# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:46:58 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1ncccc1CNc2nc(Nc3ccc4NC(=O)Cc4c3)ncc2C(F)(F)F)[S](C)(=O)=O
#
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
 YAM  YAM  N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide  ligand  55  35  .  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_YAM
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
 YAM  C35   C  CH3   0  -0.547  -2.4290   0.1094  -1.5527
 YAM  C34   C  CH3   0  -0.795  -2.9551  -3.1471  -1.1472
 YAM  N2    N  N     0  -0.487   1.7178   1.4689  -0.1687
 YAM  C7    C  CR16  0  -0.019   1.0215   2.5736  -0.3872
 YAM  C6    C  CR6   0  -0.452  -0.2338   2.8181   0.1295
 YAM  C13   C  CR6   0   0.032  -3.8981   0.3598   1.6055
 YAM  C20   C  CR6   0   0.395  -3.8934  -0.2949   0.3734
 YAM  C21   C  CR56  0   0.397   5.3210  -2.2476  -0.4827
 YAM  C8    C  CT    0   1.073  -0.9608   4.0705  -0.1832
 YAM  C18   C  CR16  0  -0.319  -6.2934   0.2051   1.5215
 YAM  C16   C  CR16  0  -0.345   3.0605  -2.4709   0.1977
 YAM  C19   C  CR16  0  -0.070  -6.1656  -0.4234   0.2946
 YAM  O33   O  OS    0  -0.663  -2.3219  -2.4566   1.3081
 YAM  S31   S  S     0   1.342  -2.0300  -2.0785  -0.0661
 YAM  O32   O  OS    0  -0.649  -0.6538  -2.0665  -0.5340
 YAM  N30   N  N     0  -0.634  -2.6496  -0.5516  -0.2703
 YAM  C17   C  CR16  0  -0.188  -5.1391   0.6033   2.1784
 YAM  N1    N  N     0  -0.386  -4.9868  -0.6684  -0.2645
 YAM  N10   N  NH1   0  -0.672  -1.9940   1.8756   1.5121
 YAM  C5    C  CR6   0   0.612  -0.7762   1.7889   0.9540
 YAM  F29   F  F     0  -0.321  -2.1265   3.8451  -0.8224
 YAM  F28   F  F     0  -0.322  -1.2846   4.7698   0.9219
 YAM  F27   F  F     0  -0.300  -0.2511   4.8908  -0.9615
 YAM  N4    N  N     0  -0.522  -0.0678   0.6965   1.1889
 YAM  C3    C  CR6   0   0.612   1.1240   0.5695   0.6149
 YAM  N9    N  NH1   0  -0.750   1.7527  -0.5980   0.8861
 YAM  C11   C  CR6   0   0.350   2.9620  -1.0920   0.3857
 YAM  C14   C  CR16  0  -0.361   4.0745  -0.2785   0.1354
 YAM  C22   C  CR56  0   0.008   5.2388  -0.8684  -0.3045
 YAM  C23   C  CH2   0  -0.621   6.5672  -0.2761  -0.6537
 YAM  C15   C  CR16  0  -0.297   4.2409  -3.0684  -0.2298
 YAM  N25   N  NR15  0  -0.739   6.5997  -2.5787  -0.9197
 YAM  C24   C  CR5   0   0.512   7.4017  -1.4863  -1.0474
 YAM  O26   O  O     0  -0.462   8.5611  -1.4941  -1.4074
 YAM  H35   H  HCH3  0   0.259  -2.6560   1.1659  -1.4310
 YAM  H35A  H  HCH3  0   0.267  -1.3829   0.0249  -1.8353
 YAM  H35B  H  HCH3  0   0.252  -3.0540  -0.2900  -2.3542
 YAM  H34   H  HCH3  0   0.292  -4.0119  -3.0884  -0.9007
 YAM  H34A  H  HCH3  0   0.289  -2.7937  -2.8451  -2.1797
 YAM  H34B  H  HCH3  0   0.305  -2.5880  -4.1617  -1.0005
 YAM  H7    H  HCR6  0   0.278   1.5017   3.3062  -1.0254
