# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 17:45:42 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{[6-(pentyloxy)naphthalen-2-yl]sulfonyl}-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCOc1ccc2cc(ccc2c1)[S](=O)(=O)N[C@H](CCC(O)=O)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
 LK3  LK3  'N-{[6-(pentyloxy)naphthalen-2-yl]sulfonyl}-D-glutamic acid'  ligand  54  29  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK3
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
 LK3  O28   O  OS    0  -0.651  -1.2882   3.1093    2.7747
 LK3  S11   S  S     0   1.376  -1.8668   2.3203    1.7017
 LK3  O27   O  OS    0  -0.648  -3.2750   1.9632    1.7299
 LK3  N     N  NC1   0  -0.712  -1.0180   0.8983    1.6912
 LK3  CA    C  CH1   0  -0.254  -1.3058  -0.0706    0.6493
 LK3  C     C  C     0   0.555  -0.4289   0.1530   -0.5753
 LK3  OXT   O  OH1   0  -0.581  -0.9404  -0.4263   -1.6477
 LK3  O     O  O     0  -0.422   0.6176   0.7470   -0.5540
 LK3  CB    C  CH2   0  -0.419  -1.1512  -1.5022    1.1798
 LK3  CG    C  CH2   0  -0.606   0.2561  -1.8333    1.6491
 LK3  CD    C  C     0   0.562   0.3645  -3.2285    2.2024
 LK3  OE2   O  O     0  -0.440  -0.5468  -4.0126    2.2881
 LK3  OE1   O  OH1   0  -0.594   1.6030  -3.5056    2.5937
 LK3  C12   C  CR6   0  -0.229  -1.5292   3.1104    0.1611
 LK3  C17   C  CR16  0  -0.227  -0.3298   3.8453    0.0214
 LK3  C16   C  CR16  0  -0.311  -0.0184   4.3958   -1.1851
 LK3  C15   C  CR66  0   0.157  -0.8745   4.2379   -2.3061
 LK3  C21   C  CR16  0  -0.436  -0.5648   4.7942   -3.5575
 LK3  C20   C  CR6   0   0.416  -1.4158   4.6329   -4.6305
 LK3  C19   C  CR16  0  -0.374  -2.6182   3.9020   -4.4714
 LK3  C18   C  CR16  0  -0.285  -2.9321   3.3550   -3.2576
 LK3  C14   C  CR66  0   0.110  -2.0777   3.5021   -2.1454
 LK3  C13   C  CR16  0  -0.292  -2.3898   2.9409   -0.8889
 LK3  O22   O  O2    0  -0.472  -1.0401   5.1900   -5.7900
 LK3  C23   C  CH2   0  -0.175  -1.9169   5.1570   -6.9106
 LK3  C24   C  CH2   0  -0.456  -1.2533   5.9027   -8.0486
 LK3  C25   C  CH2   0  -0.421  -2.1612   5.9800   -9.2703
 LK3  C26   C  CH2   0  -0.419  -1.5184   6.7247  -10.4343
 LK3  C30   C  CH3   0  -0.663  -2.4369   6.8236  -11.6441
 LK3  H     H  HNC1  0   0.413  -0.0292   1.0548    1.8616
 LK3  HA    H  HCH1  0   0.320  -2.3525   0.0361    0.3566
 LK3  HBC1  H  HCH2  0   0.267  -1.4642  -2.1944    0.3970
 LK3  HBC2  H  HCH2  0   0.272  -1.8580  -1.6129    2.0024
 LK3  HXT   H  HOH1  0   0.488  -0.3448  -0.3227   -2.4059
 LK3  HGC1  H  HCH2  0   0.291   0.9873  -1.7368    0.8414
 LK3  HGC2  H  HCH2  0   0.286   0.5850  -1.1435    2.4326
 LK3  HE1   H  HOH1  0   0.481   1.6434  -4.4055    2.9506
 LK3  H17   H  HCR6  0   0.280   0.3363   3.9787    0.8632
 LK3  H13   H  HCR6  0   0.287  -3.3144   2.3878   -0.7785
 LK3  H16   H  HCR6  0   0.266   0.8953   4.9665   -1.2953
 LK3  H21   H  HCR6  0   0.265   0.3519   5.3589   -3.6806
 LK3  H19   H  HCR6  0   0.289  -3.3004   3.7623   -5.2983
