# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:43:35 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-phosphono-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cn(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
 NEP  NEP  '1-phosphono-L-histidine  '  L-peptide  22  15  .  2012-08-28  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_NEP
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
 NEP  N    N  NH2    0  -0.797  13.9327  -8.0744  17.7692
 NEP  CA   C  CH1    0  -0.215  14.1246  -6.8691  16.9807
 NEP  C    C  C      0   0.403  12.8133  -6.4485  16.2736
 NEP  O    O  O      0  -0.599  11.9261  -7.3158  16.1488
 NEP  CB   C  CH2    0  -0.518  15.2357  -6.9742  15.9182
 NEP  CG   C  CR5    0   0.113  16.5674  -7.3830  16.4629
 NEP  ND1  N  N      0  -0.489  17.4384  -8.1488  15.7391
 NEP  CD2  C  CR15   0  -0.162  17.1336  -7.0902  17.6796
 NEP  CE1  C  CR15   0   0.037  18.4921  -8.2983  16.5186
 NEP  NE2  N  NR5    0  -0.545  18.3638  -7.6823  17.7028
 NEP  P    P  P      0   1.206  19.5174  -7.7875  19.1452
 NEP  O1P  O  OP    -1  -0.856  20.7079  -8.4724  18.5005
 NEP  O2P  O  OP    -1  -0.862  19.6917  -6.3269  19.5154
 NEP  O3P  O  O      0  -0.862  18.7120  -8.6250  20.1195
 NEP  OXT  O  OC    -1  -0.615  12.7758  -5.2743  15.8532
 NEP  H    H  HNH2   0   0.331  14.8344  -8.4761  17.9975
 NEP  H2   H  HNH2   0   0.321  13.4419  -8.7535  17.2012
 NEP  HA   H  HCH1   0   0.197  14.4022  -6.0572  17.6647
 NEP  HB2  H  HCH2   0   0.210  14.9380  -7.7044  15.1573
 NEP  HB3  H  HCH2   0   0.220  15.3155  -6.0136  15.4001
 NEP  HD2  H  HCR5   0   0.246  16.7580  -6.5198  18.5148
 NEP  HE1  H  HCR5   0   0.235  19.3758  -8.8625  16.2627

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
 NEP  N    CA   single    1.458  0.019  1.458
 NEP  N    H    single    0.860  0.020  0.860
 NEP  N    H2   single    0.890  0.020  1.040
 NEP  CA   C    single    1.525  0.021  1.525
 NEP  CA   CB   single    1.530  0.020  1.530
 NEP  CA   HA   single    0.970  0.020  0.970
 NEP  C    O    deloc     1.231  0.020  1.231
 NEP  C    OXT  deloc     1.248  0.020  1.248
 NEP  CB   CG   single    1.496  0.020  1.496
 NEP  CB   HB2  single    0.970  0.020  1.090
 NEP  CB   HB3  single    0.970  0.020  1.090
 NEP  CG   ND1  aromatic  1.367  0.020  1.367
 NEP  CG   CD2  aromatic  1.374  0.020  1.374
 NEP  ND1  CE1  aromatic  1.319  0.020  1.319
 NEP  CD2  NE2  aromatic  1.366  0.020  1.366
 NEP  CD2  HD2  single    0.930  0.020  1.080
 NEP  CE1  NE2  aromatic  1.341  0.020  1.341
 NEP  CE1  HE1  single    0.930  0.020  1.080
 NEP  NE2  P    single    1.850  0.020  1.850
 NEP  P    O1P  deloc     1.517  0.020  1.517
 NEP  P    O2P  deloc     1.517  0.020  1.517
 NEP  P    O3P  deloc     1.516  0.020  1.516

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
 NEP  H2   N    H    106.98  3.000
 NEP  H2   N    CA   108.42  3.000
 NEP  H    N    CA   114.00  3.000
 NEP  HA   CA   CB   109.00  3.000
 NEP  HA   CA   C    109.00  3.000
 NEP  CB   CA   C    110.10  1.900
 NEP  HA   CA   N    110.00  3.000
 NEP  CB   CA   N    110.50  1.700
 NEP  C    CA   N    111.00  2.800
 NEP  OXT  C    O    126.83  3.000
 NEP  OXT  C    CA   115.79  3.000
 NEP  O    C    CA   120.80  1.700
 NEP  HB3  CB   HB2  106.02  3.000
 NEP  HB3  CB   CG   110.33  3.000
 NEP  HB2  CB   CG   108.22  3.000
 NEP  HB3  CB   CA   108.61  3.000
 NEP  HB2  CB   CA   109.17  3.000
 NEP  CG   CB   CA   114.18  3.000
 NEP  CD2  CG   ND1  109.01  3.000
 NEP  CD2  CG   CB   129.15  3.000
 NEP  ND1  CG   CB   121.84  3.000
 NEP  CE1  ND1  CG   105.04  3.000
 NEP  HD2  CD2  NE2  121.98  3.000
 NEP  HD2  CD2  CG   130.92  3.000
 NEP  NE2  CD2  CG   107.10  3.000
 NEP  HE1  CE1  NE2  121.85  3.000
 NEP  HE1  CE1  ND1  124.98  3.000
 NEP  NE2  CE1  ND1  113.17  3.000
 NEP  P    NE2  CE1  127.07  3.000
 NEP  P    NE2  CD2  126.85  3.000
 NEP  CE1  NE2  CD2  105.68  3.000
 NEP  O3P  P    O2P  115.85  3.000
 NEP  O3P  P    O1P  116.13  3.000
 NEP  O2P  P    O1P  116.63  3.000
 NEP  O3P  P    NE2  101.61  3.000
 NEP  O2P  P    NE2  101.96  3.000
 NEP  O1P  P    NE2  100.59  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
 NEP  CONST_01  NE2  CE1  ND1  CG      0.00   0.0  0
 NEP  CONST_02  CE1  NE2  CD2  CG      0.00   0.0  0
 NEP  CONST_03  NE2  CD2  CG   ND1     0.00   0.0  0
 NEP  CONST_04  CD2  NE2  CE1  ND1     0.00   0.0  0
 NEP  CONST_05  CE1  ND1  CG   CD2     0.00   0.0  0
 NEP  CONST_06  CE1  ND1  CG   CB    180.00   0.0  0
 NEP  CONST_07  NE2  CD2  CG   CB    180.00   0.0  0
 NEP  CONST_08  P    NE2  CD2  CG    180.00   0.0  0
 NEP  CONST_09  P    NE2  CE1  ND1   180.00   0.0  0
 NEP  CONST_10  HE1  CE1  ND1  CG    180.00   0.0  0
 NEP  CONST_11  HD2  CD2  CG   ND1   180.00   0.0  0
 NEP  Var_01    ND1  CG   CB   CA    146.54  30.0  2
 NEP  Var_02    O1P  P    NE2  CD2  -176.70  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
 NEP  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
 NEP  plan-1  CB   0.020
 NEP  plan-1  CG   0.020
 NEP  plan-1  ND1  0.020
 NEP  plan-1  CD2  0.020
 NEP  plan-1  CE1  0.020
 NEP  plan-1  NE2  0.020
 NEP  plan-1  P    0.020
 NEP  plan-1  HD2  0.020
 NEP  plan-1  HE1  0.020
 NEP  plan-2  CA   0.020
 NEP  plan-2  C    0.020
 NEP  plan-2  O    0.020
 NEP  plan-2  OXT  0.020

