# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:47:44 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: N-[(2R)-2-{[(7-chloro-2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}-2-(2-methoxyphenyl)acetyl]-N-[(thiophen-2-yl)methyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1[C@@H](N[S](=O)(=O)c2cc3C=CC(=O)Nc3cc2Cl)C(=O)N(CC(O)=O)Cc4sccc4
#
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
 JA4  JA4  N-[(2R)-2-{[(7-chloro-2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}-2-(2-methoxyphenyl)acetyl]-N-[(thiophen-2-yl)methyl]glycine  ligand  59  38  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JA4
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
 JA4  C10   C   CR16   0  -0.457   5.3534   1.7846  -1.8768
 JA4  C13   C   CR6    0  -0.023   2.4545  -0.2964   1.6367
 JA4  C20   C   CR6    0   0.013  -0.3859   0.3775   0.0875
 JA4  C21   C   CR6    0   0.379   0.3890   0.9943  -0.9062
 JA4  C24   C   CR16   0  -0.368   0.9034   2.2704  -0.6956
 JA4  C26   C   CR16   0  -0.263  -0.1220   2.3356   1.4844
 JA4  C02   C   C      0   0.607  -2.4049  -1.1017   0.2344
 JA4  C03   C   CH1    0  -0.292  -0.9099  -1.0362  -0.0949
 JA4  N04   N   NC1    0  -0.729  -0.2593  -2.0072   0.7754
 JA4  S05   S   S      0   1.399   1.2554  -2.5417   0.4846
 JA4  C06   C   CR6    0  -0.162   2.3378  -1.1331   0.5154
 JA4  C07   C   CR16   0  -0.313   3.0547  -0.8337  -0.6230
 JA4  C08   C   CR66   0   0.024   3.8643   0.2990  -0.6807
 JA4  C09   C   CR16   0  -0.125   4.6186   0.6576  -1.8446
 JA4  C11   C   CR66   0   0.425   3.9299   1.1485   0.4325
 JA4  C12   C   CR16   0  -0.247   3.2297   0.8356   1.5999
 JA4  CL1   CL  CL     0  -0.080   1.6198  -0.6486   3.1007
 JA4  N15   N   NR16   0  -0.760   4.6849   2.2803   0.3580
 JA4  C16   C   CR6    0   0.534   5.4177   2.6846  -0.7360
 JA4  O17   O   O      0  -0.474   6.0590   3.7233  -0.7100
 JA4  O18   O   OS     0  -0.650   1.5935  -3.4218   1.5877
 JA4  O19   O   OS     0  -0.644   1.2875  -3.0476  -0.8766
 JA4  O22   O   O2     0  -0.472   0.5917   0.2845  -2.0302
 JA4  C23   C   CH3    0  -0.440   1.1354   0.9291  -3.1632
 JA4  C25   C   CR16   0  -0.241   0.6494   2.9298   0.4993
 JA4  C27   C   CR16   0  -0.269  -0.6371   1.0662   1.2663
 JA4  C29   C   CH2    0  -0.494  -2.8907  -0.0245  -1.9321
 JA4  C30   C   C      0   0.428  -2.6266  -1.0674  -3.0423
 JA4  O31   O   OC    -1  -0.609  -2.4565  -0.5806  -4.1746
 JA4  O32   O   O      0  -0.591  -2.5924  -2.2626  -2.7062
 JA4  C33   C   CH2    0  -0.413  -4.6806  -0.7001  -0.3540
 JA4  C34   C   CR5    0  -0.123  -5.1901   0.4215   0.4936
 JA4  C35   C   CR15   0  -0.239  -6.0468   1.4136   0.1188
 JA4  C36   C   CR15   0  -0.185  -6.3246   2.3394   1.1627
 JA4  C37   C   CR15   0  -0.474  -5.6687   2.0304   2.3138
 JA4  S38   S   S2     0   0.216  -4.7123   0.6174   2.1399
 JA4  H101  H   HCR6   0   0.287   5.9237   2.0594  -2.7531
 JA4  H241  H   HCR6   0   0.278   1.5065   2.7611  -1.4477
 JA4  H261  H   HCR6   0   0.252  -0.3235   2.8517   2.4135
