# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:12:00 2021
#   Inital geometry file: a 160 line input string
#   Ligand name: N-({6-[(4-cyanobenzyl)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(cc3)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
 LK4  LK4  'N-({6-[(4-cyanobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid'  ligand  53  33  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LK4
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
 LK4  N31   N  NS    0  -0.249  -12.2382   3.3096  -24.8924
 LK4  C30   C  CSP   0   0.058  -12.9437   2.8542  -24.1035
 LK4  C27   C  CR6   0  -0.004  -13.8195   2.2906  -23.1266
 LK4  C28   C  CR16  0  -0.222  -13.2953   1.7458  -21.9572
 LK4  C29   C  CR16  0  -0.292  -14.1550   1.2004  -21.0173
 LK4  C26   C  CR16  0  -0.226  -15.1975   2.2922  -23.3506
 LK4  C25   C  CR16  0  -0.270  -16.0416   1.7480  -22.4023
 LK4  C24   C  CR6   0   0.112  -15.5283   1.1994  -21.2282
 LK4  C23   C  CH2   0  -0.267  -16.4614   0.6170  -20.2087
 LK4  O22   O  O2    0  -0.466  -17.1130  -0.4864  -20.8199
 LK4  C20   C  CR6   0   0.418  -18.1223  -1.0983  -20.1761
 LK4  C19   C  CR16  0  -0.371  -18.5335  -0.7497  -18.8667
 LK4  C18   C  CR16  0  -0.284  -19.5778  -1.4089  -18.2807
 LK4  C21   C  CR16  0  -0.433  -18.7628  -2.1117  -20.8533
 LK4  C15   C  CR66  0   0.157  -19.8357  -2.8006  -20.2623
 LK4  C16   C  CR66  0   0.107  -20.2619  -2.4426  -18.9555
 LK4  C17   C  CR16  0  -0.280  -21.3513  -3.1162  -18.3691
 LK4  C14   C  CR16  0  -0.311  -20.5116  -3.8483  -20.9356
 LK4  C13   C  CR16  0  -0.241  -21.5594  -4.4997  -20.3515
 LK4  C12   C  CR6   0  -0.209  -21.9827  -4.1145  -19.0607
 LK4  S11   S  S     0   1.379  -23.3753  -4.9127  -18.3247
 LK4  O33   O  OS    0  -0.648  -23.2585  -4.8661  -16.8772
 LK4  O32   O  OS    0  -0.643  -23.5483  -6.1932  -18.9985
 LK4  N     N  NC1   0  -0.741  -24.6182  -3.8905  -18.7133
 LK4  CA    C  CH1   0  -0.194  -25.1987  -3.9943  -20.0377
 LK4  C     C  C     0   0.551  -25.9801  -5.2796  -20.2739
 LK4  O     O  O     0  -0.433  -26.0057  -5.8564  -21.3303
 LK4  OXT   O  OH1   0  -0.585  -26.6751  -5.6421  -19.2084
 LK4  CB    C  CH2   0  -0.455  -26.0860  -2.7654  -20.2697
 LK4  CG    C  CH2   0  -0.584  -26.6345  -2.6960  -21.6907
 LK4  CD    C  C     0   0.551  -27.3355  -1.4105  -22.0445
 LK4  OE1   O  O     0  -0.450  -27.4341  -0.9905  -23.1706
 LK4  OE2   O  OH1   0  -0.588  -27.8693  -0.8006  -20.9942
 LK4  H28   H  HCR6  0   0.285  -12.2277   1.7440  -21.7857
 LK4  H26   H  HCR6  0   0.285  -15.5997   2.7200  -24.2585
 LK4  H29   H  HCR6  0   0.275  -13.7469   0.7707  -20.1117
 LK4  H25   H  HCR6  0   0.273  -17.1098   1.7583  -22.5778
 LK4  H231  H  HCH2  0   0.257  -15.9098   0.2996  -19.3187
 LK4  H232  H  HCH2  0   0.256  -17.1921   1.3732  -19.9031
 LK4  H19   H  HCR6  0   0.293  -18.0345   0.0322  -18.3113
 LK4  H21   H  HCR6  0   0.269  -18.4410  -2.3762  -21.8533
 LK4  H18   H  HCR6  0   0.273  -19.8875  -1.1357  -17.2799
 LK4  H14   H  HCR6  0   0.268  -20.1867  -4.1343  -21.9278
 LK4  H17   H  HCR6  0   0.285  -21.6718  -2.8304  -17.3749
 LK4  H13   H  HCR6  0   0.284  -22.0541  -5.3053  -20.8765
