# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 21:32:57 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)[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
 P4D  P4D  '(2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid'  peptide  40  22  .  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_P4D
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
 P4D  C1    C  CH2   0  -0.537  -2.7125   1.8983   0.3634
 P4D  N1    N  NH2   0  -0.786  -0.6946   3.0638   1.2959
 P4D  C2    C  CH1   0  -0.339  -1.2925   1.7871   0.9453
 P4D  P3    P  P     0   1.258  -0.1182   0.9015  -0.1429
 P4D  C4    C  CH2   0  -0.718   1.5225   1.0987   0.6417
 P4D  C5    C  CH1   0  -0.395   2.5139  -0.0052   0.2797
 P4D  C6    C  C     0   0.619   2.9414   0.0902  -1.1667
 P4D  C7    C  CH2   0  -0.570   3.7109  -0.0030   1.2321
 P4D  C8    C  C     0   0.553   4.4741  -1.3021   1.2559
 P4D  CG    C  CR6   0   0.123  -3.4034   0.5869   0.1198
 P4D  CZ    C  CR6   0   0.335  -4.6810  -1.8781  -0.3088
 P4D  O31   O  OH1   0  -0.775  -0.1485   1.8705  -1.4386
 P4D  O32   O  O     0  -0.709  -0.4292  -0.5352  -0.4090
 P4D  O61   O  OH1   0  -0.581   4.0589  -0.5664  -1.4123
 P4D  O62   O  O     0  -0.460   2.3313   0.6843  -2.0270
 P4D  O81   O  O     0  -0.443   3.9784  -2.3890   1.0961
 P4D  O82   O  OH1   0  -0.590   5.7563  -1.1197   1.5426
 P4D  CD1   C  CR16  0  -0.276  -3.5670   0.0763  -1.1619
 P4D  CD2   C  CR16  0  -0.298  -3.8965  -0.1652   1.1834
 P4D  CE1   C  CR16  0  -0.376  -4.2008  -1.1375  -1.3843
 P4D  CE2   C  CR16  0  -0.325  -4.5247  -1.3836   0.9840
 P4D  H1    H  HCH2  0   0.257  -3.2908   2.4895   1.0806
 P4D  H1A   H  HCH2  0   0.251  -2.6811   2.4860  -0.5578
 P4D  HN1   H  HNH2  0   0.350  -0.7581   3.7037   0.5136
 P4D  HN1A  H  HNH2  0   0.361  -1.2238   3.4844   2.0500
 P4D  H2    H  HCH1  0   0.278  -1.3341   1.1781   1.8551
 P4D  H4    H  HCH2  0   0.291   1.9255   2.0922   0.4429
 P4D  H4A   H  HCH2  0   0.293   1.3385   1.0559   1.7178
 P4D  H5    H  HCH1  0   0.312   2.0030  -0.9706   0.3755
 P4D  H7    H  HCH2  0   0.286   4.3783   0.8376   1.0377
 P4D  H7A   H  HCH2  0   0.306   3.3380   0.1389   2.2517
 P4D  HOH   H  HOH1  0   0.472  -5.3432  -3.3052  -1.3928
 P4D  HO31  H  HOH1  0   0.485   0.6320   1.7106  -1.9938
 P4D  HO61  H  HOH1  0   0.491   4.2944  -0.5039  -2.3512
 P4D  HO82  H  HOH1  0   0.481   6.2033  -1.9763   1.6219
 P4D  HD1   H  HCR6  0   0.244  -3.1944   0.6343  -2.0129
 P4D  HD2   H  HCR6  0   0.246  -3.7932   0.2077   2.1963
 P4D  HE1   H  HCR6  0   0.265  -4.3199  -1.5054  -2.3976
 P4D  HE2   H  HCR6  0   0.257  -4.9004  -1.9506   1.8270
 P4D  OH    O  OH1   0  -0.637  -5.3081  -3.0643  -0.4609

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
 P4D  C1   CG    single    1.502  0.020  1.502
 P4D  C1   C2    single    1.539  0.020  1.539
 P4D  C1   H1    single    0.970  0.020  1.090
 P4D  C1   H1A   single    0.970  0.020  1.090
 P4D  N1   C2    single    1.453  0.020  1.453
