# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:40:00 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: ~{N}-[3-[(7-nitrodibenzofuran-2-yl)sulfonylamino]phenyl]-1-oxidanyl-cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1(CC1)C(=O)Nc2cccc(N[S](=O)(=O)c3ccc4oc5cc(ccc5c4c3)[N+]([O-])=O)c2
#
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
 L5K  L5K  ~{N}-[3-[(7-nitrodibenzofuran-2-yl)sulfonylamino]phenyl]-1-oxidanyl-cyclopropane-1-carboxamide  ligand  50  33  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L5K
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
 L5K  CAX  C  CH2    0  -0.497  31.5364  180.4620  327.1860
 L5K  CAY  C  CH2    0  -0.479  31.8276  180.8995  328.5824
 L5K  CAW  C  CT     0   0.105  30.8027  179.8297  328.3334
 L5K  OAZ  O  OH1    0  -0.651  29.4767  180.1698  328.5615
 L5K  CAU  C  C      0   0.529  31.2011  178.4290  328.7053
 L5K  OAV  O  O      0  -0.473  32.3327  178.0171  328.5131
 L5K  NAT  N  NH1    0  -0.759  30.2016  177.7094  329.2669
 L5K  CAS  C  CR6    0   0.392  30.2002  176.3794  329.6895
 L5K  CBA  C  CR16   0  -0.359  28.9607  175.8495  330.0519
 L5K  CAR  C  CR16   0  -0.314  31.3367  175.5723  329.7608
 L5K  CAQ  C  CR16   0  -0.243  31.2126  174.2588  330.1906
 L5K  CAP  C  CR16   0  -0.288  29.9896  173.7330  330.5699
 L5K  CAO  C  CR6    0   0.272  28.8608  174.5413  330.4961
 L5K  NAN  N  NC1    0  -0.800  27.5894  174.0291  330.8669
 L5K  SAM  S  S      0   1.357  26.9579  174.4977  332.3367
 L5K  OBB  O  OS     0  -0.635  26.8541  175.9442  332.3200
 L5K  OBC  O  OS     0  -0.644  25.7759  173.6788  332.5314
 L5K  CAL  C  CR6    0  -0.210  28.1795  174.0522  333.5355
 L5K  CBD  C  CR16   0  -0.330  29.1508  174.9790  333.8772
 L5K  CBE  C  CR56   0   0.098  30.1337  174.5676  334.7652
 L5K  CBF  C  CR56   0   0.105  31.2830  175.1935  335.3650
 L5K  CBG  C  CR16   0  -0.363  31.8740  176.4491  335.2929
 L5K  CAA  C  CR16   0  -0.268  33.0091  176.6893  336.0436
 L5K  CAB  C  CR6    0   0.250  33.5344  175.6780  336.8499
 L5K  NAC  N  N      1   0.331  34.7290  175.9582  337.6334
 L5K  OAE  O  O      0  -0.374  35.1747  175.0724  338.3240
 L5K  OAD  O  O     -1  -0.374  35.2141  177.0617  337.5545
 L5K  CAF  C  CR16   0  -0.372  32.9738  174.4120  336.9455
 L5K  CAG  C  CR56   0   0.379  31.8460  174.2110  336.1834
 L5K  OAH  O  O      0  -0.468  31.1401  173.0526  336.1268
 L5K  CAI  C  CR56   0   0.381  30.1123  173.2668  335.2763
 L5K  CAJ  C  CR16   0  -0.322  29.1463  172.3363  334.9383
 L5K  CAK  C  CR16   0  -0.243  28.1723  172.7498  334.0484
 L5K  H1   H  HCH2   0   0.276  30.9594  181.1274  326.5558
 L5K  H2   H  HCH2   0   0.266  32.2718  179.8631  326.6663
 L5K  H3   H  HCH2   0   0.267  32.7669  180.6075  329.0331
 L5K  H4   H  HCH2   0   0.273  31.4423  181.8584  328.9045
 L5K  H5   H  HOH1   0   0.468  28.9620  179.9711  327.7709
