# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:06:56 2021
#   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  53  34  .  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_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  -0.244   0.9597  -11.5701  -22.1613
 LKM  C30   C  CSP   0   0.064   0.4551  -12.6050  -22.1292
 LKM  C27   C  CR6   0   0.009  -0.1693  -13.8877  -22.0830
 LKM  C28   C  CR16  0  -0.233  -0.4207  -14.4933  -20.8546
 LKM  C29   C  CR16  0  -0.249  -1.0260  -15.7375  -20.8195
 LKM  C26   C  CR16  0  -0.389  -0.5237  -14.5200  -23.2726
 LKM  C25   C  CR6   0   0.563  -1.1237  -15.7566  -23.1931
 LKM  C24   C  CR6   0  -0.168  -1.3849  -16.3980  -21.9903
 LKM  C23   C  CH2   0  -0.245  -2.0663  -17.7434  -21.9748
 LKM  O22   O  O2    0  -0.478  -1.8527  -18.4450  -20.7717
 LKM  C20   C  CR6   0   0.418  -0.6553  -19.0220  -20.5372
 LKM  C19   C  CR16  0  -0.345   0.4341  -18.9552  -21.4361
 LKM  C18   C  CR16  0  -0.289   1.6150  -19.5698  -21.1208
 LKM  C21   C  CR16  0  -0.434  -0.5293  -19.7016  -19.3467
 LKM  C15   C  CR66  0   0.157   0.6779  -20.3362  -19.0106
 LKM  C16   C  CR66  0   0.112   1.7740  -20.2722  -19.9092
 LKM  C17   C  CR16  0  -0.287   2.9903  -20.9060  -19.5732
 LKM  C14   C  CR16  0  -0.311   0.8353  -21.0439  -17.7899
 LKM  C13   C  CR16  0  -0.226   2.0148  -21.6496  -17.4774
 LKM  C12   C  CR6   0  -0.216   3.0959  -21.5749  -18.3867
 LKM  S11   S  S     0   1.377   4.6182  -22.3460  -17.9435
 LKM  O33   O  OS    0  -0.644   5.5831  -22.0775  -19.0030
 LKM  O32   O  OS    0  -0.651   4.9563  -22.0049  -16.5718
 LKM  N     N  NC1   0  -0.731   4.1856  -23.9433  -17.9207
 LKM  CA    C  CH1   0  -0.200   4.0811  -24.6231  -19.1980
 LKM  C     C  C     0   0.549   5.4562  -24.8952  -19.7935
 LKM  OXT   O  OH1   0  -0.581   5.4658  -24.7770  -21.1100
 LKM  O     O  O     0  -0.430   6.4045  -25.2295  -19.1321
 LKM  CB    C  CH2   0  -0.442   3.3150  -25.9322  -18.9797
 LKM  CG    C  CH2   0  -0.598   3.0425  -26.6897  -20.2688
 LKM  CD    C  C     0   0.560   2.1560  -27.8865  -20.0521
 LKM  OE1   O  OH1   0  -0.595   1.9455  -28.5493  -21.1834
 LKM  OE2   O  O     0  -0.441   1.6855  -28.2194  -18.9936
 LKM  F2    F  F     0  -0.301  -1.4689  -16.3709  -24.3324
 LKM  H28   H  HCR6  0   0.289  -0.1486  -13.9962  -19.9343
 LKM  H26   H  HCR6  0   0.306  -0.3348  -14.0610  -24.2336
 LKM  H29   H  HCR6  0   0.287  -1.2200  -16.1950  -19.8593
 LKM  H231  H  HCH2  0   0.306  -3.1465  -17.6018  -22.0403
 LKM  H232  H  HCH2  0   0.261  -1.7759  -18.3467  -22.8392
 LKM  H19   H  HCR6  0   0.288   0.3631  -18.4259  -22.3761
 LKM  H21   H  HCR6  0   0.272  -1.3680  -19.7465  -18.6624
 LKM  H18   H  HCR6  0   0.274   2.4453  -19.5139  -21.8131
 LKM  H14   H  HCR6  0   0.269   0.0024  -21.0975  -17.1007
 LKM  H17   H  HCR6  0   0.286   3.8203  -20.8525  -20.2659
 LKM  H13   H  HCR6  0   0.283   2.1178  -22.1876  -16.5444
 LKM  H     H  HNC1  0   0.417   4.6887  -24.4561  -17.2018
 LKM  HA    H  HCH1  0   0.299   3.5003  -23.9940  -19.8785
 LKM  HBC1  H  HCH2  0   0.258   3.8687  -26.5618  -18.2787
