# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:45:45 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(CN2C(=O)c3cccc(NC(=O)c4sc(Cl)cc4)c3C2=O)cc1
#
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
 L5N  L5N  '4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid'  ligand  42  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L5N
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
 L5N  CAT  C   CR16   0  -0.289  25.2298  176.5949  27.5972
 L5N  CAX  C   CR16   0  -0.277  24.5005  176.8508  28.7504
 L5N  CBA  C   CR6    0  -0.105  23.3604  176.1139  29.0562
 L5N  CBB  C   C      0   0.392  22.5692  176.3869  30.3336
 L5N  OBD  O   O      0  -0.586  21.5377  175.7096  30.5048
 L5N  OBC  O   OC    -1  -0.586  23.0279  177.2620  31.0924
 L5N  CAY  C   CR16   0  -0.276  22.9641  175.1194  28.1636
 L5N  CAU  C   CR16   0  -0.282  23.6880  174.8623  27.0099
 L5N  CAQ  C   CR6    0   0.122  24.8349  175.5957  26.7157
 L5N  CAN  C   CH2    0  -0.422  25.6371  175.3004  25.4751
 L5N  NAI  N   NR5    0  -0.591  26.3511  174.0395  25.5709
 L5N  CAE  C   CR5    0   0.595  25.9348  172.8479  24.9967
 L5N  OAK  O   O      0  -0.394  24.9505  172.6993  24.3197
 L5N  CAD  C   CR5    0   0.625  27.5071  173.8754  26.3108
 L5N  OAJ  O   O      0  -0.412  28.0755  174.7544  26.9177
 L5N  CAA  C   CR56   0  -0.138  27.8821  172.4529  26.1934
 L5N  CAB  C   CR56   0  -0.046  26.9381  171.8300  25.3944
 L5N  CAF  C   CR16   0  -0.325  27.0003  170.4917  25.0900
 L5N  CAL  C   CR16   0  -0.236  28.0762  169.7882  25.6304
 L5N  CAH  C   CR16   0  -0.306  29.0315  170.3906  26.4359
 L5N  CAC  C   CR6    0   0.385  28.9531  171.7594  26.7473
 L5N  NAG  N   NH1    0  -0.785  29.8393  172.4526  27.5566
 L5N  CAM  C   C      0   0.570  30.8946  171.9601  28.2613
 L5N  OAP  O   O      0  -0.447  31.2764  170.8043  28.2172
 L5N  CAO  C   CR5    0  -0.307  31.5854  172.9236  29.1298
 L5N  CAS  C   CR15   0  -0.219  31.3768  174.2473  29.4043
 L5N  CAW  C   CR15   0  -0.114  32.2967  174.7676  30.3424
 L5N  CAV  C   CR5    0  -0.247  33.1794  173.8141  30.7544
 L5N  CLA  CL  CL     0  -0.061  34.4418  174.0202  31.8789
 L5N  SAR  S   S2     0   0.332  32.9170  172.2895  30.0214
 L5N  H1   H   HCR6   0   0.244  26.1164  177.1792  27.3810
 L5N  H2   H   HCR6   0   0.240  24.8260  177.6328  29.4237
 L5N  H4   H   HCR6   0   0.240  22.0758  174.5394  28.3758
 L5N  H5   H   HCR6   0   0.244  23.3530  174.0856  26.3319
 L5N  H6   H   HCH2   0   0.290  26.3619  176.0922  25.2861
 L5N  H7   H   HCH2   0   0.289  24.9926  175.2387  24.5987
 L5N  H8   H   HCR6   0   0.275  26.2615  170.0059  24.4677
 L5N  H9   H   HCR6   0   0.281  28.1788  168.7316  25.4217
 L5N  H10  H   HCR6   0   0.302  29.8362  169.7884  26.8219
 L5N  H11  H   HNH1   0   0.443  29.6251  173.4355  27.6627
 L5N  H12  H   HCR5   0   0.285  30.5940  174.8514  28.9661