 YAM  H18   H  HCR6  0   0.279  -7.2709   0.3846   1.9464
 YAM  H16   H  HCR6  0   0.267   2.1946  -3.0942   0.3859
 YAM  H19   H  HCR6  0   0.273  -7.0413  -0.7418  -0.2584
 YAM  H17   H  HCR6  0   0.278  -5.2011   1.1099   3.1336
 YAM  H12   H  HCH2  0   0.274  -2.8612   1.1850   3.2729
 YAM  H12A  H  HCH2  0   0.286  -1.9226   0.0017   2.3763
 YAM  HN10  H  HNH1  0   0.402  -2.5328   2.7180   1.4108
 YAM  HN9   H  HNH1  0   0.401   1.1527  -1.2760   1.3301
 YAM  H14   H  HCR6  0   0.267   4.0239   0.7893   0.2841
 YAM  H23   H  HCH2  0   0.303   6.5188   0.4309  -1.4854
 YAM  H23A  H  HCH2  0   0.303   7.0416   0.2472   0.1803
 YAM  H15   H  HCR6  0   0.269   4.2942  -4.1407  -0.3632
 YAM  HN25  H  HNR5  0   0.410   6.9117  -3.5181  -1.1134
 YAM  C12   C  CH2   0  -0.368  -2.6285   0.8202   2.2704

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
 YAM  N30  C35   single    1.459  0.020  1.459
 YAM  C35  H35   single    0.970  0.020  1.090
 YAM  C35  H35A  single    0.970  0.020  1.090
 YAM  C35  H35B  single    0.970  0.020  1.090
 YAM  S31  C34   single    1.779  0.020  1.779
 YAM  C34  H34   single    0.970  0.020  1.090
 YAM  C34  H34A  single    0.970  0.020  1.090
 YAM  C34  H34B  single    0.970  0.020  1.090
 YAM  C3   N2    aromatic  1.332  0.020  1.332
 YAM  N2   C7    aromatic  1.324  0.020  1.324
 YAM  C7   C6    aromatic  1.379  0.020  1.379
 YAM  C7   H7    single    0.930  0.020  1.080
 YAM  C5   C6    aromatic  1.426  0.020  1.426
 YAM  C6   C8    single    1.481  0.020  1.481
 YAM  C17  C13   aromatic  1.388  0.020  1.388
 YAM  C13  C12   single    1.505  0.020  1.505
 YAM  C13  C20   aromatic  1.395  0.020  1.395
 YAM  N1   C20   aromatic  1.320  0.020  1.320
 YAM  C20  N30   single    1.424  0.020  1.424
 YAM  N25  C21   single    1.391  0.020  1.391
 YAM  C22  C21   aromatic  1.393  0.020  1.393
 YAM  C21  C15   aromatic  1.380  0.020  1.380
 YAM  F28  C8    single    1.347  0.020  1.347
 YAM  C8   F27   single    1.335  0.020  1.335
 YAM  C8   F29   single    1.348  0.020  1.348
 YAM  C18  C17   aromatic  1.387  0.020  1.387
 YAM  C18  C19   aromatic  1.384  0.020  1.384
 YAM  C18  H18   single    0.930  0.020  1.080
 YAM  C15  C16   aromatic  1.390  0.020  1.390
 YAM  C11  C16   aromatic  1.395  0.020  1.395
 YAM  C16  H16   single    0.930  0.020  1.080
 YAM  C19  N1    aromatic  1.327  0.020  1.327
 YAM  C19  H19   single    0.930  0.020  1.080
 YAM  O33  S31   double    1.455  0.020  1.455
 YAM  N30  S31   single    1.660  0.020  1.660
 YAM  S31  O32   double    1.454  0.020  1.454
 YAM  C17  H17   single    0.930  0.020  1.080
 YAM  C12  N10   single    1.446  0.020  1.446
 YAM  C12  H12   single    0.970  0.020  1.090
 YAM  C12  H12A  single    0.970  0.020  1.090
 YAM  C5   N10   single    1.342  0.020  1.342
 YAM  N10  HN10  single    0.860  0.020  1.020
