# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 02:11:03 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-[(E)-{2-[3-(methylsulfanyl)propanoyl]-5-oxo-1-(2-oxoethyl)-1,5-dihydro-4H-imidazol-4-ylidene}methyl]phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCC(=O)C1=NC(=C/c2ccc([O-])cc2)/C(=O)N1CC=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
 CRK  CRK  4-[(E)-{2-[3-(methylsulfanyl)propanoyl]-5-oxo-1-(2-oxoethyl)-1,5-dihydro-4H-imidazol-4-ylidene}methyl]phenolate  L-peptide  38  23  .  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_CRK
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
 CRK  C1    C  CR5    0   0.402  -1.1208  -0.6392   0.1043
 CRK  C2    C  CR5    0   0.501   1.0184  -1.2865   0.2652
 CRK  C3    C  C1     0   0.178  -1.3650  -3.7481  -0.5990
 CRK  CA1   C  C      0   0.352  -2.5791  -0.7146   0.0396
 CRK  CA2   C  CR5    0   0.048   0.8824   0.1438   0.0369
 CRK  CA3   C  CH2    0  -0.410  -0.6600  -3.0949   0.5634
 CRK  CB    C  CH2    0  -0.552  -3.3132   0.5928  -0.1203
 CRK  CB2   C  C1     0  -0.355   1.8111   1.1733  -0.1037
 CRK  CD2   C  CR16   0  -0.298   4.1251   0.1979   0.1448
 CRK  CD1   C  CR16   0  -0.254   3.7720   2.5610  -0.2891
 CRK  CE    C  CH3    0  -0.764  -7.3155   1.6191   0.1180
 CRK  CE2   C  CR16   0  -0.400   5.4675   0.4057   0.1487
 CRK  CE1   C  CR16   0  -0.422   5.1110   2.7834  -0.2894
 CRK  CG    C  CH2    0  -0.551  -4.8124   0.4476   0.0714
 CRK  CG2   C  CR6    0   0.065   3.2025   1.2662  -0.0758
 CRK  CZ    C  CR6    0   0.355   6.0595   1.7115  -0.0704
 CRK  N2    N  N      0  -0.442  -0.4524   0.4588  -0.0471
 CRK  N3    N  NR5    0  -0.571  -0.2941  -1.7308   0.2940
 CRK  O1    O  O      0  -0.407  -3.1535  -1.7870   0.0969
 CRK  O2    O  O      0  -0.496   1.9917  -2.0192   0.4168
 CRK  O3    O  O      0  -0.382  -1.9380  -4.8017  -0.5088
 CRK  OH    O  OC    -1  -0.528   7.2878   1.8946  -0.0688
 CRK  SD    S  S2     0  -0.040  -5.5921   2.0668  -0.1793
 CRK  H3    H  H      0   0.202  -1.2710  -3.2148  -1.5625
 CRK  HA31  H  HCH2   0   0.297  -1.2623  -3.1832   1.4683
 CRK  HA32  H  HCH2   0   0.301   0.2678  -3.6466   0.7406
 CRK  HB1   H  HCH2   0   0.279  -2.8995   1.3246   0.5766
 CRK  HB2A  H  HCH2   0   0.287  -3.0887   0.9808  -1.1192
 CRK  HB2   H  H      0   0.263   1.3123   2.1236  -0.2790
 CRK  HD2   H  HCR6   0   0.283   3.7414  -0.7978   0.3149
 CRK  HD1   H  HCR6   0   0.251   3.0982   3.3944  -0.4577
 CRK  HE1A  H  HCH3   0   0.262  -7.6458   0.8484  -0.5773
 CRK  HE2A  H  HCH3   0   0.262  -7.4621   1.2712   1.1395
 CRK  HE3   H  HCH3   0   0.274  -7.9208   2.5101  -0.0378
 CRK  HE2   H  HCR6   0   0.238   6.1394  -0.4279   0.3208
 CRK  HE1   H  HCR6   0   0.238   5.4965   3.7824  -0.4577
 CRK  HG1   H  HCH2   0   0.268  -5.2344  -0.2629  -0.6402
 CRK  HG2   H  HCH2   0   0.268  -5.0400   0.0940   1.0786

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
 CRK  C1   CA1   single    1.462  0.020  1.462
 CRK  C1   N2    double    1.294  0.020  1.294
 CRK  C1   N3    single    1.382  0.020  1.382
 CRK  C2   CA2   single    1.455  0.020  1.455
 CRK  C2   N3    single    1.386  0.020  1.386
 CRK  C2   O2    double    1.228  0.020  1.228
 CRK  C3   CA3   single    1.508  0.020  1.508
 CRK  C3   O3    double    1.203  0.020  1.203
