# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:25:39 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(1H-pyrrolo[2,3-b]pyridin-4-yl)pyrimidin-4-yl}cyclopropane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COCCN1c2cc(nc(n2)c3ccnc4[nH]ccc34)C5(CC5)[S](N)(=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
 XXV  XXV  1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(1H-pyrrolo[2,3-b]pyridin-4-yl)pyrimidin-4-yl}cyclopropane-1-sulfonamide  ligand  51  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XXV
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
 XXV  C10  C  CH1   0  -0.162  -130.7694  -173.7501  114.8754
 XXV  C15  C  CH2   0  -0.330  -131.3399  -173.4280  117.2498
 XXV  C17  C  CR6   0   0.346  -126.9632  -172.5902  115.6520
 XXV  C20  C  CR16  0  -0.080  -123.9876  -171.7991  113.4752
 XXV  C22  C  CR56  0   0.463  -125.2271  -173.2685  112.3452
 XXV  C24  C  CR15  0  -0.490  -127.1777  -174.3203  112.8772
 XXV  C03  C  CT    0  -0.317  -126.8163  -171.4563  119.0676
 XXV  C04  C  CH2   0  -0.453  -126.1569  -172.3661  120.0619
 XXV  C05  C  CH2   0  -0.460  -127.4610  -171.7246  120.3922
 XXV  C06  C  CR6   0   0.333  -127.3627  -172.0275  117.8016
 XXV  C07  C  CR16  0  -0.466  -128.6691  -172.4373  117.6910
 XXV  C08  C  CR6   0   0.609  -129.0624  -173.0006  116.4557
 XXV  C11  C  CH3   0  -0.659  -131.3577  -172.4841  114.2606
 XXV  C12  C  CH2   0  -0.183  -131.7561  -174.9081  114.8908
 XXV  C14  C  CH2   0  -0.184  -132.3163  -174.5823  117.0970
 XXV  C18  C  CR6   0   0.075  -126.0217  -172.6063  114.5103
 XXV  C19  C  CR16  0  -0.395  -124.8762  -171.8182  114.5491
 XXV  C23  C  CR56  0   0.016  -126.2206  -173.3760  113.3556
 XXV  C25  C  CR15  0   0.010  -126.7464  -174.7278  111.6475
 XXV  N01  N  NC2   0  -0.883  -125.9468  -169.0443  120.1804
 XXV  N09  N  NT    0  -0.509  -130.2972  -173.5062  116.2407
 XXV  N16  N  N     0  -0.498  -128.1886  -173.0417  115.4439
 XXV  N21  N  N     0  -0.418  -124.1438  -172.5137  112.3701
 XXV  N26  N  NR15  0  -0.665  -125.5812  -174.0958  111.3252
 XXV  N27  N  N     0  -0.460  -126.4954  -172.1070  116.7925
 XXV  O13  O  O2    0  -0.472  -132.8179  -174.6849  115.7874
 XXV  O28  O  OS    0  -0.656  -126.9175  -169.1168  117.8961
 XXV  O29  O  OS    0  -0.656  -124.6464  -170.0978  118.3640
 XXV  S02  S  S     0   1.378  -126.0245  -169.8672  118.7640
 XXV  H1   H  HCH1  0   0.292  -129.9173  -174.0684  114.2791
 XXV  H2   H  HCH2  0   0.269  -130.9084  -173.5056  118.2460
 XXV  H3   H  HCH2  0   0.247  -131.8668  -172.4686  117.1960
 XXV  H4   H  HCR6  0   0.255  -123.1072  -171.1685  113.5217
