# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:31:30 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[(S)-[(2R)-2-(benzoylamino)-2-carboxyethoxy](hydroxy)phosphoryl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[P](O)(=O)OC[C@@H](NC(=O)c1ccccc1)C(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
 2H9  2H9  'N-[(S)-[(2R)-2-(benzoylamino)-2-carboxyethoxy](hydroxy)phosphoryl]-L-glutamic acid'  ligand  47  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2H9
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
 2H9  CAM  C  CR16  0  -0.304   2.1874   1.0902   1.1287
 2H9  CAK  C  CR16  0  -0.228   2.7147   2.2030   1.7655
 2H9  CAJ  C  CR16  0  -0.248   3.9517   2.7012   1.3828
 2H9  CAL  C  CR16  0  -0.240   4.6549   2.0860   0.3552
 2H9  CAN  C  CR16  0  -0.258   4.1220   0.9817  -0.2897
 2H9  CAY  C  CR6   0  -0.021   2.8863   0.4661   0.0955
 2H9  CAX  C  C     0   0.537   2.3524  -0.7037  -0.6674
 2H9  OAD  O  O     0  -0.462   2.8177  -1.0187  -1.7504
 2H9  NAR  N  NH1   0  -0.662   1.3180  -1.3681  -0.1016
 2H9  CBA  C  CH1   0  -0.261   0.6785  -2.4874  -0.7366
 2H9  CAW  C  C     0   0.556   0.6687  -3.6829   0.2050
 2H9  OAH  O  O     0  -0.423   1.1253  -3.6730   1.3170
 2H9  OAC  O  OH1   0  -0.585   0.1017  -4.7326  -0.3625
 2H9  CAQ  C  CH2   0  -0.169  -0.7272  -2.1452  -1.2123
 2H9  OAT  O  O2    0  -0.606  -1.5191  -1.9031  -0.0525
 2H9  PBB  P  P     0   1.456  -2.9431  -1.1606  -0.1897
 2H9  OAI  O  OH1   0  -0.737  -3.4492  -1.2762   1.3218
 2H9  OAE  O  O     0  -0.702  -3.8263  -1.6857  -1.2517
 2H9  N    N  NH1   0  -0.766  -2.5760   0.4369  -0.3837
 2H9  CA   C  CH1   0  -0.226  -1.7942   1.1776   0.5765
 2H9  C    C  C     0   0.557  -2.6497   1.7080   1.7183
 2H9  OXT  O  OH1   0  -0.587  -1.9176   1.9520   2.7944
 2H9  O    O  O     0  -0.429  -3.8305   1.9206   1.6374
 2H9  CB   C  CH2   0  -0.446  -1.0594   2.3508  -0.0826
 2H9  CG   C  CH2   0  -0.588  -0.2247   1.8902  -1.2667
 2H9  CD   C  C     0   0.561   0.8800   2.8465  -1.6218
 2H9  OE2  O  OH1   0  -0.591   1.6712   2.3469  -2.5643
 2H9  OE1  O  O     0  -0.437   1.0371   3.9382  -1.1362
 2H9  H1   H  HCR6  0   0.246   1.2134   0.7383   1.4451
 2H9  H2   H  HCR6  0   0.265   2.1542   2.6818   2.5573
 2H9  H3   H  HCR6  0   0.266   4.3647   3.5682   1.8814
 2H9  H4   H  HCR6  0   0.264   5.6200   2.4700   0.0526
 2H9  H5   H  HCR6  0   0.261   4.6720   0.5147  -1.0952
 2H9  H6   H  HNH1  0   0.412   1.0836  -1.1890   0.8613
 2H9  H7   H  HCH1  0   0.329   1.2599  -2.7641  -1.6204
 2H9  H8   H  HOH1  0   0.491   0.1002  -5.4877   0.2456
 2H9  H9   H  HCH2  0   0.259  -0.6781  -1.2598  -1.8515