 LKM  HBC2  H  HCH2  0   0.274   2.3733  -25.6663  -18.4985
 LKM  HB    H  HOH1  0   0.486   6.3345  -25.0229  -21.4645
 LKM  HGC1  H  HCH2  0   0.291   2.5592  -26.0403  -21.0051
 LKM  HGC2  H  HCH2  0   0.291   3.9626  -27.0430  -20.7413
 LKM  HE1   H  HOH1  0   0.481   1.3720  -29.3128  -21.0188

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    1.427  0.020  1.427
 LKM  C27  C28   aromatic  1.392  0.020  1.392
 LKM  C27  C26   aromatic  1.393  0.020  1.393
 LKM  C28  C29   aromatic  1.384  0.020  1.384
 LKM  C29  C24   aromatic  1.391  0.020  1.391
 LKM  C26  C25   aromatic  1.377  0.020  1.377
 LKM  C25  C24   aromatic  1.388  0.020  1.388
 LKM  C25  F2    single    1.340  0.020  1.340
 LKM  C24  C23   single    1.508  0.020  1.508
 LKM  C23  O22   single    1.409  0.020  1.409
 LKM  O22  C20   single    1.350  0.020  1.350
 LKM  C20  C19   aromatic  1.414  0.020  1.414
 LKM  C20  C21   aromatic  1.377  0.020  1.377
 LKM  C19  C18   aromatic  1.368  0.020  1.368
 LKM  C18  C16   aromatic  1.410  0.020  1.410
 LKM  C21  C15   aromatic  1.405  0.020  1.405
 LKM  C15  C16   aromatic  1.419  0.020  1.419
 LKM  C15  C14   aromatic  1.420  0.020  1.420
 LKM  C16  C17   aromatic  1.412  0.020  1.412
 LKM  C17  C12   aromatic  1.366  0.020  1.366
 LKM  C14  C13   aromatic  1.362  0.020  1.362
 LKM  C13  C12   aromatic  1.415  0.020  1.415
 LKM  C12  S11   single    1.763  0.020  1.763
 LKM  S11  O33   double    1.458  0.020  1.458
 LKM  S11  O32   double    1.453  0.020  1.453
 LKM  S11  N     single    1.655  0.020  1.655
 LKM  N    CA    single    1.451  0.020  1.451
 LKM  CA   C     single    1.523  0.020  1.523
 LKM  CA   CB    single    1.532  0.020  1.532
 LKM  C    OXT   single    1.322  0.020  1.322
 LKM  C    O     double    1.204  0.020  1.204
 LKM  CB   CG    single    1.520  0.020  1.520
 LKM  CG   CD    single    1.505  0.020  1.505
 LKM  CD   OE1   single    1.328  0.020  1.328
 LKM  CD   OE2   double    1.205  0.020  1.205
 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  OXT  HB    single    0.850  0.020  0.980
 LKM  CG   HGC1  single    0.970  0.020  1.090
 LKM  CG   HGC2  single    0.970  0.020  1.090
 LKM  OE1  HE1   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
 LKM  C27   C30  N31   180.00  3.000
 LKM  C26   C27  C28   120.66  3.000
 LKM  C26   C27  C30   119.45  3.000
 LKM  C28   C27  C30   119.89  3.000
 LKM  H28   C28  C29   120.14  3.000
 LKM  H28   C28  C27   120.38  3.000
 LKM  C29   C28  C27   119.49  3.000
 LKM  H29   C29  C24   120.01  3.000
 LKM  H29   C29  C28   118.77  3.000
 LKM  C24   C29  C28   121.22  3.000
 LKM  H26   C26  C25   120.57  3.000
 LKM  H26   C26  C27   121.44  3.000
 LKM  C25   C26  C27   117.99  3.000
 LKM  F2    C25  C24   118.46  3.000
 LKM  F2    C25  C26   118.37  3.000
 LKM  C24   C25  C26   123.17  3.000
 LKM  C23   C24  C25   120.41  3.000
 LKM  C23   C24  C29   122.10  3.000
 LKM  C25   C24  C29   117.47  3.000
 LKM  H232  C23  H231  106.68  3.000
 LKM  H232  C23  O22   111.10  3.000
 LKM  H231  C23  O22   105.42  3.000
 LKM  H232  C23  C24   111.35  3.000
