# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:01:09 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-({7-[(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)c1ccc2ccc(OCc3ccc(cc3)C#N)cc2c1)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
 IK4  IK4  'N-({7-[(4-cyanobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid'  ligand  53  33  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IK4
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
 IK4  N31   N  NS    0  -0.248  -9.9804  -1.3167   2.5618
 IK4  C30   C  CSP   0   0.058  -9.0738  -1.0435   1.9053
 IK4  C27   C  CR6   0  -0.003  -7.9498  -0.7063   1.0920
 IK4  C28   C  CR16  0  -0.225  -7.6469   0.6335   0.8520
 IK4  C29   C  CR16  0  -0.277  -6.5580   0.9504   0.0595
 IK4  C26   C  CR16  0  -0.225  -7.1682  -1.7205   0.5399
 IK4  C25   C  CR16  0  -0.278  -6.0829  -1.3856  -0.2504
 IK4  C24   C  CR6   0   0.114  -5.7714  -0.0525  -0.4993
 IK4  C23   C  CH2   0  -0.272  -4.5742   0.3002  -1.3300
 IK4  C19   C  CR16  0  -0.367  -2.0070   0.9313  -2.3010
 IK4  C20   C  CR6   0   0.410  -2.2653   0.7450  -0.9217
 IK4  C21   C  CR16  0  -0.428  -1.2474   0.8913  -0.0087
 IK4  C18   C  CR16  0  -0.289  -0.7475   1.2505  -2.7283
 IK4  C16   C  CR66  0   0.111   0.3179   1.4042  -1.8175
 IK4  C15   C  CR66  0   0.159   0.0533   1.2195  -0.4353
 IK4  C14   C  CR16  0  -0.302   1.1145   1.3689   0.4864
 IK4  C17   C  CR16  0  -0.292   1.6236   1.7421  -2.2375
 IK4  C12   C  CR16  0  -0.263   2.6393   1.8859  -1.3347
 IK4  C13   C  CR6   0  -0.201   2.3670   1.6840   0.0353
 IK4  S11   S  S     0   1.384   3.7031   1.7349   1.1999
 IK4  O33   O  OS    0  -0.648   4.7976   2.4586   0.5750
 IK4  O32   O  OS    0  -0.651   3.1816   2.1475   2.4905
 IK4  N     N  NC1   0  -0.737   4.1915   0.1872   1.3796
 IK4  CA    C  CH1   0  -0.212   4.9323  -0.5147   0.3606
 IK4  C     C  C     0   0.568   6.3934  -0.6377   0.7764
 IK4  O     O  O     0  -0.420   6.8200  -0.3629   1.8648
 IK4  OXT   O  OH1   0  -0.590   7.1333  -1.0991  -0.2211
 IK4  CB    C  CH2   0  -0.448   4.3256  -1.8910   0.0660
 IK4  CG    C  CH2   0  -0.584   2.8900  -1.7776  -0.4205
 IK4  CD    C  C     0   0.559   2.3065  -3.1043  -0.8212
 IK4  OE1   O  O     0  -0.443   2.8803  -4.1627  -0.7554
 IK4  OE2   O  OH1   0  -0.589   1.0597  -2.9777  -1.2590
 IK4  O22   O  O2    0  -0.466  -3.4781   0.4223  -0.4336
 IK4  H28   H  HCR6  0   0.285  -8.2595   1.4157   1.2787
 IK4  H26   H  HCR6  0   0.285  -7.4104  -2.7576   0.7264
 IK4  H29   H  HCR6  0   0.273  -6.3232   1.9901  -0.1308
 IK4  H25   H  HCR6  0   0.273  -5.4769  -2.1720  -0.6822
 IK4  H231  H  HCH2  0   0.254  -4.3842  -0.4806  -2.0728
