# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:20:04 2021
#   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  43  30  .  2022-03-22  2022-11-17
;
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  -0.283  25.2381  176.4990  27.7716
 L5N  CAX  C   CR16  0  -0.245  24.4505  176.7338  28.8880
 L5N  CBA  C   CR6   0  -0.091  23.2403  176.0615  29.0410
 L5N  CBB  C   C     0   0.534  22.3561  176.2767  30.2130
 L5N  OBD  O   O     0  -0.438  21.3093  175.6968  30.3780
 L5N  OBC  O   OH1   0  -0.593  22.8299  177.1750  31.0641
 L5N  CAY  C   CR16  0  -0.241  22.8314  175.1578  28.0613
 L5N  CAU  C   CR16  0  -0.280  23.6195  174.9317  26.9475
 L5N  CAQ  C   CR6   0   0.144  24.8318  175.6003  26.7927
 L5N  CAN  C   CH2   0  -0.430  25.6947  175.3421  25.5853
 L5N  NAI  N   NR5   0  -0.593  26.3789  174.0670  25.6720
 L5N  CAE  C   CR5   0   0.598  25.9734  172.9040  25.0330
 L5N  OAK  O   O     0  -0.397  25.0087  172.7968  24.3208
 L5N  CAD  C   CR5   0   0.633  27.5138  173.8649  26.4339
 L5N  OAJ  O   O     0  -0.418  28.0699  174.7151  27.0924
 L5N  CAA  C   CR56  0  -0.139  27.8832  172.4484  26.2657
 L5N  CAB  C   CR56  0  -0.044  26.9587  171.8633  25.4169
 L5N  CAF  C   CR16  0  -0.325  27.0313  170.5396  25.0556
 L5N  CAL  C   CR16  0  -0.238  28.0935  169.8122  25.5933
 L5N  CAH  C   CR16  0  -0.306  29.0294  170.3780  26.4471
 L5N  CAC  C   CR6   0   0.395  28.9442  171.7331  26.8091
 L5N  NAG  N   NH1   0  -0.787  29.8212  172.4030  27.6457
 L5N  CAM  C   C     0   0.572  30.9065  171.9138  28.3045
 L5N  OAP  O   O     0  -0.450  31.2687  170.7513  28.2758
 L5N  CAO  C   CR5   0  -0.309  31.6543  172.9038  29.0907
 L5N  CAS  C   CR15  0  -0.217  31.5039  174.2539  29.2522
 L5N  CAW  C   CR15  0  -0.114  32.4724  174.8184  30.1120
 L5N  CAV  C   CR5   0  -0.247  33.3348  173.8709  30.5775
 L5N  CLA  CL  CL    0  -0.060  34.6450  174.1264  31.6347
 L5N  SAR  S   S2    0   0.336  32.9938  172.2993  29.9898
 L5N  H1   H   HCR6  0   0.264  26.1789  177.0231  27.6632
 L5N  H2   H   HCR6  0   0.270  24.7917  177.4407  29.6315
 L5N  H3   H   HOH1  0   0.488  22.2129  177.2878  31.8024
 L5N  H4   H   HCR6  0   0.268  21.8908  174.6340  28.1651
 L5N  H5   H   HCR6  0   0.261  23.2821  174.2356  26.1894
 L5N  H6   H   HCH2  0   0.298  26.4408  176.1275  25.4679
 L5N  H7   H   HCH2  0   0.300  25.0929  175.3312  24.6772
 L5N  H8   H   HCR6  0   0.277  26.3115  170.0807  24.3923
 L5N  H9   H   HCR6  0   0.284  28.2022  168.7662  25.3402
 L5N  H10  H   HCR6  0   0.303  29.8232  169.7584  26.8288
 L5N  H11  H   HNH1  0   0.437  29.5978  173.3797  27.7812
 L5N  H12  H   HCR5  0   0.278  30.7358  174.8508  28.7800
 L5N  H13  H   HCR5  0   0.301  32.5264  175.8656  30.3683

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  1.395  0.020  1.395
 L5N  CAE  CAB  single    1.484  0.020  1.484
 L5N  CAE  NAI  single    1.388  0.020  1.388
 L5N  CAB  CAA  aromatic  1.385  0.020  1.385
 L5N  CAL  CAH  aromatic  1.387  0.020  1.387
 L5N  CAN  NAI  single    1.450  0.020  1.450
 L5N  CAN  CAQ  single    1.506  0.020  1.506
 L5N  NAI  CAD  single    1.382  0.020  1.382
 L5N  CAA  CAD  single    1.474  0.020  1.474
 L5N  CAA  CAC  aromatic  1.390  0.020  1.390
 L5N  CAH  CAC  aromatic  1.405  0.020  1.405
 L5N  CAD  OAJ  double    1.211  0.020  1.211
 L5N  CAC  NAG  single    1.385  0.020  1.385
 L5N  CAQ  CAU  aromatic  1.393  0.020  1.393
 L5N  CAQ  CAT  aromatic  1.390  0.020  1.390
 L5N  CAU  CAY  aromatic  1.383  0.020  1.383
 L5N  NAG  CAM  single    1.361  0.020  1.361
 L5N  CAT  CAX  aromatic  1.386  0.020  1.386
 L5N  OAP  CAM  double    1.218  0.020  1.218
