# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:54:35 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[(S)-[(2S)-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
 2G5  2G5  'N-[(S)-[(2S)-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_2G5
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
 2G5  CAM  C  CR16  0  -0.266   5.9923   0.6720   0.7478
 2G5  CAK  C  CR16  0  -0.242   7.1460  -0.0940   0.8034
 2G5  CAJ  C  CR16  0  -0.249   7.2089  -1.3087   0.1318
 2G5  CAL  C  CR16  0  -0.241   6.1127  -1.7555  -0.5934
 2G5  CAN  C  CR16  0  -0.289   4.9523  -0.9965  -0.6392
 2G5  CAY  C  CR6   0  -0.040   4.8825   0.2209   0.0362
 2G5  CAX  C  C     0   0.548   3.6677   1.0864   0.0020
 2G5  OAD  O  O     0  -0.477   3.7380   2.2966   0.1470
 2G5  NAR  N  NH1   0  -0.647   2.4961   0.4505  -0.2161
 2G5  CBA  C  CH1   0  -0.249   1.2491   1.1591  -0.2142
 2G5  CAW  C  C     0   0.563   0.7722   1.4144   1.2130
 2G5  OAH  O  OH1   0  -0.593  -0.3801   2.0703   1.2244
 2G5  OAC  O  O     0  -0.416   1.3663   1.0733   2.1983
 2G5  CAQ  C  CH2   0  -0.196   0.2054   0.4096  -1.0228
 2G5  OAT  O  O2    0  -0.603  -0.0737  -0.8062  -0.3317
 2G5  PBB  P  P     0   1.440  -1.1279  -1.8565  -0.9534
 2G5  OAI  O  OH1   0  -0.765  -0.9099  -3.0700   0.0516
 2G5  OAE  O  O     0  -0.707  -0.9138  -2.1865  -2.3779
 2G5  N    N  NH1   0  -0.787  -2.6092  -1.1658  -0.6774
 2G5  CA   C  CH1   0  -0.236  -3.0690  -0.5603   0.5507
 2G5  C    C  C     0   0.623  -3.5133  -1.6148   1.5632
 2G5  O    O  O     0  -0.468  -3.1453  -2.7697   1.5338
 2G5  OXT  O  OH1   0  -0.566  -4.3025  -1.1400   2.4975
 2G5  CB   C  CH2   0  -0.447  -4.1540   0.4797   0.2572
 2G5  CG   C  CH2   0  -0.590  -3.6487   1.5624  -0.6808
 2G5  CD   C  C     0   0.563  -4.6895   2.6065  -0.9777
 2G5  OE2  O  OH1   0  -0.595  -4.2266   3.5354  -1.8073
 2G5  OE1  O  O     0  -0.443  -5.8095   2.6200  -0.5316
 2G5  H1   H  HCR6  0   0.261   5.9501   1.6197   1.2681
 2G5  H2   H  HCR6  0   0.264   7.9979   0.2576   1.3703
 2G5  H3   H  HCR6  0   0.266   8.1120  -1.9038   0.1684
 2G5  H4   H  HCR6  0   0.266   6.1610  -2.6936  -1.1302
 2G5  H5   H  HCR6  0   0.262   4.1175  -1.3536  -1.2293
 2G5  H6   H  HNH1  0   0.410   2.4568  -0.5501  -0.0971
 2G5  H7   H  HCH1  0   0.325   1.3893   2.1303  -0.6972
 2G5  H8   H  HOH1  0   0.490  -0.6725   2.2273   2.1354
 2G5  H9   H  HCH2  0   0.265  -0.6959   1.0151  -1.1292
 2G5  H10  H  HCH2  0   0.278   0.6018   0.2087  -2.0201
 2G5  H11  H  HOH1  0   0.499  -1.6849  -3.1788   0.6466
