# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 03:45:34 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-1-(2-oxoethyl)-1H-imidazol-5-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)c1nc(Cc2ccc(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
 C12  C12  2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-1-(2-oxoethyl)-1H-imidazol-5-olate  L-peptide  40  22  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C12
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
 C12  C1    C  CR5    0   0.414   1.4995   0.3830   0.1725
 C12  N2    N  N      0  -0.471   0.4525   1.0748   0.5056
 C12  CA2   C  CR5    0  -0.049  -0.2782   0.3116   1.3901
 C12  CG1   C  CH3    0  -0.689   5.0816   1.1945  -0.9900
 C12  OG1   O  OH1    0  -0.681   3.7723   2.2867   0.7391
 C12  C2    C  CR5    0   0.380   0.3345  -0.9209   1.6018
 C12  O2    O  OC    -1  -0.636   0.0479  -1.9472   2.2749
 C12  N3    N  NR5    0  -0.542   1.5029  -0.8319   0.8115
 C12  CA1   C  CH1    0  -0.214   2.5807   0.8400  -0.7590
 C12  N1    N  NH2    0  -0.820   2.1786   2.0928  -1.3854
 C12  CB1   C  CH1    0   0.051   3.9146   1.1095  -0.0152
 C12  CA3   C  CH2    0  -0.432   2.3836  -1.9364   0.5953
 C12  C3    C  C1     0   0.165   2.2047  -2.5547  -0.7682
 C12  O3    O  O      0  -0.374   3.0622  -3.1705  -1.3469
 C12  CB2   C  CH2    0  -0.591  -1.6085   0.7435   1.9074
 C12  CG2   C  CR6    0   0.126  -2.7308   0.5529   0.9117
 C12  CD1   C  CR16   0  -0.331  -3.5204   1.6083   0.4755
 C12  CE1   C  CR16   0  -0.371  -4.5387   1.4241  -0.4556
 C12  CD2   C  CR16   0  -0.277  -2.9960  -0.7115   0.3829
 C12  CE2   C  CR16   0  -0.325  -4.0069  -0.9167  -0.5396
 C12  CZ    C  CR6    0   0.329  -4.7868   0.1576  -0.9690
 C12  OH    O  OH1    0  -0.640  -5.7582  -0.0900  -1.8774
 C12  HG12  H  HCH3   0   0.218   5.2003   0.2557  -1.5348
 C12  HG13  H  HCH3   0   0.222   4.9349   1.9920  -1.7212
 C12  HG1   H  HOH1   0   0.432   3.2222   2.8518   0.1674
 C12  HA1   H  HCH1   0   0.230   2.7650   0.0571  -1.5099
 C12  HN11  H  HNH2   0   0.362   2.4289   2.1075  -2.3632
 C12  HN12  H  HNH2   0   0.361   1.1760   2.2068  -1.3167
 C12  HB1   H  HCH1   0   0.217   4.1119   0.2959   0.6899
 C12  HA31  H  HCH2   0   0.277   3.4346  -1.6912   0.7625
 C12  HA32  H  HCH2   0   0.296   2.1195  -2.7049   1.3315
 C12  H3    H  H      0   0.200   1.1961  -2.4167  -1.2019
 C12  HB21  H  HCH2   0   0.231  -1.8395   0.1746   2.8142
 C12  HB22  H  HCH2   0   0.225  -1.5873   1.7948   2.2137
 C12  HD1   H  HCR6   0   0.242  -3.3430   2.6053   0.8629
 C12  HE1   H  HCR6   0   0.261  -5.1345   2.2717  -0.7779
 C12  HD2   H  HCR6   0   0.249  -2.3904  -1.5528   0.7009
 C12  HE2   H  HCR6   0   0.253  -4.1962  -1.9079  -0.9343
 C12  HOH   H  HOH1   0   0.470  -6.2239   0.7248  -2.0939
 C12  HG11  H  HCH3   0   0.234   6.0159   1.3913  -0.4629

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
 C12  C1   N2    aromatic  1.298  0.020  1.298
 C12  C1   N3    aromatic  1.373  0.020  1.373
 C12  C1   CA1   single    1.499  0.020  1.499
 C12  N2   CA2   aromatic  1.378  0.020  1.378
 C12  CA2  C2    aromatic  1.393  0.020  1.393
 C12  CA2  CB2   single    1.491  0.020  1.491
 C12  CG1  CB1   single    1.523  0.020  1.523
 C12  CG1  HG11  single    0.970  0.020  1.090
