# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 22:49:21 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN1C(=O)CO[P](O)(=O)O[P](O)(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
 2P0  2P0  1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline  L-peptide  29  20  .  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_2P0
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
 2P0  C     C  C      0   0.334  -24.9460  -23.3176  -18.4999
 2P0  N     N  NT     0  -0.388  -26.8657  -22.4065  -19.9124
 2P0  OXT   O  OC     0  -0.607  -24.4129  -23.2516  -17.3760
 2P0  CA    C  CH1    0  -0.223  -26.3441  -22.6569  -18.5730
 2P0  CB    C  CH2    0  -0.472  -27.3808  -23.6211  -17.9696
 2P0  CD    C  CH2    0  -0.259  -28.1223  -23.0962  -20.1658
 2P0  CG    C  CH2    0  -0.521  -28.6525  -23.3589  -18.7641
 2P0  OAB   O  O      0  -0.568  -26.8601  -21.3715  -21.9106
 2P0  OAC   O  OP    -1  -0.948  -25.8926  -15.2486  -20.5476
 2P0  OAD   O  O      0  -0.870  -23.5765  -17.7410  -22.0451
 2P0  OAF   O  OP    -1  -0.891  -25.9327  -16.1348  -18.1412
 2P0  OAG   O  O      0  -0.885  -23.6855  -15.6468  -19.2975
 2P0  OAH   O  OP    -1  -0.890  -22.9297  -18.9079  -19.8033
 2P0  CAK   C  CH2    0  -0.222  -25.1735  -20.7171  -20.3247
 2P0  OAM   O  O2     0  -0.569  -24.8394  -19.7554  -21.2768
 2P0  OAN   O  O2     0  -0.688  -25.1657  -17.6456  -20.0149
 2P0  CAP   C  C      0   0.456  -26.3700  -21.5264  -20.7992
 2P0  PAS   P  P      0   1.168  -25.1605  -15.9985  -19.4443
 2P0  PAT   P  P      0   1.328  -23.9779  -18.4214  -20.7677
 2P0  O     O  O     -1  -0.514  -24.5170  -23.8841  -19.5200
 2P0  HA    H  HCH1   0   0.235  -26.3380  -21.7270  -17.9933
 2P0  HB    H  HCH2   0   0.255  -27.0661  -24.6570  -18.1236
 2P0  HBA   H  HCH2   0   0.270  -27.4948  -23.4712  -16.8973
 2P0  HD    H  HCH2   0   0.275  -28.7885  -22.4761  -20.7642
 2P0  HDA   H  HCH2   0   0.193  -27.9604  -24.0316  -20.7117
 2P0  HG    H  HCH2   0   0.257  -29.3509  -24.1950  -18.7331
 2P0  HGA   H  HCH2   0   0.242  -29.1697  -22.4740  -18.3869
 2P0  HAK   H  HCH2   0   0.270  -24.3390  -21.4023  -20.1416
 2P0  HAKA  H  HCH2   0   0.231  -25.4265  -20.2744  -19.3517

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
 2P0  O    C     deloc   1.231  0.020  1.231
 2P0  CA   C     single  1.525  0.021  1.525
 2P0  C    OXT   deloc   1.246  0.020  1.246
 2P0  CAP  N     single  1.344  0.020  1.344
 2P0  CD   N     single  1.473  0.014  1.473
 2P0  N    CA    single  1.466  0.015  1.466
 2P0  CA   CB    single  1.530  0.020  1.530
 2P0  CA   HA    single  0.970  0.020  0.970
 2P0  CG   CB    single  1.522  0.020  1.522
 2P0  CB   HB    single  0.970  0.020  1.090
 2P0  CB   HBA   single  0.970  0.020  1.090
 2P0  CD   CG    single  1.521  0.020  1.521
 2P0  CD   HD    single  0.970  0.020  1.090
 2P0  CD   HDA   single  0.970  0.020  1.090
 2P0  CG   HG    single  0.970  0.020  1.090
 2P0  CG   HGA   single  0.970  0.020  1.090
 2P0  OAB  CAP   double  1.225  0.020  1.225
 2P0  OAC  PAS   deloc   1.522  0.020  1.522
 2P0  OAD  PAT   deloc   1.502  0.020  1.502
 2P0  PAS  OAF   deloc   1.521  0.020  1.521
 2P0  OAG  PAS   deloc   1.523  0.020  1.523