 XXV  H5   H  HCR5  0   0.264  -128.0673  -174.6629  113.3732
 XXV  H6   H  HCH2  0   0.287  -126.1394  -173.4194  119.8138
 XXV  H7   H  HCH2  0   0.285  -125.2667  -172.0139  120.5696
 XXV  H8   H  HCH2  0   0.279  -127.4720  -170.9410  121.1369
 XXV  H9   H  HCH2  0   0.282  -128.3540  -172.3350  120.3913
 XXV  H10  H  HCR6  0   0.283  -129.3543  -172.3080  118.5123
 XXV  H11  H  HCH3  0   0.238  -130.6218  -171.6798  114.2507
 XXV  H12  H  HCH3  0   0.236  -131.6582  -172.6726  113.2294
 XXV  H13  H  HCH3  0   0.231  -132.2355  -172.1361  114.8051
 XXV  H14  H  HCH2  0   0.243  -132.1825  -175.0335  113.8944
 XXV  H15  H  HCH2  0   0.220  -131.2253  -175.8352  115.1503
 XXV  H16  H  HCH2  0   0.248  -133.1605  -174.4279  117.7699
 XXV  H17  H  HCH2  0   0.210  -131.8167  -175.5168  117.3887
 XXV  H18  H  HCR6  0   0.256  -124.6698  -171.2040  115.4139
 XXV  H19  H  HCR5  0   0.288  -127.1930  -175.4325  110.9647
 XXV  H20  H  HNC2  0   0.419  -126.8366  -168.7781  120.5843
 XXV  H21  H  HNC2  0   0.422  -125.2917  -169.4035  120.8648
 XXV  H22  H  HNR5  0   0.410  -125.0563  -174.2281  110.4758

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
 XXV  N26  C25  aromatic  1.364  0.020  1.364
 XXV  N26  C22  aromatic  1.360  0.020  1.360
 XXV  C25  C24  aromatic  1.365  0.020  1.365
 XXV  N21  C22  aromatic  1.321  0.020  1.321
 XXV  N21  C20  aromatic  1.325  0.020  1.325
 XXV  C22  C23  aromatic  1.421  0.020  1.421
 XXV  C24  C23  aromatic  1.427  0.020  1.427
 XXV  C20  C19  aromatic  1.394  0.020  1.394
 XXV  C23  C18  aromatic  1.402  0.020  1.402
 XXV  C11  C10  single    1.525  0.020  1.525
 XXV  C19  C18  aromatic  1.391  0.020  1.391
 XXV  C18  C17  single    1.480  0.020  1.480
 XXV  C12  C10  single    1.521  0.020  1.521
 XXV  C12  O13  single    1.408  0.020  1.408
 XXV  C10  N09  single    1.465  0.020  1.465
 XXV  N16  C17  aromatic  1.322  0.020  1.322
 XXV  N16  C08  aromatic  1.338  0.020  1.338
 XXV  C17  N27  aromatic  1.324  0.020  1.324
 XXV  O13  C14  single    1.406  0.020  1.406
 XXV  N09  C08  single    1.351  0.020  1.351
 XXV  N09  C15  single    1.453  0.020  1.453
 XXV  C08  C07  aromatic  1.414  0.020  1.414
 XXV  N27  C06  aromatic  1.333  0.020  1.333
 XXV  C14  C15  single    1.520  0.020  1.520
 XXV  C07  C06  aromatic  1.374  0.020  1.374
 XXV  C06  C03  single    1.492  0.020  1.492
 XXV  O29  S02  double    1.453  0.020  1.453
 XXV  O28  S02  double    1.454  0.020  1.454
 XXV  S02  C03  single    1.801  0.020  1.801
 XXV  S02  N01  single    1.640  0.020  1.640
 XXV  C03  C04  single    1.500  0.020  1.500
 XXV  C03  C05  single    1.497  0.020  1.497
 XXV  C04  C05  single    1.490  0.020  1.490
