# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:45:11 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 1-{3-tert-butyl-1-[2-(1,1-dioxidothiomorpholin-4-yl)-2-oxoethyl]-1H-pyrazol-5-yl}-3-naphthalen-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1cc(NC(=O)Nc2ccc3ccccc3c2)n(CC(=O)N4CC[S](=O)(=O)CC4)n1
#
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
 P79  P79  1-{3-tert-butyl-1-[2-(1,1-dioxidothiomorpholin-4-yl)-2-oxoethyl]-1H-pyrazol-5-yl}-3-naphthalen-2-ylurea  ligand  63  34  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P79
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
 P79  C1    C  CR15  0  -0.533  -0.4283  -3.8295   0.8397
 P79  C2    C  CR5   0   0.344   0.6257  -4.6572   0.3977
 P79  N3    N  NR5   0  -0.291   1.4390  -2.7159   0.6239
 P79  N4    N  N     0  -0.311   1.7430  -3.9621   0.2761
 P79  C5    C  CT    0  -0.186   0.5645  -6.1349   0.1111
 P79  C6    C  CR5   0   0.631   0.1387  -2.5877   0.9661
 P79  C7    C  CH2   0  -0.440   2.4009  -1.6566   0.5787
 P79  C8    C  C     0   0.553   2.1121  -0.7258  -0.5988
 P79  N9    N  NT    0  -0.456   2.7023   0.4955  -0.5807
 P79  O10   O  O     0  -0.454   1.3924  -1.0939  -1.5051
 P79  C11   C  C     0   0.726  -1.2528  -0.6556   0.5799
 P79  N12   N  NH1   0  -0.808  -1.5613   0.5732   1.0962
 P79  O13   O  O     0  -0.477  -1.6849  -1.0917  -0.4663
 P79  C14   C  CR6   0   0.380  -2.4471   1.5220   0.5777
 P79  C15   C  CR16  0  -0.331  -2.3780   2.8101   1.1697
 P79  C16   C  CR16  0  -0.303  -3.2020   3.8155   0.7610
 P79  C17   C  CR66  0   0.093  -4.1448   3.6086  -0.2724
 P79  C18   C  CR66  0   0.148  -4.2112   2.3248  -0.8689
 P79  C19   C  CR16  0  -0.395  -3.3539   1.2896  -0.4281
 P79  N20   N  NH1   0  -0.819  -0.3619  -1.3515   1.3629
 P79  C21   C  CH3   0  -0.634  -0.5342  -6.3963  -0.9254
 P79  C22   C  CH3   0  -0.639   1.9005  -6.6437  -0.4280
 P79  C23   C  CH3   0  -0.632   0.2275  -6.8778   1.4102
 P79  C24   C  CR16  0  -0.307  -5.0118   4.6301  -0.7219
 P79  C25   C  CR16  0  -0.265  -5.9134   4.3880  -1.7232
 P79  C26   C  CR16  0  -0.256  -5.9833   3.1107  -2.3179
 P79  C27   C  CR16  0  -0.323  -5.1534   2.1046  -1.9024
 P79  C28   C  CH2   0  -0.347   2.3083   1.4905  -1.5619
 P79  C29   C  CH2   0  -0.609   1.2749   2.4532  -0.9799
 P79  S30   S  S     0   1.205   1.9424   3.2959   0.4530
 P79  C31   C  CH2   0  -0.597   2.5616   1.9173   1.4162
 P79  C32   C  CH2   0  -0.377   3.4452   1.0281   0.5449
 P79  O33   O  OS    0  -0.660   0.8677   3.9623   1.1822
 P79  O34   O  OS    0  -0.678   3.0927   4.0869   0.0142
 P79  H1    H  HCR5  0   0.266  -1.4532  -4.0952   1.0401
 P79  H7    H  HCH2  0   0.286   2.3918  -1.1296   1.5321
