# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:16:33 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: N-[(1Z)-amino{[(4S)-4-amino-4-carboxybutyl]amino}methylidene]prop-2-en-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH+]CC=C)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
 ARV  ARV  N-[(1Z)-amino{[(4S)-4-amino-4-carboxybutyl]amino}methylidene]prop-2-en-1-aminium  L-peptide  33  15  .  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_ARV
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
 ARV  N     N  NH2    0  -0.798   8.5187  -1.3158  26.0414
 ARV  CA    C  CH1    0  -0.200   8.8967  -1.6363  24.6739
 ARV  C     C  C      0   0.401   8.9570  -3.1685  24.4685
 ARV  O     O  O      0  -0.613   8.8138  -3.5724  23.2970
 ARV  CB    C  CH2    0  -0.423  10.2429  -1.0477  24.2141
 ARV  CG    C  CH2    0  -0.468  10.3170   0.4698  24.3191
 ARV  CD    C  CH2    0  -0.301  11.5629   1.0661  23.6816
 ARV  NE    N  NH1    0  -0.611  12.7708   0.5768  24.3361
 ARV  CZ    C  C      0   0.798  13.8324   0.0487  23.7358
 ARV  NH1   N  NH2    0  -0.810  14.5547  -0.8585  24.3847
 ARV  NH2   N  NC1    1  -0.617  14.1996   0.4092  22.5066
 ARV  OXT   O  OC    -1  -0.603   9.1948  -3.8624  25.4775
 ARV  C1    C  CH2    0  -0.374  14.0222   1.7271  21.9011
 ARV  C2    C  C1     0  -0.170  13.2199   1.6774  20.6373
 ARV  C3    C  C2     0  -0.513  12.1930   2.4762  20.3787
 ARV  H     H  HNH2   0   0.334   8.6232  -0.3246  26.2182
 ARV  H2    H  HNH2   0   0.324   9.1481  -1.7957  26.6725
 ARV  HA    H  HCH1   0   0.198   8.1237  -1.2317  24.0098
 ARV  HB2   H  HCH2   0   0.214  10.4116  -1.3416  23.1736
 ARV  HB3   H  HCH2   0   0.213  11.0480  -1.5029  24.8017
 ARV  HG2   H  HCH2   0   0.229  10.2646   0.7911  25.3642
 ARV  HG3   H  HCH2   0   0.244   9.4558   0.9208  23.8176
 ARV  HD2   H  HCH2   0   0.261  11.5233   2.1562  23.7359
 ARV  HD3   H  HCH2   0   0.261  11.6012   0.7916  22.6284
 ARV  HE    H  HNH1   0   0.420  12.7019   0.4150  25.3308
 ARV  HH11  H  HNH2   0   0.430  14.1718  -1.3622  25.1682
 ARV  HH12  H  HNH2   0   0.429  15.4714  -1.1259  24.0655
 ARV  HH2   H  HNC1   0   0.423  14.8963  -0.1735  22.0661
 ARV  HC11  H  HCH2   0   0.292  15.0224   2.1098  21.6822
 ARV  HC12  H  HCH2   0   0.281  13.5805   2.4117  22.6229
 ARV  HC2   H  H      0   0.259  13.5455   0.9568  19.8932
 ARV  HC31  H  H      0   0.244  11.8444   3.2073  21.0990
 ARV  HC32  H  H      0   0.248  11.6646   2.4309  19.4359

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
 ARV  N    CA    single  1.458  0.019  1.458
 ARV  N    H     single  0.860  0.020  0.860
 ARV  N    H2    single  0.890  0.020  1.040
 ARV  CA   C     single  1.525  0.021  1.525
 ARV  CA   CB    single  1.521  0.033  1.521
 ARV  CA   HA    single  0.970  0.020  0.970
 ARV  C    O     deloc   1.231  0.020  1.231
 ARV  C    OXT   deloc   1.247  0.020  1.247
 ARV  CB   CG    single  1.523  0.020  1.523
 ARV  CB   HB2   single  0.970  0.020  1.090
 ARV  CB   HB3   single  0.970  0.020  1.090
 ARV  CG   CD    single  1.521  0.020  1.521
 ARV  CG   HG2   single  0.970  0.020  1.090
 ARV  CG   HG3   single  0.970  0.020  1.090
 ARV  CD   NE    single  1.458  0.020  1.458
 ARV  CD   HD2   single  0.970  0.020  1.090
 ARV  CD   HD3   single  0.970  0.020  1.090
 ARV  NE   CZ    single  1.329  0.020  1.329
 ARV  NE   HE    single  0.860  0.020  1.020
 ARV  CZ   NH1   single  1.329  0.020  1.329
 ARV  CZ   NH2   double  1.333  0.020  1.333
 ARV  NH1  HH11  single  0.860  0.020  1.020
 ARV  NH1  HH12  single  0.860  0.020  1.020
 ARV  NH2  C1    single  1.461  0.020  1.461
 ARV  NH2  HH2   single  0.890  0.020  1.040
 ARV  C1   C2    single  1.498  0.020  1.498
 ARV  C1   HC11  single  0.970  0.020  1.090
 ARV  C1   HC12  single  0.970  0.020  1.090
 ARV  C2   C3    double  1.326  0.020  1.326
 ARV  C2   HC2   single  0.930  0.020  1.080
 ARV  C3   HC31  single  0.930  0.020  1.080
 ARV  C3   HC32  single  0.930  0.020  1.080

