# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:07:33 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: benzyl (3R)-3-(hydroxycarbamoyl)-4-[(4-methoxyphenyl)sulfonyl]piperazine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[S](=O)(=O)N2CCN(C[C@@H]2C(=O)NO)C(=O)OCc3ccccc3
#
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
 SPI  SPI  'benzyl (3R)-3-(hydroxycarbamoyl)-4-[(4-methoxyphenyl)sulfonyl]piperazine-1-carboxylate'  ligand  54  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SPI
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
 SPI  S1    S  S     0   1.370  -0.2140   1.3986  -1.8265
 SPI  O1    O  OS    0  -0.639   0.3332   2.6183  -1.2508
 SPI  O2    O  OS    0  -0.639  -1.5308   1.4326  -2.4470
 SPI  C1    C  CR6   0  -0.180   0.9483   0.8147  -3.0126
 SPI  C2    C  CR16  0  -0.206   0.5127   0.2861  -4.2230
 SPI  C3    C  CR16  0  -0.339   1.4379  -0.1400  -5.1524
 SPI  C4    C  CR6   0   0.405   2.8074  -0.0475  -4.8848
 SPI  C5    C  CR16  0  -0.374   3.2370   0.4920  -3.6707
 SPI  C6    C  CR16  0  -0.225   2.3049   0.9285  -2.7444
 SPI  O3    O  O2    0  -0.459   3.6280  -0.4889  -5.8432
 SPI  C7    C  CH3   0  -0.442   5.0276  -0.4143  -5.6351
 SPI  N1    N  N     0  -0.611  -0.2454   0.2314  -0.6215
 SPI  C8    C  CH1   0  -0.172  -1.4791  -0.5406  -0.4723
 SPI  C9    C  CH2   0  -0.309  -1.2139  -1.7369   0.4573
 SPI  N2    N  NT    0  -0.496  -0.6421  -1.3073   1.7054
 SPI  C10   C  CH2   0  -0.329   0.6095  -0.6062   1.5135
 SPI  C11   C  CH2   0  -0.287   0.3882   0.6184   0.6466
 SPI  C12   C  C     0   0.773  -1.3915  -1.2845   2.8338
 SPI  O4    O  O     0  -0.519  -2.5087  -1.7527   2.9235
 SPI  O5    O  O2    0  -0.473  -0.7496  -0.7090   3.8488
 SPI  C13   C  CH2   0  -0.238  -1.4232  -0.6824   5.1141
 SPI  C14   C  CR6   0   0.078  -0.5232   0.0354   6.0723
 SPI  C15   C  CR16  0  -0.294  -0.6858   1.3964   6.3106
 SPI  C16   C  CR16  0  -0.242   0.1586   2.0646   7.1875
 SPI  C17   C  CR16  0  -0.261   1.1782   1.3755   7.8308
 SPI  C18   C  CR16  0  -0.242   1.3496   0.0168   7.5955
 SPI  C19   C  CR16  0  -0.286   0.5023  -0.6479   6.7206
 SPI  C20   C  C     0   0.506  -1.9311  -1.1493  -1.7941
 SPI  NA    N  NH1   0  -0.362  -3.2575  -1.0887  -1.9669
 SPI  OA    O  OH1   0  -0.539  -3.8438  -1.7067  -3.0246
 SPI  OB    O  O     0  -0.454  -1.1615  -1.7209  -2.5413
 SPI  HC21  H  HCR6  0   0.278  -0.5398   0.2100  -4.4520
 SPI  HC31  H  HCR6  0   0.277   1.1063  -0.5461  -6.0991
 SPI  HC51  H  HCR6  0   0.294   4.2866   0.5907  -3.4323
 SPI  HC61  H  HCR6  0   0.284   2.6605   1.3606  -1.8185
 SPI  HC71  H  HCH3  0   0.266   5.4928  -0.8189  -6.5298
 SPI  HC72  H  HCH3  0   0.235   5.3625   0.6166  -5.4990
 SPI  HC73  H  HCH3  0   0.236   5.3410  -1.0083  -4.7736
 SPI  HC81  H  HCH1  0   0.285  -2.2734   0.0709  -0.0256
 SPI  HC91  H  HCH2  0   0.274  -0.5147  -2.4181  -0.0336
 SPI  HC92  H  HCH2  0   0.291  -2.1464  -2.2694   0.6270
 SPI  H101  H  HCH2  0   0.262   1.3152  -1.2841   1.0260
 SPI  H102  H  HCH2  0   0.290   1.0442  -0.3013   2.4603
 SPI  H111  H  HCH2  0   0.277   1.3570   1.0738   0.4516
 SPI  H112  H  HCH2  0   0.251  -0.2242   1.3443   1.1915
 SPI  H131  H  HCH2  0   0.250  -2.3801  -0.1661   5.0196
 SPI  H132  H  HCH2  0   0.249  -1.6179  -1.7022   5.4528
