# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:47:15 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 1-{5-tert-butyl-3-[(1,1-dioxidothiomorpholin-4-yl)carbonyl]thiophen-2-yl}-3-naphthalen-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1sc(NC(=O)Nc2ccc3ccccc3c2)c(c1)C(=O)N4CC[S](=O)(=O)CC4
#
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
 P78  P78  1-{5-tert-butyl-3-[(1,1-dioxidothiomorpholin-4-yl)carbonyl]thiophen-2-yl}-3-naphthalen-2-ylurea  ligand  60  33  .  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_P78
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
 P78  C1    C  CR5   0  -0.094    1.9071  -2.6537   0.1051
 P78  O1    O  OS    0  -0.682    5.9975   3.0411  -1.7489
 P78  S1    S  S     0   1.207    6.1067   2.0703  -0.6584
 P78  C2    C  CR16  0  -0.317   -7.3269   2.4285  -0.7812
 P78  S2    S  S2    0   0.241    0.1750  -2.4731   0.1264
 P78  C3    C  CR5   0   0.087    0.2956  -0.7635   0.3199
 P78  C4    C  CR5   0  -0.072    1.6071  -0.3442   0.3188
 P78  C5    C  CR15  0  -0.251    2.5118  -1.4484   0.2132
 P78  C6    C  CT    0  -0.171    2.5167  -4.0285  -0.0156
 P78  C7    C  CH3   0  -0.629    2.1053  -4.8862   1.1881
 P78  C8    C  CH3   0  -0.631    2.0353  -4.6959  -1.3101
 P78  C9    C  CH3   0  -0.660    4.0409  -3.9175  -0.0494
 P78  C10   C  C     0   0.560    1.9782   1.0673   0.5184
 P78  C11   C  CR16  0  -0.308   -8.6080   0.1431   0.1863
 P78  O11   O  O     0  -0.495    1.2793   1.8019   1.2124
 P78  C12   C  CR16  0  -0.262   -9.3382   1.1619  -0.3631
 P78  N12   N  NH1   0  -0.759   -0.8010   0.0453   0.4740
 P78  C13   C  C     0   0.741   -2.0955  -0.3775   0.3317
 P78  C14   C  CR16  0  -0.257   -8.6889   2.3157  -0.8519
 P78  O14   O  O     0  -0.489   -2.3686  -1.5370   0.0751
 P78  N15   N  NH1   0  -0.789   -3.0103   0.6145   0.5126
 P78  C16   C  CR6   0   0.371   -4.3986   0.4576   0.4084
 P78  C17   C  CR16  0  -0.289   -5.0519  -0.6916   0.9185
 P78  C18   C  CR16  0  -0.311   -6.4113  -0.7954   0.8396
 P78  C19   C  CR66  0   0.102   -7.1997   0.2314   0.2711
 P78  C20   C  CR66  0   0.135   -6.5464   1.3908  -0.2179
 P78  C21   C  CR16  0  -0.412   -5.1389   1.4730  -0.1439
 P78  N26   N  NT    0  -0.472    3.1272   1.5179  -0.0575
 P78  C27   C  CH2   0  -0.327    3.6694   2.8060   0.3341
 P78  C28   C  CH2   0  -0.609    5.1392   2.6731   0.7193
 P78  C31   C  CH2   0  -0.611    5.1678   0.6160  -1.1142
 P78  C32   C  CH2   0  -0.358    3.6970   0.9762  -1.2779
 P78  H2    H  HCR6  0   0.255   -6.8310   3.3144  -1.1588
 P78  H5    H  HCR5  0   0.260    3.5854  -1.3370   0.2548
 P78  H7    H  HCH3  0   0.228    1.0215  -4.9962   1.2580
 P78  H7A   H  HCH3  0   0.233    2.5317  -5.8875   1.1031
 P78  H7B   H  HCH3  0   0.234    2.4588  -4.4467   2.1222
 P78  H8    H  HCH3  0   0.234    2.3171  -4.1063  -2.1840
 P78  H8A   H  HCH3  0   0.234    2.4813  -5.6866  -1.4138
 P78  H8B   H  HCH3  0   0.228    0.9512  -4.8242  -1.3258
 P78  H9    H  HCH3  0   0.234    4.4352  -3.4746   0.8668
 P78  H9A   H  HCH3  0   0.243    4.4801  -4.9108  -0.1514