 LK3  H18   H  HCR6  0   0.270  -3.8527   2.7950   -3.1482
 LK3  H231  H  HCH2  0   0.226  -2.1232   4.1223   -7.2051
 LK3  H232  H  HCH2  0   0.225  -2.8722   5.6292   -6.6560
 LK3  H241  H  HCH2  0   0.230  -0.9975   6.9138   -7.7188
 LK3  H242  H  HCH2  0   0.231  -0.3162   5.4055   -8.3159
 LK3  H251  H  HCH2  0   0.216  -3.0988   6.4764   -8.9982
 LK3  H252  H  HCH2  0   0.217  -2.4336   4.9698   -9.5938
 LK3  H261  H  HCH2  0   0.214  -1.2337   7.7289  -10.1060
 LK3  H262  H  HCH2  0   0.215  -0.5882   6.2219  -10.7151
 LK3  H301  H  HCH3  0   0.217  -2.7062   5.8341  -12.0180
 LK3  H302  H  HCH3  0   0.217  -3.3631   7.3431  -11.3908
 LK3  H303  H  HCH3  0   0.228  -1.9660   7.3693  -12.4622

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
 LK3  O27  S11   double    1.453  0.020  1.453
 LK3  S11  N     single    1.656  0.020  1.656
 LK3  N    CA    single    1.452  0.020  1.452
 LK3  CA   C     single    1.523  0.020  1.523
 LK3  C    OXT   single    1.322  0.020  1.322
 LK3  C    O     double    1.203  0.020  1.203
 LK3  CA   CB    single    1.535  0.020  1.535
 LK3  CB   CG    single    1.520  0.020  1.520
 LK3  CG   CD    single    1.505  0.020  1.505
 LK3  CD   OE2   double    1.205  0.020  1.205
 LK3  CD   OE1   single    1.328  0.020  1.328
 LK3  S11  C12   single    1.764  0.020  1.764
 LK3  C12  C17   aromatic  1.414  0.020  1.414
 LK3  C17  C16   aromatic  1.362  0.020  1.362
 LK3  C16  C15   aromatic  1.419  0.020  1.419
 LK3  C15  C21   single    1.404  0.020  1.404
 LK3  C21  C20   double    1.379  0.020  1.379
 LK3  C20  C19   single    1.416  0.020  1.416
 LK3  C19  C18   double    1.368  0.020  1.368
 LK3  C15  C14   aromatic  1.420  0.020  1.420
 LK3  C18  C14   single    1.410  0.020  1.410
 LK3  C12  C13   aromatic  1.368  0.020  1.368
 LK3  C14  C13   aromatic  1.411  0.020  1.411
 LK3  C20  O22   single    1.340  0.020  1.340
 LK3  O22  C23   single    1.423  0.020  1.423
 LK3  S11  O28   double    1.452  0.020  1.452
 LK3  C23  C24   single    1.514  0.020  1.514
 LK3  C24  C25   single    1.524  0.020  1.524
 LK3  C25  C26   single    1.524  0.020  1.524
 LK3  C26  C30   single    1.522  0.020  1.522
 LK3  N    H     single    0.860  0.020  1.020
 LK3  CB   HBC1  single    0.970  0.020  1.090
 LK3  CB   HBC2  single    0.970  0.020  1.090
 LK3  OXT  HXT   single    0.850  0.020  0.980
 LK3  CG   HGC1  single    0.970  0.020  1.090
 LK3  CG   HGC2  single    0.970  0.020  1.090
 LK3  OE1  HE1   single    0.850  0.020  0.980
 LK3  C17  H17   single    0.930  0.020  1.080
 LK3  C13  H13   single    0.930  0.020  1.080
 LK3  C16  H16   single    0.930  0.020  1.080
 LK3  C21  H21   single    0.930  0.020  1.080
 LK3  C19  H19   single    0.930  0.020  1.080
 LK3  C18  H18   single    0.930  0.020  1.080
 LK3  C23  H231  single    0.970  0.020  1.090
 LK3  C23  H232  single    0.970  0.020  1.090
 LK3  C24  H241  single    0.970  0.020  1.090
 LK3  C24  H242  single    0.970  0.020  1.090