 SPI  H151  H  HCR6  0   0.255  -1.4813   1.9382   5.8129
 SPI  H161  H  HCR6  0   0.259   0.0181   3.1220   7.3706
 SPI  H171  H  HCR6  0   0.259   1.8346   1.8951   8.5168
 SPI  H181  H  HCR6  0   0.259   2.1407  -0.5259   8.0961
 SPI  H191  H  HCR6  0   0.255   0.6366  -1.7088   6.5440
 SPI  HNA   H  HNH1  0   0.421  -3.8650  -0.5164  -1.3987
 SPI  HOA   H  HOH1  0   0.478  -3.7915  -1.0929  -3.7703

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
 SPI  S1   O1    double    1.456  0.020  1.456
 SPI  S1   O2    double    1.456  0.020  1.456
 SPI  S1   C1    single    1.760  0.020  1.760
 SPI  S1   N1    single    1.678  0.020  1.678
 SPI  C1   C2    aromatic  1.391  0.020  1.391
 SPI  C1   C6    aromatic  1.388  0.020  1.388
 SPI  C2   C3    aromatic  1.379  0.020  1.379
 SPI  C2   HC21  single    0.930  0.020  1.080
 SPI  C3   C4    aromatic  1.398  0.020  1.398
 SPI  C3   HC31  single    0.930  0.020  1.080
 SPI  C4   C5    aromatic  1.396  0.020  1.396
 SPI  C4   O3    single    1.337  0.020  1.337
 SPI  C5   C6    aromatic  1.385  0.020  1.385
 SPI  C5   HC51  single    0.930  0.020  1.080
 SPI  C6   HC61  single    0.930  0.020  1.080
 SPI  O3   C7    single    1.417  0.020  1.417
 SPI  C7   HC71  single    0.970  0.020  1.090
 SPI  C7   HC72  single    0.970  0.020  1.090
 SPI  C7   HC73  single    0.970  0.020  1.090
 SPI  N1   C8    single    1.463  0.020  1.463
 SPI  N1   C11   single    1.469  0.020  1.469
 SPI  C8   C9    single    1.538  0.020  1.538
 SPI  C8   C20   single    1.524  0.020  1.524
 SPI  C8   HC81  single    0.970  0.020  1.090
 SPI  C9   N2    single    1.439  0.020  1.439
 SPI  C9   HC91  single    0.970  0.020  1.090
 SPI  C9   HC92  single    0.970  0.020  1.090
 SPI  N2   C10   single    1.447  0.020  1.447
 SPI  N2   C12   single    1.355  0.020  1.355
 SPI  C10  C11   single    1.517  0.020  1.517
 SPI  C10  H101  single    0.970  0.020  1.090
 SPI  C10  H102  single    0.970  0.020  1.090
 SPI  C11  H111  single    0.970  0.020  1.090
 SPI  C11  H112  single    0.970  0.020  1.090
 SPI  C12  O4    double    1.215  0.020  1.215
 SPI  C12  O5    single    1.332  0.020  1.332
 SPI  O5   C13   single    1.434  0.020  1.434
 SPI  C13  C14   single    1.498  0.020  1.498
 SPI  C13  H131  single    0.970  0.020  1.090
 SPI  C13  H132  single    0.970  0.020  1.090
 SPI  C14  C15   aromatic  1.391  0.020  1.391
 SPI  C14  C19   aromatic  1.392  0.020  1.392
 SPI  C15  C16   aromatic  1.389  0.020  1.389
 SPI  C15  H151  single    0.930  0.020  1.080
 SPI  C16  C17   aromatic  1.389  0.020  1.389
 SPI  C16  H161  single    0.930  0.020  1.080
 SPI  C17  C18   aromatic  1.390  0.020  1.390
 SPI  C17  H171  single    0.930  0.020  1.080
 SPI  C18  C19   aromatic  1.388  0.020  1.388
 SPI  C18  H181  single    0.930  0.020  1.080
 SPI  C19  H191  single    0.930  0.020  1.080
 SPI  C20  NA    single    1.339  0.020  1.339
 SPI  C20  OB    double    1.215  0.020  1.215
 SPI  NA   OA    single    1.358  0.020  1.358
 SPI  NA   HNA   single    0.860  0.020  1.020
 SPI  OA   HOA   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
 SPI  N1    S1   C1    105.40  3.000
 SPI  N1    S1   O2    107.78  3.000
 SPI  C1    S1   O2    108.53  3.000
 SPI  N1    S1   O1    107.82  3.000
 SPI  C1    S1   O1    107.23  3.000
 SPI  O2    S1   O1    119.27  3.000
