# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:16:30 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: methyl 3-(1H-imidazol-3-ium-4-yl)-L-alaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)Cc1c[nH]c[nH+]1
#
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
 PVH  PVH  'methyl 3-(1H-imidazol-3-ium-4-yl)-L-alaninate'  L-peptide  24  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PVH
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
 PVH  N    N  NH2   0  -0.769   0.2760  -1.6241  -0.8909
 PVH  CA   C  CH1   0  -0.212   0.7342  -0.3235  -0.4849
 PVH  C    C  C     0   0.571   2.2121  -0.2716  -0.1053
 PVH  O    O  O     0  -0.438   2.8965  -1.2428   0.0928
 PVH  CB   C  CH2   0  -0.546  -0.0983   0.1840   0.7092
 PVH  CG   C  CR5   0   0.354  -1.5527   0.1509   0.4226
 PVH  ND1  N  NR15  1  -0.589  -2.1573   0.9625  -0.5073
 PVH  CD2  C  CR15  0  -0.121  -2.5433  -0.6224   0.9336
 PVH  CE1  C  CR15  0   0.242  -3.4527   0.7027  -0.5677
 PVH  NE2  N  NR15  0  -0.538  -3.7026  -0.2562   0.3026
 PVH  OE   O  O2    0  -0.451   2.6492   0.9739  -0.0134
 PVH  CM   C  CH3   0  -0.423   4.0156   1.1729   0.3561
 PVH  H    H  HNH2  0   0.361   0.7805  -1.9359  -1.7103
 PVH  H2   H  HNH2  0   0.349   0.4543  -2.3078  -0.1652
 PVH  HA   H  HCH1  0   0.283   0.5954   0.3685  -1.3217
 PVH  HB2  H  HCH2  0   0.288   0.0873  -0.4458   1.5813
 PVH  HB3  H  HCH2  0   0.297   0.2037   1.1978   0.9772
 PVH  HD1  H  HNR5  0   0.457  -1.6979   1.6686  -1.0662
 PVH  HD2  H  HCR5  0   0.329  -2.5123  -1.3946   1.6811
 PVH  HE1  H  HCR5  0   0.358  -4.1693   1.1884  -1.2063
 PVH  HE2  H  HNR5  0   0.461  -4.6157  -0.6558   0.4681
 PVH  HM1  H  HCH3  0   0.241   4.2223   0.7659   1.3453
 PVH  HM2  H  HCH3  0   0.241   4.6913   0.7201  -0.3689
 PVH  HM3  H  HCH3  0   0.254   4.1677   2.2479   0.3688

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
 PVH  N    CA   single    1.458  0.019  1.458
 PVH  N    H    single    0.860  0.020  0.860
 PVH  N    H2   single    0.890  0.020  1.040
 PVH  CA   C    single    1.525  0.021  1.525
 PVH  CA   CB   single    1.530  0.020  1.530
 PVH  CA   HA   single    0.970  0.020  0.970
 PVH  C    O    double    1.231  0.020  1.231
 PVH  C    OE   single    1.323  0.020  1.323
 PVH  CB   CG   single    1.483  0.020  1.483
 PVH  CB   HB2  single    0.970  0.020  1.090
 PVH  CB   HB3  single    0.970  0.020  1.090
 PVH  CG   ND1  aromatic  1.374  0.020  1.374
 PVH  CG   CD2  aromatic  1.357  0.020  1.357
 PVH  ND1  CE1  aromatic  1.323  0.020  1.323
 PVH  ND1  HD1  single    0.860  0.020  1.020
 PVH  CD2  NE2  aromatic  1.370  0.020  1.370
 PVH  CD2  HD2  single    0.930  0.020  1.080
 PVH  CE1  NE2  aromatic  1.319  0.020  1.319
 PVH  CE1  HE1  single    0.930  0.020  1.080
 PVH  NE2  HE2  single    0.860  0.020  1.020