 IK4  H232  H  HCH2  0   0.254  -4.7436   1.2414  -1.8618
 IK4  H18   H  HCR6  0   0.270  -0.5629   1.3888  -3.7862
 IK4  H21   H  HCR6  0   0.267  -1.4449   0.7501   1.0472
 IK4  H17   H  HCR6  0   0.269   1.8156   1.8937  -3.2923
 IK4  H14   H  HCR6  0   0.285   0.9191   1.2189   1.5412
 IK4  H12   H  HCR6  0   0.283   3.6293   2.1620  -1.6685
 IK4  H     H  HNC1  0   0.426   3.7129  -0.3497   2.0914
 IK4  HA    H  HCH1  0   0.301   4.9114   0.0623  -0.5698
 IK4  HB1C  H  HCH2  0   0.275   4.9361  -2.3798  -0.6925
 IK4  HB2C  H  HCH2  0   0.263   4.3754  -2.5126   0.9633
 IK4  HXT   H  HOH1  0   0.488   8.0565  -1.1922   0.0591
 IK4  HG1C  H  HCH2  0   0.285   2.2405  -1.3528   0.3491
 IK4  HG2C  H  HCH2  0   0.285   2.8168  -1.0945  -1.2729
 IK4  HE2   H  HOH1  0   0.480   0.7049  -3.8464  -1.5002
 IK4  H19   H  HCR6  0   0.294  -2.7936   0.8260  -3.0351

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
 IK4  N31  C30   triple    1.152  0.020  1.152
 IK4  C30  C27   single    1.428  0.020  1.428
 IK4  C27  C28   aromatic  1.394  0.020  1.394
 IK4  C27  C26   aromatic  1.394  0.020  1.394
 IK4  C28  C29   aromatic  1.384  0.020  1.384
 IK4  C29  C24   aromatic  1.392  0.020  1.392
 IK4  C26  C25   aromatic  1.384  0.020  1.384
 IK4  C25  C24   aromatic  1.391  0.020  1.391
 IK4  C24  C23   single    1.499  0.020  1.499
 IK4  C23  O22   single    1.421  0.020  1.421
 IK4  C19  C20   aromatic  1.416  0.020  1.416
 IK4  C19  C18   aromatic  1.368  0.020  1.368
 IK4  C20  C21   aromatic  1.375  0.020  1.375
 IK4  C20  O22   single    1.347  0.020  1.347
 IK4  C21  C15   aromatic  1.408  0.020  1.408
 IK4  C18  C16   aromatic  1.410  0.020  1.410
 IK4  C16  C15   aromatic  1.419  0.020  1.419
 IK4  C16  C17   aromatic  1.413  0.020  1.413
 IK4  C15  C14   aromatic  1.414  0.020  1.414
 IK4  C14  C13   aromatic  1.368  0.020  1.368
 IK4  C17  C12   aromatic  1.366  0.020  1.366
 IK4  C12  C13   aromatic  1.411  0.020  1.411
 IK4  C13  S11   single    1.773  0.020  1.773
 IK4  S11  O33   double    1.453  0.020  1.453
 IK4  S11  O32   double    1.452  0.020  1.452
 IK4  S11  N     single    1.633  0.020  1.633
 IK4  N    CA    single    1.442  0.020  1.442
 IK4  CA   C     single    1.524  0.020  1.524
 IK4  CA   CB    single    1.533  0.020  1.533
 IK4  C    O     double    1.201  0.020  1.201
 IK4  C    OXT   single    1.325  0.020  1.325
 IK4  CB   CG    single    1.520  0.020  1.520
 IK4  CG   CD    single    1.504  0.020  1.504
 IK4  CD   OE1   double    1.206  0.020  1.206
 IK4  CD   OE2   single    1.327  0.020  1.327
 IK4  C28  H28   single    0.930  0.020  1.080
 IK4  C26  H26   single    0.930  0.020  1.080
