# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 17:40:21 2022
#   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  48  30  .  2022-03-18  2022-03-18
;
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  OC    -1  -0.624  14.1574  49.2957  40.4872
 G8W  CAZ  C  C      0   0.412  14.0612  48.0510  40.5234
 G8W  OBB  O  O      0  -0.604  13.0391  47.3790  40.2799
 G8W  CAY  C  CH2    0  -0.596  15.3567  47.2911  40.8825
 G8W  CAX  C  CH2    0  -0.432  15.1906  45.8059  41.1793
 G8W  CAT  C  CH1    0  -0.187  16.4872  45.0550  41.5030
 G8W  CAU  C  C      0   0.402  17.4831  45.1440  40.3162
 G8W  OAW  O  O      0  -0.615  17.1539  44.4999  39.2985
 G8W  OAV  O  OC    -1  -0.603  18.4948  45.8557  40.4604
 G8W  NAS  N  NH1    0  -0.671  17.0323  45.5352  42.7564
 G8W  CAA  C  C      0   0.719  18.1498  44.9375  43.2707
 G8W  OBD  O  O      0  -0.559  18.4888  43.7986  42.9563
 G8W  N    N  NH1    0  -0.685  18.8072  45.6612  44.2109
 G8W  CA   C  CH1    0  -0.164  20.1022  45.2869  44.7354
 G8W  C    C  C      0   0.405  20.3518  46.0684  46.0476
 G8W  O    O  O     -1  -0.601  19.8980  47.2310  46.0849
 G8W  OXT  O  OC     0  -0.598  21.0067  45.4876  46.9321
 G8W  CB   C  CH2    0  -0.427  21.2067  45.5885  43.7090
 G8W  CAL  C  CH2    0  -0.431  22.5971  45.1086  44.1057
 G8W  CAK  C  CH2    0  -0.592  23.6293  45.3440  43.0105
 G8W  CAB  C  C      0   0.546  23.9398  46.8088  42.7857
 G8W  OBC  O  O      0  -0.460  23.9341  47.6282  43.6855
 G8W  NAJ  N  NH1    0  -0.747  24.2621  47.1208  41.4999
 G8W  CAD  C  CR6    0   0.282  24.7179  48.3382  40.9946
 G8W  CAC  C  CR16   0  -0.221  25.2717  48.3454  39.7097
 G8W  CAE  C  CR16   0  -0.437  25.7341  49.5206  39.1583
 G8W  CAG  C  CR6    0   0.557  25.6189  50.6572  39.9402
 G8W  FAI  F  F      0  -0.305  26.0584  51.8250  39.4575
 G8W  NAH  N  N      0  -0.413  25.1037  50.6901  41.1307
 G8W  CAF  C  CR16   0  -0.102  24.6498  49.5576  41.6667
 G8W  H2   H  HCH2   0   0.224  16.0543  47.4262  40.0480
 G8W  H3   H  HCH2   0   0.206  15.8236  47.8134  41.7244
 G8W  H4   H  HCH2   0   0.208  14.4940  45.6729  42.0123
 G8W  H5   H  HCH2   0   0.213  14.7318  45.3157  40.3205
 G8W  H6   H  HCH1   0   0.220  16.2186  44.0034  41.6355
 G8W  H8   H  HNH1   0   0.368  16.9794  46.5341  42.8841
 G8W  H9   H  HNH1   0   0.366  18.5496  46.6202  44.3913
 G8W  H10  H  HCH1   0   0.212  20.1035  44.2163  44.9512
 G8W  H12  H  HCH2   0   0.212  21.2155  46.6679  43.5266
 G8W  H13  H  HCH2   0   0.221  20.9293  45.1165  42.7616
 G8W  H14  H  HCH2   0   0.228  22.5628  44.0364  44.3157
 G8W  H15  H  HCH2   0   0.229  22.9261  45.5884  45.0274
 G8W  H16  H  HCH2   0   0.255  23.3081  44.8695  42.0797