 PVH  OE   CM   single    1.429  0.020  1.429
 PVH  CM   HM1  single    0.970  0.020  1.090
 PVH  CM   HM2  single    0.970  0.020  1.090
 PVH  CM   HM3  single    0.970  0.020  1.090

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
 PVH  H2   N    H    106.53  3.000
 PVH  H2   N    CA   110.62  3.000
 PVH  H    N    CA   114.00  3.000
 PVH  HA   CA   CB   109.00  3.000
 PVH  HA   CA   C    109.00  3.000
 PVH  CB   CA   C    110.10  1.900
 PVH  HA   CA   N    110.00  3.000
 PVH  CB   CA   N    110.50  1.700
 PVH  C    CA   N    111.00  2.800
 PVH  OE   C    O    124.05  3.000
 PVH  OE   C    CA   111.66  3.000
 PVH  O    C    CA   120.80  1.700
 PVH  HB3  CB   HB2  107.02  3.000
 PVH  HB3  CB   CG   109.86  3.000
 PVH  HB2  CB   CG   107.95  3.000
 PVH  HB3  CB   CA   110.28  3.000
 PVH  HB2  CB   CA   109.70  3.000
 PVH  CG   CB   CA   111.88  3.000
 PVH  CD2  CG   ND1  105.67  3.000
 PVH  CD2  CG   CB   131.01  3.000
 PVH  ND1  CG   CB   123.30  3.000
 PVH  HD1  ND1  CE1  123.86  3.000
 PVH  HD1  ND1  CG   125.91  3.000
 PVH  CE1  ND1  CG   110.23  3.000
 PVH  HD2  CD2  NE2  122.46  3.000
 PVH  HD2  CD2  CG   130.55  3.000
 PVH  NE2  CD2  CG   106.99  3.000
 PVH  HE1  CE1  NE2  126.42  3.000
 PVH  HE1  CE1  ND1  126.22  3.000
 PVH  NE2  CE1  ND1  107.36  3.000
 PVH  HE2  NE2  CE1  124.53  3.000
 PVH  HE2  NE2  CD2  125.71  3.000
 PVH  CE1  NE2  CD2  109.75  3.000
 PVH  CM   OE   C    117.70  3.000
 PVH  HM3  CM   HM2  109.41  3.000
 PVH  HM3  CM   HM1  109.43  3.000
 PVH  HM2  CM   HM1  109.34  3.000
 PVH  HM3  CM   OE   105.95  3.000
 PVH  HM2  CM   OE   111.28  3.000
 PVH  HM1  CM   OE   111.35  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
 PVH  CONST_01  NE2  CE1  ND1  CG     0.00   0.0  0
 PVH  CONST_02  CE1  NE2  CD2  CG     0.00   0.0  0
 PVH  CONST_03  NE2  CD2  CG   ND1    0.00   0.0  0
 PVH  CONST_04  CD2  NE2  CE1  ND1    0.00   0.0  0
 PVH  CONST_05  CE1  ND1  CG   CD2    0.00   0.0  0
 PVH  CONST_06  CE1  ND1  CG   CB   180.00   0.0  0
 PVH  CONST_07  NE2  CD2  CG   CB   180.00   0.0  0
 PVH  CONST_08  HE1  CE1  ND1  CG   180.00   0.0  0
 PVH  CONST_09  HE2  NE2  CD2  CG   180.00   0.0  0
 PVH  CONST_10  HD2  CD2  CG   ND1  180.00   0.0  0
 PVH  CONST_11  HD1  ND1  CG   CD2  180.00   0.0  0
 PVH  Var_01    ND1  CG   CB   CA   -67.51  30.0  2
 PVH  Var_02    HM1  CM   OE   C    -61.37  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
 PVH  chir_01  CA  N  C  CB  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
 PVH  plan-1  CB   0.020
 PVH  plan-1  CG   0.020
 PVH  plan-1  ND1  0.020
 PVH  plan-1  CD2  0.020
 PVH  plan-1  CE1  0.020
 PVH  plan-1  NE2  0.020
 PVH  plan-1  HD1  0.020
 PVH  plan-1  HD2  0.020
 PVH  plan-1  HE1  0.020
 PVH  plan-1  HE2  0.020
 PVH  plan-2  CA   0.020
 PVH  plan-2  C    0.020
 PVH  plan-2  O    0.020
 PVH  plan-2  OE   0.020

