# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:41:38 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-[(S)-[2-(benzoylamino)ethoxy](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)OCCNC(=O)c1ccccc1)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
 2GR  2GR  'N-[(S)-[2-(benzoylamino)ethoxy](hydroxy)phosphoryl]-L-glutamic acid'  ligand  44  25  .  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_2GR
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
 2GR  CAK  C  CR16  0  -0.270   5.9345   0.9123  -0.3212
 2GR  CAI  C  CR16  0  -0.243   7.0520   0.2174   0.1139
 2GR  CAH  C  CR16  0  -0.251   6.9038  -0.9792   0.8049
 2GR  CAJ  C  CR16  0  -0.241   5.6334  -1.4753   1.0631
 2GR  CAL  C  CR16  0  -0.291   4.5133  -0.7720   0.6426
 2GR  CAW  C  CR6   0  -0.027   4.6563   0.4302  -0.0473
 2GR  CAV  C  C     0   0.525   3.4810   1.2028  -0.5536
 2GR  OAC  O  O     0  -0.488   3.5557   1.8741  -1.5741
 2GR  NAQ  N  NH1   0  -0.636   2.3627   1.1208   0.1864
 2GR  CAM  C  CH2   0  -0.336   1.1049   1.6997  -0.2204
 2GR  CAN  C  CH2   0  -0.185   0.3334   0.8156  -1.1768
 2GR  OAS  O  O2    0  -0.596   0.0866  -0.4320  -0.5236
 2GR  PAY  P  P     0   1.450  -0.9283  -1.4839  -1.1874
 2GR  OAG  O  OH1   0  -0.740  -0.7579  -2.7067  -0.1691
 2GR  OAD  O  O     0  -0.709  -0.7095  -1.7540  -2.6249
 2GR  N    N  NH1   0  -0.768  -2.4383  -0.8969  -0.8690
 2GR  CA   C  CH1   0  -0.220  -2.9375  -0.7032   0.4718
 2GR  C    C  C     0   0.555  -3.5568  -1.9798   1.0231
 2GR  OXT  O  OH1   0  -0.589  -3.6161  -1.9581   2.3464
 2GR  O    O  O     0  -0.430  -3.9737  -2.8793   0.3421
 2GR  CB   C  CH2   0  -0.432  -3.9767   0.4241   0.5105
 2GR  CG   C  CH2   0  -0.588  -3.3652   1.7519   0.1008
 2GR  CD   C  C     0   0.558  -4.3374   2.8964   0.1736
 2GR  OE2  O  O     0  -0.442  -5.5096   2.7973   0.4374
 2GR  OE1  O  OH1   0  -0.595  -3.7473   4.0560  -0.0952
 2GR  H1   H  HCR6  0   0.261   6.0546   1.8378  -0.8688
 2GR  H2   H  HCR6  0   0.263   8.0405   0.6073  -0.0895
 2GR  H3   H  HCR6  0   0.264   7.7774  -1.5265   1.1342
 2GR  H4   H  HCR6  0   0.264   5.5114  -2.4137   1.5876
 2GR  H5   H  HCR6  0   0.257   3.5317  -1.1896   0.8316
 2GR  H6   H  HNH1  0   0.411   2.3773   0.5980   1.0461
 2GR  H7   H  HCH2  0   0.264   0.5160   1.8857   0.6779
 2GR  H8   H  HCH2  0   0.264   1.2731   2.6641  -0.6998
 2GR  H9   H  HCH2  0   0.242  -0.6059   1.3072  -1.4468
 2GR  H10  H  HCH2  0   0.248   0.9029   0.6504  -2.0933
 2GR  H11  H  HOH1  0   0.496   0.1301  -3.0867  -0.1255
 2GR  H12  H  HNH1  0   0.406  -3.1425  -1.1099  -1.5635
 2GR  H13  H  HCH1  0   0.288  -2.1043  -0.4172   1.1197
 2GR  H14  H  HOH1  0   0.486  -4.0561  -2.7553   2.6789
 2GR  H15  H  HCH2  0   0.255  -4.8088   0.1658  -0.1491
 2GR  H16  H  HCH2  0   0.266  -4.3824   0.4978   1.5203
 2GR  H17  H  HCH2  0   0.279  -2.5060   1.9914   0.7351
 2GR  H18  H  HCH2  0   0.293  -2.9776   1.7032  -0.9204
 2GR  H19  H  HOH1  0   0.480  -4.3922   4.7772  -0.0433

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
 2GR  O    C    double    1.203  0.020  1.203
 2GR  OE2  CD   double    1.206  0.020  1.206
 2GR  CD   OE1  single    1.329  0.020  1.329
 2GR  CD   CG   single    1.503  0.020  1.503
 2GR  C    OXT  single    1.325  0.020  1.325