 SPI  C6    C1   C2    120.38  3.000
 SPI  C6    C1   S1    119.22  3.000
 SPI  C2    C1   S1    120.38  3.000
 SPI  HC21  C2   C3    119.29  3.000
 SPI  HC21  C2   C1    121.11  3.000
 SPI  C3    C2   C1    119.60  3.000
 SPI  HC31  C3   C4    119.49  3.000
 SPI  HC31  C3   C2    120.00  3.000
 SPI  C4    C3   C2    120.51  3.000
 SPI  O3    C4   C5    124.21  3.000
 SPI  O3    C4   C3    116.24  3.000
 SPI  C5    C4   C3    119.55  3.000
 SPI  HC51  C5   C6    118.51  3.000
 SPI  HC51  C5   C4    121.72  3.000
 SPI  C6    C5   C4    119.76  3.000
 SPI  HC61  C6   C5    118.50  3.000
 SPI  HC61  C6   C1    121.30  3.000
 SPI  C5    C6   C1    120.20  3.000
 SPI  C7    O3   C4    118.93  3.000
 SPI  HC73  C7   HC72  109.08  3.000
 SPI  HC73  C7   HC71  108.91  3.000
 SPI  HC72  C7   HC71  108.83  3.000
 SPI  HC73  C7   O3    111.75  3.000
 SPI  HC72  C7   O3    111.76  3.000
 SPI  HC71  C7   O3    106.40  3.000
 SPI  C11   N1   C8    114.49  3.000
 SPI  C11   N1   S1    115.37  3.000
 SPI  C8    N1   S1    117.14  3.000
 SPI  HC81  C8   C20   111.16  3.000
 SPI  HC81  C8   C9    108.19  3.000
 SPI  C20   C8   C9    105.35  3.000
 SPI  HC81  C8   N1    110.96  3.000
 SPI  C20   C8   N1    111.87  3.000
 SPI  C9    C8   N1    109.07  3.000
 SPI  HC92  C9   HC91  108.28  3.000
 SPI  HC92  C9   N2    110.60  3.000
 SPI  HC91  C9   N2    108.76  3.000
 SPI  HC92  C9   C8    109.12  3.000
 SPI  HC91  C9   C8    108.89  3.000
 SPI  N2    C9   C8    111.14  3.000
 SPI  C12   N2   C10   125.49  3.000
 SPI  C12   N2   C9    120.52  3.000
 SPI  C10   N2   C9    111.93  3.000
 SPI  H102  C10  H101  107.74  3.000
 SPI  H102  C10  C11   109.28  3.000
 SPI  H101  C10  C11   109.87  3.000
 SPI  H102  C10  N2    111.51  3.000
 SPI  H101  C10  N2    108.48  3.000
 SPI  C11   C10  N2    109.92  3.000
 SPI  H112  C11  H111  108.04  3.000
 SPI  H112  C11  C10   109.42  3.000
 SPI  H111  C11  C10   108.09  3.000
 SPI  H112  C11  N1    111.28  3.000
 SPI  H111  C11  N1    109.85  3.000
 SPI  C10   C11  N1    110.09  3.000
 SPI  O5    C12  O4    123.62  3.000
 SPI  O5    C12  N2    112.05  3.000
 SPI  O4    C12  N2    124.32  3.000
 SPI  C13   O5   C12   117.01  3.000
 SPI  H132  C13  H131  108.20  3.000
 SPI  H132  C13  C14   110.87  3.000
 SPI  H131  C13  C14   110.82  3.000
 SPI  H132  C13  O5    109.89  3.000
 SPI  H131  C13  O5    110.14  3.000
 SPI  C14   C13  O5    106.93  3.000
 SPI  C19   C14  C15   119.10  3.000
 SPI  C19   C14  C13   120.34  3.000
 SPI  C15   C14  C13   120.55  3.000
 SPI  H151  C15  C16   119.72  3.000
 SPI  H151  C15  C14   119.75  3.000
 SPI  C16   C15  C14   120.52  3.000
 SPI  H161  C16  C17   120.12  3.000
 SPI  H161  C16  C15   119.87  3.000
 SPI  C17   C16  C15   120.01  3.000
 SPI  H171  C17  C18   120.12  3.000
 SPI  H171  C17  C16   120.05  3.000
 SPI  C18   C17  C16   119.83  3.000
 SPI  H181  C18  C19   119.85  3.000
 SPI  H181  C18  C17   120.15  3.000
 SPI  C19   C18  C17   120.00  3.000
 SPI  H191  C19  C18   119.74  3.000
 SPI  H191  C19  C14   119.72  3.000
 SPI  C18   C19  C14   120.54  3.000
 SPI  OB    C20  NA    124.69  3.000
 SPI  OB    C20  C8    122.23  3.000
 SPI  NA    C20  C8    112.81  3.000
 SPI  HNA   NA   OA    115.88  3.000
 SPI  HNA   NA   C20   123.31  3.000
 SPI  OA    NA   C20   120.50  3.000
