# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:07:32 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: N-({6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H](N[S](=O)(=O)c1ccc2cc(OCc3ccc(cc3F)C#N)ccc2c1)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
 LKM  LKM  'N-({6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid'  ligand  51  34  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LKM
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
 LKM  N31   N  NS     0  -0.240   1.2085  -11.8108  -21.3641
 LKM  C30   C  CSP    0   0.061   0.6322  -12.7978  -21.5047
 LKM  C27   C  CR6    0   0.012  -0.0826  -14.0224  -21.6692
 LKM  C28   C  CR16   0  -0.235  -0.5869  -14.6848  -20.5522
 LKM  C29   C  CR16   0  -0.245  -1.2623  -15.8797  -20.7195
 LKM  C26   C  CR16   0  -0.390  -0.2588  -14.5483  -22.9461
 LKM  C25   C  CR6    0   0.561  -0.9363  -15.7423  -23.0687
 LKM  C24   C  CR6    0  -0.162  -1.4434  -16.4391  -21.9815
 LKM  C23   C  CH2    0  -0.247  -2.1738  -17.7477  -22.1539
 LKM  O22   O  O2     0  -0.476  -1.9832  -18.6072  -21.0512
 LKM  C20   C  CR6    0   0.414  -0.7586  -19.1312  -20.8246
 LKM  C19   C  CR16   0  -0.349   0.3112  -19.0371  -21.7444
 LKM  C18   C  CR16   0  -0.287   1.5224  -19.5943  -21.4390
 LKM  C21   C  CR16   0  -0.433  -0.5851  -19.7894  -19.6289
 LKM  C15   C  CR66   0   0.152   0.6542  -20.3673  -19.3028
 LKM  C16   C  CR66   0   0.112   1.7324  -20.2672  -20.2185
 LKM  C17   C  CR16   0  -0.294   2.9832  -20.8339  -19.8893
 LKM  C14   C  CR16   0  -0.310   0.8661  -21.0434  -18.0728
 LKM  C13   C  CR16   0  -0.228   2.0811  -21.5804  -17.7675
 LKM  C12   C  CR6    0  -0.209   3.1442  -21.4732  -18.6937
 LKM  S11   S  S      0   1.367   4.7268  -22.1277  -18.2547
 LKM  O33   O  OS     0  -0.653   5.6232  -21.8854  -19.3810
 LKM  O32   O  OS     0  -0.666   5.1091  -21.6147  -16.9449
 LKM  N     N  NC1    0  -0.724   4.3720  -23.7208  -18.0363
 LKM  CA    C  CH1    0  -0.210   4.2912  -24.5569  -19.2437
 LKM  C     C  C      0   0.423   5.7015  -25.0305  -19.6741
 LKM  OXT   O  OC     0  -0.595   5.9032  -25.1787  -20.8915
 LKM  O     O  O     -1  -0.602   6.4931  -25.2587  -18.7360
 LKM  CB    C  CH2    0  -0.407   3.3718  -25.7378  -18.9226
 LKM  CG    C  CH2    0  -0.587   3.0670  -26.6270  -20.1160
 LKM  CD    C  C      0   0.410   2.0560  -27.7633  -19.8572
 LKM  OE1   O  OC    -1  -0.625   1.7572  -28.4527  -20.8551
 LKM  OE2   O  O      0  -0.605   1.6254  -27.9112  -18.6960
 LKM  F2    F  F      0  -0.301  -1.0953  -16.2543  -24.2957
 LKM  H28   H  HCR6   0   0.286  -0.4502  -14.2699  -19.5634
 LKM  H26   H  HCR6   0   0.304   0.1292  -14.0453  -23.8219
 LKM  H29   H  HCR6   0   0.288  -1.6496  -16.3886  -19.8471
 LKM  H231  H  HCH2   0   0.299  -3.2487  -17.5637  -22.1923
 LKM  H232  H  HCH2   0   0.262  -1.9040  -18.2369  -23.0926
 LKM  H19   H  HCR6   0   0.290   0.1990  -18.5399  -22.6975
 LKM  H21   H  HCR6   0   0.268  -1.4083  -19.8576  -18.9277
 LKM  H18   H  HCR6   0   0.270   2.3379  -19.5168  -22.1473
 LKM  H14   H  HCR6   0   0.265   0.0472  -21.1257  -17.3691
 LKM  H17   H  HCR6   0   0.281   3.7991  -20.7517  -20.5960
 LKM  H13   H  HCR6   0   0.277   2.2255  -22.0935  -16.8260
 LKM  H     H  HNC1   0   0.390   5.0460  -24.1282  -17.3876