 P79  H7A   H  HCH2  0   0.335   3.3927  -2.0972   0.4690
 P79  HN12  H  HNH1  0   0.412  -1.1256   0.8340   1.9681
 P79  H15   H  HCR6  0   0.268  -1.6527   2.9940   1.9523
 P79  H16   H  HCR6  0   0.259  -3.1323   4.7902   1.2283
 P79  H19   H  HCR6  0   0.275  -3.4355   0.3216  -0.8965
 P79  HN20  H  HNH1  0   0.418  -0.1769  -1.0509   2.3092
 P79  H21   H  HCH3  0   0.228  -0.3092  -5.8976  -1.8699
 P79  H21A  H  HCH3  0   0.228  -0.6242  -7.4659  -1.1243
 P79  H21B  H  HCH3  0   0.227  -1.5070  -6.0409  -0.5814
 P79  H22   H  HCH3  0   0.226   2.7052  -6.5085   0.2956
 P79  H22A  H  HCH3  0   0.226   1.8266  -7.7093  -0.6512
 P79  H22B  H  HCH3  0   0.226   2.1855  -6.1290  -1.3462
 P79  H23   H  HCH3  0   0.227  -0.7250  -6.5480   1.8290
 P79  H23A  H  HCH3  0   0.227   0.1549  -7.9523   1.2294
 P79  H23B  H  HCH3  0   0.228   0.9992  -6.7180   2.1654
 P79  H24   H  HCR6  0   0.254  -4.9533   5.6092  -0.2615
 P79  H25   H  HCR6  0   0.256  -6.5758   5.1739  -2.0617
 P79  H26   H  HCR6  0   0.257  -6.6998   2.9298  -3.1087
 P79  H27   H  HCR6  0   0.253  -5.2100   1.1247  -2.3615
 P79  H28   H  HCH2  0   0.287   3.1921   2.0379  -1.8926
 P79  H28A  H  HCH2  0   0.306   1.8825   1.0041  -2.4346
 P79  H29   H  HCH2  0   0.337   1.0029   3.2306  -1.6961
 P79  H29A  H  HCH2  0   0.293   0.3691   1.9315  -0.6659
 P79  H31   H  HCH2  0   0.339   3.1154   2.3444   2.2541
 P79  H31A  H  HCH2  0   0.284   1.6993   1.3739   1.8068
 P79  H32   H  HCH2  0   0.318   3.8759   0.2359   1.1512
 P79  H32A  H  HCH2  0   0.301   4.2937   1.6003   0.1660

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
 P79  C1   C2    aromatic  1.411  0.020  1.411
 P79  C1   C6    aromatic  1.371  0.020  1.371
 P79  C2   N4    aromatic  1.321  0.020  1.321
 P79  C2   C5    single    1.506  0.020  1.506
 P79  N3   N4    aromatic  1.329  0.020  1.329
 P79  N3   C6    aromatic  1.351  0.020  1.351
 P79  N3   C7    single    1.432  0.020  1.432
 P79  C5   C21   single    1.533  0.020  1.533
 P79  C5   C22   single    1.528  0.020  1.528
 P79  C5   C23   single    1.534  0.020  1.534
 P79  C6   N20   single    1.391  0.020  1.391
 P79  C7   C8    single    1.528  0.020  1.528
 P79  C8   N9    single    1.357  0.020  1.357
 P79  C8   O10   double    1.215  0.020  1.215
 P79  N9   C28   single    1.452  0.020  1.452
 P79  N9   C32   single    1.450  0.020  1.450
 P79  C11  N12   single    1.368  0.020  1.368
 P79  C11  O13   double    1.213  0.020  1.213
 P79  C11  N20   single    1.375  0.020  1.375
 P79  N12  C14   single    1.398  0.020  1.398
 P79  C14  C15   aromatic  1.419  0.020  1.419
 P79  C14  C19   aromatic  1.374  0.020  1.374
 P79  C15  C16   aromatic  1.363  0.020  1.363
