# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:55:02 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: {(2S)-2-[(1S)-1-aminoethyl]-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H]1N=CC(=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
 CLV  CLV  '{(2S)-2-[(1S)-1-aminoethyl]-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  24  13  .  2022-09-22  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_CLV
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
 CLV  N1    N  NH2   0  -0.798   2.3786   0.5670   1.4176
 CLV  CA1   C  CH1   0  -0.103   1.8044   1.2956   0.3020
 CLV  CB1   C  CH3   0  -0.664   2.9014   1.8993  -0.5600
 CLV  C1    C  CR15  0   0.082   0.9239   0.3531  -0.5281
 CLV  N2    N  N     0  -0.312   1.6826  -0.7430  -1.0731
 CLV  N3    N  NR5   0  -0.485  -0.1194  -0.2702   0.2621
 CLV  C2    C  CR5   0   0.474  -0.0383  -1.6146   0.1796
 CLV  O2    O  O     0  -0.464  -0.7780  -2.4408   0.6764
 CLV  CA2   C  CR15  0  -0.144   1.1698  -1.8268  -0.6714
 CLV  CA3   C  CH2   0  -0.455  -1.2307   0.4215   0.8297
 CLV  C3    C  C     0   0.551  -2.3604   0.5807  -0.1685
 CLV  O3    O  O     0  -0.428  -2.3371   0.1517  -1.2911
 CLV  OXT   O  OH1   0  -0.587  -3.3696   1.2500   0.3633
 CLV  HN11  H  HNH2  0   0.355   3.0435   1.1636   1.8939
 CLV  HN12  H  HNH2  0   0.349   1.6648   0.3545   2.1033
 CLV  HA1   H  HCH1  0   0.226   1.1509   2.1221   0.6213
 CLV  HB11  H  HCH3  0   0.233   3.5850   1.1335  -0.9241
 CLV  HB12  H  HCH3  0   0.233   2.4806   2.4240  -1.4184
 CLV  HB13  H  HCH3  0   0.239   3.4745   2.6254   0.0177
 CLV  H1    H  HCR5  0   0.286   0.4914   0.9205  -1.3606
 CLV  HA2   H  HCR5  0   0.291   1.5546  -2.8052  -0.9345
 CLV  HA31  H  HCH2  0   0.318  -1.5977  -0.1235   1.7025
 CLV  HA32  H  HCH2  0   0.313  -0.9248   1.4064   1.1899
 CLV  HXT   H  HOH1  0   0.488  -4.0876   1.3495  -0.2803

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
 CLV  N1   CA1   single  1.451  0.020  1.451
 CLV  N1   HN11  single  0.890  0.020  1.040
 CLV  N1   HN12  single  0.890  0.020  1.040
 CLV  CA1  CB1   single  1.520  0.020  1.520
 CLV  CA1  C1    single  1.534  0.020  1.534
 CLV  CA1  HA1   single  0.970  0.020  1.090
 CLV  CB1  HB11  single  0.970  0.020  1.090
 CLV  CB1  HB12  single  0.970  0.020  1.090
 CLV  CB1  HB13  single  0.970  0.020  1.090
 CLV  C1   N2    single  1.440  0.020  1.440
 CLV  C1   N3    single  1.450  0.020  1.450
 CLV  C1   H1    single  0.970  0.020  1.090
 CLV  N2   CA2   double  1.265  0.020  1.265
 CLV  N3   CA3   single  1.427  0.020  1.427
 CLV  N3   C2    single  1.349  0.020  1.349
 CLV  C2   CA2   single  1.493  0.020  1.493
 CLV  C2   O2    double  1.215  0.020  1.215
 CLV  CA2  HA2   single  0.930  0.020  1.080