 P78  H9B   H  HCH3  0   0.231    4.3842  -3.3188  -0.8954
 P78  H11   H  HCR6  0   0.256   -9.1019  -0.7436   0.5656
 P78  H12   H  HCR6  0   0.258  -10.4160   1.0874  -0.4244
 P78  HN12  H  HNH1  0   0.429   -0.5936   0.9892   0.7762
 P78  H14   H  HCR6  0   0.259   -9.2749   3.1161  -1.2845
 P78  HN15  H  HNH1  0   0.418   -2.6748   1.5665   0.5255
 P78  H17   H  HCR6  0   0.271   -4.4833  -1.4817   1.3847
 P78  H18   H  HCR6  0   0.260   -6.9019  -1.6763   1.2348
 P78  H21   H  HCR6  0   0.266   -4.6431   2.3540  -0.5359
 P78  H27   H  HCH2  0   0.271    3.5494   3.5341  -0.4732
 P78  H27A  H  HCH2  0   0.301    3.1244   3.1862   1.1933
 P78  H28   H  HCH2  0   0.310    5.2717   1.9725   1.5445
 P78  H28A  H  HCH2  0   0.331    5.5646   3.6391   0.9973
 P78  H31   H  HCH2  0   0.333    5.5914   0.2486  -2.0507
 P78  H31A  H  HCH2  0   0.305    5.3274  -0.1301  -0.3343
 P78  H32   H  HCH2  0   0.312    3.1467   0.0985  -1.6048
 P78  H32A  H  HCH2  0   0.293    3.5903   1.7177  -2.0754
 P78  O33   O  OS    0  -0.672    7.4390   1.6790  -0.2051

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
 P78  C1   S2    aromatic  1.742  0.020  1.742
 P78  C1   C5    aromatic  1.353  0.020  1.353
 P78  C1   C6    single    1.509  0.020  1.509
 P78  O1   S1    double    1.464  0.020  1.464
 P78  S1   C28   single    1.788  0.020  1.788
 P78  S1   C31   single    1.790  0.020  1.790
 P78  S1   O33   double    1.461  0.020  1.461
 P78  C2   C14   aromatic  1.368  0.020  1.368
 P78  C2   C20   aromatic  1.415  0.020  1.415
 P78  S2   C3    aromatic  1.725  0.020  1.725
 P78  C3   C4    aromatic  1.377  0.020  1.377
 P78  C3   N12   single    1.371  0.020  1.371
 P78  C4   C5    aromatic  1.431  0.020  1.431
 P78  C4   C10   single    1.473  0.020  1.473
 P78  C6   C7    single    1.534  0.020  1.534
 P78  C6   C8    single    1.534  0.020  1.534
 P78  C6   C9    single    1.529  0.020  1.529
 P78  C10  O11   double    1.229  0.020  1.229
 P78  C10  N26   single    1.362  0.020  1.362
 P78  C11  C12   aromatic  1.369  0.020  1.369
 P78  C11  C19   aromatic  1.414  0.020  1.414
 P78  C12  C14   aromatic  1.411  0.020  1.411
 P78  N12  C13   single    1.369  0.020  1.369
 P78  C13  O14   double    1.219  0.020  1.219
 P78  C13  N15   single    1.361  0.020  1.361
 P78  N15  C16   single    1.401  0.020  1.401
 P78  C16  C17   aromatic  1.417  0.020  1.417
 P78  C16  C21   aromatic  1.373  0.020  1.373
 P78  C17  C18   aromatic  1.366  0.020  1.366
 P78  C18  C19   aromatic  1.414  0.020  1.414
 P78  C19  C20   aromatic  1.418  0.020  1.418
 P78  C20  C21   aromatic  1.412  0.020  1.412
 P78  N26  C27   single    1.451  0.020  1.451
 P78  N26  C32   single    1.452  0.020  1.452
 P78  C27  C28   single    1.525  0.020  1.525
 P78  C31  C32   single    1.523  0.020  1.523
 P78  C2   H2    single    0.930  0.020  1.080
 P78  C5   H5    single    0.930  0.020  1.080
 P78  C7   H7    single    0.970  0.020  1.090
 P78  C7   H7A   single    0.970  0.020  1.090
 P78  C7   H7B   single    0.970  0.020  1.090
 P78  C8   H8    single    0.970  0.020  1.090
 P78  C8   H8A   single    0.970  0.020  1.090