 P79  C16  C17   aromatic  1.414  0.020  1.414
 P79  C17  C18   aromatic  1.417  0.020  1.417
 P79  C17  C24   aromatic  1.413  0.020  1.413
 P79  C18  C19   aromatic  1.415  0.020  1.415
 P79  C18  C27   aromatic  1.416  0.020  1.416
 P79  C24  C25   aromatic  1.369  0.020  1.369
 P79  C25  C26   aromatic  1.411  0.020  1.411
 P79  C26  C27   aromatic  1.369  0.020  1.369
 P79  C28  C29   single    1.528  0.020  1.528
 P79  C29  S30   single    1.791  0.020  1.791
 P79  S30  C31   single    1.792  0.020  1.792
 P79  S30  O33   double    1.460  0.020  1.460
 P79  S30  O34   double    1.463  0.020  1.463
 P79  C31  C32   single    1.527  0.020  1.527
 P79  C1   H1    single    0.930  0.020  1.080
 P79  C7   H7    single    0.970  0.020  1.090
 P79  C7   H7A   single    0.970  0.020  1.090
 P79  N12  HN12  single    0.860  0.020  1.020
 P79  C15  H15   single    0.930  0.020  1.080
 P79  C16  H16   single    0.930  0.020  1.080
 P79  C19  H19   single    0.930  0.020  1.080
 P79  N20  HN20  single    0.860  0.020  1.020
 P79  C21  H21   single    0.970  0.020  1.090
 P79  C21  H21A  single    0.970  0.020  1.090
 P79  C21  H21B  single    0.970  0.020  1.090
 P79  C22  H22   single    0.970  0.020  1.090
 P79  C22  H22A  single    0.970  0.020  1.090
 P79  C22  H22B  single    0.970  0.020  1.090
 P79  C23  H23   single    0.970  0.020  1.090
 P79  C23  H23A  single    0.970  0.020  1.090
 P79  C23  H23B  single    0.970  0.020  1.090
 P79  C24  H24   single    0.930  0.020  1.080
 P79  C25  H25   single    0.930  0.020  1.080
 P79  C26  H26   single    0.930  0.020  1.080
 P79  C27  H27   single    0.930  0.020  1.080
 P79  C28  H28   single    0.970  0.020  1.090
 P79  C28  H28A  single    0.970  0.020  1.090
 P79  C29  H29   single    0.970  0.020  1.090
 P79  C29  H29A  single    0.970  0.020  1.090
 P79  C31  H31   single    0.970  0.020  1.090
 P79  C31  H31A  single    0.970  0.020  1.090
 P79  C32  H32   single    0.970  0.020  1.090
 P79  C32  H32A  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
 P79  H1    C1   C6    126.83  3.000
 P79  H1    C1   C2    128.62  3.000
 P79  C6    C1   C2    104.55  3.000
 P79  C5    C2   N4    122.19  3.000
 P79  C5    C2   C1    127.19  3.000
 P79  N4    C2   C1    110.60  3.000
 P79  C7    N3   C6    125.77  3.000
 P79  C7    N3   N4    122.13  3.000
 P79  C6    N3   N4    112.06  3.000
 P79  N3    N4   C2    106.00  3.000
 P79  C23   C5   C22   109.25  3.000
 P79  C23   C5   C21   109.42  3.000
 P79  C22   C5   C21   109.35  3.000
 P79  C23   C5   C2    108.84  3.000
 P79  C22   C5   C2    110.99  3.000
 P79  C21   C5   C2    108.97  3.000
 P79  N20   C6   N3    120.19  3.000
 P79  N20   C6   C1    133.02  3.000
