# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:02:29 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: ~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc(Nc2ncc(c(NCc3nccnc3N(C)[S](C)(=O)=O)n2)C(F)(F)F)cc1
#
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
 7KD  7KD  ~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide  ligand  56  35  .  2022-07-23  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_7KD
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
 7KD  C1   C  CR6   0  -0.450  -0.8383   3.0030   0.1452
 7KD  C2   C  CR6   0   0.623  -1.1908   1.9312  -0.7256
 7KD  C8   C  CT    0   1.076  -1.7592   4.1198   0.4692
 7KD  C13  C  CR6   0   0.373   3.0194  -0.2751  -0.4060
 7KD  C14  C  CR16  0  -0.299   3.8430   0.5229   0.3941
 7KD  C15  C  CR16  0  -0.261   5.1402   0.1217   0.6623
 7KD  C16  C  CR6   0  -0.051   5.6595  -1.0730   0.1729
 7KD  C19  C  C     0   0.526   7.0691  -1.4269   0.5038
 7KD  C22  C  CH3   0  -0.514   8.7490  -3.1824   0.6695
 7KD  C24  C  CR6   0   0.221  -3.9314  -0.0621  -1.5795
 7KD  N26  N  N     0  -0.335  -4.8865  -1.3353   0.1841
 7KD  C27  C  CR16  0  -0.102  -5.9922  -1.4156  -0.5409
 7KD  N29  N  N     0  -0.370  -5.0387  -0.1571  -2.3009
 7KD  C32  C  CH3   0  -0.551  -2.8050   0.1040   1.7314
 7KD  C33  C  CH3   0  -0.792  -2.4057  -3.1988   1.3011
 7KD  N20  N  NH1   0  -0.643   7.4138  -2.7176   0.3788
 7KD  O21  O  O     0  -0.499   7.8701  -0.5749   0.8739
 7KD  C17  C  CR16  0  -0.281   4.8346  -1.8605  -0.6308
 7KD  C18  C  CR16  0  -0.344   3.5427  -1.4701  -0.9167
 7KD  N12  N  NH1   0  -0.764   1.7162   0.0248  -0.7612
 7KD  C4   C  CR6   0   0.644   0.8915   1.0487  -0.4149
 7KD  N3   N  N     0  -0.527  -0.3012   0.9894  -0.9922
 7KD  N5   N  N     0  -0.495   1.3108   1.9909   0.4228
 7KD  C6   C  CR16  0  -0.003   0.4323   2.9514   0.6767
 7KD  F10  F  F     0  -0.298  -1.2036   5.0162   1.2870
 7KD  F11  F  F     0  -0.320  -2.1557   4.7888  -0.6298
 7KD  F9   F  F     0  -0.319  -2.8914   3.7015   1.0676
 7KD  N7   N  NH1   0  -0.677  -2.3990   1.8234  -1.3000
 7KD  C23  C  CH2   0  -0.375  -2.7922   0.7323  -2.1589
 7KD  C28  C  CR16  0  -0.108  -6.0612  -0.8325  -1.7959
 7KD  C25  C  CR6   0   0.395  -3.8623  -0.6813  -0.3270
 7KD  N30  N  N     0  -0.648  -2.6812  -0.5873   0.4507
 7KD  S31  S  S     0   1.345  -1.6470  -1.8896   0.3638
 7KD  O34  O  OS    0  -0.646  -0.4197  -1.5141   1.0430
 7KD  O35  O  OS    0  -0.660  -1.6155  -2.2953  -1.0321
 7KD  H1   H  HCR6  0   0.289   3.4745   1.4486   0.8028
 7KD  H2   H  HCR6  0   0.258   5.7598   0.7592   1.2789
 7KD  H3   H  HCH3  0   0.240   9.4904  -2.6682   0.0585
 7KD  H4   H  HCH3  0   0.236   9.0131  -3.0400   1.7188
 7KD  H5   H  HCH3  0   0.250   8.7994  -4.2439   0.4451
