# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:28:49 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N~2~-[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-N~2~-[(4-methoxyphenyl)sulfonyl]-3-thiophen-2-yl-D-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[S](=O)(=O)N(Cc2ccc3OCOc3c2)[C@H](Cc4sccc4)C(=O)NO
#
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
 E8S  E8S  N~2~-[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-N~2~-[(4-methoxyphenyl)sulfonyl]-3-thiophen-2-yl-D-alaninamide  ligand  55  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E8S
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
 E8S  C14  C  CR16  0  -0.335   4.4471   0.0370   0.3209
 E8S  O17  O  OS    0  -0.646   0.5519  -2.3349  -1.7087
 E8S  N19  N  N     0  -0.583   0.1275   0.0061  -0.7468
 E8S  C23  C  CR6   0   0.084  -1.7743  -0.6854   0.7139
 E8S  C24  C  CR16  0  -0.280  -2.4103  -1.6729  -0.0269
 E8S  C28  C  CR56  0   0.297  -4.4903  -1.0765   0.9177
 E8S  C30  C  CH2   0   0.066  -6.0503   0.0719   1.9960
 E8S  O33  O  O     0  -0.487  -4.7819   0.5242   2.4515
 E8S  C01  C  CH3   0  -0.442   6.5630  -2.3420   2.0708
 E8S  O05  O  O2    0  -0.459   6.0411  -1.1384   1.5350
 E8S  C06  C  CR6   0   0.405   4.9055  -1.1848   0.8318
 E8S  C07  C  CR16  0  -0.376   4.1771  -2.3490   0.5906
 E8S  C09  C  CR16  0  -0.227   3.0077  -2.2910  -0.1541
 E8S  C11  C  CR6   0  -0.228   2.5655  -1.0784  -0.6547
 E8S  C12  C  CR16  0  -0.186   3.2883   0.0895  -0.4180
 E8S  S16  S  S     0   1.392   1.1024  -0.9881  -1.6343
 E8S  O18  O  OS    0  -0.652   1.4075  -0.2879  -2.8733
 E8S  C20  C  CH2   0  -0.399  -0.2914  -0.4491   0.5769
 E8S  C26  C  CR16  0  -0.320  -3.7876  -1.8869   0.0603
 E8S  O29  O  O     0  -0.485  -5.8153  -1.0827   1.2006
 E8S  C34  C  CR56  0   0.309  -3.8638  -0.1015   1.6740
 E8S  C35  C  CR16  0  -0.405  -2.5107   0.1168   1.5993
 E8S  C37  C  CH1   0  -0.209  -0.5234   1.1445  -1.3675
 E8S  C39  C  CH2   0  -0.584  -0.5368   2.3693  -0.4445
 E8S  C42  C  CR5   0  -0.127   0.8483   2.8469  -0.1406
 E8S  C43  C  CR15  0  -0.224   1.7237   3.4555  -0.9928
 E8S  C45  C  CR15  0  -0.192   2.9676   3.7732  -0.3821
 E8S  C47  C  CR15  0  -0.458   3.0172   3.4045   0.9279
 E8S  S49  S  S2    0   0.203   1.5520   2.6687   1.4192
 E8S  C50  C  C     0   0.569  -1.8621   0.7121  -1.9894
 E8S  O51  O  O     0  -0.463  -1.8750  -0.1565  -2.8388
 E8S  N52  N  NH1   0  -0.376  -2.9466   1.4020  -1.6011
 E8S  O54  O  OH1   0  -0.532  -4.1778   1.0018  -2.0251
 E8S  H1   H  HCR6  0   0.272   5.0099   0.9420   0.5103
 E8S  H2   H  HCR6  0   0.260  -1.8299  -2.2830  -0.7053
 E8S  H3   H  HCH2  0   0.248  -6.6780  -0.1878   2.8478
 E8S  H4   H  HCH2  0   0.233  -6.5269   0.8503   1.3897
