# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 11:20:26 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N~5~-[N-(3-hydroxypropyl)carbamimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCCCO)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
 C6D  C6D  N~5~-[N-(3-hydroxypropyl)carbamimidoyl]-L-ornithine  ligand  35  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C6D
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
 C6D  N    N  NH2    0  -0.788   4.3387   1.8330  -0.4481
 C6D  CA   C  CH1    0  -0.211   4.2131   0.6868   0.4401
 C6D  C    C  C      0   0.384   5.4876  -0.1805   0.5871
 C6D  O    O  O      0  -0.609   6.3820  -0.0454  -0.2719
 C6D  CB   C  CH2    0  -0.417   3.0546  -0.2080  -0.0112
 C6D  CG   C  CH2    0  -0.450   1.7030   0.4909  -0.0034
 C6D  CD   C  CH2    0  -0.227   0.5757  -0.4452  -0.4097
 C6D  NE   N  NH1    0  -0.666  -0.6999   0.2339  -0.3290
 C6D  CZ   C  C      0   0.610  -1.8573  -0.4414  -0.6206
 C6D  NH1  N  N      0  -0.733  -1.8068  -1.5718  -1.2269
 C6D  NH2  N  NH1    0  -0.670  -2.9993   0.2391  -0.2659
 C6D  C01  C  CH2    0  -0.496  -5.3646   0.5102   0.2475
 C6D  C02  C  CH2    0  -0.276  -4.2789  -0.4347  -0.2413
 C6D  C03  C  CH2    0  -0.138  -6.7139  -0.1798   0.2936
 C6D  O2   O  OH1    0  -0.673  -7.6782   0.7405   0.7558
 C6D  H1   H  HNH2   0   0.334   4.9815   2.4969  -0.0330
 C6D  H2   H  HNH2   0   0.322   4.8110   1.5197  -1.2892
 C6D  H4   H  HCH1   0   0.206   3.9573   1.0686   1.4355
 C6D  H6   H  HCH2   0   0.207   3.2676  -0.5887  -1.0180
 C6D  H7   H  HCH2   0   0.217   3.0168  -1.0805   0.6458
 C6D  H8   H  HCH2   0   0.209   1.5068   0.8771   1.0041
 C6D  H9   H  HCH2   0   0.225   1.7267   1.3545  -0.6709
 C6D  H10  H  HCH2   0   0.219   0.7326  -0.7900  -1.4336
 C6D  H11  H  HCH2   0   0.201   0.5901  -1.3410   0.2249
 C6D  H12  H  HNH1   0   0.373  -0.7632   0.9108   0.4160
 C6D  H13  H  H      0   0.327  -2.7329  -1.9337  -1.4159
 C6D  H14  H  HNH1   0   0.379  -2.8859   0.9450   0.4459
 C6D  H15  H  HCH2   0   0.234  -5.1081   0.8736   1.2478
 C6D  H16  H  HCH2   0   0.238  -5.4151   1.3797  -0.4133
 C6D  H17  H  HCH2   0   0.230  -4.5299  -0.7749  -1.2501
 C6D  H18  H  HCH2   0   0.222  -4.2518  -1.3277   0.3975
 C6D  H19  H  HCH2   0   0.193  -6.9647  -0.5533  -0.7082
 C6D  H20  H  HCH2   0   0.193  -6.6512  -1.0572   0.9511
 C6D  H21  H  HOH1   0   0.454  -8.5293   0.2941   0.7784
 C6D  O1   O  OC    -1  -0.625   5.5003  -0.9765   1.5499

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
 C6D  N    CA   single  1.455  0.020  1.455
 C6D  C03  O2   single  1.411  0.020  1.411
 C6D  C03  C01  single  1.516  0.020  1.516
 C6D  C01  C02  single  1.520  0.020  1.520
 C6D  CA   C    single  1.549  0.020  1.549
 C6D  CA   CB   single  1.532  0.020  1.532
 C6D  C02  NH2  single  1.446  0.020  1.446
 C6D  CG   CB   single  1.522  0.020  1.522
 C6D  CG   CD   single  1.521  0.020  1.521
 C6D  C    O    deloc   1.247  0.020  1.247
 C6D  NE   CD   single  1.447  0.020  1.447
 C6D  NE   CZ   single  1.371  0.020  1.371
 C6D  NH2  CZ   single  1.376  0.020  1.376
 C6D  CZ   NH1  double  1.284  0.020  1.284
 C6D  N    H1   single  0.890  0.020  1.040
 C6D  N    H2   single  0.890  0.020  1.040
 C6D  CA   H4   single  0.970  0.020  1.090
 C6D  CB   H6   single  0.970  0.020  1.090
 C6D  CB   H7   single  0.970  0.020  1.090
 C6D  CG   H8   single  0.970  0.020  1.090
 C6D  CG   H9   single  0.970  0.020  1.090
 C6D  CD   H10  single  0.970  0.020  1.090
 C6D  CD   H11  single  0.970  0.020  1.090
 C6D  NE   H12  single  0.890  0.020  1.040
 C6D  NH1  H13  single  0.890  0.020  1.040
 C6D  NH2  H14  single  0.890  0.020  1.040
 C6D  C01  H15  single  0.970  0.020  1.090
 C6D  C01  H16  single  0.970  0.020  1.090
 C6D  C02  H17  single  0.970  0.020  1.090
 C6D  C02  H18  single  0.970  0.020  1.090
 C6D  C03  H19  single  0.970  0.020  1.090
 C6D  C03  H20  single  0.970  0.020  1.090
 C6D  O2   H21  single  0.850  0.020  0.980
 C6D  C    O1   deloc   1.249  0.020  1.249