 LK4  H     H  HNC1  0   0.419  -25.2731  -3.7743  -17.9460
 LK4  HA    H  HCH1  0   0.303  -24.3909  -3.9695  -20.7744
 LK4  HBC1  H  HCH2  0   0.264  -26.8983  -2.7590  -19.5398
 LK4  HBC2  H  HCH2  0   0.277  -25.4628  -1.8929  -20.0673
 LK4  HXT   H  HOH1  0   0.488  -27.1818  -6.4474  -19.3929
 LK4  HGC1  H  HCH2  0   0.281  -25.8368  -2.8405  -22.4209
 LK4  HGC2  H  HCH2  0   0.294  -27.3604  -3.4948  -21.8731
 LK4  HE2   H  HOH1  0   0.484  -28.3251   0.0065  -21.2772

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
 LK4  N31  C30   triple    1.152  0.020  1.152
 LK4  C30  C27   single    1.428  0.020  1.428
 LK4  C27  C28   aromatic  1.392  0.020  1.392
 LK4  C28  C29   aromatic  1.386  0.020  1.386
 LK4  C27  C26   aromatic  1.396  0.020  1.396
 LK4  C26  C25   aromatic  1.381  0.020  1.381
 LK4  C29  C24   aromatic  1.389  0.020  1.389
 LK4  C25  C24   aromatic  1.394  0.020  1.394
 LK4  C24  C23   single    1.500  0.020  1.500
 LK4  C23  O22   single    1.420  0.020  1.420
 LK4  O22  C20   single    1.344  0.020  1.344
 LK4  C20  C19   aromatic  1.416  0.020  1.416
 LK4  C19  C18   aromatic  1.367  0.020  1.367
 LK4  C20  C21   aromatic  1.377  0.020  1.377
 LK4  C21  C15   aromatic  1.405  0.020  1.405
 LK4  C18  C16   aromatic  1.411  0.020  1.411
 LK4  C15  C16   aromatic  1.420  0.020  1.420
 LK4  C16  C17   single    1.409  0.020  1.409
 LK4  C15  C14   single    1.417  0.020  1.417
 LK4  C14  C13   double    1.365  0.020  1.365
 LK4  C17  C12   double    1.369  0.020  1.369
 LK4  C13  C12   single    1.412  0.020  1.412
 LK4  C12  S11   single    1.766  0.020  1.766
 LK4  S11  O33   double    1.453  0.020  1.453
 LK4  S11  O32   double    1.457  0.020  1.457
 LK4  S11  N     single    1.655  0.020  1.655
 LK4  N    CA    single    1.450  0.020  1.450
 LK4  CA   C     single    1.523  0.020  1.523
 LK4  C    O     double    1.204  0.020  1.204
 LK4  C    OXT   single    1.323  0.020  1.323
 LK4  CA   CB    single    1.533  0.020  1.533
 LK4  CB   CG    single    1.525  0.020  1.525
 LK4  CG   CD    single    1.506  0.020  1.506
 LK4  CD   OE1   double    1.206  0.020  1.206
 LK4  CD   OE2   single    1.327  0.020  1.327
 LK4  C28  H28   single    0.930  0.020  1.080
 LK4  C26  H26   single    0.930  0.020  1.080
 LK4  C29  H29   single    0.930  0.020  1.080
 LK4  C25  H25   single    0.930  0.020  1.080
 LK4  C23  H231  single    0.970  0.020  1.090
 LK4  C23  H232  single    0.970  0.020  1.090
 LK4  C19  H19   single    0.930  0.020  1.080
 LK4  C21  H21   single    0.930  0.020  1.080
 LK4  C18  H18   single    0.930  0.020  1.080
 LK4  C14  H14   single    0.930  0.020  1.080
 LK4  C17  H17   single    0.930  0.020  1.080
 LK4  C13  H13   single    0.930  0.020  1.080
 LK4  N    H     single    0.860  0.020  1.020
 LK4  CA   HA    single    0.970  0.020  1.090
 LK4  CB   HBC1  single    0.970  0.020  1.090
 LK4  CB   HBC2  single    0.970  0.020  1.090
 LK4  OXT  HXT   single    0.850  0.020  0.980
 LK4  CG   HGC1  single    0.970  0.020  1.090
 LK4  CG   HGC2  single    0.970  0.020  1.090
 LK4  OE2  HE2   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