 CRK  C3   H3    single    0.930  0.020  1.080
 CRK  CA1  CB    single    1.508  0.020  1.508
 CRK  CA1  O1    double    1.218  0.020  1.218
 CRK  CA2  CB2   double    1.394  0.020  1.394
 CRK  CA2  N2    single    1.374  0.020  1.374
 CRK  CA3  N3    single    1.438  0.020  1.438
 CRK  CA3  HA31  single    0.970  0.020  1.090
 CRK  CA3  HA32  single    0.970  0.020  1.090
 CRK  CB   CG    single    1.518  0.020  1.518
 CRK  CB   HB1   single    0.970  0.020  1.090
 CRK  CB   HB2A  single    0.970  0.020  1.090
 CRK  CB2  CG2   single    1.395  0.020  1.395
 CRK  CB2  HB2   single    0.930  0.020  1.080
 CRK  CD2  CE2   aromatic  1.358  0.020  1.358
 CRK  CD2  CG2   aromatic  1.429  0.020  1.429
 CRK  CD2  HD2   single    0.930  0.020  1.080
 CRK  CD1  CE1   aromatic  1.357  0.020  1.357
 CRK  CD1  CG2   aromatic  1.431  0.020  1.431
 CRK  CD1  HD1   single    0.930  0.020  1.080
 CRK  CE   SD    single    1.805  0.020  1.805
 CRK  CE   HE1A  single    0.970  0.020  1.090
 CRK  CE   HE2A  single    0.970  0.020  1.090
 CRK  CE   HE3   single    0.970  0.020  1.090
 CRK  CE2  CZ    aromatic  1.450  0.020  1.450
 CRK  CE2  HE2   single    0.930  0.020  1.080
 CRK  CE1  CZ    aromatic  1.448  0.020  1.448
 CRK  CE1  HE1   single    0.930  0.020  1.080
 CRK  CG   SD    single    1.815  0.020  1.815
 CRK  CG   HG1   single    0.970  0.020  1.090
 CRK  CG   HG2   single    0.970  0.020  1.090
 CRK  CZ   OH    single    1.242  0.020  1.242

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
 CRK  N3    C1   N2    112.15  3.000
 CRK  N3    C1   CA1   124.19  3.000
 CRK  N2    C1   CA1   123.63  3.000
 CRK  O2    C2   N3    123.84  3.000
 CRK  O2    C2   CA2   132.87  3.000
 CRK  N3    C2   CA2   103.29  3.000
 CRK  H3    C3   O3    121.90  3.000
 CRK  H3    C3   CA3   115.04  3.000
 CRK  O3    C3   CA3   122.98  3.000
 CRK  O1    CA1  CB    122.60  3.000
 CRK  O1    CA1  C1    120.93  3.000
 CRK  CB    CA1  C1    116.46  3.000
 CRK  N2    CA2  CB2   118.16  3.000
 CRK  N2    CA2  C2    109.01  3.000
 CRK  CB2   CA2  C2    132.83  3.000
 CRK  HA32  CA3  HA31  107.05  3.000
 CRK  HA32  CA3  N3    107.04  3.000
 CRK  HA31  CA3  N3    111.89  3.000
 CRK  HA32  CA3  C3    107.63  3.000
 CRK  HA31  CA3  C3    110.26  3.000
 CRK  N3    CA3  C3    112.67  3.000
 CRK  HB2A  CB   HB1   105.49  3.000
 CRK  HB2A  CB   CG    110.58  3.000
 CRK  HB1   CB   CG    110.95  3.000
 CRK  HB2A  CB   CA1   107.71  3.000
 CRK  HB1   CB   CA1   109.21  3.000
 CRK  CG    CB   CA1   112.60  3.000
 CRK  HB2   CB2  CG2   113.74  3.000
 CRK  HB2   CB2  CA2   110.86  3.000
 CRK  CG2   CB2  CA2   135.40  3.000
 CRK  HD2   CD2  CG2   118.95  3.000
 CRK  HD2   CD2  CE2   119.43  3.000
 CRK  CG2   CD2  CE2   121.62  3.000
 CRK  HD1   CD1  CG2   118.11  3.000
 CRK  HD1   CD1  CE1   119.13  3.000
 CRK  CG2   CD1  CE1   122.76  3.000
 CRK  HE3   CE   HE2A  108.72  3.000
 CRK  HE3   CE   HE1A  108.62  3.000
 CRK  HE2A  CE   HE1A  109.38  3.000
 CRK  HE3   CE   SD    107.72  3.000
 CRK  HE2A  CE   SD    111.23  3.000
 CRK  HE1A  CE   SD    111.09  3.000
 CRK  HE2   CE2  CZ    117.59  3.000
 CRK  HE2   CE2  CD2   119.68  3.000
 CRK  CZ    CE2  CD2   122.73  3.000
 CRK  HE1   CE1  CZ    118.21  3.000
 CRK  HE1   CE1  CD1   120.13  3.000
 CRK  CZ    CE1  CD1   121.66  3.000
