# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Sep 24 18:46:16 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: [(2S,4S)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(1H-imidazol-4-ylmethyl)-5-oxoimidazolidin-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)[C@H]1N[C@@H](Cc2c[nH]cn2)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
 CSH  CSH  "[2-(2-HYDROXY-1-METHYL-ETHYL)-4-(1H-IMIDAZOL-4-YLMETHYL)-5-OXO-IMIDAZOLIDIN-1-YL]-ACETIC ACID"  L-peptide  37  20  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CSH
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
 CSH  C1    C  CR15  0   0.163  14.1940  64.1355  77.1289
 CSH  N2    N  NR15  0  -0.652  14.0059  64.7785  75.8360
 CSH  CA2   C  CR15  0  -0.193  12.8399  65.6419  75.8598
 CSH  C2    C  CR5   0   0.550  12.1495  65.2706  77.1499
 CSH  O2    O  O     0  -0.485  11.0597  65.6566  77.5360
 CSH  N3    N  NR5   0  -0.479  12.9561  64.4333  77.8169
 CSH  CA3   C  CH2   0  -0.431  12.5919  63.9212  79.1007
 CSH  C3    C  C     0   0.538  12.5573  64.9607  80.2014
 CSH  O3    O  O     0  -0.436  11.9373  64.8053  81.2213
 CSH  OXT   O  OH1   0  -0.580  13.3092  66.0180  79.9414
 CSH  CA1   C  CH1   0  -0.173  14.4256  62.6291  76.9619
 CSH  N1    N  NH2   0  -0.793  13.2590  62.0183  76.3593
 CSH  CB1   C  CH2   0  -0.169  15.7058  62.3652  76.1640
 CSH  OG2   O  OH1   0  -0.660  16.8560  62.9853  76.6923
 CSH  CB2   C  CH2   0  -0.509  11.9308  65.4428  74.6455
 CSH  CG    C  CR5   0   0.153  12.6355  65.7570  73.3720
 CSH  ND1   N  N     0  -0.459  13.0154  67.0320  73.0471
 CSH  CD2   C  CR15  0  -0.134  13.0405  64.8924  72.3937
 CSH  CE1   C  CR15  0   0.083  13.6318  66.9375  71.8961
 CSH  NE2   N  NR15  0  -0.563  13.6705  65.6650  71.4603
 CSH  H1    H  HCR5  0   0.245  15.0375  64.5622  77.6845
 CSH  HN2   H  HNR5  0   0.371  14.8380  65.2685  75.5460
 CSH  HA2   H  HCR5  0   0.268  13.1100  66.7044  75.9213
 CSH  HA31  H  HCH2  0   0.296  11.6169  63.4323  79.0686
 CSH  HA32  H  HCH2  0   0.308  13.3087  63.1559  79.4057
 CSH  HXT   H  HOH1  0   0.483  13.2707  66.6401  80.6843
 CSH  HA1   H  HCH1  0   0.236  14.5575  62.1903  77.9593
 CSH  HN11  H  HNH2  0   0.342  13.1415  62.3794  75.4192
 CSH  HN12  H  HNH2  0   0.351  13.3950  61.0193  76.2707
 CSH  HB11  H  HCH2  0   0.210  15.8357  61.2781  76.0772
 CSH  HB12  H  HCH2  0   0.215  15.5769  62.7515  75.1496
 CSH  HOG   H  HOH1  0   0.447  17.0288  62.6131  77.5625
 CSH  HB21  H  HCH2  0   0.245  11.5823  64.4074  74.6274
 CSH  HB22  H  HCH2  0   0.243  11.0497  66.0801  74.7563
 CSH  HD2   H  HCR5  0   0.279  12.9334  63.8259  72.2877
 CSH  HE1   H  HCR5  0   0.273  14.0622  67.7542  71.3369
 CSH  HE2   H  HNR5  0   0.417  14.0859  65.3432  70.6005

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
 CSH  C1   N2    single    1.456  0.020  1.456
 CSH  C1   N3    single    1.447  0.020  1.447
 CSH  C1   CA1   single    1.533  0.020  1.533
 CSH  C1   H1    single    0.970  0.020  1.090
 CSH  N2   CA2   single    1.451  0.020  1.451
 CSH  N2   HN2   single    0.890  0.020  1.040
 CSH  CA2  C2    single    1.510  0.020  1.510
 CSH  CA2  CB2   single    1.530  0.020  1.530
 CSH  CA2  HA2   single    0.970  0.020  1.090
 CSH  C2   O2    double    1.219  0.020  1.219