 L5K  H6   H  HNH1   0   0.415  29.3238  178.1996  329.3666
 L5K  H7   H  HCR6   0   0.279  28.0687  176.4567  329.9693
 L5K  H8   H  HCR6   0   0.283  32.3062  175.9522  329.4865
 L5K  H9   H  HCR6   0   0.266  32.0974  173.6386  330.2440
 L5K  H10  H  HCR6   0   0.267  29.9102  172.7114  330.9196
 L5K  H11  H  HNC1   0   0.421  27.4986  173.0255  330.7383
 L5K  H12  H  HCR6   0   0.291  29.1444  175.9838  333.4778
 L5K  H13  H  HCR6   0   0.279  31.4624  177.2293  334.6680
 L5K  H14  H  HCR6   0   0.304  33.4805  177.6595  336.0023
 L5K  H15  H  HCR6   0   0.316  33.3857  173.6341  337.5719
 L5K  H16  H  HCR6   0   0.295  29.1445  171.3356  335.3470
 L5K  H17  H  HCR6   0   0.297  27.3976  172.0526  333.7603

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
 L5K  OAV  CAU  double    1.219  0.020  1.219
 L5K  CAY  CAX  single    1.492  0.020  1.492
 L5K  CAY  CAW  single    1.502  0.020  1.502
 L5K  CAX  CAW  single    1.502  0.020  1.502
 L5K  CAU  CAW  single    1.503  0.020  1.503
 L5K  CAU  NAT  single    1.354  0.020  1.354
 L5K  CAR  CAQ  aromatic  1.388  0.020  1.388
 L5K  CAR  CAS  aromatic  1.396  0.020  1.396
 L5K  CAQ  CAP  aromatic  1.384  0.020  1.384
 L5K  CAW  OAZ  single    1.388  0.020  1.388
 L5K  CAS  NAT  single    1.395  0.020  1.395
 L5K  CAS  CBA  aromatic  1.396  0.020  1.396
 L5K  CAP  CAO  aromatic  1.390  0.020  1.390
 L5K  CBA  CAO  aromatic  1.385  0.020  1.385
 L5K  CAO  NAN  single    1.420  0.020  1.420
 L5K  NAN  SAM  single    1.667  0.020  1.667
 L5K  OBB  SAM  double    1.450  0.020  1.450
 L5K  SAM  OBC  double    1.451  0.020  1.451
 L5K  SAM  CAL  single    1.769  0.020  1.769
 L5K  CAK  CAL  aromatic  1.400  0.020  1.400
 L5K  CAK  CAJ  aromatic  1.383  0.020  1.383
 L5K  CAL  CBD  aromatic  1.385  0.020  1.385
 L5K  CAJ  CAI  aromatic  1.383  0.020  1.383
 L5K  CBD  CBE  aromatic  1.387  0.020  1.387
 L5K  CAI  CBE  aromatic  1.398  0.020  1.398
 L5K  CAI  OAH  aromatic  1.351  0.020  1.351
 L5K  CBE  CBF  aromatic  1.440  0.020  1.440
 L5K  OAH  CAG  aromatic  1.358  0.020  1.358
 L5K  CBF  CAG  aromatic  1.397  0.020  1.397
 L5K  CBF  CBG  aromatic  1.390  0.020  1.390
 L5K  CAG  CAF  aromatic  1.376  0.020  1.376
 L5K  CBG  CAA  aromatic  1.382  0.020  1.382
 L5K  CAF  CAB  aromatic  1.388  0.020  1.388
 L5K  CAA  CAB  aromatic  1.396  0.020  1.396
 L5K  CAB  NAC  single    1.456  0.020  1.456
 L5K  NAC  OAE  double    1.208  0.020  1.208
 L5K  NAC  OAD  single    1.208  0.020  1.208
 L5K  CAX  H1   single    0.970  0.020  1.090
 L5K  CAX  H2   single    0.970  0.020  1.090
 L5K  CAY  H3   single    0.970  0.020  1.090
 L5K  CAY  H4   single    0.970  0.020  1.090
 L5K  OAZ  H5   single    0.850  0.020  0.980
 L5K  NAT  H6   single    0.860  0.020  1.020
 L5K  CBA  H7   single    0.930  0.020  1.080