 G8W  H17  H  HCH2   0   0.285  24.5750  44.8635  43.2838
 G8W  H18  H  HNH1   0   0.419  24.2566  46.3576  40.8393
 G8W  H19  H  HCR6   0   0.297  25.3407  47.4246  39.1428
 G8W  H20  H  HCR6   0   0.293  26.1668  49.5496  38.1682
 G8W  H21  H  HCR6   0   0.290  24.2239  49.6351  42.6539

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  1.384  0.020  1.384
 G8W  OAW  CAU  deloc     1.249  0.020  1.249
 G8W  FAI  CAG  single    1.338  0.020  1.338
 G8W  OBB  CAZ  deloc     1.247  0.020  1.247
 G8W  CAC  CAD  aromatic  1.399  0.020  1.399
 G8W  CAG  NAH  aromatic  1.298  0.020  1.298
 G8W  CAU  OAV  deloc     1.245  0.020  1.245
 G8W  CAU  CAT  single    1.552  0.020  1.552
 G8W  CAZ  OBA  deloc     1.249  0.020  1.249
 G8W  CAZ  CAY  single    1.544  0.020  1.544
 G8W  CAD  NAJ  single    1.395  0.020  1.395
 G8W  CAD  CAF  aromatic  1.394  0.020  1.394
 G8W  CAY  CAX  single    1.524  0.020  1.524
 G8W  NAH  CAF  aromatic  1.333  0.020  1.333
 G8W  CAX  CAT  single    1.533  0.020  1.533
 G8W  NAJ  CAB  single    1.362  0.020  1.362
 G8W  CAT  NAS  single    1.449  0.020  1.449
 G8W  CAB  CAK  single    1.514  0.020  1.514
 G8W  CAB  OBC  double    1.217  0.020  1.217
 G8W  OBD  CAA  double    1.229  0.020  1.229
 G8W  NAS  CAA  single    1.368  0.020  1.368
 G8W  CAK  CAL  single    1.523  0.020  1.523
 G8W  CAA  N    single    1.356  0.020  1.356
 G8W  CB   CAL  single    1.523  0.020  1.523
 G8W  CB   CA   single    1.538  0.020  1.538
 G8W  N    CA   single    1.446  0.020  1.446
 G8W  CA   C    single    1.548  0.020  1.548
 G8W  C    O    deloc     1.249  0.020  1.249
 G8W  C    OXT  deloc     1.245  0.020  1.245
 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  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  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  CAY  CAZ  OBB  117.89  3.000
 G8W  CAY  CAZ  OBA  115.63  3.000
 G8W  OBB  CAZ  OBA  126.47  3.000
 G8W  H3   CAY  H2   104.78  3.000
 G8W  H3   CAY  CAX  111.19  3.000
 G8W  H2   CAY  CAX  109.75  3.000
 G8W  H3   CAY  CAZ  107.56  3.000
 G8W  H2   CAY  CAZ  107.24  3.000
 G8W  CAX  CAY  CAZ  115.69  3.000
 G8W  H5   CAX  H4   106.09  3.000
 G8W  H5   CAX  CAT  107.59  3.000
 G8W  H4   CAX  CAT  108.56  3.000
 G8W  H5   CAX  CAY  109.32  3.000
 G8W  H4   CAX  CAY  109.65  3.000
 G8W  CAT  CAX  CAY  115.24  3.000
 G8W  H6   CAT  NAS  107.84  3.000
 G8W  H6   CAT  CAU  107.79  3.000
 G8W  NAS  CAT  CAU  113.65  3.000
 G8W  H6   CAT  CAX  106.79  3.000
 G8W  NAS  CAT  CAX  109.79  3.000
 G8W  CAU  CAT  CAX  110.68  3.000
 G8W  OAV  CAU  OAW  127.12  3.000
 G8W  OAV  CAU  CAT  117.74  3.000
 G8W  OAW  CAU  CAT  115.12  3.000
 G8W  H8   NAS  CAA  115.35  3.000
