# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:26:44 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-[(3R,4R)-3-[({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-(trifluoromethyl)pyrrolidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1C[C@H](COc2nc(Nc3cnn(C)c3)nc4[nH]ccc24)[C@H](C1)C(F)(F)F
#
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
 63A  63A  1-[(3R,4R)-3-[({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-(trifluoromethyl)pyrrolidin-1-yl]propan-1-one  ligand  53  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_63A
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
 63A  N3   N  NT    0  -0.463   2.9708  -0.8633  -1.1068
 63A  C4   C  CH2   0  -0.294   3.2307   0.3218  -0.3075
 63A  C5   C  CH1   0  -0.520   2.8190  -0.0809   1.1113
 63A  C6   C  CT    0   1.043   3.9921  -0.5329   1.9485
 63A  C10  C  C     0   0.566   3.3199  -1.0209  -2.3978
 63A  C20  C  CR56  0   0.501  -4.0013  -1.8471  -0.2810
 63A  C21  C  CR56  0  -0.135  -2.6960  -2.2892  -0.0137
 63A  C22  C  CR15  0  -0.432  -2.7011  -3.7167  -0.0787
 63A  C26  C  CR5   0   0.077  -3.0072   2.7215   0.0994
 63A  C1   C  CH1   0  -0.355   1.7769  -1.1908   0.8896
 63A  C2   C  CH2   0  -0.265   2.2482  -1.8964  -0.3822
 63A  F7   F  F     0  -0.306   3.6084  -0.9201   3.1722
 63A  F8   F  F     0  -0.307   4.6576  -1.5634   1.4056
 63A  F9   F  F     0  -0.309   4.8856   0.4524   2.1174
 63A  C11  C  CH2   0  -0.587   3.9962   0.1624  -3.0557
 63A  C12  C  CH3   0  -0.653   4.3534  -0.0827  -4.5107
 63A  O13  O  O     0  -0.505   3.0881  -2.0636  -2.9966
 63A  C14  C  CH2   0  -0.149   0.4129  -0.5393   0.7208
 63A  O15  O  O2    0  -0.461  -0.5297  -1.5811   0.4970
 63A  C16  C  CR6   0   0.535  -1.7874  -1.2585   0.2313
 63A  N17  N  N     0  -0.531  -2.1525   0.0035   0.2062
 63A  C18  C  CR6   0   0.578  -3.4358   0.2893  -0.0666
 63A  N19  N  N     0  -0.515  -4.4057  -0.5808  -0.3158
 63A  C23  C  CR15  0  -0.024  -3.9803  -4.0733  -0.3760
 63A  N24  N  NR15  0  -0.669  -4.7613  -2.9431  -0.4975
 63A  N25  N  NH1   0  -0.758  -3.7983   1.5980  -0.0923
 63A  C27  C  CR15  0  -0.034  -3.4386   4.0172  -0.1102
 63A  N28  N  NR5   0  -0.250  -2.4031   4.8227   0.1979
 63A  N29  N  N     0  -0.285  -1.3379   4.1479   0.5870
 63A  C30  C  CR15  0  -0.083  -1.6767   2.8678   0.5381
 63A  C31  C  CH3   0  -0.505  -2.3787   6.2644   0.1504
 63A  H1   H  HCH2  0   0.278   4.2731   0.6372  -0.3762
 63A  H2   H  HCH2  0   0.272   2.6263   1.1697  -0.6402
 63A  H3   H  HCH1  0   0.324   2.3856   0.7751   1.6370
 63A  H4   H  HCR5  0   0.253  -1.8719  -4.3880   0.0727
 63A  H5   H  HCH1  0   0.298   1.7241  -1.8877   1.7283
 63A  H6   H  HCH2  0   0.260   1.4149  -2.2778  -0.9720
 63A  H7   H  HCH2  0   0.257   2.8934  -2.7469  -0.1530
 63A  H8   H  HCH2  0   0.266   3.3370   1.0327  -2.9716
 63A  H9   H  HCH2  0   0.266   4.8931   0.4251  -2.4871
 63A  H10  H  HCH3  0   0.232   4.8124   0.8097  -4.9346
 63A  H11  H  HCH3  0   0.227   5.0618  -0.9030  -4.6200
 63A  H12  H  HCH3  0   0.228   3.4730  -0.3180  -5.1070
 63A  H13  H  HCH2  0   0.255   0.1479   0.0169   1.6239
 63A  H14  H  HCH2  0   0.238   0.4076   0.1595  -0.1213
 63A  H15  H  HCR5  0   0.285  -4.4120  -5.0502  -0.5167