 L5K  CAR  H8   single    0.930  0.020  1.080
 L5K  CAQ  H9   single    0.930  0.020  1.080
 L5K  CAP  H10  single    0.930  0.020  1.080
 L5K  NAN  H11  single    0.890  0.020  1.040
 L5K  CBD  H12  single    0.930  0.020  1.080
 L5K  CBG  H13  single    0.930  0.020  1.080
 L5K  CAA  H14  single    0.930  0.020  1.080
 L5K  CAF  H15  single    0.930  0.020  1.080
 L5K  CAJ  H16  single    0.930  0.020  1.080
 L5K  CAK  H17  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
 L5K  H2   CAX  H1   115.02  3.000
 L5K  H2   CAX  CAW  117.79  3.000
 L5K  H1   CAX  CAW  116.30  3.000
 L5K  H2   CAX  CAY  118.65  3.000
 L5K  H1   CAX  CAY  117.93  3.000
 L5K  CAW  CAX  CAY   60.24  3.000
 L5K  H4   CAY  H3   115.10  3.000
 L5K  H4   CAY  CAW  115.94  3.000
 L5K  H3   CAY  CAW  117.98  3.000
 L5K  H4   CAY  CAX  117.95  3.000
 L5K  H3   CAY  CAX  118.69  3.000
 L5K  CAW  CAY  CAX   60.19  3.000
 L5K  CAU  CAW  OAZ  116.17  3.000
 L5K  OAZ  CAW  CAY  116.75  3.000
 L5K  CAU  CAW  CAY  116.22  3.000
 L5K  OAZ  CAW  CAX  119.29  3.000
 L5K  CAU  CAW  CAX  116.87  3.000
 L5K  CAY  CAW  CAX   59.57  3.000
 L5K  H5   OAZ  CAW  108.95  3.000
 L5K  NAT  CAU  OAV  124.82  3.000
 L5K  NAT  CAU  CAW  113.72  3.000
 L5K  OAV  CAU  CAW  121.45  3.000
 L5K  H6   NAT  CAS  115.57  3.000
 L5K  H6   NAT  CAU  115.12  3.000
 L5K  CAS  NAT  CAU  129.27  3.000
 L5K  CAR  CAS  CBA  119.36  3.000
 L5K  CBA  CAS  NAT  116.19  3.000
 L5K  CAR  CAS  NAT  124.46  3.000
 L5K  H7   CBA  CAO  119.67  3.000
 L5K  H7   CBA  CAS  119.94  3.000
 L5K  CAO  CBA  CAS  120.38  3.000
 L5K  H8   CAR  CAQ  119.56  3.000
 L5K  H8   CAR  CAS  121.07  3.000
 L5K  CAQ  CAR  CAS  119.37  3.000
 L5K  H9   CAQ  CAP  119.42  3.000
 L5K  H9   CAQ  CAR  119.00  3.000
 L5K  CAP  CAQ  CAR  121.57  3.000
 L5K  H10  CAP  CAO  120.41  3.000
 L5K  H10  CAP  CAQ  120.78  3.000
 L5K  CAO  CAP  CAQ  118.81  3.000
 L5K  NAN  CAO  CAP  120.22  3.000
 L5K  NAN  CAO  CBA  119.27  3.000
 L5K  CAP  CAO  CBA  120.50  3.000
 L5K  H11  NAN  SAM  110.82  3.000
 L5K  H11  NAN  CAO  113.79  3.000
 L5K  SAM  NAN  CAO  117.91  3.000
 L5K  CAL  SAM  OBC  109.24  3.000
 L5K  CAL  SAM  OBB  107.96  3.000
 L5K  OBC  SAM  OBB  120.41  3.000
 L5K  CAL  SAM  NAN  105.38  3.000
 L5K  OBC  SAM  NAN  105.56  3.000
 L5K  OBB  SAM  NAN  107.30  3.000
 L5K  CAK  CAL  CBD  122.39  3.000
 L5K  CBD  CAL  SAM  118.88  3.000
 L5K  CAK  CAL  SAM  118.63  3.000
 L5K  H12  CBD  CBE  121.08  3.000
 L5K  H12  CBD  CAL  121.77  3.000
 L5K  CBE  CBD  CAL  117.15  3.000
 L5K  CAI  CBE  CBF  105.34  3.000
 L5K  CBF  CBE  CBD  134.71  3.000
 L5K  CAI  CBE  CBD  119.95  3.000
 L5K  CAG  CBF  CBG  119.62  3.000
 L5K  CBG  CBF  CBE  135.30  3.000
 L5K  CAG  CBF  CBE  105.08  3.000
 L5K  H13  CBG  CAA  120.09  3.000
 L5K  H13  CBG  CBF  121.34  3.000
 L5K  CAA  CBG  CBF  118.57  3.000
 L5K  H14  CAA  CAB  120.59  3.000
