# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 06:45:39 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-(1-phosphono-1H-imidazol-3-ium-5-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH+]cn1[P](O)(O)=O)C(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
 HIP  HIP  3-(1-phosphono-1H-imidazol-3-ium-5-yl)-L-alanine  L-peptide  23  15  .  2016-04-22  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_HIP
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
 HIP  N    N  NH2    0  -0.804  5.7819   7.4312  3.9443
 HIP  CA   C  CH1    0  -0.211  6.6474   6.5658  4.7279
 HIP  CB   C  CH2    0  -0.541  7.3765   7.2659  5.8856
 HIP  CG   C  CR5    0   0.279  6.5058   7.8796  6.9289
 HIP  CD2  C  CR15   0  -0.135  5.1788   7.7136  7.1960
 HIP  NE2  N  NR15   1  -0.571  4.8954   8.5080  8.2742
 HIP  CE1  C  CR15   0   0.186  6.0071   9.1334  8.6482
 HIP  ND1  N  NR5    0  -0.587  6.9952   8.7762  7.8546
 HIP  P    P  P      0   1.245  8.7754   9.4948  8.0358
 HIP  O1P  O  O      0  -0.827  8.5436  10.3215  9.2792
 HIP  O2P  O  OP    -1  -0.830  8.9068  10.2396  6.7294
 HIP  O3P  O  OP    -1  -0.830  9.5782   8.2272  8.1903
 HIP  C    C  C      0   0.405  5.9055   5.2940  5.2193
 HIP  O    O  O      0  -0.597  4.6609   5.2746  5.1195
 HIP  OXT  O  OC    -1  -0.598  6.6323   4.3963  5.6845
 HIP  H    H  HNH2   0   0.334  4.8556   7.4320  4.3488
 HIP  H2   H  HNH2   0   0.332  6.1190   8.3854  3.9645
 HIP  HA   H  HCH1   0   0.219  7.4529   6.2070  4.0753
 HIP  HB2  H  HCH2   0   0.244  8.0145   8.0546  5.4788
 HIP  HB3  H  HCH2   0   0.245  8.0574   6.5550  6.3581
 HIP  HD2  H  HCR5   0   0.296  4.4352   7.0973  6.7218
 HIP  HE2  H  HNR5   0   0.432  3.9941   8.6103  8.7150
 HIP  HE1  H  HCR5   0   0.314  6.0835   9.8247  9.4689

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
 HIP  N    CA   single    1.458  0.019  1.458
 HIP  N    H    single    0.860  0.020  0.860
 HIP  N    H2   single    0.890  0.020  1.040
 HIP  CA   CB   single    1.530  0.020  1.530
 HIP  CA   C    single    1.525  0.021  1.525
 HIP  CA   HA   single    0.970  0.020  0.970
 HIP  CB   CG   single    1.491  0.020  1.491
 HIP  CB   HB2  single    0.970  0.020  1.090
 HIP  CB   HB3  single    0.970  0.020  1.090
 HIP  CG   CD2  aromatic  1.364  0.020  1.364
 HIP  CG   ND1  aromatic  1.378  0.020  1.378
 HIP  CD2  NE2  aromatic  1.369  0.020  1.369
 HIP  CD2  HD2  single    0.930  0.020  1.080
 HIP  NE2  CE1  aromatic  1.329  0.020  1.329
 HIP  NE2  HE2  single    0.860  0.020  1.020
 HIP  CE1  ND1  aromatic  1.317  0.020  1.317
 HIP  CE1  HE1  single    0.930  0.020  1.080
 HIP  ND1  P    single    1.928  0.020  1.928
 HIP  P    O1P  deloc     1.511  0.020  1.511
 HIP  P    O2P  deloc     1.510  0.020  1.510
 HIP  P    O3P  deloc     1.508  0.020  1.508
 HIP  C    O    deloc     1.231  0.020  1.231
 HIP  C    OXT  deloc     1.245  0.020  1.245