 LKM  H231  C23  C24   109.32  3.000
 LKM  O22   C23  C24   112.61  3.000
 LKM  C20   O22  C23   119.72  3.000
 LKM  C21   C20  C19   120.18  3.000
 LKM  C21   C20  O22   116.26  3.000
 LKM  C19   C20  O22   123.56  3.000
 LKM  H19   C19  C18   118.49  3.000
 LKM  H19   C19  C20   121.69  3.000
 LKM  C18   C19  C20   119.82  3.000
 LKM  H18   C18  C16   119.27  3.000
 LKM  H18   C18  C19   119.44  3.000
 LKM  C16   C18  C19   121.29  3.000
 LKM  H21   C21  C15   119.70  3.000
 LKM  H21   C21  C20   119.73  3.000
 LKM  C15   C21  C20   120.57  3.000
 LKM  C14   C15  C16   118.77  3.000
 LKM  C14   C15  C21   121.75  3.000
 LKM  C16   C15  C21   119.47  3.000
 LKM  C17   C16  C15   119.64  3.000
 LKM  C17   C16  C18   121.69  3.000
 LKM  C15   C16  C18   118.67  3.000
 LKM  H17   C17  C12   121.38  3.000
 LKM  H17   C17  C16   119.08  3.000
 LKM  C12   C17  C16   119.54  3.000
 LKM  H14   C14  C13   119.89  3.000
 LKM  H14   C14  C15   119.13  3.000
 LKM  C13   C14  C15   120.99  3.000
 LKM  H13   C13  C12   120.52  3.000
 LKM  H13   C13  C14   120.09  3.000
 LKM  C12   C13  C14   119.40  3.000
 LKM  S11   C12  C13   118.37  3.000
 LKM  S11   C12  C17   119.95  3.000
 LKM  C13   C12  C17   121.66  3.000
 LKM  N     S11  O32   105.92  3.000
 LKM  N     S11  O33   111.15  3.000
 LKM  O32   S11  O33   119.25  3.000
 LKM  N     S11  C12   101.53  3.000
 LKM  O32   S11  C12   109.60  3.000
 LKM  O33   S11  C12   107.95  3.000
 LKM  H     N    CA    114.96  3.000
 LKM  H     N    S11   111.55  3.000
 LKM  CA    N    S11   117.32  3.000
 LKM  HA    CA   CB    108.33  3.000
 LKM  HA    CA   C     109.81  3.000
 LKM  CB    CA   C     110.76  3.000
 LKM  HA    CA   N     108.45  3.000
 LKM  CB    CA   N     108.11  3.000
 LKM  C     CA   N     111.28  3.000
 LKM  O     C    OXT   124.50  3.000
 LKM  O     C    CA    123.10  3.000
 LKM  OXT   C    CA    112.33  3.000
 LKM  HB    OXT  C     110.36  3.000
 LKM  HBC2  CB   HBC1  107.16  3.000
 LKM  HBC2  CB   CG    109.94  3.000
 LKM  HBC1  CB   CG    110.35  3.000
 LKM  HBC2  CB   CA    106.64  3.000
 LKM  HBC1  CB   CA    109.28  3.000
 LKM  CG    CB   CA    113.24  3.000
 LKM  HGC2  CG   HGC1  105.83  3.000
 LKM  HGC2  CG   CD    107.53  3.000
 LKM  HGC1  CG   CD    107.98  3.000
 LKM  HGC2  CG   CB    112.14  3.000
 LKM  HGC1  CG   CB    110.74  3.000
 LKM  CD    CG   CB    112.32  3.000
 LKM  OE2   CD   OE1   123.26  3.000
 LKM  OE2   CD   CG    125.17  3.000
 LKM  OE1   CD   CG    111.57  3.000
 LKM  HE1   OE1  CD    110.02  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  CONST_44  HB   OXT  C    CA    180.00   0.0  0
 LKM  CONST_45  HE1  OE1  CD   CG    180.00   0.0  0
 LKM  Var_01    O22  C23  C24  C29   -21.91  30.0  2
 LKM  Var_02    C19  C20  O22  C23     0.75  30.0  2
 LKM  Var_03    O33  S11  C12  C17     1.52  30.0  2
 LKM  Var_04    CA   N    S11  C12    78.72  30.0  3
 LKM  Var_05    CD   CG   CB   CA   -173.43  30.0  3
 LKM  Var_06    OE1  CD   CG   CB   -178.98  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-3  HB   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
 LKM  plan-4  HE1  0.020

