# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:30:56 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: 4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]sulfonyl}-2-(3-methylphenoxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Oc2cc(ccc2C(O)=O)[S](=O)(=O)N3CCC[C@@H](C3)N4C=C(C)C(=O)NC4=O)c1
#
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
 T05  T05  '4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]sulfonyl}-2-(3-methylphenoxy)benzoic acid'  ligand  59  35  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T05
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
 T05  C4   C  CR16   0  -0.235  -4.1853   1.3277   1.6068
 T05  C13  C  CR16   0  -0.280   0.2366  -2.5046  -1.9106
 T05  C3   C  CR16   0  -0.308  -3.2144   1.4492   2.5915
 T05  C5   C  CR16   0  -0.342  -4.0742   0.3617   0.6156
 T05  C12  C  CR16   0  -0.245   0.5615  -1.3815  -2.6561
 T05  C7   C  CR16   0  -0.368  -2.0085  -0.3793   1.6222
 T05  C10  C  CR16   0  -0.300  -1.4495  -0.3060  -1.8573
 T05  C14  C  CR6    0  -0.110  -0.8811  -2.5308  -1.0829
 T05  C2   C  CR6    0   0.110  -2.1182   0.5900   2.6146
 T05  C6   C  CR6    0   0.341  -2.9773  -0.4857   0.6351
 T05  C9   C  CR6    0   0.337  -1.7274  -1.4232  -1.0861
 T05  C11  C  CR6    0  -0.216  -0.2867  -0.2853  -2.6147
 T05  C28  C  CR16   0   0.050   1.7906  -0.5691   1.2732
 T05  C29  C  CR6    0  -0.171   2.5478  -1.2802   2.1252
 T05  C30  C  CR6    0   0.558   3.7050  -0.6271   2.7043
 T05  C33  C  CR6    0   0.741   3.1186   1.4074   1.4157
 T05  C23  C  CH2    0  -0.454  -0.7396   3.0284  -0.3487
 T05  C24  C  CH2    0  -0.452   0.3565   2.5915   0.6182
 T05  C22  C  CH2    0  -0.306  -0.1670   3.3279  -1.7280
 T05  C26  C  CH2    0  -0.322   1.7125   1.7744  -1.3374
 T05  C25  C  CH1    0  -0.074   1.0873   1.3993   0.0102
 T05  C1   C  CH3    0  -0.729  -1.0847   0.6692   3.7010
 T05  C35  C  CH3    0  -0.725   2.2446  -2.6946   2.4948
 T05  N32  N  NR16   0  -0.733   3.8854   0.6802   2.2898
 T05  N27  N  NR6    0  -0.552   2.0299   0.7347   0.9154
 T05  N21  N  N      0  -0.578   0.6637   2.2363  -2.2391
 T05  O16  O  OC    -1  -0.581  -1.2719  -4.8212  -0.7455
 T05  O17  O  O      0  -0.565  -1.0895  -3.4883   1.0420
 T05  O8   O  O2     0  -0.522  -2.8720  -1.4537  -0.3366
 T05  S18  S  S      0   1.389   0.1686   1.2203  -3.4323
 T05  H1   H  HCR6   0   0.260  -5.0336   1.9997   1.6013
 T05  H2   H  HCR6   0   0.273   0.8934  -3.3643  -1.9431
 T05  H3   H  HCR6   0   0.250  -3.3134   2.2149   3.3512
 T05  H4   H  HCR6   0   0.268  -4.8226   0.2693  -0.1608
 T05  H5   H  HCR6   0   0.285   1.4607  -1.3706  -3.2555
 T05  H6   H  HCR6   0   0.271  -1.1923  -1.0915   1.6416
 T05  H7   H  HCR6   0   0.293  -2.1316   0.5359  -1.8552
 T05  H8   H  HCR6   0   0.293   0.9161  -1.0158   0.8174
 T05  H9   H  HCH2   0   0.231  -1.5084   2.2528  -0.4172