 L5N  CAM  CAO  single    1.469  0.020  1.469
 L5N  CAY  CBA  aromatic  1.394  0.020  1.394
 L5N  CAX  CBA  aromatic  1.393  0.020  1.393
 L5N  CAO  CAS  aromatic  1.368  0.020  1.368
 L5N  CAO  SAR  aromatic  1.723  0.020  1.723
 L5N  CBA  CBB  single    1.484  0.020  1.484
 L5N  CAS  CAW  aromatic  1.413  0.020  1.413
 L5N  SAR  CAV  aromatic  1.712  0.020  1.712
 L5N  OBD  CBB  double    1.208  0.020  1.208
 L5N  CAW  CAV  aromatic  1.363  0.020  1.363
 L5N  CBB  OBC  single    1.325  0.020  1.325
 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  OBC  H3   single    0.850  0.020  0.980
 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  119.78  3.000
 L5N  H1   CAT  CAX  119.51  3.000
 L5N  CAQ  CAT  CAX  120.71  3.000
 L5N  H2   CAX  CBA  120.95  3.000
 L5N  H2   CAX  CAT  119.02  3.000
 L5N  CBA  CAX  CAT  120.02  3.000
 L5N  CAY  CBA  CBB  118.31  3.000
 L5N  CBB  CBA  CAX  122.31  3.000
 L5N  CAY  CBA  CAX  119.38  3.000
 L5N  OBC  CBB  OBD  123.20  3.000
 L5N  OBC  CBB  CBA  113.11  3.000
 L5N  OBD  CBB  CBA  123.69  3.000
 L5N  H3   OBC  CBB  109.92  3.000
 L5N  H4   CAY  CAU  119.58  3.000
 L5N  H4   CAY  CBA  120.10  3.000
 L5N  CAU  CAY  CBA  120.32  3.000
 L5N  H5   CAU  CAQ  120.12  3.000
 L5N  H5   CAU  CAY  119.42  3.000
 L5N  CAQ  CAU  CAY  120.46  3.000
 L5N  CAN  CAQ  CAU  120.35  3.000
 L5N  CAU  CAQ  CAT  119.11  3.000
 L5N  CAN  CAQ  CAT  120.53  3.000
 L5N  H7   CAN  H6   107.19  3.000
 L5N  H7   CAN  NAI  107.56  3.000
 L5N  H6   CAN  NAI  108.50  3.000
 L5N  H7   CAN  CAQ  110.70  3.000
 L5N  H6   CAN  CAQ  110.80  3.000
 L5N  NAI  CAN  CAQ  111.91  3.000
 L5N  CAD  NAI  CAE  111.80  3.000
 L5N  CAD  NAI  CAN  123.31  3.000
 L5N  CAE  NAI  CAN  124.87  3.000
 L5N  CAB  CAE  OAK  128.52  3.000
 L5N  CAB  CAE  NAI  105.94  3.000
 L5N  OAK  CAE  NAI  125.54  3.000
 L5N  CAA  CAD  OAJ  128.47  3.000
 L5N  OAJ  CAD  NAI  125.06  3.000
 L5N  CAA  CAD  NAI  106.47  3.000
 L5N  CAC  CAA  CAB  122.13  3.000
 L5N  CAC  CAA  CAD  129.89  3.000
 L5N  CAB  CAA  CAD  107.98  3.000
 L5N  CAF  CAB  CAA  122.20  3.000
 L5N  CAA  CAB  CAE  107.80  3.000
 L5N  CAF  CAB  CAE  130.00  3.000
 L5N  H8   CAF  CAL  121.47  3.000
 L5N  H8   CAF  CAB  122.35  3.000
 L5N  CAL  CAF  CAB  116.18  3.000
 L5N  H9   CAL  CAH  118.07  3.000
 L5N  H9   CAL  CAF  119.37  3.000
 L5N  CAH  CAL  CAF  122.55  3.000
 L5N  H10  CAH  CAC  120.54  3.000
 L5N  H10  CAH  CAL  118.73  3.000
 L5N  CAC  CAH  CAL  120.72  3.000
 L5N  NAG  CAC  CAH  125.71  3.000
 L5N  NAG  CAC  CAA  118.07  3.000
 L5N  CAH  CAC  CAA  116.21  3.000
 L5N  H11  NAG  CAM  117.31  3.000
 L5N  H11  NAG  CAC  114.10  3.000
 L5N  CAM  NAG  CAC  128.59  3.000
 L5N  CAO  CAM  OAP  120.30  3.000
 L5N  CAO  CAM  NAG  115.02  3.000
 L5N  OAP  CAM  NAG  124.68  3.000
 L5N  SAR  CAO  CAS  111.73  3.000
 L5N  SAR  CAO  CAM  116.02  3.000
 L5N  CAS  CAO  CAM  132.25  3.000
 L5N  H12  CAS  CAW  122.15  3.000
 L5N  H12  CAS  CAO  124.84  3.000
 L5N  CAW  CAS  CAO  113.01  3.000
 L5N  H13  CAW  CAV  124.17  3.000
 L5N  H13  CAW  CAS  124.50  3.000
 L5N  CAV  CAW  CAS  111.33  3.000
 L5N  SAR  CAV  CLA  120.27  3.000
 L5N  CLA  CAV  CAW  126.48  3.000
 L5N  SAR  CAV  CAW  113.26  3.000
 L5N  CAV  SAR  CAO   90.68  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  CONST_47  H3   OBC  CBB  CBA   180.00   0.0  0
 L5N  Var_01    NAI  CAN  CAQ  CAT   104.43  30.0  3
 L5N  Var_02    CAE  NAI  CAN  CAQ    99.98  30.0  3
 L5N  Var_03    OBD  CBB  CBA  CAX  -179.16  30.0  2
 L5N  Var_04    CAS  CAO  CAM  NAG    -3.07  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
 L5N  plan-5  H3   0.020

