# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 07:52:57 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (2~{R})-6-azanyl-2-carbamimidamido-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@@H](NC(N)=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
 V7T  V7T  "(2R)-6-azanyl-2-carbamimidamido-hexanoic acid"  peptide  28  13  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V7T
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
 V7T  N1   N  N      0  -0.727   6.3378  -10.0872  4.7713
 V7T  N2   N  NH2    0  -0.812   4.9394  -10.4467  2.9874
 V7T  CA   C  CH1    0  -0.167   3.4212  -12.2776  4.4628
 V7T  CD   C  CH2    0  -0.430   0.7804  -14.4493  6.3694
 V7T  CE   C  CH2    0  -0.286  -0.3307  -15.4194  5.9925
 V7T  NZ   N  NH2    0  -0.794  -1.3787  -14.7643  5.2203
 V7T  CB   C  CH2    0  -0.454   2.6620  -12.9455  5.6114
 V7T  C2   C  C      0   0.521   5.2515  -10.6048  4.3173
 V7T  N    N  NH1    0  -0.644   4.3368  -11.3120  5.0522
 V7T  C    C  C      0   0.403   4.1274  -13.3471  3.5882
 V7T  O    O  O      0  -0.604   5.2170  -13.7748  4.0141
 V7T  H1   H  H      0   0.305   6.4877  -10.3597  5.7360
 V7T  H2   H  HNH2   0   0.382   3.9637  -10.4058  2.7404
 V7T  H3   H  HNH2   0   0.376   5.4834   -9.7324  2.5313
 V7T  HA   H  HCH1   0   0.209   2.6851  -11.7448  3.8505
 V7T  HD2  H  HCH2   0   0.209   0.3616  -13.6348  6.9721
 V7T  HD3  H  HCH2   0   0.214   1.4833  -14.9733  7.0247
 V7T  HE2  H  HCH2   0   0.209   0.0911  -16.2218  5.3802
 V7T  HE3  H  HCH2   0   0.197  -0.7044  -15.8971  6.9093
 V7T  HZ1  H  HNH2   0   0.344  -2.0841  -15.4434  4.9650
 V7T  HZ2  H  HNH2   0   0.334  -1.8502  -14.0896  5.8106
 V7T  HG2  H  HCH2   0   0.213   1.9346  -14.7016  4.5825
 V7T  HG3  H  HCH2   0   0.209   0.8459  -13.3352  4.5258
 V7T  HB2  H  HCH2   0   0.213   3.3777  -13.4995  6.2300
 V7T  HB3  H  HCH2   0   0.223   2.2453  -12.1603  6.2517
 V7T  H    H  HNH1   0   0.370   4.6834  -11.5764  5.9621
 V7T  OXT  O  OC    -1  -0.605   3.5191  -13.7074  2.5614
 V7T  CG   C  CH2    0  -0.407   1.5371  -13.8753  5.1775

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
 V7T  N1  C2   double  1.286  0.020  1.286
 V7T  N2  C2   single  1.375  0.020  1.375
 V7T  CA  CB   single  1.530  0.020  1.530
 V7T  CA  N    single  1.458  0.019  1.458
 V7T  CA  C    single  1.525  0.021  1.525
 V7T  CD  CE   single  1.522  0.020  1.522
 V7T  CD  CG   single  1.524  0.020  1.524
 V7T  CE  NZ   single  1.457  0.020  1.457
 V7T  CG  CB   single  1.523  0.020  1.523
 V7T  C2  N    single  1.370  0.020  1.370
 V7T  C   O    deloc   1.231  0.020  1.231
 V7T  N1  H1   single  0.890  0.020  1.040
 V7T  N2  H2   single  0.890  0.020  1.040
 V7T  N2  H3   single  0.890  0.020  1.040
 V7T  CA  HA   single  0.970  0.020  0.970
 V7T  CD  HD2  single  0.970  0.020  1.090
 V7T  CD  HD3  single  0.970  0.020  1.090
 V7T  CE  HE2  single  0.970  0.020  1.090
 V7T  CE  HE3  single  0.970  0.020  1.090
 V7T  NZ  HZ1  single  0.890  0.020  1.040
 V7T  NZ  HZ2  single  0.890  0.020  1.040
 V7T  CG  HG2  single  0.970  0.020  1.090
 V7T  CG  HG3  single  0.970  0.020  1.090
 V7T  CB  HB2  single  0.970  0.020  1.090
 V7T  CB  HB3  single  0.970  0.020  1.090
 V7T  N   H    single  0.860  0.020  0.860
