# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:04:22 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-{2,4-difluoro-3-[({6-[(2-hydroxyethyl)amino]pyrimidin-4-yl}carbamoyl)amino]phenyl}propane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[S](=O)(=O)Nc1ccc(F)c(NC(=O)Nc2cc(NCCO)ncn2)c1F
#
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
 RI9  RI9  N-{2,4-difluoro-3-[({6-[(2-hydroxyethyl)amino]pyrimidin-4-yl}carbamoyl)amino]phenyl}propane-1-sulfonamide  ligand  49  29  .  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_RI9
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
 RI9  O1    O  O     0  -0.460   0.1374   0.0584  -0.8626
 RI9  C2    C  C     0   0.731  -0.5343  -0.7849  -0.3139
 RI9  N3    N  NH1   0  -0.769  -1.8964  -0.7304  -0.1213
 RI9  C4    C  CR6   0   0.559  -2.7894   0.2435  -0.5218
 RI9  N5    N  N     0  -0.450  -2.3654   1.2757  -1.2455
 RI9  C6    C  CR16  0   0.055  -3.3015   2.1500  -1.5834
 RI9  N7    N  N     0  -0.472  -4.5822   2.1268  -1.2904
 RI9  C8    C  CR6   0   0.541  -5.0100   1.0836  -0.5539
 RI9  C9    C  CR16  0  -0.521  -4.1176   0.0867  -0.1468
 RI9  N10   N  NH1   0  -0.650  -6.3132   1.0742  -0.2347
 RI9  N11   N  NH1   0  -0.771   0.0109  -1.9307   0.2142
 RI9  C12   C  CR6   0  -0.010   1.3851  -2.1559   0.1205
 RI9  C13   C  CR6   0   0.572   2.2942  -1.3116   0.7411
 RI9  C14   C  CR6   0   0.073   3.6678  -1.4698   0.6189
 RI9  C15   C  CR16  0  -0.251   4.1442  -2.5510  -0.1119
 RI9  C16   C  CR16  0  -0.445   3.2694  -3.4319  -0.7254
 RI9  C17   C  CR6   0   0.548   1.9116  -3.2121  -0.6119
 RI9  F18   F  F     0  -0.294   1.0565  -4.0384  -1.2171
 RI9  F19   F  F     0  -0.288   1.8280  -0.3045   1.4769
 RI9  N20   N  NC1   0  -0.798   4.5590  -0.5560   1.2248
 RI9  S21   S  S     0   1.335   5.2008   0.6639   0.2830
 RI9  C22   C  CH2   0  -0.607   3.8338   1.7119  -0.2047
 RI9  O23   O  OS    0  -0.663   6.0787   1.4179   1.1624
 RI9  O24   O  OS    0  -0.655   5.7445   0.0319  -0.9074
 RI9  C25   C  CH2   0  -0.434   4.3027   2.8745  -1.0705
 RI9  C26   C  CH3   0  -0.663   3.1214   3.7460  -1.4752
 RI9  C27   C  CH2   0  -0.300  -6.9828  -0.0159   0.4330
 RI9  C28   C  CH2   0  -0.180  -8.3694   0.3986   0.8717
 RI9  O29   O  OH1   0  -0.672  -9.1207   0.7482  -0.2694
 RI9  HN3   H  HNH1  0   0.421  -2.3105  -1.4841   0.4062
 RI9  H6    H  HCR6  0   0.252  -2.9651   2.9931  -2.1796
 RI9  H9    H  HCR6  0   0.286  -4.4352  -0.7706   0.4300
 RI9  HN10  H  HNH1  0   0.388  -6.8859   1.7606  -0.7016
 RI9  HN11  H  HNH1  0   0.418  -0.5773  -2.6924   0.5184
 RI9  H15   H  HCR6  0   0.292   5.2105  -2.7050  -0.1946
 RI9  H16   H  HCR6  0   0.296   3.6387  -4.2746  -1.2933
 RI9  HN20  H  HNC1  0   0.423   4.3079  -0.2349   2.1543
 RI9  H22   H  HCH2  0   0.292   3.1189   1.0857  -0.7429
 RI9  H22A  H  HCH2  0   0.298   3.3663   2.0632   0.7163
 RI9  H25   H  HCH2  0   0.248   5.0312   3.4734  -0.5214
 RI9  H25A  H  HCH2  0   0.248   4.8031   2.4937  -1.9623
 RI9  H26   H  HCH3  0   0.243   3.4548   4.5795  -2.0926
 RI9  H26A  H  HCH3  0   0.228   2.3881   3.1781  -2.0490