 E8S  H5   H  HCH3  0   0.236   5.8746  -2.7986   2.7856
 E8S  H6   H  HCH3  0   0.236   6.7951  -3.0658   1.2862
 E8S  H7   H  HCH3  0   0.265   7.4813  -2.0754   2.5871
 E8S  H8   H  HCR6  0   0.293   4.5006  -3.3082   0.9692
 E8S  H9   H  HCR6  0   0.284   2.4536  -3.2021  -0.3321
 E8S  H10  H  HCR6  0   0.289   2.9450   1.0427  -0.7993
 E8S  H11  H  HCH2  0   0.295   0.2554  -1.3618   0.8198
 E8S  H12  H  HCH2  0   0.267   0.0341   0.2814   1.3201
 E8S  H13  H  HCR6  0   0.272  -4.2741  -2.6571  -0.5225
 E8S  H14  H  HCR6  0   0.271  -2.0346   0.8803   2.2027
 E8S  H15  H  HCH1  0   0.322   0.0772   1.4315  -2.2321
 E8S  H16  H  HCH2  0   0.303  -1.0705   3.1705  -0.9602
 E8S  H17  H  HCH2  0   0.272  -1.0889   2.1805   0.4778
 E8S  H18  H  HCR5  0   0.266   1.4856   3.6758  -2.0249
 E8S  H19  H  HCR5  0   0.268   3.7856   4.2585  -0.8948
 E8S  H20  H  HCR5  0   0.296   3.8286   3.5281   1.6280
 E8S  H21  H  HNH1  0   0.421  -2.9663   1.9480  -0.7524
 E8S  H22  H  HOH1  0   0.477  -4.4179   1.6051  -2.7403

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
 E8S  C01  O05  single    1.417  0.020  1.417
 E8S  O05  C06  single    1.337  0.020  1.337
 E8S  C07  C06  aromatic  1.394  0.020  1.394
 E8S  C07  C09  aromatic  1.388  0.020  1.388
 E8S  C06  C14  aromatic  1.401  0.020  1.401
 E8S  C09  C11  aromatic  1.384  0.020  1.384
 E8S  C14  C12  aromatic  1.375  0.020  1.375
 E8S  C11  C12  aromatic  1.394  0.020  1.394
 E8S  C11  S16  single    1.763  0.020  1.763
 E8S  C20  C23  single    1.508  0.020  1.508
 E8S  C20  N19  single    1.461  0.020  1.461
 E8S  C35  C34  aromatic  1.373  0.020  1.373
 E8S  C35  C23  aromatic  1.403  0.020  1.403
 E8S  O33  C34  single    1.356  0.020  1.356
 E8S  O33  C30  single    1.422  0.020  1.422
 E8S  C34  C28  aromatic  1.384  0.020  1.384
 E8S  C23  C24  aromatic  1.389  0.020  1.389
 E8S  O17  S16  double    1.457  0.020  1.457
 E8S  O51  C50  double    1.215  0.020  1.215
 E8S  C30  O29  single    1.422  0.020  1.422
 E8S  S16  N19  single    1.651  0.020  1.651
 E8S  S16  O18  double    1.456  0.020  1.456
 E8S  C28  O29  single    1.355  0.020  1.355
 E8S  C28  C26  aromatic  1.373  0.020  1.373
 E8S  C24  C26  aromatic  1.397  0.020  1.397
 E8S  N19  C37  single    1.451  0.020  1.451
 E8S  C50  C37  single    1.538  0.020  1.538
 E8S  C50  N52  single    1.343  0.020  1.343
 E8S  O54  N52  single    1.362  0.020  1.362
 E8S  C37  C39  single    1.534  0.020  1.534
 E8S  C39  C42  single    1.496  0.020  1.496
 E8S  S49  C42  aromatic  1.720  0.020  1.720
 E8S  S49  C47  aromatic  1.712  0.020  1.712
 E8S  C42  C43  aromatic  1.365  0.020  1.365
 E8S  C47  C45  aromatic  1.362  0.020  1.362