 T05  H10  H  HCH2   0   0.259  -1.2335   3.9257   0.0272
 T05  H11  H  HCH2   0   0.251   1.0461   3.4188   0.7919
 T05  H12  H  HCH2   0   0.265  -0.0773   2.3142   1.5801
 T05  H13  H  HCH2   0   0.281  -0.9545   3.5513  -2.4429
 T05  H14  H  HCH2   0   0.257   0.4740   4.2133  -1.6773
 T05  H15  H  HCH2   0   0.284   2.4396   2.5778  -1.2176
 T05  H16  H  HCH2   0   0.288   2.2441   0.9251  -1.7678
 T05  H17  H  HCH1   0   0.256   0.3312   0.6376  -0.1886
 T05  H18  H  HCH3   0   0.261  -1.2149  -0.1409   4.4209
 T05  H19  H  HCH3   0   0.234  -0.0725   0.5792   3.3033
 T05  H20  H  HCH3   0   0.250  -1.1461   1.6089   4.2479
 T05  H21  H  HCH3   0   0.246   3.0541  -3.3642   2.2003
 T05  H22  H  HCH3   0   0.246   2.1147  -2.8010   3.5727
 T05  H23  H  HCH3   0   0.256   1.3299  -3.0342   2.0109
 T05  H24  H  HNR6   0   0.426   4.6861   1.1719   2.6681
 T05  O31  O  O      0  -0.453   4.4788  -1.1420   3.4901
 T05  C15  C  C      0   0.392  -1.1177  -3.7303  -0.1775
 T05  O19  O  OS     0  -0.649   1.3216   0.9155  -4.2638
 T05  O34  O  O      0  -0.482   3.3951   2.5526   1.1196
 T05  O20  O  OS     0  -0.651  -1.0126   1.8104  -4.0414

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
 T05  O31  C30  double    1.217  0.020  1.217
 T05  N32  C30  single    1.383  0.020  1.383
 T05  N32  C33  single    1.371  0.020  1.371
 T05  C30  C29  single    1.449  0.020  1.449
 T05  O34  C33  double    1.215  0.020  1.215
 T05  C33  N27  single    1.374  0.020  1.374
 T05  C29  C35  single    1.493  0.020  1.493
 T05  C29  C28  double    1.343  0.020  1.343
 T05  C1   C2   single    1.502  0.020  1.502
 T05  N27  C28  single    1.373  0.020  1.373
 T05  N27  C25  single    1.466  0.020  1.466
 T05  C3   C2   aromatic  1.393  0.020  1.393
 T05  C3   C4   aromatic  1.388  0.020  1.388
 T05  C2   C7   aromatic  1.392  0.020  1.392
 T05  C25  C26  single    1.532  0.020  1.532
 T05  C25  C24  single    1.525  0.020  1.525
 T05  C4   C5   aromatic  1.388  0.020  1.388
 T05  C7   C6   aromatic  1.387  0.020  1.387
 T05  C26  N21  single    1.458  0.020  1.458
 T05  C24  C23  single    1.526  0.020  1.526
 T05  O20  S18  double    1.454  0.020  1.454
 T05  C5   C6   aromatic  1.386  0.020  1.386
 T05  C6   O8   single    1.376  0.020  1.376
 T05  N21  S18  single    1.643  0.020  1.643
 T05  N21  C22  single    1.464  0.020  1.464
 T05  C23  C22  single    1.523  0.020  1.523
 T05  S18  C11  single    1.773  0.020  1.773
 T05  S18  O19  double    1.454  0.020  1.454
 T05  C10  C9   aromatic  1.386  0.020  1.386
 T05  C10  C11  aromatic  1.388  0.020  1.388
 T05  O8   C9   single    1.369  0.020  1.369
 T05  C9   C14  aromatic  1.394  0.020  1.394
 T05  C11  C12  aromatic  1.387  0.020  1.387
 T05  C12  C13  aromatic  1.387  0.020  1.387
 T05  C14  C13  aromatic  1.391  0.020  1.391
 T05  C14  C15  single    1.521  0.020  1.521
 T05  O17  C15  deloc     1.244  0.020  1.244