 2H9  H10  H  HCH2  0   0.268  -1.1480  -2.9626  -1.7988
 2H9  H11  H  HOH1  0   0.499  -3.6223  -2.1756   1.6326
 2H9  H12  H  HNH1  0   0.409  -3.2540   0.9791  -0.9029
 2H9  H13  H  HCH1  0   0.276  -1.0421   0.5051   0.9970
 2H9  H14  H  HOH1  0   0.486  -2.4621   2.3466   3.4925
 2H9  H15  H  HCH2  0   0.267  -1.7816   3.1066  -0.4008
 2H9  H16  H  HCH2  0   0.266  -0.4253   2.8248   0.6680
 2H9  H17  H  HCH2  0   0.265   0.2121   0.9094  -1.0716
 2H9  H18  H  HCH2  0   0.302  -0.8485   1.7483  -2.1527
 2H9  H19  H  HOH1  0   0.477   2.3747   2.9788  -2.7736

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
 2H9  O    C    double    1.203  0.020  1.203
 2H9  OE1  CD   double    1.205  0.020  1.205
 2H9  CD   OE2  single    1.328  0.020  1.328
 2H9  CD   CG   single    1.504  0.020  1.504
 2H9  C    OXT  single    1.324  0.020  1.324
 2H9  C    CA   single    1.522  0.020  1.522
 2H9  CG   CB   single    1.520  0.020  1.520
 2H9  CB   CA   single    1.533  0.020  1.533
 2H9  CA   N    single    1.443  0.020  1.443
 2H9  CAL  CAJ  aromatic  1.389  0.020  1.389
 2H9  CAL  CAN  aromatic  1.385  0.020  1.385
 2H9  CAJ  CAK  aromatic  1.387  0.020  1.387
 2H9  CAN  CAY  aromatic  1.393  0.020  1.393
 2H9  OAE  PBB  double    1.478  0.020  1.478
 2H9  N    PBB  single    1.651  0.020  1.651
 2H9  CAK  CAM  aromatic  1.386  0.020  1.386
 2H9  CAY  CAM  aromatic  1.395  0.020  1.395
 2H9  CAY  CAX  single    1.495  0.020  1.495
 2H9  CAQ  OAT  single    1.425  0.020  1.425
 2H9  CAQ  CBA  single    1.523  0.020  1.523
 2H9  PBB  OAT  single    1.612  0.020  1.612
 2H9  PBB  OAI  single    1.598  0.020  1.598
 2H9  NAR  CAX  single    1.353  0.020  1.353
 2H9  NAR  CBA  single    1.437  0.020  1.437
 2H9  CAX  OAD  double    1.220  0.020  1.220
 2H9  CBA  CAW  single    1.522  0.020  1.522
 2H9  CAW  OAH  double    1.202  0.020  1.202
 2H9  CAW  OAC  single    1.321  0.020  1.321
 2H9  CAM  H1   single    0.930  0.020  1.080
 2H9  CAK  H2   single    0.930  0.020  1.080
 2H9  CAJ  H3   single    0.930  0.020  1.080
 2H9  CAL  H4   single    0.930  0.020  1.080
 2H9  CAN  H5   single    0.930  0.020  1.080
 2H9  NAR  H6   single    0.860  0.020  1.020
 2H9  CBA  H7   single    0.970  0.020  1.090
 2H9  OAC  H8   single    0.850  0.020  0.980
 2H9  CAQ  H9   single    0.970  0.020  1.090
 2H9  CAQ  H10  single    0.970  0.020  1.090
 2H9  OAI  H11  single    0.850  0.020  0.980
 2H9  N    H12  single    0.890  0.020  1.040
 2H9  CA   H13  single    0.970  0.020  1.090
 2H9  OXT  H14  single    0.850  0.020  0.980
 2H9  CB   H15  single    0.970  0.020  1.090
 2H9  CB   H16  single    0.970  0.020  1.090