 P79  N3    C6   C1    106.79  3.000
 P79  H7A   C7   H7    106.92  3.000
 P79  H7A   C7   C8    109.89  3.000
 P79  H7    C7   C8    112.21  3.000
 P79  H7A   C7   N3    108.37  3.000
 P79  H7    C7   N3    108.95  3.000
 P79  C8    C7   N3    110.36  3.000
 P79  O10   C8   N9    122.72  3.000
 P79  O10   C8   C7    120.16  3.000
 P79  N9    C8   C7    117.11  3.000
 P79  C32   N9   C28   114.32  3.000
 P79  C32   N9   C8    124.33  3.000
 P79  C28   N9   C8    119.33  3.000
 P79  N20   C11  O13   122.68  3.000
 P79  N20   C11  N12   112.69  3.000
 P79  O13   C11  N12   124.62  3.000
 P79  HN12  N12  C14   114.76  3.000
 P79  HN12  N12  C11   117.45  3.000
 P79  C14   N12  C11   127.77  3.000
 P79  C19   C14  C15   119.41  3.000
 P79  C19   C14  N12   125.10  3.000
 P79  C15   C14  N12   115.49  3.000
 P79  H15   C15  C16   119.77  3.000
 P79  H15   C15  C14   119.23  3.000
 P79  C16   C15  C14   121.00  3.000
 P79  H16   C16  C17   119.33  3.000
 P79  H16   C16  C15   119.71  3.000
 P79  C17   C16  C15   120.96  3.000
 P79  C24   C17  C18   119.48  3.000
 P79  C24   C17  C16   122.39  3.000
 P79  C18   C17  C16   118.12  3.000
 P79  C27   C18  C19   121.13  3.000
 P79  C27   C18  C17   118.64  3.000
 P79  C19   C18  C17   120.23  3.000
 P79  H19   C19  C18   118.40  3.000
 P79  H19   C19  C14   121.31  3.000
 P79  C18   C19  C14   120.29  3.000
 P79  HN20  N20  C11   120.10  3.000
 P79  HN20  N20  C6    117.76  3.000
 P79  C11   N20  C6    121.35  3.000
 P79  H21B  C21  H21A  107.64  3.000
 P79  H21B  C21  H21   107.92  3.000
 P79  H21A  C21  H21   107.87  3.000
 P79  H21B  C21  C5    111.73  3.000
 P79  H21A  C21  C5    110.45  3.000
 P79  H21   C21  C5    111.07  3.000
 P79  H22B  C22  H22A  107.84  3.000
 P79  H22B  C22  H22   107.90  3.000
 P79  H22A  C22  H22   107.87  3.000
 P79  H22B  C22  C5    111.62  3.000
 P79  H22A  C22  C5    109.76  3.000
 P79  H22   C22  C5    111.70  3.000
 P79  H23B  C23  H23A  107.80  3.000
 P79  H23B  C23  H23   107.89  3.000
 P79  H23A  C23  H23   107.62  3.000
 P79  H23B  C23  C5    111.08  3.000
 P79  H23A  C23  C5    110.55  3.000
 P79  H23   C23  C5    111.74  3.000
 P79  H24   C24  C25   120.41  3.000
 P79  H24   C24  C17   119.00  3.000
 P79  C25   C24  C17   120.59  3.000
 P79  H25   C25  C26   119.69  3.000
 P79  H25   C25  C24   120.24  3.000
 P79  C26   C25  C24   120.07  3.000
 P79  H26   C26  C27   120.02  3.000
 P79  H26   C26  C25   119.48  3.000
 P79  C27   C26  C25   120.50  3.000
 P79  H27   C27  C26   120.29  3.000
 P79  H27   C27  C18   118.99  3.000
 P79  C26   C27  C18   120.72  3.000
 P79  H28A  C28  H28   107.38  3.000
 P79  H28A  C28  C29   108.85  3.000
 P79  H28   C28  C29   110.32  3.000
 P79  H28A  C28  N9    110.03  3.000