 C12  CG1  HG12  single    0.970  0.020  1.090
 C12  CG1  HG13  single    0.970  0.020  1.090
 C12  OG1  CB1   single    1.405  0.020  1.405
 C12  OG1  HG1   single    0.850  0.020  0.980
 C12  C2   O2    single    1.260  0.020  1.260
 C12  C2   N3    aromatic  1.413  0.020  1.413
 C12  N3   CA3   single    1.429  0.020  1.429
 C12  CA1  N1    single    1.457  0.020  1.457
 C12  CA1  CB1   single    1.551  0.020  1.551
 C12  CA1  HA1   single    0.970  0.020  1.090
 C12  N1   HN11  single    0.890  0.020  1.040
 C12  N1   HN12  single    0.890  0.020  1.040
 C12  CB1  HB1   single    0.970  0.020  1.090
 C12  CA3  C3    single    1.508  0.020  1.508
 C12  CA3  HA31  single    0.970  0.020  1.090
 C12  CA3  HA32  single    0.970  0.020  1.090
 C12  C3   O3    double    1.204  0.020  1.204
 C12  C3   H3    single    0.930  0.020  1.080
 C12  CB2  CG2   single    1.512  0.020  1.512
 C12  CB2  HB21  single    0.970  0.020  1.090
 C12  CB2  HB22  single    0.970  0.020  1.090
 C12  CG2  CD1   aromatic  1.388  0.020  1.388
 C12  CG2  CD2   aromatic  1.396  0.020  1.396
 C12  CD1  CE1   aromatic  1.392  0.020  1.392
 C12  CD1  HD1   single    0.930  0.020  1.080
 C12  CE1  CZ    aromatic  1.389  0.020  1.389
 C12  CE1  HE1   single    0.930  0.020  1.080
 C12  CD2  CE2   aromatic  1.384  0.020  1.384
 C12  CD2  HD2   single    0.930  0.020  1.080
 C12  CE2  CZ    aromatic  1.395  0.020  1.395
 C12  CE2  HE2   single    0.930  0.020  1.080
 C12  CZ   OH    single    1.353  0.020  1.353
 C12  OH   HOH   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
 C12  CA1   C1   N3    123.88  3.000
 C12  CA1   C1   N2    125.37  3.000
 C12  N3    C1   N2    110.74  3.000
 C12  CA2   N2   C1    107.29  3.000
 C12  CB2   CA2  C2    126.59  3.000
 C12  CB2   CA2  N2    122.37  3.000
 C12  C2    CA2  N2    110.76  3.000
 C12  HG13  CG1  HG12  107.97  3.000
 C12  HG13  CG1  HG11  107.87  3.000
 C12  HG12  CG1  HG11  107.65  3.000
 C12  HG13  CG1  CB1   111.50  3.000
 C12  HG12  CG1  CB1   110.78  3.000
 C12  HG11  CG1  CB1   110.92  3.000
 C12  HG1   OG1  CB1   103.18  3.000
 C12  N3    C2   O2    122.54  3.000
 C12  N3    C2   CA2   102.89  3.000
 C12  O2    C2   CA2   134.57  3.000
 C12  CA3   N3   C2    123.05  3.000
 C12  CA3   N3   C1    127.96  3.000
 C12  C2    N3   C1    108.30  3.000
 C12  HA1   CA1  CB1   107.87  3.000
 C12  HA1   CA1  N1    111.38  3.000
 C12  CB1   CA1  N1    107.10  3.000
 C12  HA1   CA1  C1    109.15  3.000
 C12  CB1   CA1  C1    112.05  3.000
 C12  N1    CA1  C1    109.28  3.000
 C12  HN12  N1   HN11  108.06  3.000
 C12  HN12  N1   CA1   109.95  3.000
 C12  HN11  N1   CA1   111.13  3.000
 C12  HB1   CB1  CA1   109.56  3.000
 C12  HB1   CB1  OG1   107.16  3.000
 C12  CA1   CB1  OG1   108.41  3.000
 C12  HB1   CB1  CG1   108.41  3.000
 C12  CA1   CB1  CG1   111.21  3.000
 C12  OG1   CB1  CG1   111.99  3.000
 C12  HA32  CA3  HA31  106.64  3.000
 C12  HA32  CA3  C3    106.93  3.000
 C12  HA31  CA3  C3    110.17  3.000
 C12  HA32  CA3  N3    106.96  3.000
 C12  HA31  CA3  N3    113.35  3.000
 C12  C3    CA3  N3    112.37  3.000
 C12  H3    C3   O3    121.64  3.000
 C12  H3    C3   CA3   114.30  3.000
 C12  O3    C3   CA3   124.05  3.000
 C12  HB22  CB2  HB21  105.73  3.000
 C12  HB22  CB2  CG2   108.62  3.000
 C12  HB21  CB2  CG2   108.85  3.000