 V7T  C   OXT  deloc   1.247  0.020  1.247

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
 V7T  H1   N1  C2   110.65  3.000
 V7T  H3   N2  H2   112.54  3.000
 V7T  H3   N2  C2   113.39  3.000
 V7T  H2   N2  C2   117.49  3.000
 V7T  HA   CA  C    109.00  3.000
 V7T  HA   CA  N    110.00  3.000
 V7T  C    CA  N    111.00  2.800
 V7T  HA   CA  CB   109.00  3.000
 V7T  C    CA  CB   110.10  1.900
 V7T  N    CA  CB   110.50  1.700
 V7T  HD3  CD  HD2  105.77  3.000
 V7T  HD3  CD  CG   109.25  3.000
 V7T  HD2  CD  CG   109.86  3.000
 V7T  HD3  CD  CE   108.17  3.000
 V7T  HD2  CD  CE   109.31  3.000
 V7T  CG   CD  CE   114.12  3.000
 V7T  HE3  CE  HE2  106.21  3.000
 V7T  HE3  CE  NZ   113.13  3.000
 V7T  HE2  CE  NZ   108.09  3.000
 V7T  HE3  CE  CD   108.57  3.000
 V7T  HE2  CE  CD   108.94  3.000
 V7T  NZ   CE  CD   111.69  3.000
 V7T  HZ2  NZ  HZ1  105.65  3.000
 V7T  HZ2  NZ  CE   108.99  3.000
 V7T  HZ1  NZ  CE   109.47  3.000
 V7T  HB3  CB  HB2  106.30  3.000
 V7T  HB3  CB  CG   108.86  3.000
 V7T  HB2  CB  CG   109.55  3.000
 V7T  HB3  CB  CA   108.33  3.000
 V7T  HB2  CB  CA   108.67  3.000
 V7T  CG   CB  CA   114.78  3.000
 V7T  N    C2  N2   115.25  3.000
 V7T  N    C2  N1   125.61  3.000
 V7T  N2   C2  N1   119.13  3.000
 V7T  H    N   C2   112.93  3.000
 V7T  H    N   CA   114.00  3.000
 V7T  C2   N   CA   123.04  3.000
 V7T  OXT  C   O    127.54  3.000
 V7T  OXT  C   CA   116.19  3.000
 V7T  O    C   CA   120.80  1.700
 V7T  HG3  CG  HG2  106.20  3.000
 V7T  HG3  CG  CB   109.60  3.000
 V7T  HG2  CG  CB   110.37  3.000
 V7T  HG3  CG  CD   109.79  3.000
 V7T  HG2  CG  CD   108.76  3.000
 V7T  CB   CG  CD   111.96  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
 V7T  CONST_04  H3   N2  C2  N1     0.00   0.0  0
 V7T  CONST_05  H    N   C2  N1     0.00   0.0  0
 V7T  CONST_06  H1   N1  C2  N2   180.00   0.0  0
 V7T  CONST_07  H    N   C2  N2   180.00   0.0  0
 V7T  CONST_08  H1   N1  C2  N      0.00   0.0  0
 V7T  Var_01    CD   CG  CB  CA  -177.11  30.0  1
 V7T  Var_02    CB   CG  CD  CE  -178.29  30.0  3
 V7T  Var_03    CG   CD  CE  NZ   -63.55  30.0  1
 V7T  Var_04    HG2  CG  CB  CA    61.59  30.0  1
 V7T  Var_05    HG3  CG  CB  CA   -55.03  30.0  1
 V7T  Var_06    HZ1  NZ  CE  CD   178.33  30.0  3
 V7T  Var_07    HZ2  NZ  CE  CD   -66.57  30.0  3
 V7T  Var_08    HB2  CB  CG  CD    60.33  30.0  3
 V7T  Var_09    HB3  CB  CG  CD   -55.52  30.0  3
 V7T  Var_10    HG2  CG  CD  CE   -56.06  30.0  3
 V7T  Var_11    HG3  CG  CD  CE    59.74  30.0  3
 V7T  Var_12    HD2  CD  CE  NZ    59.91  30.0  1
 V7T  Var_13    HD3  CD  CE  NZ   174.63  30.0  1
 V7T  Var_14    HE2  CE  CD  CG    55.77  30.0  3
 V7T  Var_15    HE3  CE  CD  CG   171.02  30.0  3
 V7T  Var_16    HD2  CD  CG  CB    58.54  30.0  1
 V7T  Var_17    HD3  CD  CG  CB   -57.07  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
 V7T  chir_01  CA  CB  N  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
 V7T  plan-1  N1   0.020
 V7T  plan-1  N2   0.020
 V7T  plan-1  CA   0.020
 V7T  plan-1  C2   0.020
 V7T  plan-1  N    0.020
 V7T  plan-1  H1   0.020
 V7T  plan-1  H2   0.020
 V7T  plan-1  H3   0.020
 V7T  plan-1  H    0.020
 V7T  plan-2  CA   0.020
 V7T  plan-2  C    0.020
 V7T  plan-2  O    0.020
 V7T  plan-2  OXT  0.020

