# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 10:47:58 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: [(2S,4S)-2-[(1S)-1-aminoethyl]-4-(aminomethyl)-5-oxoimidazolidin-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H]1N[C@@H](CN)C(=O)N1CC(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
 175  175  '[(2S,4S)-2-[(1S)-1-aminoethyl]-4-(aminomethyl)-5-oxoimidazolidin-1-yl]acetic acid'  L-peptide  30  15  .  2022-08-09  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_175
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
 175  N     N  NH2    0  -0.803  -0.8030   3.3898   0.3029
 175  C0    C  CH1    0  -0.137  -1.0912   1.9996  -0.0123
 175  C2    C  CH1    0   0.140   0.1407   1.1490   0.2939
 175  CB    C  CH3    0  -0.657  -1.4787   1.8654  -1.4775
 175  N2    N  NH1    0  -0.626   1.3099   1.6210  -0.4207
 175  C3    C  CH1    0  -0.232   2.4556   1.3550   0.4375
 175  C5    C  C      0   0.542   1.8687   1.2218   1.8326
 175  O6    O  O      0  -0.505   2.4904   1.1493   2.8830
 175  C4    C  CH2    0  -0.319   3.5367   2.4319   0.3168
 175  N0    N  NT     0  -0.464   0.5309   1.2025   1.7020
 175  CA    C  CH2    0  -0.475  -0.3078   0.6872   2.7490
 175  N5    N  NH2    0  -0.792   4.7925   2.1536   0.9819
 175  C     C  C      0   0.413  -0.2665  -0.8545   2.8818
 175  O     O  O      0  -0.589   0.5335  -1.4715   2.1595
 175  OXT   O  OC    -1  -0.619  -1.0529  -1.3222   3.7274
 175  H     H  HNH2   0   0.351  -0.6797   3.5007   1.3017
 175  H2    H  HNH2   0   0.354  -1.5924   3.9691   0.0474
 175  HC0   H  HCH1   0   0.225  -1.9223   1.5925   0.5821
 175  HC2   H  HCH1   0   0.229  -0.0799   0.1075   0.0276
 175  HB1   H  HCH3   0   0.226  -0.6900   2.2309  -2.1353
 175  HB2   H  HCH3   0   0.230  -1.6784   0.8238  -1.7299
 175  HB3   H  HCH3   0   0.234  -2.3843   2.4360  -1.6890
 175  HN2A  H  HNH1   0   0.348   1.2005   2.6292  -0.5089
 175  H3    H  HCH1   0   0.256   2.8986   0.3831   0.1791
 175  H41   H  HCH2   0   0.223   3.1379   3.3780   0.6966
 175  H42   H  HCH2   0   0.240   3.7339   2.5895  -0.7467
 175  HA1   H  HCH2   0   0.255  -1.3371   1.0122   2.5856
 175  HA2   H  HCH2   0   0.261   0.0006   1.1310   3.6980
 175  HN51  H  HNH2   0   0.342   5.2019   1.3116   0.5959
 175  HN52  H  HNH2   0   0.345   4.6226   1.9587   1.9601

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
 175  N   C0    single  1.454  0.020  1.454
 175  N   H     single  0.860  0.020  1.020
 175  N   H2    single  0.890  0.020  1.040
 175  C0  C2    single  1.528  0.020  1.528
 175  C0  CB    single  1.521  0.020  1.521
 175  C0  HC0   single  0.970  0.020  1.090
 175  C2  N2    single  1.449  0.020  1.449
 175  C2  N0    single  1.462  0.020  1.462
 175  C2  HC2   single  0.970  0.020  1.090
 175  CB  HB1   single  0.970  0.020  1.090
 175  CB  HB2   single  0.970  0.020  1.090
 175  CB  HB3   single  0.970  0.020  1.090
 175  N2  C3    single  1.456  0.020  1.456
 175  N2  HN2A  single  0.890  0.020  1.040
 175  C3  C5    single  1.519  0.020  1.519
 175  C3  C4    single  1.531  0.020  1.531
 175  C3  H3    single  0.970  0.020  1.090
 175  C5  O6    double  1.223  0.020  1.223
 175  C5  N0    single  1.344  0.020  1.344