 CSH  C2   N3    single    1.340  0.020  1.340
 CSH  N3   CA3   single    1.429  0.020  1.429
 CSH  CA3  C3    single    1.514  0.020  1.514
 CSH  CA3  HA31  single    0.970  0.020  1.090
 CSH  CA3  HA32  single    0.970  0.020  1.090
 CSH  C3   O3    double    1.204  0.020  1.204
 CSH  C3   OXT   single    1.323  0.020  1.323
 CSH  OXT  HXT   single    0.850  0.020  0.980
 CSH  CA1  N1    single    1.448  0.020  1.448
 CSH  CA1  CB1   single    1.531  0.020  1.531
 CSH  CA1  HA1   single    0.970  0.020  1.090
 CSH  N1   HN11  single    0.890  0.020  1.040
 CSH  N1   HN12  single    0.890  0.020  1.040
 CSH  CB1  OG2   single    1.410  0.020  1.410
 CSH  CB1  HB11  single    0.970  0.020  1.090
 CSH  CB1  HB12  single    0.970  0.020  1.090
 CSH  OG2  HOG   single    0.850  0.020  0.980
 CSH  CB2  CG    single    1.489  0.020  1.489
 CSH  CB2  HB21  single    0.970  0.020  1.090
 CSH  CB2  HB22  single    0.970  0.020  1.090
 CSH  CG   ND1   aromatic  1.370  0.020  1.370
 CSH  CG   CD2   aromatic  1.367  0.020  1.367
 CSH  ND1  CE1   aromatic  1.309  0.020  1.309
 CSH  CD2  NE2   aromatic  1.366  0.020  1.366
 CSH  CD2  HD2   single    0.930  0.020  1.080
 CSH  CE1  NE2   aromatic  1.346  0.020  1.346
 CSH  CE1  HE1   single    0.930  0.020  1.080
 CSH  NE2  HE2   single    0.860  0.020  1.020

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
 CSH  H1    C1   CA1   108.74  3.000
 CSH  H1    C1   N3    109.70  3.000
 CSH  CA1   C1   N3    112.53  3.000
 CSH  H1    C1   N2    112.17  3.000
 CSH  CA1   C1   N2    110.89  3.000
 CSH  N3    C1   N2    102.75  3.000
 CSH  HN2   N2   CA2   112.26  3.000
 CSH  HN2   N2   C1    111.31  3.000
 CSH  CA2   N2   C1    110.61  3.000
 CSH  HA2   CA2  CB2   108.45  3.000
 CSH  HA2   CA2  C2    107.62  3.000
 CSH  CB2   CA2  C2    111.99  3.000
 CSH  HA2   CA2  N2    112.27  3.000
 CSH  CB2   CA2  N2    112.77  3.000
 CSH  C2    CA2  N2    103.60  3.000
 CSH  N3    C2   O2    125.33  3.000
 CSH  N3    C2   CA2   107.68  3.000
 CSH  O2    C2   CA2   126.99  3.000
 CSH  CA3   N3   C2    121.16  3.000
 CSH  CA3   N3   C1    124.83  3.000
 CSH  C2    N3   C1    114.00  3.000
 CSH  HA32  CA3  HA31  106.31  3.000
 CSH  HA32  CA3  C3    107.04  3.000
 CSH  HA31  CA3  C3    107.97  3.000
 CSH  HA32  CA3  N3    109.55  3.000
 CSH  HA31  CA3  N3    111.21  3.000
 CSH  C3    CA3  N3    114.37  3.000
 CSH  OXT   C3   O3    124.22  3.000
 CSH  OXT   C3   CA3   113.12  3.000
 CSH  O3    C3   CA3   122.62  3.000
 CSH  HXT   OXT  C3    109.84  3.000
 CSH  HA1   CA1  CB1   107.71  3.000
 CSH  HA1   CA1  N1    107.84  3.000
 CSH  CB1   CA1  N1    112.58  3.000
 CSH  HA1   CA1  C1    108.18  3.000
 CSH  CB1   CA1  C1    110.63  3.000
 CSH  N1    CA1  C1    109.75  3.000
 CSH  HN12  N1   HN11  106.61  3.000
 CSH  HN12  N1   CA1   110.15  3.000
 CSH  HN11  N1   CA1   109.21  3.000
 CSH  HB12  CB1  HB11  106.88  3.000
 CSH  HB12  CB1  OG2   106.77  3.000
 CSH  HB11  CB1  OG2   111.63  3.000
 CSH  HB12  CB1  CA1   108.91  3.000
 CSH  HB11  CB1  CA1   108.10  3.000
 CSH  OG2   CB1  CA1   114.27  3.000
 CSH  HOG   OG2  CB1   108.38  3.000
 CSH  HB22  CB2  HB21  107.28  3.000
 CSH  HB22  CB2  CG    110.19  3.000
 CSH  HB21  CB2  CG    109.68  3.000
 CSH  HB22  CB2  CA2   108.82  3.000
 CSH  HB21  CB2  CA2   109.03  3.000