 E8S  C43  C45  aromatic  1.422  0.020  1.422
 E8S  C14  H1   single    0.930  0.020  1.080
 E8S  C24  H2   single    0.930  0.020  1.080
 E8S  C30  H3   single    0.970  0.020  1.090
 E8S  C30  H4   single    0.970  0.020  1.090
 E8S  C01  H5   single    0.970  0.020  1.090
 E8S  C01  H6   single    0.970  0.020  1.090
 E8S  C01  H7   single    0.970  0.020  1.090
 E8S  C07  H8   single    0.930  0.020  1.080
 E8S  C09  H9   single    0.930  0.020  1.080
 E8S  C12  H10  single    0.930  0.020  1.080
 E8S  C20  H11  single    0.970  0.020  1.090
 E8S  C20  H12  single    0.970  0.020  1.090
 E8S  C26  H13  single    0.930  0.020  1.080
 E8S  C35  H14  single    0.930  0.020  1.080
 E8S  C37  H15  single    0.970  0.020  1.090
 E8S  C39  H16  single    0.970  0.020  1.090
 E8S  C39  H17  single    0.970  0.020  1.090
 E8S  C43  H18  single    0.930  0.020  1.080
 E8S  C45  H19  single    0.930  0.020  1.080
 E8S  C47  H20  single    0.930  0.020  1.080
 E8S  N52  H21  single    0.890  0.020  1.040
 E8S  O54  H22  single    0.850  0.020  0.980

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
 E8S  H1   C14  C12  120.01  3.000
 E8S  H1   C14  C06  119.68  3.000
 E8S  C12  C14  C06  120.31  3.000
 E8S  C37  N19  C20  120.23  3.000
 E8S  C37  N19  S16  120.49  3.000
 E8S  C20  N19  S16  117.94  3.000
 E8S  C35  C23  C20  118.94  3.000
 E8S  C35  C23  C24  120.18  3.000
 E8S  C20  C23  C24  120.89  3.000
 E8S  H2   C24  C26  118.82  3.000
 E8S  H2   C24  C23  119.35  3.000
 E8S  C26  C24  C23  121.82  3.000
 E8S  C34  C28  O29  109.38  3.000
 E8S  O29  C28  C26  128.91  3.000
 E8S  C34  C28  C26  121.69  3.000
 E8S  H4   C30  H3   110.57  3.000
 E8S  H4   C30  O29  109.83  3.000
 E8S  H3   C30  O29  109.82  3.000
 E8S  H4   C30  O33  109.84  3.000
 E8S  H3   C30  O33  109.84  3.000
 E8S  O29  C30  O33  106.87  3.000
 E8S  C34  O33  C30  105.88  3.000
 E8S  H7   C01  H6   108.92  3.000
 E8S  H7   C01  H5   108.91  3.000
 E8S  H6   C01  H5   109.08  3.000
 E8S  H7   C01  O05  106.41  3.000
 E8S  H6   C01  O05  111.68  3.000
 E8S  H5   C01  O05  111.74  3.000
 E8S  C06  O05  C01  118.84  3.000
 E8S  C07  C06  O05  124.33  3.000
 E8S  C07  C06  C14  119.61  3.000
 E8S  O05  C06  C14  116.06  3.000
 E8S  H8   C07  C09  118.52  3.000
 E8S  H8   C07  C06  121.61  3.000
 E8S  C09  C07  C06  119.88  3.000
 E8S  H9   C09  C11  120.99  3.000
 E8S  H9   C09  C07  119.01  3.000
 E8S  C11  C09  C07  120.00  3.000
 E8S  S16  C11  C12  118.81  3.000
 E8S  S16  C11  C09  120.72  3.000
 E8S  C12  C11  C09  120.46  3.000
 E8S  H10  C12  C11  120.90  3.000
 E8S  H10  C12  C14  119.34  3.000
 E8S  C11  C12  C14  119.75  3.000
 E8S  O18  S16  C11  108.88  3.000
 E8S  O18  S16  N19  106.95  3.000