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
 C6D  H2   N    H1   104.29  3.000
 C6D  H2   N    CA   107.64  3.000
 C6D  H1   N    CA   108.71  3.000
 C6D  H4   CA   CB   107.12  3.000
 C6D  H4   CA   C    107.51  3.000
 C6D  CB   CA   C    108.86  3.000
 C6D  H4   CA   N    107.46  3.000
 C6D  CB   CA   N    110.21  3.000
 C6D  C    CA   N    115.34  3.000
 C6D  O1   C    O    126.33  3.000
 C6D  O1   C    CA   116.00  3.000
 C6D  O    C    CA   117.65  3.000
 C6D  H7   CB   H6   106.34  3.000
 C6D  H7   CB   CG   109.44  3.000
 C6D  H6   CB   CG   109.67  3.000
 C6D  H7   CB   CA   108.38  3.000
 C6D  H6   CB   CA   109.04  3.000
 C6D  CG   CB   CA   113.70  3.000
 C6D  H9   CG   H8   106.68  3.000
 C6D  H9   CG   CD   109.86  3.000
 C6D  H8   CG   CD   109.25  3.000
 C6D  H9   CG   CB   109.93  3.000
 C6D  H8   CG   CB   108.99  3.000
 C6D  CD   CG   CB   111.99  3.000
 C6D  H11  CD   H10  106.41  3.000
 C6D  H11  CD   NE   111.23  3.000
 C6D  H10  CD   NE   109.10  3.000
 C6D  H11  CD   CG   109.76  3.000
 C6D  H10  CD   CG   109.78  3.000
 C6D  NE   CD   CG   110.46  3.000
 C6D  H12  NE   CZ   115.76  3.000
 C6D  H12  NE   CD   114.29  3.000
 C6D  CZ   NE   CD   120.06  3.000
 C6D  NH2  CZ   NH1  126.15  3.000
 C6D  NH1  CZ   NE   120.06  3.000
 C6D  NH2  CZ   NE   113.71  3.000
 C6D  H13  NH1  CZ   111.54  3.000
 C6D  H14  NH2  C02  114.42  3.000
 C6D  H14  NH2  CZ   115.77  3.000
 C6D  C02  NH2  CZ   120.55  3.000
 C6D  H16  C01  H15  107.40  3.000
 C6D  H16  C01  C03  109.83  3.000
 C6D  H15  C01  C03  109.38  3.000
 C6D  H16  C01  C02  109.45  3.000
 C6D  H15  C01  C02  109.44  3.000
 C6D  C03  C01  C02  111.26  3.000
 C6D  H18  C02  H17  106.81  3.000
 C6D  H18  C02  C01  109.63  3.000
 C6D  H17  C02  C01  109.02  3.000
 C6D  H18  C02  NH2  111.52  3.000
 C6D  H17  C02  NH2  109.41  3.000
 C6D  C01  C02  NH2  110.35  3.000
 C6D  H20  C03  H19  106.71  3.000
 C6D  H20  C03  O2   111.35  3.000
 C6D  H19  C03  O2   111.39  3.000
 C6D  H20  C03  C01  109.32  3.000
 C6D  H19  C03  C01  109.29  3.000
 C6D  O2   C03  C01  108.75  3.000
 C6D  H21  O2   C03  108.06  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
 C6D  CONST_01  NH2  CZ   NE   CD    180.00   0.0  0
 C6D  CONST_02  NH1  CZ   NE   CD      0.00   0.0  0
 C6D  CONST_03  C02  NH2  CZ   NE    180.00   0.0  0
 C6D  CONST_06  H13  NH1  CZ   NE    180.00   0.0  0
 C6D  Var_01    CD   CG   CB   CA   -177.97  30.0  1
 C6D  Var_02    NE   CD   CG   CB    177.25  30.0  3
 C6D  Var_03    CZ   NE   CD   CG   -178.32  30.0  1
 C6D  Var_04    C01  C02  NH2  CZ    177.15  30.0  2
 C6D  Var_05    C03  C01  C02  NH2  -179.47  30.0  2
 C6D  Var_06    O2   C03  C01  C02   179.85  30.0  1

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
 C6D  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
 C6D  plan-1  CD   0.020
 C6D  plan-1  NE   0.020
 C6D  plan-1  CZ   0.020
 C6D  plan-1  NH1  0.020
 C6D  plan-1  NH2  0.020
 C6D  plan-1  C02  0.020
 C6D  plan-1  H12  0.020
 C6D  plan-1  H13  0.020
 C6D  plan-1  H14  0.020
 C6D  plan-2  CA   0.020
 C6D  plan-2  C    0.020
 C6D  plan-2  O    0.020
 C6D  plan-2  O1   0.020

