# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:23:12 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R)-2-(aminomethyl)-3-(carboxymethyl)-2,4-dihydroxy-5-oxo-2,5-dihydro-1H-imidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@]1(O)NC(=O)C(=[N+]1CC(O)=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
 CR5  CR5  (2R)-2-(aminomethyl)-3-(carboxymethyl)-2,4-dihydroxy-5-oxo-2,5-dihydro-1H-imidazol-3-ium  L-peptide  24  14  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CR5
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
 CR5  N     N  NH2   0  -0.770  -1.3852   0.8094  -1.3033
 CR5  CA1   C  CH2   0  -0.318  -0.4256   0.9408  -0.2465
 CR5  C1    C  CR5   0   0.564  -0.9305   1.6713   1.0183
 CR5  N2    N  NR15  0  -0.681  -2.0172   0.9674   1.6480
 CR5  N3    N  NR5   1  -0.448   0.1052   1.5841   2.0900
 CR5  C2    C  CR5   0   0.572  -0.3154   0.9035   3.0976
 CR5  O2    O  OH1   0  -0.493   0.3582   0.6738   4.1518
 CR5  CA2   C  CR5   0   0.513  -1.7293   0.4394   2.8404
 CR5  CA3   C  CH2   0  -0.479   1.3381   2.3346   2.0121
 CR5  C     C  C     0   0.574   1.2369   3.7161   2.6365
 CR5  O3    O  O     0  -0.416   2.0103   4.5901   2.3601
 CR5  O4    O  OH1   0  -0.596  -1.2647   2.9791   0.8175
 CR5  O5    O  O     0  -0.392  -2.3666  -0.2374   3.6035
 CR5  OXT   O  OH1   0  -0.577   0.2624   3.7960   3.5177
 CR5  HN1   H  HNH2  0   0.363  -1.7124   1.6961  -1.6598
 CR5  HN2A  H  HNH2  0   0.363  -2.1856   0.2534  -1.0372
 CR5  HA11  H  HCH2  0   0.275  -0.0836  -0.0489   0.0587
 CR5  HA12  H  HCH2  0   0.267   0.4486   1.4779  -0.6241
 CR5  HN2   H  HNR5  0   0.447  -2.9022   0.8259   1.1785
 CR5  HO2   H  HOH1  0   0.536  -0.1292   0.1220   4.7907
 CR5  HA31  H  HCH2  0   0.341   1.6406   2.4323   0.9718
 CR5  HA32  H  HCH2  0   0.362   2.1330   1.7819   2.5170
 CR5  HO4   H  HOH1  0   0.492  -0.8899   3.3152  -0.0064
 CR5  HXT   H  HOH1  0   0.501   0.2361   4.6747   3.9288

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
 CR5  N    CA1   single  1.433  0.020  1.433
 CR5  N    HN1   single  0.890  0.020  1.040
 CR5  N    HN2A  single  0.890  0.020  1.040
 CR5  CA1  C1    single  1.545  0.020  1.545
 CR5  CA1  HA11  single  0.970  0.020  1.090
 CR5  CA1  HA12  single  0.970  0.020  1.090
 CR5  C1   N2    single  1.440  0.020  1.440
 CR5  C1   N3    single  1.493  0.020  1.493
 CR5  C1   O4    single  1.365  0.020  1.365
 CR5  N2   CA2   single  1.336  0.020  1.336
 CR5  N2   HN2   single  0.860  0.020  1.020
 CR5  N3   C2    double  1.287  0.020  1.287
 CR5  N3   CA3   single  1.445  0.020  1.445
 CR5  C2   O2    single  1.272  0.020  1.272
 CR5  C2   CA2   single  1.510  0.020  1.510
 CR5  O2   HO2   single  0.850  0.020  0.980
 CR5  CA2  O5    double  1.203  0.020  1.203
