# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:27:50 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-6-[(6-fluoranylpyridin-3-yl)amino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](NC(=O)N[C@@H](CCCC(=O)Nc1ccc(F)nc1)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
 G8W  G8W  '(2~{S})-2-[[(2~{S})-6-[(6-fluoranylpyridin-3-yl)amino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid'  ligand  51  30  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G8W
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
 G8W  OBA  O  OH1   0  -0.570  14.9412  49.1792  39.3027
 G8W  CAZ  C  C     0   0.576  14.5038  48.2769  40.1743
 G8W  OBB  O  O     0  -0.438  13.3944  48.2999  40.6456
 G8W  CAY  C  CH2   0  -0.557  15.5574  47.2475  40.4803
 G8W  CAX  C  CH2   0  -0.488  15.0682  46.1876  41.4571
 G8W  CAT  C  CH1   0  -0.162  16.1403  45.1911  41.9136
 G8W  CAU  C  C     0   0.548  16.6707  44.4116  40.7230
 G8W  OAW  O  O     0  -0.457  16.1166  43.4298  40.2943
 G8W  OAV  O  OH1   0  -0.559  17.7412  44.9529  40.1662
 G8W  NAS  N  NH1   0  -0.682  17.1832  45.8741  42.6291
 G8W  CAA  C  C     0   0.791  18.1976  45.1582  43.1851
 G8W  OBD  O  O     0  -0.548  18.3164  43.9547  42.9843
 G8W  N    N  NH1   0  -0.679  19.0472  45.8775  43.9637
 G8W  CA   C  CH1   0  -0.185  20.2615  45.3110  44.4932
 G8W  C    C  C     0   0.543  20.4574  45.8270  45.9068
 G8W  O    O  O     0  -0.422  20.2262  46.9613  46.2396
 G8W  OXT  O  OH1   0  -0.562  20.9409  44.9022  46.7199
 G8W  CB   C  CH2   0  -0.421  21.4745  45.6681  43.6209
 G8W  CAL  C  CH2   0  -0.438  22.8004  45.0830  44.0941
 G8W  CAK  C  CH2   0  -0.571  23.9185  45.3212  43.0831
 G8W  CAB  C  C     0   0.541  24.2606  46.7898  42.9526
 G8W  OBC  O  O     0  -0.417  24.4420  47.4977  43.9270
 G8W  NAJ  N  NH1   0  -0.743  24.3513  47.2375  41.6735
 G8W  CAD  C  CR6   0   0.295  24.6858  48.5116  41.2140
 G8W  CAC  C  CR16  0  -0.215  24.8579  48.6752  39.8354
 G8W  CAE  C  CR16  0  -0.422  25.1769  49.9112  39.3175
 G8W  CAG  C  CR6   0   0.581  25.3142  50.9451  40.2280
 G8W  FAI  F  F     0  -0.290  25.6277  52.1656  39.7796
 G8W  NAH  N  N     0  -0.375  25.1599  50.8306  41.5111
 G8W  CAF  C  CR16  0  -0.086  24.8477  49.6383  42.0178
 G8W  H1   H  HOH1  0   0.457  14.2452  49.8282  39.1216
 G8W  H2   H  HCH2  0   0.277  15.8688  46.8053  39.5304
 G8W  H3   H  HCH2  0   0.267  16.4382  47.7735  40.8599
 G8W  H4   H  HCH2  0   0.275  14.6653  46.6608  42.3550
 G8W  H5   H  HCH2  0   0.268  14.2483  45.6200  41.0155
 G8W  H6   H  HCH1  0   0.289  15.6375  44.4583  42.5527
 G8W  H7   H  HOH1  0   0.455  18.0066  44.4313  39.3937
 G8W  H8   H  HNH1  0   0.374  16.9910  46.8046  42.9646
 G8W  H9   H  HNH1  0   0.375  18.9665  46.8831  43.9739
 G8W  H10  H  HCH1  0   0.279  20.1460  44.2277  44.5178
 G8W  H11  H  HOH1  0   0.459  21.1054  45.2793  47.5982
 G8W  H12  H  HCH2  0   0.245  21.5413  46.7580  43.5491