 P4D  N1   HN1   single    0.890  0.020  1.040
 P4D  N1   HN1A  single    0.890  0.020  1.040
 P4D  C2   P3    single    1.830  0.020  1.830
 P4D  C2   H2    single    0.970  0.020  1.090
 P4D  O32  P3    double    1.494  0.020  1.494
 P4D  O31  P3    single    1.618  0.020  1.618
 P4D  P3   C4    single    1.829  0.020  1.829
 P4D  C4   C5    single    1.527  0.020  1.527
 P4D  C4   H4    single    0.970  0.020  1.090
 P4D  C4   H4A   single    0.970  0.020  1.090
 P4D  C6   C5    single    1.511  0.020  1.511
 P4D  C5   C7    single    1.530  0.020  1.530
 P4D  C5   H5    single    0.970  0.020  1.090
 P4D  O62  C6    double    1.210  0.020  1.210
 P4D  O61  C6    single    1.319  0.020  1.319
 P4D  C7   C8    single    1.507  0.020  1.507
 P4D  C7   H7    single    0.970  0.020  1.090
 P4D  C7   H7A   single    0.970  0.020  1.090
 P4D  O81  C8    double    1.205  0.020  1.205
 P4D  C8   O82   single    1.326  0.020  1.326
 P4D  CD1  CG    aromatic  1.389  0.020  1.389
 P4D  CG   CD2   aromatic  1.393  0.020  1.393
 P4D  CZ   OH    single    1.350  0.020  1.350
 P4D  OH   HOH   single    0.850  0.020  0.980
 P4D  CE1  CZ    aromatic  1.391  0.020  1.391
 P4D  CZ   CE2   aromatic  1.393  0.020  1.393
 P4D  O31  HO31  single    0.850  0.020  0.980
 P4D  O61  HO61  single    0.850  0.020  0.980
 P4D  O82  HO82  single    0.850  0.020  0.980
 P4D  CD1  CE1   aromatic  1.387  0.020  1.387
 P4D  CD1  HD1   single    0.930  0.020  1.080
 P4D  CD2  CE2   aromatic  1.385  0.020  1.385
 P4D  CD2  HD2   single    0.930  0.020  1.080
 P4D  CE1  HE1   single    0.930  0.020  1.080
 P4D  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
 P4D  H1A   C1   H1   106.07  3.000
 P4D  H1A   C1   CG   110.23  3.000
 P4D  H1    C1   CG   109.56  3.000
 P4D  H1A   C1   C2   109.33  3.000
 P4D  H1    C1   C2   106.19  3.000
 P4D  CG    C1   C2   115.01  3.000
 P4D  HN1A  N1   HN1  106.26  3.000
 P4D  HN1A  N1   C2   109.24  3.000
 P4D  HN1   N1   C2   110.06  3.000
 P4D  H2    C2   P3   104.43  3.000
 P4D  H2    C2   N1   107.68  3.000
 P4D  P3    C2   N1   107.75  3.000
 P4D  H2    C2   C1   108.61  3.000
 P4D  P3    C2   C1   113.73  3.000
 P4D  N1    C2   C1   114.06  3.000
 P4D  O32   P3   O31  115.43  3.000
 P4D  O31   P3   C4   107.19  3.000
 P4D  O32   P3   C4   111.52  3.000
 P4D  C4    P3   C2   105.56  3.000
 P4D  O31   P3   C2   100.04  3.000
 P4D  O32   P3   C2   115.97  3.000
 P4D  H4A   C4   H4   106.11  3.000
 P4D  H4A   C4   C5   108.33  3.000
 P4D  H4    C4   C5   112.05  3.000
 P4D  H4A   C4   P3   105.50  3.000
 P4D  H4    C4   P3   110.58  3.000
 P4D  C5    C4   P3   113.74  3.000
 P4D  H5    C5   C7   108.15  3.000
 P4D  H5    C5   C6   105.73  3.000
 P4D  C7    C5   C6   111.99  3.000
 P4D  H5    C5   C4   108.25  3.000
 P4D  C7    C5   C4   111.06  3.000
 P4D  C6    C5   C4   111.40  3.000
 P4D  O62   C6   O61  122.61  3.000
 P4D  O61   C6   C5   112.73  3.000
 P4D  O62   C6   C5   124.66  3.000
 P4D  H7A   C7   H7   105.93  3.000