 T05  C15  O16  deloc     1.240  0.020  1.240
 T05  C4   H1   single    0.930  0.020  1.080
 T05  C13  H2   single    0.930  0.020  1.080
 T05  C3   H3   single    0.930  0.020  1.080
 T05  C5   H4   single    0.930  0.020  1.080
 T05  C12  H5   single    0.930  0.020  1.080
 T05  C7   H6   single    0.930  0.020  1.080
 T05  C10  H7   single    0.930  0.020  1.080
 T05  C28  H8   single    0.930  0.020  1.080
 T05  C23  H9   single    0.970  0.020  1.090
 T05  C23  H10  single    0.970  0.020  1.090
 T05  C24  H11  single    0.970  0.020  1.090
 T05  C24  H12  single    0.970  0.020  1.090
 T05  C22  H13  single    0.970  0.020  1.090
 T05  C22  H14  single    0.970  0.020  1.090
 T05  C26  H15  single    0.970  0.020  1.090
 T05  C26  H16  single    0.970  0.020  1.090
 T05  C25  H17  single    0.970  0.020  1.090
 T05  C1   H18  single    0.970  0.020  1.090
 T05  C1   H19  single    0.970  0.020  1.090
 T05  C1   H20  single    0.970  0.020  1.090
 T05  C35  H21  single    0.970  0.020  1.090
 T05  C35  H22  single    0.970  0.020  1.090
 T05  C35  H23  single    0.970  0.020  1.090
 T05  N32  H24  single    0.860  0.020  1.020

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
 T05  H1   C4   C5   119.41  3.000
 T05  H1   C4   C3   119.83  3.000
 T05  C5   C4   C3   120.75  3.000
 T05  H2   C13  C14  119.37  3.000
 T05  H2   C13  C12  119.02  3.000
 T05  C14  C13  C12  121.56  3.000
 T05  H3   C3   C2   119.75  3.000
 T05  H3   C3   C4   119.71  3.000
 T05  C2   C3   C4   120.54  3.000
 T05  H4   C5   C6   120.33  3.000
 T05  H4   C5   C4   121.07  3.000
 T05  C6   C5   C4   118.59  3.000
 T05  H5   C12  C11  121.16  3.000
 T05  H5   C12  C13  120.09  3.000
 T05  C11  C12  C13  118.75  3.000
 T05  H6   C7   C6   119.24  3.000
 T05  H6   C7   C2   120.30  3.000
 T05  C6   C7   C2   120.39  3.000
 T05  H7   C10  C11  121.13  3.000
 T05  H7   C10  C9   119.94  3.000
 T05  C11  C10  C9   118.93  3.000
 T05  C15  C14  C9   122.24  3.000
 T05  C15  C14  C13  119.60  3.000
 T05  C9   C14  C13  118.13  3.000
 T05  C1   C2   C7   119.90  3.000
 T05  C7   C2   C3   118.68  3.000
 T05  C1   C2   C3   121.41  3.000
 T05  O8   C6   C7   120.21  3.000
 T05  O8   C6   C5   118.74  3.000
 T05  C7   C6   C5   121.05  3.000
 T05  O8   C9   C14  119.26  3.000
 T05  C14  C9   C10  121.35  3.000
 T05  O8   C9   C10  119.38  3.000
 T05  S18  C11  C10  118.65  3.000
 T05  C10  C11  C12  121.13  3.000
 T05  S18  C11  C12  120.04  3.000
 T05  H8   C28  N27  115.02  3.000
 T05  H8   C28  C29  120.26  3.000
 T05  N27  C28  C29  124.72  3.000
 T05  C35  C29  C30  119.35  3.000
 T05  C35  C29  C28  122.95  3.000
 T05  C30  C29  C28  117.70  3.000
 T05  O31  C30  N32  120.69  3.000
 T05  N32  C30  C29  114.22  3.000
 T05  O31  C30  C29  125.09  3.000
 T05  O34  C33  N27  123.58  3.000
 T05  N27  C33  N32  114.55  3.000
 T05  O34  C33  N32  121.87  3.000