 2G5  H12  H  HNH1  0   0.414  -3.3453  -1.4647  -1.3045
 2G5  H13  H  HCH1  0   0.302  -2.2253  -0.0439   1.0239
 2G5  H14  H  HOH1  0   0.496  -4.5200  -1.8288   3.1457
 2G5  H15  H  HCH2  0   0.259  -5.0251  -0.0200  -0.1744
 2G5  H16  H  HCH2  0   0.271  -4.4783   0.9322   1.1928
 2G5  H17  H  HCH2  0   0.280  -2.7777   2.0691  -0.2530
 2G5  H18  H  HCH2  0   0.288  -3.3125   1.1410  -1.6317
 2G5  H19  H  HOH1  0   0.481  -4.9142   4.1950  -1.9826

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
 2G5  O    C    double    1.212  0.020  1.212
 2G5  OE1  CD   double    1.206  0.020  1.206
 2G5  CD   OE2  single    1.329  0.020  1.329
 2G5  CD   CG   single    1.504  0.020  1.504
 2G5  C    OXT  single    1.312  0.020  1.312
 2G5  C    CA   single    1.528  0.020  1.528
 2G5  CG   CB   single    1.519  0.020  1.519
 2G5  CB   CA   single    1.531  0.020  1.531
 2G5  CA   N    single    1.444  0.020  1.444
 2G5  CAK  CAJ  aromatic  1.389  0.020  1.389
 2G5  CAK  CAM  aromatic  1.386  0.020  1.386
 2G5  CAJ  CAL  aromatic  1.388  0.020  1.388
 2G5  CAM  CAY  aromatic  1.393  0.020  1.393
 2G5  OAE  PBB  double    1.478  0.020  1.478
 2G5  N    PBB  single    1.658  0.020  1.658
 2G5  CAL  CAN  aromatic  1.387  0.020  1.387
 2G5  CAY  CAN  aromatic  1.394  0.020  1.394
 2G5  CAY  CAX  single    1.492  0.020  1.492
 2G5  CAQ  CBA  single    1.518  0.020  1.518
 2G5  CAQ  OAT  single    1.426  0.020  1.426
 2G5  NAR  CAX  single    1.351  0.020  1.351
 2G5  NAR  CBA  single    1.434  0.020  1.434
 2G5  PBB  OAT  single    1.613  0.020  1.613
 2G5  PBB  OAI  single    1.591  0.020  1.591
 2G5  CAX  OAD  double    1.221  0.020  1.221
 2G5  CBA  CAW  single    1.526  0.020  1.526
 2G5  CAW  OAC  double    1.200  0.020  1.200
 2G5  CAW  OAH  single    1.326  0.020  1.326
 2G5  CAM  H1   single    0.930  0.020  1.080
 2G5  CAK  H2   single    0.930  0.020  1.080
 2G5  CAJ  H3   single    0.930  0.020  1.080
 2G5  CAL  H4   single    0.930  0.020  1.080
 2G5  CAN  H5   single    0.930  0.020  1.080
 2G5  NAR  H6   single    0.860  0.020  1.020
 2G5  CBA  H7   single    0.970  0.020  1.090
 2G5  OAH  H8   single    0.850  0.020  0.980
 2G5  CAQ  H9   single    0.970  0.020  1.090
 2G5  CAQ  H10  single    0.970  0.020  1.090
 2G5  OAI  H11  single    0.850  0.020  0.980
 2G5  N    H12  single    0.890  0.020  1.040
 2G5  CA   H13  single    0.970  0.020  1.090
 2G5  OXT  H14  single    0.850  0.020  0.980
 2G5  CB   H15  single    0.970  0.020  1.090
 2G5  CB   H16  single    0.970  0.020  1.090
 2G5  CG   H17  single    0.970  0.020  1.090