 JA4  H031  H   HCH1   0   0.319  -0.7658  -1.3736  -1.1198
 JA4  H041  H   HNC1   0   0.412  -0.5015  -1.9515   1.7577
 JA4  H071  H   HCR6   0   0.298   2.9919  -1.4736  -1.4919
 JA4  H091  H   HCR6   0   0.295   4.5887   0.0004  -2.7051
 JA4  H121  H   HCR6   0   0.307   3.2894   1.4845   2.4634
 JA4  H151  H   HNR6   0   0.423   4.7181   2.8865   1.1678
 JA4  H232  H   HCH3   0   0.224   2.1611   1.2661  -2.9952
 JA4  H233  H   HCH3   0   0.262   1.1379   0.1938  -3.9634
 JA4  H231  H   HCH3   0   0.236   0.5305   1.7864  -3.4685
 JA4  H251  H   HCR6   0   0.259   1.0624   3.9181   0.6540
 JA4  H271  H   HCR6   0   0.254  -1.2403   0.5982   2.0353
 JA4  H292  H   HCH2   0   0.270  -3.6932   0.6455  -2.2448
 JA4  H291  H   HCH2   0   0.276  -2.0174   0.6206  -1.8346
 JA4  H332  H   HCH2   0   0.281  -5.2252  -0.6886  -1.2979
 JA4  H331  H   HCH2   0   0.278  -4.8794  -1.6663   0.1095
 JA4  H351  H   HCR5   0   0.262  -6.4689   1.4770  -0.8754
 JA4  H361  H   HCR5   0   0.264  -6.9797   3.1922   1.0568
 JA4  H371  H   HCR5   0   0.291  -5.6963   2.5599   3.2540
 JA4  O01   O   O      0  -0.505  -2.7746  -1.5818   1.3011
 JA4  N28   N   NT     0  -0.411  -3.2612  -0.5808  -0.6498

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
 JA4  C10  C09   double    1.346  0.020  1.346
 JA4  C10  C16   single    1.455  0.020  1.455
 JA4  C09  C08   single    1.433  0.020  1.433
 JA4  O17  C16   double    1.221  0.020  1.221
 JA4  C37  C36   aromatic  1.360  0.020  1.360
 JA4  C37  S38   aromatic  1.715  0.020  1.715
 JA4  C16  N15   single    1.377  0.020  1.377
 JA4  C36  C35   aromatic  1.423  0.020  1.423
 JA4  C08  C07   aromatic  1.394  0.020  1.394
 JA4  C08  C11   aromatic  1.402  0.020  1.402
 JA4  C07  C06   aromatic  1.378  0.020  1.378
 JA4  O18  S05   double    1.451  0.020  1.451
 JA4  N15  C11   single    1.363  0.020  1.363
 JA4  C11  C12   aromatic  1.397  0.020  1.397
 JA4  S38  C34   aromatic  1.725  0.020  1.725
 JA4  C06  S05   single    1.777  0.020  1.777
 JA4  C06  C13   aromatic  1.404  0.020  1.404
 JA4  O19  S05   double    1.452  0.020  1.452
 JA4  C35  C34   aromatic  1.363  0.020  1.363
 JA4  S05  N04   single    1.632  0.020  1.632
 JA4  C12  C13   aromatic  1.372  0.020  1.372
 JA4  C13  CL1   single    1.722  0.020  1.722
 JA4  C34  C33   single    1.495  0.020  1.495
 JA4  C23  O22   single    1.412  0.020  1.412
 JA4  O22  C21   single    1.345  0.020  1.345
 JA4  N04  C03   single    1.457  0.020  1.457
 JA4  C03  C02   single    1.532  0.020  1.532
 JA4  C03  C20   single    1.519  0.020  1.519
 JA4  C33  N28   single    1.455  0.020  1.455
 JA4  C02  N28   single    1.337  0.020  1.337
 JA4  C02  O01   double    1.227  0.020  1.227
 JA4  C21  C20   aromatic  1.403  0.020  1.403
 JA4  C21  C24   aromatic  1.392  0.020  1.392
 JA4  N28  C29   single    1.446  0.020  1.446
 JA4  C20  C27   aromatic  1.388  0.020  1.388
 JA4  C29  C30   single    1.546  0.020  1.546
 JA4  C24  C25   aromatic  1.388  0.020  1.388
 JA4  C27  C26   aromatic  1.387  0.020  1.387