 YAM  N4   C5    aromatic  1.323  0.020  1.323
 YAM  N4   C3    aromatic  1.329  0.020  1.329
 YAM  N9   C3    single    1.353  0.020  1.353
 YAM  C11  N9    single    1.399  0.020  1.399
 YAM  N9   HN9   single    0.860  0.020  1.020
 YAM  C14  C11   aromatic  1.401  0.020  1.401
 YAM  C22  C14   aromatic  1.377  0.020  1.377
 YAM  C14  H14   single    0.930  0.020  1.080
 YAM  C23  C22   single    1.496  0.020  1.496
 YAM  C24  C23   single    1.522  0.020  1.522
 YAM  C23  H23   single    0.970  0.020  1.090
 YAM  C23  H23A  single    0.970  0.020  1.090
 YAM  C15  H15   single    0.930  0.020  1.080
 YAM  C24  N25   single    1.361  0.020  1.361
 YAM  N25  HN25  single    0.860  0.020  1.020
 YAM  O26  C24   double    1.214  0.020  1.214

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
 YAM  H35B  C35  H35A  109.37  3.000
 YAM  H35B  C35  H35   108.54  3.000
 YAM  H35A  C35  H35   107.79  3.000
 YAM  H35B  C35  N30   113.13  3.000
 YAM  H35A  C35  N30   109.81  3.000
 YAM  H35   C35  N30   108.07  3.000
 YAM  H34B  C34  H34A  109.66  3.000
 YAM  H34B  C34  H34   110.34  3.000
 YAM  H34A  C34  H34   110.16  3.000
 YAM  H34B  C34  S31   107.60  3.000
 YAM  H34A  C34  S31   109.44  3.000
 YAM  H34   C34  S31   109.60  3.000
 YAM  C3    N2   C7    115.20  3.000
 YAM  H7    C7   C6    120.26  3.000
 YAM  H7    C7   N2    115.35  3.000
 YAM  C6    C7   N2    124.38  3.000
 YAM  C5    C6   C8    123.06  3.000
 YAM  C8    C6   C7    121.16  3.000
 YAM  C5    C6   C7    115.77  3.000
 YAM  C12   C13  C17   121.20  3.000
 YAM  C12   C13  C20   122.06  3.000
 YAM  C17   C13  C20   116.72  3.000
 YAM  N1    C20  N30   117.01  3.000
 YAM  N30   C20  C13   119.13  3.000
 YAM  N1    C20  C13   123.84  3.000
 YAM  N25   C21  C15   129.45  3.000
 YAM  C15   C21  C22   121.28  3.000
 YAM  N25   C21  C22   109.27  3.000
 YAM  F27   C8   F28   106.68  3.000
 YAM  F27   C8   F29   106.61  3.000
 YAM  F28   C8   F29   105.54  3.000
 YAM  F29   C8   C6    112.52  3.000
 YAM  F27   C8   C6    112.43  3.000
 YAM  F28   C8   C6    112.55  3.000
 YAM  H18   C18  C17   121.26  3.000
 YAM  H18   C18  C19   120.48  3.000
 YAM  C17   C18  C19   118.25  3.000
 YAM  H16   C16  C15   119.00  3.000
 YAM  H16   C16  C11   119.26  3.000
 YAM  C15   C16  C11   121.74  3.000
 YAM  H19   C19  N1    116.65  3.000
 YAM  H19   C19  C18   120.73  3.000
 YAM  N1    C19  C18   122.62  3.000
 YAM  N30   S31  O32   107.83  3.000
 YAM  O32   S31  O33   119.75  3.000
 YAM  N30   S31  O33   106.27  3.000
 YAM  O32   S31  C34   107.55  3.000
 YAM  N30   S31  C34   106.47  3.000
 YAM  O33   S31  C34   108.27  3.000
 YAM  S31   N30  C20   115.86  3.000
 YAM  S31   N30  C35   117.91  3.000
 YAM  C20   N30  C35   116.60  3.000
 YAM  H17   C17  C18   120.30  3.000
 YAM  H17   C17  C13   119.81  3.000
 YAM  C18   C17  C13   119.89  3.000
