# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 06:58:56 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-[(1R,2R)-1-amino-2-hydroxypropyl]-1-(carboxymethyl)-4-(1H-imidazol-5-ylmethyl)-1H-imidazol-5-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)c1nc(Cc2[nH]cnc2)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
 XXY  XXY  2-[(1R,2R)-1-amino-2-hydroxypropyl]-1-(carboxymethyl)-4-(1H-imidazol-5-ylmethyl)-1H-imidazol-5-olate  L-peptide  37  21  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XXY
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
 XXY  C1    C  CR5    0   0.461  -0.7419   1.0050   0.3621
 XXY  N2    N  N      0  -0.481   0.3113   1.5104  -0.2072
 XXY  CA2   C  CR5    0  -0.067   1.1755   0.4692  -0.4663
 XXY  C2    C  CR5    0   0.422   0.6204  -0.7304  -0.0399
 XXY  O2    O  OC    -1  -0.657   1.0164  -1.9462  -0.0286
 XXY  N3    N  NR5    0  -0.512  -0.6078  -0.3518   0.4999
 XXY  CA1   C  CH1    0  -0.230  -1.9667   1.7733   0.7496
 XXY  N1    N  NH2    0  -0.796  -1.5840   3.1498   1.0118
 XXY  CB1   C  CH1    0   0.023  -3.0778   1.6030  -0.3171
 XXY  CG1   C  CH3    0  -0.695  -4.4047   2.1915   0.1423
 XXY  OG1   O  OH1    0  -0.659  -2.6782   2.1205  -1.5665
 XXY  CA3   C  CH2    0  -0.450  -1.4905  -1.2981   1.0961
 XXY  C3    C  C      0   0.545  -2.1594  -2.1854   0.0693
 XXY  OXT   O  OH1    0  -0.592  -2.7330  -3.2312   0.6497
 XXY  CB2   C  CH2    0  -0.583   2.4879   0.6782  -1.1643
 XXY  CG2   C  CR5    0   0.275   3.6586   0.0469  -0.4806
 XXY  ND1   N  NR15   0  -0.630   3.5899  -1.2010   0.0668
 XXY  CE1   C  CR15   0   0.060   4.8016  -1.4912   0.5770
 XXY  NE2   N  N      0  -0.456   5.6575  -0.5156   0.3889
 XXY  CD2   C  CR15   0  -0.285   4.9513   0.4530  -0.2730
 XXY  O3    O  O      0  -0.433  -2.1953  -1.9674  -1.1126
 XXY  HA1   H  HCH1   0   0.233  -2.3728   1.3632   1.6838
 XXY  HN11  H  HNH2   0   0.342  -1.0528   3.5220   0.2350
 XXY  HN12  H  HNH2   0   0.348  -2.3959   3.7378   1.1469
 XXY  HB1   H  HCH1   0   0.226  -3.2204   0.5319  -0.4829
 XXY  HG11  H  HCH3   0   0.216  -4.3366   3.2688   0.3125
 XXY  HG12  H  HCH3   0   0.243  -5.1812   2.0262  -0.6050
 XXY  HG13  H  HCH3   0   0.229  -4.7321   1.7277   1.0738
 XXY  HOG1  H  HOH1   0   0.431  -2.5148   3.0639  -1.4614
 XXY  HA31  H  HCH2   0   0.295  -0.9533  -1.9254   1.8112
 XXY  HA32  H  HCH2   0   0.304  -2.2697  -0.7875   1.6669
 XXY  HOXT  H  HOH1   0   0.483  -3.1914  -3.7716  -0.0111
 XXY  HB21  H  HCH2   0   0.234   2.4463   0.3113  -2.1994
 XXY  HB22  H  HCH2   0   0.244   2.6749   1.7509  -1.2456
 XXY  HND1  H  HNR5   0   0.423   2.6992  -1.7401   0.1013
 XXY  HE1   H  HCR5   0   0.257   5.0100  -2.4236   1.0799
 XXY  HD2   H  HCR5   0   0.235   5.4022   1.3909  -0.5644

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
 XXY  CG1  CB1   single    1.523  0.020  1.523
 XXY  OG1  CB1   single    1.410  0.020  1.410
 XXY  CB1  CA1   single    1.550  0.020  1.550
 XXY  N1   CA1   single    1.453  0.020  1.453
 XXY  CA1  C1    single    1.497  0.020  1.497
 XXY  N2   C1    aromatic  1.300  0.020  1.300