 7KD  H6   H  HCR6  0   0.286  -6.8337  -1.9528  -0.1228
 7KD  H7   H  HCH3  0   0.254  -3.4086  -0.4442   2.4571
 7KD  H8   H  HCH3  0   0.270  -1.8176   0.2880   2.1457
 7KD  H9   H  HCH3  0   0.262  -3.2722   1.0686   1.5486
 7KD  H10  H  HCH3  0   0.291  -2.5581  -2.8729   2.3275
 7KD  H11  H  HCH3  0   0.291  -3.3546  -3.4698   0.8471
 7KD  H12  H  HCH3  0   0.307  -1.7246  -4.0483   1.2845
 7KD  H13  H  HNH1  0   0.409   6.7066  -3.4095   0.2005
 7KD  H14  H  HCR6  0   0.258   5.1916  -2.7828  -1.0713
 7KD  H15  H  HCR6  0   0.274   2.9295  -2.0951  -1.5549
 7KD  H16  H  HNH1  0   0.406   1.2554  -0.6609  -1.3407
 7KD  H17  H  HCR6  0   0.282   0.7740   3.7257   1.3532
 7KD  H18  H  HNH1  0   0.408  -3.0795   2.5541  -1.1836
 7KD  H19  H  HCH2  0   0.295  -1.9293   0.0918  -2.3225
 7KD  H20  H  HCH2  0   0.282  -3.1115   1.1206  -3.1267
 7KD  H21  H  HCR6  0   0.286  -6.9600  -0.9045  -2.3953

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
 7KD  C33  S31  single    1.780  0.020  1.780
 7KD  O35  S31  double    1.454  0.020  1.454
 7KD  S31  O34  double    1.452  0.020  1.452
 7KD  S31  N30  single    1.665  0.020  1.665
 7KD  C32  N30  single    1.461  0.020  1.461
 7KD  N26  C27  aromatic  1.325  0.020  1.325
 7KD  N26  C25  aromatic  1.318  0.020  1.318
 7KD  N30  C25  single    1.417  0.020  1.417
 7KD  F9   C8   single    1.347  0.020  1.347
 7KD  C27  C28  aromatic  1.385  0.020  1.385
 7KD  C25  C24  aromatic  1.399  0.020  1.399
 7KD  F11  C8   single    1.346  0.020  1.346
 7KD  F10  C8   single    1.334  0.020  1.334
 7KD  C8   C1   single    1.483  0.020  1.483
 7KD  C28  N29  aromatic  1.325  0.020  1.325
 7KD  C24  N29  aromatic  1.325  0.020  1.325
 7KD  C24  C23  single    1.505  0.020  1.505
 7KD  N7   C23  single    1.443  0.020  1.443
 7KD  N7   C2   single    1.342  0.020  1.342
 7KD  C1   C2   aromatic  1.425  0.020  1.425
 7KD  C1   C6   aromatic  1.378  0.020  1.378
 7KD  C2   N3   aromatic  1.323  0.020  1.323
 7KD  C6   N5   aromatic  1.326  0.020  1.326
 7KD  N3   C4   aromatic  1.326  0.020  1.326
 7KD  N5   C4   aromatic  1.329  0.020  1.329
 7KD  C4   N12  single    1.360  0.020  1.360
 7KD  C18  C17  aromatic  1.380  0.020  1.380
 7KD  C18  C13  aromatic  1.401  0.020  1.401
 7KD  N12  C13  single    1.384  0.020  1.384
 7KD  C17  C16  aromatic  1.395  0.020  1.395
 7KD  C13  C14  aromatic  1.398  0.020  1.398
 7KD  C16  C19  single    1.491  0.020  1.491
 7KD  C16  C15  aromatic  1.392  0.020  1.392
 7KD  C14  C15  aromatic  1.384  0.020  1.384
 7KD  O21  C19  double    1.227  0.020  1.227
 7KD  C19  N20  single    1.342  0.020  1.342
 7KD  N20  C22  single    1.443  0.020  1.443
 7KD  C14  H1   single    0.930  0.020  1.080
 7KD  C15  H2   single    0.930  0.020  1.080
 7KD  C22  H3   single    0.970  0.020  1.090
