# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:18:21 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  31  15  .  2022-08-09  2022-11-17
;
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  -0.801  -0.8209   3.3786   0.2914
 175  C0    C  CH1   0  -0.142  -1.1095   1.9968  -0.0553
 175  C2    C  CH1   0   0.141   0.1187   1.1372   0.2415
 175  CB    C  CH3   0  -0.658  -1.4800   1.8925  -1.5276
 175  N2    N  NH1   0  -0.622   1.3004   1.6409  -0.4241
 175  C3    C  CH1   0  -0.235   2.4338   1.3513   0.4428
 175  C5    C  C     0   0.551   1.8275   1.1722   1.8233
 175  O6    O  O     0  -0.484   2.4161   1.0644   2.8855
 175  C4    C  CH2   0  -0.319   3.5133   2.4355   0.3740
 175  N0    N  NT    0  -0.486   0.4872   1.1406   1.6616
 175  CA    C  CH2   0  -0.459  -0.3720   0.6802   2.7057
 175  N5    N  NH2   0  -0.790   4.7579   2.1411   1.0505
 175  C     C  C     0   0.546  -0.3087  -0.8251   2.8731
 175  O     O  O     0  -0.428   0.4010  -1.5525   2.2301
 175  OXT   O  OH1   0  -0.589  -1.1360  -1.2315   3.8234
 175  H     H  HNH2  0   0.354  -0.7471   3.4841   1.2956
 175  H2    H  HNH2  0   0.358  -1.5871   3.9718  -0.0002
 175  HC0   H  HCH1  0   0.231  -1.9484   1.5785   0.5200
 175  HC2   H  HCH1  0   0.242  -0.0936   0.1066  -0.0703
 175  HB1   H  HCH3  0   0.230  -0.6833   2.2706  -2.1685
 175  HB2   H  HCH3  0   0.233  -1.6785   0.8569  -1.8042
 175  HB3   H  HCH3  0   0.238  -2.3826   2.4686  -1.7359
 175  HN2A  H  HNH1  0   0.353   1.1839   2.6509  -0.4799
 175  H3    H  HCH1  0   0.267   2.8851   0.3899   0.1616
 175  H41   H  HCH2  0   0.226   3.1053   3.3685   0.7748
 175  H42   H  HCH2  0   0.245   3.7253   2.6234  -0.6816
 175  HA1   H  HCH2  0   0.310  -1.4045   0.9759   2.5113
 175  HA2   H  HCH2  0   0.314  -0.0943   1.1503   3.6518
 175  HN51  H  HNH2  0   0.343   5.1721   1.3043   0.6587
 175  HN52  H  HNH2  0   0.348   4.5804   1.9377   2.0253
 175  HXT   H  HOH1  0   0.486  -1.0817  -2.1932   3.9302

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  1.522  0.020  1.522
 175  C0   HC0   single  0.970  0.020  1.090
 175  C2   N2    single  1.447  0.020  1.447
 175  C2   N0    single  1.467  0.020  1.467
 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  1.518  0.020  1.518
 175  C3   C4    single  1.532  0.020  1.532
 175  C3   H3    single  0.970  0.020  1.090
 175  C5   O6    double  1.219  0.020  1.219
 175  C5   N0    single  1.350  0.020  1.350
 175  C4   N5    single  1.447  0.020  1.447
 175  C4   H41   single  0.970  0.020  1.090
 175  C4   H42   single  0.970  0.020  1.090
 175  N0   CA    single  1.428  0.020  1.428
 175  CA   C     single  1.516  0.020  1.516
 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     double  1.203  0.020  1.203
 175  C    OXT   single  1.324  0.020  1.324
 175  OXT  HXT   single  0.850  0.020  0.980

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     106.25  3.000
 175  H2    N    C0    109.77  3.000
 175  H     N    C0    110.49  3.000
 175  HC0   C0   CB    107.11  3.000
 175  HC0   C0   C2    107.30  3.000
 175  CB    C0   C2    110.18  3.000
 175  HC0   C0   N     112.85  3.000
 175  CB    C0   N     110.14  3.000
 175  C2    C0   N     109.20  3.000
 175  HC2   C2   N0    109.01  3.000
 175  HC2   C2   N2    110.75  3.000
 175  N0    C2   N2    103.85  3.000
 175  HC2   C2   C0    108.51  3.000
 175  N0    C2   C0    112.87  3.000
 175  N2    C2   C0    111.79  3.000
 175  HB3   CB   HB2   107.61  3.000
 175  HB3   CB   HB1   108.01  3.000
 175  HB2   CB   HB1   108.27  3.000
 175  HB3   CB   C0    110.49  3.000
 175  HB2   CB   C0    110.79  3.000
 175  HB1   CB   C0    111.53  3.000
 175  HN2A  N2   C3    108.60  3.000
 175  HN2A  N2   C2    106.08  3.000
 175  C3    N2   C2    107.02  3.000
 175  H3    C3   C4    108.57  3.000
 175  H3    C3   C5    107.07  3.000
 175  C4    C3   C5    113.94  3.000
 175  H3    C3   N2    109.97  3.000
 175  C4    C3   N2    112.41  3.000
 175  C5    C3   N2    104.71  3.000
 175  N0    C5   O6    125.56  3.000
 175  N0    C5   C3    106.87  3.000
 175  O6    C5   C3    127.57  3.000
 175  H42   C4   H41   106.23  3.000
 175  H42   C4   N5    108.65  3.000
 175  H41   C4   N5    108.85  3.000
 175  H42   C4   C3    107.56  3.000
 175  H41   C4   C3    108.92  3.000
 175  N5    C4   C3    116.19  3.000
 175  CA    N0   C5    121.13  3.000
 175  CA    N0   C2    123.76  3.000
 175  C5    N0   C2    111.42  3.000
 175  HA2   CA   HA1   106.15  3.000
 175  HA2   CA   C     108.73  3.000
 175  HA1   CA   C     109.16  3.000
 175  HA2   CA   N0    109.97  3.000
 175  HA1   CA   N0    110.58  3.000
 175  C     CA   N0    112.06  3.000
 175  HN52  N5   HN51  106.17  3.000
 175  HN52  N5   C4    109.91  3.000
 175  HN51  N5   C4    109.83  3.000
 175  OXT   C    O     124.53  3.000
 175  OXT   C    CA    110.98  3.000
 175  O     C    CA    124.49  3.000
 175  HXT   OXT  C     110.41  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  CONST_03  CA    N0   C5  C3  180.00   0.0  0
 175  CONST_04  CA    N0   C5  O6    0.00   0.0  0
 175  CONST_05  HXT   OXT  C   CA  180.00   0.0  0
 175  Var_01    C     CA   N0  C2   83.01  30.0  3
 175  Var_02    O     C    CA  N0    1.66  30.0  3
 175  Var_03    HN51  N5   C4  C3   59.45  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
 175  plan-2  HXT  0.020