 P79  H28   C28  N9    109.20  3.000
 P79  C29   C28  N9    110.98  3.000
 P79  H29A  C29  H29   108.81  3.000
 P79  H29A  C29  S30   107.70  3.000
 P79  H29   C29  S30   106.42  3.000
 P79  H29A  C29  C28   111.70  3.000
 P79  H29   C29  C28   111.56  3.000
 P79  S30   C29  C28   110.43  3.000
 P79  O34   S30  O33   118.80  3.000
 P79  O34   S30  C31   107.78  3.000
 P79  O33   S30  C31   109.70  3.000
 P79  O34   S30  C29   107.90  3.000
 P79  O33   S30  C29   109.88  3.000
 P79  C31   S30  C29   101.35  3.000
 P79  H31A  C31  H31   108.73  3.000
 P79  H31A  C31  C32   111.81  3.000
 P79  H31   C31  C32   111.86  3.000
 P79  H31A  C31  S30   107.60  3.000
 P79  H31   C31  S30   106.68  3.000
 P79  C32   C31  S30   109.95  3.000
 P79  H32A  C32  H32   105.54  3.000
 P79  H32A  C32  C31   110.05  3.000
 P79  H32   C32  C31   109.60  3.000
 P79  H32A  C32  N9    108.75  3.000
 P79  H32   C32  N9    111.62  3.000
 P79  C31   C32  N9    111.13  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
 P79  CONST_01  N3    N4   C2   C1     0.00   0.0  0
 P79  CONST_02  N4    N3   C6   C1     0.00   0.0  0
 P79  CONST_03  N3    C6   C1   C2     0.00   0.0  0
 P79  CONST_04  C6    N3   N4   C2     0.00   0.0  0
 P79  CONST_05  C6    C1   C2   N4     0.00   0.0  0
 P79  CONST_06  C17   C16  C15  C14    0.00   0.0  0
 P79  CONST_07  C17   C18  C19  C14    0.00   0.0  0
 P79  CONST_08  C27   C18  C19  C14  180.00   0.0  0
 P79  CONST_09  C18   C19  C14  C15    0.00   0.0  0
 P79  CONST_10  C18   C17  C16  C15    0.00   0.0  0
 P79  CONST_11  C24   C17  C16  C15  180.00   0.0  0
 P79  CONST_12  C19   C14  C15  C16    0.00   0.0  0
 P79  CONST_13  C19   C18  C17  C16    0.00   0.0  0
 P79  CONST_14  C27   C18  C17  C16  180.00   0.0  0
 P79  CONST_15  C25   C24  C17  C16  180.00   0.0  0
 P79  CONST_16  C26   C27  C18  C17    0.00   0.0  0
 P79  CONST_17  C26   C25  C24  C17    0.00   0.0  0
 P79  CONST_18  C25   C24  C17  C18    0.00   0.0  0
 P79  CONST_19  C25   C26  C27  C18    0.00   0.0  0
 P79  CONST_20  C24   C17  C18  C19  180.00   0.0  0
 P79  CONST_21  C26   C27  C18  C19  180.00   0.0  0
 P79  CONST_22  C27   C18  C17  C24    0.00   0.0  0
 P79  CONST_23  C27   C26  C25  C24    0.00   0.0  0
 P79  CONST_24  C7    N3   C6   C1   180.00   0.0  0
 P79  CONST_25  N20   C6   C1   C2   180.00   0.0  0
 P79  CONST_26  C7    N3   N4   C2   180.00   0.0  0
 P79  CONST_27  C5    C2   N4   N3   180.00   0.0  0
 P79  CONST_28  N20   C6   N3   N4   180.00   0.0  0
 P79  CONST_29  C6    C1   C2   C5   180.00   0.0  0
 P79  CONST_30  C16   C15  C14  N12  180.00   0.0  0
 P79  CONST_31  C18   C19  C14  N12  180.00   0.0  0
 P79  CONST_32  H1    C1   C6   N3   180.00   0.0  0