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
 HIP  H2   N    H    107.25  3.000
 HIP  H2   N    CA   110.63  3.000
 HIP  H    N    CA   114.00  3.000
 HIP  HA   CA   C    109.00  3.000
 HIP  HA   CA   CB   109.00  3.000
 HIP  C    CA   CB   110.10  1.900
 HIP  HA   CA   N    110.00  3.000
 HIP  C    CA   N    111.00  2.800
 HIP  CB   CA   N    110.50  1.700
 HIP  HB3  CB   HB2  105.47  3.000
 HIP  HB3  CB   CG   109.23  3.000
 HIP  HB2  CB   CG   107.71  3.000
 HIP  HB3  CB   CA   108.98  3.000
 HIP  HB2  CB   CA   108.98  3.000
 HIP  CG   CB   CA   115.95  3.000
 HIP  ND1  CG   CD2  107.04  3.000
 HIP  ND1  CG   CB   122.02  3.000
 HIP  CD2  CG   CB   130.93  3.000
 HIP  HD2  CD2  NE2  122.45  3.000
 HIP  HD2  CD2  CG   130.98  3.000
 HIP  NE2  CD2  CG   106.56  3.000
 HIP  HE2  NE2  CE1  125.22  3.000
 HIP  HE2  NE2  CD2  126.02  3.000
 HIP  CE1  NE2  CD2  108.76  3.000
 HIP  HE1  CE1  ND1  125.51  3.000
 HIP  HE1  CE1  NE2  125.20  3.000
 HIP  ND1  CE1  NE2  109.29  3.000
 HIP  P    ND1  CE1  122.35  3.000
 HIP  P    ND1  CG   129.29  3.000
 HIP  CE1  ND1  CG   108.35  3.000
 HIP  O3P  P    O2P  117.19  3.000
 HIP  O3P  P    O1P  117.20  3.000
 HIP  O2P  P    O1P  117.10  3.000
 HIP  O3P  P    ND1  100.82  3.000
 HIP  O2P  P    ND1  100.54  3.000
 HIP  O1P  P    ND1   98.03  3.000
 HIP  OXT  C    O    126.89  3.000
 HIP  OXT  C    CA   115.47  3.000
 HIP  O    C    CA   120.80  1.700

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
 HIP  CONST_01  CE1  NE2  CD2  CG      0.00   0.0  0
 HIP  CONST_02  NE2  CE1  ND1  CG      0.00   0.0  0
 HIP  CONST_03  CE1  ND1  CG   CD2     0.00   0.0  0
 HIP  CONST_04  ND1  CE1  NE2  CD2     0.00   0.0  0
 HIP  CONST_05  ND1  CG   CD2  NE2     0.00   0.0  0
 HIP  CONST_06  NE2  CD2  CG   CB    180.00   0.0  0
 HIP  CONST_07  CE1  ND1  CG   CB    180.00   0.0  0
 HIP  CONST_08  P    ND1  CG   CD2   180.00   0.0  0
 HIP  CONST_09  P    ND1  CE1  NE2   180.00   0.0  0
 HIP  CONST_10  HE2  NE2  CD2  CG    180.00   0.0  0
 HIP  CONST_11  HE1  CE1  ND1  CG    180.00   0.0  0
 HIP  CONST_12  HD2  CD2  NE2  CE1   180.00   0.0  0
 HIP  Var_01    CD2  CG   CB   CA     15.00  30.0  2
 HIP  Var_02    O1P  P    ND1  CG   -177.36  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
 HIP  chir_01  CA  N  CB  C  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
 HIP  plan-1  CB   0.020
 HIP  plan-1  CG   0.020
 HIP  plan-1  CD2  0.020
 HIP  plan-1  NE2  0.020
 HIP  plan-1  CE1  0.020
 HIP  plan-1  ND1  0.020
 HIP  plan-1  P    0.020
 HIP  plan-1  HD2  0.020
 HIP  plan-1  HE2  0.020
 HIP  plan-1  HE1  0.020
 HIP  plan-2  CA   0.020
 HIP  plan-2  C    0.020
 HIP  plan-2  O    0.020
 HIP  plan-2  OXT  0.020

