# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:33:16 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-ethyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(cc1)[S](=O)(=O)Nc2cc3N(C)C(=O)N(C)c3cc2OC
#
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
 5XD  5XD  4-ethyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)benzenesulfonamide  ligand  47  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XD
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
 5XD  CAA  C  CH3   0  -0.655   5.1671   2.6716   2.3257
 5XD  CAN  C  CH2   0  -0.505   3.8385   2.0227   2.7133
 5XD  CAQ  C  CR6   0   0.141   3.2875   1.1840   1.5967
 5XD  CAI  C  CR16  0  -0.293   3.7025  -0.1376   1.4318
 5XD  CAK  C  CR16  0  -0.211   3.2332  -0.9081   0.3837
 5XD  CAH  C  CR16  0  -0.297   2.3929   1.7219   0.6755
 5XD  CAJ  C  CR16  0  -0.207   1.9146   0.9669  -0.3839
 5XD  CAR  C  CR6   0  -0.210   2.3422  -0.3459  -0.5215
 5XD  SAZ  S  S     0   1.357   1.6576  -1.3518  -1.7994
 5XD  OAF  O  OS    0  -0.649   1.1885  -0.4740  -2.8571
 5XD  OAG  O  OS    0  -0.659   2.5822  -2.4316  -2.1038
 5XD  NAO  N  NC1   0  -0.786   0.3103  -2.0905  -1.1546
 5XD  CAS  C  CR6   0   0.139  -0.7286  -1.2556  -0.6691
 5XD  CAL  C  CR16  0  -0.325  -1.6832  -0.7836  -1.5669
 5XD  CAV  C  CR56  0   0.311  -2.6705   0.0441  -1.0816
 5XD  NAX  N  NR5   0  -0.583  -3.7373   0.6692  -1.6956
 5XD  CAC  C  CH3   0  -0.535  -4.0611   0.5713  -3.0946
 5XD  CAU  C  CR5   0   0.654  -4.4531   1.3830  -0.7684
 5XD  OAE  O  O     0  -0.504  -5.4556   2.0476  -0.9645
 5XD  NAY  N  NR5   0  -0.586  -3.8115   1.1991   0.4396
 5XD  CAD  C  CH3   0  -0.536  -4.2323   1.7776   1.6894
 5XD  CAW  C  CR56  0   0.374  -2.7195   0.3846   0.2697
 5XD  CAM  C  CR16  0  -0.466  -1.7907  -0.0838   1.1803
 5XD  CAT  C  CR6   0   0.402  -0.7780  -0.9112   0.6936
 5XD  OAP  O  O2    0  -0.469   0.1860  -1.4419   1.4639
 5XD  CAB  C  CH3   0  -0.434   0.3057  -1.0085   2.8035
 5XD  H1   H  HCH3  0   0.235   5.5597   3.2693   3.1486
 5XD  H2   H  HCH3  0   0.228   5.9136   1.9176   2.0730
 5XD  H3   H  HCH3  0   0.229   5.0468   3.3271   1.4625
 5XD  H4   H  HCH2  0   0.246   3.9807   1.4038   3.6017
 5XD  H5   H  HCH2  0   0.246   3.1182   2.7984   2.9812
 5XD  H6   H  HCR6  0   0.260   4.3996  -0.5734   2.1375
 5XD  H7   H  HCR6  0   0.277   3.5611  -1.9337   0.2791
 5XD  H8   H  HCR6  0   0.260   2.0606   2.7469   0.7866
 5XD  H9   H  HCR6  0   0.279   1.2227   1.4062  -1.0893
 5XD  H10  H  HNC1  0   0.414   0.5710  -2.8571  -0.5422
 5XD  H11  H  HCR6  0   0.280  -1.6353  -1.0772  -2.6065
 5XD  H12  H  HCH3  0   0.255  -4.3072  -0.4555  -3.3652
 5XD  H13  H  HCH3  0   0.268  -4.9183   1.2030  -3.3082
 5XD  H14  H  HCH3  0   0.255  -3.2229   0.9051  -3.7061
 5XD  H15  H  HCH3  0   0.269  -5.1546   2.3288   1.5325
 5XD  H16  H  HCH3  0   0.256  -4.4128   0.9987   2.4300
 5XD  H17  H  HCH3  0   0.256  -3.4770   2.4623   2.0745
