# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:43:23 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (2Z,4E)-5-carbamimidamido-2-iminopent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N/C=C/CC(=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
 4VI  4VI  "(2Z,4E)-5-carbamimidamido-2-iminopent-4-enoic acid"  ligand  21  12  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VI
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
 4VI  CZ    C  C      0   0.526  28.2337  26.6163  44.4302
 4VI  CD    C  C1     0   0.020  26.1704  27.9452  44.1804
 4VI  CG    C  C1     0  -0.347  25.0528  28.2626  43.5218
 4VI  CB    C  CH2    0  -0.556  24.0792  29.2806  44.0205
 4VI  CA    C  C      0   0.048  24.0064  30.5413  43.1820
 4VI  C     C  C      0   0.384  22.8530  31.5108  43.5040
 4VI  NH1   N  N      0  -0.699  28.7562  25.4848  44.1389
 4VI  NE    N  NH1    0  -0.658  27.0734  26.9801  43.7839
 4VI  N     N  N      0  -0.563  24.8446  30.8547  42.2849
 4VI  NH2   N  NH2    0  -0.829  28.6818  27.5136  45.3700
 4VI  OXT   O  OC    -1  -0.587  22.3312  31.3498  44.6244
 4VI  O     O  O      0  -0.586  22.5588  32.3521  42.6405
 4VI  HD2   H  H      0   0.267  26.4085  28.4472  45.1109
 4VI  HG2   H  H      0   0.247  24.8163  27.7547  42.5902
 4VI  HB2   H  HCH2   0   0.258  24.3247  29.5726  45.0458
 4VI  HB3   H  HCH2   0   0.246  23.0758  28.8494  44.0805
 4VI  HH11  H  H      0   0.322  29.6426  25.3640  44.6144
 4VI  H     H  H      0   0.323  25.5650  30.1344  42.2138
 4VI  HH21  H  HNH2   0   0.394  29.5906  27.3043  45.7519
 4VI  HH22  H  HNH2   0   0.393  28.5878  28.4942  45.1522
 4VI  H1    H  HNH1   0   0.396  26.7983  26.3559  43.0411

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
 4VI  N    CA    double  1.267  0.020  1.267
 4VI  O    C     deloc   1.241  0.020  1.241
 4VI  CA   C     single  1.541  0.020  1.541
 4VI  CA   CB    single  1.516  0.020  1.516
 4VI  CG   CB    single  1.494  0.020  1.494
 4VI  CG   CD    double  1.335  0.020  1.335
 4VI  C    OXT   deloc   1.246  0.020  1.246
 4VI  NE   CD    single  1.380  0.020  1.380
 4VI  NE   CZ    single  1.377  0.020  1.377
 4VI  NH1  CZ    double  1.280  0.020  1.280
 4VI  CZ   NH2   single  1.375  0.020  1.375
 4VI  CD   HD2   single  0.930  0.020  1.080
 4VI  CG   HG2   single  0.930  0.020  1.080
 4VI  CB   HB2   single  0.970  0.020  1.090
 4VI  CB   HB3   single  0.970  0.020  1.090
 4VI  NH1  HH11  single  0.890  0.020  1.040
 4VI  N    H     single  0.860  0.020  1.020
 4VI  NH2  HH21  single  0.890  0.020  1.040
 4VI  NH2  HH22  single  0.890  0.020  1.040
 4VI  NE   H1    single  0.860  0.020  1.020