 P79  CONST_33  H16   C16  C15  C14  180.00   0.0  0
 P79  CONST_34  H19   C19  C14  C15  180.00   0.0  0
 P79  CONST_35  H24   C24  C17  C16    0.00   0.0  0
 P79  CONST_36  H15   C15  C16  C17  180.00   0.0  0
 P79  CONST_37  H27   C27  C18  C17  180.00   0.0  0
 P79  CONST_38  H25   C25  C24  C17  180.00   0.0  0
 P79  CONST_39  H26   C26  C27  C18  180.00   0.0  0
 P79  CONST_40  C28   N9   C8   C7   180.00   0.0  0
 P79  CONST_41  C32   N9   C8   C7     0.00   0.0  0
 P79  CONST_42  C28   N9   C8   O10    0.00   0.0  0
 P79  CONST_43  C32   N9   C8   O10  180.00   0.0  0
 P79  CONST_46  C15   C14  N12  C11  180.00   0.0  0
 P79  CONST_47  C19   C14  N12  C11    0.00   0.0  0
 P79  CONST_49  HN12  N12  C14  C15    0.00   0.0  0
 P79  CONST_50  O13   C11  N20  C6     0.00   0.0  0
 P79  CONST_51  C14   N12  C11  O13    0.00   0.0  0
 P79  CONST_52  N12   C11  N20  C6   180.00   0.0  0
 P79  CONST_53  N20   C11  N12  C14  180.00   0.0  0
 P79  Var_01    S30   C29  C28  N9    59.48  30.0  1
 P79  Var_02    S30   C31  C32  N9   -60.28  30.0  1
 P79  Var_03    C31   C32  N9   C28   67.96  30.0  1
 P79  Var_04    C31   S30  C29  C28  -50.66  30.0  1
 P79  Var_05    C32   N9   C28  C29  -67.32  30.0  1
 P79  Var_06    C32   C31  S30  C29   50.84  30.0  1
 P79  Var_07    C21   C5   C2   C1    56.10  30.0  2
 P79  Var_08    N9    C8   C7   N3   163.36  30.0  3
 P79  Var_09    C8    C7   N3   N4   106.65  30.0  2
 P79  Var_10    H21   C21  C5   C2    62.41  30.0  3
 P79  Var_11    H22   C22  C5   C2    61.77  30.0  3
 P79  Var_12    H23   C23  C5   C2    58.95  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
 P79  plan-1  C1    0.020
 P79  plan-1  C2    0.020
 P79  plan-1  N3    0.020
 P79  plan-1  N4    0.020
 P79  plan-1  C5    0.020
 P79  plan-1  C6    0.020
 P79  plan-1  C7    0.020
 P79  plan-1  N20   0.020
 P79  plan-1  H1    0.020
 P79  plan-2  N12   0.020
 P79  plan-2  C14   0.020
 P79  plan-2  C15   0.020
 P79  plan-2  C16   0.020
 P79  plan-2  C17   0.020
 P79  plan-2  C18   0.020
 P79  plan-2  C19   0.020
 P79  plan-2  C24   0.020
 P79  plan-2  C25   0.020
 P79  plan-2  C26   0.020
 P79  plan-2  C27   0.020
 P79  plan-2  H15   0.020
 P79  plan-2  H16   0.020
 P79  plan-2  H19   0.020
 P79  plan-2  H24   0.020
 P79  plan-2  H25   0.020
 P79  plan-2  H26   0.020
 P79  plan-2  H27   0.020
 P79  plan-3  C6    0.020
 P79  plan-3  C11   0.020
 P79  plan-3  N12   0.020
 P79  plan-3  O13   0.020
 P79  plan-3  C14   0.020
 P79  plan-3  N20   0.020
 P79  plan-3  HN12  0.020
 P79  plan-3  HN20  0.020
 P79  plan-4  C7    0.020
 P79  plan-4  C8    0.020
 P79  plan-4  N9    0.020
 P79  plan-4  O10   0.020
 P79  plan-4  C28   0.020
 P79  plan-4  C32   0.020

