# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 18:16:29 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(=O)CC(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
 PTA  PTA  '[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]acetic acid'  peptide  29  13  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PTA
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
 PTA  N     N  NH2   0  -0.788   1.1083   1.6536  -1.0147
 PTA  CA    C  CH1   0  -0.357   0.9906   0.3176  -0.4654
 PTA  CB    C  CH2   0  -0.419   2.1535   0.0003   0.4739
 PTA  CG    C  CH1   0  -0.220   3.5337   0.0958  -0.1804
 PTA  CD1   C  CH3   0  -0.653   4.6122  -0.1732   0.8645
 PTA  CD2   C  CH3   0  -0.666   3.6752  -0.8627  -1.3578
 PTA  P     P  P     0   1.235  -0.6002   0.1014   0.4242
 PTA  O1P   O  O     0  -0.706  -0.7609   0.9510   1.6359
 PTA  O2P   O  OH1   0  -0.753  -0.7466  -1.4594   0.8242
 PTA  CM    C  CH2   0  -0.834  -1.8947   0.3852  -0.8435
 PTA  C     C  C     0   0.533  -3.2386  -0.0103  -0.3068
 PTA  O     O  O     0  -0.432  -3.9029   0.6767   0.4262
 PTA  OXT   O  OH1   0  -0.580  -3.5973  -1.2216  -0.7095
 PTA  H     H  HNH2  0   0.367   0.4297   1.8316  -1.7425
 PTA  H2    H  HNH2  0   0.355   0.9897   2.3594  -0.2984
 PTA  HA    H  HCH1  0   0.282   0.9879  -0.3936  -1.2977
 PTA  HB2   H  HCH2  0   0.236   2.1140   0.6836   1.3289
 PTA  HB3   H  HCH2  0   0.231   2.0250  -1.0089   0.8795
 PTA  HG    H  HCH1  0   0.222   3.6648   1.1162  -0.5505
 PTA  HD11  H  HCH3  0   0.213   4.5227  -1.1834   1.2721
 PTA  HD12  H  HCH3  0   0.226   5.6103  -0.0808   0.4324
 PTA  HD13  H  HCH3  0   0.224   4.5468   0.5277   1.6988
 PTA  HD21  H  HCH3  0   0.229   2.9988  -0.6133  -2.1764
 PTA  HD22  H  HCH3  0   0.229   4.6894  -0.8380  -1.7602
 PTA  HD23  H  HCH3  0   0.214   3.4643  -1.8911  -1.0524
 PTA  HOP2  H  HOH1  0   0.490  -0.6469  -2.0925   0.1014
 PTA  HM1   H  HCH2  0   0.323  -1.8990   1.4503  -1.0782
 PTA  HM2   H  HCH2  0   0.315  -1.6377  -0.1689  -1.7481
 PTA  HXT   H  HOH1  0   0.485  -4.4520  -1.4629  -0.3207

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
 PTA  N    CA    single  1.458  0.019  1.458
 PTA  N    H     single  0.860  0.020  0.860
 PTA  N    H2    single  0.890  0.020  1.040
 PTA  CA   CB    single  1.521  0.033  1.521
 PTA  CA   P     single  1.835  0.020  1.835
 PTA  CA   HA    single  0.970  0.020  0.970
 PTA  CB   CG    single  1.530  0.020  1.530
 PTA  CB   HB2   single  0.970  0.020  1.090
 PTA  CB   HB3   single  0.970  0.020  1.090
 PTA  CG   CD1   single  1.526  0.020  1.526
 PTA  CG   CD2   single  1.525  0.020  1.525
 PTA  CG   HG    single  0.970  0.020  1.090
 PTA  CD1  HD11  single  0.970  0.020  1.090
 PTA  CD1  HD12  single  0.970  0.020  1.090
 PTA  CD1  HD13  single  0.970  0.020  1.090
 PTA  CD2  HD21  single  0.970  0.020  1.090
 PTA  CD2  HD22  single  0.970  0.020  1.090
 PTA  CD2  HD23  single  0.970  0.020  1.090
 PTA  P    O1P   double  1.489  0.020  1.489
 PTA  P    O2P   single  1.618  0.020  1.618
 PTA  P    CM    single  1.834  0.020  1.834
 PTA  O2P  HOP2  single  0.850  0.020  0.980
 PTA  CM   C     single  1.500  0.020  1.500
 PTA  CM   HM1   single  0.970  0.020  1.090
 PTA  CM   HM2   single  0.970  0.020  1.090
 PTA  C    O     double  1.231  0.020  1.231
 PTA  C    OXT   single  1.326  0.020  1.326
 PTA  OXT  HXT   single  0.850  0.020  0.980