 XXV  C10  H1   single    0.970  0.020  1.090
 XXV  C15  H2   single    0.970  0.020  1.090
 XXV  C15  H3   single    0.970  0.020  1.090
 XXV  C20  H4   single    0.930  0.020  1.080
 XXV  C24  H5   single    0.930  0.020  1.080
 XXV  C04  H6   single    0.970  0.020  1.090
 XXV  C04  H7   single    0.970  0.020  1.090
 XXV  C05  H8   single    0.970  0.020  1.090
 XXV  C05  H9   single    0.970  0.020  1.090
 XXV  C07  H10  single    0.930  0.020  1.080
 XXV  C11  H11  single    0.970  0.020  1.090
 XXV  C11  H12  single    0.970  0.020  1.090
 XXV  C11  H13  single    0.970  0.020  1.090
 XXV  C12  H14  single    0.970  0.020  1.090
 XXV  C12  H15  single    0.970  0.020  1.090
 XXV  C14  H16  single    0.970  0.020  1.090
 XXV  C14  H17  single    0.970  0.020  1.090
 XXV  C19  H18  single    0.930  0.020  1.080
 XXV  C25  H19  single    0.930  0.020  1.080
 XXV  N01  H20  single    0.890  0.020  1.040
 XXV  N01  H21  single    0.890  0.020  1.040
 XXV  N26  H22  single    0.860  0.020  1.020

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
 XXV  H1   C10  N09  107.89  3.000
 XXV  H1   C10  C12  106.91  3.000
 XXV  N09  C10  C12  109.04  3.000
 XXV  H1   C10  C11  108.91  3.000
 XXV  N09  C10  C11  111.21  3.000
 XXV  C12  C10  C11  112.68  3.000
 XXV  H3   C15  H2   107.33  3.000
 XXV  H3   C15  N09  110.98  3.000
 XXV  H2   C15  N09  110.32  3.000
 XXV  H3   C15  C14  110.56  3.000
 XXV  H2   C15  C14  107.02  3.000
 XXV  N09  C15  C14  110.51  3.000
 XXV  N27  C17  N16  125.99  3.000
 XXV  N27  C17  C18  116.34  3.000
 XXV  N16  C17  C18  117.67  3.000
 XXV  H4   C20  N21  116.44  3.000
 XXV  H4   C20  C19  119.52  3.000
 XXV  N21  C20  C19  124.04  3.000
 XXV  N26  C22  N21  125.13  3.000
 XXV  N21  C22  C23  127.10  3.000
 XXV  N26  C22  C23  107.77  3.000
 XXV  H5   C24  C25  125.60  3.000
 XXV  H5   C24  C23  127.69  3.000
 XXV  C25  C24  C23  106.71  3.000
 XXV  S02  C03  C06  110.83  3.000
 XXV  S02  C03  C05  119.77  3.000
 XXV  C06  C03  C05  121.61  3.000
 XXV  C05  C03  C04   59.63  3.000
 XXV  S02  C03  C04  116.97  3.000
 XXV  C06  C03  C04  119.40  3.000
 XXV  H7   C04  H6   114.23  3.000
 XXV  H7   C04  C05  118.37  3.000
 XXV  H6   C04  C05  118.94  3.000
 XXV  H7   C04  C03  118.32  3.000
 XXV  H6   C04  C03  116.45  3.000
 XXV  C05  C04  C03   60.09  3.000
 XXV  H9   C05  H8   113.65  3.000
 XXV  H9   C05  C04  118.64  3.000
 XXV  H8   C05  C04  118.26  3.000
 XXV  H9   C05  C03  117.12  3.000
 XXV  H8   C05  C03  118.94  3.000
 XXV  C04  C05  C03   60.29  3.000
 XXV  N27  C06  C07  122.69  3.000
 XXV  C07  C06  C03  122.05  3.000
 XXV  N27  C06  C03  115.26  3.000