 5XD  H18  H  HCR6  0   0.300  -1.8507   0.1911   2.2242
 5XD  H19  H  HCH3  0   0.261   1.1990  -1.4833   3.2002
 5XD  H20  H  HCH3  0   0.229   0.4259   0.0757   2.8684
 5XD  H21  H  HCH3  0   0.233  -0.5534  -1.3090   3.4090

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
 5XD  CAA  CAN  single    1.528  0.020  1.528
 5XD  OAE  CAU  double    1.219  0.020  1.219
 5XD  CAD  NAY  single    1.440  0.020  1.440
 5XD  CAN  CAQ  single    1.501  0.020  1.501
 5XD  CAU  NAY  single    1.380  0.020  1.380
 5XD  CAU  NAX  single    1.372  0.020  1.372
 5XD  NAY  CAW  single    1.373  0.020  1.373
 5XD  CAQ  CAI  aromatic  1.395  0.020  1.395
 5XD  CAQ  CAH  aromatic  1.392  0.020  1.392
 5XD  CAC  NAX  single    1.439  0.020  1.439
 5XD  NAX  CAV  single    1.381  0.020  1.381
 5XD  CAI  CAK  aromatic  1.383  0.020  1.383
 5XD  CAW  CAV  aromatic  1.394  0.020  1.394
 5XD  CAW  CAM  aromatic  1.382  0.020  1.382
 5XD  CAH  CAJ  aromatic  1.386  0.020  1.386
 5XD  CAV  CAL  aromatic  1.377  0.020  1.377
 5XD  CAM  CAT  aromatic  1.395  0.020  1.395
 5XD  CAK  CAR  aromatic  1.389  0.020  1.389
 5XD  CAL  CAS  aromatic  1.393  0.020  1.393
 5XD  CAJ  CAR  aromatic  1.387  0.020  1.387
 5XD  CAB  OAP  single    1.413  0.020  1.413
 5XD  CAR  SAZ  single    1.765  0.020  1.765
 5XD  CAT  CAS  aromatic  1.406  0.020  1.406
 5XD  CAT  OAP  single    1.343  0.020  1.343
 5XD  CAS  NAO  single    1.418  0.020  1.418
 5XD  OAG  SAZ  double    1.454  0.020  1.454
 5XD  SAZ  NAO  single    1.666  0.020  1.666
 5XD  SAZ  OAF  double    1.452  0.020  1.452
 5XD  CAA  H1   single    0.970  0.020  1.090
 5XD  CAA  H2   single    0.970  0.020  1.090
 5XD  CAA  H3   single    0.970  0.020  1.090
 5XD  CAN  H4   single    0.970  0.020  1.090
 5XD  CAN  H5   single    0.970  0.020  1.090
 5XD  CAI  H6   single    0.930  0.020  1.080
 5XD  CAK  H7   single    0.930  0.020  1.080
 5XD  CAH  H8   single    0.930  0.020  1.080
 5XD  CAJ  H9   single    0.930  0.020  1.080
 5XD  NAO  H10  single    0.890  0.020  1.040
 5XD  CAL  H11  single    0.930  0.020  1.080
 5XD  CAC  H12  single    0.970  0.020  1.090
 5XD  CAC  H13  single    0.970  0.020  1.090
 5XD  CAC  H14  single    0.970  0.020  1.090
 5XD  CAD  H15  single    0.970  0.020  1.090
 5XD  CAD  H16  single    0.970  0.020  1.090
 5XD  CAD  H17  single    0.970  0.020  1.090
 5XD  CAM  H18  single    0.930  0.020  1.080
 5XD  CAB  H19  single    0.970  0.020  1.090
 5XD  CAB  H20  single    0.970  0.020  1.090
 5XD  CAB  H21  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
 5XD  H3   CAA  H2   107.91  3.000
 5XD  H3   CAA  H1   107.91  3.000
 5XD  H2   CAA  H1   107.90  3.000
 5XD  H3   CAA  CAN  111.10  3.000
 5XD  H2   CAA  CAN  111.12  3.000
 5XD  H1   CAA  CAN  110.76  3.000
 5XD  H5   CAN  H4   106.79  3.000
 5XD  H5   CAN  CAQ  109.71  3.000
 5XD  H4   CAN  CAQ  109.65  3.000
 5XD  H5   CAN  CAA  109.52  3.000
 5XD  H4   CAN  CAA  109.49  3.000
 5XD  CAQ  CAN  CAA  111.57  3.000
