# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 06:17:07 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-oxo-5-(phosphonooxy)-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(=O)O[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
 RGP  RGP  "GAMMA-GLUTAMYL PHOSPHATE"  L-peptide  21  14  .  2022-09-22  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_RGP
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
 RGP  PA   P  P      0   1.224   3.4567  -0.0777   0.0693
 RGP  OA1  O  O      0  -0.875   3.4660  -1.5130   0.5493
 RGP  OA2  O  OP    -1  -0.875   3.6040   0.1403  -1.4212
 RGP  OA3  O  OP    -1  -0.875   4.1783   0.9181   0.9554
 RGP  OE2  O  O2     0  -0.617   1.7769   0.4630   0.4132
 RGP  CD   C  C      0   0.572   0.7145  -0.0847  -0.1035
 RGP  OE1  O  O      0  -0.498   0.7095  -1.0050  -0.8961
 RGP  CG   C  CH2    0  -0.582  -0.5628   0.5647   0.3960
 RGP  CB   C  CH2    0  -0.422  -1.8416  -0.0829  -0.1086
 RGP  CA   C  CH1    0  -0.206  -3.1113   0.5707   0.4627
 RGP  C    C  C      0   0.405  -4.3270  -0.2928   0.0630
 RGP  O    O  O     -1  -0.609  -5.0266   0.1078  -0.8883
 RGP  OXT  O  OC     0  -0.622  -4.4843  -1.3523   0.7037
 RGP  N    N  NH2    0  -0.798  -3.3161   1.9554   0.0683
 RGP  HG1  H  HCH2   0   0.243  -0.5215   1.6245   0.1213
 RGP  HG2  H  HCH2   0   0.250  -0.5467   0.5515   1.4911
 RGP  HB1  H  HCH2   0   0.217  -1.8392  -1.1408   0.1631
 RGP  HB2  H  HCH2   0   0.212  -1.8808  -0.0409  -1.2019
 RGP  HA   H  HCH1   0   0.199  -3.0286   0.5422   1.5561
 RGP  HN1  H  HNH2   0   0.332  -2.4665   2.4908   0.1961
 RGP  HN2  H  HNH2   0   0.326  -3.5317   1.9806  -0.9205

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
 RGP  PA   OA1  deloc   1.513  0.020  1.513
 RGP  PA   OA2  deloc   1.514  0.020  1.514
 RGP  PA   OA3  deloc   1.516  0.020  1.516
 RGP  PA   OE2  single  1.798  0.020  1.798
 RGP  OE2  CD   single  1.302  0.020  1.302
 RGP  CD   OE1  double  1.215  0.020  1.215
 RGP  CD   CG   single  1.517  0.020  1.517
 RGP  CG   CB   single  1.520  0.020  1.520
 RGP  CG   HG1  single  0.970  0.020  1.090
 RGP  CG   HG2  single  0.970  0.020  1.090
 RGP  CB   CA   single  1.530  0.020  1.530
 RGP  CB   HB1  single  0.970  0.020  1.090
 RGP  CB   HB2  single  0.970  0.020  1.090
 RGP  CA   C    single  1.525  0.021  1.525
 RGP  CA   N    single  1.458  0.019  1.458
 RGP  CA   HA   single  0.970  0.020  0.970
 RGP  C    O    deloc   1.231  0.020  1.231
 RGP  C    OXT  deloc   1.248  0.020  1.248
 RGP  N    HN1  single  0.890  0.020  1.040
 RGP  N    HN2  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
 RGP  OE2  PA   OA3   97.78  3.000
 RGP  OE2  PA   OA2  103.65  3.000
 RGP  OA3  PA   OA2  115.77  3.000
 RGP  OE2  PA   OA1  103.31  3.000
 RGP  OA3  PA   OA1  115.77  3.000
 RGP  OA2  PA   OA1  116.64  3.000
 RGP  CD   OE2  PA   124.05  3.000
 RGP  CG   CD   OE1  122.39  3.000
 RGP  CG   CD   OE2  112.09  3.000
 RGP  OE1  CD   OE2  125.52  3.000
 RGP  HG2  CG   HG1  105.18  3.000
 RGP  HG2  CG   CB   109.83  3.000
 RGP  HG1  CG   CB   111.15  3.000
 RGP  HG2  CG   CD   108.15  3.000
 RGP  HG1  CG   CD   107.44  3.000
 RGP  CB   CG   CD   114.62  3.000
 RGP  HB2  CB   HB1  106.60  3.000
 RGP  HB2  CB   CA   108.97  3.000
 RGP  HB1  CB   CA   108.72  3.000
 RGP  HB2  CB   CG   110.21  3.000
 RGP  HB1  CB   CG   109.16  3.000
 RGP  CA   CB   CG   112.97  3.000
 RGP  HA   CA   N    110.00  3.000
 RGP  HA   CA   C    109.00  3.000
 RGP  N    CA   C    111.00  2.800
 RGP  HA   CA   CB   109.00  3.000
 RGP  N    CA   CB   110.50  1.700
 RGP  C    CA   CB   110.10  1.900
 RGP  OXT  C    O    126.42  3.000
 RGP  OXT  C    CA   116.18  3.000
 RGP  O    C    CA   120.80  1.700
 RGP  HN2  N    HN1  106.79  3.000
 RGP  HN2  N    CA   108.58  3.000
 RGP  HN1  N    CA   110.56  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
 RGP  Var_01  OE1  CD   OE2  PA     -1.46  30.0  3
 RGP  Var_02  CG   CD   OE2  PA    178.70  30.0  3
 RGP  Var_03  CD   OE2  PA   OA1   -60.51  30.0  3
 RGP  Var_04  CD   OE2  PA   OA2    61.60  30.0  3
 RGP  Var_05  CD   OE2  PA   OA3  -179.40  30.0  3
 RGP  Var_06  CB   CG   CD   OE2  -176.62  30.0  3
 RGP  Var_07  CA   CB   CG   CD    177.81  30.0  3
 RGP  Var_08  CB   CG   CD   OE1     3.54  30.0  3
 RGP  Var_09  HG1  CG   CD   OE2    59.34  30.0  3
 RGP  Var_10  HG2  CG   CD   OE2   -53.73  30.0  3
 RGP  Var_11  HB1  CB   CG   CD     56.72  30.0  3
 RGP  Var_12  HB2  CB   CG   CD    -60.04  30.0  3
 RGP  Var_13  HG1  CG   CD   OE1  -120.51  30.0  3
 RGP  Var_14  HG2  CG   CD   OE1   126.43  30.0  3
 RGP  Var_15  HG1  CG   CB   CA    -60.14  30.0  1
 RGP  Var_16  HG2  CG   CB   CA     55.83  30.0  1

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
 RGP  chir_01  CA  CB  C  N  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
 RGP  plan-1  CA   0.020
 RGP  plan-1  C    0.020
 RGP  plan-1  O    0.020
 RGP  plan-1  OXT  0.020
 RGP  plan-2  OE2  0.020
 RGP  plan-2  CD   0.020
 RGP  plan-2  OE1  0.020
 RGP  plan-2  CG   0.020