 YAM  C19   N1   C20   118.68  3.000
 YAM  HN10  N10  C5    119.90  3.000
 YAM  HN10  N10  C12   115.43  3.000
 YAM  C5    N10  C12   124.67  3.000
 YAM  N4    C5   N10   117.73  3.000
 YAM  N4    C5   C6    119.66  3.000
 YAM  N10   C5   C6    122.61  3.000
 YAM  C3    N4   C5    118.85  3.000
 YAM  N9    C3   N4    114.36  3.000
 YAM  N9    C3   N2    119.54  3.000
 YAM  N4    C3   N2    126.10  3.000
 YAM  HN9   N9   C11   115.75  3.000
 YAM  HN9   N9   C3    113.07  3.000
 YAM  C11   N9   C3    129.38  3.000
 YAM  C14   C11  N9    123.05  3.000
 YAM  C14   C11  C16   119.59  3.000
 YAM  N9    C11  C16   117.28  3.000
 YAM  H14   C14  C22   120.49  3.000
 YAM  H14   C14  C11   120.85  3.000
 YAM  C22   C14  C11   118.66  3.000
 YAM  C23   C22  C14   130.97  3.000
 YAM  C23   C22  C21   108.04  3.000
 YAM  C14   C22  C21   120.98  3.000
 YAM  H23A  C23  H23   106.88  3.000
 YAM  H23A  C23  C24   109.89  3.000
 YAM  H23   C23  C24   109.99  3.000
 YAM  H23A  C23  C22   113.38  3.000
 YAM  H23   C23  C22   113.24  3.000
 YAM  C24   C23  C22   103.44  3.000
 YAM  H15   C15  C16   120.38  3.000
 YAM  H15   C15  C21   121.90  3.000
 YAM  C16   C15  C21   117.72  3.000
 YAM  HN25  N25  C24   123.18  3.000
 YAM  HN25  N25  C21   124.49  3.000
 YAM  C24   N25  C21   112.33  3.000
 YAM  O26   C24  N25   125.83  3.000
 YAM  O26   C24  C23   127.26  3.000
 YAM  N25   C24  C23   106.91  3.000
 YAM  H12A  C12  H12   107.51  3.000
 YAM  H12A  C12  N10   108.42  3.000
 YAM  H12   C12  N10   109.34  3.000
 YAM  H12A  C12  C13   111.15  3.000
 YAM  H12   C12  C13   109.15  3.000
 YAM  N10   C12  C13   111.20  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
 YAM  CONST_01  C5    N4   C3   N2      0.00   0.0  0
 YAM  CONST_02  C5    C6   C7   N2      0.00   0.0  0
 YAM  CONST_03  N4    C3   N2   C7      0.00   0.0  0
 YAM  CONST_04  N4    C5   C6   C7      0.00   0.0  0
 YAM  CONST_05  C3    N2   C7   C6      0.00   0.0  0
 YAM  CONST_06  C3    N4   C5   C6      0.00   0.0  0
 YAM  CONST_07  C19   C18  C17  C13     0.00   0.0  0
 YAM  CONST_08  C19   N1   C20  C13     0.00   0.0  0
 YAM  CONST_09  C18   C17  C13  C20     0.00   0.0  0
 YAM  CONST_10  C18   C19  N1   C20     0.00   0.0  0
 YAM  CONST_11  C11   C14  C22  C21     0.00   0.0  0
 YAM  CONST_12  C11   C16  C15  C21     0.00   0.0  0
 YAM  CONST_13  C22   C21  C15  C16     0.00   0.0  0
 YAM  CONST_14  C22   C14  C11  C16     0.00   0.0  0
 YAM  CONST_15  N1    C20  C13  C17     0.00   0.0  0
 YAM  CONST_16  N1    C19  C18  C17     0.00   0.0  0
 YAM  CONST_17  C15   C16  C11  C14     0.00   0.0  0
 YAM  CONST_18  C15   C21  C22  C14     0.00   0.0  0
 YAM  CONST_19  C23   C24  N25  C21     0.00   0.0  0
 YAM  CONST_20  C8    C6   C7   N2    180.00   0.0  0
 YAM  CONST_21  N9    C3   N2   C7    180.00   0.0  0
 YAM  CONST_22  N10   C5   C6   C7    180.00   0.0  0