 L5N  H13  H   HCR5   0   0.298  32.3014  175.7889  30.6928

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
 L5N  OAK  CAE  double    1.204  0.020  1.204
 L5N  CAF  CAB  aromatic  1.374  0.020  1.374
 L5N  CAF  CAL  aromatic  1.394  0.020  1.394
 L5N  CAE  CAB  single    1.483  0.020  1.483
 L5N  CAE  NAI  single    1.387  0.020  1.387
 L5N  CAB  CAA  aromatic  1.385  0.020  1.385
 L5N  CAL  CAH  aromatic  1.387  0.020  1.387
 L5N  CAN  NAI  single    1.452  0.020  1.452
 L5N  CAN  CAQ  single    1.507  0.020  1.507
 L5N  NAI  CAD  single    1.382  0.020  1.382
 L5N  CAA  CAD  single    1.476  0.020  1.476
 L5N  CAA  CAC  aromatic  1.391  0.020  1.391
 L5N  CAH  CAC  aromatic  1.406  0.020  1.406
 L5N  CAD  OAJ  double    1.210  0.020  1.210
 L5N  CAC  NAG  single    1.386  0.020  1.386
 L5N  CAQ  CAU  aromatic  1.393  0.020  1.393
 L5N  CAQ  CAT  aromatic  1.390  0.020  1.390
 L5N  CAU  CAY  aromatic  1.386  0.020  1.386
 L5N  NAG  CAM  single    1.361  0.020  1.361
 L5N  CAT  CAX  aromatic  1.388  0.020  1.388
 L5N  OAP  CAM  double    1.218  0.020  1.218
 L5N  CAM  CAO  single    1.470  0.020  1.470
 L5N  CAY  CBA  aromatic  1.394  0.020  1.394
 L5N  CAX  CBA  aromatic  1.391  0.020  1.391
 L5N  CAO  CAS  aromatic  1.368  0.020  1.368
 L5N  CAO  SAR  aromatic  1.723  0.020  1.723
 L5N  CBA  CBB  single    1.527  0.020  1.527
 L5N  CAS  CAW  aromatic  1.413  0.020  1.413
 L5N  SAR  CAV  aromatic  1.712  0.020  1.712
 L5N  OBD  CBB  deloc     1.246  0.020  1.246
 L5N  CAW  CAV  aromatic  1.363  0.020  1.363
 L5N  CBB  OBC  deloc     1.246  0.020  1.246
 L5N  CAV  CLA  single    1.703  0.020  1.703
 L5N  CAT  H1   single    0.930  0.020  1.080
 L5N  CAX  H2   single    0.930  0.020  1.080
 L5N  CAY  H4   single    0.930  0.020  1.080
 L5N  CAU  H5   single    0.930  0.020  1.080
 L5N  CAN  H6   single    0.970  0.020  1.090
 L5N  CAN  H7   single    0.970  0.020  1.090
 L5N  CAF  H8   single    0.930  0.020  1.080
 L5N  CAL  H9   single    0.930  0.020  1.080
 L5N  CAH  H10  single    0.930  0.020  1.080
 L5N  NAG  H11  single    0.860  0.020  1.020
 L5N  CAS  H12  single    0.930  0.020  1.080
 L5N  CAW  H13  single    0.930  0.020  1.080

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
 L5N  H1   CAT  CAQ  119.57  3.000
 L5N  H1   CAT  CAX  119.75  3.000
 L5N  CAQ  CAT  CAX  120.68  3.000
 L5N  H2   CAX  CBA  119.51  3.000
 L5N  H2   CAX  CAT  119.47  3.000
 L5N  CBA  CAX  CAT  121.02  3.000
 L5N  CAY  CBA  CBB  121.06  3.000
 L5N  CBB  CBA  CAX  120.90  3.000
 L5N  CAY  CBA  CAX  118.04  3.000
 L5N  OBC  CBB  OBD  127.09  3.000
 L5N  OBC  CBB  CBA  116.38  3.000
 L5N  OBD  CBB  CBA  116.53  3.000
 L5N  H4   CAY  CAU  119.51  3.000
 L5N  H4   CAY  CBA  119.37  3.000
 L5N  CAU  CAY  CBA  121.12  3.000
 L5N  H5   CAU  CAQ  119.97  3.000
 L5N  H5   CAU  CAY  119.48  3.000
 L5N  CAQ  CAU  CAY  120.55  3.000
 L5N  CAN  CAQ  CAU  120.61  3.000
