# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:22:34 2022
#   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  51  33  .  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_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  -0.246  -11.2223   2.6573  -24.0763
 LK4  C30   C  CSP    0   0.054  -12.1737   2.3777  -23.4896
 LK4  C27   C  CR6    0  -0.003  -13.3537   2.0294  -22.7652
 LK4  C28   C  CR16   0  -0.221  -13.3103   1.9275  -21.3771
 LK4  C29   C  CR16   0  -0.292  -14.4573   1.5742  -20.6854
 LK4  C26   C  CR16   0  -0.225  -14.5431   1.7871  -23.4547
 LK4  C25   C  CR16   0  -0.268  -15.6803   1.4411  -22.7501
 LK4  C24   C  CR6    0   0.105  -15.6470   1.3286  -21.3609
 LK4  C23   C  CH2    0  -0.257  -16.8861   0.9506  -20.6036
 LK4  O22   O  O2     0  -0.466  -17.3247  -0.2992  -21.1108
 LK4  C20   C  CR6    0   0.416  -18.3811  -0.9113  -20.5471
 LK4  C19   C  CR16   0  -0.371  -19.1138  -0.3606  -19.4676
 LK4  C18   C  CR16   0  -0.284  -20.1634  -1.0532  -18.9313
 LK4  C21   C  CR16   0  -0.431  -18.7358  -2.1350  -21.0680
 LK4  C15   C  CR66   0   0.152  -19.8116  -2.8599  -20.5258
 LK4  C16   C  CR66   0   0.104  -20.5394  -2.3182  -19.4328
 LK4  C17   C  CR16   0  -0.268  -21.6019  -3.0545  -18.8725
 LK4  C14   C  CR16   0  -0.307  -20.1916  -4.1254  -21.0360
 LK4  C13   C  CR16   0  -0.244  -21.2282  -4.8237  -20.4858
 LK4  C12   C  CR6    0  -0.222  -21.9328  -4.2771  -19.3929
 LK4  S11   S  S      0   1.373  -23.2118  -5.2256  -18.6144
 LK4  O33   O  OS     0  -0.666  -22.9023  -5.3913  -17.1993
 LK4  O32   O  OS     0  -0.654  -23.4016  -6.4324  -19.4132
 LK4  N     N  NC1    0  -0.725  -24.4849  -4.1828  -18.6807
 LK4  CA    C  CH1    0  -0.208  -25.1614  -4.0186  -19.9760
 LK4  C     C  C      0   0.421  -26.1049  -5.2066  -20.2828
 LK4  O     O  O      0  -0.598  -26.2008  -5.5572  -21.4722
 LK4  OXT   O  OC    -1  -0.604  -26.7164  -5.6708  -19.2990
 LK4  CB    C  CH2    0  -0.409  -25.9290  -2.6954  -19.9010
 LK4  CG    C  CH2    0  -0.589  -26.6724  -2.3228  -21.1730
 LK4  CD    C  C      0   0.412  -27.3534  -0.9377  -21.1528
 LK4  OE1   O  O      0  -0.625  -28.0127  -0.6473  -22.1730
 LK4  OE2   O  OC    -1  -0.604  -27.1953  -0.2257  -20.1411
 LK4  H28   H  HCR6   0   0.283  -12.3879   2.1144  -20.8440
 LK4  H26   H  HCR6   0   0.282  -14.5742   1.8719  -24.5326
 LK4  H29   H  HCR6   0   0.274  -14.4190   1.4854  -19.6071
 LK4  H25   H  HCR6   0   0.271  -16.6008   1.2594  -23.2899
 LK4  H231  H  HCH2   0   0.257  -16.6672   0.8876  -19.5334
 LK4  H232  H  HCH2   0   0.255  -17.6596   1.7140  -20.7437
 LK4  H19   H  HCR6   0   0.292  -18.8568   0.6041  -19.0521
 LK4  H21   H  HCR6   0   0.265  -18.1750  -2.5491  -21.8976
 LK4  H18   H  HCR6   0   0.270  -20.7184  -0.6288  -18.1039
 LK4  H14   H  HCR6   0   0.263  -19.6459  -4.5395  -21.8746
 LK4  H17   H  HCR6   0   0.281  -22.1504  -2.6344  -18.0376
 LK4  H13   H  HCR6   0   0.277  -21.5071  -5.7869  -20.8894