 SPI  HOA   OA   NA    106.76  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
 SPI  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SPI  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 SPI  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 SPI  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 SPI  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 SPI  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 SPI  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 SPI  CONST_08  C17   C18  C19  C14     0.00   0.0  0
 SPI  CONST_09  C18   C19  C14  C15     0.00   0.0  0
 SPI  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 SPI  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 SPI  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 SPI  CONST_13  C3    C2   C1   S1    180.00   0.0  0
 SPI  CONST_14  C5    C6   C1   S1    180.00   0.0  0
 SPI  CONST_15  O3    C4   C3   C2    180.00   0.0  0
 SPI  CONST_16  O3    C4   C5   C6    180.00   0.0  0
 SPI  CONST_17  C16   C15  C14  C13   180.00   0.0  0
 SPI  CONST_18  C18   C19  C14  C13   180.00   0.0  0
 SPI  CONST_19  HC31  C3   C2   C1    180.00   0.0  0
 SPI  CONST_20  HC51  C5   C6   C1    180.00   0.0  0
 SPI  CONST_21  HC61  C6   C1   C2    180.00   0.0  0
 SPI  CONST_22  HC21  C2   C3   C4    180.00   0.0  0
 SPI  CONST_23  H161  C16  C15  C14   180.00   0.0  0
 SPI  CONST_24  H181  C18  C19  C14   180.00   0.0  0
 SPI  CONST_25  H191  C19  C14  C15   180.00   0.0  0
 SPI  CONST_26  H171  C17  C16  C15   180.00   0.0  0
 SPI  CONST_27  H151  C15  C16  C17   180.00   0.0  0
 SPI  CONST_28  OA    NA   C20  C8    180.00   0.0  0
 SPI  CONST_29  HNA   NA   C20  C8      0.00   0.0  0
 SPI  CONST_30  OB    C20  NA   OA      0.00   0.0  0
 SPI  Var_01    N2    C10  C11  N1    -55.27  30.0  1
 SPI  Var_02    C10   C11  N1   C8     53.89  30.0  1
 SPI  Var_03    C10   N2   C9   C8    -59.25  30.0  1
 SPI  Var_04    C11   C10  N2   C9     59.70  30.0  1
 SPI  Var_05    C8    N1   S1   C1   -112.58  30.0  3
 SPI  Var_06    N1    S1   C1   C2    105.37  30.0  3
 SPI  Var_07    O4    C12  N2   C9      8.89  30.0  2
 SPI  Var_08    C15   C14  C13  O5     95.31  30.0  2
 SPI  Var_09    C14   C13  O5   C12  -178.71  30.0  3
 SPI  Var_10    HC71  C7   O3   C4   -179.83  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
 SPI  chir_01  C8  N1  C9  C20  positiv

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
 SPI  plan-1  S1    0.020
 SPI  plan-1  C1    0.020
 SPI  plan-1  C2    0.020
 SPI  plan-1  C3    0.020
 SPI  plan-1  C4    0.020
 SPI  plan-1  C5    0.020
 SPI  plan-1  C6    0.020
 SPI  plan-1  O3    0.020
 SPI  plan-1  HC21  0.020
 SPI  plan-1  HC31  0.020
 SPI  plan-1  HC51  0.020
 SPI  plan-1  HC61  0.020
 SPI  plan-2  C13   0.020
 SPI  plan-2  C14   0.020
 SPI  plan-2  C15   0.020
 SPI  plan-2  C16   0.020
 SPI  plan-2  C17   0.020
 SPI  plan-2  C18   0.020
 SPI  plan-2  C19   0.020
 SPI  plan-2  H151  0.020
 SPI  plan-2  H161  0.020
 SPI  plan-2  H171  0.020
 SPI  plan-2  H181  0.020
 SPI  plan-2  H191  0.020
 SPI  plan-3  C8    0.020
 SPI  plan-3  C20   0.020
 SPI  plan-3  NA    0.020
 SPI  plan-3  OA    0.020
 SPI  plan-3  OB    0.020
 SPI  plan-3  HNA   0.020
 SPI  plan-4  N2    0.020
 SPI  plan-4  C12   0.020
 SPI  plan-4  O4    0.020
 SPI  plan-4  O5    0.020