 P78  C8   H8B   single    0.970  0.020  1.090
 P78  C9   H9    single    0.970  0.020  1.090
 P78  C9   H9A   single    0.970  0.020  1.090
 P78  C9   H9B   single    0.970  0.020  1.090
 P78  C11  H11   single    0.930  0.020  1.080
 P78  C12  H12   single    0.930  0.020  1.080
 P78  N12  HN12  single    0.860  0.020  1.020
 P78  C14  H14   single    0.930  0.020  1.080
 P78  N15  HN15  single    0.860  0.020  1.020
 P78  C17  H17   single    0.930  0.020  1.080
 P78  C18  H18   single    0.930  0.020  1.080
 P78  C21  H21   single    0.930  0.020  1.080
 P78  C27  H27   single    0.970  0.020  1.090
 P78  C27  H27A  single    0.970  0.020  1.090
 P78  C28  H28   single    0.970  0.020  1.090
 P78  C28  H28A  single    0.970  0.020  1.090
 P78  C31  H31   single    0.970  0.020  1.090
 P78  C31  H31A  single    0.970  0.020  1.090
 P78  C32  H32   single    0.970  0.020  1.090
 P78  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
 P78  C6    C1   C5   129.61  3.000
 P78  C6    C1   S2   119.82  3.000
 P78  C5    C1   S2   110.56  3.000
 P78  O33   S1   C31  109.86  3.000
 P78  O33   S1   C28  110.16  3.000
 P78  C31   S1   C28  100.74  3.000
 P78  O33   S1   O1   118.48  3.000
 P78  C31   S1   O1   108.05  3.000
 P78  C28   S1   O1   108.06  3.000
 P78  H2    C2   C20  119.07  3.000
 P78  H2    C2   C14  120.34  3.000
 P78  C20   C2   C14  120.59  3.000
 P78  C3    S2   C1    91.99  3.000
 P78  N12   C3   C4   125.60  3.000
 P78  N12   C3   S2   122.78  3.000
 P78  C4    C3   S2   111.61  3.000
 P78  C10   C4   C5   126.15  3.000
 P78  C10   C4   C3   122.12  3.000
 P78  C5    C4   C3   111.54  3.000
 P78  H5    C5   C4   123.08  3.000
 P78  H5    C5   C1   122.64  3.000
 P78  C4    C5   C1   114.25  3.000
 P78  C9    C6   C8   109.02  3.000
 P78  C9    C6   C7   108.99  3.000
 P78  C8    C6   C7   109.55  3.000
 P78  C9    C6   C1   109.79  3.000
 P78  C8    C6   C1   109.70  3.000
 P78  C7    C6   C1   109.77  3.000
 P78  H7B   C7   H7A  108.04  3.000
 P78  H7B   C7   H7   107.91  3.000
 P78  H7A   C7   H7   107.49  3.000
 P78  H7B   C7   C6   111.07  3.000
 P78  H7A   C7   C6   110.30  3.000
 P78  H7    C7   C6   111.88  3.000
 P78  H8B   C8   H8A  107.33  3.000
 P78  H8B   C8   H8   107.96  3.000
 P78  H8A   C8   H8   107.99  3.000
 P78  H8B   C8   C6   112.02  3.000
 P78  H8A   C8   C6   110.30  3.000
 P78  H8    C8   C6   111.08  3.000
 P78  H9B   C9   H9A  107.48  3.000
 P78  H9B   C9   H9   108.32  3.000
 P78  H9A   C9   H9   107.61  3.000
 P78  H9B   C9   C6   111.74  3.000
 P78  H9A   C9   C6   109.72  3.000
 P78  H9    C9   C6   111.78  3.000
 P78  N26   C10  O11  121.39  3.000
 P78  N26   C10  C4   118.18  3.000
 P78  O11   C10  C4   120.40  3.000
 P78  H11   C11  C19  118.96  3.000
 P78  H11   C11  C12  120.43  3.000
 P78  C19   C11  C12  120.60  3.000
 P78  H12   C12  C14  119.67  3.000
 P78  H12   C12  C11  120.19  3.000
 P78  C14   C12  C11  120.14  3.000
 P78  HN12  N12  C13  120.83  3.000
 P78  HN12  N12  C3   114.81  3.000
 P78  C13   N12  C3   124.21  3.000
 P78  N15   C13  O14  124.80  3.000
 P78  N15   C13  N12  113.36  3.000