 L5K  H14  CAA  CBG  119.61  3.000
 L5K  CAB  CAA  CBG  119.80  3.000
 L5K  CAF  CAB  NAC  118.03  3.000
 L5K  NAC  CAB  CAA  118.70  3.000
 L5K  CAF  CAB  CAA  123.27  3.000
 L5K  OAD  NAC  OAE  123.97  3.000
 L5K  OAD  NAC  CAB  118.05  3.000
 L5K  OAE  NAC  CAB  117.98  3.000
 L5K  H15  CAF  CAG  121.90  3.000
 L5K  H15  CAF  CAB  122.87  3.000
 L5K  CAG  CAF  CAB  115.22  3.000
 L5K  OAH  CAG  CAF  125.02  3.000
 L5K  CAF  CAG  CBF  123.51  3.000
 L5K  OAH  CAG  CBF  111.47  3.000
 L5K  CAI  OAH  CAG  106.65  3.000
 L5K  CAJ  CAI  OAH  125.34  3.000
 L5K  OAH  CAI  CBE  111.47  3.000
 L5K  CAJ  CAI  CBE  123.19  3.000
 L5K  H16  CAJ  CAK  121.27  3.000
 L5K  H16  CAJ  CAI  122.11  3.000
 L5K  CAK  CAJ  CAI  116.62  3.000
 L5K  H17  CAK  CAJ  118.91  3.000
 L5K  H17  CAK  CAL  120.39  3.000
 L5K  CAJ  CAK  CAL  120.70  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
 L5K  CONST_01  CAP  CAQ  CAR  CAS    0.00   0.0  0
 L5K  CONST_02  CAP  CAO  CBA  CAS    0.00   0.0  0
 L5K  CONST_03  CAQ  CAR  CAS  CBA    0.00   0.0  0
 L5K  CONST_04  CAQ  CAP  CAO  CBA    0.00   0.0  0
 L5K  CONST_05  CAO  CAP  CAQ  CAR    0.00   0.0  0
 L5K  CONST_06  CAO  CBA  CAS  CAR    0.00   0.0  0
 L5K  CONST_07  CAI  CAJ  CAK  CAL    0.00   0.0  0
 L5K  CONST_08  CAI  CBE  CBD  CAL    0.00   0.0  0
 L5K  CONST_09  CBF  CBE  CBD  CAL  180.00   0.0  0
 L5K  CONST_10  CAJ  CAK  CAL  CBD    0.00   0.0  0
 L5K  CONST_11  CAJ  CAI  CBE  CBD    0.00   0.0  0
 L5K  CONST_12  OAH  CAI  CBE  CBD  180.00   0.0  0
 L5K  CONST_13  CAG  CBF  CBE  CBD  180.00   0.0  0
 L5K  CONST_14  CBG  CBF  CBE  CBD    0.00   0.0  0
 L5K  CONST_15  CAK  CAL  CBD  CBE    0.00   0.0  0
 L5K  CONST_16  CAK  CAJ  CAI  CBE    0.00   0.0  0
 L5K  CONST_17  CAG  OAH  CAI  CBE    0.00   0.0  0
 L5K  CONST_18  OAH  CAG  CBF  CBE    0.00   0.0  0
 L5K  CONST_19  CAF  CAG  CBF  CBE  180.00   0.0  0
 L5K  CONST_20  CAA  CBG  CBF  CBE  180.00   0.0  0
 L5K  CONST_21  CAJ  CAI  CBE  CBF  180.00   0.0  0
 L5K  CONST_22  OAH  CAI  CBE  CBF    0.00   0.0  0
 L5K  CONST_23  CAI  OAH  CAG  CBF    0.00   0.0  0
 L5K  CONST_24  CAB  CAF  CAG  CBF    0.00   0.0  0
 L5K  CONST_25  CAB  CAA  CBG  CBF    0.00   0.0  0
 L5K  CONST_26  CAI  CBE  CBF  CBG  180.00   0.0  0
 L5K  CONST_27  OAH  CAG  CBF  CBG  180.00   0.0  0
 L5K  CONST_28  CAF  CAG  CBF  CBG    0.00   0.0  0
 L5K  CONST_29  CAF  CAB  CAA  CBG    0.00   0.0  0
 L5K  CONST_30  CAG  CBF  CBG  CAA    0.00   0.0  0
 L5K  CONST_31  CAG  CAF  CAB  CAA    0.00   0.0  0
 L5K  CONST_32  OAH  CAG  CAF  CAB  180.00   0.0  0
 L5K  CONST_33  CAI  OAH  CAG  CAF  180.00   0.0  0
 L5K  CONST_34  CAJ  CAI  OAH  CAG  180.00   0.0  0
 L5K  CONST_35  CAI  CBE  CBF  CAG    0.00   0.0  0
 L5K  CONST_36  CAK  CAJ  CAI  OAH  180.00   0.0  0
 L5K  CONST_37  CAQ  CAR  CAS  NAT  180.00   0.0  0
 L5K  CONST_38  CAO  CBA  CAS  NAT  180.00   0.0  0