 LKM  HA    H  HCH1   0   0.233   3.8311  -23.9685  -20.0433
 LKM  HBC1  H  HCH2   0   0.206   3.8234  -26.3258  -18.1181
 LKM  HBC2  H  HCH2   0   0.216   2.4399  -25.3332  -18.5204
 LKM  HGC1  H  HCH2   0   0.211   2.6871  -26.0156  -20.9426
 LKM  HGC2  H  HCH2   0   0.224   3.9860  -27.0785  -20.5007

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
 LKM  N31  C30   triple    1.152  0.020  1.152
 LKM  C30  C27   single    1.428  0.020  1.428
 LKM  C27  C28   aromatic  1.393  0.020  1.393
 LKM  C27  C26   aromatic  1.392  0.020  1.392
 LKM  C28  C29   aromatic  1.383  0.020  1.383
 LKM  C29  C24   aromatic  1.392  0.020  1.392
 LKM  C26  C25   aromatic  1.378  0.020  1.378
 LKM  C25  C24   aromatic  1.387  0.020  1.387
 LKM  C25  F2    single    1.339  0.020  1.339
 LKM  C24  C23   single    1.509  0.020  1.509
 LKM  C23  O22   single    1.411  0.020  1.411
 LKM  O22  C20   single    1.351  0.020  1.351
 LKM  C20  C19   aromatic  1.414  0.020  1.414
 LKM  C20  C21   aromatic  1.376  0.020  1.376
 LKM  C19  C18   aromatic  1.368  0.020  1.368
 LKM  C18  C16   aromatic  1.409  0.020  1.409
 LKM  C21  C15   aromatic  1.406  0.020  1.406
 LKM  C15  C16   aromatic  1.418  0.020  1.418
 LKM  C15  C14   aromatic  1.419  0.020  1.419
 LKM  C16  C17   aromatic  1.412  0.020  1.412
 LKM  C17  C12   aromatic  1.365  0.020  1.365
 LKM  C14  C13   aromatic  1.363  0.020  1.363
 LKM  C13  C12   aromatic  1.414  0.020  1.414
 LKM  C12  S11   single    1.768  0.020  1.768
 LKM  S11  O33   double    1.460  0.020  1.460
 LKM  S11  O32   double    1.458  0.020  1.458
 LKM  S11  N     single    1.647  0.020  1.647
 LKM  N    CA    single    1.471  0.020  1.471
 LKM  CA   C     single    1.549  0.020  1.549
 LKM  CA   CB    single    1.531  0.020  1.531
 LKM  C    OXT   deloc     1.243  0.020  1.243
 LKM  C    O     deloc     1.248  0.020  1.248
 LKM  CB   CG    single    1.519  0.020  1.519
 LKM  CG   CD    single    1.543  0.020  1.543
 LKM  CD   OE1   deloc     1.249  0.020  1.249
 LKM  CD   OE2   deloc     1.247  0.020  1.247
 LKM  C28  H28   single    0.930  0.020  1.080
 LKM  C26  H26   single    0.930  0.020  1.080
 LKM  C29  H29   single    0.930  0.020  1.080
 LKM  C23  H231  single    0.970  0.020  1.090
 LKM  C23  H232  single    0.970  0.020  1.090
 LKM  C19  H19   single    0.930  0.020  1.080
 LKM  C21  H21   single    0.930  0.020  1.080
 LKM  C18  H18   single    0.930  0.020  1.080
 LKM  C14  H14   single    0.930  0.020  1.080
 LKM  C17  H17   single    0.930  0.020  1.080
 LKM  C13  H13   single    0.930  0.020  1.080
 LKM  N    H     single    0.860  0.020  1.020
 LKM  CA   HA    single    0.970  0.020  1.090
 LKM  CB   HBC1  single    0.970  0.020  1.090
 LKM  CB   HBC2  single    0.970  0.020  1.090
 LKM  CG   HGC1  single    0.970  0.020  1.090
 LKM  CG   HGC2  single    0.970  0.020  1.090

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
 LKM  C27   C30  N31   180.00  3.000
 LKM  C26   C27  C28   120.66  3.000
 LKM  C26   C27  C30   119.55  3.000
 LKM  C28   C27  C30   119.78  3.000
 LKM  H28   C28  C29   120.28  3.000
 LKM  H28   C28  C27   120.34  3.000
 LKM  C29   C28  C27   119.38  3.000
 LKM  H29   C29  C24   119.70  3.000
 LKM  H29   C29  C28   118.94  3.000
 LKM  C24   C29  C28   121.36  3.000
 LKM  H26   C26  C25   120.46  3.000
 LKM  H26   C26  C27   121.43  3.000