 LK4  H     H  HNC1   0   0.391  -25.1629  -4.4409  -17.9644
 LK4  HA    H  HCH1   0   0.234  -24.3963  -3.9321  -20.7539
 LK4  HBC1  H  HCH2   0   0.205  -26.6300  -2.7508  -19.0625
 LK4  HBC2  H  HCH2   0   0.217  -25.2150  -1.9077  -19.6510
 LK4  HGC1  H  HCH2   0   0.214  -25.9844  -2.3507  -22.0262
 LK4  HGC2  H  HCH2   0   0.221  -27.4360  -3.0702  -21.4039

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  1.393  0.020  1.393
 LK4  C28  C29   aromatic  1.385  0.020  1.385
 LK4  C27  C26   aromatic  1.396  0.020  1.396
 LK4  C26  C25   aromatic  1.382  0.020  1.382
 LK4  C29  C24   aromatic  1.390  0.020  1.390
 LK4  C25  C24   aromatic  1.394  0.020  1.394
 LK4  C24  C23   single    1.501  0.020  1.501
 LK4  C23  O22   single    1.418  0.020  1.418
 LK4  O22  C20   single    1.345  0.020  1.345
 LK4  C20  C19   aromatic  1.416  0.020  1.416
 LK4  C19  C18   aromatic  1.367  0.020  1.367
 LK4  C20  C21   aromatic  1.376  0.020  1.376
 LK4  C21  C15   aromatic  1.406  0.020  1.406
 LK4  C18  C16   aromatic  1.412  0.020  1.412
 LK4  C15  C16   aromatic  1.421  0.020  1.421
 LK4  C16  C17   single    1.409  0.020  1.409
 LK4  C15  C14   single    1.416  0.020  1.416
 LK4  C14  C13   double    1.366  0.020  1.366
 LK4  C17  C12   double    1.369  0.020  1.369
 LK4  C13  C12   single    1.410  0.020  1.410
 LK4  C12  S11   single    1.772  0.020  1.772
 LK4  S11  O33   double    1.458  0.020  1.458
 LK4  S11  O32   double    1.460  0.020  1.460
 LK4  S11  N     single    1.647  0.020  1.647
 LK4  N    CA    single    1.470  0.020  1.470
 LK4  CA   C     single    1.548  0.020  1.548
 LK4  C    O     deloc     1.244  0.020  1.244
 LK4  C    OXT   deloc     1.248  0.020  1.248
 LK4  CA   CB    single    1.532  0.020  1.532
 LK4  CB   CG    single    1.520  0.020  1.520
 LK4  CG   CD    single    1.544  0.020  1.544
 LK4  CD   OE1   deloc     1.249  0.020  1.249
 LK4  CD   OE2   deloc     1.247  0.020  1.247
 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  CG   HGC1  single    0.970  0.020  1.090
 LK4  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
 LK4  C27   C30  N31   180.00  3.000
 LK4  C26   C27  C28   120.41  3.000
 LK4  C26   C27  C30   119.73  3.000
 LK4  C28   C27  C30   119.85  3.000
 LK4  H28   C28  C29   120.27  3.000
 LK4  H28   C28  C27   120.35  3.000
 LK4  C29   C28  C27   119.38  3.000
 LK4  H29   C29  C24   119.99  3.000
 LK4  H29   C29  C28   119.27  3.000
 LK4  C24   C29  C28   120.74  3.000
 LK4  H26   C26  C25   120.27  3.000
 LK4  H26   C26  C27   120.20  3.000
 LK4  C25   C26  C27   119.52  3.000
 LK4  H25   C25  C24   120.24  3.000
 LK4  H25   C25  C26   119.18  3.000
 LK4  C24   C25  C26   120.58  3.000
 LK4  C23   C24  C25   120.23  3.000
 LK4  C23   C24  C29   120.40  3.000
 LK4  C25   C24  C29   119.37  3.000
 LK4  H232  C23  H231  107.84  3.000
 LK4  H232  C23  O22   110.48  3.000
 LK4  H231  C23  O22   111.16  3.000
 LK4  H232  C23  C24   110.05  3.000
