# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:06:55 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-2-amino-4-(2-amino-1H-imidazol-5-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCc1[nH]c(N)nc1)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
 Z70  Z70  '(2S)-2-amino-4-(2-amino-1H-imidazol-5-yl)butanoic acid'  L-peptide  24  13  .  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_Z70
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
 Z70  CA    C  CH1    0  -0.227  -23.6751  12.6435  -39.3968
 Z70  C     C  C      0   0.410  -23.0620  11.7217  -40.4832
 Z70  C3    C  CR5    0   0.312  -23.2005  16.2405  -40.7913
 Z70  C4    C  CR5    0   0.569  -23.8538  18.3291  -40.4720
 Z70  C5    C  CR15   0  -0.282  -23.2654  16.9251  -41.9644
 Z70  C6    C  CH2    0  -0.400  -24.0441  14.0318  -39.9171
 Z70  C7    C  CH2    0  -0.511  -22.8581  14.8322  -40.4593
 Z70  N     N  NH2    0  -0.808  -22.7918  12.7541  -38.2447
 Z70  N2    N  NR15   0  -0.664  -23.5808  17.1665  -39.8373
 Z70  N3    N  N      0  -0.494  -23.6766  18.2263  -41.7628
 Z70  N4    N  NH2    0  -0.848  -24.1940  19.4762  -39.7882
 Z70  OXT   O  OC    -1  -0.602  -22.1911  10.9120  -40.1051
 Z70  O     O  O      0  -0.605  -23.5317  11.8275  -41.6334
 Z70  H1    H  HCH1   0   0.205  -24.6293  12.1557  -39.1276
 Z70  H5    H  HCR5   0   0.234  -23.0440  16.5487  -42.9524
 Z70  H6    H  HCH2   0   0.212  -24.8005  13.9335  -40.6975
 Z70  H6A   H  HCH2   0   0.208  -24.5175  14.5898  -39.1019
 Z70  H7    H  HCH2   0   0.236  -22.4809  14.3554  -41.3653
 Z70  H7A   H  HCH2   0   0.228  -22.0433  14.8048  -39.7297
 Z70  H     H  HNH2   0   0.328  -23.3310  12.9699  -37.4165
 Z70  H2    H  HNH2   0   0.332  -22.3573  11.8540  -38.0923
 Z70  HN4   H  HNH2   0   0.378  -24.5865  20.1792  -40.3957
 Z70  HN4A  H  HNH2   0   0.382  -24.7930  19.3264  -38.9895
 Z70  HN2   H  HNR5   0   0.406  -23.6323  17.0053  -38.8435

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
 Z70  C   CA    single    1.525  0.021  1.525
 Z70  C6  CA    single    1.528  0.020  1.528
 Z70  CA  N     single    1.458  0.019  1.458
 Z70  CA  H1    single    0.970  0.020  1.090
 Z70  O   C     deloc     1.231  0.020  1.231
 Z70  C   OXT   deloc     1.248  0.020  1.248
 Z70  C5  C3    aromatic  1.360  0.020  1.360
 Z70  C3  C7    single    1.487  0.020  1.487
 Z70  C3  N2    aromatic  1.383  0.020  1.383
 Z70  N3  C4    aromatic  1.307  0.020  1.307
 Z70  C4  N4    single    1.378  0.020  1.378
 Z70  C4  N2    aromatic  1.352  0.020  1.352
 Z70  N3  C5    aromatic  1.379  0.020  1.379
 Z70  C5  H5    single    0.930  0.020  1.080
 Z70  C7  C6    single    1.530  0.020  1.530
 Z70  C6  H6    single    0.970  0.020  1.090
 Z70  C6  H6A   single    0.970  0.020  1.090
 Z70  C7  H7    single    0.970  0.020  1.090
 Z70  C7  H7A   single    0.970  0.020  1.090
 Z70  N   H     single    0.860  0.020  0.860