 5XD  CAH  CAQ  CAI  118.62  3.000
 5XD  CAH  CAQ  CAN  120.81  3.000
 5XD  CAI  CAQ  CAN  120.53  3.000
 5XD  H6   CAI  CAK  119.20  3.000
 5XD  H6   CAI  CAQ  119.70  3.000
 5XD  CAK  CAI  CAQ  121.10  3.000
 5XD  H7   CAK  CAR  121.01  3.000
 5XD  H7   CAK  CAI  119.92  3.000
 5XD  CAR  CAK  CAI  119.08  3.000
 5XD  H8   CAH  CAJ  119.21  3.000
 5XD  H8   CAH  CAQ  119.66  3.000
 5XD  CAJ  CAH  CAQ  121.13  3.000
 5XD  H9   CAJ  CAR  121.13  3.000
 5XD  H9   CAJ  CAH  119.87  3.000
 5XD  CAR  CAJ  CAH  119.00  3.000
 5XD  SAZ  CAR  CAJ  119.44  3.000
 5XD  SAZ  CAR  CAK  119.34  3.000
 5XD  CAJ  CAR  CAK  121.07  3.000
 5XD  NAO  SAZ  OAG  105.42  3.000
 5XD  NAO  SAZ  OAF  106.78  3.000
 5XD  OAG  SAZ  OAF  120.12  3.000
 5XD  OAF  SAZ  CAR  107.95  3.000
 5XD  NAO  SAZ  CAR  106.63  3.000
 5XD  OAG  SAZ  CAR  109.17  3.000
 5XD  H10  NAO  CAS  115.22  3.000
 5XD  H10  NAO  SAZ  111.13  3.000
 5XD  CAS  NAO  SAZ  117.63  3.000
 5XD  CAT  CAS  CAL  121.17  3.000
 5XD  CAT  CAS  NAO  120.09  3.000
 5XD  CAL  CAS  NAO  118.74  3.000
 5XD  H11  CAL  CAV  122.27  3.000
 5XD  H11  CAL  CAS  119.82  3.000
 5XD  CAV  CAL  CAS  117.90  3.000
 5XD  CAW  CAV  NAX  107.06  3.000
 5XD  CAW  CAV  CAL  120.91  3.000
 5XD  NAX  CAV  CAL  132.03  3.000
 5XD  CAU  NAX  CAC  125.11  3.000
 5XD  CAC  NAX  CAV  125.13  3.000
 5XD  CAU  NAX  CAV  109.76  3.000
 5XD  H14  CAC  H13  108.57  3.000
 5XD  H14  CAC  H12  108.84  3.000
 5XD  H13  CAC  H12  108.72  3.000
 5XD  H14  CAC  NAX  110.57  3.000
 5XD  H13  CAC  NAX  109.22  3.000
 5XD  H12  CAC  NAX  110.86  3.000
 5XD  NAY  CAU  OAE  126.58  3.000
 5XD  NAY  CAU  NAX  106.25  3.000
 5XD  OAE  CAU  NAX  127.17  3.000
 5XD  CAW  NAY  CAD  125.33  3.000
 5XD  CAW  NAY  CAU  109.91  3.000
 5XD  CAD  NAY  CAU  124.77  3.000
 5XD  H17  CAD  H16  108.88  3.000
 5XD  H17  CAD  H15  108.71  3.000
 5XD  H16  CAD  H15  108.69  3.000
 5XD  H17  CAD  NAY  110.89  3.000
 5XD  H16  CAD  NAY  110.55  3.000
 5XD  H15  CAD  NAY  109.07  3.000
 5XD  CAM  CAW  NAY  130.84  3.000
 5XD  CAM  CAW  CAV  122.14  3.000
 5XD  NAY  CAW  CAV  107.02  3.000
 5XD  H18  CAM  CAT  121.86  3.000
 5XD  H18  CAM  CAW  120.83  3.000
 5XD  CAT  CAM  CAW  117.31  3.000
 5XD  OAP  CAT  CAM  123.72  3.000
 5XD  OAP  CAT  CAS  115.70  3.000
 5XD  CAM  CAT  CAS  120.57  3.000
 5XD  CAB  OAP  CAT  118.90  3.000
 5XD  H21  CAB  H20  109.04  3.000
 5XD  H21  CAB  H19  108.88  3.000
 5XD  H20  CAB  H19  108.75  3.000
 5XD  H21  CAB  OAP  111.98  3.000
 5XD  H20  CAB  OAP  111.71  3.000
 5XD  H19  CAB  OAP  106.36  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
 5XD  CONST_01  CAR  CAK  CAI  CAQ     0.00   0.0  0
 5XD  CONST_02  CAR  CAJ  CAH  CAQ     0.00   0.0  0
 5XD  CONST_03  CAJ  CAH  CAQ  CAI     0.00   0.0  0
 5XD  CONST_04  CAJ  CAR  CAK  CAI     0.00   0.0  0
 5XD  CONST_05  CAH  CAQ  CAI  CAK     0.00   0.0  0
 5XD  CONST_06  CAH  CAJ  CAR  CAK     0.00   0.0  0