 LK4  H231  C23  C24   110.05  3.000
 LK4  O22   C23  C24   107.27  3.000
 LK4  C20   O22  C23   119.61  3.000
 LK4  C21   C20  C19   120.06  3.000
 LK4  C21   C20  O22   116.65  3.000
 LK4  C19   C20  O22   123.29  3.000
 LK4  H19   C19  C18   118.92  3.000
 LK4  H19   C19  C20   121.12  3.000
 LK4  C18   C19  C20   119.95  3.000
 LK4  H18   C18  C16   119.08  3.000
 LK4  H18   C18  C19   119.65  3.000
 LK4  C16   C18  C19   121.27  3.000
 LK4  H21   C21  C15   119.62  3.000
 LK4  H21   C21  C20   119.75  3.000
 LK4  C15   C21  C20   120.64  3.000
 LK4  C14   C15  C16   118.71  3.000
 LK4  C14   C15  C21   121.80  3.000
 LK4  C16   C15  C21   119.48  3.000
 LK4  C17   C16  C15   119.54  3.000
 LK4  C17   C16  C18   121.86  3.000
 LK4  C15   C16  C18   118.59  3.000
 LK4  H17   C17  C12   121.10  3.000
 LK4  H17   C17  C16   119.04  3.000
 LK4  C12   C17  C16   119.85  3.000
 LK4  H14   C14  C13   119.94  3.000
 LK4  H14   C14  C15   119.05  3.000
 LK4  C13   C14  C15   121.02  3.000
 LK4  H13   C13  C12   120.38  3.000
 LK4  H13   C13  C14   120.06  3.000
 LK4  C12   C13  C14   119.56  3.000
 LK4  S11   C12  C13   119.57  3.000
 LK4  S11   C12  C17   119.03  3.000
 LK4  C13   C12  C17   121.31  3.000
 LK4  N     S11  O32   113.64  3.000
 LK4  N     S11  O33   105.97  3.000
 LK4  O32   S11  O33   117.70  3.000
 LK4  N     S11  C12   101.61  3.000
 LK4  O32   S11  C12   107.21  3.000
 LK4  O33   S11  C12   109.51  3.000
 LK4  H     N    CA    109.95  3.000
 LK4  H     N    S11   108.99  3.000
 LK4  CA    N    S11   117.50  3.000
 LK4  HA    CA   CB    108.47  3.000
 LK4  HA    CA   C     110.23  3.000
 LK4  CB    CA   C     111.55  3.000
 LK4  HA    CA   N     108.26  3.000
 LK4  CB    CA   N     106.49  3.000
 LK4  C     CA   N     111.68  3.000
 LK4  OXT   C    O     127.69  3.000
 LK4  OXT   C    CA    115.33  3.000
 LK4  O     C    CA    116.93  3.000
 LK4  HBC2  CB   HBC1  106.25  3.000
 LK4  HBC2  CB   CG    109.55  3.000
 LK4  HBC1  CB   CG    109.90  3.000
 LK4  HBC2  CB   CA    107.86  3.000
 LK4  HBC1  CB   CA    108.34  3.000
 LK4  CG    CB   CA    114.58  3.000
 LK4  HGC2  CG   HGC1  104.87  3.000
 LK4  HGC2  CG   CD    107.94  3.000
 LK4  HGC1  CG   CD    108.05  3.000
 LK4  HGC2  CG   CB    110.54  3.000
 LK4  HGC1  CG   CB    109.76  3.000
 LK4  CD    CG   CB    115.14  3.000
 LK4  OE2   CD   OE1   126.64  3.000
 LK4  OE2   CD   CG    117.84  3.000
 LK4  OE1   CD   CG    115.52  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  Var_01    O22  C23  C24  C29  -122.61  30.0  2
 LK4  Var_02    C19  C20  O22  C23     1.15  30.0  2
 LK4  Var_03    O33  S11  C12  C17   -54.32  30.0  3
 LK4  Var_04    CA   N    S11  C12    76.17  30.0  3
 LK4  Var_05    CD   CG   CB   CA   -175.15  30.0  3
 LK4  Var_06    OE1  CD   CG   CB   -177.15  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-4  CG   0.020
 LK4  plan-4  CD   0.020
 LK4  plan-4  OE1  0.020
 LK4  plan-4  OE2  0.020