 LKM  C25   C26  C27   118.11  3.000
 LKM  F2    C25  C24   118.86  3.000
 LKM  F2    C25  C26   118.11  3.000
 LKM  C24   C25  C26   123.03  3.000
 LKM  C23   C24  C25   121.54  3.000
 LKM  C23   C24  C29   121.00  3.000
 LKM  C25   C24  C29   117.45  3.000
 LKM  H232  C23  H231  106.77  3.000
 LKM  H232  C23  O22   111.43  3.000
 LKM  H231  C23  O22   105.26  3.000
 LKM  H232  C23  C24   111.54  3.000
 LKM  H231  C23  C24   109.56  3.000
 LKM  O22   C23  C24   111.94  3.000
 LKM  C20   O22  C23   119.32  3.000
 LKM  C21   C20  C19   120.11  3.000
 LKM  C21   C20  O22   116.46  3.000
 LKM  C19   C20  O22   123.43  3.000
 LKM  H19   C19  C18   118.44  3.000
 LKM  H19   C19  C20   121.71  3.000
 LKM  C18   C19  C20   119.85  3.000
 LKM  H18   C18  C16   119.23  3.000
 LKM  H18   C18  C19   119.45  3.000
 LKM  C16   C18  C19   121.32  3.000
 LKM  H21   C21  C15   119.59  3.000
 LKM  H21   C21  C20   119.78  3.000
 LKM  C15   C21  C20   120.63  3.000
 LKM  C14   C15  C16   118.67  3.000
 LKM  C14   C15  C21   121.90  3.000
 LKM  C16   C15  C21   119.44  3.000
 LKM  C17   C16  C15   119.64  3.000
 LKM  C17   C16  C18   121.70  3.000
 LKM  C15   C16  C18   118.66  3.000
 LKM  H17   C17  C12   121.22  3.000
 LKM  H17   C17  C16   119.01  3.000
 LKM  C12   C17  C16   119.77  3.000
 LKM  H14   C14  C13   119.91  3.000
 LKM  H14   C14  C15   119.11  3.000
 LKM  C13   C14  C15   120.98  3.000
 LKM  H13   C13  C12   120.37  3.000
 LKM  H13   C13  C14   120.04  3.000
 LKM  C12   C13  C14   119.58  3.000
 LKM  S11   C12  C13   118.83  3.000
 LKM  S11   C12  C17   119.76  3.000
 LKM  C13   C12  C17   121.36  3.000
 LKM  N     S11  O32   106.13  3.000
 LKM  N     S11  O33   113.28  3.000
 LKM  O32   S11  O33   118.29  3.000
 LKM  N     S11  C12   101.43  3.000
 LKM  O32   S11  C12   109.12  3.000
 LKM  O33   S11  C12   107.25  3.000
 LKM  H     N    CA    109.34  3.000
 LKM  H     N    S11   109.16  3.000
 LKM  CA    N    S11   116.93  3.000
 LKM  HA    CA   CB    108.40  3.000
 LKM  HA    CA   C     110.14  3.000
 LKM  CB    CA   C     111.67  3.000
 LKM  HA    CA   N     108.50  3.000
 LKM  CB    CA   N     107.41  3.000
 LKM  C     CA   N     110.61  3.000
 LKM  O     C    OXT   127.69  3.000
 LKM  O     C    CA    115.12  3.000
 LKM  OXT   C    CA    117.16  3.000
 LKM  HBC2  CB   HBC1  106.28  3.000
 LKM  HBC2  CB   CG    109.56  3.000
 LKM  HBC1  CB   CG    110.23  3.000
 LKM  HBC2  CB   CA    107.69  3.000
 LKM  HBC1  CB   CA    108.73  3.000
 LKM  CG    CB   CA    114.03  3.000
 LKM  HGC2  CG   HGC1  104.85  3.000
 LKM  HGC2  CG   CD    107.79  3.000
 LKM  HGC1  CG   CD    108.07  3.000
 LKM  HGC2  CG   CB    110.44  3.000
 LKM  HGC1  CG   CB    109.60  3.000
 LKM  CD    CG   CB    115.52  3.000
 LKM  OE2   CD   OE1   126.56  3.000
 LKM  OE2   CD   CG    118.02  3.000
 LKM  OE1   CD   CG    115.42  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
 LKM  CONST_01  C24  C29  C28  C27     0.00   0.0  0
 LKM  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 LKM  CONST_03  C25  C26  C27  C28     0.00   0.0  0
 LKM  CONST_04  C25  C24  C29  C28     0.00   0.0  0
 LKM  CONST_05  C26  C27  C28  C29     0.00   0.0  0
 LKM  CONST_06  C26  C25  C24  C29     0.00   0.0  0
 LKM  CONST_07  C16  C18  C19  C20     0.00   0.0  0
 LKM  CONST_08  C16  C15  C21  C20     0.00   0.0  0