 JA4  C30  O32   deloc     1.242  0.020  1.242
 JA4  C30  O31   deloc     1.244  0.020  1.244
 JA4  C25  C26   aromatic  1.385  0.020  1.385
 JA4  C10  H101  single    0.930  0.020  1.080
 JA4  C24  H241  single    0.930  0.020  1.080
 JA4  C26  H261  single    0.930  0.020  1.080
 JA4  C03  H031  single    0.970  0.020  1.090
 JA4  N04  H041  single    0.890  0.020  1.040
 JA4  C07  H071  single    0.930  0.020  1.080
 JA4  C09  H091  single    0.930  0.020  1.080
 JA4  C12  H121  single    0.930  0.020  1.080
 JA4  N15  H151  single    0.860  0.020  1.020
 JA4  C23  H232  single    0.970  0.020  1.090
 JA4  C23  H233  single    0.970  0.020  1.090
 JA4  C23  H231  single    0.970  0.020  1.090
 JA4  C25  H251  single    0.930  0.020  1.080
 JA4  C27  H271  single    0.930  0.020  1.080
 JA4  C29  H292  single    0.970  0.020  1.090
 JA4  C29  H291  single    0.970  0.020  1.090
 JA4  C33  H332  single    0.970  0.020  1.090
 JA4  C33  H331  single    0.970  0.020  1.090
 JA4  C35  H351  single    0.930  0.020  1.080
 JA4  C36  H361  single    0.930  0.020  1.080
 JA4  C37  H371  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
 JA4  H101  C10  C16   117.08  3.000
 JA4  H101  C10  C09   121.35  3.000
 JA4  C16   C10  C09   121.57  3.000
 JA4  CL1   C13  C12   117.74  3.000
 JA4  CL1   C13  C06   121.13  3.000
 JA4  C12   C13  C06   121.14  3.000
 JA4  C27   C20  C03   120.09  3.000
 JA4  C27   C20  C21   118.90  3.000
 JA4  C03   C20  C21   120.98  3.000
 JA4  O22   C21  C24   123.69  3.000
 JA4  C24   C21  C20   120.01  3.000
 JA4  O22   C21  C20   116.31  3.000
 JA4  H241  C24  C25   119.02  3.000
 JA4  H241  C24  C21   121.11  3.000
 JA4  C25   C24  C21   119.87  3.000
 JA4  H261  C26  C27   120.16  3.000
 JA4  H261  C26  C25   120.66  3.000
 JA4  C27   C26  C25   119.18  3.000
 JA4  N28   C02  C03   117.79  3.000
 JA4  N28   C02  O01   122.32  3.000
 JA4  C03   C02  O01   119.85  3.000
 JA4  H031  C03  N04   107.26  3.000
 JA4  H031  C03  C02   108.56  3.000
 JA4  N04   C03  C02   106.19  3.000
 JA4  H031  C03  C20   110.85  3.000
 JA4  C02   C03  C20   110.53  3.000
 JA4  N04   C03  C20   113.23  3.000
 JA4  H041  N04  S05   114.36  3.000
 JA4  H041  N04  C03   115.83  3.000
 JA4  S05   N04  C03   121.74  3.000
 JA4  O19   S05  O18   119.74  3.000
 JA4  O19   S05  C06   106.19  3.000
 JA4  O18   S05  C06   109.01  3.000
 JA4  O19   S05  N04   107.55  3.000
 JA4  C06   S05  N04   107.61  3.000
 JA4  O18   S05  N04   106.22  3.000
 JA4  C07   C06  S05   118.35  3.000
 JA4  S05   C06  C13   122.48  3.000
 JA4  C07   C06  C13   119.15  3.000
 JA4  H071  C07  C08   118.80  3.000
 JA4  H071  C07  C06   120.34  3.000
 JA4  C08   C07  C06   120.86  3.000
 JA4  C11   C08  C09   117.96  3.000
 JA4  C11   C08  C07   119.14  3.000
 JA4  C09   C08  C07   122.89  3.000
 JA4  H091  C09  C08   118.63  3.000
 JA4  H091  C09  C10   120.27  3.000
 JA4  C08   C09  C10   121.10  3.000
 JA4  N15   C11  C12   120.63  3.000
 JA4  C12   C11  C08   120.30  3.000
 JA4  N15   C11  C08   119.07  3.000