 LK4  C27   C30  N31   180.00  3.000
 LK4  C26   C27  C28   120.45  3.000
 LK4  C26   C27  C30   119.68  3.000
 LK4  C28   C27  C30   119.87  3.000
 LK4  H28   C28  C29   120.29  3.000
 LK4  H28   C28  C27   120.37  3.000
 LK4  C29   C28  C27   119.35  3.000
 LK4  H29   C29  C24   119.97  3.000
 LK4  H29   C29  C28   119.33  3.000
 LK4  C24   C29  C28   120.70  3.000
 LK4  H26   C26  C25   120.33  3.000
 LK4  H26   C26  C27   120.16  3.000
 LK4  C25   C26  C27   119.51  3.000
 LK4  H25   C25  C24   120.24  3.000
 LK4  H25   C25  C26   119.21  3.000
 LK4  C24   C25  C26   120.55  3.000
 LK4  C23   C24  C25   119.76  3.000
 LK4  C23   C24  C29   120.80  3.000
 LK4  C25   C24  C29   119.44  3.000
 LK4  H232  C23  H231  108.05  3.000
 LK4  H232  C23  O22   110.52  3.000
 LK4  H231  C23  O22   110.85  3.000
 LK4  H232  C23  C24   109.68  3.000
 LK4  H231  C23  C24   110.61  3.000
 LK4  O22   C23  C24   107.14  3.000
 LK4  C20   O22  C23   119.48  3.000
 LK4  C21   C20  C19   120.06  3.000
 LK4  C21   C20  O22   116.66  3.000
 LK4  C19   C20  O22   123.28  3.000
 LK4  H19   C19  C18   118.76  3.000
 LK4  H19   C19  C20   121.27  3.000
 LK4  C18   C19  C20   119.97  3.000
 LK4  H18   C18  C16   119.22  3.000
 LK4  H18   C18  C19   119.55  3.000
 LK4  C16   C18  C19   121.24  3.000
 LK4  H21   C21  C15   119.69  3.000
 LK4  H21   C21  C20   119.70  3.000
 LK4  C15   C21  C20   120.61  3.000
 LK4  C14   C15  C16   118.71  3.000
 LK4  C14   C15  C21   121.79  3.000
 LK4  C16   C15  C21   119.50  3.000
 LK4  C17   C16  C15   119.64  3.000
 LK4  C17   C16  C18   121.74  3.000
 LK4  C15   C16  C18   118.62  3.000
 LK4  H17   C17  C12   121.32  3.000
 LK4  H17   C17  C16   119.00  3.000
 LK4  C12   C17  C16   119.68  3.000
 LK4  H14   C14  C13   119.77  3.000
 LK4  H14   C14  C15   119.19  3.000
 LK4  C13   C14  C15   121.04  3.000
 LK4  H13   C13  C12   120.66  3.000
 LK4  H13   C13  C14   119.93  3.000
 LK4  C12   C13  C14   119.41  3.000
 LK4  S11   C12  C13   119.61  3.000
 LK4  S11   C12  C17   118.87  3.000
 LK4  C13   C12  C17   121.50  3.000
 LK4  N     S11  O32   110.18  3.000
 LK4  N     S11  O33   105.93  3.000
 LK4  O32   S11  O33   119.89  3.000
 LK4  N     S11  C12   102.42  3.000
 LK4  O32   S11  C12   107.34  3.000
 LK4  O33   S11  C12   109.72  3.000
 LK4  H     N    CA    116.11  3.000
 LK4  H     N    S11   112.18  3.000
 LK4  CA    N    S11   118.09  3.000
 LK4  HA    CA   CB    107.90  3.000
 LK4  HA    CA   C     107.08  3.000
 LK4  CB    CA   C     110.86  3.000
 LK4  HA    CA   N     108.54  3.000
 LK4  CB    CA   N     108.21  3.000
 LK4  C     CA   N     114.06  3.000
 LK4  OXT   C    O     124.36  3.000
 LK4  OXT   C    CA    112.08  3.000
 LK4  O     C    CA    123.47  3.000
 LK4  HXT   OXT  C     110.43  3.000
 LK4  HBC2  CB   HBC1  107.22  3.000
 LK4  HBC2  CB   CG    110.00  3.000
 LK4  HBC1  CB   CG    110.79  3.000
 LK4  HBC2  CB   CA    106.40  3.000
 LK4  HBC1  CB   CA    109.51  3.000
 LK4  CG    CB   CA    112.68  3.000
 LK4  HGC2  CG   HGC1  106.06  3.000
 LK4  HGC2  CG   CD    105.96  3.000
 LK4  HGC1  CG   CD    107.22  3.000
 LK4  HGC2  CG   CB    111.14  3.000