 G8W  H13  H  HCH2  0   0.231  21.2571  45.2998  42.6149
 G8W  H14  H  HCH2  0   0.234  22.6964  44.0058  44.2415
 G8W  H15  H  HCH2  0   0.256  23.0973  45.5030  45.0565
 G8W  H16  H  HCH2  0   0.216  23.6495  44.8840  42.1188
 G8W  H17  H  HCH2  0   0.285  24.8257  44.8084  43.4154
 G8W  H18  H  HNH1  0   0.371  24.1972  46.5530  40.9492
 G8W  H19  H  HCR6  0   0.240  24.7409  47.8300  39.1680
 G8W  H20  H  HCR6  0   0.264  25.3136  50.0627  38.2562
 G8W  H21  H  HCR6  0   0.296  24.7277  49.5915  43.0880

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
 G8W  CAE  CAC  aromatic  1.378  0.020  1.378
 G8W  CAE  CAG  aromatic  1.385  0.020  1.385
 G8W  OAW  CAU  double    1.206  0.020  1.206
 G8W  FAI  CAG  single    1.338  0.020  1.338
 G8W  OBB  CAZ  double    1.206  0.020  1.206
 G8W  CAC  CAD  aromatic  1.399  0.020  1.399
 G8W  CAG  NAH  aromatic  1.297  0.020  1.297
 G8W  CAU  OAV  single    1.322  0.020  1.322
 G8W  CAU  CAT  single    1.519  0.020  1.519
 G8W  CAZ  OBA  single    1.329  0.020  1.329
 G8W  CAZ  CAY  single    1.504  0.020  1.504
 G8W  CAD  NAJ  single    1.395  0.020  1.395
 G8W  CAD  CAF  aromatic  1.393  0.020  1.393
 G8W  CAY  CAX  single    1.522  0.020  1.522
 G8W  NAH  CAF  aromatic  1.333  0.020  1.333
 G8W  CAX  CAT  single    1.533  0.020  1.533
 G8W  NAJ  CAB  single    1.358  0.020  1.358
 G8W  CAT  NAS  single    1.437  0.020  1.437
 G8W  CAB  CAK  single    1.514  0.020  1.514
 G8W  CAB  OBC  double    1.218  0.020  1.218
 G8W  OBD  CAA  double    1.226  0.020  1.226
 G8W  NAS  CAA  single    1.360  0.020  1.360
 G8W  CAK  CAL  single    1.526  0.020  1.526
 G8W  CAA  N    single    1.358  0.020  1.358
 G8W  CB   CAL  single    1.525  0.020  1.525
 G8W  CB   CA   single    1.536  0.020  1.536
 G8W  N    CA   single    1.441  0.020  1.441
 G8W  CA   C    single    1.518  0.020  1.518
 G8W  C    O    double    1.204  0.020  1.204
 G8W  C    OXT  single    1.323  0.020  1.323
 G8W  OBA  H1   single    0.850  0.020  0.980
 G8W  CAY  H2   single    0.970  0.020  1.090
 G8W  CAY  H3   single    0.970  0.020  1.090
 G8W  CAX  H4   single    0.970  0.020  1.090
 G8W  CAX  H5   single    0.970  0.020  1.090
 G8W  CAT  H6   single    0.970  0.020  1.090
 G8W  OAV  H7   single    0.850  0.020  0.980
 G8W  NAS  H8   single    0.890  0.020  1.040
 G8W  N    H9   single    0.860  0.020  1.020
 G8W  CA   H10  single    0.970  0.020  1.090
 G8W  OXT  H11  single    0.850  0.020  0.980
 G8W  CB   H12  single    0.970  0.020  1.090
 G8W  CB   H13  single    0.970  0.020  1.090
 G8W  CAL  H14  single    0.970  0.020  1.090
 G8W  CAL  H15  single    0.970  0.020  1.090
 G8W  CAK  H16  single    0.970  0.020  1.090
 G8W  CAK  H17  single    0.970  0.020  1.090
 G8W  NAJ  H18  single    0.860  0.020  1.020
 G8W  CAC  H19  single    0.930  0.020  1.080
 G8W  CAE  H20  single    0.930  0.020  1.080
 G8W  CAF  H21  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
