# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:07:16 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N~5~-(N,N-dimethylcarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=N)NCCC[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
 DA2  DA2  N~5~-(N,N-dimethylcarbamimidoyl)-L-ornithine  L-peptide  31  14  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DA2
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
 DA2  C1    C  CH3    0  -0.533   8.3632  10.9363  30.1471
 DA2  C2    C  CH3    0  -0.549   6.4625  12.3588  29.6890
 DA2  N     N  NH2    0  -0.786   7.6695  16.0119  34.9151
 DA2  CA    C  CH1    0  -0.208   8.1494  16.0713  33.5408
 DA2  CB    C  CH2    0  -0.423   8.1476  14.6690  32.9253
 DA2  CG    C  CH2    0  -0.411   9.0254  13.6699  33.6689
 DA2  CD    C  CH2    0  -0.319   9.1668  12.3201  32.9724
 DA2  NE    N  NH1    0  -0.626   7.9407  11.5357  32.9150
 DA2  CZ    C  C      0   0.549   6.9548  11.7547  31.9770
 DA2  NH2   N  N      0  -0.701   5.7332  11.8158  32.3642
 DA2  NH1   N  NT     0  -0.450   7.4088  11.8950  30.6763
 DA2  C     C  C      0   0.380   7.3753  17.0376  32.6052
 DA2  O     O  O      0  -0.603   6.2639  17.4487  32.9946
 DA2  OXT   O  OC    -1  -0.618   7.9315  17.3027  31.5186
 DA2  HC11  H  HCH3   0   0.257   9.0240  10.5649  30.9239
 DA2  HC12  H  HCH3   0   0.227   7.8564  10.0744  29.6982
 DA2  HC13  H  HCH3   0   0.237   8.9747  11.4059  29.3759
 DA2  HC21  H  HCH3   0   0.248   5.9204  13.2307  30.0535
 DA2  HC22  H  HCH3   0   0.249   7.0075  12.6587  28.7946
 DA2  HC23  H  HCH3   0   0.219   5.7339  11.5938  29.3934
 DA2  HCA   H  HCH1   0   0.200   9.1914  16.4124  33.5741
 DA2  HCB1  H  HCH2   0   0.210   7.1144  14.3059  32.8874
 DA2  HCB2  H  HCH2   0   0.211   8.4865  14.7447  31.8890
 DA2  HCG1  H  HCH2   0   0.209  10.0303  14.0918  33.7821
 DA2  HCG2  H  HCH2   0   0.216   8.6475  13.5149  34.6825
 DA2  HCD1  H  HCH2   0   0.238   9.5494  12.4666  31.9622
 DA2  HCD2  H  HCH2   0   0.237   9.9153  11.7224  33.4978
 DA2  HNE   H  HNH1   0   0.364   7.5305  11.3920  33.8266
 DA2  HNH2  H  H      0   0.326   5.0908  11.7980  31.5813
 DA2  HN1   H  HNH2   0   0.330   7.7538  16.9338  35.3268
 DA2  HN2   H  HNH2   0   0.319   6.6698  15.8437  34.8854

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
 DA2  C1   NH1   single  1.453  0.020  1.453
 DA2  C1   HC11  single  0.970  0.020  1.090
 DA2  C1   HC12  single  0.970  0.020  1.090
 DA2  C1   HC13  single  0.970  0.020  1.090
 DA2  C2   NH1   single  1.444  0.020  1.444
 DA2  C2   HC21  single  0.970  0.020  1.090
 DA2  C2   HC22  single  0.970  0.020  1.090
 DA2  C2   HC23  single  0.970  0.020  1.090
 DA2  N    CA    single  1.458  0.019  1.458
 DA2  N    HN1   single  0.890  0.020  1.040
 DA2  N    HN2   single  0.890  0.020  1.040
 DA2  CA   CB    single  1.530  0.020  1.530
 DA2  CA   C     single  1.525  0.021  1.525
 DA2  CA   HCA   single  0.970  0.020  1.090
 DA2  CB   CG    single  1.524  0.020  1.524
 DA2  CB   HCB1  single  0.970  0.020  1.090
 DA2  CB   HCB2  single  0.970  0.020  1.090
 DA2  CG   CD    single  1.525  0.020  1.525
 DA2  CG   HCG1  single  0.970  0.020  1.090
 DA2  CG   HCG2  single  0.970  0.020  1.090
 DA2  CD   NE    single  1.457  0.020  1.457
 DA2  CD   HCD1  single  0.970  0.020  1.090