 2H9  CG   H17  single    0.970  0.020  1.090
 2H9  CG   H18  single    0.970  0.020  1.090
 2H9  OE2  H19  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
 2H9  H1   CAM  CAY  121.45  3.000
 2H9  H1   CAM  CAK  117.95  3.000
 2H9  CAY  CAM  CAK  120.59  3.000
 2H9  H2   CAK  CAJ  120.33  3.000
 2H9  H2   CAK  CAM  119.63  3.000
 2H9  CAJ  CAK  CAM  120.04  3.000
 2H9  H3   CAJ  CAL  120.17  3.000
 2H9  H3   CAJ  CAK  120.07  3.000
 2H9  CAL  CAJ  CAK  119.76  3.000
 2H9  H4   CAL  CAN  119.73  3.000
 2H9  H4   CAL  CAJ  120.09  3.000
 2H9  CAN  CAL  CAJ  120.18  3.000
 2H9  H5   CAN  CAY  119.81  3.000
 2H9  H5   CAN  CAL  119.69  3.000
 2H9  CAY  CAN  CAL  120.50  3.000
 2H9  CAX  CAY  CAN  117.73  3.000
 2H9  CAX  CAY  CAM  123.30  3.000
 2H9  CAN  CAY  CAM  118.92  3.000
 2H9  NAR  CAX  OAD  122.40  3.000
 2H9  OAD  CAX  CAY  121.24  3.000
 2H9  NAR  CAX  CAY  116.34  3.000
 2H9  H6   NAR  CBA  117.22  3.000
 2H9  H6   NAR  CAX  119.36  3.000
 2H9  CBA  NAR  CAX  122.54  3.000
 2H9  H7   CBA  CAQ  107.17  3.000
 2H9  H7   CBA  CAW  107.74  3.000
 2H9  CAQ  CBA  CAW  111.34  3.000
 2H9  H7   CBA  NAR  108.51  3.000
 2H9  CAW  CBA  NAR  109.96  3.000
 2H9  CAQ  CBA  NAR  111.94  3.000
 2H9  OAC  CAW  OAH  124.53  3.000
 2H9  OAC  CAW  CBA  111.17  3.000
 2H9  OAH  CAW  CBA  124.30  3.000
 2H9  H8   OAC  CAW  110.49  3.000
 2H9  H10  CAQ  H9   108.05  3.000
 2H9  H10  CAQ  OAT  110.52  3.000
 2H9  H9   CAQ  OAT  111.30  3.000
 2H9  H10  CAQ  CBA  110.84  3.000
 2H9  H9   CAQ  CBA  108.86  3.000
 2H9  OAT  CAQ  CBA  107.27  3.000
 2H9  PBB  OAT  CAQ  119.99  3.000
 2H9  N    PBB  OAE  113.11  3.000
 2H9  N    PBB  OAI  104.57  3.000
 2H9  OAE  PBB  OAI  117.69  3.000
 2H9  OAI  PBB  OAT   99.55  3.000
 2H9  N    PBB  OAT  105.03  3.000
 2H9  OAE  PBB  OAT  115.18  3.000
 2H9  H11  OAI  PBB  115.34  3.000
 2H9  H12  N    CA   115.43  3.000
 2H9  H12  N    PBB  115.47  3.000
 2H9  CA   N    PBB  122.63  3.000
 2H9  H13  CA   CB   107.84  3.000
 2H9  H13  CA   C    108.21  3.000
 2H9  CB   CA   C    108.98  3.000
 2H9  H13  CA   N    108.23  3.000
 2H9  CB   CA   N    111.50  3.000
 2H9  C    CA   N    111.94  3.000
 2H9  O    C    OXT  124.40  3.000
 2H9  OXT  C    CA   111.29  3.000
 2H9  O    C    CA   124.26  3.000
 2H9  H14  OXT  C    110.47  3.000
 2H9  H16  CB   H15  106.50  3.000
 2H9  H16  CB   CG   110.39  3.000
 2H9  H15  CB   CG   110.22  3.000
 2H9  H16  CB   CA   108.38  3.000
 2H9  H15  CB   CA   109.74  3.000
 2H9  CG   CB   CA   111.48  3.000
 2H9  H18  CG   H17  104.87  3.000
 2H9  H18  CG   CD   108.09  3.000
 2H9  H17  CG   CD   108.65  3.000
 2H9  H18  CG   CB   110.94  3.000