 JA4  H121  C12  C11   120.34  3.000
 JA4  H121  C12  C13   120.30  3.000
 JA4  C11   C12  C13   119.36  3.000
 JA4  H151  N15  C16   116.25  3.000
 JA4  H151  N15  C11   118.16  3.000
 JA4  C16   N15  C11   125.59  3.000
 JA4  O17   C16  N15   120.81  3.000
 JA4  N15   C16  C10   114.69  3.000
 JA4  O17   C16  C10   124.49  3.000
 JA4  C23   O22  C21   119.19  3.000
 JA4  H231  C23  H233  109.05  3.000
 JA4  H231  C23  H232  108.70  3.000
 JA4  H233  C23  H232  108.65  3.000
 JA4  H231  C23  O22   111.66  3.000
 JA4  H233  C23  O22   106.43  3.000
 JA4  H232  C23  O22   112.26  3.000
 JA4  H251  C25  C26   120.17  3.000
 JA4  H251  C25  C24   119.14  3.000
 JA4  C26   C25  C24   120.69  3.000
 JA4  H271  C27  C26   119.36  3.000
 JA4  H271  C27  C20   119.28  3.000
 JA4  C26   C27  C20   121.35  3.000
 JA4  H291  C29  H292  104.56  3.000
 JA4  H291  C29  C30   109.06  3.000
 JA4  H292  C29  C30   109.51  3.000
 JA4  H291  C29  N28   110.71  3.000
 JA4  H292  C29  N28   107.57  3.000
 JA4  C30   C29  N28   114.90  3.000
 JA4  O32   C30  O31   128.24  3.000
 JA4  O31   C30  C29   114.39  3.000
 JA4  O32   C30  C29   117.36  3.000
 JA4  H331  C33  H332  106.65  3.000
 JA4  H331  C33  C34   111.20  3.000
 JA4  H332  C33  C34   108.22  3.000
 JA4  H331  C33  N28   109.70  3.000
 JA4  H332  C33  N28   108.10  3.000
 JA4  C34   C33  N28   112.72  3.000
 JA4  S38   C34  C35   110.71  3.000
 JA4  C35   C34  C33   127.16  3.000
 JA4  S38   C34  C33   122.12  3.000
 JA4  H351  C35  C36   124.05  3.000
 JA4  H351  C35  C34   122.71  3.000
 JA4  C36   C35  C34   113.24  3.000
 JA4  H361  C36  C37   123.67  3.000
 JA4  H361  C36  C35   124.06  3.000
 JA4  C37   C36  C35   112.27  3.000
 JA4  H371  C37  S38   120.45  3.000
 JA4  H371  C37  C36   127.83  3.000
 JA4  S38   C37  C36   111.73  3.000
 JA4  C37   S38  C34    92.05  3.000
 JA4  C33   N28  C29   117.51  3.000
 JA4  C29   N28  C02   124.92  3.000
 JA4  C33   N28  C02   117.30  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
 JA4  CONST_01  C08   C07  C06  C13    0.00   0.0  0
 JA4  CONST_02  C08   C11  C12  C13    0.00   0.0  0
 JA4  CONST_03  C25   C24  C21  C20    0.00   0.0  0
 JA4  CONST_04  C25   C26  C27  C20    0.00   0.0  0
 JA4  CONST_05  C26   C27  C20  C21    0.00   0.0  0
 JA4  CONST_06  C26   C25  C24  C21    0.00   0.0  0
 JA4  CONST_07  C27   C20  C21  C24    0.00   0.0  0
 JA4  CONST_08  C27   C26  C25  C24    0.00   0.0  0
 JA4  CONST_09  C11   C08  C07  C06    0.00   0.0  0
 JA4  CONST_10  C11   C12  C13  C06    0.00   0.0  0
 JA4  CONST_11  C12   C11  C08  C07    0.00   0.0  0
 JA4  CONST_12  C12   C13  C06  C07    0.00   0.0  0
 JA4  CONST_13  C36   C37  S38  C34    0.00   0.0  0
 JA4  CONST_14  C37   C36  C35  C34    0.00   0.0  0
 JA4  CONST_15  S38   C37  C36  C35    0.00   0.0  0
 JA4  CONST_16  C37   S38  C34  C35    0.00   0.0  0
 JA4  CONST_17  S38   C34  C35  C36    0.00   0.0  0
 JA4  CONST_18  C11   N15  C16  C10    0.00   0.0  0
 JA4  CONST_19  C03   C20  C21  C24  180.00   0.0  0