 L5K  CONST_39  NAN  CAO  CBA  CAS  180.00   0.0  0
 L5K  CONST_40  NAN  CAO  CAP  CAQ  180.00   0.0  0
 L5K  CONST_41  CAJ  CAK  CAL  SAM  180.00   0.0  0
 L5K  CONST_42  CBE  CBD  CAL  SAM  180.00   0.0  0
 L5K  CONST_43  NAC  CAB  CAA  CBG  180.00   0.0  0
 L5K  CONST_44  CAG  CAF  CAB  NAC  180.00   0.0  0
 L5K  CONST_45  H9   CAQ  CAR  CAS  180.00   0.0  0
 L5K  CONST_46  H8   CAR  CAS  CBA  180.00   0.0  0
 L5K  CONST_47  H10  CAP  CAO  CBA  180.00   0.0  0
 L5K  CONST_48  H7   CBA  CAS  CAR  180.00   0.0  0
 L5K  CONST_49  H16  CAJ  CAK  CAL  180.00   0.0  0
 L5K  CONST_50  H17  CAK  CAL  CBD  180.00   0.0  0
 L5K  CONST_51  H13  CBG  CBF  CBE    0.00   0.0  0
 L5K  CONST_52  H12  CBD  CBE  CBF    0.00   0.0  0
 L5K  CONST_53  H15  CAF  CAG  CBF  180.00   0.0  0
 L5K  CONST_54  H14  CAA  CBG  CBF  180.00   0.0  0
 L5K  CONST_55  CAS  NAT  CAU  CAW  180.00   0.0  0
 L5K  CONST_56  CAR  CAS  NAT  CAU    0.00   0.0  0
 L5K  CONST_57  CBA  CAS  NAT  CAU  180.00   0.0  0
 L5K  CONST_60  OAE  NAC  CAB  CAA  180.00   0.0  0
 L5K  CONST_61  OAD  NAC  CAB  CAA    0.00   0.0  0
 L5K  CONST_62  CAF  CAB  NAC  OAE    0.00   0.0  0
 L5K  CONST_63  CAF  CAB  NAC  OAD  180.00   0.0  0
 L5K  CONST_64  H6   NAT  CAS  CBA    0.00   0.0  0
 L5K  CONST_66  CAS  NAT  CAU  OAV    0.00   0.0  0
 L5K  Var_01    CAU  CAW  CAY  CAX  107.16  30.0  1
 L5K  Var_02    OAV  CAU  CAW  CAX   28.71  30.0  1
 L5K  Var_03    CAL  SAM  NAN  CAO  -56.14  30.0  3
 L5K  Var_04    CAK  CAL  SAM  NAN  -85.69  30.0  2

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
 L5K  chir_01  CAW  CAX  CAU  OAZ  both

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
 L5K  plan-1  NAT  0.020
 L5K  plan-1  CAS  0.020
 L5K  plan-1  CBA  0.020
 L5K  plan-1  CAR  0.020
 L5K  plan-1  CAQ  0.020
 L5K  plan-1  CAP  0.020
 L5K  plan-1  CAO  0.020
 L5K  plan-1  NAN  0.020
 L5K  plan-1  H7   0.020
 L5K  plan-1  H8   0.020
 L5K  plan-1  H9   0.020
 L5K  plan-1  H10  0.020
 L5K  plan-2  SAM  0.020
 L5K  plan-2  CAL  0.020
 L5K  plan-2  CBD  0.020
 L5K  plan-2  CBE  0.020
 L5K  plan-2  CBF  0.020
 L5K  plan-2  CBG  0.020
 L5K  plan-2  CAA  0.020
 L5K  plan-2  CAB  0.020
 L5K  plan-2  NAC  0.020
 L5K  plan-2  CAF  0.020
 L5K  plan-2  CAG  0.020
 L5K  plan-2  OAH  0.020
 L5K  plan-2  CAI  0.020
 L5K  plan-2  CAJ  0.020
 L5K  plan-2  CAK  0.020
 L5K  plan-2  H12  0.020
 L5K  plan-2  H13  0.020
 L5K  plan-2  H14  0.020
 L5K  plan-2  H15  0.020
 L5K  plan-2  H16  0.020
 L5K  plan-2  H17  0.020
 L5K  plan-3  CAO  0.020
 L5K  plan-3  NAN  0.020
 L5K  plan-3  SAM  0.020
 L5K  plan-3  H11  0.020
 L5K  plan-4  CAB  0.020
 L5K  plan-4  NAC  0.020
 L5K  plan-4  OAE  0.020
 L5K  plan-4  OAD  0.020
 L5K  plan-5  CAW  0.020
 L5K  plan-5  CAU  0.020
 L5K  plan-5  OAV  0.020
 L5K  plan-5  NAT  0.020
 L5K  plan-5  CAS  0.020
 L5K  plan-5  H6   0.020

