# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 07:31:55 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2S)-2-{[(S)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(=O)O[C@@H](Cc1ccccc1)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
 P0L  P0L  '(2S)-2-{[(S)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoic acid'  peptide  43  21  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_P0L
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
 P0L  C    C  C     0   0.540  -1.4577   2.8101   0.0031
 P0L  N    N  NH2   0  -0.776   1.2651  -1.2300   1.7807
 P0L  O    O  O     0  -0.430  -0.5117   3.3943   0.4627
 P0L  P1   P  P     0   1.386   0.8397   0.1930  -0.4172
 P0L  C2   C  CR16  0  -0.270  -2.9628  -3.5298  -0.2422
 P0L  O2   O  O     0  -0.699   0.4999  -0.8207  -1.4425
 P0L  O3   O  OH1   0  -0.748   1.4371   1.5016  -1.1450
 P0L  C3   C  CH1   0  -0.368   2.0024  -0.3607   0.8746
 P0L  C4   C  CH1   0  -0.070  -1.5398   1.2982  -0.1432
 P0L  O4   O  O2    0  -0.583  -0.3932   0.7404   0.4632
 P0L  C5   C  CH2   0  -0.434   3.2471  -1.0290   0.2737
 P0L  C6   C  CH2   0  -0.548  -2.7811   0.6976   0.5227
 P0L  C7   C  CR16  0  -0.246  -2.2427  -3.0491   0.8438
 P0L  C8   C  CH1   0  -0.254   4.1892  -0.1809  -0.5834
 P0L  C9   C  CR6   0   0.136  -2.8607  -0.7838   0.2791
 P0L  C10  C  CR16  0  -0.276  -2.1916  -1.6863   1.1014
 P0L  C11  C  CH3   0  -0.656   4.6940   1.0504   0.1624
 P0L  C12  C  CH3   0  -0.648   5.3618  -1.0445  -1.0396
 P0L  C13  C  CR16  0  -0.306  -3.5808  -1.2751  -0.8066
 P0L  C14  C  CR16  0  -0.242  -3.6329  -2.6376  -1.0685
 P0L  H1   H  HCR6  0   0.252  -3.0027  -4.5927  -0.4434
 P0L  H3   H  HOH1  0   0.485   1.5383   2.2807  -0.5816
 P0L  H4   H  HCH1  0   0.279   2.2983   0.5281   1.4400
 P0L  H5   H  HCH1  0   0.290  -1.5817   1.0722  -1.2171
 P0L  H6   H  HCH2  0   0.236   3.8186  -1.4182   1.1244
 P0L  H7   H  HCH2  0   0.235   2.9256  -1.9048  -0.2992
 P0L  H8   H  HCH2  0   0.272  -2.7511   0.9157   1.5931
 P0L  H9   H  HCH2  0   0.276  -3.6676   1.1865   0.1183
 P0L  H10  H  HCR6  0   0.250  -1.7169  -3.7376   1.4934
 P0L  H11  H  HCH1  0   0.227   3.6601   0.1514  -1.4814
 P0L  H12  H  HCR6  0   0.242  -1.6146  -1.3230   1.9419
 P0L  H13  H  HCH3  0   0.231   5.3984   1.6145  -0.4508
 P0L  H14  H  HCH3  0   0.220   3.8895   1.7335   0.4387
 P0L  H15  H  HCH3  0   0.217   5.2100   0.7622   1.0818
 P0L  H16  H  HCH3  0   0.226   5.0218  -1.9128  -1.6071
 P0L  H17  H  HCH3  0   0.228   6.0453  -0.4792  -1.6753
 P0L  H18  H  HCH3  0   0.214   5.9325  -1.4121  -0.1830
 P0L  H19  H  HCR6  0   0.246  -4.1113  -0.5853  -1.4534
 P0L  H20  H  HCR6  0   0.252  -4.1990  -3.0020  -1.9163
 P0L  OXT  O  OH1   0  -0.585  -2.5479   3.3969  -0.4577
 P0L  H2   H  HNH2  0   0.360   1.8616  -1.4587   2.5667
 P0L  HXT  H  HOH1  0   0.492  -2.4789   4.3601  -0.3696
 P0L  H    H  HNH2  0   0.348   1.0577  -2.1101   1.3234

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
 P0L  N    C3   single    1.456  0.020  1.456
 P0L  N    H    single    0.860  0.020  0.860
