# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:28:31 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  23  13  .  2022-09-22  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_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  -0.800   2.4443   0.5097   1.4016
 CLV  CA1   C  CH1    0  -0.097   1.8241   1.2366   0.3084
 CLV  CB1   C  CH3    0  -0.664   2.8849   1.8388  -0.5980
 CLV  C1    C  CR15   0   0.080   0.9056   0.2952  -0.4794
 CLV  N2    N  N      0  -0.320   1.6376  -0.8029  -1.0604
 CLV  N3    N  NR5    0  -0.459  -0.1078  -0.3137   0.3528
 CLV  C2    C  CR5    0   0.463  -0.0658  -1.6511   0.2336
 CLV  O2    O  O      0  -0.486  -0.8075  -2.4809   0.7314
 CLV  CA2   C  CR15   0  -0.155   1.1131  -1.8799  -0.6543
 CLV  CA3   C  CH2    0  -0.470  -1.2409   0.4053   0.8627
 CLV  C3    C  C      0   0.417  -2.3636   0.6108  -0.1847
 CLV  O3    O  O      0  -0.590  -2.2041   0.0881  -1.2991
 CLV  OXT   O  OC    -1  -0.614  -3.3275   1.2878   0.2171
 CLV  HN11  H  HNH2   0   0.351   3.0918   1.1235   1.8800
 CLV  HN12  H  HNH2   0   0.347   1.7445   0.2627   2.0903
 CLV  HA1   H  HCH1   0   0.220   1.1852   2.0627   0.6569
 CLV  HB11  H  HCH3   0   0.230   3.5470   1.0716  -0.9977
 CLV  HB12  H  HCH3   0   0.230   2.4293   2.3707  -1.4341
 CLV  HB13  H  HCH3   0   0.236   3.4909   2.5578  -0.0447
 CLV  H1    H  HCR5   0   0.275   0.4360   0.8616  -1.2925
 CLV  HA2   H  HCR5   0   0.282   1.4704  -2.8629  -0.9405
 CLV  HA31  H  HCH2   0   0.266  -1.6417  -0.1373   1.7214
 CLV  HA32  H  HCH2   0   0.259  -0.9119   1.3757   1.2419

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  1.452  0.020  1.452
 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  1.533  0.020  1.533
 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  1.442  0.020  1.442
 CLV  C1   N3    single  1.446  0.020  1.446
 CLV  C1   H1    single  0.970  0.020  1.090
 CLV  N2   CA2   double  1.265  0.020  1.265
 CLV  N3   CA3   single  1.436  0.020  1.436
 CLV  N3   C2    single  1.343  0.020  1.343
 CLV  C2   CA2   single  1.493  0.020  1.493
 CLV  C2   O2    double  1.219  0.020  1.219
 CLV  CA2  HA2   single  0.930  0.020  1.080
 CLV  CA3  C3    single  1.549  0.020  1.549
 CLV  CA3  HA31  single  0.970  0.020  1.090
 CLV  CA3  HA32  single  0.970  0.020  1.090
 CLV  C3   OXT   deloc   1.245  0.020  1.245
 CLV  C3   O3    deloc   1.241  0.020  1.241

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  105.58  3.000
 CLV  HN12  N1   CA1   109.82  3.000
 CLV  HN11  N1   CA1   108.99  3.000
 CLV  HA1   CA1  C1    106.00  3.000
 CLV  HA1   CA1  CB1   107.25  3.000
 CLV  C1    CA1  CB1   110.79  3.000
 CLV  HA1   CA1  N1    112.66  3.000
 CLV  C1    CA1  N1    109.59  3.000
 CLV  CB1   CA1  N1    110.44  3.000
 CLV  HB13  CB1  HB12  107.42  3.000
 CLV  HB13  CB1  HB11  108.22  3.000
 CLV  HB12  CB1  HB11  108.43  3.000
 CLV  HB13  CB1  CA1   110.26  3.000
 CLV  HB12  CB1  CA1   111.03  3.000
 CLV  HB11  CB1  CA1   111.35  3.000
 CLV  H1    C1   N3    110.13  3.000
 CLV  H1    C1   N2    108.18  3.000
 CLV  N3    C1   N2    105.49  3.000
 CLV  H1    C1   CA1   108.69  3.000
 CLV  N3    C1   CA1   112.50  3.000
 CLV  N2    C1   CA1   111.75  3.000
 CLV  CA2   N2   C1    107.97  3.000
 CLV  CA3   N3   C2    123.70  3.000
 CLV  C2    N3   C1    110.26  3.000
 CLV  CA3   N3   C1    123.14  3.000
 CLV  CA2   C2   O2    128.22  3.000
 CLV  O2    C2   N3    128.48  3.000
 CLV  CA2   C2   N3    103.30  3.000
 CLV  HA2   CA2  C2    123.77  3.000
 CLV  HA2   CA2  N2    123.40  3.000
 CLV  C2    CA2  N2    112.81  3.000
 CLV  HA32  CA3  HA31  106.19  3.000
 CLV  HA32  CA3  C3    109.58  3.000
 CLV  HA31  CA3  C3    109.37  3.000
 CLV  HA32  CA3  N3    109.30  3.000
 CLV  HA31  CA3  N3    108.67  3.000
 CLV  C3    CA3  N3    113.47  3.000
 CLV  OXT   C3   O3    128.21  3.000
 CLV  O3    C3   CA3   117.26  3.000
 CLV  OXT   C3   CA3   114.53  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  Var_01    C2   CA2  N2   C1      1.29  30.0  1
 CLV  Var_02    N3   C2   CA2  N2     -3.50  30.0  1
 CLV  Var_03    C3   CA3  N3   C1     78.37  30.0  3
 CLV  Var_04    OXT  C3   CA3  N3   -176.69  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