 P4D  H7A   C7   C8   105.63  3.000
 P4D  H7    C7   C8   110.94  3.000
 P4D  H7A   C7   C5   108.27  3.000
 P4D  H7    C7   C5   111.65  3.000
 P4D  C8    C7   C5   113.89  3.000
 P4D  O82   C8   O81  123.38  3.000
 P4D  O82   C8   C7   111.99  3.000
 P4D  O81   C8   C7   124.54  3.000
 P4D  CD2   CG   CD1  117.67  3.000
 P4D  CD2   CG   C1   120.69  3.000
 P4D  CD1   CG   C1   121.64  3.000
 P4D  CE2   CZ   CE1  119.32  3.000
 P4D  CE2   CZ   OH   117.94  3.000
 P4D  CE1   CZ   OH   122.73  3.000
 P4D  HO31  O31  P3   110.13  3.000
 P4D  HO61  O61  C6   110.72  3.000
 P4D  HO82  O82  C8   109.99  3.000
 P4D  HD1   CD1  CE1  118.79  3.000
 P4D  HD1   CD1  CG   119.65  3.000
 P4D  CE1   CD1  CG   121.55  3.000
 P4D  HD2   CD2  CE2  118.69  3.000
 P4D  HD2   CD2  CG   119.60  3.000
 P4D  CE2   CD2  CG   121.70  3.000
 P4D  HE1   CE1  CD1  119.79  3.000
 P4D  HE1   CE1  CZ   120.25  3.000
 P4D  CD1   CE1  CZ   119.96  3.000
 P4D  HE2   CE2  CD2  120.37  3.000
 P4D  HE2   CE2  CZ   119.84  3.000
 P4D  CD2   CE2  CZ   119.79  3.000
 P4D  HOH   OH   CZ   110.22  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
 P4D  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 P4D  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 P4D  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 P4D  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 P4D  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 P4D  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 P4D  CONST_07  CE1   CD1  CG   C1    180.00   0.0  0
 P4D  CONST_08  CE2   CD2  CG   C1    180.00   0.0  0
 P4D  CONST_09  CD1   CE1  CZ   OH    180.00   0.0  0
 P4D  CONST_10  CD2   CE2  CZ   OH    180.00   0.0  0
 P4D  CONST_11  HE1   CE1  CD1  CG    180.00   0.0  0
 P4D  CONST_12  HE2   CE2  CD2  CG    180.00   0.0  0
 P4D  CONST_13  HD1   CD1  CE1  CZ    180.00   0.0  0
 P4D  CONST_14  HD2   CD2  CE2  CZ    180.00   0.0  0
 P4D  CONST_15  HO61  O61  C6   C5    180.00   0.0  0
 P4D  CONST_16  HO82  O82  C8   C7    180.00   0.0  0
 P4D  Var_01    CD1   CG   C1   C2   -105.74  30.0  2
 P4D  Var_02    C5    C4   P3   C2    155.04  30.0  3
 P4D  Var_03    O81   C8   C7   C5    -32.48  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
 P4D  chir_01  C2  C1   N1   P3  positiv
 P4D  chir_03  C5  C4   C6   C7  negativ
 P4D  chir_04  P3  O32  O31  C4  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
 P4D  plan-1  C1    0.020
 P4D  plan-1  CG    0.020
 P4D  plan-1  CZ    0.020
 P4D  plan-1  CD1   0.020
 P4D  plan-1  CD2   0.020
 P4D  plan-1  CE1   0.020
 P4D  plan-1  CE2   0.020
 P4D  plan-1  HD1   0.020
 P4D  plan-1  HD2   0.020
 P4D  plan-1  HE1   0.020
 P4D  plan-1  HE2   0.020
 P4D  plan-1  OH    0.020
 P4D  plan-2  C5    0.020
 P4D  plan-2  C6    0.020
 P4D  plan-2  O61   0.020
 P4D  plan-2  O62   0.020
 P4D  plan-2  HO61  0.020
 P4D  plan-3  C7    0.020
 P4D  plan-3  C8    0.020
 P4D  plan-3  O81   0.020
 P4D  plan-3  O82   0.020
 P4D  plan-3  HO82  0.020