 63A  H16  H  HNR5  0   0.411  -5.7456  -2.9359  -0.7102
 63A  H17  H  HNH1  0   0.404  -4.7660   1.7621  -0.3192
 63A  H18  H  HCR5  0   0.294  -4.3882   4.4008  -0.4472
 63A  H19  H  HCR5  0   0.272  -0.9719   2.1037   0.8126
 63A  H20  H  HCH3  0   0.259  -2.2302   6.6774   1.1468
 63A  H21  H  HCH3  0   0.260  -1.5778   6.6072  -0.5015
 63A  H22  H  HCH3  0   0.258  -3.3269   6.6214  -0.2405

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
 63A  C23  N24  aromatic  1.379  0.020  1.379
 63A  C23  C22  aromatic  1.361  0.020  1.361
 63A  N24  C20  aromatic  1.351  0.020  1.351
 63A  C22  C21  aromatic  1.429  0.020  1.429
 63A  C20  C21  aromatic  1.404  0.020  1.404
 63A  C20  N19  aromatic  1.330  0.020  1.330
 63A  C21  C16  aromatic  1.396  0.020  1.396
 63A  N19  C18  aromatic  1.327  0.020  1.327
 63A  C16  O15  single    1.325  0.020  1.325
 63A  C16  N17  aromatic  1.314  0.020  1.314
 63A  C18  N17  aromatic  1.343  0.020  1.343
 63A  C18  N25  single    1.358  0.020  1.358
 63A  O15  C14  single    1.423  0.020  1.423
 63A  N25  C26  single    1.387  0.020  1.387
 63A  F7   C6   single    1.340  0.020  1.340
 63A  C26  C27  aromatic  1.382  0.020  1.382
 63A  C26  C30  aromatic  1.409  0.020  1.409
 63A  C27  N28  aromatic  1.348  0.020  1.348
 63A  C14  C1   single    1.521  0.020  1.521
 63A  C30  N29  aromatic  1.325  0.020  1.325
 63A  C1   C5   single    1.539  0.020  1.539
 63A  C1   C2   single    1.529  0.020  1.529
 63A  C6   C5   single    1.510  0.020  1.510
 63A  C6   F9   single    1.341  0.020  1.341
 63A  C6   F8   single    1.341  0.020  1.341
 63A  N28  N29  aromatic  1.320  0.020  1.320
 63A  N28  C31  single    1.443  0.020  1.443
 63A  C5   C4   single    1.531  0.020  1.531
 63A  C2   N3   single    1.454  0.020  1.454
 63A  C4   N3   single    1.453  0.020  1.453
 63A  N3   C10  single    1.347  0.020  1.347
 63A  C10  O13  double    1.225  0.020  1.225
 63A  C10  C11  single    1.513  0.020  1.513
 63A  C11  C12  single    1.518  0.020  1.518
 63A  C4   H1   single    0.970  0.020  1.090
 63A  C4   H2   single    0.970  0.020  1.090
 63A  C5   H3   single    0.970  0.020  1.090
 63A  C22  H4   single    0.930  0.020  1.080
 63A  C1   H5   single    0.970  0.020  1.090
 63A  C2   H6   single    0.970  0.020  1.090
 63A  C2   H7   single    0.970  0.020  1.090
 63A  C11  H8   single    0.970  0.020  1.090
 63A  C11  H9   single    0.970  0.020  1.090
 63A  C12  H10  single    0.970  0.020  1.090
 63A  C12  H11  single    0.970  0.020  1.090
 63A  C12  H12  single    0.970  0.020  1.090
 63A  C14  H13  single    0.970  0.020  1.090
 63A  C14  H14  single    0.970  0.020  1.090
 63A  C23  H15  single    0.930  0.020  1.080
 63A  N24  H16  single    0.860  0.020  1.020
 63A  N25  H17  single    0.860  0.020  1.020
 63A  C27  H18  single    0.930  0.020  1.080
 63A  C30  H19  single    0.930  0.020  1.080
 63A  C31  H20  single    0.970  0.020  1.090
 63A  C31  H21  single    0.970  0.020  1.090
 63A  C31  H22  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
 63A  C2   N3   C10  121.56  3.000
 63A  C10  N3   C4   125.20  3.000
 63A  C2   N3   C4   113.22  3.000
 63A  H2   C4   H1   106.55  3.000
 63A  H2   C4   C5   109.71  3.000
 63A  H1   C4   C5   113.03  3.000
 63A  H2   C4   N3   111.49  3.000