 P78  O14   C13  N12  121.84  3.000
 P78  H14   C14  C12  119.60  3.000
 P78  H14   C14  C2   119.91  3.000
 P78  C12   C14  C2   120.49  3.000
 P78  HN15  N15  C16  115.84  3.000
 P78  HN15  N15  C13  117.75  3.000
 P78  C16   N15  C13  125.05  3.000
 P78  C21   C16  C17  119.75  3.000
 P78  C21   C16  N15  118.78  3.000
 P78  C17   C16  N15  121.40  3.000
 P78  H17   C17  C18  119.59  3.000
 P78  H17   C17  C16  120.42  3.000
 P78  C18   C17  C16  119.98  3.000
 P78  H18   C18  C19  119.00  3.000
 P78  H18   C18  C17  119.45  3.000
 P78  C19   C18  C17  121.55  3.000
 P78  C20   C19  C18  118.40  3.000
 P78  C20   C19  C11  119.30  3.000
 P78  C18   C19  C11  122.30  3.000
 P78  C21   C20  C19  119.27  3.000
 P78  C21   C20  C2   121.86  3.000
 P78  C19   C20  C2   118.86  3.000
 P78  H21   C21  C20  118.96  3.000
 P78  H21   C21  C16  120.00  3.000
 P78  C20   C21  C16  121.04  3.000
 P78  C32   N26  C27  114.29  3.000
 P78  C32   N26  C10  124.28  3.000
 P78  C27   N26  C10  119.65  3.000
 P78  H27A  C27  H27  107.21  3.000
 P78  H27A  C27  C28  108.31  3.000
 P78  H27   C27  C28  110.49  3.000
 P78  H27A  C27  N26  109.67  3.000
 P78  H27   C27  N26  110.53  3.000
 P78  C28   C27  N26  110.53  3.000
 P78  H28A  C28  H28  109.18  3.000
 P78  H28A  C28  C27  111.27  3.000
 P78  H28   C28  C27  111.35  3.000
 P78  H28A  C28  S1   106.48  3.000
 P78  H28   C28  S1   107.50  3.000
 P78  C27   C28  S1   110.87  3.000
 P78  H31A  C31  H31  109.05  3.000
 P78  H31A  C31  C32  112.32  3.000
 P78  H31   C31  C32  111.23  3.000
 P78  H31A  C31  S1   107.26  3.000
 P78  H31   C31  S1   106.76  3.000
 P78  C32   C31  S1   109.98  3.000
 P78  H32A  C32  H32  106.19  3.000
 P78  H32A  C32  C31  109.44  3.000
 P78  H32   C32  C31  109.30  3.000
 P78  H32A  C32  N26  108.76  3.000
 P78  H32   C32  N26  110.83  3.000
 P78  C31   C32  N26  112.15  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
 P78  CONST_01  C4    C3   S2   C1      0.00   0.0  0
 P78  CONST_02  C3    C4   C5   C1      0.00   0.0  0
 P78  CONST_03  C11   C12  C14  C2      0.00   0.0  0
 P78  CONST_04  C11   C19  C20  C2      0.00   0.0  0
 P78  CONST_05  C18   C19  C20  C2    180.00   0.0  0
 P78  CONST_06  C16   C21  C20  C2    180.00   0.0  0
 P78  CONST_07  C4    C5   C1   S2      0.00   0.0  0
 P78  CONST_08  C5    C4   C3   S2      0.00   0.0  0
 P78  CONST_09  C5    C1   S2   C3      0.00   0.0  0
 P78  CONST_10  C17   C18  C19  C11   180.00   0.0  0
 P78  CONST_11  C21   C20  C19  C11   180.00   0.0  0
 P78  CONST_12  C18   C19  C11  C12   180.00   0.0  0
 P78  CONST_13  C20   C19  C11  C12     0.00   0.0  0
 P78  CONST_14  C20   C2   C14  C12     0.00   0.0  0
 P78  CONST_15  C19   C20  C2   C14     0.00   0.0  0
 P78  CONST_16  C21   C20  C2   C14   180.00   0.0  0
 P78  CONST_17  C19   C11  C12  C14     0.00   0.0  0
 P78  CONST_18  C19   C18  C17  C16     0.00   0.0  0
 P78  CONST_19  C19   C20  C21  C16     0.00   0.0  0
 P78  CONST_20  C20   C21  C16  C17     0.00   0.0  0
 P78  CONST_21  C20   C19  C18  C17     0.00   0.0  0
 P78  CONST_22  C21   C16  C17  C18     0.00   0.0  0