 CRK  HG2   CG   HG1   108.09  3.000
 CRK  HG2   CG   SD    109.09  3.000
 CRK  HG1   CG   SD    108.96  3.000
 CRK  HG2   CG   CB    110.69  3.000
 CRK  HG1   CG   CB    111.22  3.000
 CRK  SD    CG   CB    108.75  3.000
 CRK  CD1   CG2  CD2   116.28  3.000
 CRK  CD1   CG2  CB2   117.03  3.000
 CRK  CD2   CG2  CB2   126.69  3.000
 CRK  OH    CZ   CE1   122.62  3.000
 CRK  OH    CZ   CE2   122.43  3.000
 CRK  CE1   CZ   CE2   114.95  3.000
 CRK  CA2   N2   C1    107.46  3.000
 CRK  CA3   N3   C2    123.30  3.000
 CRK  CA3   N3   C1    128.51  3.000
 CRK  C2    N3   C1    108.08  3.000
 CRK  CG    SD   CE     99.56  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
 CRK  CONST_01  CE1   CZ   CE2  CD2     0.00   0.0  0
 CRK  CONST_02  CE1   CD1  CG2  CD2     0.00   0.0  0
 CRK  CONST_03  CE2   CZ   CE1  CD1     0.00   0.0  0
 CRK  CONST_04  CE2   CD2  CG2  CD1     0.00   0.0  0
 CRK  CONST_05  CZ    CE2  CD2  CG2     0.00   0.0  0
 CRK  CONST_06  CZ    CE1  CD1  CG2     0.00   0.0  0
 CRK  CONST_07  C2    CA2  N2   C1      0.00   0.0  0
 CRK  CONST_08  CA2   C2   N3   C1      0.00   0.0  0
 CRK  CONST_09  N2    C1   N3   C2      0.00   0.0  0
 CRK  CONST_10  N3    C1   N2   CA2     0.00   0.0  0
 CRK  CONST_11  N3    C2   CA2  N2      0.00   0.0  0
 CRK  CONST_12  CE2   CD2  CG2  CB2   180.00   0.0  0
 CRK  CONST_13  CE1   CD1  CG2  CB2   180.00   0.0  0
 CRK  CONST_14  OH    CZ   CE2  CD2   180.00   0.0  0
 CRK  CONST_15  OH    CZ   CE1  CD1   180.00   0.0  0
 CRK  CONST_16  O2    C2   N3   C1    180.00   0.0  0
 CRK  CONST_17  CA1   C1   N3   C2    180.00   0.0  0
 CRK  CONST_18  CA2   N2   C1   CA1   180.00   0.0  0
 CRK  CONST_19  CA3   N3   C2   CA2   180.00   0.0  0
 CRK  CONST_20  N2    C1   N3   CA3   180.00   0.0  0
 CRK  CONST_21  HD1   CD1  CG2  CD2   180.00   0.0  0
 CRK  CONST_22  HD2   CD2  CG2  CD1   180.00   0.0  0
 CRK  CONST_23  HE1   CE1  CZ   CE2   180.00   0.0  0
 CRK  CONST_24  HE2   CE2  CZ   CE1   180.00   0.0  0
 CRK  CONST_25  CA3   N3   C1   CA1     0.00   0.0  0
 CRK  CONST_26  O2    C2   N3   CA3     0.00   0.0  0
 CRK  Var_01    CG2   CB2  CA2  C2     -0.60  30.0  2
 CRK  Var_02    CD2   CG2  CB2  CA2    -0.80  30.0  2
 CRK  Var_03    C3    CA3  N3   C1     66.89  30.0  2
 CRK  Var_04    N2    C1   CA1  CB     -4.26  30.0  2
 CRK  Var_05    CG    CB   CA1  C1   -169.71  30.0  3
 CRK  Var_06    O3    C3   CA3  N3   -167.81  30.0  2
 CRK  Var_07    SD    CG   CB   CA1  -178.75  30.0  3
 CRK  Var_08    HE1A  CE   SD   CG    -59.08  30.0  3

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
 CRK  plan-1  C1   0.020
 CRK  plan-1  C2   0.020
 CRK  plan-1  CA1  0.020
 CRK  plan-1  CA2  0.020
 CRK  plan-1  CA3  0.020
 CRK  plan-1  CB2  0.020
 CRK  plan-1  N2   0.020
 CRK  plan-1  N3   0.020
 CRK  plan-1  O2   0.020
 CRK  plan-2  CB2  0.020
 CRK  plan-2  CD2  0.020
 CRK  plan-2  CD1  0.020
 CRK  plan-2  CE2  0.020
 CRK  plan-2  CE1  0.020
 CRK  plan-2  CG2  0.020
 CRK  plan-2  CZ   0.020
 CRK  plan-2  OH   0.020
 CRK  plan-2  HD2  0.020
 CRK  plan-2  HD1  0.020
 CRK  plan-2  HE2  0.020
 CRK  plan-2  HE1  0.020
 CRK  plan-3  C1   0.020
 CRK  plan-3  CA1  0.020
 CRK  plan-3  CB   0.020
 CRK  plan-3  O1   0.020
 CRK  plan-4  C3   0.020
 CRK  plan-4  CA3  0.020
 CRK  plan-4  O3   0.020
 CRK  plan-4  H3   0.020