 IK4  C29  H29   single    0.930  0.020  1.080
 IK4  C25  H25   single    0.930  0.020  1.080
 IK4  C23  H231  single    0.970  0.020  1.090
 IK4  C23  H232  single    0.970  0.020  1.090
 IK4  C19  H19   single    0.930  0.020  1.080
 IK4  C18  H18   single    0.930  0.020  1.080
 IK4  C21  H21   single    0.930  0.020  1.080
 IK4  C17  H17   single    0.930  0.020  1.080
 IK4  C14  H14   single    0.930  0.020  1.080
 IK4  C12  H12   single    0.930  0.020  1.080
 IK4  N    H     single    0.860  0.020  1.020
 IK4  CA   HA    single    0.970  0.020  1.090
 IK4  CB   HB1C  single    0.970  0.020  1.090
 IK4  CB   HB2C  single    0.970  0.020  1.090
 IK4  OXT  HXT   single    0.850  0.020  0.980
 IK4  CG   HG1C  single    0.970  0.020  1.090
 IK4  CG   HG2C  single    0.970  0.020  1.090
 IK4  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
 IK4  C27   C30  N31   180.00  3.000
 IK4  C26   C27  C28   120.59  3.000
 IK4  C26   C27  C30   119.68  3.000
 IK4  C28   C27  C30   119.73  3.000
 IK4  H28   C28  C29   120.41  3.000
 IK4  H28   C28  C27   120.27  3.000
 IK4  C29   C28  C27   119.32  3.000
 IK4  H29   C29  C24   119.92  3.000
 IK4  H29   C29  C28   119.43  3.000
 IK4  C24   C29  C28   120.65  3.000
 IK4  H26   C26  C25   120.42  3.000
 IK4  H26   C26  C27   120.25  3.000
 IK4  C25   C26  C27   119.33  3.000
 IK4  H25   C25  C24   119.94  3.000
 IK4  H25   C25  C26   119.41  3.000
 IK4  C24   C25  C26   120.64  3.000
 IK4  C23   C24  C25   120.22  3.000
 IK4  C23   C24  C29   120.28  3.000
 IK4  C25   C24  C29   119.47  3.000
 IK4  H232  C23  H231  108.11  3.000
 IK4  H232  C23  O22   110.61  3.000
 IK4  H231  C23  O22   110.82  3.000
 IK4  H232  C23  C24   110.37  3.000
 IK4  H231  C23  C24   110.30  3.000
 IK4  O22   C23  C24   106.65  3.000
 IK4  H19   C19  C18   118.72  3.000
 IK4  H19   C19  C20   121.07  3.000
 IK4  C18   C19  C20   120.21  3.000
 IK4  O22   C20  C21   116.84  3.000
 IK4  O22   C20  C19   123.31  3.000
 IK4  C21   C20  C19   119.85  3.000
 IK4  H21   C21  C15   119.61  3.000
 IK4  H21   C21  C20   119.88  3.000
 IK4  C15   C21  C20   120.50  3.000
 IK4  H18   C18  C16   119.23  3.000
 IK4  H18   C18  C19   119.47  3.000
 IK4  C16   C18  C19   121.29  3.000
 IK4  C17   C16  C15   119.54  3.000
 IK4  C17   C16  C18   122.17  3.000
 IK4  C15   C16  C18   118.29  3.000
 IK4  C14   C15  C16   118.76  3.000
 IK4  C14   C15  C21   121.39  3.000
 IK4  C16   C15  C21   119.85  3.000
 IK4  H14   C14  C13   121.22  3.000
 IK4  H14   C14  C15   119.00  3.000
 IK4  C13   C14  C15   119.78  3.000
 IK4  H17   C17  C12   119.81  3.000
 IK4  H17   C17  C16   119.14  3.000
 IK4  C12   C17  C16   121.05  3.000
 IK4  H12   C12  C13   120.88  3.000