 LK3  C25  H251  single    0.970  0.020  1.090
 LK3  C25  H252  single    0.970  0.020  1.090
 LK3  C26  H261  single    0.970  0.020  1.090
 LK3  C26  H262  single    0.970  0.020  1.090
 LK3  C30  H301  single    0.970  0.020  1.090
 LK3  C30  H302  single    0.970  0.020  1.090
 LK3  C30  H303  single    0.970  0.020  1.090
 LK3  CA   HA    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
 LK3  C12   S11  N     106.32  3.000
 LK3  C12   S11  O27   108.21  3.000
 LK3  N     S11  O27   106.61  3.000
 LK3  C12   S11  O28   109.01  3.000
 LK3  N     S11  O28   105.48  3.000
 LK3  O27   S11  O28   120.35  3.000
 LK3  H     N    CA    114.61  3.000
 LK3  H     N    S11   111.45  3.000
 LK3  CA    N    S11   118.42  3.000
 LK3  HA    CA   CB    106.28  3.000
 LK3  HA    CA   C     108.79  3.000
 LK3  CB    CA   C     110.92  3.000
 LK3  HA    CA   N     108.50  3.000
 LK3  CB    CA   N     110.76  3.000
 LK3  C     CA   N     111.41  3.000
 LK3  O     C    OXT   124.55  3.000
 LK3  O     C    CA    123.99  3.000
 LK3  OXT   C    CA    111.43  3.000
 LK3  HXT   OXT  C     110.48  3.000
 LK3  HBC2  CB   HBC1  106.92  3.000
 LK3  HBC2  CB   CG    110.20  3.000
 LK3  HBC1  CB   CG    110.43  3.000
 LK3  HBC2  CB   CA    106.87  3.000
 LK3  HBC1  CB   CA    108.36  3.000
 LK3  CG    CB   CA    113.78  3.000
 LK3  HGC2  CG   HGC1  105.79  3.000
 LK3  HGC2  CG   CD    107.43  3.000
 LK3  HGC1  CG   CD    107.77  3.000
 LK3  HGC2  CG   CB    111.23  3.000
 LK3  HGC1  CG   CB    111.82  3.000
 LK3  CD    CG   CB    112.47  3.000
 LK3  OE1   CD   OE2   123.26  3.000
 LK3  OE1   CD   CG    111.65  3.000
 LK3  OE2   CD   CG    125.09  3.000
 LK3  HE1   OE1  CD    109.95  3.000
 LK3  C13   C12  C17   121.49  3.000
 LK3  C13   C12  S11   119.63  3.000
 LK3  C17   C12  S11   118.79  3.000
 LK3  H17   C17  C16   119.91  3.000
 LK3  H17   C17  C12   120.64  3.000
 LK3  C16   C17  C12   119.45  3.000
 LK3  H16   C16  C15   119.16  3.000
 LK3  H16   C16  C17   119.74  3.000
 LK3  C15   C16  C17   121.11  3.000
 LK3  C14   C15  C21   119.56  3.000
 LK3  C14   C15  C16   118.65  3.000
 LK3  C21   C15  C16   121.79  3.000
 LK3  H21   C21  C20   119.65  3.000
 LK3  H21   C21  C15   119.62  3.000
 LK3  C20   C21  C15   120.73  3.000
 LK3  O22   C20  C19   123.36  3.000
 LK3  O22   C20  C21   116.84  3.000
 LK3  C19   C20  C21   119.80  3.000
 LK3  H19   C19  C18   118.83  3.000
 LK3  H19   C19  C20   121.10  3.000
 LK3  C18   C19  C20   120.07  3.000
 LK3  H18   C18  C14   119.29  3.000
 LK3  H18   C18  C19   119.44  3.000
 LK3  C14   C18  C19   121.27  3.000
 LK3  C13   C14  C18   121.79  3.000
 LK3  C13   C14  C15   119.63  3.000
 LK3  C18   C14  C15   118.57  3.000
 LK3  H13   C13  C14   118.86  3.000
 LK3  H13   C13  C12   121.47  3.000
 LK3  C14   C13  C12   119.67  3.000
 LK3  C23   O22  C20   119.92  3.000
 LK3  H232  C23  H231  107.78  3.000
 LK3  H232  C23  C24   110.16  3.000
 LK3  H231  C23  C24   110.23  3.000
 LK3  H232  C23  O22   110.13  3.000