 P0L  O    C    double    1.231  0.020  1.231
 P0L  P1   O4   single    1.611  0.020  1.611
 P0L  P1   O3   single    1.612  0.020  1.612
 P0L  C2   H1   single    0.930  0.020  1.080
 P0L  O2   P1   double    1.481  0.020  1.481
 P0L  O3   H3   single    0.850  0.020  0.980
 P0L  C3   P1   single    1.824  0.020  1.824
 P0L  C3   H4   single    0.970  0.020  1.090
 P0L  C4   C    single    1.521  0.020  1.521
 P0L  C4   C6   single    1.531  0.020  1.531
 P0L  C4   H5   single    0.970  0.020  1.090
 P0L  O4   C4   single    1.412  0.020  1.412
 P0L  C5   C3   single    1.535  0.020  1.535
 P0L  C5   H6   single    0.970  0.020  1.090
 P0L  C5   H7   single    0.970  0.020  1.090
 P0L  C6   C9   single    1.503  0.020  1.503
 P0L  C6   H8   single    0.970  0.020  1.090
 P0L  C6   H9   single    0.970  0.020  1.090
 P0L  C7   C2   aromatic  1.389  0.020  1.389
 P0L  C7   H10  single    0.930  0.020  1.080
 P0L  C8   C5   single    1.530  0.020  1.530
 P0L  C8   H11  single    0.970  0.020  1.090
 P0L  C9   C10  aromatic  1.392  0.020  1.392
 P0L  C9   C13  aromatic  1.392  0.020  1.392
 P0L  C10  C7   aromatic  1.388  0.020  1.388
 P0L  C10  H12  single    0.930  0.020  1.080
 P0L  C11  C8   single    1.525  0.020  1.525
 P0L  C11  H13  single    0.970  0.020  1.090
 P0L  C11  H14  single    0.970  0.020  1.090
 P0L  C11  H15  single    0.970  0.020  1.090
 P0L  C12  C8   single    1.526  0.020  1.526
 P0L  C12  H16  single    0.970  0.020  1.090
 P0L  C12  H17  single    0.970  0.020  1.090
 P0L  C12  H18  single    0.970  0.020  1.090
 P0L  C13  C14  aromatic  1.388  0.020  1.388
 P0L  C13  H19  single    0.930  0.020  1.080
 P0L  C14  C2   aromatic  1.388  0.020  1.388
 P0L  C14  H20  single    0.930  0.020  1.080
 P0L  C    OXT  single    1.321  0.020  1.321
 P0L  N    H2   single    0.890  0.020  1.040
 P0L  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
 P0L  OXT  C    C4   111.31  3.000
 P0L  OXT  C    O    124.51  3.000
 P0L  C4   C    O    124.18  3.000
 P0L  H2   N    H    105.94  3.000
 P0L  H2   N    C3   108.64  3.000
 P0L  H    N    C3   109.96  3.000
 P0L  O4   P1   C3   101.77  3.000
 P0L  C3   P1   O3   109.26  3.000
 P0L  O4   P1   O3   104.74  3.000
 P0L  C3   P1   O2   115.38  3.000
 P0L  O3   P1   O2   109.15  3.000
 P0L  O4   P1   O2   115.81  3.000
 P0L  H1   C2   C14  120.17  3.000
 P0L  C14  C2   C7   119.55  3.000
 P0L  H1   C2   C7   120.28  3.000
 P0L  H3   O3   P1   115.46  3.000
 P0L  H4   C3   C5   109.67  3.000
 P0L  C5   C3   P1   111.82  3.000
 P0L  H4   C3   P1   106.97  3.000
 P0L  C5   C3   N    113.21  3.000
 P0L  H4   C3   N    107.47  3.000
 P0L  P1   C3   N    107.41  3.000
 P0L  H5   C4   C6   108.28  3.000
 P0L  H5   C4   O4   111.69  3.000
 P0L  C6   C4   O4   108.46  3.000
 P0L  O4   C4   C    107.90  3.000
 P0L  H5   C4   C    107.49  3.000
 P0L  C6   C4   C    113.06  3.000
 P0L  C4   O4   P1   121.40  3.000
 P0L  H7   C5   H6   105.98  3.000
 P0L  H7   C5   C8   109.33  3.000
 P0L  H6   C5   C8   108.08  3.000
 P0L  C8   C5   C3   118.49  3.000