 RI9  H26B  H  HCH3  0   0.230   2.6155   4.1590  -0.6017
 RI9  H27   H  HCH2  0   0.240  -7.0389  -0.9036  -0.2087
 RI9  H27A  H  HCH2  0   0.248  -6.4271  -0.3035   1.3282
 RI9  H28   H  HCH2  0   0.217  -8.8178  -0.4402   1.4165
 RI9  H28A  H  HCH2  0   0.212  -8.2871   1.2366   1.5736
 RI9  HO29  H  HOH1  0   0.461  -9.9384   1.1620   0.0206

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
 RI9  O1   C2    double    1.210  0.020  1.210
 RI9  C2   N11   single    1.374  0.020  1.374
 RI9  C2   N3    single    1.377  0.020  1.377
 RI9  N3   C4    single    1.381  0.020  1.381
 RI9  N3   HN3   single    0.860  0.020  1.020
 RI9  C4   N5    aromatic  1.330  0.020  1.330
 RI9  C4   C9    aromatic  1.389  0.020  1.389
 RI9  N5   C6    aromatic  1.325  0.020  1.325
 RI9  C6   N7    aromatic  1.314  0.020  1.314
 RI9  C6   H6    single    0.930  0.020  1.080
 RI9  C8   N7    aromatic  1.347  0.020  1.347
 RI9  C9   C8    aromatic  1.399  0.020  1.399
 RI9  C8   N10   single    1.342  0.020  1.342
 RI9  C9   H9    single    0.930  0.020  1.080
 RI9  C27  N10   single    1.443  0.020  1.443
 RI9  N10  HN10  single    0.860  0.020  1.020
 RI9  C12  N11   single    1.396  0.020  1.396
 RI9  N11  HN11  single    0.860  0.020  1.020
 RI9  C13  C12   aromatic  1.387  0.020  1.387
 RI9  C12  C17   aromatic  1.389  0.020  1.389
 RI9  F19  C13   single    1.331  0.020  1.331
 RI9  C14  C13   aromatic  1.388  0.020  1.388
 RI9  N20  C14   single    1.413  0.020  1.413
 RI9  C14  C15   aromatic  1.389  0.020  1.389
 RI9  C15  C16   aromatic  1.385  0.020  1.385
 RI9  C15  H15   single    0.930  0.020  1.080
 RI9  C16  C17   aromatic  1.380  0.020  1.380
 RI9  C16  H16   single    0.930  0.020  1.080
 RI9  C17  F18   single    1.334  0.020  1.334
 RI9  S21  N20   single    1.669  0.020  1.669
 RI9  N20  HN20  single    0.890  0.020  1.040
 RI9  O24  S21   double    1.453  0.020  1.453
 RI9  S21  C22   single    1.790  0.020  1.790
 RI9  S21  O23   double    1.454  0.020  1.454
 RI9  C25  C22   single    1.524  0.020  1.524
 RI9  C22  H22   single    0.970  0.020  1.090
 RI9  C22  H22A  single    0.970  0.020  1.090
 RI9  C25  C26   single    1.523  0.020  1.523
 RI9  C25  H25   single    0.970  0.020  1.090
 RI9  C25  H25A  single    0.970  0.020  1.090
 RI9  C26  H26   single    0.970  0.020  1.090
 RI9  C26  H26A  single    0.970  0.020  1.090
 RI9  C26  H26B  single    0.970  0.020  1.090
 RI9  C27  C28   single    1.512  0.020  1.512
 RI9  C27  H27   single    0.970  0.020  1.090
 RI9  C27  H27A  single    0.970  0.020  1.090
 RI9  C28  O29   single    1.410  0.020  1.410
 RI9  C28  H28   single    0.970  0.020  1.090
 RI9  C28  H28A  single    0.970  0.020  1.090
 RI9  O29  HO29  single    0.850  0.020  0.980

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
 RI9  N11   C2   N3    111.82  3.000
 RI9  N3    C2   O1    125.82  3.000
 RI9  N11   C2   O1    122.36  3.000
 RI9  HN3   N3   C4    114.40  3.000
 RI9  HN3   N3   C2    116.72  3.000
 RI9  C4    N3   C2    128.85  3.000
 RI9  C9    C4   N5    122.64  3.000
 RI9  C9    C4   N3    117.42  3.000