 E8S  C11  S16  N19  102.84  3.000
 E8S  O18  S16  O17  118.72  3.000
 E8S  N19  S16  O17  111.16  3.000
 E8S  C11  S16  O17  107.13  3.000
 E8S  H12  C20  H11  104.99  3.000
 E8S  H12  C20  C23  109.64  3.000
 E8S  H11  C20  C23  109.96  3.000
 E8S  H12  C20  N19  108.83  3.000
 E8S  H11  C20  N19  108.58  3.000
 E8S  C23  C20  N19  114.40  3.000
 E8S  H13  C26  C28  121.78  3.000
 E8S  H13  C26  C24  121.27  3.000
 E8S  C28  C26  C24  116.95  3.000
 E8S  C30  O29  C28  105.95  3.000
 E8S  C35  C34  O33  128.70  3.000
 E8S  O33  C34  C28  109.39  3.000
 E8S  C35  C34  C28  121.90  3.000
 E8S  H14  C35  C34  121.00  3.000
 E8S  H14  C35  C23  121.57  3.000
 E8S  C34  C35  C23  117.44  3.000
 E8S  H15  C37  C50  103.45  3.000
 E8S  H15  C37  C39  105.76  3.000
 E8S  C50  C37  C39  117.40  3.000
 E8S  H15  C37  N19  107.37  3.000
 E8S  C39  C37  N19  111.91  3.000
 E8S  C50  C37  N19  110.05  3.000
 E8S  H17  C39  H16  106.19  3.000
 E8S  H17  C39  C42  110.60  3.000
 E8S  H16  C39  C42  108.31  3.000
 E8S  H17  C39  C37  112.01  3.000
 E8S  H16  C39  C37  107.82  3.000
 E8S  C42  C39  C37  111.65  3.000
 E8S  S49  C42  C43  110.48  3.000
 E8S  C43  C42  C39  127.53  3.000
 E8S  S49  C42  C39  121.99  3.000
 E8S  H18  C43  C45  123.83  3.000
 E8S  H18  C43  C42  123.05  3.000
 E8S  C45  C43  C42  113.12  3.000
 E8S  H19  C45  C47  123.40  3.000
 E8S  H19  C45  C43  123.98  3.000
 E8S  C47  C45  C43  112.61  3.000
 E8S  H20  C47  S49  120.46  3.000
 E8S  H20  C47  C45  128.36  3.000
 E8S  S49  C47  C45  111.19  3.000
 E8S  C47  S49  C42   92.60  3.000
 E8S  N52  C50  O51  124.12  3.000
 E8S  N52  C50  C37  116.21  3.000
 E8S  O51  C50  C37  119.53  3.000
 E8S  H21  N52  O54  113.76  3.000
 E8S  H21  N52  C50  122.47  3.000
 E8S  O54  N52  C50  119.28  3.000
 E8S  H22  O54  N52  105.76  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
 E8S  CONST_01  C09  C07  C06  C14     0.00   0.0  0
 E8S  CONST_02  C09  C11  C12  C14     0.00   0.0  0
 E8S  CONST_03  C28  C34  C35  C23     0.00   0.0  0
 E8S  CONST_04  C28  C26  C24  C23     0.00   0.0  0
 E8S  CONST_05  C34  C35  C23  C24     0.00   0.0  0
 E8S  CONST_06  C34  C28  C26  C24     0.00   0.0  0
 E8S  CONST_07  C11  C09  C07  C06     0.00   0.0  0
 E8S  CONST_08  C11  C12  C14  C06     0.00   0.0  0
 E8S  CONST_09  C12  C14  C06  C07     0.00   0.0  0
 E8S  CONST_10  C12  C11  C09  C07     0.00   0.0  0
 E8S  CONST_11  C35  C34  C28  C26     0.00   0.0  0
 E8S  CONST_12  C35  C23  C24  C26     0.00   0.0  0
 E8S  CONST_13  C45  C47  S49  C42     0.00   0.0  0
 E8S  CONST_14  C47  C45  C43  C42     0.00   0.0  0
 E8S  CONST_15  C47  S49  C42  C43     0.00   0.0  0
 E8S  CONST_16  S49  C47  C45  C43     0.00   0.0  0
 E8S  CONST_17  S49  C42  C43  C45     0.00   0.0  0