 LK3  H231  C23  O22   110.46  3.000
 LK3  C24   C23  O22   108.09  3.000
 LK3  H242  C24  H241  107.07  3.000
 LK3  H242  C24  C25   109.72  3.000
 LK3  H241  C24  C25   109.52  3.000
 LK3  H242  C24  C23   109.59  3.000
 LK3  H241  C24  C23   109.34  3.000
 LK3  C25   C24  C23   111.50  3.000
 LK3  H252  C25  H251  106.17  3.000
 LK3  H252  C25  C26   109.27  3.000
 LK3  H251  C25  C26   109.23  3.000
 LK3  H252  C25  C24   109.77  3.000
 LK3  H251  C25  C24   109.50  3.000
 LK3  C26   C25  C24   112.69  3.000
 LK3  H262  C26  H261  106.11  3.000
 LK3  H262  C26  C30   109.81  3.000
 LK3  H261  C26  C30   109.63  3.000
 LK3  H262  C26  C25   109.27  3.000
 LK3  H261  C26  C25   109.21  3.000
 LK3  C30   C26  C25   112.60  3.000
 LK3  H303  C30  H302  107.60  3.000
 LK3  H303  C30  H301  107.65  3.000
 LK3  H302  C30  H301  107.55  3.000
 LK3  H303  C30  C26   111.61  3.000
 LK3  H302  C30  C26   111.00  3.000
 LK3  H301  C30  C26   111.24  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
 LK3  CONST_01  C15   C16  C17  C12     0.00   0.0  0
 LK3  CONST_02  C15   C14  C13  C12     0.00   0.0  0
 LK3  CONST_03  C14   C13  C12  C17     0.00   0.0  0
 LK3  CONST_04  C14   C15  C16  C17     0.00   0.0  0
 LK3  CONST_05  C13   C12  C17  C16     0.00   0.0  0
 LK3  CONST_06  C13   C14  C15  C16     0.00   0.0  0
 LK3  CONST_07  C16   C17  C12  S11   180.00   0.0  0
 LK3  CONST_08  C14   C13  C12  S11   180.00   0.0  0
 LK3  CONST_09  H16   C16  C17  C12   180.00   0.0  0
 LK3  CONST_10  H13   C13  C12  C17   180.00   0.0  0
 LK3  CONST_11  H17   C17  C16  C15   180.00   0.0  0
 LK3  CONST_12  HXT   OXT  C    CA    180.00   0.0  0
 LK3  CONST_13  HE1   OE1  CD   CG    180.00   0.0  0
 LK3  Var_01    C17   C12  S11  O28    31.78  30.0  2
 LK3  Var_02    C12   S11  N    CA    -59.87  30.0  2
 LK3  Var_03    C24   C23  O22  C20   177.82  30.0  3
 LK3  Var_04    CD    CG   CB   CA    178.22  30.0  3
 LK3  Var_05    OE2   CD   CG   CB     -0.67  30.0  3
 LK3  Var_06    C25   C24  C23  O22  -176.94  30.0  3
 LK3  Var_07    C26   C25  C24  C23  -179.93  30.0  3
 LK3  Var_08    C30   C26  C25  C24  -178.91  30.0  3
 LK3  Var_09    H301  C30  C26  C25   -60.43  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
 LK3  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
 LK3  plan-1  S11  0.020
 LK3  plan-1  C12  0.020
 LK3  plan-1  C17  0.020
 LK3  plan-1  C16  0.020
 LK3  plan-1  C15  0.020
 LK3  plan-1  C21  0.020
 LK3  plan-1  C20  0.020
 LK3  plan-1  C19  0.020
 LK3  plan-1  C18  0.020
 LK3  plan-1  C14  0.020
 LK3  plan-1  C13  0.020
 LK3  plan-1  O22  0.020
 LK3  plan-1  H17  0.020
 LK3  plan-1  H13  0.020
 LK3  plan-1  H16  0.020
 LK3  plan-1  H21  0.020
 LK3  plan-1  H19  0.020
 LK3  plan-1  H18  0.020
 LK3  plan-2  CA   0.020
 LK3  plan-2  C    0.020
 LK3  plan-2  OXT  0.020
 LK3  plan-2  O    0.020
 LK3  plan-2  HXT  0.020
 LK3  plan-3  CG   0.020
 LK3  plan-3  CD   0.020
 LK3  plan-3  OE2  0.020
 LK3  plan-3  OE1  0.020
 LK3  plan-3  HE1  0.020