 RI9  N5    C4   N3    119.94  3.000
 RI9  C6    N5   C4    115.20  3.000
 RI9  H6    C6   N7    115.98  3.000
 RI9  H6    C6   N5    115.69  3.000
 RI9  N7    C6   N5    128.33  3.000
 RI9  C8    N7   C6    116.44  3.000
 RI9  N10   C8   C9    123.06  3.000
 RI9  N10   C8   N7    116.36  3.000
 RI9  C9    C8   N7    120.57  3.000
 RI9  H9    C9   C8    122.22  3.000
 RI9  H9    C9   C4    120.96  3.000
 RI9  C8    C9   C4    116.82  3.000
 RI9  HN10  N10  C27   117.70  3.000
 RI9  HN10  N10  C8    115.89  3.000
 RI9  C27   N10  C8    124.47  3.000
 RI9  HN11  N11  C12   118.19  3.000
 RI9  HN11  N11  C2    120.91  3.000
 RI9  C12   N11  C2    119.95  3.000
 RI9  C17   C12  C13   116.77  3.000
 RI9  C17   C12  N11   122.09  3.000
 RI9  C13   C12  N11   121.13  3.000
 RI9  F19   C13  C14   118.77  3.000
 RI9  C14   C13  C12   122.67  3.000
 RI9  F19   C13  C12   118.56  3.000
 RI9  N20   C14  C15   120.84  3.000
 RI9  C15   C14  C13   118.32  3.000
 RI9  N20   C14  C13   120.85  3.000
 RI9  H15   C15  C16   119.93  3.000
 RI9  H15   C15  C14   119.31  3.000
 RI9  C16   C15  C14   120.76  3.000
 RI9  H16   C16  C17   120.22  3.000
 RI9  H16   C16  C15   120.84  3.000
 RI9  C17   C16  C15   118.93  3.000
 RI9  F18   C17  C16   119.65  3.000
 RI9  F18   C17  C12   117.85  3.000
 RI9  C16   C17  C12   122.50  3.000
 RI9  HN20  N20  S21   112.37  3.000
 RI9  HN20  N20  C14   116.18  3.000
 RI9  S21   N20  C14   118.24  3.000
 RI9  O24   S21  O23   119.69  3.000
 RI9  O23   S21  C22   108.81  3.000
 RI9  O24   S21  C22   108.49  3.000
 RI9  O23   S21  N20   105.66  3.000
 RI9  C22   S21  N20   106.73  3.000
 RI9  O24   S21  N20   106.75  3.000
 RI9  H22A  C22  H22   108.67  3.000
 RI9  H22A  C22  C25   111.46  3.000
 RI9  H22   C22  C25   111.04  3.000
 RI9  H22A  C22  S21   106.60  3.000
 RI9  H22   C22  S21   107.37  3.000
 RI9  C25   C22  S21   111.50  3.000
 RI9  H25A  C25  H25   107.25  3.000
 RI9  H25A  C25  C26   109.77  3.000
 RI9  H25   C25  C26   109.73  3.000
 RI9  H25A  C25  C22   109.83  3.000
 RI9  H25   C25  C22   109.78  3.000
 RI9  C26   C25  C22   110.43  3.000
 RI9  H26B  C26  H26A  107.86  3.000
 RI9  H26B  C26  H26   107.82  3.000
 RI9  H26A  C26  H26   107.82  3.000
 RI9  H26B  C26  C25   111.33  3.000
 RI9  H26A  C26  C25   111.31  3.000
 RI9  H26   C26  C25   110.55  3.000
 RI9  H27A  C27  H27   107.00  3.000
 RI9  H27A  C27  C28   107.51  3.000
 RI9  H27   C27  C28   110.16  3.000
 RI9  H27A  C27  N10   110.00  3.000
 RI9  H27   C27  N10   111.38  3.000
 RI9  C28   C27  N10   110.65  3.000
 RI9  H28A  C28  H28   107.31  3.000
 RI9  H28A  C28  O29   111.63  3.000
 RI9  H28   C28  O29   111.96  3.000
 RI9  H28A  C28  C27   109.06  3.000
 RI9  H28   C28  C27   108.03  3.000
 RI9  O29   C28  C27   108.76  3.000
 RI9  HO29  O29  C28   108.41  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
 RI9  CONST_01  N7    C6   N5   C4     0.00   0.0  0
 RI9  CONST_02  N7    C8   C9   C4     0.00   0.0  0
 RI9  CONST_03  C8    C9   C4   N5     0.00   0.0  0
 RI9  CONST_04  C8    N7   C6   N5     0.00   0.0  0
 RI9  CONST_05  C9    C4   N5   C6     0.00   0.0  0