 G8W  H1   OBA  CAZ  109.95  3.000
 G8W  CAY  CAZ  OBB  125.31  3.000
 G8W  CAY  CAZ  OBA  111.57  3.000
 G8W  OBB  CAZ  OBA  123.12  3.000
 G8W  H3   CAY  H2   105.46  3.000
 G8W  H3   CAY  CAX  111.77  3.000
 G8W  H2   CAY  CAX  111.56  3.000
 G8W  H3   CAY  CAZ  107.78  3.000
 G8W  H2   CAY  CAZ  107.44  3.000
 G8W  CAX  CAY  CAZ  112.45  3.000
 G8W  H5   CAX  H4   106.32  3.000
 G8W  H5   CAX  CAT  107.93  3.000
 G8W  H4   CAX  CAT  107.15  3.000
 G8W  H5   CAX  CAY  110.13  3.000
 G8W  H4   CAX  CAY  110.15  3.000
 G8W  CAT  CAX  CAY  114.77  3.000
 G8W  H6   CAT  NAS  111.14  3.000
 G8W  H6   CAT  CAU  105.94  3.000
 G8W  NAS  CAT  CAU  112.38  3.000
 G8W  H6   CAT  CAX  106.72  3.000
 G8W  NAS  CAT  CAX  110.28  3.000
 G8W  CAU  CAT  CAX  110.15  3.000
 G8W  OAV  CAU  OAW  123.74  3.000
 G8W  OAV  CAU  CAT  113.74  3.000
 G8W  OAW  CAU  CAT  122.41  3.000
 G8W  H7   OAV  CAU  109.69  3.000
 G8W  H8   NAS  CAA  119.48  3.000
 G8W  H8   NAS  CAT  117.79  3.000
 G8W  CAA  NAS  CAT  119.63  3.000
 G8W  N    CAA  OBD  123.58  3.000
 G8W  N    CAA  NAS  114.96  3.000
 G8W  OBD  CAA  NAS  121.47  3.000
 G8W  H9   N    CA   117.10  3.000
 G8W  H9   N    CAA  118.92  3.000
 G8W  CA   N    CAA  121.97  3.000
 G8W  H10  CA   CB   109.12  3.000
 G8W  H10  CA   C    109.31  3.000
 G8W  CB   CA   C    110.36  3.000
 G8W  H10  CA   N    108.05  3.000
 G8W  C    CA   N    108.51  3.000
 G8W  CB   CA   N    111.44  3.000
 G8W  OXT  C    O    123.97  3.000
 G8W  OXT  C    CA   112.46  3.000
 G8W  O    C    CA   123.56  3.000
 G8W  H11  OXT  C    110.29  3.000
 G8W  H13  CB   H12  106.70  3.000
 G8W  H13  CB   CAL  109.23  3.000
 G8W  H12  CB   CAL  110.46  3.000
 G8W  H13  CB   CA   106.69  3.000
 G8W  H12  CB   CA   108.47  3.000
 G8W  CAL  CB   CA   114.92  3.000
 G8W  H15  CAL  H14  106.65  3.000
 G8W  H15  CAL  CAK  108.96  3.000
 G8W  H14  CAL  CAK  108.25  3.000
 G8W  H15  CAL  CB   111.26  3.000
 G8W  H14  CAL  CB   109.72  3.000
 G8W  CAK  CAL  CB   111.82  3.000
 G8W  H17  CAK  H16  106.54  3.000
 G8W  H17  CAK  CAB  107.08  3.000
 G8W  H16  CAK  CAB  111.58  3.000
 G8W  H17  CAK  CAL  109.46  3.000
 G8W  H16  CAK  CAL  109.99  3.000
 G8W  CAB  CAK  CAL  111.98  3.000
 G8W  NAJ  CAB  OBC  123.49  3.000
 G8W  OBC  CAB  CAK  121.91  3.000
 G8W  NAJ  CAB  CAK  114.59  3.000
 G8W  H18  NAJ  CAD  114.83  3.000
 G8W  H18  NAJ  CAB  116.26  3.000
 G8W  CAD  NAJ  CAB  128.85  3.000
 G8W  CAF  CAD  CAC  117.37  3.000
 G8W  CAF  CAD  NAJ  125.18  3.000
 G8W  CAC  CAD  NAJ  117.44  3.000
 G8W  H19  CAC  CAE  119.56  3.000
 G8W  H19  CAC  CAD  120.18  3.000
 G8W  CAE  CAC  CAD  120.26  3.000
 G8W  H20  CAE  CAG  121.91  3.000
 G8W  H20  CAE  CAC  121.62  3.000
 G8W  CAG  CAE  CAC  116.47  3.000
 G8W  NAH  CAG  FAI  116.11  3.000
 G8W  NAH  CAG  CAE  124.94  3.000
 G8W  FAI  CAG  CAE  118.96  3.000
 G8W  CAF  NAH  CAG  118.87  3.000
 G8W  H21  CAF  NAH  116.26  3.000
 G8W  H21  CAF  CAD  121.65  3.000