 2GR  C    CA   single    1.522  0.020  1.522
 2GR  CG   CB   single    1.518  0.020  1.518
 2GR  CB   CA   single    1.534  0.020  1.534
 2GR  CA   N    single    1.444  0.020  1.444
 2GR  OAD  PAY  double    1.479  0.020  1.479
 2GR  N    PAY  single    1.651  0.020  1.651
 2GR  CAN  CAM  single    1.514  0.020  1.514
 2GR  CAN  OAS  single    1.430  0.020  1.430
 2GR  PAY  OAS  single    1.605  0.020  1.605
 2GR  PAY  OAG  single    1.600  0.020  1.600
 2GR  CAM  NAQ  single    1.443  0.020  1.443
 2GR  NAQ  CAV  single    1.343  0.020  1.343
 2GR  CAH  CAJ  aromatic  1.388  0.020  1.388
 2GR  CAH  CAI  aromatic  1.390  0.020  1.390
 2GR  CAJ  CAL  aromatic  1.388  0.020  1.388
 2GR  CAI  CAK  aromatic  1.386  0.020  1.386
 2GR  CAL  CAW  aromatic  1.394  0.020  1.394
 2GR  CAK  CAW  aromatic  1.393  0.020  1.393
 2GR  CAW  CAV  single    1.495  0.020  1.495
 2GR  CAV  OAC  double    1.224  0.020  1.224
 2GR  CAK  H1   single    0.930  0.020  1.080
 2GR  CAI  H2   single    0.930  0.020  1.080
 2GR  CAH  H3   single    0.930  0.020  1.080
 2GR  CAJ  H4   single    0.930  0.020  1.080
 2GR  CAL  H5   single    0.930  0.020  1.080
 2GR  NAQ  H6   single    0.860  0.020  1.020
 2GR  CAM  H7   single    0.970  0.020  1.090
 2GR  CAM  H8   single    0.970  0.020  1.090
 2GR  CAN  H9   single    0.970  0.020  1.090
 2GR  CAN  H10  single    0.970  0.020  1.090
 2GR  OAG  H11  single    0.850  0.020  0.980
 2GR  N    H12  single    0.890  0.020  1.040
 2GR  CA   H13  single    0.970  0.020  1.090
 2GR  OXT  H14  single    0.850  0.020  0.980
 2GR  CB   H15  single    0.970  0.020  1.090
 2GR  CB   H16  single    0.970  0.020  1.090
 2GR  CG   H17  single    0.970  0.020  1.090
 2GR  CG   H18  single    0.970  0.020  1.090
 2GR  OE1  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
 2GR  H1   CAK  CAW  119.82  3.000
 2GR  H1   CAK  CAI  119.88  3.000
 2GR  CAW  CAK  CAI  120.30  3.000
 2GR  H2   CAI  CAH  120.08  3.000
 2GR  H2   CAI  CAK  119.79  3.000
 2GR  CAH  CAI  CAK  120.12  3.000
 2GR  H3   CAH  CAJ  120.10  3.000
 2GR  H3   CAH  CAI  120.05  3.000
 2GR  CAJ  CAH  CAI  119.85  3.000
 2GR  H4   CAJ  CAL  119.69  3.000
 2GR  H4   CAJ  CAH  120.23  3.000
 2GR  CAL  CAJ  CAH  120.08  3.000
 2GR  H5   CAL  CAW  120.79  3.000
 2GR  H5   CAL  CAJ  118.89  3.000
 2GR  CAW  CAL  CAJ  120.29  3.000
 2GR  CAV  CAW  CAL  122.20  3.000
 2GR  CAV  CAW  CAK  118.42  3.000
 2GR  CAL  CAW  CAK  119.34  3.000
 2GR  NAQ  CAV  OAC  122.93  3.000
 2GR  OAC  CAV  CAW  121.19  3.000
 2GR  NAQ  CAV  CAW  115.87  3.000
 2GR  H6   NAQ  CAM  117.51  3.000
 2GR  H6   NAQ  CAV  119.35  3.000
 2GR  CAM  NAQ  CAV  123.07  3.000
 2GR  H8   CAM  H7   107.15  3.000
 2GR  H8   CAM  CAN  108.51  3.000
 2GR  H7   CAM  CAN  110.18  3.000
 2GR  H8   CAM  NAQ  110.14  3.000
 2GR  H7   CAM  NAQ  107.88  3.000
 2GR  CAN  CAM  NAQ  112.83  3.000
 2GR  H10  CAN  H9   107.98  3.000
 2GR  H10  CAN  OAS  109.97  3.000
 2GR  H9   CAN  OAS  110.90  3.000
 2GR  H10  CAN  CAM  110.67  3.000
 2GR  H9   CAN  CAM  109.33  3.000
 2GR  OAS  CAN  CAM  107.99  3.000
 2GR  PAY  OAS  CAN  119.47  3.000
 2GR  N    PAY  OAD  112.81  3.000
 2GR  N    PAY  OAG  104.26  3.000
 2GR  OAD  PAY  OAG  117.59  3.000
 2GR  OAG  PAY  OAS   99.80  3.000
 2GR  N    PAY  OAS  105.40  3.000
 2GR  OAD  PAY  OAS  115.34  3.000