 XXV  H10  C07  C08  122.48  3.000
 XXV  H10  C07  C06  120.51  3.000
 XXV  C08  C07  C06  117.00  3.000
 XXV  N16  C08  N09  117.71  3.000
 XXV  N09  C08  C07  122.84  3.000
 XXV  N16  C08  C07  119.44  3.000
 XXV  H13  C11  H12  107.79  3.000
 XXV  H13  C11  H11  108.21  3.000
 XXV  H12  C11  H11  107.75  3.000
 XXV  H13  C11  C10  111.98  3.000
 XXV  H12  C11  C10  110.12  3.000
 XXV  H11  C11  C10  110.83  3.000
 XXV  H15  C12  H14  107.90  3.000
 XXV  H15  C12  O13  110.34  3.000
 XXV  H14  C12  O13  107.77  3.000
 XXV  H15  C12  C10  109.34  3.000
 XXV  H14  C12  C10  109.37  3.000
 XXV  O13  C12  C10  112.02  3.000
 XXV  H17  C14  H16  107.97  3.000
 XXV  H17  C14  O13  110.33  3.000
 XXV  H16  C14  O13  108.00  3.000
 XXV  H17  C14  C15  109.09  3.000
 XXV  H16  C14  C15  109.13  3.000
 XXV  O13  C14  C15  112.23  3.000
 XXV  C23  C18  C19  116.80  3.000
 XXV  C19  C18  C17  119.75  3.000
 XXV  C23  C18  C17  123.45  3.000
 XXV  H18  C19  C18  120.11  3.000
 XXV  H18  C19  C20  119.14  3.000
 XXV  C18  C19  C20  120.74  3.000
 XXV  C18  C23  C24  137.27  3.000
 XXV  C18  C23  C22  116.42  3.000
 XXV  C24  C23  C22  106.29  3.000
 XXV  H19  C25  N26  120.47  3.000
 XXV  H19  C25  C24  129.39  3.000
 XXV  N26  C25  C24  110.14  3.000
 XXV  H21  N01  H20  113.06  3.000
 XXV  H21  N01  S02  115.86  3.000
 XXV  H20  N01  S02  115.77  3.000
 XXV  C08  N09  C15  121.67  3.000
 XXV  C15  N09  C10  115.14  3.000
 XXV  C08  N09  C10  120.33  3.000
 XXV  C08  N16  C17  118.41  3.000
 XXV  C22  N21  C20  114.88  3.000
 XXV  H22  N26  C25  125.70  3.000
 XXV  H22  N26  C22  125.21  3.000
 XXV  C25  N26  C22  109.09  3.000
 XXV  C06  N27  C17  116.35  3.000
 XXV  C14  O13  C12  109.62  3.000
 XXV  O29  S02  O28  120.00  3.000
 XXV  O28  S02  N01  106.60  3.000
 XXV  O29  S02  N01  105.80  3.000
 XXV  N01  S02  C03  108.54  3.000
 XXV  O28  S02  C03  106.62  3.000
 XXV  O29  S02  C03  108.86  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
 XXV  CONST_01  C22  C23  C18  C17   180.00   0.0  0
 XXV  CONST_02  C24  C23  C18  C17     0.00   0.0  0
 XXV  CONST_03  C20  C19  C18  C17   180.00   0.0  0
 XXV  CONST_04  C07  C08  N16  C17     0.00   0.0  0
 XXV  CONST_05  C07  C06  N27  C17     0.00   0.0  0
 XXV  CONST_06  N26  C22  N21  C20   180.00   0.0  0
 XXV  CONST_07  C23  C22  N21  C20     0.00   0.0  0
 XXV  CONST_08  C23  C18  C19  C20     0.00   0.0  0
 XXV  CONST_09  C24  C25  N26  C22     0.00   0.0  0
 XXV  CONST_10  C19  C20  N21  C22     0.00   0.0  0
 XXV  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 XXV  CONST_12  C19  C18  C23  C22     0.00   0.0  0
 XXV  CONST_13  N26  C22  C23  C24     0.00   0.0  0
