# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 08:45:56 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[P@](=O)(C[C@@H](Cc1ccccc1)C(O)=O)O[P](O)(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
 P0D  P0D  '(2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid'  ligand  41  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P0D
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
 P0D  O2   O  OH1   0  -0.580   1.6858   0.2501  -1.8436
 P0D  C    C  C     0   0.568   1.4721  -0.8159  -1.0906
 P0D  O1   O  O     0  -0.444   1.6280  -1.9489  -1.4736
 P0D  C2'  C  CH1   0  -0.358   1.0866  -0.4607   0.3296
 P0D  C1'  C  CH2   0  -0.744  -0.1112  -1.2887   0.7973
 P0D  P1   P  P     0   1.297  -1.6251  -0.8765  -0.0999
 P0D  O1P  O  O     0  -0.692  -1.4674  -0.8059  -1.5785
 P0D  C2   C  CH3   0  -0.682  -3.3103  -1.7964   1.9743
 P0D  C1   C  CH1   0  -0.352  -2.9689  -1.9608   0.4980
 P0D  N1   N  NH2   0  -0.799  -2.5585  -3.2987   0.0990
 P0D  O2P  O  O2    0  -0.712  -1.9472   0.6081   0.5672
 P0D  P2   P  P     0   1.460  -3.0476   1.6439   0.0147
 P0D  O4P  O  OH1   0  -0.724  -3.4801   2.4528   1.3115
 P0D  O3P  O  OH1   0  -0.724  -2.1145   2.5850  -0.8651
 P0D  O5P  O  O     0  -0.699  -4.2108   1.0222  -0.6402
 P0D  C3'  C  CH2   0  -0.499   2.2924  -0.7338   1.2516
 P0D  C31  C  CR6   0   0.121   3.5159   0.0456   0.8586
 P0D  C33  C  CR16  0  -0.306   4.5514  -0.5563   0.1494
 P0D  C35  C  CR16  0  -0.240   5.6639   0.1772  -0.2438
 P0D  C36  C  CR16  0  -0.270   5.7541   1.5265   0.0684
 P0D  C34  C  CR16  0  -0.238   4.7274   2.1366   0.7793
 P0D  C32  C  CR16  0  -0.306   3.6186   1.4002   1.1695
 P0D  H1   H  HOH1  0   0.478   1.9815  -0.0213  -2.7260
 P0D  H2   H  HCH1  0   0.285   0.8503   0.6042   0.3873
 P0D  H3   H  HCH2  0   0.297   0.0844  -2.3540   0.6558
 P0D  H4   H  HCH2  0   0.307  -0.2733  -1.1324   1.8661
 P0D  H6   H  HCH3  0   0.257  -4.1273  -2.4719   2.2299
 P0D  H7   H  HCH3  0   0.236  -2.4632  -2.0482   2.6157
 P0D  H8   H  HCH1  0   0.294  -3.8348  -1.6762  -0.1063
 P0D  H9   H  HNH2  0   0.358  -2.0296  -3.7410   0.8401
 P0D  H10  H  HNH2  0   0.373  -3.3726  -3.8782  -0.0565
 P0D  H12  H  HOH1  0   0.502  -2.7878   2.9586   1.7589
 P0D  H13  H  HOH1  0   0.505  -2.5912   3.2575  -1.3717
 P0D  H14  H  HCH2  0   0.271   1.9922  -0.4705   2.2684
 P0D  H15  H  HCH2  0   0.261   2.5076  -1.8045   1.2503
 P0D  H16  H  HCR6  0   0.249   4.4894  -1.6099  -0.0972
 P0D  H17  H  HCR6  0   0.254   6.4612  -0.3077  -0.7922
 P0D  H18  H  HCR6  0   0.255   6.6200   2.0995  -0.2374
 P0D  H19  H  HCR6  0   0.254   4.7930   3.1870   1.0326
 P0D  H20  H  HCR6  0   0.248   2.8222   1.8836   1.7241
 P0D  H5   H  HCH3  0   0.240  -3.6302  -0.7847   2.2203

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
 P0D  O1P  P1   double    1.489  0.020  1.489
 P0D  C2   C1   single    1.524  0.020  1.524
 P0D  N1   C1   single    1.455  0.020  1.455