 2GR  H11  OAG  PAY  115.26  3.000
 2GR  H12  N    CA   115.16  3.000
 2GR  H12  N    PAY  115.43  3.000
 2GR  CA   N    PAY  122.89  3.000
 2GR  H13  CA   CB   108.00  3.000
 2GR  H13  CA   C    108.34  3.000
 2GR  CB   CA   C    109.36  3.000
 2GR  H13  CA   N    108.78  3.000
 2GR  CB   CA   N    110.87  3.000
 2GR  C    CA   N    111.38  3.000
 2GR  O    C    OXT  124.22  3.000
 2GR  OXT  C    CA   111.48  3.000
 2GR  O    C    CA   124.27  3.000
 2GR  H14  OXT  C    110.45  3.000
 2GR  H16  CB   H15  106.95  3.000
 2GR  H16  CB   CG   109.91  3.000
 2GR  H15  CB   CG   110.52  3.000
 2GR  H16  CB   CA   108.97  3.000
 2GR  H15  CB   CA   109.09  3.000
 2GR  CG   CB   CA   111.29  3.000
 2GR  H18  CG   H17  105.82  3.000
 2GR  H18  CG   CD   107.96  3.000
 2GR  H17  CG   CD   108.24  3.000
 2GR  H18  CG   CB   110.85  3.000
 2GR  H17  CG   CB   110.56  3.000
 2GR  CD   CG   CB   113.10  3.000
 2GR  OE1  CD   OE2  123.22  3.000
 2GR  OE1  CD   CG   111.56  3.000
 2GR  OE2  CD   CG   125.22  3.000
 2GR  H19  OE1  CD   110.07  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
 2GR  CONST_01  CAJ  CAH  CAI  CAK     0.00   0.0  0
 2GR  CONST_02  CAJ  CAL  CAW  CAK     0.00   0.0  0
 2GR  CONST_03  CAL  CAJ  CAH  CAI     0.00   0.0  0
 2GR  CONST_04  CAL  CAW  CAK  CAI     0.00   0.0  0
 2GR  CONST_05  CAW  CAL  CAJ  CAH     0.00   0.0  0
 2GR  CONST_06  CAW  CAK  CAI  CAH     0.00   0.0  0
 2GR  CONST_07  CAV  CAW  CAK  CAI   180.00   0.0  0
 2GR  CONST_08  CAV  CAW  CAL  CAJ   180.00   0.0  0
 2GR  CONST_09  H3   CAH  CAI  CAK   180.00   0.0  0
 2GR  CONST_10  H5   CAL  CAW  CAK   180.00   0.0  0
 2GR  CONST_11  H4   CAJ  CAH  CAI   180.00   0.0  0
 2GR  CONST_12  H1   CAK  CAI  CAH   180.00   0.0  0
 2GR  CONST_13  H2   CAI  CAH  CAJ   180.00   0.0  0
 2GR  CONST_14  CAM  NAQ  CAV  CAW   180.00   0.0  0
 2GR  CONST_15  H6   NAQ  CAV  CAW     0.00   0.0  0
 2GR  CONST_16  CAM  NAQ  CAV  OAC     0.00   0.0  0
 2GR  CONST_17  H14  OXT  C    CA    180.00   0.0  0
 2GR  CONST_18  H19  OE1  CD   CG    180.00   0.0  0
 2GR  Var_01    NAQ  CAV  CAW  CAK  -150.00  30.0  2
 2GR  Var_02    CAN  CAM  NAQ  CAV    82.57  30.0  1
 2GR  Var_03    OAS  CAN  CAM  NAQ    59.24  30.0  2
 2GR  Var_04    OAD  PAY  OAS  CAN    48.55  30.0  2
 2GR  Var_05    CA   N    PAY  OAS   -60.59  30.0  2
 2GR  Var_06    CD   CG   CB   CA   -177.86  30.0  1
 2GR  Var_07    OE2  CD   CG   CB     -4.80  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
 2GR  chir_02  CA   C  CB   N    positiv
 2GR  chir_03  PAY  N  OAS  OAG  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
 2GR  plan-1  CAK  0.020
 2GR  plan-1  CAI  0.020
 2GR  plan-1  CAH  0.020
 2GR  plan-1  CAJ  0.020
 2GR  plan-1  CAL  0.020
 2GR  plan-1  CAW  0.020
 2GR  plan-1  CAV  0.020
 2GR  plan-1  H1   0.020
 2GR  plan-1  H2   0.020
 2GR  plan-1  H3   0.020
 2GR  plan-1  H4   0.020
 2GR  plan-1  H5   0.020
 2GR  plan-2  CAW  0.020
 2GR  plan-2  CAV  0.020
 2GR  plan-2  OAC  0.020
 2GR  plan-2  NAQ  0.020
 2GR  plan-2  CAM  0.020
 2GR  plan-2  H6   0.020
 2GR  plan-3  CA   0.020
 2GR  plan-3  C    0.020
 2GR  plan-3  OXT  0.020
 2GR  plan-3  O    0.020
 2GR  plan-3  H14  0.020
 2GR  plan-4  CG   0.020
 2GR  plan-4  CD   0.020
 2GR  plan-4  OE2  0.020
 2GR  plan-4  OE1  0.020
 2GR  plan-4  H19  0.020