 2H9  H17  CG   CB   110.66  3.000
 2H9  CD   CG   CB   113.25  3.000
 2H9  OE1  CD   OE2  123.30  3.000
 2H9  OE2  CD   CG   111.47  3.000
 2H9  OE1  CD   CG   125.22  3.000
 2H9  H19  OE2  CD   109.92  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
 2H9  CONST_01  CAL  CAJ  CAK  CAM     0.00   0.0  0
 2H9  CONST_02  CAL  CAN  CAY  CAM     0.00   0.0  0
 2H9  CONST_03  CAN  CAL  CAJ  CAK     0.00   0.0  0
 2H9  CONST_04  CAN  CAY  CAM  CAK     0.00   0.0  0
 2H9  CONST_05  CAY  CAN  CAL  CAJ     0.00   0.0  0
 2H9  CONST_06  CAY  CAM  CAK  CAJ     0.00   0.0  0
 2H9  CONST_07  CAX  CAY  CAM  CAK   180.00   0.0  0
 2H9  CONST_08  CAX  CAY  CAN  CAL   180.00   0.0  0
 2H9  CONST_09  H3   CAJ  CAK  CAM   180.00   0.0  0
 2H9  CONST_10  H5   CAN  CAY  CAM   180.00   0.0  0
 2H9  CONST_11  H4   CAL  CAJ  CAK   180.00   0.0  0
 2H9  CONST_12  H1   CAM  CAK  CAJ   180.00   0.0  0
 2H9  CONST_13  H2   CAK  CAJ  CAL   180.00   0.0  0
 2H9  CONST_14  CBA  NAR  CAX  CAY   180.00   0.0  0
 2H9  CONST_15  H6   NAR  CAX  CAY     0.00   0.0  0
 2H9  CONST_16  CBA  NAR  CAX  OAD     0.00   0.0  0
 2H9  CONST_17  H8   OAC  CAW  CBA   180.00   0.0  0
 2H9  CONST_18  H14  OXT  C    CA    180.00   0.0  0
 2H9  CONST_19  H19  OE2  CD   CG    180.00   0.0  0
 2H9  Var_01    NAR  CAX  CAY  CAM   -16.89  30.0  2
 2H9  Var_02    OAE  PBB  OAT  CAQ    47.86  30.0  2
 2H9  Var_03    CA   N    PBB  OAT   -57.36  30.0  1
 2H9  Var_04    CD   CG   CB   CA   -158.55  30.0  1
 2H9  Var_05    OE1  CD   CG   CB     -7.39  30.0  2
 2H9  Var_06    H9   CAQ  OAT  PBB    45.57  30.0  2

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
 2H9  chir_01  CBA  CAQ  NAR  CAW  negativ
 2H9  chir_03  CA   C    CB   N    positiv
 2H9  chir_04  PBB  N    OAT  OAI  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
 2H9  plan-1  CAM  0.020
 2H9  plan-1  CAK  0.020
 2H9  plan-1  CAJ  0.020
 2H9  plan-1  CAL  0.020
 2H9  plan-1  CAN  0.020
 2H9  plan-1  CAY  0.020
 2H9  plan-1  CAX  0.020
 2H9  plan-1  H1   0.020
 2H9  plan-1  H2   0.020
 2H9  plan-1  H3   0.020
 2H9  plan-1  H4   0.020
 2H9  plan-1  H5   0.020
 2H9  plan-2  CAY  0.020
 2H9  plan-2  CAX  0.020
 2H9  plan-2  OAD  0.020
 2H9  plan-2  NAR  0.020
 2H9  plan-2  CBA  0.020
 2H9  plan-2  H6   0.020
 2H9  plan-3  CBA  0.020
 2H9  plan-3  CAW  0.020
 2H9  plan-3  OAH  0.020
 2H9  plan-3  OAC  0.020
 2H9  plan-3  H8   0.020
 2H9  plan-4  CA   0.020
 2H9  plan-4  C    0.020
 2H9  plan-4  OXT  0.020
 2H9  plan-4  O    0.020
 2H9  plan-4  H14  0.020
 2H9  plan-5  CG   0.020
 2H9  plan-5  CD   0.020
 2H9  plan-5  OE2  0.020
 2H9  plan-5  OE1  0.020
 2H9  plan-5  H19  0.020