 XXY  N2   CA2   aromatic  1.378  0.020  1.378
 XXY  C1   N3    aromatic  1.370  0.020  1.370
 XXY  N3   CA3   single    1.425  0.020  1.425
 XXY  N3   C2    aromatic  1.394  0.020  1.394
 XXY  CA2  CB2   single    1.501  0.020  1.501
 XXY  CA2  C2    aromatic  1.389  0.020  1.389
 XXY  CA3  C3    single    1.513  0.020  1.513
 XXY  CB2  CG2   single    1.496  0.020  1.496
 XXY  O3   C3    double    1.202  0.020  1.202
 XXY  C2   O2    single    1.279  0.020  1.279
 XXY  CD2  CG2   aromatic  1.371  0.020  1.371
 XXY  CD2  NE2   aromatic  1.369  0.020  1.369
 XXY  CG2  ND1   aromatic  1.364  0.020  1.364
 XXY  C3   OXT   single    1.326  0.020  1.326
 XXY  NE2  CE1   aromatic  1.311  0.020  1.311
 XXY  ND1  CE1   aromatic  1.346  0.020  1.346
 XXY  CA1  HA1   single    0.970  0.020  1.090
 XXY  N1   HN11  single    0.890  0.020  1.040
 XXY  N1   HN12  single    0.890  0.020  1.040
 XXY  CB1  HB1   single    0.970  0.020  1.090
 XXY  CG1  HG11  single    0.970  0.020  1.090
 XXY  CG1  HG12  single    0.970  0.020  1.090
 XXY  CG1  HG13  single    0.970  0.020  1.090
 XXY  OG1  HOG1  single    0.850  0.020  0.980
 XXY  CA3  HA31  single    0.970  0.020  1.090
 XXY  CA3  HA32  single    0.970  0.020  1.090
 XXY  OXT  HOXT  single    0.850  0.020  0.980
 XXY  CB2  HB21  single    0.970  0.020  1.090
 XXY  CB2  HB22  single    0.970  0.020  1.090
 XXY  ND1  HND1  single    0.860  0.020  1.020
 XXY  CE1  HE1   single    0.930  0.020  1.080
 XXY  CD2  HD2   single    0.930  0.020  1.080

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
 XXY  CA1   C1   N3    124.21  3.000
 XXY  N3    C1   N2    110.48  3.000
 XXY  CA1   C1   N2    125.24  3.000
 XXY  CA2   N2   C1    107.27  3.000
 XXY  CB2   CA2  C2    127.77  3.000
 XXY  C2    CA2  N2    110.14  3.000
 XXY  CB2   CA2  N2    122.05  3.000
 XXY  N3    C2   O2    121.85  3.000
 XXY  O2    C2   CA2   134.44  3.000
 XXY  N3    C2   CA2   103.68  3.000
 XXY  CA3   N3   C2    121.84  3.000
 XXY  C2    N3   C1    108.43  3.000
 XXY  CA3   N3   C1    129.72  3.000
 XXY  HA1   CA1  CB1   106.22  3.000
 XXY  HA1   CA1  N1    107.32  3.000
 XXY  CB1   CA1  N1    114.67  3.000
 XXY  HA1   CA1  C1    109.34  3.000
 XXY  N1    CA1  C1    108.51  3.000
 XXY  CB1   CA1  C1    110.61  3.000
 XXY  HN12  N1   HN11  108.06  3.000
 XXY  HN12  N1   CA1   111.32  3.000
 XXY  HN11  N1   CA1   110.38  3.000
 XXY  HB1   CB1  OG1   105.20  3.000
 XXY  HB1   CB1  CG1   108.11  3.000
 XXY  OG1   CB1  CG1   111.87  3.000
 XXY  HB1   CB1  CA1   107.79  3.000
 XXY  OG1   CB1  CA1   111.49  3.000
 XXY  CG1   CB1  CA1   112.01  3.000
 XXY  HG13  CG1  HG12  107.88  3.000
 XXY  HG13  CG1  HG11  107.75  3.000
 XXY  HG12  CG1  HG11  107.49  3.000
 XXY  HG13  CG1  CB1   110.79  3.000
 XXY  HG12  CG1  CB1   110.81  3.000
 XXY  HG11  CG1  CB1   111.95  3.000
 XXY  HOG1  OG1  CB1   108.11  3.000
 XXY  HA32  CA3  HA31  106.09  3.000
 XXY  HA32  CA3  C3    108.26  3.000
 XXY  HA31  CA3  C3    108.96  3.000
 XXY  HA32  CA3  N3    110.49  3.000
 XXY  HA31  CA3  N3    110.53  3.000
 XXY  C3    CA3  N3    112.29  3.000
 XXY  O3    C3   OXT   124.07  3.000