 IK4  H12   C12  C17   120.25  3.000
 IK4  C13   C12  C17   118.87  3.000
 IK4  S11   C13  C12   119.21  3.000
 IK4  S11   C13  C14   118.68  3.000
 IK4  C12   C13  C14   121.99  3.000
 IK4  N     S11  O32   106.20  3.000
 IK4  N     S11  O33   107.10  3.000
 IK4  O32   S11  O33   120.75  3.000
 IK4  N     S11  C13   105.69  3.000
 IK4  O32   S11  C13   108.74  3.000
 IK4  O33   S11  C13   107.42  3.000
 IK4  H     N    CA    118.80  3.000
 IK4  H     N    S11   116.03  3.000
 IK4  CA    N    S11   122.49  3.000
 IK4  HA    CA   CB    107.60  3.000
 IK4  HA    CA   C     107.01  3.000
 IK4  CB    CA   C     111.07  3.000
 IK4  HA    CA   N     109.52  3.000
 IK4  CB    CA   N     111.69  3.000
 IK4  C     CA   N     109.81  3.000
 IK4  OXT   C    O     124.31  3.000
 IK4  OXT   C    CA    110.98  3.000
 IK4  O     C    CA    124.71  3.000
 IK4  HXT   OXT  C     110.35  3.000
 IK4  HB2C  CB   HB1C  106.91  3.000
 IK4  HB2C  CB   CG    110.38  3.000
 IK4  HB1C  CB   CG    109.87  3.000
 IK4  HB2C  CB   CA    109.57  3.000
 IK4  HB1C  CB   CA    108.36  3.000
 IK4  CG    CB   CA    111.62  3.000
 IK4  HG2C  CG   HG1C  105.42  3.000
 IK4  HG2C  CG   CD    108.49  3.000
 IK4  HG1C  CG   CD    107.46  3.000
 IK4  HG2C  CG   CB    111.03  3.000
 IK4  HG1C  CG   CB    111.40  3.000
 IK4  CD    CG   CB    112.71  3.000
 IK4  OE2   CD   OE1   123.28  3.000
 IK4  OE2   CD   CG    111.60  3.000
 IK4  OE1   CD   CG    125.12  3.000
 IK4  HE2   OE2  CD    109.91  3.000
 IK4  C20   O22  C23   119.12  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
 IK4  CONST_01  C24  C29  C28  C27     0.00   0.0  0
 IK4  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 IK4  CONST_03  C25  C26  C27  C28     0.00   0.0  0
 IK4  CONST_04  C25  C24  C29  C28     0.00   0.0  0
 IK4  CONST_05  C26  C27  C28  C29     0.00   0.0  0
 IK4  CONST_06  C26  C25  C24  C29     0.00   0.0  0
 IK4  CONST_07  C15  C21  C20  C19     0.00   0.0  0
 IK4  CONST_08  C15  C16  C18  C19     0.00   0.0  0
 IK4  CONST_09  C17  C16  C18  C19   180.00   0.0  0
 IK4  CONST_10  C16  C18  C19  C20     0.00   0.0  0
 IK4  CONST_11  C16  C15  C21  C20     0.00   0.0  0
 IK4  CONST_12  C14  C15  C21  C20   180.00   0.0  0
 IK4  CONST_13  C18  C19  C20  C21     0.00   0.0  0
 IK4  CONST_14  C18  C16  C15  C21     0.00   0.0  0
 IK4  CONST_15  C17  C16  C15  C21   180.00   0.0  0
 IK4  CONST_16  C13  C14  C15  C21   180.00   0.0  0
 IK4  CONST_17  C14  C15  C16  C18   180.00   0.0  0
 IK4  CONST_18  C12  C17  C16  C18   180.00   0.0  0
 IK4  CONST_19  C13  C14  C15  C16     0.00   0.0  0
 IK4  CONST_20  C13  C12  C17  C16     0.00   0.0  0
 IK4  CONST_21  C12  C17  C16  C15     0.00   0.0  0