 5XD  CONST_07  CAW  CAV  CAL  CAS     0.00   0.0  0
 5XD  CONST_08  CAW  CAM  CAT  CAS     0.00   0.0  0
 5XD  CONST_09  CAM  CAW  CAV  CAL     0.00   0.0  0
 5XD  CONST_10  CAM  CAT  CAS  CAL     0.00   0.0  0
 5XD  CONST_11  CAT  CAM  CAW  CAV     0.00   0.0  0
 5XD  CONST_12  CAT  CAS  CAL  CAV     0.00   0.0  0
 5XD  CONST_13  NAY  CAU  NAX  CAV     0.00   0.0  0
 5XD  CONST_14  CAU  NAY  CAW  CAV     0.00   0.0  0
 5XD  CONST_15  CAW  NAY  CAU  NAX     0.00   0.0  0
 5XD  CONST_16  NAY  CAW  CAV  NAX     0.00   0.0  0
 5XD  CONST_17  CAW  CAV  NAX  CAU     0.00   0.0  0
 5XD  CONST_18  CAK  CAI  CAQ  CAN   180.00   0.0  0
 5XD  CONST_19  CAJ  CAH  CAQ  CAN   180.00   0.0  0
 5XD  CONST_20  SAZ  CAR  CAK  CAI   180.00   0.0  0
 5XD  CONST_21  SAZ  CAR  CAJ  CAH   180.00   0.0  0
 5XD  CONST_22  CAV  CAL  CAS  NAO   180.00   0.0  0
 5XD  CONST_23  CAM  CAT  CAS  NAO   180.00   0.0  0
 5XD  CONST_24  OAP  CAT  CAS  CAL   180.00   0.0  0
 5XD  CONST_25  OAP  CAT  CAM  CAW   180.00   0.0  0
 5XD  CONST_26  OAE  CAU  NAX  CAV   180.00   0.0  0
 5XD  CONST_27  CAD  NAY  CAW  CAV   180.00   0.0  0
 5XD  CONST_28  CAD  NAY  CAU  NAX   180.00   0.0  0
 5XD  CONST_29  NAY  CAU  NAX  CAC   180.00   0.0  0
 5XD  CONST_30  CAW  CAV  NAX  CAC   180.00   0.0  0
 5XD  CONST_31  CAW  NAY  CAU  OAE   180.00   0.0  0
 5XD  CONST_32  H7   CAK  CAI  CAQ   180.00   0.0  0
 5XD  CONST_33  H9   CAJ  CAH  CAQ   180.00   0.0  0
 5XD  CONST_34  H8   CAH  CAQ  CAI   180.00   0.0  0
 5XD  CONST_35  H6   CAI  CAQ  CAH   180.00   0.0  0
 5XD  CONST_36  H18  CAM  CAT  CAS   180.00   0.0  0
 5XD  CONST_37  H11  CAL  CAV  NAX     0.00   0.0  0
 5XD  CONST_40  OAE  CAU  NAX  CAC     0.00   0.0  0
 5XD  CONST_41  CAD  NAY  CAU  OAE     0.00   0.0  0
 5XD  Var_01    CAI  CAQ  CAN  CAA    84.77  30.0  2
 5XD  Var_02    OAG  SAZ  CAR  CAK   -27.08  30.0  2
 5XD  Var_03    CAS  NAO  SAZ  CAR    59.42  30.0  3
 5XD  Var_04    H12  CAC  NAX  CAV    63.03  30.0  3
 5XD  Var_05    H15  CAD  NAY  CAU     3.01  30.0  3
 5XD  Var_06    H1   CAA  CAN  CAQ  -179.46  30.0  3
 5XD  Var_07    H19  CAB  OAP  CAT  -174.27  30.0  3

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
 5XD  plan-1  CAN  0.020
 5XD  plan-1  CAQ  0.020
 5XD  plan-1  CAI  0.020
 5XD  plan-1  CAK  0.020
 5XD  plan-1  CAH  0.020
 5XD  plan-1  CAJ  0.020
 5XD  plan-1  CAR  0.020
 5XD  plan-1  SAZ  0.020
 5XD  plan-1  H6   0.020
 5XD  plan-1  H7   0.020
 5XD  plan-1  H8   0.020
 5XD  plan-1  H9   0.020
 5XD  plan-2  NAO  0.020
 5XD  plan-2  CAS  0.020
 5XD  plan-2  CAL  0.020
 5XD  plan-2  CAV  0.020
 5XD  plan-2  NAX  0.020
 5XD  plan-2  CAC  0.020
 5XD  plan-2  CAU  0.020
 5XD  plan-2  OAE  0.020
 5XD  plan-2  NAY  0.020
 5XD  plan-2  CAD  0.020
 5XD  plan-2  CAW  0.020
 5XD  plan-2  CAM  0.020
 5XD  plan-2  CAT  0.020
 5XD  plan-2  OAP  0.020
 5XD  plan-2  H11  0.020
 5XD  plan-2  H18  0.020
 5XD  plan-3  SAZ  0.020
 5XD  plan-3  NAO  0.020
 5XD  plan-3  CAS  0.020
 5XD  plan-3  H10  0.020

