# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 00:09:48 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (R)-[(1R)-1-amino-3-methylbutyl](2-ethoxy-2-oxoethyl)phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C[P](O)(=O)[C@@H](N)CC(C)C
#
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
 PT0  PT0  '(R)-[(1R)-1-amino-3-methylbutyl](2-ethoxy-2-oxoethyl)phosphinic acid'  peptide  35  15  .  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_PT0
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
 PT0  N     N  NH2   0  -0.791   1.7641   2.2751  -0.9914
 PT0  O     O  O     0  -0.442  -2.8921   1.2066   1.3366
 PT0  P     P  P     0   1.221   0.2689   0.5710   0.4880
 PT0  C5    C  C     0   0.584  -2.4429   0.8301   0.2840
 PT0  C6    C  CH2   0  -0.182  -4.1656  -0.7746   0.0298
 PT0  O6    O  O2    0  -0.444  -2.9810  -0.1218  -0.4592
 PT0  C7    C  CH3   0  -0.689  -4.5486  -1.8369  -0.9707
 PT0  CA    C  CH1   0  -0.347   1.6759   0.8623  -0.6599
 PT0  CB    C  CH2   0  -0.406   3.0102   0.4094  -0.0656
 PT0  CG    C  CH1   0  -0.261   3.1727  -1.0702   0.2851
 PT0  CP    C  CH2   0  -0.846  -1.1755   1.3575  -0.3271
 PT0  O1P   O  O     0  -0.706   0.5055   1.0474   1.8788
 PT0  O2P   O  OH1   0  -0.753  -0.1130  -1.0037   0.5069
 PT0  CD1   C  CH3   0  -0.654   2.9519  -1.9804  -0.9184
 PT0  CD2   C  CH3   0  -0.647   4.5659  -1.2948   0.8660
 PT0  HN    H  HNH2  0   0.370   0.9740   2.5955  -1.5345
 PT0  HNA   H  HNH2  0   0.357   1.8260   2.8513  -0.1610
 PT0  H6    H  HCH2  0   0.239  -3.9630  -1.2125   1.0090
 PT0  H6A   H  HCH2  0   0.239  -4.9644  -0.0400   0.1471
 PT0  H7    H  HCH3  0   0.238  -4.7572  -1.4091  -1.9511
 PT0  H7A   H  HCH3  0   0.237  -3.7674  -2.5895  -1.0774
 PT0  H7B   H  HCH3  0   0.241  -5.4520  -2.3400  -0.6272
 PT0  HA    H  HCH1  0   0.282   1.4690   0.3180  -1.5864
 PT0  HB    H  HCH2  0   0.238   3.7783   0.6848  -0.7959
 PT0  HBA   H  HCH2  0   0.235   3.2117   1.0094   0.8277
 PT0  HG    H  HCH1  0   0.228   2.4490  -1.3380   1.0609
 PT0  HP    H  HCH2  0   0.323  -1.1132   2.4343  -0.1682
 PT0  HPA   H  HCH2  0   0.314  -1.1380   1.1600  -1.4000
 PT0  HO2P  H  HOH1  0   0.487  -0.2690  -1.4113  -0.3546
 PT0  HD1   H  HCH3  0   0.217   1.9437  -1.9050  -1.3276
 PT0  HD1A  H  HCH3  0   0.218   3.6509  -1.7357  -1.7219
 PT0  HD1B  H  HCH3  0   0.232   3.1122  -3.0255  -0.6485
 PT0  HD2   H  HCH3  0   0.226   4.7466  -0.6556   1.7320
 PT0  HD2A  H  HCH3  0   0.228   4.6973  -2.3308   1.1815
 PT0  HD2B  H  HCH3  0   0.215   5.3369  -1.0739   0.1236

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
 PT0  CA   N     single  1.458  0.019  1.458
 PT0  N    HN    single  0.890  0.020  1.040
 PT0  N    HNA   single  0.890  0.020  1.040
 PT0  C5   O     double  1.205  0.020  1.205
 PT0  O1P  P     double  1.489  0.020  1.489
 PT0  CA   P     single  1.839  0.020  1.839
 PT0  O2P  P     single  1.621  0.020  1.621
 PT0  P    CP    single  1.836  0.020  1.836
 PT0  CP   C5    single  1.503  0.020  1.503
 PT0  C5   O6    single  1.322  0.020  1.322
 PT0  O6   C6    single  1.438  0.020  1.438
 PT0  C7   C6    single  1.509  0.020  1.509
 PT0  C6   H6    single  0.970  0.020  1.090
 PT0  C6   H6A   single  0.970  0.020  1.090
 PT0  C7   H7    single  0.970  0.020  1.090
 PT0  C7   H7A   single  0.970  0.020  1.090
 PT0  C7   H7B   single  0.970  0.020  1.090
 PT0  CB   CA    single  1.521  0.033  1.521
 PT0  CA   HA    single  0.970  0.020  0.970
 PT0  CG   CB    single  1.529  0.020  1.529
 PT0  CB   HB    single  0.970  0.020  1.090