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
 PTA  H2    N    H     107.93  3.000
 PTA  H2    N    CA    111.40  3.000
 PTA  H     N    CA    114.00  3.000
 PTA  HA    CA   P     106.85  3.000
 PTA  HA    CA   CB    109.00  3.000
 PTA  P     CA   CB    109.71  3.000
 PTA  HA    CA   N     110.00  3.000
 PTA  P     CA   N     111.26  3.000
 PTA  CB    CA   N     110.40  1.500
 PTA  HB3   CB   HB2   106.35  3.000
 PTA  HB3   CB   CG    108.76  3.000
 PTA  HB2   CB   CG    109.11  3.000
 PTA  HB3   CB   CA    109.25  3.000
 PTA  HB2   CB   CA    108.84  3.000
 PTA  CG    CB   CA    114.24  3.000
 PTA  HG    CG   CD2   108.31  3.000
 PTA  HG    CG   CD1   108.16  3.000
 PTA  CD2   CG   CD1   110.64  3.000
 PTA  HG    CG   CB    108.12  3.000
 PTA  CD2   CG   CB    112.00  3.000
 PTA  CD1   CG   CB    109.50  3.000
 PTA  HD13  CD1  HD12  107.64  3.000
 PTA  HD13  CD1  HD11  107.67  3.000
 PTA  HD12  CD1  HD11  107.50  3.000
 PTA  HD13  CD1  CG    111.59  3.000
 PTA  HD12  CD1  CG    111.12  3.000
 PTA  HD11  CD1  CG    111.13  3.000
 PTA  HD23  CD2  HD22  107.67  3.000
 PTA  HD23  CD2  HD21  107.76  3.000
 PTA  HD22  CD2  HD21  107.12  3.000
 PTA  HD23  CD2  CG    110.96  3.000
 PTA  HD22  CD2  CG    110.90  3.000
 PTA  HD21  CD2  CG    112.23  3.000
 PTA  CM    P    O2P   104.85  3.000
 PTA  CM    P    O1P   113.47  3.000
 PTA  O2P   P    O1P   109.85  3.000
 PTA  CM    P    CA    104.98  3.000
 PTA  O2P   P    CA    108.17  3.000
 PTA  O1P   P    CA    114.89  3.000
 PTA  HOP2  O2P  P     115.97  3.000
 PTA  HM2   CM   HM1   108.56  3.000
 PTA  HM2   CM   C     111.94  3.000
 PTA  HM1   CM   C     109.33  3.000
 PTA  HM2   CM   P     109.16  3.000
 PTA  HM1   CM   P     107.62  3.000
 PTA  C     CM   P     110.13  3.000
 PTA  OXT   C    O     123.83  3.000
 PTA  OXT   C    CM    112.00  3.000
 PTA  O     C    CM    124.16  3.000
 PTA  HXT   OXT  C     110.12  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
 PTA  CONST_01  HXT   OXT  C   CM  180.00   0.0  0
 PTA  Var_01    CD1   CG   CB  CA  177.24  30.0  3
 PTA  Var_02    C     CM   P   CA  169.54  30.0  3
 PTA  Var_03    O     C    CM  P    79.90  30.0  3
 PTA  Var_04    HD11  CD1  CG  CB   62.11  30.0  3
 PTA  Var_05    HD21  CD2  CG  CB   64.77  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
 PTA  chir_01  CA  N    CB   P   negativ
 PTA  chir_02  P   O1P  O2P  CM  both

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
 PTA  plan-1  CM   0.020
 PTA  plan-1  C    0.020
 PTA  plan-1  O    0.020
 PTA  plan-1  OXT  0.020
 PTA  plan-1  HXT  0.020