 CSH  CG    CB2  CA2   111.72  3.000
 CSH  CD2   CG   ND1   109.69  3.000
 CSH  CD2   CG   CB2   128.23  3.000
 CSH  ND1   CG   CB2   122.05  3.000
 CSH  CE1   ND1  CG    105.78  3.000
 CSH  HD2   CD2  NE2   122.60  3.000
 CSH  HD2   CD2  CG    131.85  3.000
 CSH  NE2   CD2  CG    105.54  3.000
 CSH  HE1   CE1  NE2   122.43  3.000
 CSH  HE1   CE1  ND1   126.06  3.000
 CSH  NE2   CE1  ND1   111.51  3.000
 CSH  HE2   NE2  CE1   126.17  3.000
 CSH  HE2   NE2  CD2   126.35  3.000
 CSH  CE1   NE2  CD2   107.48  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
 CSH  CONST_01  NE2   CE1  ND1  CG      0.00   0.0  0
 CSH  CONST_02  CE1   NE2  CD2  CG      0.00   0.0  0
 CSH  CONST_03  NE2   CD2  CG   ND1     0.00   0.0  0
 CSH  CONST_04  CD2   NE2  CE1  ND1     0.00   0.0  0
 CSH  CONST_05  CE1   ND1  CG   CD2     0.00   0.0  0
 CSH  CONST_06  CA2   C2   N3   C1      0.00   0.0  0
 CSH  CONST_07  CE1   ND1  CG   CB2   180.00   0.0  0
 CSH  CONST_08  NE2   CD2  CG   CB2   180.00   0.0  0
 CSH  CONST_09  O2    C2   N3   C1    180.00   0.0  0
 CSH  CONST_10  CA3   N3   C2   CA2   180.00   0.0  0
 CSH  CONST_11  HE1   CE1  ND1  CG    180.00   0.0  0
 CSH  CONST_12  HE2   NE2  CD2  CG    180.00   0.0  0
 CSH  CONST_13  HD2   CD2  CG   ND1   180.00   0.0  0
 CSH  CONST_14  HE2   NE2  CE1  ND1   180.00   0.0  0
 CSH  CONST_15  HE1   CE1  NE2  CD2   180.00   0.0  0
 CSH  CONST_16  HD2   CD2  NE2  CE1   180.00   0.0  0
 CSH  CONST_17  CA3   N3   C2   O2      0.00   0.0  0
 CSH  CONST_18  HXT   OXT  C3   CA3   180.00   0.0  0
 CSH  CONST_19  HXT   OXT  C3   O3      0.00   0.0  0
 CSH  Var_01    ND1   CG   CB2  CA2   -68.06  30.0  2
 CSH  Var_02    CD2   CG   CB2  CA2   109.63  30.0  2
 CSH  Var_03    C3    CA3  N3   C1    111.22  30.0  3
 CSH  Var_04    C3    CA3  N3   C2    -67.81  30.0  3
 CSH  Var_05    HA31  CA3  N3   C1   -126.16  30.0  3
 CSH  Var_06    HA32  CA3  N3   C1     -8.93  30.0  3
 CSH  Var_07    HA31  CA3  N3   C2     54.81  30.0  3
 CSH  Var_08    HA32  CA3  N3   C2    172.04  30.0  3
 CSH  Var_09    HB21  CB2  CG   ND1   170.92  30.0  1
 CSH  Var_10    HB22  CB2  CG   ND1    53.04  30.0  1
 CSH  Var_11    HB21  CB2  CG   CD2   -11.38  30.0  1
 CSH  Var_12    HB22  CB2  CG   CD2  -129.26  30.0  1
 CSH  Var_13    O3    C3   CA3  N3    158.97  30.0  3
 CSH  Var_14    OXT   C3   CA3  N3    -23.26  30.0  3
 CSH  Var_15    HA31  CA3  C3   O3     34.60  30.0  2
 CSH  Var_16    HA32  CA3  C3   O3    -79.48  30.0  2
 CSH  Var_17    HA31  CA3  C3   OXT  -147.62  30.0  2
 CSH  Var_18    HA32  CA3  C3   OXT    98.29  30.0  2

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
 CSH  chir_01  C1   N2  N3   CA1  negativ
 CSH  chir_02  CA2  N2  CB2  C2   negativ
 CSH  chir_03  CA1  N1  CB1  C1   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
 CSH  plan-1  CB2  0.020
 CSH  plan-1  CG   0.020
 CSH  plan-1  ND1  0.020
 CSH  plan-1  CD2  0.020
 CSH  plan-1  CE1  0.020
 CSH  plan-1  NE2  0.020
 CSH  plan-1  HD2  0.020
 CSH  plan-1  HE1  0.020
 CSH  plan-1  HE2  0.020
 CSH  plan-2  CA3  0.020
 CSH  plan-2  C3   0.020
 CSH  plan-2  O3   0.020
 CSH  plan-2  OXT  0.020
 CSH  plan-2  HXT  0.020
 CSH  plan-3  C1   0.020
 CSH  plan-3  CA2  0.020
 CSH  plan-3  C2   0.020
 CSH  plan-3  O2   0.020
 CSH  plan-3  N3   0.020
 CSH  plan-3  CA3  0.020