 YAM  CONST_23  N4    C5   C6   C8    180.00   0.0  0
 YAM  CONST_24  C12   C13  C17  C18   180.00   0.0  0
 YAM  CONST_25  N30   C20  N1   C19   180.00   0.0  0
 YAM  CONST_26  C17   C13  C20  N30   180.00   0.0  0
 YAM  CONST_27  C12   C13  C20  N1    180.00   0.0  0
 YAM  CONST_28  C3    N4   C5   N10   180.00   0.0  0
 YAM  CONST_29  N9    C3   N4   C5    180.00   0.0  0
 YAM  CONST_30  C15   C16  C11  N9    180.00   0.0  0
 YAM  CONST_31  C22   C14  C11  N9    180.00   0.0  0
 YAM  CONST_32  O26   C24  N25  C21   180.00   0.0  0
 YAM  CONST_33  H18   C18  C17  C13   180.00   0.0  0
 YAM  CONST_34  H17   C17  C13  C20   180.00   0.0  0
 YAM  CONST_35  H19   C19  N1   C20   180.00   0.0  0
 YAM  CONST_36  H14   C14  C22  C21   180.00   0.0  0
 YAM  CONST_37  H16   C16  C15  C21   180.00   0.0  0
 YAM  CONST_38  H7    C7   C6   C5    180.00   0.0  0
 YAM  CONST_39  H15   C15  C16  C11   180.00   0.0  0
 YAM  CONST_40  HN25  N25  C24  C23   180.00   0.0  0
 YAM  CONST_43  C12   N10  C5   C6    180.00   0.0  0
 YAM  CONST_46  N4    C5   N10  C12     0.00   0.0  0
 YAM  CONST_47  HN10  N10  C5   C6      0.00   0.0  0
 YAM  Var_01    C11   N9   C3   N2     -4.79  30.0  1
 YAM  Var_02    C3    N9   C11  C16  -145.71  30.0  2
 YAM  Var_03    H23   C23  C22  C21   119.00  30.0  1
 YAM  Var_04    F28   C8   C6   C7   -122.06  30.0  2
 YAM  Var_05    C5    N10  C12  C13  -117.67  30.0  3
 YAM  Var_06    N10   C12  C13  C20    66.59  30.0  2
 YAM  Var_07    C20   N30  S31  C34    76.95  30.0  1
 YAM  Var_08    H35   C35  N30  C20    49.96  30.0  3
 YAM  Var_09    H34   C34  S31  O33    55.98  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
 YAM  plan-1  C13   0.020
 YAM  plan-1  C20   0.020
 YAM  plan-1  C18   0.020
 YAM  plan-1  C19   0.020
 YAM  plan-1  N30   0.020
 YAM  plan-1  C17   0.020
 YAM  plan-1  N1    0.020
 YAM  plan-1  H18   0.020
 YAM  plan-1  H19   0.020
 YAM  plan-1  H17   0.020
 YAM  plan-1  C12   0.020
 YAM  plan-2  N2    0.020
 YAM  plan-2  C7    0.020
 YAM  plan-2  C6    0.020
 YAM  plan-2  C8    0.020
 YAM  plan-2  N10   0.020
 YAM  plan-2  C5    0.020
 YAM  plan-2  N4    0.020
 YAM  plan-2  C3    0.020
 YAM  plan-2  N9    0.020
 YAM  plan-2  H7    0.020
 YAM  plan-3  C35   0.020
 YAM  plan-3  C20   0.020
 YAM  plan-3  S31   0.020
 YAM  plan-3  N30   0.020
 YAM  plan-4  N10   0.020
 YAM  plan-4  C5    0.020
 YAM  plan-4  HN10  0.020
 YAM  plan-4  C12   0.020
 YAM  plan-5  C21   0.020
 YAM  plan-5  C16   0.020
 YAM  plan-5  N9    0.020
 YAM  plan-5  C11   0.020
 YAM  plan-5  C14   0.020
 YAM  plan-5  C22   0.020
 YAM  plan-5  C23   0.020
 YAM  plan-5  C15   0.020
 YAM  plan-5  N25   0.020
 YAM  plan-5  C24   0.020
 YAM  plan-5  O26   0.020
 YAM  plan-5  H16   0.020
 YAM  plan-5  H14   0.020
 YAM  plan-5  H15   0.020
 YAM  plan-5  HN25  0.020