 E8S  CONST_18  S16  C11  C12  C14   180.00   0.0  0
 E8S  CONST_19  C09  C07  C06  O05   180.00   0.0  0
 E8S  CONST_20  C12  C14  C06  O05   180.00   0.0  0
 E8S  CONST_21  S16  C11  C09  C07   180.00   0.0  0
 E8S  CONST_22  C34  C35  C23  C20   180.00   0.0  0
 E8S  CONST_23  C26  C24  C23  C20   180.00   0.0  0
 E8S  CONST_24  C47  S49  C42  C39   180.00   0.0  0
 E8S  CONST_25  C45  C43  C42  C39   180.00   0.0  0
 E8S  CONST_26  H8   C07  C06  C14   180.00   0.0  0
 E8S  CONST_27  H13  C26  C24  C23   180.00   0.0  0
 E8S  CONST_28  H14  C35  C23  C24   180.00   0.0  0
 E8S  CONST_29  H2   C24  C26  C28   180.00   0.0  0
 E8S  CONST_30  H9   C09  C07  C06   180.00   0.0  0
 E8S  CONST_31  H10  C12  C14  C06   180.00   0.0  0
 E8S  CONST_32  H1   C14  C06  C07   180.00   0.0  0
 E8S  CONST_33  H20  C47  S49  C42   180.00   0.0  0
 E8S  CONST_34  H19  C45  C43  C42   180.00   0.0  0
 E8S  CONST_35  H18  C43  C45  C47   180.00   0.0  0
 E8S  CONST_36  O54  N52  C50  C37   180.00   0.0  0
 E8S  CONST_37  O54  N52  C50  O51     0.00   0.0  0
 E8S  Var_01    O33  C30  O29  C28   -15.45  30.0  1
 E8S  Var_02    C35  C34  O33  C30   171.12  30.0  1
 E8S  Var_03    C34  C28  O29  C30     9.59  30.0  1
 E8S  Var_04    C09  C11  S16  O17     1.90  30.0  2
 E8S  Var_05    C35  C23  C20  N19  -115.57  30.0  2
 E8S  Var_06    C07  C06  O05  C01     0.54  30.0  2
 E8S  Var_07    S49  C42  C39  C37  -109.55  30.0  2
 E8S  Var_08    S16  N19  C20  C23  -115.12  30.0  3
 E8S  Var_09    C20  N19  S16  C11   -63.41  30.0  3
 E8S  Var_10    H5   C01  O05  C06   -61.81  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
 E8S  chir_01  C37  N19  C50  C39  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
 E8S  plan-1  C39  0.020
 E8S  plan-1  C42  0.020
 E8S  plan-1  C43  0.020
 E8S  plan-1  C45  0.020
 E8S  plan-1  C47  0.020
 E8S  plan-1  S49  0.020
 E8S  plan-1  H18  0.020
 E8S  plan-1  H19  0.020
 E8S  plan-1  H20  0.020
 E8S  plan-2  C14  0.020
 E8S  plan-2  O05  0.020
 E8S  plan-2  C06  0.020
 E8S  plan-2  C07  0.020
 E8S  plan-2  C09  0.020
 E8S  plan-2  C11  0.020
 E8S  plan-2  C12  0.020
 E8S  plan-2  S16  0.020
 E8S  plan-2  H1   0.020
 E8S  plan-2  H8   0.020
 E8S  plan-2  H9   0.020
 E8S  plan-2  H10  0.020
 E8S  plan-3  C23  0.020
 E8S  plan-3  C24  0.020
 E8S  plan-3  C28  0.020
 E8S  plan-3  O33  0.020
 E8S  plan-3  C20  0.020
 E8S  plan-3  C26  0.020
 E8S  plan-3  O29  0.020
 E8S  plan-3  C34  0.020
 E8S  plan-3  C35  0.020
 E8S  plan-3  H2   0.020
 E8S  plan-3  H13  0.020
 E8S  plan-3  H14  0.020
 E8S  plan-4  C37  0.020
 E8S  plan-4  C50  0.020
 E8S  plan-4  O51  0.020
 E8S  plan-4  N52  0.020
 E8S  plan-4  O54  0.020
 E8S  plan-4  H21  0.020