 63A  H1   C4   N3   111.84  3.000
 63A  C5   C4   N3   104.31  3.000
 63A  H3   C5   C1   111.43  3.000
 63A  H3   C5   C6   105.99  3.000
 63A  C1   C5   C6   112.95  3.000
 63A  H3   C5   C4   110.25  3.000
 63A  C6   C5   C4   112.55  3.000
 63A  C1   C5   C4   103.79  3.000
 63A  F9   C6   F8   106.55  3.000
 63A  F8   C6   F7   106.85  3.000
 63A  F9   C6   F7   106.75  3.000
 63A  F8   C6   C5   113.01  3.000
 63A  F9   C6   C5   111.56  3.000
 63A  F7   C6   C5   111.74  3.000
 63A  O13  C10  C11  122.53  3.000
 63A  C11  C10  N3   116.17  3.000
 63A  O13  C10  N3   121.29  3.000
 63A  N24  C20  N19  126.67  3.000
 63A  N19  C20  C21  125.99  3.000
 63A  N24  C20  C21  107.35  3.000
 63A  C16  C21  C22  138.42  3.000
 63A  C16  C21  C20  113.97  3.000
 63A  C22  C21  C20  107.61  3.000
 63A  H4   C22  C23  126.21  3.000
 63A  H4   C22  C21  127.82  3.000
 63A  C23  C22  C21  105.97  3.000
 63A  C30  C26  C27  104.17  3.000
 63A  C30  C26  N25  131.74  3.000
 63A  C27  C26  N25  124.09  3.000
 63A  H5   C1   C14  108.38  3.000
 63A  H5   C1   C2   111.06  3.000
 63A  C14  C1   C2   112.45  3.000
 63A  H5   C1   C5   112.49  3.000
 63A  C2   C1   C5   104.12  3.000
 63A  C14  C1   C5   108.32  3.000
 63A  H7   C2   H6   107.03  3.000
 63A  H7   C2   C1   111.53  3.000
 63A  H6   C2   C1   112.08  3.000
 63A  H7   C2   N3   111.37  3.000
 63A  H6   C2   N3   111.03  3.000
 63A  C1   C2   N3   103.88  3.000
 63A  H9   C11  H8   105.23  3.000
 63A  H9   C11  C12  110.12  3.000
 63A  H8   C11  C12  110.10  3.000
 63A  H9   C11  C10  109.16  3.000
 63A  H8   C11  C10  108.60  3.000
 63A  C12  C11  C10  113.30  3.000
 63A  H12  C12  H11  107.94  3.000
 63A  H12  C12  H10  107.73  3.000
 63A  H11  C12  H10  107.69  3.000
 63A  H12  C12  C11  111.68  3.000
 63A  H11  C12  C11  111.77  3.000
 63A  H10  C12  C11  109.87  3.000
 63A  H14  C14  H13  108.04  3.000
 63A  H14  C14  O15  110.08  3.000
 63A  H13  C14  O15  110.00  3.000
 63A  H14  C14  C1   111.30  3.000
 63A  H13  C14  C1   110.10  3.000
 63A  O15  C14  C1   107.33  3.000
 63A  C16  O15  C14  118.82  3.000
 63A  N17  C16  O15  120.08  3.000
 63A  N17  C16  C21  121.67  3.000
 63A  O15  C16  C21  118.24  3.000
 63A  C18  N17  C16  118.28  3.000
 63A  N25  C18  N19  115.68  3.000
 63A  N25  C18  N17  117.64  3.000
 63A  N19  C18  N17  126.67  3.000
 63A  C18  N19  C20  113.41  3.000
 63A  H15  C23  N24  120.31  3.000
 63A  H15  C23  C22  130.01  3.000
 63A  N24  C23  C22  109.68  3.000
 63A  H16  N24  C23  125.31  3.000
 63A  H16  N24  C20  125.30  3.000
 63A  C23  N24  C20  109.39  3.000
 63A  H17  N25  C18  114.68  3.000
 63A  H17  N25  C26  116.55  3.000
 63A  C18  N25  C26  128.72  3.000
 63A  H18  C27  N28  122.38  3.000
 63A  H18  C27  C26  131.00  3.000
 63A  N28  C27  C26  106.61  3.000
 63A  C31  N28  N29  120.47  3.000
 63A  C31  N28  C27  127.07  3.000
 63A  N29  N28  C27  112.46  3.000
 63A  C30  N29  N28  106.07  3.000
 63A  H19  C30  N29  120.64  3.000
 63A  H19  C30  C26  128.67  3.000
 63A  N29  C30  C26  110.69  3.000
 63A  H22  C31  H21  108.87  3.000
 63A  H22  C31  H20  108.90  3.000
 63A  H21  C31  H20  109.17  3.000
 63A  H22  C31  N28  109.00  3.000
 63A  H21  C31  N28  110.30  3.000
 63A  H20  C31  N28  110.56  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