 C12  HB22  CB2  CA2   110.97  3.000
 C12  HB21  CB2  CA2   108.97  3.000
 C12  CG2   CB2  CA2   113.39  3.000
 C12  CD2   CG2  CD1   117.48  3.000
 C12  CD2   CG2  CB2   120.30  3.000
 C12  CD1   CG2  CB2   122.21  3.000
 C12  HD1   CD1  CE1   118.70  3.000
 C12  HD1   CD1  CG2   119.59  3.000
 C12  CE1   CD1  CG2   121.71  3.000
 C12  HE1   CE1  CZ    120.29  3.000
 C12  HE1   CE1  CD1   119.81  3.000
 C12  CZ    CE1  CD1   119.90  3.000
 C12  HD2   CD2  CE2   119.24  3.000
 C12  HD2   CD2  CG2   119.05  3.000
 C12  CE2   CD2  CG2   121.71  3.000
 C12  HE2   CE2  CZ    119.64  3.000
 C12  HE2   CE2  CD2   120.40  3.000
 C12  CZ    CE2  CD2   119.96  3.000
 C12  OH    CZ   CE2   117.85  3.000
 C12  OH    CZ   CE1   122.91  3.000
 C12  CE2   CZ   CE1   119.24  3.000
 C12  HOH   OH   CZ    110.08  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
 C12  CONST_01  C2   CA2  N2   C1      0.00   0.0  0
 C12  CONST_02  CA2  C2   N3   C1      0.00   0.0  0
 C12  CONST_03  C2   N3   C1   N2      0.00   0.0  0
 C12  CONST_04  N3   C2   CA2  N2      0.00   0.0  0
 C12  CONST_05  N3   C1   N2   CA2     0.00   0.0  0
 C12  CONST_06  CZ   CE1  CD1  CG2     0.00   0.0  0
 C12  CONST_07  CZ   CE2  CD2  CG2     0.00   0.0  0
 C12  CONST_08  CE2  CD2  CG2  CD1     0.00   0.0  0
 C12  CONST_09  CE2  CZ   CE1  CD1     0.00   0.0  0
 C12  CONST_10  CD2  CG2  CD1  CE1     0.00   0.0  0
 C12  CONST_11  CD2  CE2  CZ   CE1     0.00   0.0  0
 C12  CONST_12  CB2  CA2  N2   C1    180.00   0.0  0
 C12  CONST_13  O2   C2   N3   C1    180.00   0.0  0
 C12  CONST_14  CA3  N3   C1   N2    180.00   0.0  0
 C12  CONST_15  O2   C2   CA2  N2    180.00   0.0  0
 C12  CONST_16  CA1  C1   N2   CA2   180.00   0.0  0
 C12  CONST_17  CA3  N3   C2   CA2   180.00   0.0  0
 C12  CONST_18  CA1  C1   N3   C2    180.00   0.0  0
 C12  CONST_19  CB2  CA2  C2   N3    180.00   0.0  0
 C12  CONST_20  CE1  CD1  CG2  CB2   180.00   0.0  0
 C12  CONST_21  CE2  CD2  CG2  CB2   180.00   0.0  0
 C12  CONST_22  OH   CZ   CE1  CD1   180.00   0.0  0
 C12  CONST_23  OH   CZ   CE2  CD2   180.00   0.0  0
 C12  CONST_24  HE1  CE1  CD1  CG2   180.00   0.0  0
 C12  CONST_25  HE2  CE2  CD2  CG2   180.00   0.0  0
 C12  CONST_26  HD2  CD2  CG2  CD1   180.00   0.0  0
 C12  CONST_27  HD1  CD1  CG2  CD2   180.00   0.0  0
 C12  Var_01    CG2  CB2  CA2  N2     77.19  30.0  2
 C12  Var_02    CD1  CG2  CB2  CA2  -121.59  30.0  2
 C12  Var_03    C3   CA3  N3   C1    -66.35  30.0  2
 C12  Var_04    O3   C3   CA3  N3    154.91  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
 C12  chir_01  CA1  C1   N1   CB1  negativ
 C12  chir_02  CB1  OG1  CA1  CG1  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
 C12  plan-1  C1   0.020
 C12  plan-1  N2   0.020
 C12  plan-1  CA2  0.020
 C12  plan-1  C2   0.020
 C12  plan-1  O2   0.020
 C12  plan-1  N3   0.020
 C12  plan-1  CA1  0.020
 C12  plan-1  CA3  0.020
 C12  plan-1  CB2  0.020
 C12  plan-2  CB2  0.020
 C12  plan-2  CG2  0.020
 C12  plan-2  CD1  0.020
 C12  plan-2  CE1  0.020
 C12  plan-2  CD2  0.020
 C12  plan-2  CE2  0.020
 C12  plan-2  CZ   0.020
 C12  plan-2  OH   0.020
 C12  plan-2  HD1  0.020
 C12  plan-2  HE1  0.020
 C12  plan-2  HD2  0.020
 C12  plan-2  HE2  0.020
 C12  plan-3  CA3  0.020
 C12  plan-3  C3   0.020
 C12  plan-3  O3   0.020
 C12  plan-3  H3   0.020

