# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:46:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R)-2-{[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]methyl}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[P](O)(=O)C[C@H](CC(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
 P5D  P5D  '(2R)-2-{[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]methyl}butanedioic acid'  peptide  36  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P5D
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
 P5D  C1    C  CH2    0  -0.534  -3.0490   1.3113   0.2384
 P5D  N1    N  NH2    0  -0.792  -1.2418   2.6393   1.3008
 P5D  C2    C  CH1    0  -0.311  -1.6943   1.2920   0.9704
 P5D  P3    P  P      0   1.193  -0.3855   0.4464  -0.0496
 P5D  C4    C  CH2    0  -0.668   1.1523   0.7975   0.8953
 P5D  C5    C  CH1    0  -0.315   2.3571  -0.0005   0.3924
 P5D  C6    C  C      0   0.417   2.8056   0.4702  -1.0026
 P5D  C7    C  CH2    0  -0.528   3.5242   0.1172   1.3775
 P5D  C8    C  C      0   0.390   4.7420  -0.7391   1.0015
 P5D  CG    C  CR6    0   0.159  -3.6746  -0.0278  -0.0265
 P5D  CZ    C  CR16   0  -0.279  -4.8870  -2.5052  -0.5301
 P5D  O31   O  OP    -1  -0.823  -0.3552   1.1668  -1.3875
 P5D  O32   O  O      0  -0.814  -0.6272  -1.0497  -0.0195
 P5D  O61   O  OC    -1  -0.632   2.8024  -0.3642  -1.9311
 P5D  O62   O  O      0  -0.633   3.1789   1.6603  -1.0951
 P5D  O81   O  O      0  -0.627   4.5265  -1.9503   0.7794
 P5D  O82   O  OC    -1  -0.628   5.8590  -0.1796   0.9652
 P5D  CD1   C  CR16   0  -0.275  -3.5317  -0.6556  -1.2617
 P5D  CD2   C  CR16   0  -0.326  -4.4299  -0.6664   0.9538
 P5D  CE1   C  CR16   0  -0.251  -4.1371  -1.8764  -1.5174
 P5D  CE2   C  CR16   0  -0.246  -5.0287  -1.8965   0.7099
 P5D  H1    H  HCH2   0   0.228  -3.7416   1.9088   0.8419
 P5D  H1A   H  HCH2   0   0.229  -2.9181   1.8477  -0.7054
 P5D  HN1   H  HNH2   0   0.329  -1.0329   3.1326   0.4400
 P5D  HN1A  H  HNH2   0   0.336  -1.9994   3.1558   1.7346
 P5D  H2    H  HCH1   0   0.214  -1.8100   0.7327   1.9064
 P5D  H4    H  HCH2   0   0.213   1.3750   1.8656   0.8738
 P5D  H4A   H  HCH2   0   0.204   0.9622   0.5442   1.9452
 P5D  H5    H  HCH1   0   0.181   2.0697  -1.0519   0.3340
 P5D  H7    H  HCH2   0   0.184   3.8093   1.1670   1.4763
 P5D  H7A   H  HCH2   0   0.202   3.1756  -0.2057   2.3673
 P5D  HZ    H  HCR6   0   0.245  -5.3601  -3.4586  -0.7284
 P5D  HD1   H  HCR6   0   0.232  -2.9340  -0.1757  -2.0270
 P5D  HD2   H  HCR6   0   0.237  -4.5605  -0.1918   1.9203
 P5D  HE1   H  HCR6   0   0.243  -4.0230  -2.3410  -2.4891
 P5D  HE2   H  HCR6   0   0.245  -5.6154  -2.3737   1.4848

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
 P5D  C1   CG    single    1.502  0.020  1.502
 P5D  C1   C2    single    1.540  0.020  1.540
 P5D  C1   H1    single    0.970  0.020  1.090
 P5D  C1   H1A   single    0.970  0.020  1.090
 P5D  N1   C2    single    1.459  0.020  1.459
 P5D  N1   HN1   single    0.890  0.020  1.040
 P5D  N1   HN1A  single    0.890  0.020  1.040
 P5D  C2   P3    single    1.862  0.020  1.862
 P5D  C2   H2    single    0.970  0.020  1.090
 P5D  O32  P3    deloc     1.516  0.020  1.516
 P5D  O31  P3    deloc     1.520  0.020  1.520
 P5D  P3   C4    single    1.839  0.020  1.839
 P5D  C4   C5    single    1.530  0.020  1.530
 P5D  C4   H4    single    0.970  0.020  1.090
 P5D  C4   H4A   single    0.970  0.020  1.090
 P5D  C6   C5    single    1.539  0.020  1.539
 P5D  C5   C7    single    1.532  0.020  1.532
 P5D  C5   H5    single    0.970  0.020  1.090
 P5D  O62  C6    deloc     1.251  0.020  1.251
 P5D  O61  C6    deloc     1.248  0.020  1.248
 P5D  C7   C8    single    1.535  0.020  1.535
 P5D  C7   H7    single    0.970  0.020  1.090
 P5D  C7   H7A   single    0.970  0.020  1.090
 P5D  O81  C8    deloc     1.250  0.020  1.250
 P5D  C8   O82   deloc     1.250  0.020  1.250
 P5D  CD1  CG    aromatic  1.393  0.020  1.393
 P5D  CG   CD2   aromatic  1.393  0.020  1.393
 P5D  CE1  CZ    aromatic  1.390  0.020  1.390
 P5D  CZ   CE2   aromatic  1.389  0.020  1.389
 P5D  CZ   HZ    single    0.930  0.020  1.080
 P5D  CD1  CE1   aromatic  1.387  0.020  1.387
 P5D  CD1  HD1   single    0.930  0.020  1.080
 P5D  CD2  CE2   aromatic  1.390  0.020  1.390
 P5D  CD2  HD2   single    0.930  0.020  1.080
 P5D  CE1  HE1   single    0.930  0.020  1.080
 P5D  CE2  HE2   single    0.930  0.020  1.080

