# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 08:04:08 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)NC(=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
 VR0  VR0  N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithine  L-peptide  32  16  .  2012-08-28  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_VR0
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
 VR0  C1    C  CH3    0  -0.506  89.2348  66.8014  -2.6413
 VR0  NH2   N  N      0  -0.701  92.8081  70.5471  -4.0850
 VR0  O1    O  O      0  -0.517  91.6022  68.1624  -3.0530
 VR0  O     O  O      0  -0.602  96.8234  73.9012  -9.2519
 VR0  CG    C  CH2    0  -0.417  92.9867  72.1287  -7.0781
 VR0  CD    C  CH2    0  -0.269  92.2107  72.6185  -5.8586
 VR0  CB    C  CH2    0  -0.422  93.9905  73.1704  -7.5534
 VR0  NH3   N  NH1    0  -0.668  89.3751  68.0377  -3.3722
 VR0  NE    N  NH1    0  -0.668  91.2398  71.6799  -5.3434
 VR0  NH1   N  NH1    0  -0.767  90.5326  69.8133  -4.2376
 VR0  N     N  NH2    0  -0.785  95.4532  71.5550  -8.6698
 VR0  CZ    C  C      0   0.617  91.6177  70.6484  -4.5276
 VR0  C6    C  C      0   0.750  90.5743  68.6343  -3.5198
 VR0  C     C  C      0   0.380  95.5828  74.0175  -9.3047
 VR0  CA    C  CH1    0  -0.209  94.7278  72.8050  -8.8448
 VR0  H5    H  HCH3   0   0.249  88.1824  66.5320  -2.6333
 VR0  H4    H  HCH3   0   0.235  89.7908  65.9847  -3.1036
 VR0  H3    H  HCH3   0   0.236  89.5671  66.9003  -1.6075
 VR0  HH22  H  H      0   0.340  92.8868  69.7770  -3.4358
 VR0  HG2   H  HCH2   0   0.217  93.4921  71.1938  -6.8332
 VR0  HG3   H  HCH2   0   0.203  92.2815  71.9061  -7.8861
 VR0  HD2   H  HCH2   0   0.229  92.9027  72.8663  -5.0537
 VR0  HD3   H  HCH2   0   0.231  91.6767  73.5381  -6.1096
 VR0  HB2   H  HCH2   0   0.214  93.4741  74.1205  -7.7101
 VR0  HB3   H  HCH2   0   0.204  94.7275  73.3516  -6.7603
 VR0  HH33  H  HNH1   0   0.403  88.5493  68.4343  -3.7875
 VR0  HE    H  HNH1   0   0.381  90.4425  71.5243  -5.9405
 VR0  HH11  H  HNH1   0   0.407  89.6258  70.1454  -4.5311
 VR0  H2    H  HNH2   0   0.330  95.8712  71.2952  -9.5552
 VR0  H     H  HNH2   0   0.320  96.2456  71.7374  -8.0640
 VR0  OXT   O  OC    -1  -0.618  94.9417  75.0250  -9.6725
 VR0  HA    H  HCH1   0   0.202  93.9672  72.6339  -9.6170

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
 VR0  C1   NH3   single  1.443  0.020  1.443
 VR0  C1   H5    single  0.970  0.020  1.090
 VR0  C1   H4    single  0.970  0.020  1.090
 VR0  C1   H3    single  0.970  0.020  1.090
 VR0  NH2  CZ    double  1.274  0.020  1.274
 VR0  NH2  HH22  single  0.890  0.020  1.040
 VR0  O1   C6    double  1.224  0.020  1.224
 VR0  O    C     deloc   1.231  0.020  1.231
 VR0  CG   CD    single  1.526  0.020  1.526
 VR0  CG   CB    single  1.523  0.020  1.523
 VR0  CG   HG2   single  0.970  0.020  1.090
 VR0  CG   HG3   single  0.970  0.020  1.090
 VR0  CD   NE    single  1.445  0.020  1.445
 VR0  CD   HD2   single  0.970  0.020  1.090
 VR0  CD   HD3   single  0.970  0.020  1.090
 VR0  CB   CA    single  1.530  0.020  1.530
 VR0  CB   HB2   single  0.970  0.020  1.090
 VR0  CB   HB3   single  0.970  0.020  1.090
 VR0  NH3  C6    single  1.348  0.020  1.348
 VR0  NH3  HH33  single  0.860  0.020  1.020
 VR0  NE   CZ    single  1.368  0.020  1.368
 VR0  NE   HE    single  0.890  0.020  1.040
 VR0  NH1  CZ    single  1.400  0.020  1.400
 VR0  NH1  C6    single  1.381  0.020  1.381
 VR0  NH1  HH11  single  0.860  0.020  1.020
 VR0  N    CA    single  1.458  0.019  1.458
 VR0  N    H2    single  0.890  0.020  1.040