 LKM  CONST_09  C14  C15  C21  C20   180.00   0.0  0
 LKM  CONST_10  C15  C21  C20  C19     0.00   0.0  0
 LKM  CONST_11  C15  C16  C18  C19     0.00   0.0  0
 LKM  CONST_12  C17  C16  C18  C19   180.00   0.0  0
 LKM  CONST_13  C21  C20  C19  C18     0.00   0.0  0
 LKM  CONST_14  C21  C15  C16  C18     0.00   0.0  0
 LKM  CONST_15  C14  C15  C16  C18   180.00   0.0  0
 LKM  CONST_16  C12  C17  C16  C18   180.00   0.0  0
 LKM  CONST_17  C17  C16  C15  C21   180.00   0.0  0
 LKM  CONST_18  C13  C14  C15  C21   180.00   0.0  0
 LKM  CONST_19  C12  C17  C16  C15     0.00   0.0  0
 LKM  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 LKM  CONST_21  C13  C14  C15  C16     0.00   0.0  0
 LKM  CONST_22  C13  C12  C17  C16     0.00   0.0  0
 LKM  CONST_23  C14  C15  C16  C17     0.00   0.0  0
 LKM  CONST_24  C14  C13  C12  C17     0.00   0.0  0
 LKM  CONST_25  C29  C28  C27  C30   180.00   0.0  0
 LKM  CONST_26  C25  C26  C27  C30   180.00   0.0  0
 LKM  CONST_27  F2   C25  C26  C27   180.00   0.0  0
 LKM  CONST_28  C23  C24  C29  C28   180.00   0.0  0
 LKM  CONST_29  F2   C25  C24  C29   180.00   0.0  0
 LKM  CONST_30  C23  C24  C25  C26   180.00   0.0  0
 LKM  CONST_31  C18  C19  C20  O22   180.00   0.0  0
 LKM  CONST_32  C15  C21  C20  O22   180.00   0.0  0
 LKM  CONST_33  S11  C12  C17  C16   180.00   0.0  0
 LKM  CONST_34  S11  C12  C13  C14   180.00   0.0  0
 LKM  CONST_35  H29  C29  C28  C27   180.00   0.0  0
 LKM  CONST_36  H26  C26  C27  C28   180.00   0.0  0
 LKM  CONST_37  H28  C28  C27  C26   180.00   0.0  0
 LKM  CONST_38  H18  C18  C19  C20   180.00   0.0  0
 LKM  CONST_39  H21  C21  C20  C19   180.00   0.0  0
 LKM  CONST_40  H17  C17  C16  C18     0.00   0.0  0
 LKM  CONST_41  H19  C19  C20  C21   180.00   0.0  0
 LKM  CONST_42  H14  C14  C15  C21     0.00   0.0  0
 LKM  CONST_43  H13  C13  C14  C15   180.00   0.0  0
 LKM  Var_01    O22  C23  C24  C29   -32.08  30.0  2
 LKM  Var_02    C19  C20  O22  C23   -10.08  30.0  2
 LKM  Var_03    O33  S11  C12  C17    -2.54  30.0  2
 LKM  Var_04    CA   N    S11  C12    81.29  30.0  3
 LKM  Var_05    CD   CG   CB   CA   -175.40  30.0  3
 LKM  Var_06    OE1  CD   CG   CB    176.66  30.0  3

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
 LKM  chir_01  CA  N  C  CB  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
 LKM  plan-1  N31  0.020
 LKM  plan-1  C30  0.020
 LKM  plan-1  C27  0.020
 LKM  plan-1  C28  0.020
 LKM  plan-1  C29  0.020
 LKM  plan-1  C26  0.020
 LKM  plan-1  C25  0.020
 LKM  plan-1  C24  0.020
 LKM  plan-1  C23  0.020
 LKM  plan-1  F2   0.020
 LKM  plan-1  H28  0.020
 LKM  plan-1  H26  0.020
 LKM  plan-1  H29  0.020
 LKM  plan-2  O22  0.020
 LKM  plan-2  C20  0.020
 LKM  plan-2  C19  0.020
 LKM  plan-2  C18  0.020
 LKM  plan-2  C21  0.020
 LKM  plan-2  C15  0.020
 LKM  plan-2  C16  0.020
 LKM  plan-2  C17  0.020
 LKM  plan-2  C14  0.020
 LKM  plan-2  C13  0.020
 LKM  plan-2  C12  0.020
 LKM  plan-2  S11  0.020
 LKM  plan-2  H19  0.020
 LKM  plan-2  H21  0.020
 LKM  plan-2  H18  0.020
 LKM  plan-2  H14  0.020
 LKM  plan-2  H17  0.020
 LKM  plan-2  H13  0.020
 LKM  plan-3  CA   0.020
 LKM  plan-3  C    0.020
 LKM  plan-3  OXT  0.020
 LKM  plan-3  O    0.020
 LKM  plan-4  CG   0.020
 LKM  plan-4  CD   0.020
 LKM  plan-4  OE1  0.020
 LKM  plan-4  OE2  0.020