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
 P5D  H1A   C1   H1   106.47  3.000
 P5D  H1A   C1   CG   109.58  3.000
 P5D  H1    C1   CG   108.67  3.000
 P5D  H1A   C1   C2   108.13  3.000
 P5D  H1    C1   C2   107.52  3.000
 P5D  CG    C1   C2   116.05  3.000
 P5D  HN1A  N1   HN1  105.62  3.000
 P5D  HN1A  N1   C2   109.60  3.000
 P5D  HN1   N1   C2   108.71  3.000
 P5D  H2    C2   P3   108.07  3.000
 P5D  H2    C2   N1   108.08  3.000
 P5D  P3    C2   N1   108.99  3.000
 P5D  H2    C2   C1   108.62  3.000
 P5D  P3    C2   C1   111.32  3.000
 P5D  N1    C2   C1   111.64  3.000
 P5D  O32   P3   O31  119.24  3.000
 P5D  O31   P3   C4   110.19  3.000
 P5D  O32   P3   C4   108.16  3.000
 P5D  C4    P3   C2   102.69  3.000
 P5D  O31   P3   C2   106.32  3.000
 P5D  O32   P3   C2   108.98  3.000
 P5D  H4A   C4   H4   106.28  3.000
 P5D  H4A   C4   C5   109.31  3.000
 P5D  H4    C4   C5   110.08  3.000
 P5D  H4A   C4   P3   107.63  3.000
 P5D  H4    C4   P3   110.33  3.000
 P5D  C5    C4   P3   112.96  3.000
 P5D  H5    C5   C7   108.00  3.000
 P5D  H5    C5   C6   108.83  3.000
 P5D  C7    C5   C6   109.71  3.000
 P5D  H5    C5   C4   108.22  3.000
 P5D  C7    C5   C4   110.39  3.000
 P5D  C6    C5   C4   111.58  3.000
 P5D  O62   C6   O61  125.58  3.000
 P5D  O61   C6   C5   117.97  3.000
 P5D  O62   C6   C5   116.43  3.000
 P5D  H7A   C7   H7   106.50  3.000
 P5D  H7A   C7   C8   107.97  3.000
 P5D  H7    C7   C8   110.55  3.000
 P5D  H7A   C7   C5   108.38  3.000
 P5D  H7    C7   C5   109.32  3.000
 P5D  C8    C7   C5   113.83  3.000
 P5D  O82   C8   O81  125.64  3.000
 P5D  O82   C8   C7   117.80  3.000
 P5D  O81   C8   C7   116.55  3.000
 P5D  CD2   CG   CD1  118.24  3.000
 P5D  CD2   CG   C1   120.71  3.000
 P5D  CD1   CG   C1   121.04  3.000
 P5D  HZ    CZ   CE2  120.33  3.000
 P5D  HZ    CZ   CE1  120.26  3.000
 P5D  CE2   CZ   CE1  119.41  3.000
 P5D  HD1   CD1  CE1  120.05  3.000
 P5D  HD1   CD1  CG   118.92  3.000
 P5D  CE1   CD1  CG   121.04  3.000
 P5D  HD2   CD2  CE2  119.46  3.000
 P5D  HD2   CD2  CG   119.47  3.000
 P5D  CE2   CD2  CG   121.07  3.000
 P5D  HE1   CE1  CD1  119.81  3.000
 P5D  HE1   CE1  CZ   120.00  3.000
 P5D  CD1   CE1  CZ   120.19  3.000
 P5D  HE2   CE2  CD2  119.87  3.000
 P5D  HE2   CE2  CZ   120.08  3.000
 P5D  CD2   CE2  CZ   120.05  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
 P5D  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 P5D  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 P5D  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 P5D  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 P5D  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 P5D  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 P5D  CONST_07  CE1  CD1  CG   C1   180.00   0.0  0
 P5D  CONST_08  CE2  CD2  CG   C1   180.00   0.0  0
 P5D  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 P5D  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 P5D  CONST_11  HD1  CD1  CE1  CZ   180.00   0.0  0
 P5D  CONST_12  HD2  CD2  CE2  CZ   180.00   0.0  0
 P5D  CONST_13  HZ   CZ   CE1  CD1  180.00   0.0  0
 P5D  Var_01    CD1  CG   C1   C2   -97.40  30.0  2
 P5D  Var_02    C5   C4   P3   C2   169.94  30.0  3
 P5D  Var_03    O81  C8   C7   C5   -52.28  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
 P5D  chir_01  C2  C1  N1  P3  positiv
 P5D  chir_03  C5  C4  C6  C7  negativ

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
 P5D  plan-1  C1   0.020
 P5D  plan-1  CG   0.020
 P5D  plan-1  CZ   0.020
 P5D  plan-1  CD1  0.020
 P5D  plan-1  CD2  0.020
 P5D  plan-1  CE1  0.020
 P5D  plan-1  CE2  0.020
 P5D  plan-1  HZ   0.020
 P5D  plan-1  HD1  0.020
 P5D  plan-1  HD2  0.020
 P5D  plan-1  HE1  0.020
 P5D  plan-1  HE2  0.020
 P5D  plan-2  C5   0.020
 P5D  plan-2  C6   0.020
 P5D  plan-2  O61  0.020
 P5D  plan-2  O62  0.020
 P5D  plan-3  C7   0.020
 P5D  plan-3  C8   0.020
 P5D  plan-3  O81  0.020
 P5D  plan-3  O82  0.020