 175  C4  N5    single  1.448  0.020  1.448
 175  C4  H41   single  0.970  0.020  1.090
 175  C4  H42   single  0.970  0.020  1.090
 175  N0  CA    single  1.437  0.020  1.437
 175  CA  C     single  1.548  0.020  1.548
 175  CA  HA1   single  0.970  0.020  1.090
 175  CA  HA2   single  0.970  0.020  1.090
 175  N5  HN51  single  0.890  0.020  1.040
 175  N5  HN52  single  0.890  0.020  1.040
 175  C   O     deloc   1.242  0.020  1.242
 175  C   OXT   deloc   1.246  0.020  1.246

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
 175  H2    N   H     106.35  3.000
 175  H2    N   C0    109.75  3.000
 175  H     N   C0    110.04  3.000
 175  HC0   C0  CB    107.18  3.000
 175  HC0   C0  C2    107.15  3.000
 175  CB    C0  C2    110.44  3.000
 175  HC0   C0  N     112.73  3.000
 175  CB    C0  N     110.09  3.000
 175  C2    C0  N     109.20  3.000
 175  HC2   C2  N0    108.79  3.000
 175  HC2   C2  N2    110.59  3.000
 175  N0    C2  N2    104.34  3.000
 175  HC2   C2  C0    108.51  3.000
 175  N0    C2  C0    112.82  3.000
 175  N2    C2  C0    111.73  3.000
 175  HB3   CB  HB2   107.62  3.000
 175  HB3   CB  HB1   107.95  3.000
 175  HB2   CB  HB1   108.25  3.000
 175  HB3   CB  C0    110.61  3.000
 175  HB2   CB  C0    110.72  3.000
 175  HB1   CB  C0    111.55  3.000
 175  HN2A  N2  C3    108.46  3.000
 175  HN2A  N2  C2    106.17  3.000
 175  C3    N2  C2    106.54  3.000
 175  H3    C3  C4    108.60  3.000
 175  H3    C3  C5    107.11  3.000
 175  C4    C3  C5    114.01  3.000
 175  H3    C3  N2    109.89  3.000
 175  C4    C3  N2    112.38  3.000
 175  C5    C3  N2    104.67  3.000
 175  N0    C5  O6    126.06  3.000
 175  N0    C5  C3    107.25  3.000
 175  O6    C5  C3    126.69  3.000
 175  H42   C4  H41   106.18  3.000
 175  H42   C4  N5    108.55  3.000
 175  H41   C4  N5    108.82  3.000
 175  H42   C4  C3    107.79  3.000
 175  H41   C4  C3    108.87  3.000
 175  N5    C4  C3    116.17  3.000
 175  CA    N0  C5    121.01  3.000
 175  CA    N0  C2    122.19  3.000
 175  C5    N0  C2    111.08  3.000
 175  HA2   CA  HA1   105.98  3.000
 175  HA2   CA  C     108.83  3.000
 175  HA1   CA  C     109.54  3.000
 175  HA2   CA  N0    108.82  3.000
 175  HA1   CA  N0    109.54  3.000
 175  C     CA  N0    113.83  3.000
 175  HN52  N5  HN51  106.03  3.000
 175  HN52  N5  C4    109.60  3.000
 175  HN51  N5  C4    109.59  3.000
 175  OXT   C   O     127.94  3.000
 175  OXT   C   CA    114.54  3.000
 175  O     C   CA    117.52  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
 175  CONST_01  C3    C5  N0  C2    0.00   0.0  0
 175  CONST_02  O6    C5  N0  C2  180.00   0.0  0
 175  Var_01    C     CA  N0  C2   77.92  30.0  3
 175  Var_02    O     C   CA  N0    4.92  30.0  3
 175  Var_03    HN51  N5  C4  C3   60.43  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
 175  chir_01  C0  N   C2  CB  positiv
 175  chir_02  C2  N2  N0  C0  negativ
 175  chir_03  C3  N2  C5  C4  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
 175  plan-1  C2   0.020
 175  plan-1  C3   0.020
 175  plan-1  C5   0.020
 175  plan-1  O6   0.020
 175  plan-1  N0   0.020
 175  plan-1  CA   0.020
 175  plan-2  CA   0.020
 175  plan-2  C    0.020
 175  plan-2  O    0.020
 175  plan-2  OXT  0.020