 DA2  CD   HCD2  single  0.970  0.020  1.090
 DA2  NE   CZ    single  1.378  0.020  1.378
 DA2  NE   HNE   single  0.890  0.020  1.040
 DA2  CZ   NH2   double  1.283  0.020  1.283
 DA2  CZ   NH1   single  1.385  0.020  1.385
 DA2  NH2  HNH2  single  0.890  0.020  1.040
 DA2  C    O     deloc   1.231  0.020  1.231
 DA2  C    OXT   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
 DA2  HC13  C1   HC12  107.95  3.000
 DA2  HC13  C1   HC11  108.19  3.000
 DA2  HC12  C1   HC11  107.79  3.000
 DA2  HC13  C1   NH1   109.99  3.000
 DA2  HC12  C1   NH1   111.37  3.000
 DA2  HC11  C1   NH1   111.42  3.000
 DA2  HC23  C2   HC22  107.64  3.000
 DA2  HC23  C2   HC21  108.53  3.000
 DA2  HC22  C2   HC21  107.66  3.000
 DA2  HC23  C2   NH1   113.29  3.000
 DA2  HC22  C2   NH1   108.78  3.000
 DA2  HC21  C2   NH1   110.75  3.000
 DA2  HN2   N    HN1   104.17  3.000
 DA2  HN2   N    CA    107.69  3.000
 DA2  HN1   N    CA    108.60  3.000
 DA2  HCA   CA   C     107.37  3.000
 DA2  HCA   CA   CB    107.34  3.000
 DA2  C     CA   CB    110.10  1.900
 DA2  HCA   CA   N     107.27  3.000
 DA2  C     CA   N     111.00  2.800
 DA2  CB    CA   N     110.50  1.700
 DA2  HCB2  CB   HCB1  106.41  3.000
 DA2  HCB2  CB   CG    109.24  3.000
 DA2  HCB1  CB   CG    110.05  3.000
 DA2  HCB2  CB   CA    108.50  3.000
 DA2  HCB1  CB   CA    108.56  3.000
 DA2  CG    CB   CA    113.80  3.000
 DA2  HCG2  CG   HCG1  106.02  3.000
 DA2  HCG2  CG   CD    109.27  3.000
 DA2  HCG1  CG   CD    107.63  3.000
 DA2  HCG2  CG   CB    110.27  3.000
 DA2  HCG1  CG   CB    109.04  3.000
 DA2  CD    CG   CB    114.25  3.000
 DA2  HCD2  CD   HCD1  106.18  3.000
 DA2  HCD2  CD   NE    107.52  3.000
 DA2  HCD1  CD   NE    109.35  3.000
 DA2  HCD2  CD   CG    109.15  3.000
 DA2  HCD1  CD   CG    109.68  3.000
 DA2  NE    CD   CG    114.61  3.000
 DA2  HNE   NE   CZ    110.27  3.000
 DA2  HNE   NE   CD    112.52  3.000
 DA2  CZ    NE   CD    122.91  3.000
 DA2  NH1   CZ   NH2   126.21  3.000
 DA2  NH1   CZ   NE    114.89  3.000
 DA2  NH2   CZ   NE    118.90  3.000
 DA2  HNH2  NH2  CZ    111.71  3.000
 DA2  CZ    NH1  C2    117.38  3.000
 DA2  CZ    NH1  C1    119.39  3.000
 DA2  C2    NH1  C1    113.17  3.000
 DA2  OXT   C    O     126.75  3.000
 DA2  OXT   C    CA    115.75  3.000
 DA2  O     C    CA    120.80  1.700

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
 DA2  CONST_03  NE    CZ   NH1  C2    180.00   0.0  0
 DA2  CONST_04  NH2   CZ   NH1  C2      0.00   0.0  0
 DA2  CONST_07  HNH2  NH2  CZ   NE    180.00   0.0  0
 DA2  CONST_08  HNE   NE   CZ   NH2     0.00   0.0  0
 DA2  Var_01    CD    CG   CB   CA   -172.93  30.0  3
 DA2  Var_02    NE    CD   CG   CB    -67.13  30.0  3
 DA2  Var_03    CZ    NE   CD   CG     80.77  30.0  3
 DA2  Var_04    HC21  C2   NH1  C1   -166.97  30.0  3
 DA2  Var_05    HC11  C1   NH1  C2   -176.79  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
 DA2  chir_01  CA  N  CB  C  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
 DA2  plan-1  C1    0.020
 DA2  plan-1  C2    0.020
 DA2  plan-1  CD    0.020
 DA2  plan-1  NE    0.020
 DA2  plan-1  CZ    0.020
 DA2  plan-1  NH2   0.020
 DA2  plan-1  NH1   0.020
 DA2  plan-1  HNE   0.020
 DA2  plan-1  HNH2  0.020
 DA2  plan-2  CA    0.020
 DA2  plan-2  C     0.020
 DA2  plan-2  O     0.020
 DA2  plan-2  OXT   0.020

