# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 06:55:31 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (2~{S})-2-azanyl-5-[(~{N}-phosphonocarbamimidoyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)N[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
 RPI  RPI  '(2~{S})-2-azanyl-5-[(~{N}-phosphonocarbamimidoyl)amino]pentanoic acid'  L-peptide  28  16  .  2017-07-05  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_RPI
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
 RPI  P    P  P      0   1.196  22.3265  27.8469   8.7290
 RPI  N    N  NH2    0  -0.787  26.3196  27.1920  14.4873
 RPI  CA   C  CH1    0  -0.209  25.1672  27.7344  13.7812
 RPI  CB   C  CH2    0  -0.451  24.3386  26.5906  13.1866
 RPI  CG   C  CH2    0  -0.439  25.1140  25.6460  12.2705
 RPI  CD   C  CH2    0  -0.282  25.7796  26.3070  11.0713
 RPI  NE   N  NH1    0  -0.693  24.8079  26.9353  10.2192
 RPI  CZ   C  C      0   0.543  25.1206  27.5070   9.0224
 RPI  NH1  N  N      0  -0.775  26.2870  27.4896   8.4528
 RPI  NH2  N  NH1    0  -0.842  24.0700  28.1462   8.4223
 RPI  O1P  O  OP    -1  -0.874  22.0242  26.4667   8.1605
 RPI  O2P  O  O      0  -0.874  21.6702  29.0101   8.0030
 RPI  O3P  O  OP    -1  -0.871  22.2535  27.9147  10.2654
 RPI  C    C  C      0   0.385  24.2350  28.6402  14.6257
 RPI  O    O  O      0  -0.617  23.4487  29.3645  13.9802
 RPI  OXT  O  OC    -1  -0.605  24.3270  28.5585  15.8675
 RPI  H4   H  HCH1   0   0.207  25.5454  28.3437  12.9525
 RPI  H5   H  HCH2   0   0.219  23.4807  27.0148  12.6606
 RPI  H6   H  HCH2   0   0.214  23.9174  25.9988  14.0079
 RPI  H7   H  HCH2   0   0.217  24.4386  24.8631  11.9119
 RPI  H8   H  HCH2   0   0.220  25.8918  25.1444  12.8478
 RPI  H9   H  HCH2   0   0.217  26.3228  25.5340  10.5151
 RPI  H10  H  HCH2   0   0.203  26.5424  27.0161  11.4224
 RPI  H11  H  HNH1   0   0.407  23.8867  27.1998  10.5827
 RPI  H12  H  H      0   0.302  26.9697  27.0364   9.0486
 RPI  H14  H  HNH1   0   0.338  24.3133  28.4867   7.5040
 RPI  H1   H  HNH2   0   0.330  26.9040  27.9606  14.7940
 RPI  H2   H  HNH2   0   0.320  25.9841  26.7741  15.3486

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
 RPI  O2P  P    deloc   1.520  0.020  1.520
 RPI  NH2  P    single  1.795  0.020  1.795
 RPI  NH2  CZ   single  1.368  0.020  1.368
 RPI  O1P  P    deloc   1.523  0.020  1.523
 RPI  NH1  CZ   double  1.298  0.020  1.298
 RPI  P    O3P  deloc   1.540  0.020  1.540
 RPI  CZ   NE   single  1.363  0.020  1.363
 RPI  NE   CD   single  1.437  0.020  1.437
 RPI  CD   CG   single  1.522  0.020  1.522
 RPI  CG   CB   single  1.527  0.020  1.527
 RPI  CB   CA   single  1.530  0.020  1.530
 RPI  CA   C    single  1.525  0.021  1.525
 RPI  CA   N    single  1.458  0.019  1.458
 RPI  O    C    deloc   1.231  0.020  1.231
 RPI  C    OXT  deloc   1.248  0.020  1.248
 RPI  N    H1   single  0.890  0.020  1.040
 RPI  N    H2   single  0.890  0.020  1.040
 RPI  CA   H4   single  0.970  0.020  1.090
