C67  H4   CA   CB   107.92  3.000
 C67  H4   CA   C    107.20  3.000
 C67  CB   CA   C    109.04  3.000
 C67  H4   CA   N    108.21  3.000
 C67  CB   CA   N    110.75  3.000
 C67  C    CA   N    113.51  3.000
 C67  O1   C    O    123.27  3.000
 C67  O1   C    CA   112.09  3.000
 C67  O    C    CA   124.64  3.000
 C67  H7   CB   H6   106.52  3.000
 C67  H7   CB   CG   109.11  3.000
 C67  H6   CB   CG   109.93  3.000
 C67  H7   CB   CA   109.44  3.000
 C67  H6   CB   CA   108.94  3.000
 C67  CG   CB   CA   112.71  3.000
 C67  H9   CG   H8   106.91  3.000
 C67  H9   CG   CD   109.83  3.000
 C67  H8   CG   CD   109.51  3.000
 C67  H9   CG   CB   109.65  3.000
 C67  H8   CG   CB   109.44  3.000
 C67  CD   CG   CB   111.40  3.000
 C67  H11  CD   H10  106.41  3.000
 C67  H11  CD   NE   108.84  3.000
 C67  H10  CD   NE   111.66  3.000
 C67  H11  CD   CG   109.88  3.000
 C67  H10  CD   CG   109.66  3.000
 C67  NE   CD   CG   110.30  3.000
 C67  H12  NE   CZ   116.48  3.000
 C67  H12  NE   CD   115.15  3.000
 C67  CZ   NE   CD   120.35  3.000
 C67  NH2  CZ   NH1  126.67  3.000
 C67  NH1  CZ   NE   119.83  3.000
 C67  NH2  CZ   NE   113.39  3.000
 C67  H13  NH1  CZ   111.96  3.000
 C67  H14  NH2  C02  114.58  3.000
 C67  H14  NH2  CZ   115.71  3.000
 C67  C02  NH2  CZ   121.22  3.000
 C67  H16  C01  H15  105.95  3.000
 C67  H16  C01  C03  108.46  3.000
 C67  H15  C01  C03  108.45  3.000
 C67  H16  C01  C02  110.94  3.000
 C67  H15  C01  C02  110.06  3.000
 C67  C03  C01  C02  112.72  3.000
 C67  H18  C02  H17  107.17  3.000
 C67  H18  C02  C01  108.78  3.000
 C67  H17  C02  C01  110.27  3.000
 C67  H18  C02  NH2  109.21  3.000
 C67  H17  C02  NH2  112.16  3.000
 C67  C01  C02  NH2  109.18  3.000
 C67  O03  C03  O02  123.29  3.000
 C67  O02  C03  C01  111.69  3.000
 C67  O03  C03  C01  125.03  3.000
 C67  H19  O02  C03  110.04  3.000
 C67  H3   O1   C    110.29  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
 C67  CONST_01  NH2  CZ   NE   CD    180.00   0.0  0
 C67  CONST_02  NH1  CZ   NE   CD      0.00   0.0  0
 C67  CONST_03  C02  NH2  CZ   NE    180.00   0.0  0
 C67  CONST_05  H3   O1   C    CA    180.00   0.0  0
 C67  CONST_07  H13  NH1  CZ   NE    180.00   0.0  0
 C67  CONST_09  H19  O02  C03  C01   180.00   0.0  0
 C67  Var_01    CD   CG   CB   CA    178.43  30.0  1
 C67  Var_02    NE   CD   CG   CB    177.08  30.0  3
 C67  Var_03    CZ   NE   CD   CG    178.58  30.0  1
 C67  Var_04    C01  C02  NH2  CZ    171.26  30.0  1
 C67  Var_05    C03  C01  C02  NH2  -178.59  30.0  1
 C67  Var_06    O03  C03  C01  C02     3.17  30.0  2

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
 C67  chir_01  CA  N  C  CB  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
 C67  plan-1  CD   0.020
 C67  plan-1  NE   0.020
 C67  plan-1  CZ   0.020
 C67  plan-1  NH1  0.020
 C67  plan-1  NH2  0.020
 C67  plan-1  C02  0.020
 C67  plan-1  H12  0.020
 C67  plan-1  H13  0.020
 C67  plan-1  H14  0.020
 C67  plan-2  CA   0.020
 C67  plan-2  C    0.020
 C67  plan-2  O    0.020
 C67  plan-2  O1   0.020
 C67  plan-2  H3   0.020
 C67  plan-3  C01  0.020
 C67  plan-3  C03  0.020
 C67  plan-3  O02  0.020
 C67  plan-3  O03  0.020
 C67  plan-3  H19  0.020