 7KD  C22  H4   single    0.970  0.020  1.090
 7KD  C22  H5   single    0.970  0.020  1.090
 7KD  C27  H6   single    0.930  0.020  1.080
 7KD  C32  H7   single    0.970  0.020  1.090
 7KD  C32  H8   single    0.970  0.020  1.090
 7KD  C32  H9   single    0.970  0.020  1.090
 7KD  C33  H10  single    0.970  0.020  1.090
 7KD  C33  H11  single    0.970  0.020  1.090
 7KD  C33  H12  single    0.970  0.020  1.090
 7KD  N20  H13  single    0.860  0.020  1.020
 7KD  C17  H14  single    0.930  0.020  1.080
 7KD  C18  H15  single    0.930  0.020  1.080
 7KD  N12  H16  single    0.860  0.020  1.020
 7KD  C6   H17  single    0.930  0.020  1.080
 7KD  N7   H18  single    0.860  0.020  1.020
 7KD  C23  H19  single    0.970  0.020  1.090
 7KD  C23  H20  single    0.970  0.020  1.090
 7KD  C28  H21  single    0.930  0.020  1.080

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
 7KD  C6   C1   C8   121.08  3.000
 7KD  C6   C1   C2   115.82  3.000
 7KD  C8   C1   C2   123.10  3.000
 7KD  N7   C2   N3   117.52  3.000
 7KD  N3   C2   C1   119.49  3.000
 7KD  N7   C2   C1   122.99  3.000
 7KD  F9   C8   F11  105.62  3.000
 7KD  F11  C8   F10  106.80  3.000
 7KD  F9   C8   F10  106.63  3.000
 7KD  F10  C8   C1   112.41  3.000
 7KD  F11  C8   C1   112.25  3.000
 7KD  F9   C8   C1   112.65  3.000
 7KD  N12  C13  C18  116.30  3.000
 7KD  N12  C13  C14  125.31  3.000
 7KD  C18  C13  C14  118.38  3.000
 7KD  H1   C14  C15  119.75  3.000
 7KD  H1   C14  C13  120.41  3.000
 7KD  C15  C14  C13  119.84  3.000
 7KD  H2   C15  C16  119.52  3.000
 7KD  H2   C15  C14  118.45  3.000
 7KD  C16  C15  C14  122.04  3.000
 7KD  C17  C16  C19  123.58  3.000
 7KD  C19  C16  C15  118.60  3.000
 7KD  C17  C16  C15  117.81  3.000
 7KD  O21  C19  N20  121.91  3.000
 7KD  N20  C19  C16  116.78  3.000
 7KD  O21  C19  C16  121.31  3.000
 7KD  H5   C22  H4   108.36  3.000
 7KD  H5   C22  H3   108.29  3.000
 7KD  H4   C22  H3   108.23  3.000
 7KD  H5   C22  N20  108.42  3.000
 7KD  H4   C22  N20  112.05  3.000
 7KD  H3   C22  N20  111.38  3.000
 7KD  C25  C24  C23  122.75  3.000
 7KD  C23  C24  N29  117.44  3.000
 7KD  C25  C24  N29  119.80  3.000
 7KD  C25  N26  C27  117.80  3.000
 7KD  H6   C27  C28  121.33  3.000
 7KD  H6   C27  N26  117.88  3.000
 7KD  C28  C27  N26  120.79  3.000
 7KD  C28  N29  C24  118.28  3.000
 7KD  H9   C32  H8   107.72  3.000
 7KD  H9   C32  H7   108.65  3.000
 7KD  H8   C32  H7   109.52  3.000
 7KD  H9   C32  N30  107.99  3.000
 7KD  H8   C32  N30  109.72  3.000
 7KD  H7   C32  N30  113.08  3.000
 7KD  H12  C33  H11  110.20  3.000
 7KD  H12  C33  H10  109.62  3.000
 7KD  H11  C33  H10  110.29  3.000
 7KD  H12  C33  S31  107.41  3.000
 7KD  H11  C33  S31  109.62  3.000
 7KD  H10  C33  S31  109.65  3.000
 7KD  H13  N20  C22  117.70  3.000
 7KD  H13  N20  C19  119.86  3.000