 RPI  CB   H5   single  0.970  0.020  1.090
 RPI  CB   H6   single  0.970  0.020  1.090
 RPI  CG   H7   single  0.970  0.020  1.090
 RPI  CG   H8   single  0.970  0.020  1.090
 RPI  CD   H9   single  0.970  0.020  1.090
 RPI  CD   H10  single  0.970  0.020  1.090
 RPI  NE   H11  single  0.860  0.020  1.020
 RPI  NH1  H12  single  0.890  0.020  1.040
 RPI  NH2  H14  single  0.890  0.020  1.040

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
 RPI  O3P  P    O2P  114.99  3.000
 RPI  O3P  P    O1P  113.77  3.000
 RPI  O2P  P    O1P  115.43  3.000
 RPI  O3P  P    NH2  102.08  3.000
 RPI  O1P  P    NH2  106.26  3.000
 RPI  O2P  P    NH2  102.13  3.000
 RPI  H2   N    H1   104.25  3.000
 RPI  H2   N    CA   107.66  3.000
 RPI  H1   N    CA   108.71  3.000
 RPI  H4   CA   C    107.13  3.000
 RPI  H4   CA   CB   107.95  3.000
 RPI  C    CA   CB   110.10  1.900
 RPI  H4   CA   N    107.49  3.000
 RPI  C    CA   N    111.00  2.800
 RPI  CB   CA   N    110.50  1.700
 RPI  H6   CB   H5   105.59  3.000
 RPI  H6   CB   CG   108.08  3.000
 RPI  H5   CB   CG   110.50  3.000
 RPI  H6   CB   CA   108.66  3.000
 RPI  H5   CB   CA   108.77  3.000
 RPI  CG   CB   CA   114.82  3.000
 RPI  H8   CG   H7   106.53  3.000
 RPI  H8   CG   CD   107.74  3.000
 RPI  H7   CG   CD   108.80  3.000
 RPI  H8   CG   CB   109.21  3.000
 RPI  H7   CG   CB   109.01  3.000
 RPI  CD   CG   CB   115.21  3.000
 RPI  H10  CD   H9   105.85  3.000
 RPI  H10  CD   NE   112.12  3.000
 RPI  H9   CD   NE   110.03  3.000
 RPI  H10  CD   CG   109.38  3.000
 RPI  H9   CD   CG   108.07  3.000
 RPI  NE   CD   CG   111.18  3.000
 RPI  H11  NE   CZ   114.17  3.000
 RPI  H11  NE   CD   120.68  3.000
 RPI  CZ   NE   CD   123.30  3.000
 RPI  NH2  CZ   NH1  120.25  3.000
 RPI  NH1  CZ   NE   125.87  3.000
 RPI  NH2  CZ   NE   113.89  3.000
 RPI  H12  NH1  CZ   110.70  3.000
 RPI  H14  NH2  CZ   111.81  3.000
 RPI  H14  NH2  P    116.48  3.000
 RPI  CZ   NH2  P    126.35  3.000
 RPI  OXT  C    O    126.78  3.000
 RPI  OXT  C    CA   117.36  3.000
 RPI  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
 RPI  CONST_03  NH2  CZ   NE   CD    180.00   0.0  0
 RPI  CONST_04  NH1  CZ   NE   CD      0.00   0.0  0
 RPI  CONST_05  H14  NH2  CZ   NE    180.00   0.0  0
 RPI  CONST_06  H12  NH1  CZ   NE      0.00   0.0  0
 RPI  CONST_07  H11  NE   CZ   NH1   180.00   0.0  0
 RPI  Var_01    CD   CG   CB   CA    -58.13  30.0  1
 RPI  Var_02    NE   CD   CG   CB    -60.78  30.0  1
 RPI  Var_03    CZ   NE   CD   CG   -174.58  30.0  2
 RPI  Var_04    O2P  P    NH2  CZ    169.35  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
 RPI  chir_01  CA  CB  C  N  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
 RPI  plan-1  P    0.020
 RPI  plan-1  CD   0.020
 RPI  plan-1  NE   0.020
 RPI  plan-1  CZ   0.020
 RPI  plan-1  NH1  0.020
 RPI  plan-1  NH2  0.020
 RPI  plan-1  H11  0.020
 RPI  plan-1  H12  0.020
 RPI  plan-1  H14  0.020
 RPI  plan-2  CA   0.020
 RPI  plan-2  C    0.020
 RPI  plan-2  O    0.020
 RPI  plan-2  OXT  0.020