 IK4  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 IK4  CONST_23  C17  C16  C15  C14     0.00   0.0  0
 IK4  CONST_24  C17  C12  C13  C14     0.00   0.0  0
 IK4  CONST_25  C29  C28  C27  C30   180.00   0.0  0
 IK4  CONST_26  C25  C26  C27  C30   180.00   0.0  0
 IK4  CONST_27  C23  C24  C29  C28   180.00   0.0  0
 IK4  CONST_28  C23  C24  C25  C26   180.00   0.0  0
 IK4  CONST_29  O22  C20  C19  C18   180.00   0.0  0
 IK4  CONST_30  O22  C20  C21  C15   180.00   0.0  0
 IK4  CONST_31  S11  C13  C14  C15   180.00   0.0  0
 IK4  CONST_32  S11  C13  C12  C17   180.00   0.0  0
 IK4  CONST_33  H29  C29  C28  C27   180.00   0.0  0
 IK4  CONST_34  H25  C25  C26  C27   180.00   0.0  0
 IK4  CONST_35  H26  C26  C27  C28   180.00   0.0  0
 IK4  CONST_36  H28  C28  C27  C26   180.00   0.0  0
 IK4  CONST_37  H21  C21  C20  C19   180.00   0.0  0
 IK4  CONST_38  H18  C18  C19  C20   180.00   0.0  0
 IK4  CONST_39  H19  C19  C20  C21   180.00   0.0  0
 IK4  CONST_40  H14  C14  C15  C21     0.00   0.0  0
 IK4  CONST_41  H17  C17  C16  C18     0.00   0.0  0
 IK4  CONST_42  H12  C12  C17  C16   180.00   0.0  0
 IK4  CONST_43  HXT  OXT  C    CA    180.00   0.0  0
 IK4  CONST_44  HE2  OE2  CD   CG    180.00   0.0  0
 IK4  Var_01    O22  C23  C24  C29    88.36  30.0  2
 IK4  Var_02    C19  C20  O22  C23    -2.07  30.0  1
 IK4  Var_03    O33  S11  C13  C14  -163.43  30.0  2
 IK4  Var_04    CA   N    S11  C13    73.09  30.0  3
 IK4  Var_05    CD   CG   CB   CA    175.43  30.0  3
 IK4  Var_06    OE1  CD   CG   CB      1.15  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
 IK4  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
 IK4  plan-1  N31  0.020
 IK4  plan-1  C30  0.020
 IK4  plan-1  C27  0.020
 IK4  plan-1  C28  0.020
 IK4  plan-1  C29  0.020
 IK4  plan-1  C26  0.020
 IK4  plan-1  C25  0.020
 IK4  plan-1  C24  0.020
 IK4  plan-1  C23  0.020
 IK4  plan-1  H28  0.020
 IK4  plan-1  H26  0.020
 IK4  plan-1  H29  0.020
 IK4  plan-1  H25  0.020
 IK4  plan-2  C19  0.020
 IK4  plan-2  C20  0.020
 IK4  plan-2  C21  0.020
 IK4  plan-2  C18  0.020
 IK4  plan-2  C16  0.020
 IK4  plan-2  C15  0.020
 IK4  plan-2  C14  0.020
 IK4  plan-2  C17  0.020
 IK4  plan-2  C12  0.020
 IK4  plan-2  C13  0.020
 IK4  plan-2  S11  0.020
 IK4  plan-2  O22  0.020
 IK4  plan-2  H18  0.020
 IK4  plan-2  H21  0.020
 IK4  plan-2  H17  0.020
 IK4  plan-2  H14  0.020
 IK4  plan-2  H12  0.020
 IK4  plan-2  H19  0.020
 IK4  plan-3  CA   0.020
 IK4  plan-3  C    0.020
 IK4  plan-3  O    0.020
 IK4  plan-3  OXT  0.020
 IK4  plan-3  HXT  0.020
 IK4  plan-4  CG   0.020
 IK4  plan-4  CD   0.020
 IK4  plan-4  OE1  0.020
 IK4  plan-4  OE2  0.020
 IK4  plan-4  HE2  0.020