 RI9  CONST_06  C9    C8   N7   C6     0.00   0.0  0
 RI9  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 RI9  CONST_08  C15   C16  C17  C12    0.00   0.0  0
 RI9  CONST_09  C16   C17  C12  C13    0.00   0.0  0
 RI9  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 RI9  CONST_11  C17   C12  C13  C14    0.00   0.0  0
 RI9  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 RI9  CONST_13  C6    N5   C4   N3   180.00   0.0  0
 RI9  CONST_14  C8    C9   C4   N3   180.00   0.0  0
 RI9  CONST_15  N10   C8   C9   C4   180.00   0.0  0
 RI9  CONST_16  N10   C8   N7   C6   180.00   0.0  0
 RI9  CONST_17  C14   C13  C12  N11  180.00   0.0  0
 RI9  CONST_18  C16   C17  C12  N11  180.00   0.0  0
 RI9  CONST_19  N20   C14  C13  C12  180.00   0.0  0
 RI9  CONST_20  F18   C17  C12  C13  180.00   0.0  0
 RI9  CONST_21  F19   C13  C14  C15  180.00   0.0  0
 RI9  CONST_22  F18   C17  C16  C15  180.00   0.0  0
 RI9  CONST_23  N20   C14  C15  C16  180.00   0.0  0
 RI9  CONST_24  F19   C13  C12  C17  180.00   0.0  0
 RI9  CONST_25  H6    C6   N5   C4   180.00   0.0  0
 RI9  CONST_26  H9    C9   C4   N5   180.00   0.0  0
 RI9  CONST_27  H16   C16  C17  C12  180.00   0.0  0
 RI9  CONST_28  H15   C15  C14  C13  180.00   0.0  0
 RI9  CONST_31  N5    C4   N3   C2     0.00   0.0  0
 RI9  CONST_32  C9    C4   N3   C2   180.00   0.0  0
 RI9  CONST_33  C27   N10  C8   N7   180.00   0.0  0
 RI9  CONST_34  C27   N10  C8   C9     0.00   0.0  0
 RI9  CONST_37  HN3   N3   C4   N5   180.00   0.0  0
 RI9  CONST_38  HN10  N10  C8   N7     0.00   0.0  0
 RI9  CONST_41  C12   N11  C2   O1     0.00   0.0  0
 RI9  CONST_42  C4    N3   C2   O1     0.00   0.0  0
 RI9  CONST_43  C12   N11  C2   N3   180.00   0.0  0
 RI9  CONST_44  N11   C2   N3   C4   180.00   0.0  0
 RI9  Var_01    C28   C27  N10  C8   169.32  30.0  2
 RI9  Var_02    O24   S21  N20  C14  -50.83  30.0  1
 RI9  Var_03    O29   C28  C27  N10   61.13  30.0  3
 RI9  Var_04    C25   C22  S21  N20  179.74  30.0  3
 RI9  Var_05    C26   C25  C22  S21  179.79  30.0  1
 RI9  Var_06    H26   C26  C25  C22  179.87  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
 RI9  plan-1  N3    0.020
 RI9  plan-1  C4    0.020
 RI9  plan-1  N5    0.020
 RI9  plan-1  C6    0.020
 RI9  plan-1  N7    0.020
 RI9  plan-1  C8    0.020
 RI9  plan-1  C9    0.020
 RI9  plan-1  N10   0.020
 RI9  plan-1  H6    0.020
 RI9  plan-1  H9    0.020
 RI9  plan-2  C14   0.020
 RI9  plan-2  N20   0.020
 RI9  plan-2  S21   0.020
 RI9  plan-2  HN20  0.020
 RI9  plan-3  N11   0.020
 RI9  plan-3  C12   0.020
 RI9  plan-3  C13   0.020
 RI9  plan-3  C14   0.020
 RI9  plan-3  C15   0.020
 RI9  plan-3  C16   0.020
 RI9  plan-3  C17   0.020
 RI9  plan-3  F18   0.020
 RI9  plan-3  F19   0.020
 RI9  plan-3  N20   0.020
 RI9  plan-3  H15   0.020
 RI9  plan-3  H16   0.020
 RI9  plan-4  O1    0.020
 RI9  plan-4  C2    0.020
 RI9  plan-4  N3    0.020
 RI9  plan-4  C4    0.020
 RI9  plan-4  N11   0.020
 RI9  plan-4  C12   0.020
 RI9  plan-4  HN3   0.020
 RI9  plan-4  HN11  0.020
 RI9  plan-5  C8    0.020
 RI9  plan-5  N10   0.020
 RI9  plan-5  C27   0.020
 RI9  plan-5  HN10  0.020