 CLV  CA3  C3    single  1.516  0.020  1.516
 CLV  CA3  HA31  single  0.970  0.020  1.090
 CLV  CA3  HA32  single  0.970  0.020  1.090
 CLV  C3   OXT   single  1.323  0.020  1.323
 CLV  C3   O3    double  1.202  0.020  1.202
 CLV  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
 CLV  HN12  N1   HN11  105.55  3.000
 CLV  HN12  N1   CA1   110.32  3.000
 CLV  HN11  N1   CA1   109.01  3.000
 CLV  HA1   CA1  C1    106.11  3.000
 CLV  HA1   CA1  CB1   107.14  3.000
 CLV  C1    CA1  CB1   110.57  3.000
 CLV  HA1   CA1  N1    112.89  3.000
 CLV  C1    CA1  N1    109.56  3.000
 CLV  CB1   CA1  N1    110.48  3.000
 CLV  HB13  CB1  HB12  107.42  3.000
 CLV  HB13  CB1  HB11  108.38  3.000
 CLV  HB12  CB1  HB11  108.50  3.000
 CLV  HB13  CB1  CA1   110.07  3.000
 CLV  HB12  CB1  CA1   111.04  3.000
 CLV  HB11  CB1  CA1   111.30  3.000
 CLV  H1    C1   N3    110.64  3.000
 CLV  H1    C1   N2    108.32  3.000
 CLV  N3    C1   N2    104.96  3.000
 CLV  H1    C1   CA1   108.63  3.000
 CLV  N3    C1   CA1   112.48  3.000
 CLV  N2    C1   CA1   111.72  3.000
 CLV  CA2   N2   C1    108.57  3.000
 CLV  CA3   N3   C2    123.65  3.000
 CLV  C2    N3   C1    110.60  3.000
 CLV  CA3   N3   C1    124.68  3.000
 CLV  CA2   C2   O2    128.98  3.000
 CLV  O2    C2   N3    128.02  3.000
 CLV  CA2   C2   N3    103.00  3.000
 CLV  HA2   CA2  C2    123.65  3.000
 CLV  HA2   CA2  N2    123.55  3.000
 CLV  C2    CA2  N2    112.80  3.000
 CLV  HA32  CA3  HA31  106.28  3.000
 CLV  HA32  CA3  C3    109.34  3.000
 CLV  HA31  CA3  C3    109.16  3.000
 CLV  HA32  CA3  N3    110.50  3.000
 CLV  HA31  CA3  N3    109.73  3.000
 CLV  C3    CA3  N3    111.68  3.000
 CLV  OXT   C3   O3    124.82  3.000
 CLV  O3    C3   CA3   124.27  3.000
 CLV  OXT   C3   CA3   110.92  3.000
 CLV  HXT   OXT  C3    110.50  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
 CLV  CONST_01  CA2  C2   N3   C1      0.00   0.0  0
 CLV  CONST_02  O2   C2   N3   C1    180.00   0.0  0
 CLV  CONST_03  CA3  N3   C2   CA2   180.00   0.0  0
 CLV  CONST_04  CA3  N3   C2   O2      0.00   0.0  0
 CLV  CONST_05  HXT  OXT  C3   CA3   180.00   0.0  0
 CLV  Var_01    C2   CA2  N2   C1      1.50  30.0  1
 CLV  Var_02    N3   C2   CA2  N2     -2.54  30.0  1
 CLV  Var_03    C3   CA3  N3   C1     84.15  30.0  3
 CLV  Var_04    OXT  C3   CA3  N3   -178.56  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
 CLV  chir_01  CA1  N1  CB1  C1   negativ
 CLV  chir_02  C1   N2  N3   CA1  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
 CLV  plan-1  C1   0.020
 CLV  plan-1  N3   0.020
 CLV  plan-1  C2   0.020
 CLV  plan-1  O2   0.020
 CLV  plan-1  CA2  0.020
 CLV  plan-1  CA3  0.020
 CLV  plan-2  CA3  0.020
 CLV  plan-2  C3   0.020
 CLV  plan-2  O3   0.020
 CLV  plan-2  OXT  0.020
 CLV  plan-2  HXT  0.020