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
 ARV  H2    N    H     106.93  3.000
 ARV  H2    N    CA    108.66  3.000
 ARV  H     N    CA    114.00  3.000
 ARV  HA    CA   CB    109.00  3.000
 ARV  HA    CA   C     110.00  3.000
 ARV  CB    CA   C     110.50  1.500
 ARV  HA    CA   N     110.00  3.000
 ARV  CB    CA   N     110.40  1.500
 ARV  C     CA   N     111.00  2.800
 ARV  OXT   C    O     126.97  3.000
 ARV  OXT   C    CA    120.80  1.700
 ARV  O     C    CA    120.80  1.700
 ARV  HB3   CB   HB2   106.56  3.000
 ARV  HB3   CB   CG    109.95  3.000
 ARV  HB2   CB   CG    109.00  3.000
 ARV  HB3   CB   CA    108.88  3.000
 ARV  HB2   CB   CA    108.43  3.000
 ARV  CG    CB   CA    113.77  3.000
 ARV  HG3   CG   HG2   106.20  3.000
 ARV  HG3   CG   CD    106.93  3.000
 ARV  HG2   CG   CD    108.92  3.000
 ARV  HG3   CG   CB    109.93  3.000
 ARV  HG2   CG   CB    110.85  3.000
 ARV  CD    CG   CB    113.68  3.000
 ARV  HD3   CD   HD2   107.51  3.000
 ARV  HD3   CD   NE    108.68  3.000
 ARV  HD2   CD   NE    110.03  3.000
 ARV  HD3   CD   CG    109.59  3.000
 ARV  HD2   CD   CG    109.92  3.000
 ARV  NE    CD   CG    111.02  3.000
 ARV  HE    NE   CZ    115.83  3.000
 ARV  HE    NE   CD    116.05  3.000
 ARV  CZ    NE   CD    126.31  3.000
 ARV  NH2   CZ   NH1   119.04  3.000
 ARV  NH2   CZ   NE    121.96  3.000
 ARV  NH1   CZ   NE    119.00  3.000
 ARV  HH12  NH1  HH11  117.39  3.000
 ARV  HH12  NH1  CZ    121.43  3.000
 ARV  HH11  NH1  CZ    120.97  3.000
 ARV  HH2   NH2  C1    115.07  3.000
 ARV  HH2   NH2  CZ    115.88  3.000
 ARV  C1    NH2  CZ    126.36  3.000
 ARV  HC12  C1   HC11  106.49  3.000
 ARV  HC12  C1   C2    111.29  3.000
 ARV  HC11  C1   C2    109.44  3.000
 ARV  HC12  C1   NH2   109.98  3.000
 ARV  HC11  C1   NH2   106.72  3.000
 ARV  C2    C1   NH2   112.63  3.000
 ARV  HC2   C2   C3    119.89  3.000
 ARV  HC2   C2   C1    116.08  3.000
 ARV  C3    C2   C1    124.00  3.000
 ARV  HC32  C3   HC31  116.77  3.000
 ARV  HC32  C3   C2    121.52  3.000
 ARV  HC31  C3   C2    121.71  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
 ARV  CONST_06  HH12  NH1  CZ   NE    180.00   0.0  0
 ARV  CONST_07  HH2   NH2  CZ   NE    180.00   0.0  0
 ARV  CONST_08  HE    NE   CZ   NH1     0.00   0.0  0
 ARV  Var_01    CD    CG   CB   CA   -171.67  30.0  3
 ARV  Var_02    NE    CD   CG   CB    -61.56  30.0  3
 ARV  Var_03    CZ    NE   CD   CG    129.18  30.0  3
 ARV  Var_04    C2    C1   NH2  CZ   -121.98  30.0  3
 ARV  Var_05    C3    C2   C1   NH2   131.08  30.0  3
 ARV  Var_06    HC31  C3   C2   C1     -2.18   0.0  2

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
 ARV  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
 ARV  plan-1  CD    0.020
 ARV  plan-1  NE    0.020
 ARV  plan-1  CZ    0.020
 ARV  plan-1  NH1   0.020
 ARV  plan-1  NH2   0.020
 ARV  plan-1  C1    0.020
 ARV  plan-1  HE    0.020
 ARV  plan-1  HH11  0.020
 ARV  plan-1  HH12  0.020
 ARV  plan-1  HH2   0.020
 ARV  plan-2  CA    0.020
 ARV  plan-2  C     0.020
 ARV  plan-2  O     0.020
 ARV  plan-2  OXT   0.020
 ARV  plan-3  C1    0.020
 ARV  plan-3  C2    0.020
 ARV  plan-3  C3    0.020
 ARV  plan-3  HC2   0.020
 ARV  plan-3  HC31  0.020
 ARV  plan-3  HC32  0.020