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
 4VI  NH2   CZ   NE    115.03  3.000
 4VI  NH2   CZ   NH1   126.85  3.000
 4VI  NE    CZ   NH1   118.08  3.000
 4VI  HD2   CD   NE    115.27  3.000
 4VI  HD2   CD   CG    119.82  3.000
 4VI  NE    CD   CG    124.90  3.000
 4VI  HG2   CG   CB    117.56  3.000
 4VI  HG2   CG   CD    119.57  3.000
 4VI  CB    CG   CD    122.86  3.000
 4VI  HB3   CB   HB2   105.05  3.000
 4VI  HB3   CB   CA    108.31  3.000
 4VI  HB2   CB   CA    107.90  3.000
 4VI  HB3   CB   CG    110.33  3.000
 4VI  HB2   CB   CG    110.39  3.000
 4VI  CA    CB   CG    114.41  3.000
 4VI  N     CA   C     119.18  3.000
 4VI  C     CA   CB    116.33  3.000
 4VI  N     CA   CB    124.44  3.000
 4VI  O     C    OXT   127.87  3.000
 4VI  OXT   C    CA    114.84  3.000
 4VI  O     C    CA    117.29  3.000
 4VI  HH11  NH1  CZ    110.85  3.000
 4VI  H1    NE   CD    117.78  3.000
 4VI  H1    NE   CZ    114.33  3.000
 4VI  CD    NE   CZ    126.97  3.000
 4VI  H     N    CA    109.97  3.000
 4VI  HH22  NH2  HH21  111.57  3.000
 4VI  HH22  NH2  CZ    117.17  3.000
 4VI  HH21  NH2  CZ    114.68  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
 4VI  CONST_03  H1    NE   CZ  NH1     0.00   0.0  0
 4VI  CONST_04  HH21  NH2  CZ  NH1     0.00   0.0  0
 4VI  CONST_06  HH11  NH1  CZ  NE    180.00   0.0  0
 4VI  CONST_07  HH21  NH2  CZ  NE    180.00   0.0  0
 4VI  CONST_09  H1    NE   CZ  NH2   180.00   0.0  0
 4VI  CONST_10  HH11  NH1  CZ  NH2     0.00   0.0  0
 4VI  Var_01    NE    CD   CG  CB    177.59   0.0  2
 4VI  Var_02    CG    CD   NE  CZ   -179.80  30.0  2
 4VI  Var_03    CA    CB   CG  CD    111.99  30.0  3
 4VI  Var_04    N     CA   CB  CG    -12.73  30.0  2
 4VI  Var_05    C     CA   CB  CG    169.65  30.0  2
 4VI  Var_06    O     C    CA  CB   -161.83  30.0  2
 4VI  Var_07    OXT   C    CA  CB     18.58  30.0  2
 4VI  Var_08    O     C    CA  N      20.42  30.0  2
 4VI  Var_09    OXT   C    CA  N    -159.16  30.0  2
 4VI  Var_10    H     N    CA  CB      0.17   0.0  2
 4VI  Var_11    HD2   CD   CG  CB     -1.01   0.0  2
 4VI  Var_12    H     N    CA  C     177.73   0.0  2
 4VI  Var_13    HG2   CG   CD  NE     -1.23   0.0  2
 4VI  Var_14    HD2   CD   NE  CZ     -1.15  30.0  2
 4VI  Var_15    HB2   CB   CG  CD     -9.93  30.0  3
 4VI  Var_16    HB3   CB   CG  CD   -125.59  30.0  3
 4VI  Var_17    H1    NE   CD  CG    -11.50  30.0  1
 4VI  Var_18    HG2   CG   CB  CA    -69.17  30.0  2
 4VI  Var_19    HB2   CB   CA  C     -67.08  30.0  3
 4VI  Var_20    HB3   CB   CA  C      46.14  30.0  3
 4VI  Var_21    HB2   CB   CA  N     110.54  30.0  3
 4VI  Var_22    HB3   CB   CA  N    -136.24  30.0  3
 4VI  Var_23    HG2   CG   CD  HD2  -179.83   0.0  2

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
 4VI  plan-1  CZ    0.020
 4VI  plan-1  CD    0.020
 4VI  plan-1  NH1   0.020
 4VI  plan-1  NE    0.020
 4VI  plan-1  NH2   0.020
 4VI  plan-1  HH11  0.020
 4VI  plan-1  HH21  0.020
 4VI  plan-1  HH22  0.020
 4VI  plan-1  H1    0.020
 4VI  plan-2  CA    0.020
 4VI  plan-2  C     0.020
 4VI  plan-2  OXT   0.020
 4VI  plan-2  O     0.020
 4VI  plan-3  CB    0.020
 4VI  plan-3  CA    0.020
 4VI  plan-3  C     0.020
 4VI  plan-3  N     0.020
 4VI  plan-3  H     0.020
 4VI  plan-4  CD    0.020
 4VI  plan-4  CG    0.020
 4VI  plan-4  CB    0.020
 4VI  plan-4  NE    0.020
 4VI  plan-4  HD2   0.020
 4VI  plan-4  HG2   0.020