 CR5  CA3  C     single  1.519  0.020  1.519
 CR5  CA3  HA31  single  0.970  0.020  1.090
 CR5  CA3  HA32  single  0.970  0.020  1.090
 CR5  C    O3    double  1.199  0.020  1.199
 CR5  C    OXT   single  1.316  0.020  1.316
 CR5  O4   HO4   single  0.850  0.020  0.980
 CR5  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
 CR5  HN2A  N    HN1   108.62  3.000
 CR5  HN2A  N    CA1   112.75  3.000
 CR5  HN1   N    CA1   113.37  3.000
 CR5  HA12  CA1  HA11  106.95  3.000
 CR5  HA12  CA1  C1    108.16  3.000
 CR5  HA11  CA1  C1    107.59  3.000
 CR5  HA12  CA1  N     109.01  3.000
 CR5  HA11  CA1  N     109.45  3.000
 CR5  C1    CA1  N     115.34  3.000
 CR5  O4    C1   N3    109.36  3.000
 CR5  O4    C1   N2    110.37  3.000
 CR5  N3    C1   N2    100.44  3.000
 CR5  O4    C1   CA1   114.36  3.000
 CR5  N3    C1   CA1   109.47  3.000
 CR5  N2    C1   CA1   111.93  3.000
 CR5  HN2   N2   CA2   123.20  3.000
 CR5  HN2   N2   C1    121.72  3.000
 CR5  CA2   N2   C1    114.90  3.000
 CR5  CA3   N3   C2    126.56  3.000
 CR5  CA3   N3   C1    121.51  3.000
 CR5  C2    N3   C1    111.49  3.000
 CR5  CA2   C2   O2    125.55  3.000
 CR5  CA2   C2   N3    109.59  3.000
 CR5  O2    C2   N3    124.86  3.000
 CR5  HO2   O2   C2    112.37  3.000
 CR5  O5    CA2  C2    124.12  3.000
 CR5  O5    CA2  N2    132.43  3.000
 CR5  C2    CA2  N2    103.44  3.000
 CR5  HA32  CA3  HA31  106.57  3.000
 CR5  HA32  CA3  C     108.58  3.000
 CR5  HA31  CA3  C     109.26  3.000
 CR5  HA32  CA3  N3    109.46  3.000
 CR5  HA31  CA3  N3    109.60  3.000
 CR5  C     CA3  N3    113.15  3.000
 CR5  OXT   C    O3    125.97  3.000
 CR5  OXT   C    CA3   112.31  3.000
 CR5  O3    C    CA3   121.66  3.000
 CR5  HO4   O4   C1    111.35  3.000
 CR5  HXT   OXT  C     111.02  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
 CR5  CONST_01  C2   CA2  N2   C1      0.00   0.0  0
 CR5  CONST_02  O5   CA2  N2   C1    180.00   0.0  0
 CR5  CONST_03  HN2  N2   CA2  C2    180.00   0.0  0
 CR5  CONST_04  HXT  OXT  C    CA3   180.00   0.0  0
 CR5  Var_01    CA2  C2   N3   C1     -0.52  30.0  1
 CR5  Var_02    N3   C2   CA2  N2     -1.91  30.0  1
 CR5  Var_03    C    CA3  N3   C1     89.29  30.0  3
 CR5  Var_04    O3   C    CA3  N3   -159.79  30.0  3
 CR5  Var_05    HN1  N    CA1  C1     61.05  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
 CR5  chir_01  C1  N2  N3  O4  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
 CR5  plan-1  C1   0.020
 CR5  plan-1  N2   0.020
 CR5  plan-1  C2   0.020
 CR5  plan-1  CA2  0.020
 CR5  plan-1  O5   0.020
 CR5  plan-1  HN2  0.020
 CR5  plan-2  C1   0.020
 CR5  plan-2  N3   0.020
 CR5  plan-2  C2   0.020
 CR5  plan-2  CA3  0.020
 CR5  plan-3  CA3  0.020
 CR5  plan-3  C    0.020
 CR5  plan-3  O3   0.020
 CR5  plan-3  OXT  0.020
 CR5  plan-3  HXT  0.020

