# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:15:02 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: 3-[(R)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[P](O)(=O)CCC(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
 00H  00H  '3-[(R)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]propanoic acid'  peptide  33  17  .  2022-03-07  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_00H
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
 00H  N12   N  NH2   0  -0.773  15.2370  44.5915  27.9112
 00H  C13   C  CH1   0  -0.327  14.2043  45.5263  27.5091
 00H  C14   C  CH2   0  -0.541  13.8990  46.5039  28.6482
 00H  C15   C  CR6   0   0.160  13.2744  45.8053  29.8233
 00H  C16   C  CR16  0  -0.310  11.8984  45.5912  29.8632
 00H  C17   C  CR16  0  -0.241  11.3121  44.9180  30.9267
 00H  C18   C  CR16  0  -0.273  12.0983  44.4494  31.9713
 00H  C19   C  CR16  0  -0.244  13.4710  44.6594  31.9431
 00H  C20   C  CR16  0  -0.304  14.0526  45.3304  30.8753
 00H  P21   P  P     0   1.232  14.6264  46.3634  25.9249
 00H  O22   O  OH1   0  -0.755  15.6860  47.5377  26.2888
 00H  O23   O  O     0  -0.720  15.1227  45.3908  24.9024
 00H  C24   C  CH2   0  -0.732  13.1967  47.3298  25.3717
 00H  C25   C  CH2   0  -0.579  13.5073  48.1509  24.1242
 00H  C26   C  C     0   0.550  14.2093  49.4486  24.4296
 00H  O27   O  O     0  -0.444  14.0063  50.1204  25.4093
 00H  HN12  H  HNH2  0   0.359  15.4310  43.9297  27.1707
 00H  HN1A  H  HNH2  0   0.346  16.1044  45.0759  28.1086
 00H  H13   H  HCH1  0   0.280  13.2951  44.9545  27.2881
 00H  H14   H  HCH2  0   0.261  14.8251  46.9987  28.9518
 00H  H14A  H  HCH2  0   0.260  13.2295  47.2930  28.2985
 00H  H16   H  HCR6  0   0.244  11.2772  45.9583  29.0534
 00H  H17   H  HCR6  0   0.253  10.2406  44.7633  30.9413
 00H  H18   H  HCR6  0   0.253  11.6440  43.9279  32.8038
 00H  H19   H  HCR6  0   0.252  14.0908  44.2989  32.7543
 00H  H20   H  HCR6  0   0.241  15.1236  45.4916  30.8616
 00H  HO22  H  HOH1  0   0.486  16.6007  47.2316  26.3452
 00H  H24   H  HCH2  0   0.301  12.4139  46.6014  25.1500
 00H  H24A  H  HCH2  0   0.287  12.8103  47.9645  26.1699
 00H  H25   H  HCH2  0   0.278  14.0715  47.5696  23.3945
 00H  H25A  H  HCH2  0   0.312  12.5667  48.4196  23.6334
 00H  OXT   O  OH1   0  -0.591  15.0431  49.8063  23.4607
 00H  HXT   H  HOH1  0   0.479  15.4274  50.6732  23.6602

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
 00H  N12  HN12  single    0.890  0.020  1.040
 00H  N12  HN1A  single    0.890  0.020  1.040
 00H  C13  N12   single    1.450  0.020  1.450
 00H  C13  C14   single    1.532  0.020  1.532
 00H  C13  H13   single    0.970  0.020  1.090
 00H  C14  C15   single    1.503  0.020  1.503
 00H  C14  H14   single    0.970  0.020  1.090
 00H  C14  H14A  single    0.970  0.020  1.090
 00H  C15  C16   aromatic  1.393  0.020  1.393
 00H  C15  C20   aromatic  1.392  0.020  1.392
 00H  C16  C17   aromatic  1.388  0.020  1.388
 00H  C16  H16   single    0.930  0.020  1.080
 00H  C17  C18   aromatic  1.389  0.020  1.389
 00H  C17  H17   single    0.930  0.020  1.080
 00H  C18  H18   single    0.930  0.020  1.080
 00H  C19  C18   aromatic  1.389  0.020  1.389
 00H  C19  H19   single    0.930  0.020  1.080
 00H  C20  C19   aromatic  1.389  0.020  1.389
 00H  C20  H20   single    0.930  0.020  1.080
 00H  P21  C13   single    1.841  0.020  1.841
 00H  P21  O22   single    1.623  0.020  1.623
 00H  O22  HO22  single    0.850  0.020  0.980
 00H  O23  P21   double    1.496  0.020  1.496
 00H  C24  P21   single    1.812  0.020  1.812
 00H  C24  H24   single    0.970  0.020  1.090
 00H  C24  H24A  single    0.970  0.020  1.090
 00H  C25  C24   single    1.525  0.020  1.525
 00H  C25  C26   single    1.507  0.020  1.507
 00H  C25  H25   single    0.970  0.020  1.090
 00H  C25  H25A  single    0.970  0.020  1.090