 PT0  CB   HBA   single  0.970  0.020  1.090
 PT0  CD1  CG    single  1.525  0.020  1.525
 PT0  CG   CD2   single  1.526  0.020  1.526
 PT0  CG   HG    single  0.970  0.020  1.090
 PT0  CP   HP    single  0.970  0.020  1.090
 PT0  CP   HPA   single  0.970  0.020  1.090
 PT0  O2P  HO2P  single  0.850  0.020  0.980
 PT0  CD1  HD1   single  0.970  0.020  1.090
 PT0  CD1  HD1A  single  0.970  0.020  1.090
 PT0  CD1  HD1B  single  0.970  0.020  1.090
 PT0  CD2  HD2   single  0.970  0.020  1.090
 PT0  CD2  HD2A  single  0.970  0.020  1.090
 PT0  CD2  HD2B  single  0.970  0.020  1.090

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
 PT0  HNA   N    HN    107.94  3.000
 PT0  HNA   N    CA    111.69  3.000
 PT0  HN    N    CA    112.52  3.000
 PT0  O2P   P    O1P   109.72  3.000
 PT0  O2P   P    CP    103.65  3.000
 PT0  O1P   P    CP    113.75  3.000
 PT0  CP    P    CA    104.89  3.000
 PT0  O2P   P    CA    109.97  3.000
 PT0  O1P   P    CA    114.26  3.000
 PT0  CP    C5   O6    111.55  3.000
 PT0  O6    C5   O     124.36  3.000
 PT0  CP    C5   O     124.07  3.000
 PT0  H6A   C6   H6    108.02  3.000
 PT0  H6A   C6   C7    111.06  3.000
 PT0  H6    C6   C7    111.07  3.000
 PT0  H6A   C6   O6    109.50  3.000
 PT0  H6    C6   O6    109.52  3.000
 PT0  C7    C6   O6    107.65  3.000
 PT0  C6    O6   C5    118.09  3.000
 PT0  H7B   C7   H7A   107.84  3.000
 PT0  H7B   C7   H7    107.83  3.000
 PT0  H7A   C7   H7    108.67  3.000
 PT0  H7B   C7   C6    109.06  3.000
 PT0  H7A   C7   C6    111.66  3.000
 PT0  H7    C7   C6    111.64  3.000
 PT0  HA    CA   CB    109.00  3.000
 PT0  HA    CA   P     107.76  3.000
 PT0  CB    CA   P     112.21  3.000
 PT0  HA    CA   N     110.00  3.000
 PT0  CB    CA   N     110.40  1.500
 PT0  P     CA   N     110.04  3.000
 PT0  HBA   CB   HB    106.10  3.000
 PT0  HBA   CB   CG    108.88  3.000
 PT0  HB    CB   CG    108.77  3.000
 PT0  HBA   CB   CA    108.38  3.000
 PT0  HB    CB   CA    106.16  3.000
 PT0  CG    CB   CA    117.93  3.000
 PT0  HG    CG   CD2   107.33  3.000
 PT0  HG    CG   CD1   108.53  3.000
 PT0  CD2   CG   CD1   110.17  3.000
 PT0  HG    CG   CB    109.21  3.000
 PT0  CD2   CG   CB    109.07  3.000
 PT0  CD1   CG   CB    112.40  3.000
 PT0  HPA   CP   HP    108.66  3.000
 PT0  HPA   CP   C5    111.42  3.000
 PT0  HP    CP   C5    109.61  3.000
 PT0  HPA   CP   P     109.39  3.000
 PT0  HP    CP   P     108.27  3.000
 PT0  C5    CP   P     109.43  3.000
 PT0  HO2P  O2P  P     115.97  3.000
 PT0  HD1B  CD1  HD1A  107.61  3.000
 PT0  HD1B  CD1  HD1   107.14  3.000
 PT0  HD1A  CD1  HD1   107.45  3.000
 PT0  HD1B  CD1  CG    110.80  3.000
 PT0  HD1A  CD1  CG    110.73  3.000
 PT0  HD1   CD1  CG    112.87  3.000
 PT0  HD2B  CD2  HD2A  107.66  3.000
 PT0  HD2B  CD2  HD2   107.68  3.000
 PT0  HD2A  CD2  HD2   107.86  3.000
 PT0  HD2B  CD2  CG    110.84  3.000
 PT0  HD2A  CD2  CG    111.09  3.000
 PT0  HD2   CD2  CG    111.53  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
 PT0  Var_01  P    CP   C5  O     79.15  30.0  1
 PT0  Var_02  O1P  P    CP  C5   -71.94  30.0  1
 PT0  Var_03  C7   C6   O6  C5  -178.24  30.0  3
 PT0  Var_04  CD1  CG   CB  CA    57.85  30.0  1
 PT0  Var_05  H7   C7   C6  O6   -60.35  30.0  3
 PT0  Var_06  HD1  CD1  CG  CB   -62.05  30.0  3
 PT0  Var_07  HD2  CD2  CG  CB    56.37  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
 PT0  chir_02  CA  N   P    CB  positiv
 PT0  chir_03  P   CA  O2P  CP  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
 PT0  plan-1  O   0.020
 PT0  plan-1  C5  0.020
 PT0  plan-1  O6  0.020
 PT0  plan-1  CP  0.020