 XXV  CONST_14  N21  C22  C23  C24   180.00   0.0  0
 XXV  CONST_15  C19  C18  C23  C24   180.00   0.0  0
 XXV  CONST_16  C18  C17  N27  C06   180.00   0.0  0
 XXV  CONST_17  N16  C17  N27  C06     0.00   0.0  0
 XXV  CONST_18  N16  C08  C07  C06     0.00   0.0  0
 XXV  CONST_19  C18  C17  N16  C08   180.00   0.0  0
 XXV  CONST_20  N27  C17  N16  C08     0.00   0.0  0
 XXV  CONST_21  N27  C06  C07  C08     0.00   0.0  0
 XXV  CONST_22  N26  C22  C23  C18   180.00   0.0  0
 XXV  CONST_23  N21  C22  C23  C18     0.00   0.0  0
 XXV  CONST_24  C25  C24  C23  C18   180.00   0.0  0
 XXV  CONST_25  N21  C20  C19  C18     0.00   0.0  0
 XXV  CONST_28  C25  N26  C22  C23     0.00   0.0  0
 XXV  CONST_29  N26  C25  C24  C23     0.00   0.0  0
 XXV  CONST_32  N21  C22  N26  C25   180.00   0.0  0
 XXV  CONST_33  N09  C08  N16  C17   180.00   0.0  0
 XXV  CONST_34  C03  C06  N27  C17   180.00   0.0  0
 XXV  CONST_35  C08  C07  C06  C03   180.00   0.0  0
 XXV  CONST_36  N09  C08  C07  C06   180.00   0.0  0
 XXV  CONST_37  H18  C19  C18  C17     0.00   0.0  0
 XXV  CONST_38  H19  C25  N26  C22   180.00   0.0  0
 XXV  CONST_39  H4   C20  N21  C22   180.00   0.0  0
 XXV  CONST_40  H5   C24  C23  C22   180.00   0.0  0
 XXV  CONST_41  H22  N26  C25  C24   180.00   0.0  0
 XXV  CONST_42  H10  C07  C06  C03     0.00   0.0  0
 XXV  Var_01    N16  C08  N09  C10   -16.05  30.0  2
 XXV  Var_02    C14  C15  N09  C10    47.20  30.0  1
 XXV  Var_03    N27  C06  C03  C04   -87.82  30.0  2
 XXV  Var_04    C06  C03  C05  C04   107.91  30.0  1
 XXV  Var_05    O13  C14  C15  N09   -52.54  30.0  1
 XXV  Var_06    H8   C05  C04  C03  -109.01  30.0  1
 XXV  Var_07    H16  C14  O13  C12  -179.01  30.0  1
 XXV  Var_08    H14  C12  O13  C14   177.16  30.0  1
 XXV  Var_09    O29  S02  C03  C04    55.55  30.0  1
 XXV  Var_10    H20  N01  S02  C03   -65.08  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XXV  chir_01  C10  C11  C12  N09  positiv
 XXV  chir_02  C03  S02  C04  C05  both

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
 XXV  plan-1  C17  0.020
 XXV  plan-1  C03  0.020
 XXV  plan-1  C06  0.020
 XXV  plan-1  C07  0.020
 XXV  plan-1  C08  0.020
 XXV  plan-1  C18  0.020
 XXV  plan-1  N09  0.020
 XXV  plan-1  N16  0.020
 XXV  plan-1  N27  0.020
 XXV  plan-1  H10  0.020
 XXV  plan-2  C17  0.020
 XXV  plan-2  C20  0.020
 XXV  plan-2  C22  0.020
 XXV  plan-2  C24  0.020
 XXV  plan-2  C18  0.020
 XXV  plan-2  C19  0.020
 XXV  plan-2  C23  0.020
 XXV  plan-2  C25  0.020
 XXV  plan-2  N21  0.020
 XXV  plan-2  N26  0.020
 XXV  plan-2  H4   0.020
 XXV  plan-2  H5   0.020
 XXV  plan-2  H18  0.020
 XXV  plan-2  H19  0.020
 XXV  plan-2  H22  0.020