 LK4  HGC1  CG   CB    110.77  3.000
 LK4  CD    CG   CB    115.16  3.000
 LK4  OE2   CD   OE1   123.11  3.000
 LK4  OE2   CD   CG    113.18  3.000
 LK4  OE1   CD   CG    123.68  3.000
 LK4  HE2   OE2  CD    109.93  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
 LK4  CONST_01  C24  C29  C28  C27     0.00   0.0  0
 LK4  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 LK4  CONST_03  C25  C26  C27  C28     0.00   0.0  0
 LK4  CONST_04  C25  C24  C29  C28     0.00   0.0  0
 LK4  CONST_05  C26  C27  C28  C29     0.00   0.0  0
 LK4  CONST_06  C26  C25  C24  C29     0.00   0.0  0
 LK4  CONST_07  C16  C18  C19  C20     0.00   0.0  0
 LK4  CONST_08  C16  C15  C21  C20     0.00   0.0  0
 LK4  CONST_09  C15  C21  C20  C19     0.00   0.0  0
 LK4  CONST_10  C15  C16  C18  C19     0.00   0.0  0
 LK4  CONST_11  C21  C20  C19  C18     0.00   0.0  0
 LK4  CONST_12  C21  C15  C16  C18     0.00   0.0  0
 LK4  CONST_13  C29  C28  C27  C30   180.00   0.0  0
 LK4  CONST_14  C25  C26  C27  C30   180.00   0.0  0
 LK4  CONST_15  C23  C24  C29  C28   180.00   0.0  0
 LK4  CONST_16  C23  C24  C25  C26   180.00   0.0  0
 LK4  CONST_17  C18  C19  C20  O22   180.00   0.0  0
 LK4  CONST_18  C15  C21  C20  O22   180.00   0.0  0
 LK4  CONST_19  H29  C29  C28  C27   180.00   0.0  0
 LK4  CONST_20  H25  C25  C26  C27   180.00   0.0  0
 LK4  CONST_21  H26  C26  C27  C28   180.00   0.0  0
 LK4  CONST_22  H28  C28  C27  C26   180.00   0.0  0
 LK4  CONST_23  H18  C18  C19  C20   180.00   0.0  0
 LK4  CONST_24  H21  C21  C20  C19   180.00   0.0  0
 LK4  CONST_25  H19  C19  C20  C21   180.00   0.0  0
 LK4  CONST_26  HXT  OXT  C    CA    180.00   0.0  0
 LK4  CONST_27  HE2  OE2  CD   CG    180.00   0.0  0
 LK4  Var_01    O22  C23  C24  C29  -116.68  30.0  2
 LK4  Var_02    C19  C20  O22  C23    -3.76  30.0  2
 LK4  Var_03    O33  S11  C12  C17   -28.17  30.0  3
 LK4  Var_04    CA   N    S11  C12    81.06  30.0  3
 LK4  Var_05    CD   CG   CB   CA   -170.98  30.0  3
 LK4  Var_06    OE1  CD   CG   CB    154.49  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
 LK4  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
 LK4  plan-1  N31  0.020
 LK4  plan-1  C30  0.020
 LK4  plan-1  C27  0.020
 LK4  plan-1  C28  0.020
 LK4  plan-1  C29  0.020
 LK4  plan-1  C26  0.020
 LK4  plan-1  C25  0.020
 LK4  plan-1  C24  0.020
 LK4  plan-1  C23  0.020
 LK4  plan-1  H28  0.020
 LK4  plan-1  H26  0.020
 LK4  plan-1  H29  0.020
 LK4  plan-1  H25  0.020
 LK4  plan-2  O22  0.020
 LK4  plan-2  C20  0.020
 LK4  plan-2  C19  0.020
 LK4  plan-2  C18  0.020
 LK4  plan-2  C21  0.020
 LK4  plan-2  C15  0.020
 LK4  plan-2  C16  0.020
 LK4  plan-2  C17  0.020
 LK4  plan-2  C14  0.020
 LK4  plan-2  C13  0.020
 LK4  plan-2  C12  0.020
 LK4  plan-2  S11  0.020
 LK4  plan-2  H19  0.020
 LK4  plan-2  H21  0.020
 LK4  plan-2  H18  0.020
 LK4  plan-2  H14  0.020
 LK4  plan-2  H17  0.020
 LK4  plan-2  H13  0.020
 LK4  plan-3  CA   0.020
 LK4  plan-3  C    0.020
 LK4  plan-3  O    0.020
 LK4  plan-3  OXT  0.020
 LK4  plan-3  HXT  0.020
 LK4  plan-4  CG   0.020
 LK4  plan-4  CD   0.020
 LK4  plan-4  OE1  0.020
 LK4  plan-4  OE2  0.020
 LK4  plan-4  HE2  0.020