 P0D  C1   P1   single    1.827  0.020  1.827
 P0D  O1   C    double    1.206  0.020  1.206
 P0D  P1   O2P  single    1.659  0.020  1.659
 P0D  P1   C1'  single    1.807  0.020  1.807
 P0D  O2   C    single    1.322  0.020  1.322
 P0D  C    C2'  single    1.514  0.020  1.514
 P0D  O2P  P2   single    1.609  0.020  1.609
 P0D  O5P  P2   double    1.473  0.020  1.473
 P0D  C1'  C2'  single    1.529  0.020  1.529
 P0D  C2'  C3'  single    1.542  0.020  1.542
 P0D  P2   O3P  single    1.591  0.020  1.591
 P0D  P2   O4P  single    1.588  0.020  1.588
 P0D  C3'  C31  single    1.503  0.020  1.503
 P0D  C33  C31  aromatic  1.392  0.020  1.392
 P0D  C33  C35  aromatic  1.389  0.020  1.389
 P0D  C31  C32  aromatic  1.394  0.020  1.394
 P0D  C35  C36  aromatic  1.388  0.020  1.388
 P0D  C32  C34  aromatic  1.387  0.020  1.387
 P0D  C36  C34  aromatic  1.390  0.020  1.390
 P0D  O2   H1   single    0.850  0.020  0.980
 P0D  C2'  H2   single    0.970  0.020  1.090
 P0D  C1'  H3   single    0.970  0.020  1.090
 P0D  C1'  H4   single    0.970  0.020  1.090
 P0D  C2   H5   single    0.970  0.020  1.090
 P0D  C2   H6   single    0.970  0.020  1.090
 P0D  C2   H7   single    0.970  0.020  1.090
 P0D  C1   H8   single    0.970  0.020  1.090
 P0D  N1   H9   single    0.890  0.020  1.040
 P0D  N1   H10  single    0.890  0.020  1.040
 P0D  O4P  H12  single    0.850  0.020  0.980
 P0D  O3P  H13  single    0.850  0.020  0.980
 P0D  C3'  H14  single    0.970  0.020  1.090
 P0D  C3'  H15  single    0.970  0.020  1.090
 P0D  C33  H16  single    0.930  0.020  1.080
 P0D  C35  H17  single    0.930  0.020  1.080
 P0D  C36  H18  single    0.930  0.020  1.080
 P0D  C34  H19  single    0.930  0.020  1.080
 P0D  C32  H20  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
 P0D  H1   O2   C    109.99  3.000
 P0D  C2'  C    O1   123.45  3.000
 P0D  C2'  C    O2   112.72  3.000
 P0D  O1   C    O2   123.74  3.000
 P0D  H2   C2'  C3'  108.07  3.000
 P0D  H2   C2'  C1'  110.01  3.000
 P0D  C3'  C2'  C1'  109.49  3.000
 P0D  H2   C2'  C    109.47  3.000
 P0D  C3'  C2'  C    108.67  3.000
 P0D  C1'  C2'  C    111.06  3.000
 P0D  H4   C1'  H3   107.02  3.000
 P0D  H4   C1'  P1   109.19  3.000
 P0D  H3   C1'  P1   107.94  3.000
 P0D  H4   C1'  C2'  109.76  3.000
 P0D  H3   C1'  C2'  110.38  3.000
 P0D  P1   C1'  C2'  112.38  3.000
 P0D  O2P  P1   C1   104.87  3.000
 P0D  O2P  P1   O1P  112.18  3.000
 P0D  C1   P1   O1P  115.53  3.000
 P0D  O2P  P1   C1'   99.62  3.000
 P0D  C1   P1   C1'  108.56  3.000
 P0D  O1P  P1   C1'  114.52  3.000
 P0D  H7   C2   H6   107.50  3.000
 P0D  H7   C2   H5   108.02  3.000
 P0D  H6   C2   H5   107.60  3.000
 P0D  H7   C2   C1   111.73  3.000
 P0D  H6   C2   C1   109.14  3.000
 P0D  H5   C2   C1   112.63  3.000
 P0D  H8   C1   N1   108.12  3.000
 P0D  H8   C1   C2   109.26  3.000
 P0D  N1   C1   C2   115.34  3.000
 P0D  H8   C1   P1   104.30  3.000