 2G5  CG   H18  single    0.970  0.020  1.090
 2G5  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
 2G5  H1   CAM  CAY  119.87  3.000
 2G5  H1   CAM  CAK  119.82  3.000
 2G5  CAY  CAM  CAK  120.30  3.000
 2G5  H2   CAK  CAJ  120.11  3.000
 2G5  H2   CAK  CAM  119.79  3.000
 2G5  CAJ  CAK  CAM  120.10  3.000
 2G5  H3   CAJ  CAL  119.98  3.000
 2G5  H3   CAJ  CAK  120.14  3.000
 2G5  CAL  CAJ  CAK  119.88  3.000
 2G5  H4   CAL  CAN  119.69  3.000
 2G5  H4   CAL  CAJ  120.20  3.000
 2G5  CAN  CAL  CAJ  120.11  3.000
 2G5  H5   CAN  CAY  120.89  3.000
 2G5  H5   CAN  CAL  118.85  3.000
 2G5  CAY  CAN  CAL  120.24  3.000
 2G5  CAX  CAY  CAN  122.43  3.000
 2G5  CAX  CAY  CAM  118.19  3.000
 2G5  CAN  CAY  CAM  119.36  3.000
 2G5  NAR  CAX  OAD  122.40  3.000
 2G5  OAD  CAX  CAY  121.70  3.000
 2G5  NAR  CAX  CAY  115.90  3.000
 2G5  H6   NAR  CBA  117.14  3.000
 2G5  H6   NAR  CAX  118.81  3.000
 2G5  CBA  NAR  CAX  121.42  3.000
 2G5  H7   CBA  CAQ  106.94  3.000
 2G5  H7   CBA  CAW  107.73  3.000
 2G5  CAQ  CBA  CAW  111.46  3.000
 2G5  H7   CBA  NAR  109.07  3.000
 2G5  CAW  CBA  NAR  110.83  3.000
 2G5  CAQ  CBA  NAR  110.68  3.000
 2G5  OAC  CAW  OAH  124.31  3.000
 2G5  OAH  CAW  CBA  111.24  3.000
 2G5  OAC  CAW  CBA  124.44  3.000
 2G5  H8   OAH  CAW  110.50  3.000
 2G5  H10  CAQ  H9   108.23  3.000
 2G5  H10  CAQ  OAT  110.91  3.000
 2G5  H9   CAQ  OAT  111.02  3.000
 2G5  H10  CAQ  CBA  109.13  3.000
 2G5  H9   CAQ  CBA  110.24  3.000
 2G5  OAT  CAQ  CBA  107.30  3.000
 2G5  PBB  OAT  CAQ  119.76  3.000
 2G5  N    PBB  OAE  112.52  3.000
 2G5  N    PBB  OAI  109.58  3.000
 2G5  OAE  PBB  OAI  114.76  3.000
 2G5  OAI  PBB  OAT   99.42  3.000
 2G5  N    PBB  OAT  104.40  3.000
 2G5  OAE  PBB  OAT  114.98  3.000
 2G5  H11  OAI  PBB  111.03  3.000
 2G5  H12  N    CA   114.78  3.000
 2G5  H12  N    PBB  115.07  3.000
 2G5  CA   N    PBB  126.92  3.000
 2G5  H13  CA   CB   107.94  3.000
 2G5  H13  CA   C    105.24  3.000
 2G5  CB   CA   C    112.94  3.000
 2G5  H13  CA   N    108.63  3.000
 2G5  CB   CA   N    110.32  3.000
 2G5  C    CA   N    111.51  3.000
 2G5  OXT  C    O    122.99  3.000
 2G5  OXT  C    CA   113.40  3.000
 2G5  O    C    CA   123.58  3.000
 2G5  H14  OXT  C    110.71  3.000
 2G5  H16  CB   H15  106.97  3.000
 2G5  H16  CB   CG   109.48  3.000
 2G5  H15  CB   CG   110.31  3.000
 2G5  H16  CB   CA   109.18  3.000
 2G5  H15  CB   CA   109.26  3.000
 2G5  CG   CB   CA   111.52  3.000
 2G5  H18  CG   H17  105.88  3.000
 2G5  H18  CG   CD   107.99  3.000
 2G5  H17  CG   CD   107.85  3.000
 2G5  H18  CG   CB   111.39  3.000