 00H  C26  O27   double    1.205  0.020  1.205
 00H  C26  OXT   single    1.327  0.020  1.327
 00H  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
 00H  HN1A  N12  HN12  106.93  3.000
 00H  HN1A  N12  C13   110.84  3.000
 00H  HN12  N12  C13   110.82  3.000
 00H  H13   C13  P21   104.70  3.000
 00H  P21   C13  C14   113.29  3.000
 00H  H13   C13  C14   108.51  3.000
 00H  P21   C13  N12   111.62  3.000
 00H  H13   C13  N12   108.08  3.000
 00H  C14   C13  N12   110.32  3.000
 00H  H14A  C14  H14   106.34  3.000
 00H  H14A  C14  C15   109.35  3.000
 00H  H14   C14  C15   110.20  3.000
 00H  H14A  C14  C13   110.19  3.000
 00H  H14   C14  C13   109.06  3.000
 00H  C15   C14  C13   111.57  3.000
 00H  C20   C15  C16   118.56  3.000
 00H  C20   C15  C14   121.14  3.000
 00H  C16   C15  C14   120.28  3.000
 00H  H16   C16  C17   119.61  3.000
 00H  H16   C16  C15   119.49  3.000
 00H  C17   C16  C15   120.90  3.000
 00H  H17   C17  C18   120.12  3.000
 00H  H17   C17  C16   119.84  3.000
 00H  C18   C17  C16   120.04  3.000
 00H  H18   C18  C19   120.23  3.000
 00H  C19   C18  C17   119.55  3.000
 00H  H18   C18  C17   120.22  3.000
 00H  H19   C19  C20   119.82  3.000
 00H  C20   C19  C18   120.17  3.000
 00H  H19   C19  C18   120.01  3.000
 00H  H20   C20  C19   119.72  3.000
 00H  H20   C20  C15   119.50  3.000
 00H  C19   C20  C15   120.78  3.000
 00H  C24   P21  O23   113.57  3.000
 00H  C24   P21  O22   101.40  3.000
 00H  O23   P21  O22   114.03  3.000
 00H  C24   P21  C13   108.92  3.000
 00H  O23   P21  C13   111.63  3.000
 00H  O22   P21  C13   106.60  3.000
 00H  HO22  O22  P21   113.69  3.000
 00H  H24A  C24  H24   106.43  3.000
 00H  H24A  C24  C25   110.94  3.000
 00H  H24   C24  C25   109.81  3.000
 00H  C25   C24  P21   112.09  3.000
 00H  H24A  C24  P21   111.50  3.000
 00H  H24   C24  P21   105.77  3.000
 00H  H25A  C25  H25   105.99  3.000
 00H  H25A  C25  C26   106.25  3.000
 00H  H25   C25  C26   110.72  3.000
 00H  H25A  C25  C24   108.90  3.000
 00H  H25   C25  C24   111.45  3.000
 00H  C26   C25  C24   113.12  3.000
 00H  OXT   C26  O27   123.30  3.000
 00H  OXT   C26  C25   112.13  3.000
 00H  O27   C26  C25   124.51  3.000
 00H  HXT   OXT  C26   109.87  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
 00H  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 00H  CONST_02  C18  C19  C20  C15    0.00   0.0  0
 00H  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 00H  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 00H  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 00H  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 00H  CONST_07  C17  C16  C15  C14  180.00   0.0  0
 00H  CONST_08  C19  C20  C15  C14  180.00   0.0  0
 00H  CONST_09  H17  C17  C16  C15  180.00   0.0  0
 00H  CONST_10  H19  C19  C20  C15  180.00   0.0  0
 00H  CONST_11  H20  C20  C15  C16  180.00   0.0  0
 00H  CONST_12  H18  C18  C17  C16  180.00   0.0  0
 00H  CONST_13  H16  C16  C17  C18  180.00   0.0  0
 00H  CONST_14  HXT  OXT  C26  C25  180.00   0.0  0
 00H  Var_01    C16  C15  C14  C13  -85.34  30.0  2
 00H  Var_02    C25  C24  P21  C13  175.10  30.0  2
 00H  Var_03    C26  C25  C24  P21  -82.05  30.0  1
 00H  Var_04    O27  C26  C25  C24  -34.92  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
 00H  chir_01  C13  N12  C14  P21  negativ
 00H  chir_02  P21  O22  O23  C24  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
 00H  plan-1  C14  0.020
 00H  plan-1  C15  0.020
 00H  plan-1  C16  0.020
 00H  plan-1  C17  0.020
 00H  plan-1  C18  0.020
 00H  plan-1  C19  0.020
 00H  plan-1  C20  0.020
 00H  plan-1  H16  0.020
 00H  plan-1  H17  0.020
 00H  plan-1  H18  0.020
 00H  plan-1  H19  0.020
 00H  plan-1  H20  0.020
 00H  plan-2  C25  0.020
 00H  plan-2  C26  0.020
 00H  plan-2  O27  0.020
 00H  plan-2  OXT  0.020
 00H  plan-2  HXT  0.020