 Z70  N   H2    single    0.890  0.020  1.040
 Z70  N4  HN4   single    0.890  0.020  1.040
 Z70  N4  HN4A  single    0.890  0.020  1.040
 Z70  N2  HN2   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
 Z70  H1    CA  N    111.39  3.000
 Z70  H1    CA  C6   106.00  3.000
 Z70  N     CA  C6   110.30  3.000
 Z70  H1    CA  C    104.46  3.000
 Z70  N     CA  C    111.00  2.800
 Z70  C6    CA  C    113.39  3.000
 Z70  O     C   OXT  126.69  3.000
 Z70  OXT   C   CA   116.70  3.000
 Z70  O     C   CA   120.80  1.700
 Z70  N2    C3  C7   122.93  3.000
 Z70  N2    C3  C5   104.18  3.000
 Z70  C7    C3  C5   132.88  3.000
 Z70  N4    C4  N3   126.09  3.000
 Z70  N4    C4  N2   122.18  3.000
 Z70  N3    C4  N2   111.62  3.000
 Z70  H5    C5  N3   121.57  3.000
 Z70  H5    C5  C3   127.15  3.000
 Z70  N3    C5  C3   111.29  3.000
 Z70  H6A   C6  H6   106.17  3.000
 Z70  H6A   C6  C7   109.40  3.000
 Z70  H6    C6  C7   109.33  3.000
 Z70  H6A   C6  CA   108.29  3.000
 Z70  H6    C6  CA   109.21  3.000
 Z70  C7    C6  CA   114.13  3.000
 Z70  H7A   C7  H7   106.58  3.000
 Z70  H7A   C7  C6   109.14  3.000
 Z70  H7    C7  C6   109.49  3.000
 Z70  H7A   C7  C3   110.13  3.000
 Z70  H7    C7  C3   107.95  3.000
 Z70  C6    C7  C3   113.33  3.000
 Z70  H2    N   H    107.19  3.000
 Z70  H2    N   CA   108.20  3.000
 Z70  H     N   CA   114.00  3.000
 Z70  HN2   N2  C4   126.14  3.000
 Z70  HN2   N2  C3   125.95  3.000
 Z70  C4    N2  C3   107.90  3.000
 Z70  C5    N3  C4   105.01  3.000
 Z70  HN4A  N4  HN4  110.43  3.000
 Z70  HN4A  N4  C4   114.55  3.000
 Z70  HN4   N4  C4   112.18  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
 Z70  CONST_01  C4   N3  C5  C3     0.00   0.0  0
 Z70  CONST_02  N3   C4  N2  C3     0.00   0.0  0
 Z70  CONST_03  C5   C3  N2  C4     0.00   0.0  0
 Z70  CONST_04  N2   C4  N3  C5     0.00   0.0  0
 Z70  CONST_05  N3   C5  C3  N2     0.00   0.0  0
 Z70  CONST_06  N4   C4  N2  C3   180.00   0.0  0
 Z70  CONST_07  C7   C3  N2  C4   180.00   0.0  0
 Z70  CONST_08  N4   C4  N3  C5   180.00   0.0  0
 Z70  CONST_09  N3   C5  C3  C7   180.00   0.0  0
 Z70  CONST_10  H5   C5  N3  C4   180.00   0.0  0
 Z70  CONST_11  HN2  N2  C3  C5   180.00   0.0  0
 Z70  CONST_12  HN4  N4  C4  N2   180.00   0.0  0
 Z70  Var_01    C6   C7  C3  C5  -112.96  30.0  2
 Z70  Var_02    C3   C7  C6  CA  -172.29  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
 Z70  chir_01  CA  C  C6  N  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
 Z70  plan-1  C3    0.020
 Z70  plan-1  C4    0.020
 Z70  plan-1  C5    0.020
 Z70  plan-1  C7    0.020
 Z70  plan-1  N2    0.020
 Z70  plan-1  N3    0.020
 Z70  plan-1  N4    0.020
 Z70  plan-1  H5    0.020
 Z70  plan-1  HN2   0.020
 Z70  plan-2  C4    0.020
 Z70  plan-2  N4    0.020
 Z70  plan-2  HN4   0.020
 Z70  plan-2  HN4A  0.020
 Z70  plan-3  CA    0.020
 Z70  plan-3  C     0.020
 Z70  plan-3  OXT   0.020
 Z70  plan-3  O     0.020