 VR0  N    H     single  0.860  0.020  0.860
 VR0  C    CA    single  1.525  0.021  1.525
 VR0  C    OXT   deloc   1.250  0.020  1.250
 VR0  CA   HA    single  0.970  0.020  0.970

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
 VR0  H3    C1   H4   108.32  3.000
 VR0  H3    C1   H5   108.10  3.000
 VR0  H4    C1   H5   108.14  3.000
 VR0  H3    C1   NH3  111.89  3.000
 VR0  H4    C1   NH3  112.16  3.000
 VR0  H5    C1   NH3  108.08  3.000
 VR0  HH22  NH2  CZ   110.89  3.000
 VR0  HG3   CG   HG2  106.85  3.000
 VR0  HG3   CG   CB   109.47  3.000
 VR0  HG2   CG   CB   110.55  3.000
 VR0  HG3   CG   CD   109.10  3.000
 VR0  HG2   CG   CD   109.35  3.000
 VR0  CB    CG   CD   111.41  3.000
 VR0  HD3   CD   HD2  106.77  3.000
 VR0  HD3   CD   NE   107.47  3.000
 VR0  HD2   CD   NE   108.11  3.000
 VR0  HD3   CD   CG   109.58  3.000
 VR0  HD2   CD   CG   109.89  3.000
 VR0  NE    CD   CG   114.70  3.000
 VR0  HB3   CB   HB2  106.11  3.000
 VR0  HB3   CB   CA   108.99  3.000
 VR0  HB2   CB   CA   108.31  3.000
 VR0  HB3   CB   CG   109.27  3.000
 VR0  HB2   CB   CG   109.15  3.000
 VR0  CA    CB   CG   114.67  3.000
 VR0  HH33  NH3  C6   120.72  3.000
 VR0  HH33  NH3  C1   117.85  3.000
 VR0  C6    NH3  C1   121.42  3.000
 VR0  HE    NE   CZ   117.08  3.000
 VR0  HE    NE   CD   114.86  3.000
 VR0  CZ    NE   CD   121.10  3.000
 VR0  HH11  NH1  C6   117.33  3.000
 VR0  HH11  NH1  CZ   116.10  3.000
 VR0  C6    NH1  CZ   126.42  3.000
 VR0  H     N    H2   104.23  3.000
 VR0  H     N    CA   114.00  3.000
 VR0  H2    N    CA   108.71  3.000
 VR0  NH1   CZ   NE   111.05  3.000
 VR0  NH1   CZ   NH2  127.23  3.000
 VR0  NE    CZ   NH2  121.67  3.000
 VR0  NH1   C6   NH3  114.09  3.000
 VR0  NH1   C6   O1   123.57  3.000
 VR0  NH3   C6   O1   122.34  3.000
 VR0  OXT   C    CA   115.73  3.000
 VR0  OXT   C    O    126.73  3.000
 VR0  CA    C    O    120.80  1.700
 VR0  HA    CA   C    109.00  3.000
 VR0  HA    CA   N    110.00  3.000
 VR0  C     CA   N    111.00  2.800
 VR0  HA    CA   CB   109.00  3.000
 VR0  C     CA   CB   110.10  1.900
 VR0  N     CA   CB   110.50  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
 VR0  CONST_01  O1    C6   NH3  C1      0.00   0.0  0
 VR0  CONST_02  CZ    NH1  C6   O1      0.00   0.0  0
 VR0  CONST_03  NH1   C6   NH3  C1    180.00   0.0  0
 VR0  CONST_04  CD    NE   CZ   NH2     0.00   0.0  0
 VR0  CONST_05  C6    NH1  CZ   NH2     0.00   0.0  0
 VR0  CONST_06  NH1   CZ   NE   CD    180.00   0.0  0
 VR0  CONST_07  CZ    NH1  C6   NH3   180.00   0.0  0
 VR0  CONST_08  C6    NH1  CZ   NE    180.00   0.0  0
 VR0  CONST_09  HH33  NH3  C6   O1    180.00   0.0  0
 VR0  CONST_10  HH11  NH1  C6   O1    180.00   0.0  0
 VR0  CONST_12  HH22  NH2  CZ   NE    180.00   0.0  0
 VR0  Var_01    CZ    NE   CD   CG     80.99  30.0  3
 VR0  Var_02    CA    CB   CG   CD   -175.08  30.0  3
 VR0  Var_03    NE    CD   CG   CB   -179.73  30.0  3
 VR0  Var_04    H5    C1   NH3  C6    178.41  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
 VR0  chir_01  CA  CB  N  C  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
 VR0  plan-1  C1    0.020
 VR0  plan-1  NH2   0.020
 VR0  plan-1  O1    0.020
 VR0  plan-1  CD    0.020
 VR0  plan-1  NH3   0.020
 VR0  plan-1  NE    0.020
 VR0  plan-1  NH1   0.020
 VR0  plan-1  CZ    0.020
 VR0  plan-1  C6    0.020
 VR0  plan-1  HH22  0.020
 VR0  plan-1  HH33  0.020
 VR0  plan-1  HE    0.020
 VR0  plan-1  HH11  0.020
 VR0  plan-2  O     0.020
 VR0  plan-2  C     0.020
 VR0  plan-2  CA    0.020
 VR0  plan-2  OXT   0.020