 T05  H10  C23  H9   106.65  3.000
 T05  H10  C23  C22  108.69  3.000
 T05  H9   C23  C22  110.29  3.000
 T05  H10  C23  C24  110.02  3.000
 T05  H9   C23  C24  109.97  3.000
 T05  C22  C23  C24  111.11  3.000
 T05  H12  C24  H11  107.68  3.000
 T05  H12  C24  C25  110.08  3.000
 T05  H11  C24  C25  110.70  3.000
 T05  H12  C24  C23  110.24  3.000
 T05  H11  C24  C23  109.75  3.000
 T05  C25  C24  C23  108.39  3.000
 T05  H14  C22  H13  106.78  3.000
 T05  H14  C22  N21  106.69  3.000
 T05  H13  C22  N21  109.56  3.000
 T05  H14  C22  C23  109.71  3.000
 T05  H13  C22  C23  111.33  3.000
 T05  N21  C22  C23  112.51  3.000
 T05  H16  C26  H15  106.99  3.000
 T05  H16  C26  N21  110.68  3.000
 T05  H15  C26  N21  108.31  3.000
 T05  H16  C26  C25  110.82  3.000
 T05  H15  C26  C25  110.85  3.000
 T05  N21  C26  C25  109.14  3.000
 T05  H17  C25  N27  103.97  3.000
 T05  H17  C25  C26  107.06  3.000
 T05  N27  C25  C26  113.06  3.000
 T05  H17  C25  C24  106.63  3.000
 T05  C26  C25  C24  110.78  3.000
 T05  N27  C25  C24  114.60  3.000
 T05  H20  C1   H19  107.85  3.000
 T05  H20  C1   H18  107.61  3.000
 T05  H19  C1   H18  106.85  3.000
 T05  H20  C1   C2   111.71  3.000
 T05  H19  C1   C2   111.74  3.000
 T05  H18  C1   C2   110.85  3.000
 T05  H23  C35  H22  107.97  3.000
 T05  H23  C35  H21  108.17  3.000
 T05  H22  C35  H21  107.17  3.000
 T05  H23  C35  C29  110.85  3.000
 T05  H22  C35  C29  111.17  3.000
 T05  H21  C35  C29  111.34  3.000
 T05  H24  N32  C33  115.01  3.000
 T05  H24  N32  C30  116.73  3.000
 T05  C33  N32  C30  128.26  3.000
 T05  C25  N27  C33  120.82  3.000
 T05  C25  N27  C28  118.64  3.000
 T05  C33  N27  C28  120.54  3.000
 T05  S18  N21  C26  118.02  3.000
 T05  S18  N21  C22  122.93  3.000
 T05  C26  N21  C22  115.37  3.000
 T05  C9   O8   C6   115.80  3.000
 T05  O20  S18  O19  119.32  3.000
 T05  O19  S18  N21  107.82  3.000
 T05  O20  S18  N21  107.33  3.000
 T05  O19  S18  C11  106.82  3.000
 T05  N21  S18  C11  105.52  3.000
 T05  O20  S18  C11  109.22  3.000
 T05  O17  C15  O16  128.56  3.000
 T05  O16  C15  C14  116.14  3.000
 T05  O17  C15  C14  115.25  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
 T05  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 T05  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 T05  CONST_03  C10  C11  C12  C13     0.00   0.0  0
 T05  CONST_04  C10  C9   C14  C13     0.00   0.0  0
 T05  CONST_05  C6   C7   C2   C3      0.00   0.0  0
 T05  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 T05  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 T05  CONST_08  C2   C7   C6   C5      0.00   0.0  0
 T05  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 T05  CONST_10  C9   C14  C13  C12     0.00   0.0  0
 T05  CONST_11  C11  C10  C9   C14     0.00   0.0  0
 T05  CONST_12  C11  C12  C13  C14     0.00   0.0  0
 T05  CONST_13  N32  C33  N27  C28     0.00   0.0  0