 2G5  H17  CG   CB   110.69  3.000
 2G5  CD   CG   CB   112.74  3.000
 2G5  OE1  CD   OE2  123.15  3.000
 2G5  OE2  CD   CG   111.57  3.000
 2G5  OE1  CD   CG   125.29  3.000
 2G5  H19  OE2  CD   109.98  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
 2G5  CONST_01  CAL  CAJ  CAK  CAM     0.00   0.0  0
 2G5  CONST_02  CAL  CAN  CAY  CAM     0.00   0.0  0
 2G5  CONST_03  CAN  CAL  CAJ  CAK     0.00   0.0  0
 2G5  CONST_04  CAN  CAY  CAM  CAK     0.00   0.0  0
 2G5  CONST_05  CAY  CAM  CAK  CAJ     0.00   0.0  0
 2G5  CONST_06  CAY  CAN  CAL  CAJ     0.00   0.0  0
 2G5  CONST_07  CAX  CAY  CAM  CAK   180.00   0.0  0
 2G5  CONST_08  CAX  CAY  CAN  CAL   180.00   0.0  0
 2G5  CONST_09  H3   CAJ  CAK  CAM   180.00   0.0  0
 2G5  CONST_10  H5   CAN  CAY  CAM   180.00   0.0  0
 2G5  CONST_11  H4   CAL  CAJ  CAK   180.00   0.0  0
 2G5  CONST_12  H1   CAM  CAK  CAJ   180.00   0.0  0
 2G5  CONST_13  H2   CAK  CAJ  CAL   180.00   0.0  0
 2G5  CONST_14  CBA  NAR  CAX  CAY   180.00   0.0  0
 2G5  CONST_16  CBA  NAR  CAX  OAD     0.00   0.0  0
 2G5  CONST_17  H8   OAH  CAW  CBA   180.00   0.0  0
 2G5  CONST_18  H14  OXT  C    CA    180.00   0.0  0
 2G5  CONST_19  H19  OE2  CD   CG    180.00   0.0  0
 2G5  Var_01    NAR  CAX  CAY  CAM  -155.13  30.0  2
 2G5  Var_02    OAE  PBB  OAT  CAQ    49.15  30.0  1
 2G5  Var_03    CA   N    PBB  OAT   -45.57  30.0  1
 2G5  Var_04    CD   CG   CB   CA   -179.46  30.0  1
 2G5  Var_05    OE1  CD   CG   CB      0.45  30.0  2
 2G5  Var_06    H9   CAQ  OAT  PBB    60.89  30.0  1

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
 2G5  chir_01  CBA  CAQ  NAR  CAW  positiv
 2G5  chir_03  CA   C    CB   N    positiv
 2G5  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
 2G5  plan-1  CAM  0.020
 2G5  plan-1  CAK  0.020
 2G5  plan-1  CAJ  0.020
 2G5  plan-1  CAL  0.020
 2G5  plan-1  CAN  0.020
 2G5  plan-1  CAY  0.020
 2G5  plan-1  CAX  0.020
 2G5  plan-1  H1   0.020
 2G5  plan-1  H2   0.020
 2G5  plan-1  H3   0.020
 2G5  plan-1  H4   0.020
 2G5  plan-1  H5   0.020
 2G5  plan-2  CAY  0.020
 2G5  plan-2  CAX  0.020
 2G5  plan-2  OAD  0.020
 2G5  plan-2  NAR  0.020
 2G5  plan-2  CBA  0.020
 2G5  plan-2  H6   0.020
 2G5  plan-3  CBA  0.020
 2G5  plan-3  CAW  0.020
 2G5  plan-3  OAH  0.020
 2G5  plan-3  OAC  0.020
 2G5  plan-3  H8   0.020
 2G5  plan-4  CA   0.020
 2G5  plan-4  C    0.020
 2G5  plan-4  O    0.020
 2G5  plan-4  OXT  0.020
 2G5  plan-4  H14  0.020
 2G5  plan-5  CG   0.020
 2G5  plan-5  CD   0.020
 2G5  plan-5  OE2  0.020
 2G5  plan-5  OE1  0.020
 2G5  plan-5  H19  0.020