 2P0  PAT  OAH   deloc   1.505  0.020  1.505
 2P0  OAM  CAK   single  1.394  0.020  1.394
 2P0  CAP  CAK   single  1.520  0.020  1.520
 2P0  CAK  HAK   single  0.970  0.020  1.090
 2P0  CAK  HAKA  single  0.970  0.020  1.090
 2P0  OAM  PAT   single  1.668  0.020  1.668
 2P0  PAT  OAN   single  1.606  0.020  1.606
 2P0  OAN  PAS   single  1.743  0.020  1.743

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
 2P0  O     C    CA   119.00  3.000
 2P0  CA    C    OXT  113.98  3.000
 2P0  O     C    OXT  128.09  3.000
 2P0  CAP   N    CD   120.91  3.000
 2P0  CD    N    CA   112.78  3.000
 2P0  CAP   N    CA   125.88  3.000
 2P0  HA    CA   CB   109.00  3.000
 2P0  HA    CA   N    110.00  3.000
 2P0  CB    CA   N    103.00  1.100
 2P0  HA    CA   C    109.00  3.000
 2P0  CB    CA   C    110.10  1.900
 2P0  N     CA   C    112.10  2.500
 2P0  HBA   CB   HB   107.41  3.000
 2P0  HBA   CB   CG   113.76  3.000
 2P0  HB    CB   CG   109.27  3.000
 2P0  HBA   CB   CA   111.75  3.000
 2P0  HB    CB   CA   110.15  3.000
 2P0  CG    CB   CA   104.49  3.000
 2P0  HDA   CD   HD   107.63  3.000
 2P0  HDA   CD   CG   111.30  3.000
 2P0  HD    CD   CG   113.03  3.000
 2P0  HDA   CD   N    111.34  3.000
 2P0  HD    CD   N    110.73  3.000
 2P0  CG    CD   N    103.20  1.500
 2P0  HGA   CG   HG   107.95  3.000
 2P0  HGA   CG   CD   110.08  3.000
 2P0  HG    CG   CD   112.45  3.000
 2P0  HGA   CG   CB   110.79  3.000
 2P0  HG    CG   CB   112.85  3.000
 2P0  CD    CG   CB   102.68  3.000
 2P0  HAKA  CAK  HAK  106.23  3.000
 2P0  HAKA  CAK  CAP  108.04  3.000
 2P0  HAK   CAK  CAP  108.59  3.000
 2P0  HAKA  CAK  OAM  112.47  3.000
 2P0  HAK   CAK  OAM  111.30  3.000
 2P0  CAP   CAK  OAM  110.05  3.000
 2P0  PAT   OAM  CAK  117.85  3.000
 2P0  PAT   OAN  PAS  127.42  3.000
 2P0  CAK   CAP  OAB  122.07  3.000
 2P0  CAK   CAP  N    115.65  3.000
 2P0  OAB   CAP  N    122.28  3.000
 2P0  OAN   PAS  OAG  104.63  3.000
 2P0  OAN   PAS  OAF  101.20  3.000
 2P0  OAG   PAS  OAF  115.45  3.000
 2P0  OAN   PAS  OAC  103.11  3.000
 2P0  OAG   PAS  OAC  114.95  3.000
 2P0  OAF   PAS  OAC  114.91  3.000
 2P0  OAN   PAT  OAM   98.48  3.000
 2P0  OAN   PAT  OAH  111.77  3.000
 2P0  OAM   PAT  OAH  107.27  3.000
 2P0  OAN   PAT  OAD  112.17  3.000
 2P0  OAM   PAT  OAD  103.93  3.000
 2P0  OAH   PAT  OAD  120.35  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
 2P0  CONST_01  OAB  CAP  N    CA    180.00   0.0  0
 2P0  CONST_02  CAK  CAP  N    CA      0.00   0.0  0
 2P0  CONST_03  OAB  CAP  N    CD      0.00   0.0  0
 2P0  CONST_04  CAK  CAP  N    CD    180.00   0.0  0
 2P0  Var_01    CB   CG   CD   N     -35.00  30.0  1
 2P0  Var_02    CG   CD   N    CA     21.43  30.0  1
 2P0  Var_03    OAM  CAK  CAP  N    -174.13  30.0  3
 2P0  Var_04    OAN  PAT  OAM  CAK   -74.54  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
 2P0  chir_01  CA  C  N  CB  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
 2P0  plan-1  N    0.020
 2P0  plan-1  CA   0.020
 2P0  plan-1  CD   0.020
 2P0  plan-1  OAB  0.020
 2P0  plan-1  CAK  0.020
 2P0  plan-1  CAP  0.020
 2P0  plan-2  C    0.020
 2P0  plan-2  OXT  0.020
 2P0  plan-2  CA   0.020
 2P0  plan-2  O    0.020