 T05  CONST_14  C33  N32  C30  C29     0.00   0.0  0
 T05  CONST_15  N27  C33  N32  C30     0.00   0.0  0
 T05  CONST_16  N32  C33  N27  C25   180.00   0.0  0
 T05  CONST_17  C1   C2   C3   C4    180.00   0.0  0
 T05  CONST_18  O8   C6   C5   C4    180.00   0.0  0
 T05  CONST_19  S18  C11  C12  C13   180.00   0.0  0
 T05  CONST_20  O8   C9   C14  C13   180.00   0.0  0
 T05  CONST_21  C15  C14  C13  C12   180.00   0.0  0
 T05  CONST_22  C15  C14  C9   C10   180.00   0.0  0
 T05  CONST_23  O8   C6   C7   C2    180.00   0.0  0
 T05  CONST_24  C1   C2   C7   C6    180.00   0.0  0
 T05  CONST_25  S18  C11  C10  C9    180.00   0.0  0
 T05  CONST_26  O8   C9   C10  C11   180.00   0.0  0
 T05  CONST_27  O34  C33  N27  C28   180.00   0.0  0
 T05  CONST_28  O34  C33  N32  C30   180.00   0.0  0
 T05  CONST_29  O31  C30  N32  C33   180.00   0.0  0
 T05  CONST_30  O34  C33  N27  C25     0.00   0.0  0
 T05  CONST_31  H6   C7   C2   C3    180.00   0.0  0
 T05  CONST_32  H4   C5   C4   C3    180.00   0.0  0
 T05  CONST_33  H3   C3   C4   C5    180.00   0.0  0
 T05  CONST_34  H7   C10  C11  C12   180.00   0.0  0
 T05  CONST_35  H5   C12  C11  C10   180.00   0.0  0
 T05  CONST_36  H1   C4   C3   C2    180.00   0.0  0
 T05  CONST_37  H2   C13  C14  C9    180.00   0.0  0
 T05  CONST_38  H24  N32  C30  C29   180.00   0.0  0
 T05  Var_01    C26  N21  C22  C23   -51.83  30.0  1
 T05  Var_02    N21  C22  C23  C24    51.38  30.0  1
 T05  Var_03    C25  C26  N21  C22    54.43  30.0  1
 T05  Var_04    C25  C24  C23  C22   -55.52  30.0  1
 T05  Var_05    N21  S18  C11  C12  -103.33  30.0  2
 T05  Var_06    O17  C15  C14  C13   116.50  30.0  2
 T05  Var_07    H18  C1   C2   C3    103.73  30.0  2
 T05  Var_08    H21  C35  C29  C28   118.57  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
 T05  chir_01  C25  N27  C26  C24  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
 T05  plan-1  C4   0.020
 T05  plan-1  C3   0.020
 T05  plan-1  C5   0.020
 T05  plan-1  C7   0.020
 T05  plan-1  C2   0.020
 T05  plan-1  C6   0.020
 T05  plan-1  C1   0.020
 T05  plan-1  O8   0.020
 T05  plan-1  H1   0.020
 T05  plan-1  H3   0.020
 T05  plan-1  H4   0.020
 T05  plan-1  H6   0.020
 T05  plan-2  C13  0.020
 T05  plan-2  C12  0.020
 T05  plan-2  C10  0.020
 T05  plan-2  C14  0.020
 T05  plan-2  C9   0.020
 T05  plan-2  C11  0.020
 T05  plan-2  O8   0.020
 T05  plan-2  S18  0.020
 T05  plan-2  H2   0.020
 T05  plan-2  H5   0.020
 T05  plan-2  H7   0.020
 T05  plan-2  C15  0.020
 T05  plan-3  C28  0.020
 T05  plan-3  C29  0.020
 T05  plan-3  C30  0.020
 T05  plan-3  C33  0.020
 T05  plan-3  C25  0.020
 T05  plan-3  C35  0.020
 T05  plan-3  N32  0.020
 T05  plan-3  N27  0.020
 T05  plan-3  H8   0.020
 T05  plan-3  H24  0.020
 T05  plan-3  O31  0.020
 T05  plan-3  O34  0.020
 T05  plan-4  C14  0.020
 T05  plan-4  O16  0.020
 T05  plan-4  O17  0.020
 T05  plan-4  C15  0.020