 P0L  H7   C5   C3   108.36  3.000
 P0L  H6   C5   C3   105.87  3.000
 P0L  H9   C6   H8   107.23  3.000
 P0L  H9   C6   C9   109.80  3.000
 P0L  H8   C6   C9   110.90  3.000
 P0L  H9   C6   C4   108.78  3.000
 P0L  H8   C6   C4   108.99  3.000
 P0L  C9   C6   C4   111.03  3.000
 P0L  H10  C7   C10  119.68  3.000
 P0L  C10  C7   C2   120.27  3.000
 P0L  H10  C7   C2   120.05  3.000
 P0L  H11  C8   C12  107.34  3.000
 P0L  C12  C8   C11  110.40  3.000
 P0L  H11  C8   C11  108.43  3.000
 P0L  C12  C8   C5   109.08  3.000
 P0L  C11  C8   C5   112.17  3.000
 P0L  H11  C8   C5   109.29  3.000
 P0L  C13  C9   C10  118.71  3.000
 P0L  C13  C9   C6   120.10  3.000
 P0L  C10  C9   C6   121.17  3.000
 P0L  H12  C10  C9   119.82  3.000
 P0L  H12  C10  C7   119.56  3.000
 P0L  C9   C10  C7   120.61  3.000
 P0L  H15  C11  H14  107.47  3.000
 P0L  H15  C11  H13  107.72  3.000
 P0L  H14  C11  H13  107.14  3.000
 P0L  H15  C11  C8   110.77  3.000
 P0L  H14  C11  C8   112.66  3.000
 P0L  H13  C11  C8   110.87  3.000
 P0L  H18  C12  H17  107.68  3.000
 P0L  H18  C12  H16  107.61  3.000
 P0L  H17  C12  H16  107.72  3.000
 P0L  H18  C12  C8   110.93  3.000
 P0L  H17  C12  C8   111.24  3.000
 P0L  H16  C12  C8   111.48  3.000
 P0L  H19  C13  C14  119.56  3.000
 P0L  H19  C13  C9   119.58  3.000
 P0L  C14  C13  C9   120.85  3.000
 P0L  H20  C14  C13  119.85  3.000
 P0L  H20  C14  C2   120.14  3.000
 P0L  C13  C14  C2   120.01  3.000
 P0L  HXT  OXT  C    110.53  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
 P0L  CONST_01  C9   C10  C7   C2     0.00   0.0  0
 P0L  CONST_02  C9   C13  C14  C2     0.00   0.0  0
 P0L  CONST_03  C13  C14  C2   C7     0.00   0.0  0
 P0L  CONST_04  C13  C9   C10  C7     0.00   0.0  0
 P0L  CONST_05  C14  C13  C9   C10    0.00   0.0  0
 P0L  CONST_06  C14  C2   C7   C10    0.00   0.0  0
 P0L  CONST_07  C7   C10  C9   C6   180.00   0.0  0
 P0L  CONST_08  C14  C13  C9   C6   180.00   0.0  0
 P0L  CONST_09  H12  C10  C7   C2   180.00   0.0  0
 P0L  CONST_10  H19  C13  C14  C2   180.00   0.0  0
 P0L  CONST_11  H20  C14  C2   C7   180.00   0.0  0
 P0L  CONST_12  H10  C7   C10  C9   180.00   0.0  0
 P0L  CONST_13  H1   C2   C7   C10  180.00   0.0  0
 P0L  CONST_14  HXT  OXT  C    O      0.00   0.0  0
 P0L  Var_01    C10  C9   C6   C4    85.38  30.0  2
 P0L  Var_02    C11  C8   C5   C3    56.06  30.0  2
 P0L  Var_03    H13  C11  C8   C5   177.41  30.0  3
 P0L  Var_04    H16  C12  C8   C5    58.37  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
 P0L  chir_02  C3  N   P1  C5  positiv
 P0L  chir_03  C4  O4  C   C6  positiv
 P0L  chir_04  P1  O3  O2  C3  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
 P0L  plan-1  C2   0.020
 P0L  plan-1  C6   0.020
 P0L  plan-1  C7   0.020
 P0L  plan-1  C9   0.020
 P0L  plan-1  C10  0.020
 P0L  plan-1  C13  0.020
 P0L  plan-1  C14  0.020
 P0L  plan-1  H1   0.020
 P0L  plan-1  H10  0.020
 P0L  plan-1  H12  0.020
 P0L  plan-1  H19  0.020
 P0L  plan-1  H20  0.020
 P0L  plan-2  C    0.020
 P0L  plan-2  O    0.020
 P0L  plan-2  C4   0.020
 P0L  plan-2  OXT  0.020
 P0L  plan-2  HXT  0.020