 XXY  OXT   C3   CA3   110.89  3.000
 XXY  O3    C3   CA3   125.03  3.000
 XXY  HOXT  OXT  C3    110.23  3.000
 XXY  HB22  CB2  HB21  105.32  3.000
 XXY  HB22  CB2  CG2   108.34  3.000
 XXY  HB21  CB2  CG2   108.62  3.000
 XXY  HB22  CB2  CA2   108.74  3.000
 XXY  HB21  CB2  CA2   111.00  3.000
 XXY  CG2   CB2  CA2   114.39  3.000
 XXY  CD2   CG2  ND1   104.93  3.000
 XXY  ND1   CG2  CB2   122.01  3.000
 XXY  CD2   CG2  CB2   133.03  3.000
 XXY  HND1  ND1  CE1   130.20  3.000
 XXY  HND1  ND1  CG2   121.98  3.000
 XXY  CE1   ND1  CG2   107.69  3.000
 XXY  HE1   CE1  NE2   125.68  3.000
 XXY  HE1   CE1  ND1   122.43  3.000
 XXY  NE2   CE1  ND1   111.88  3.000
 XXY  CD2   NE2  CE1   105.01  3.000
 XXY  HD2   CD2  NE2   121.94  3.000
 XXY  HD2   CD2  CG2   127.57  3.000
 XXY  NE2   CD2  CG2   110.49  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
 XXY  CONST_01  C2    CA2  N2   C1      0.00   0.0  0
 XXY  CONST_02  CA2   C2   N3   C1      0.00   0.0  0
 XXY  CONST_03  C2    N3   C1   N2      0.00   0.0  0
 XXY  CONST_04  N3    C2   CA2  N2      0.00   0.0  0
 XXY  CONST_05  N3    C1   N2   CA2     0.00   0.0  0
 XXY  CONST_06  CE1   NE2  CD2  CG2     0.00   0.0  0
 XXY  CONST_07  NE2   CE1  ND1  CG2     0.00   0.0  0
 XXY  CONST_08  NE2   CD2  CG2  ND1     0.00   0.0  0
 XXY  CONST_09  CD2   NE2  CE1  ND1     0.00   0.0  0
 XXY  CONST_10  CD2   CG2  ND1  CE1     0.00   0.0  0
 XXY  CONST_11  CB2   CA2  N2   C1    180.00   0.0  0
 XXY  CONST_12  O2    C2   N3   C1    180.00   0.0  0
 XXY  CONST_13  CA3   N3   C1   N2    180.00   0.0  0
 XXY  CONST_14  O2    C2   CA2  N2    180.00   0.0  0
 XXY  CONST_15  CA1   C1   N2   CA2   180.00   0.0  0
 XXY  CONST_16  CA3   N3   C2   CA2   180.00   0.0  0
 XXY  CONST_17  CA1   C1   N3   C2    180.00   0.0  0
 XXY  CONST_18  CB2   CA2  C2   N3    180.00   0.0  0
 XXY  CONST_19  NE2   CD2  CG2  CB2   180.00   0.0  0
 XXY  CONST_20  CE1   ND1  CG2  CB2   180.00   0.0  0
 XXY  CONST_21  HE1   CE1  ND1  CG2   180.00   0.0  0
 XXY  CONST_22  HD2   CD2  CG2  ND1   180.00   0.0  0
 XXY  CONST_23  HND1  ND1  CE1  NE2   180.00   0.0  0
 XXY  CONST_24  HOXT  OXT  C3   CA3   180.00   0.0  0
 XXY  Var_01    CG2   CB2  CA2  N2    130.86  30.0  2
 XXY  Var_02    CD2   CG2  CB2  CA2  -140.47  30.0  2
 XXY  Var_03    C3    CA3  N3   C1    108.58  30.0  2
 XXY  Var_04    O3    C3   CA3  N3    -15.24  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
 XXY  chir_01  CA1  CB1  N1   C1   positiv
 XXY  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
 XXY  plan-1  C1    0.020
 XXY  plan-1  N2    0.020
 XXY  plan-1  CA2   0.020
 XXY  plan-1  C2    0.020
 XXY  plan-1  O2    0.020
 XXY  plan-1  N3    0.020
 XXY  plan-1  CA1   0.020
 XXY  plan-1  CA3   0.020
 XXY  plan-1  CB2   0.020
 XXY  plan-2  CB2   0.020
 XXY  plan-2  CG2   0.020
 XXY  plan-2  ND1   0.020
 XXY  plan-2  CE1   0.020
 XXY  plan-2  NE2   0.020
 XXY  plan-2  CD2   0.020
 XXY  plan-2  HND1  0.020
 XXY  plan-2  HE1   0.020
 XXY  plan-2  HD2   0.020
 XXY  plan-3  CA3   0.020
 XXY  plan-3  C3    0.020
 XXY  plan-3  OXT   0.020
 XXY  plan-3  O3    0.020
 XXY  plan-3  HOXT  0.020