 L5N  CAU  CAQ  CAT  118.59  3.000
 L5N  CAN  CAQ  CAT  120.79  3.000
 L5N  H7   CAN  H6   107.15  3.000
 L5N  H7   CAN  NAI  107.14  3.000
 L5N  H6   CAN  NAI  108.38  3.000
 L5N  H7   CAN  CAQ  111.00  3.000
 L5N  H6   CAN  CAQ  110.76  3.000
 L5N  NAI  CAN  CAQ  112.19  3.000
 L5N  CAD  NAI  CAE  111.76  3.000
 L5N  CAD  NAI  CAN  123.34  3.000
 L5N  CAE  NAI  CAN  124.84  3.000
 L5N  CAB  CAE  OAK  128.25  3.000
 L5N  CAB  CAE  NAI  105.99  3.000
 L5N  OAK  CAE  NAI  125.76  3.000
 L5N  CAA  CAD  OAJ  128.37  3.000
 L5N  OAJ  CAD  NAI  125.11  3.000
 L5N  CAA  CAD  NAI  106.52  3.000
 L5N  CAC  CAA  CAB  122.03  3.000
 L5N  CAC  CAA  CAD  130.14  3.000
 L5N  CAB  CAA  CAD  107.83  3.000
 L5N  CAF  CAB  CAA  122.35  3.000
 L5N  CAA  CAB  CAE  107.89  3.000
 L5N  CAF  CAB  CAE  129.76  3.000
 L5N  H8   CAF  CAL  121.57  3.000
 L5N  H8   CAF  CAB  122.29  3.000
 L5N  CAL  CAF  CAB  116.13  3.000
 L5N  H9   CAL  CAH  118.08  3.000
 L5N  H9   CAL  CAF  119.42  3.000
 L5N  CAH  CAL  CAF  122.50  3.000
 L5N  H10  CAH  CAC  120.46  3.000
 L5N  H10  CAH  CAL  118.68  3.000
 L5N  CAC  CAH  CAL  120.86  3.000
 L5N  NAG  CAC  CAH  125.49  3.000
 L5N  NAG  CAC  CAA  118.39  3.000
 L5N  CAH  CAC  CAA  116.12  3.000
 L5N  H11  NAG  CAM  117.48  3.000
 L5N  H11  NAG  CAC  114.32  3.000
 L5N  CAM  NAG  CAC  128.10  3.000
 L5N  CAO  CAM  OAP  119.74  3.000
 L5N  CAO  CAM  NAG  115.67  3.000
 L5N  OAP  CAM  NAG  124.58  3.000
 L5N  SAR  CAO  CAS  111.72  3.000
 L5N  SAR  CAO  CAM  115.32  3.000
 L5N  CAS  CAO  CAM  132.95  3.000
 L5N  H12  CAS  CAW  122.31  3.000
 L5N  H12  CAS  CAO  124.72  3.000
 L5N  CAW  CAS  CAO  112.97  3.000
 L5N  H13  CAW  CAV  124.11  3.000
 L5N  H13  CAW  CAS  124.51  3.000
 L5N  CAV  CAW  CAS  111.38  3.000
 L5N  SAR  CAV  CLA  120.27  3.000
 L5N  CLA  CAV  CAW  126.50  3.000
 L5N  SAR  CAV  CAW  113.22  3.000
 L5N  CAV  SAR  CAO   90.70  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
 L5N  CONST_01  CAY  CAU  CAQ  CAT    0.00   0.0  0
 L5N  CONST_02  CAY  CBA  CAX  CAT    0.00   0.0  0
 L5N  CONST_03  CAU  CAQ  CAT  CAX    0.00   0.0  0
 L5N  CONST_04  CAU  CAY  CBA  CAX    0.00   0.0  0
 L5N  CONST_05  CAQ  CAU  CAY  CBA    0.00   0.0  0
 L5N  CONST_06  CAQ  CAT  CAX  CBA    0.00   0.0  0
 L5N  CONST_07  CAL  CAF  CAB  CAA    0.00   0.0  0
 L5N  CONST_08  CAL  CAH  CAC  CAA    0.00   0.0  0
 L5N  CONST_09  CAH  CAL  CAF  CAB    0.00   0.0  0
 L5N  CONST_10  CAH  CAC  CAA  CAB    0.00   0.0  0
 L5N  CONST_11  CAC  CAA  CAB  CAF    0.00   0.0  0
 L5N  CONST_12  CAC  CAH  CAL  CAF    0.00   0.0  0
 L5N  CONST_13  CAV  CAW  CAS  CAO    0.00   0.0  0
 L5N  CONST_14  CAW  CAV  SAR  CAO    0.00   0.0  0
 L5N  CONST_15  CAV  SAR  CAO  CAS    0.00   0.0  0
 L5N  CONST_16  SAR  CAV  CAW  CAS    0.00   0.0  0
 L5N  CONST_17  SAR  CAO  CAS  CAW    0.00   0.0  0
 L5N  CONST_18  CAB  CAE  NAI  CAD    0.00   0.0  0