 P78  CONST_23  C21   C20  C19  C18     0.00   0.0  0
 P78  CONST_24  N12   C3   S2   C1    180.00   0.0  0
 P78  CONST_25  C10   C4   C5   C1    180.00   0.0  0
 P78  CONST_26  C10   C4   C3   S2    180.00   0.0  0
 P78  CONST_27  C6    C1   S2   C3    180.00   0.0  0
 P78  CONST_28  C6    C1   C5   C4    180.00   0.0  0
 P78  CONST_29  N12   C3   C4   C5    180.00   0.0  0
 P78  CONST_30  C18   C17  C16  N15   180.00   0.0  0
 P78  CONST_31  C20   C21  C16  N15   180.00   0.0  0
 P78  CONST_32  C27   N26  C10  C4    180.00   0.0  0
 P78  CONST_34  H12   C12  C14  C2    180.00   0.0  0
 P78  CONST_35  H21   C21  C20  C2      0.00   0.0  0
 P78  CONST_36  H5    C5   C1   S2    180.00   0.0  0
 P78  CONST_37  H14   C14  C12  C11   180.00   0.0  0
 P78  CONST_38  H18   C18  C19  C11     0.00   0.0  0
 P78  CONST_39  H2    C2   C14  C12   180.00   0.0  0
 P78  CONST_40  H11   C11  C12  C14   180.00   0.0  0
 P78  CONST_41  H17   C17  C18  C19   180.00   0.0  0
 P78  CONST_42  C27   N26  C10  O11     0.00   0.0  0
 P78  CONST_44  C13   N12  C3   S2      0.00   0.0  0
 P78  CONST_45  C13   N12  C3   C4    180.00   0.0  0
 P78  CONST_48  HN12  N12  C3   S2    180.00   0.0  0
 P78  CONST_50  O14   C13  N12  C3      0.00   0.0  0
 P78  CONST_51  C16   N15  C13  O14     0.00   0.0  0
 P78  CONST_52  N15   C13  N12  C3    180.00   0.0  0
 P78  CONST_53  C16   N15  C13  N12   180.00   0.0  0
 P78  Var_01    N26   C27  C28  S1     60.58  30.0  1
 P78  Var_02    N26   C32  C31  S1    -59.63  30.0  1
 P78  Var_03    C31   C32  N26  C27    66.63  30.0  1
 P78  Var_04    C31   S1   C28  C27   -51.99  30.0  1
 P78  Var_05    C32   C31  S1   C28    50.84  30.0  1
 P78  Var_06    C32   N26  C27  C28   -66.33  30.0  1
 P78  Var_07    N26   C10  C4   C3   -151.10  30.0  2
 P78  Var_08    C7    C6   C1   S2    -61.74  30.0  2
 P78  Var_09    H7    C7   C6   C1     59.70  30.0  3
 P78  Var_10    H8    C8   C6   C1     59.54  30.0  3
 P78  Var_11    H9    C9   C6   C1     61.53  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
 P78  plan-1  C1    0.020
 P78  plan-1  S2    0.020
 P78  plan-1  C3    0.020
 P78  plan-1  C4    0.020
 P78  plan-1  C5    0.020
 P78  plan-1  C6    0.020
 P78  plan-1  C10   0.020
 P78  plan-1  N12   0.020
 P78  plan-1  H5    0.020
 P78  plan-2  C2    0.020
 P78  plan-2  C11   0.020
 P78  plan-2  C12   0.020
 P78  plan-2  C14   0.020
 P78  plan-2  N15   0.020
 P78  plan-2  C16   0.020
 P78  plan-2  C17   0.020
 P78  plan-2  C18   0.020
 P78  plan-2  C19   0.020
 P78  plan-2  C20   0.020
 P78  plan-2  C21   0.020
 P78  plan-2  H2    0.020
 P78  plan-2  H11   0.020
 P78  plan-2  H12   0.020
 P78  plan-2  H14   0.020
 P78  plan-2  H17   0.020
 P78  plan-2  H18   0.020
 P78  plan-2  H21   0.020
 P78  plan-3  C3    0.020
 P78  plan-3  N12   0.020
 P78  plan-3  C13   0.020
 P78  plan-3  O14   0.020
 P78  plan-3  N15   0.020
 P78  plan-3  C16   0.020
 P78  plan-3  HN12  0.020
 P78  plan-3  HN15  0.020
 P78  plan-4  C4    0.020
 P78  plan-4  C10   0.020
 P78  plan-4  O11   0.020
 P78  plan-4  N26   0.020
 P78  plan-4  C27   0.020
 P78  plan-4  C32   0.020

