# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 15:41:35 2020
#   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  5-oxo-5-(phosphonooxy)-D-norvaline  L-peptide  24  14  .  2022-09-22  2022-11-17
;
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   1.458   3.3009  -0.1430   0.0305
 RGP  OA1  O  O     0  -0.683   3.6155  -1.5103   0.4655
 RGP  OA2  O  OH1   0  -0.729   3.4702   0.0256  -1.5385
 RGP  OA3  O  OH1   0  -0.723   4.0475   1.0652   0.7431
 RGP  OE2  O  O2    0  -0.585   1.7985   0.3990   0.3940
 RGP  CD   C  C     0   0.617   0.6809  -0.2108  -0.0781
 RGP  OE1  O  O     0  -0.403   0.7338  -1.1658  -0.7962
 RGP  CG   C  CH2   0  -0.591  -0.5546   0.4737   0.4181
 RGP  CB   C  CH2   0  -0.446  -1.8343  -0.1597  -0.0995
 RGP  CA   C  CH1   0  -0.219  -3.0789   0.5630   0.4527
 RGP  C    C  C     0   0.548  -4.3155  -0.1880  -0.0018
 RGP  O    O  O     0  -0.436  -5.0809   0.1991  -0.8470
 RGP  OXT  O  OH1   0  -0.594  -4.4423  -1.3532   0.6221
 RGP  N    N  NH2   0  -0.784  -3.2081   1.9546   0.0841
 RGP  HA2  H  HOH1  0   0.503   3.4100   0.9264  -1.8857
 RGP  HA3  H  HOH1  0   0.510   5.0020   0.9393   0.8397
 RGP  HG1  H  HCH2  0   0.288  -0.4847   1.5282   0.1353
 RGP  HG2  H  HCH2  0   0.296  -0.5295   0.4580   1.5128
 RGP  HB1  H  HCH2  0   0.256  -1.8603  -1.2127   0.1847
 RGP  HB2  H  HCH2  0   0.250  -1.8569  -0.1224  -1.1921
 RGP  HA   H  HCH1  0   0.276  -3.0452   0.5071   1.5457
 RGP  HO   H  HOH1  0   0.482  -5.2083  -1.8344   0.2750
 RGP  HN1  H  HNH2  0   0.361  -2.4829   2.4994   0.5304
 RGP  HN2  H  HNH2  0   0.347  -3.0834   2.0713  -0.9143

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  double  1.469  0.020  1.469
 RGP  PA   OA2  single  1.587  0.020  1.587
 RGP  PA   OA3  single  1.589  0.020  1.589
 RGP  PA   OE2  single  1.638  0.020  1.638
 RGP  OA2  HA2  single  0.850  0.020  0.980
 RGP  OA3  HA3  single  0.850  0.020  0.980
 RGP  OE2  CD   single  1.358  0.020  1.358
 RGP  CD   OE1  double  1.196  0.020  1.196
 RGP  CD   CG   single  1.497  0.020  1.497
 RGP  CG   CB   single  1.519  0.020  1.519
 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    double  1.231  0.020  1.231
 RGP  C    OXT  single  1.328  0.020  1.328
 RGP  OXT  HO   single  0.850  0.020  0.980
 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   94.58  3.000
 RGP  OE2  PA   OA2  106.38  3.000
 RGP  OA3  PA   OA2  108.21  3.000
 RGP  OE2  PA   OA1  116.02  3.000
 RGP  OA3  PA   OA1  118.32  3.000
 RGP  OA2  PA   OA1  111.64  3.000
 RGP  HA2  OA2  PA   116.56  3.000
 RGP  HA3  OA3  PA   114.16  3.000
 RGP  CD   OE2  PA   121.95  3.000
 RGP  CG   CD   OE1  126.91  3.000
 RGP  CG   CD   OE2  111.02  3.000
 RGP  OE1  CD   OE2  122.07  3.000
 RGP  HG2  CG   HG1  105.71  3.000
 RGP  HG2  CG   CB   110.73  3.000
 RGP  HG1  CG   CB   111.57  3.000
 RGP  HG2  CG   CD   107.81  3.000
 RGP  HG1  CG   CD   107.60  3.000
 RGP  CB   CG   CD   113.06  3.000
 RGP  HB2  CB   HB1  107.02  3.000
 RGP  HB2  CB   CA   108.99  3.000
 RGP  HB1  CB   CA   109.87  3.000
 RGP  HB2  CB   CG   110.10  3.000
 RGP  HB1  CB   CG   109.50  3.000
 RGP  CA   CB   CG   111.26  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    123.45  3.000
 RGP  OXT  C    CA   111.82  3.000
 RGP  O    C    CA   120.80  1.700
 RGP  HO   OXT  C    110.06  3.000
 RGP  HN2  N    HN1  106.55  3.000
 RGP  HN2  N    CA   110.57  3.000
 RGP  HN1  N    CA   110.01  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  CONST_01  HO   OXT  C    CA   180.00   0.0  0
 RGP  Var_01    OE1  CD   OE2  PA    -0.88  30.0  3
 RGP  Var_02    CB   CG   CD   OE2  179.16  30.0  3
 RGP  Var_03    CA   CB   CG   CD   179.15  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
 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-1  HO   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