 7KD  C22  N20  C19  121.91  3.000
 7KD  H14  C17  C18  117.74  3.000
 7KD  H14  C17  C16  121.35  3.000
 7KD  C18  C17  C16  120.89  3.000
 7KD  H15  C18  C17  119.26  3.000
 7KD  H15  C18  C13  119.69  3.000
 7KD  C17  C18  C13  121.04  3.000
 7KD  H16  N12  C4   112.39  3.000
 7KD  H16  N12  C13  115.48  3.000
 7KD  C4   N12  C13  132.00  3.000
 7KD  N5   C4   N3   126.15  3.000
 7KD  N5   C4   N12  120.22  3.000
 7KD  N3   C4   N12  113.64  3.000
 7KD  C4   N3   C2   119.03  3.000
 7KD  C6   N5   C4   115.17  3.000
 7KD  H17  C6   N5   115.35  3.000
 7KD  H17  C6   C1   120.32  3.000
 7KD  N5   C6   C1   124.33  3.000
 7KD  H18  N7   C23  115.73  3.000
 7KD  H18  N7   C2   120.09  3.000
 7KD  C23  N7   C2   124.10  3.000
 7KD  H20  C23  H19  107.98  3.000
 7KD  H20  C23  N7   109.79  3.000
 7KD  H19  C23  N7   108.59  3.000
 7KD  H20  C23  C24  107.94  3.000
 7KD  H19  C23  C24  110.36  3.000
 7KD  N7   C23  C24  112.10  3.000
 7KD  H21  C28  N29  117.60  3.000
 7KD  H21  C28  C27  120.99  3.000
 7KD  N29  C28  C27  121.41  3.000
 7KD  N30  C25  N26  117.88  3.000
 7KD  N30  C25  C24  120.21  3.000
 7KD  N26  C25  C24  121.89  3.000
 7KD  S31  N30  C25  115.92  3.000
 7KD  C25  N30  C32  116.22  3.000
 7KD  S31  N30  C32  117.94  3.000
 7KD  O35  S31  O34  120.19  3.000
 7KD  O34  S31  N30  107.36  3.000
 7KD  O35  S31  N30  106.36  3.000
 7KD  N30  S31  C33  106.44  3.000
 7KD  O34  S31  C33  107.70  3.000
 7KD  O35  S31  C33  108.03  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
 7KD  CONST_01  C4   N3   C2   C1     0.00   0.0  0
 7KD  CONST_02  C4   N5   C6   C1     0.00   0.0  0
 7KD  CONST_03  N5   C6   C1   C2     0.00   0.0  0
 7KD  CONST_04  N5   C4   N3   C2     0.00   0.0  0
 7KD  CONST_05  C16  C17  C18  C13    0.00   0.0  0
 7KD  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 7KD  CONST_07  C17  C18  C13  C14    0.00   0.0  0
 7KD  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 7KD  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 7KD  CONST_10  C18  C13  C14  C15    0.00   0.0  0
 7KD  CONST_11  C27  N26  C25  C24    0.00   0.0  0
 7KD  CONST_12  C27  C28  N29  C24    0.00   0.0  0
 7KD  CONST_13  N29  C28  C27  N26    0.00   0.0  0
 7KD  CONST_14  N29  C24  C25  N26    0.00   0.0  0
 7KD  CONST_15  C6   C1   C2   N3     0.00   0.0  0
 7KD  CONST_16  C6   N5   C4   N3     0.00   0.0  0
 7KD  CONST_17  C25  N26  C27  C28    0.00   0.0  0
 7KD  CONST_18  C25  C24  N29  C28    0.00   0.0  0
 7KD  CONST_19  N12  C4   N3   C2   180.00   0.0  0
 7KD  CONST_20  N3   C2   C1   C8   180.00   0.0  0
 7KD  CONST_21  N5   C6   C1   C8   180.00   0.0  0
 7KD  CONST_22  C19  C16  C15  C14  180.00   0.0  0
 7KD  CONST_23  N12  C13  C14  C15  180.00   0.0  0
 7KD  CONST_24  C18  C17  C16  C19  180.00   0.0  0