 P0D  N1   C1   P1   104.38  3.000
 P0D  C2   C1   P1   114.68  3.000
 P0D  H10  N1   H9   106.43  3.000
 P0D  H10  N1   C1   109.99  3.000
 P0D  H9   N1   C1   110.39  3.000
 P0D  P2   O2P  P1   124.80  3.000
 P0D  O5P  P2   O3P  117.85  3.000
 P0D  O3P  P2   O4P  108.06  3.000
 P0D  O5P  P2   O4P  111.29  3.000
 P0D  O4P  P2   O2P  103.52  3.000
 P0D  O3P  P2   O2P   99.76  3.000
 P0D  O5P  P2   O2P  114.91  3.000
 P0D  H12  O4P  P2   116.69  3.000
 P0D  H13  O3P  P2   114.32  3.000
 P0D  H15  C3'  H14  106.95  3.000
 P0D  H15  C3'  C31  110.35  3.000
 P0D  H14  C3'  C31  110.01  3.000
 P0D  H15  C3'  C2'  109.08  3.000
 P0D  H14  C3'  C2'  107.39  3.000
 P0D  C31  C3'  C2'  112.85  3.000
 P0D  C32  C31  C33  118.63  3.000
 P0D  C32  C31  C3'  120.38  3.000
 P0D  C33  C31  C3'  120.97  3.000
 P0D  H16  C33  C35  119.65  3.000
 P0D  H16  C33  C31  119.59  3.000
 P0D  C35  C33  C31  120.77  3.000
 P0D  H17  C35  C36  120.11  3.000
 P0D  H17  C35  C33  119.78  3.000
 P0D  C36  C35  C33  120.11  3.000
 P0D  H18  C36  C34  120.21  3.000
 P0D  H18  C36  C35  120.21  3.000
 P0D  C34  C36  C35  119.59  3.000
 P0D  H19  C34  C32  119.86  3.000
 P0D  H19  C34  C36  120.05  3.000
 P0D  C32  C34  C36  120.09  3.000
 P0D  H20  C32  C34  119.63  3.000
 P0D  H20  C32  C31  119.56  3.000
 P0D  C34  C32  C31  120.81  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
 P0D  CONST_01  C36  C35  C33  C31     0.00   0.0  0
 P0D  CONST_02  C36  C34  C32  C31     0.00   0.0  0
 P0D  CONST_03  C34  C32  C31  C33     0.00   0.0  0
 P0D  CONST_04  C34  C36  C35  C33     0.00   0.0  0
 P0D  CONST_05  C32  C31  C33  C35     0.00   0.0  0
 P0D  CONST_06  C32  C34  C36  C35     0.00   0.0  0
 P0D  CONST_07  C35  C33  C31  C3'   180.00   0.0  0
 P0D  CONST_08  C34  C32  C31  C3'   180.00   0.0  0
 P0D  CONST_09  H17  C35  C33  C31   180.00   0.0  0
 P0D  CONST_10  H19  C34  C32  C31   180.00   0.0  0
 P0D  CONST_11  H20  C32  C31  C33   180.00   0.0  0
 P0D  CONST_12  H18  C36  C35  C33   180.00   0.0  0
 P0D  CONST_13  H16  C33  C35  C36   180.00   0.0  0
 P0D  CONST_14  H1   O2   C    O1      0.00   0.0  0
 P0D  Var_01    C33  C31  C3'  C2'  -101.22  30.0  2
 P0D  Var_02    O1P  P1   C1'  C2'    47.30  30.0  1
 P0D  Var_03    O5P  P2   O2P  P1     30.21  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
 P0D  chir_01  C2'  C   C1'  C3'  negativ
 P0D  chir_03  C1   C2  N1   P1   positiv
 P0D  chir_04  P1   C1  O2P  C1'  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
 P0D  plan-1  C3'  0.020
 P0D  plan-1  C31  0.020
 P0D  plan-1  C33  0.020
 P0D  plan-1  C35  0.020
 P0D  plan-1  C36  0.020
 P0D  plan-1  C34  0.020
 P0D  plan-1  C32  0.020
 P0D  plan-1  H16  0.020
 P0D  plan-1  H17  0.020
 P0D  plan-1  H18  0.020
 P0D  plan-1  H19  0.020
 P0D  plan-1  H20  0.020
 P0D  plan-2  O2   0.020
 P0D  plan-2  C    0.020
 P0D  plan-2  O1   0.020
 P0D  plan-2  C2'  0.020
 P0D  plan-2  H1   0.020