 G8W  H8   NAS  CAT  114.72  3.000
 G8W  CAA  NAS  CAT  119.20  3.000
 G8W  N    CAA  OBD  122.54  3.000
 G8W  N    CAA  NAS  115.06  3.000
 G8W  OBD  CAA  NAS  122.28  3.000
 G8W  H9   N    CA   114.18  3.000
 G8W  H9   N    CAA  120.48  3.000
 G8W  CA   N    CAA  123.18  3.000
 G8W  H10  CA   CB   108.87  3.000
 G8W  H10  CA   C    109.10  3.000
 G8W  CB   CA   C    110.55  3.000
 G8W  H10  CA   N    109.05  3.000
 G8W  C    CA   N    108.73  3.000
 G8W  CB   CA   N    110.50  3.000
 G8W  OXT  C    O    127.20  3.000
 G8W  OXT  C    CA   116.86  3.000
 G8W  O    C    CA   115.91  3.000
 G8W  H13  CB   H12  106.44  3.000
 G8W  H13  CB   CAL  108.72  3.000
 G8W  H12  CB   CAL  110.28  3.000
 G8W  H13  CB   CA   108.13  3.000
 G8W  H12  CB   CA   108.09  3.000
 G8W  CAL  CB   CA   114.83  3.000
 G8W  H15  CAL  H14  106.19  3.000
 G8W  H15  CAL  CAK  109.60  3.000
 G8W  H14  CAL  CAK  108.11  3.000
 G8W  H15  CAL  CB   110.92  3.000
 G8W  H14  CAL  CB   109.30  3.000
 G8W  CAK  CAL  CB   112.49  3.000
 G8W  H17  CAK  H16  106.01  3.000
 G8W  H17  CAK  CAB  106.52  3.000
 G8W  H16  CAK  CAB  110.71  3.000
 G8W  H17  CAK  CAL  109.75  3.000
 G8W  H16  CAK  CAL  110.25  3.000
 G8W  CAB  CAK  CAL  113.28  3.000
 G8W  NAJ  CAB  OBC  123.02  3.000
 G8W  OBC  CAB  CAK  122.73  3.000
 G8W  NAJ  CAB  CAK  114.23  3.000
 G8W  H18  NAJ  CAD  115.13  3.000
 G8W  H18  NAJ  CAB  116.32  3.000
 G8W  CAD  NAJ  CAB  128.28  3.000
 G8W  CAF  CAD  CAC  117.24  3.000
 G8W  CAF  CAD  NAJ  124.95  3.000
 G8W  CAC  CAD  NAJ  117.81  3.000
 G8W  H19  CAC  CAE  119.61  3.000
 G8W  H19  CAC  CAD  120.09  3.000
 G8W  CAE  CAC  CAD  120.30  3.000
 G8W  H20  CAE  CAG  121.92  3.000
 G8W  H20  CAE  CAC  121.58  3.000
 G8W  CAG  CAE  CAC  116.50  3.000
 G8W  NAH  CAG  FAI  116.06  3.000
 G8W  NAH  CAG  CAE  124.90  3.000
 G8W  FAI  CAG  CAE  119.05  3.000
 G8W  CAF  NAH  CAG  118.86  3.000
 G8W  H21  CAF  NAH  116.22  3.000
 G8W  H21  CAF  CAD  121.58  3.000
 G8W  NAH  CAF  CAD  122.20  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_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_20  CA   N    CAA  OBD     0.00   0.0  0
 G8W  CONST_22  CA   N    CAA  NAS   180.00   0.0  0
 G8W  CONST_24  H9   N    CAA  OBD   180.00   0.0  0
 G8W  Var_01    CAX  CAY  CAZ  OBA   169.16  30.0  3
 G8W  Var_02    CAT  CAX  CAY  CAZ   178.66  30.0  3
 G8W  Var_03    CAK  CAL  CB   CA    175.86  30.0  3
 G8W  Var_04    CAB  CAK  CAL  CB     68.76  30.0  2
 G8W  Var_05    NAJ  CAB  CAK  CAL  -148.27  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-3  CA   0.020
 G8W  plan-3  C    0.020
 G8W  plan-3  O    0.020
 G8W  plan-3  OXT  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