 G8W  NAH  CAF  CAD  122.09  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
 G8W  CONST_01  CAG  CAE  CAC  CAD     0.00   0.0  0
 G8W  CONST_02  CAG  NAH  CAF  CAD     0.00   0.0  0
 G8W  CONST_03  NAH  CAG  CAE  CAC     0.00   0.0  0
 G8W  CONST_04  NAH  CAF  CAD  CAC     0.00   0.0  0
 G8W  CONST_05  CAF  CAD  CAC  CAE     0.00   0.0  0
 G8W  CONST_06  CAF  NAH  CAG  CAE     0.00   0.0  0
 G8W  CONST_07  CAE  CAC  CAD  NAJ   180.00   0.0  0
 G8W  CONST_08  NAH  CAF  CAD  NAJ   180.00   0.0  0
 G8W  CONST_09  FAI  CAG  CAE  CAC   180.00   0.0  0
 G8W  CONST_10  CAF  NAH  CAG  FAI   180.00   0.0  0
 G8W  CONST_11  H20  CAE  CAC  CAD   180.00   0.0  0
 G8W  CONST_12  H21  CAF  CAD  CAC   180.00   0.0  0
 G8W  CONST_13  H19  CAC  CAE  CAG   180.00   0.0  0
 G8W  CONST_14  CAC  CAD  NAJ  CAB   180.00   0.0  0
 G8W  CONST_15  CAF  CAD  NAJ  CAB     0.00   0.0  0
 G8W  CONST_16  H18  NAJ  CAD  CAC     0.00   0.0  0
 G8W  CONST_17  CAD  NAJ  CAB  CAK   180.00   0.0  0
 G8W  CONST_18  CAD  NAJ  CAB  OBC     0.00   0.0  0
 G8W  CONST_19  OBD  CAA  NAS  CAT     0.00   0.0  0
 G8W  CONST_20  CA   N    CAA  OBD     0.00   0.0  0
 G8W  CONST_21  N    CAA  NAS  CAT   180.00   0.0  0
 G8W  CONST_22  CA   N    CAA  NAS   180.00   0.0  0
 G8W  CONST_23  H8   NAS  CAA  OBD   180.00   0.0  0
 G8W  CONST_24  H9   N    CAA  OBD   180.00   0.0  0
 G8W  CONST_25  H1   OBA  CAZ  OBB     0.00   0.0  0
 G8W  CONST_26  H7   OAV  CAU  CAT   180.00   0.0  0
 G8W  CONST_27  H11  OXT  C    CA    180.00   0.0  0
 G8W  Var_01    CAX  CAY  CAZ  OBA  -178.89  30.0  3
 G8W  Var_02    CAT  CAX  CAY  CAZ  -174.25  30.0  3
 G8W  Var_03    CAK  CAL  CB   CA    172.32  30.0  3
 G8W  Var_04    CAB  CAK  CAL  CB     66.62  30.0  2
 G8W  Var_05    NAJ  CAB  CAK  CAL  -132.39  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
 G8W  chir_01  CAT  CAU  CAX  NAS  positiv
 G8W  chir_02  CA   N    CB   C    negativ

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
 G8W  plan-1  NAJ  0.020
 G8W  plan-1  CAD  0.020
 G8W  plan-1  CAC  0.020
 G8W  plan-1  CAE  0.020
 G8W  plan-1  CAG  0.020
 G8W  plan-1  FAI  0.020
 G8W  plan-1  NAH  0.020
 G8W  plan-1  CAF  0.020
 G8W  plan-1  H19  0.020
 G8W  plan-1  H20  0.020
 G8W  plan-1  H21  0.020
 G8W  plan-2  CAT  0.020
 G8W  plan-2  CAU  0.020
 G8W  plan-2  OAW  0.020
 G8W  plan-2  OAV  0.020
 G8W  plan-2  H7   0.020
 G8W  plan-3  CA   0.020
 G8W  plan-3  C    0.020
 G8W  plan-3  O    0.020
 G8W  plan-3  OXT  0.020
 G8W  plan-3  H11  0.020
 G8W  plan-4  CAT  0.020
 G8W  plan-4  NAS  0.020
 G8W  plan-4  CAA  0.020
 G8W  plan-4  OBD  0.020
 G8W  plan-4  N    0.020
 G8W  plan-4  CA   0.020
 G8W  plan-4  H8   0.020
 G8W  plan-4  H9   0.020
 G8W  plan-5  CAK  0.020
 G8W  plan-5  CAB  0.020
 G8W  plan-5  OBC  0.020
 G8W  plan-5  NAJ  0.020
 G8W  plan-5  CAD  0.020
 G8W  plan-5  H18  0.020
 G8W  plan-6  OBA  0.020
 G8W  plan-6  CAZ  0.020
 G8W  plan-6  OBB  0.020
 G8W  plan-6  CAY  0.020
 G8W  plan-6  H1   0.020