 L5N  CONST_19  CBB  CBA  CAX  CAT  180.00   0.0  0
 L5N  CONST_20  CAN  CAQ  CAT  CAX  180.00   0.0  0
 L5N  CONST_21  CAU  CAY  CBA  CBB  180.00   0.0  0
 L5N  CONST_22  CAN  CAQ  CAU  CAY  180.00   0.0  0
 L5N  CONST_23  NAG  CAC  CAA  CAD    0.00   0.0  0
 L5N  CONST_24  NAG  CAC  CAA  CAB  180.00   0.0  0
 L5N  CONST_25  NAG  CAC  CAH  CAL  180.00   0.0  0
 L5N  CONST_26  CAW  CAS  CAO  CAM  180.00   0.0  0
 L5N  CONST_27  CAV  SAR  CAO  CAM  180.00   0.0  0
 L5N  CONST_28  CLA  CAV  SAR  CAO  180.00   0.0  0
 L5N  CONST_29  CLA  CAV  CAW  CAS  180.00   0.0  0
 L5N  CONST_30  CAB  CAE  NAI  CAN  180.00   0.0  0
 L5N  CONST_31  CAD  NAI  CAE  OAK  180.00   0.0  0
 L5N  CONST_32  H5   CAU  CAQ  CAT  180.00   0.0  0
 L5N  CONST_33  H4   CAY  CBA  CAX  180.00   0.0  0
 L5N  CONST_34  H1   CAT  CAX  CBA  180.00   0.0  0
 L5N  CONST_35  H2   CAX  CBA  CAY  180.00   0.0  0
 L5N  CONST_36  H8   CAF  CAB  CAE    0.00   0.0  0
 L5N  CONST_37  H10  CAH  CAC  CAA  180.00   0.0  0
 L5N  CONST_38  H9   CAL  CAF  CAB  180.00   0.0  0
 L5N  CONST_39  H13  CAW  CAS  CAO  180.00   0.0  0
 L5N  CONST_40  H12  CAS  CAW  CAV  180.00   0.0  0
 L5N  CONST_41  CAO  CAM  NAG  CAC  180.00   0.0  0
 L5N  CONST_42  CAM  NAG  CAC  CAA  180.00   0.0  0
 L5N  CONST_43  CAM  NAG  CAC  CAH    0.00   0.0  0
 L5N  CONST_44  OAK  CAE  NAI  CAN    0.00   0.0  0
 L5N  CONST_45  H11  NAG  CAC  CAA    0.00   0.0  0
 L5N  CONST_46  OAP  CAM  NAG  CAC    0.00   0.0  0
 L5N  Var_01    NAI  CAN  CAQ  CAT  108.27  30.0  3
 L5N  Var_02    CAE  NAI  CAN  CAQ  100.14  30.0  3
 L5N  Var_03    OBD  CBB  CBA  CAX  177.70  30.0  2
 L5N  Var_04    CAS  CAO  CAM  NAG    1.10  30.0  2

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
 L5N  plan-1  CAM  0.020
 L5N  plan-1  CAO  0.020
 L5N  plan-1  CAS  0.020
 L5N  plan-1  CAW  0.020
 L5N  plan-1  CAV  0.020
 L5N  plan-1  CLA  0.020
 L5N  plan-1  SAR  0.020
 L5N  plan-1  H12  0.020
 L5N  plan-1  H13  0.020
 L5N  plan-2  CAT  0.020
 L5N  plan-2  CAX  0.020
 L5N  plan-2  CBA  0.020
 L5N  plan-2  CBB  0.020
 L5N  plan-2  CAY  0.020
 L5N  plan-2  CAU  0.020
 L5N  plan-2  CAQ  0.020
 L5N  plan-2  CAN  0.020
 L5N  plan-2  H1   0.020
 L5N  plan-2  H2   0.020
 L5N  plan-2  H4   0.020
 L5N  plan-2  H5   0.020
 L5N  plan-3  CAN  0.020
 L5N  plan-3  NAI  0.020
 L5N  plan-3  CAE  0.020
 L5N  plan-3  OAK  0.020
 L5N  plan-3  CAD  0.020
 L5N  plan-3  OAJ  0.020
 L5N  plan-3  CAA  0.020
 L5N  plan-3  CAB  0.020
 L5N  plan-3  CAF  0.020
 L5N  plan-3  CAL  0.020
 L5N  plan-3  CAH  0.020
 L5N  plan-3  CAC  0.020
 L5N  plan-3  NAG  0.020
 L5N  plan-3  H8   0.020
 L5N  plan-3  H9   0.020
 L5N  plan-3  H10  0.020
 L5N  plan-4  CAC  0.020
 L5N  plan-4  NAG  0.020
 L5N  plan-4  CAM  0.020
 L5N  plan-4  OAP  0.020
 L5N  plan-4  CAO  0.020
 L5N  plan-4  H11  0.020
 L5N  plan-5  CBA  0.020
 L5N  plan-5  CBB  0.020
 L5N  plan-5  OBD  0.020
 L5N  plan-5  OBC  0.020