 JA4  CONST_20  C03   C20  C27  C26  180.00   0.0  0
 JA4  CONST_21  C08   C07  C06  S05  180.00   0.0  0
 JA4  CONST_22  C12   C13  C06  S05  180.00   0.0  0
 JA4  CONST_23  CL1   C13  C06  C07  180.00   0.0  0
 JA4  CONST_24  CL1   C13  C12  C11  180.00   0.0  0
 JA4  CONST_25  C27   C20  C21  O22  180.00   0.0  0
 JA4  CONST_26  C25   C24  C21  O22  180.00   0.0  0
 JA4  CONST_27  C37   S38  C34  C33  180.00   0.0  0
 JA4  CONST_28  C36   C35  C34  C33  180.00   0.0  0
 JA4  CONST_29  O17   C16  N15  C11  180.00   0.0  0
 JA4  CONST_30  H071  C07  C06  C13  180.00   0.0  0
 JA4  CONST_31  H241  C24  C21  C20  180.00   0.0  0
 JA4  CONST_32  H261  C26  C27  C20  180.00   0.0  0
 JA4  CONST_33  H271  C27  C20  C21  180.00   0.0  0
 JA4  CONST_34  H251  C25  C24  C21  180.00   0.0  0
 JA4  CONST_35  H121  C12  C13  C06  180.00   0.0  0
 JA4  CONST_36  H371  C37  S38  C34  180.00   0.0  0
 JA4  CONST_37  H361  C36  C35  C34  180.00   0.0  0
 JA4  CONST_38  H351  C35  C36  C37  180.00   0.0  0
 JA4  CONST_39  H151  N15  C16  C10  180.00   0.0  0
 JA4  CONST_40  C33   N28  C02  O01    0.00   0.0  0
 JA4  CONST_41  C29   N28  C02  O01  180.00   0.0  0
 JA4  CONST_42  C33   N28  C02  C03  180.00   0.0  0
 JA4  CONST_43  C29   N28  C02  C03    0.00   0.0  0
 JA4  Var_01    O18   S05  C06  C13  -56.52  30.0  2
 JA4  Var_02    S38   C34  C33  N28  -68.14  30.0  2
 JA4  Var_03    C34   C33  N28  C02   87.10  30.0  2
 JA4  Var_04    C06   S05  N04  C03   60.01  30.0  2
 JA4  Var_05    H232  C23  O22  C21   65.54  30.0  3
 JA4  Var_06    C30   C29  N28  C02   79.29  30.0  3
 JA4  Var_07    O32   C30  C29  N28   -8.57  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
 JA4  chir_01  C03  N04  C02  C20  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
 JA4  plan-1  C33   0.020
 JA4  plan-1  C34   0.020
 JA4  plan-1  C35   0.020
 JA4  plan-1  C36   0.020
 JA4  plan-1  C37   0.020
 JA4  plan-1  S38   0.020
 JA4  plan-1  H351  0.020
 JA4  plan-1  H361  0.020
 JA4  plan-1  H371  0.020
 JA4  plan-2  C20   0.020
 JA4  plan-2  C21   0.020
 JA4  plan-2  C24   0.020
 JA4  plan-2  C26   0.020
 JA4  plan-2  C03   0.020
 JA4  plan-2  O22   0.020
 JA4  plan-2  C25   0.020
 JA4  plan-2  C27   0.020
 JA4  plan-2  H241  0.020
 JA4  plan-2  H261  0.020
 JA4  plan-2  H251  0.020
 JA4  plan-2  H271  0.020
 JA4  plan-3  C10   0.020
 JA4  plan-3  C13   0.020
 JA4  plan-3  S05   0.020
 JA4  plan-3  C06   0.020
 JA4  plan-3  C07   0.020
 JA4  plan-3  C08   0.020
 JA4  plan-3  C09   0.020
 JA4  plan-3  C11   0.020
 JA4  plan-3  C12   0.020
 JA4  plan-3  CL1   0.020
 JA4  plan-3  N15   0.020
 JA4  plan-3  C16   0.020
 JA4  plan-3  O17   0.020
 JA4  plan-3  H101  0.020
 JA4  plan-3  H071  0.020
 JA4  plan-3  H091  0.020
 JA4  plan-3  H121  0.020
 JA4  plan-3  H151  0.020
 JA4  plan-4  C02   0.020
 JA4  plan-4  C03   0.020
 JA4  plan-4  C29   0.020
 JA4  plan-4  C33   0.020
 JA4  plan-4  O01   0.020
 JA4  plan-4  N28   0.020
 JA4  plan-5  C29   0.020
 JA4  plan-5  C30   0.020
 JA4  plan-5  O31   0.020
 JA4  plan-5  O32   0.020