 7KD  CONST_25  C23  C24  C25  N26  180.00   0.0  0
 7KD  CONST_26  N30  C25  N26  C27  180.00   0.0  0
 7KD  CONST_27  N30  C25  C24  N29  180.00   0.0  0
 7KD  CONST_28  N12  C13  C18  C17  180.00   0.0  0
 7KD  CONST_29  C6   N5   C4   N12  180.00   0.0  0
 7KD  CONST_30  N7   C2   N3   C4   180.00   0.0  0
 7KD  CONST_31  N7   C2   C1   C6   180.00   0.0  0
 7KD  CONST_32  C28  N29  C24  C23  180.00   0.0  0
 7KD  CONST_33  H17  C6   C1   C2   180.00   0.0  0
 7KD  CONST_34  H14  C17  C18  C13  180.00   0.0  0
 7KD  CONST_35  H2   C15  C14  C13  180.00   0.0  0
 7KD  CONST_36  H15  C18  C13  C14  180.00   0.0  0
 7KD  CONST_37  H1   C14  C15  C16  180.00   0.0  0
 7KD  CONST_38  H21  C28  N29  C24  180.00   0.0  0
 7KD  CONST_39  H6   C27  C28  N29  180.00   0.0  0
 7KD  CONST_40  C23  N7   C2   C1   180.00   0.0  0
 7KD  CONST_45  C23  N7   C2   N3     0.00   0.0  0
 7KD  CONST_46  H18  N7   C2   C1     0.00   0.0  0
 7KD  CONST_47  C22  N20  C19  C16  180.00   0.0  0
 7KD  CONST_48  H13  N20  C19  C16    0.00   0.0  0
 7KD  CONST_49  O21  C19  N20  C22    0.00   0.0  0
 7KD  Var_01    N3   C4   N12  C13  179.13  30.0  1
 7KD  Var_02    C4   N12  C13  C14   -3.92  30.0  3
 7KD  Var_03    C24  C23  N7   C2   116.99  30.0  3
 7KD  Var_04    F9   C8   C1   C2    60.54  30.0  3
 7KD  Var_05    O21  C19  C16  C15  -19.41  30.0  2
 7KD  Var_06    N7   C23  C24  N29  121.74  30.0  2
 7KD  Var_07    C25  N30  S31  C33  -73.93  30.0  3
 7KD  Var_08    H7   C32  N30  C25   68.49  30.0  3
 7KD  Var_09    H3   C22  N20  C19  -57.93  30.0  3
 7KD  Var_10    H10  C33  S31  N30  -58.96  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
 7KD  plan-1  C1   0.020
 7KD  plan-1  C2   0.020
 7KD  plan-1  C8   0.020
 7KD  plan-1  N12  0.020
 7KD  plan-1  C4   0.020
 7KD  plan-1  N3   0.020
 7KD  plan-1  N5   0.020
 7KD  plan-1  C6   0.020
 7KD  plan-1  N7   0.020
 7KD  plan-1  H17  0.020
 7KD  plan-2  C24  0.020
 7KD  plan-2  N26  0.020
 7KD  plan-2  C27  0.020
 7KD  plan-2  N29  0.020
 7KD  plan-2  C23  0.020
 7KD  plan-2  C28  0.020
 7KD  plan-2  C25  0.020
 7KD  plan-2  N30  0.020
 7KD  plan-2  H6   0.020
 7KD  plan-2  H21  0.020
 7KD  plan-3  C13  0.020
 7KD  plan-3  C14  0.020
 7KD  plan-3  C15  0.020
 7KD  plan-3  C16  0.020
 7KD  plan-3  C19  0.020
 7KD  plan-3  C17  0.020
 7KD  plan-3  C18  0.020
 7KD  plan-3  N12  0.020
 7KD  plan-3  H1   0.020
 7KD  plan-3  H2   0.020
 7KD  plan-3  H14  0.020
 7KD  plan-3  H15  0.020
 7KD  plan-4  C16  0.020
 7KD  plan-4  C19  0.020
 7KD  plan-4  C22  0.020
 7KD  plan-4  N20  0.020
 7KD  plan-4  O21  0.020
 7KD  plan-4  H13  0.020
 7KD  plan-5  C2   0.020
 7KD  plan-5  N7   0.020
 7KD  plan-5  C23  0.020
 7KD  plan-5  H18  0.020
 7KD  plan-6  C32  0.020
 7KD  plan-6  C25  0.020
 7KD  plan-6  N30  0.020
 7KD  plan-6  S31  0.020