 63A  CONST_01  C22  C23  N24  C20     0.00   0.0  0
 63A  CONST_02  C23  C22  C21  C20     0.00   0.0  0
 63A  CONST_03  N17  C16  C21  C20     0.00   0.0  0
 63A  CONST_04  N17  C18  N19  C20     0.00   0.0  0
 63A  CONST_05  N24  C23  C22  C21     0.00   0.0  0
 63A  CONST_06  C23  N24  C20  C21     0.00   0.0  0
 63A  CONST_07  C18  N19  C20  C21     0.00   0.0  0
 63A  CONST_08  C18  N17  C16  C21     0.00   0.0  0
 63A  CONST_09  N24  C20  C21  C22     0.00   0.0  0
 63A  CONST_10  N19  C20  C21  C22   180.00   0.0  0
 63A  CONST_11  N17  C16  C21  C22   180.00   0.0  0
 63A  CONST_12  N29  N28  C27  C26     0.00   0.0  0
 63A  CONST_13  N28  N29  C30  C26     0.00   0.0  0
 63A  CONST_14  C23  C22  C21  C16   180.00   0.0  0
 63A  CONST_15  N24  C20  C21  C16   180.00   0.0  0
 63A  CONST_16  N19  C20  C21  C16     0.00   0.0  0
 63A  CONST_17  N19  C18  N17  C16     0.00   0.0  0
 63A  CONST_18  N24  C20  N19  C18   180.00   0.0  0
 63A  CONST_19  C23  N24  C20  N19   180.00   0.0  0
 63A  CONST_20  N29  C30  C26  C27     0.00   0.0  0
 63A  CONST_21  C30  N29  N28  C27     0.00   0.0  0
 63A  CONST_22  C30  C26  C27  N28     0.00   0.0  0
 63A  CONST_23  O15  C16  C21  C20   180.00   0.0  0
 63A  CONST_24  N25  C18  N19  C20   180.00   0.0  0
 63A  CONST_25  O15  C16  C21  C22     0.00   0.0  0
 63A  CONST_26  C31  N28  C27  C26   180.00   0.0  0
 63A  CONST_27  C18  N17  C16  O15   180.00   0.0  0
 63A  CONST_28  N25  C18  N17  C16   180.00   0.0  0
 63A  CONST_29  N28  C27  C26  N25   180.00   0.0  0
 63A  CONST_30  N29  C30  C26  N25   180.00   0.0  0
 63A  CONST_31  C31  N28  N29  C30   180.00   0.0  0
 63A  CONST_32  H15  C23  N24  C20   180.00   0.0  0
 63A  CONST_33  H4   C22  C21  C20   180.00   0.0  0
 63A  CONST_34  H16  N24  C20  C21   180.00   0.0  0
 63A  CONST_35  H19  C30  C26  C27   180.00   0.0  0
 63A  CONST_36  H18  C27  N28  N29   180.00   0.0  0
 63A  CONST_37  O13  C10  N3   C4    180.00   0.0  0
 63A  CONST_38  C11  C10  N3   C4      0.00   0.0  0
 63A  CONST_39  O13  C10  N3   C2      0.00   0.0  0
 63A  CONST_40  C11  C10  N3   C2    180.00   0.0  0
 63A  Var_01    C1   C2   N3   C4     11.75  30.0  1
 63A  Var_02    C2   N3   C4   C5      8.97  30.0  1
 63A  Var_03    N19  C18  N25  C26  -178.52  30.0  3
 63A  Var_04    C27  C26  N25  C18   171.62  30.0  2
 63A  Var_05    N17  C16  O15  C14    -1.46  30.0  1
 63A  Var_06    H20  C31  N28  C27   116.13  30.0  2
 63A  Var_07    C12  C11  C10  N3   -179.65  30.0  3
 63A  Var_08    H13  C14  O15  C16    64.60  30.0  3
 63A  Var_09    H10  C12  C11  C10   178.58  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
 63A  chir_01  C5  C1   C6  C4  negativ
 63A  chir_02  C1  C14  C5  C2  positiv

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
 63A  plan-1  C26  0.020
 63A  plan-1  N25  0.020
 63A  plan-1  C27  0.020
 63A  plan-1  N28  0.020
 63A  plan-1  N29  0.020
 63A  plan-1  C30  0.020
 63A  plan-1  C31  0.020
 63A  plan-1  H18  0.020
 63A  plan-1  H19  0.020
 63A  plan-2  C20  0.020
 63A  plan-2  C21  0.020
 63A  plan-2  C22  0.020
 63A  plan-2  O15  0.020
 63A  plan-2  C16  0.020
 63A  plan-2  N17  0.020
 63A  plan-2  C18  0.020
 63A  plan-2  N19  0.020
 63A  plan-2  C23  0.020
 63A  plan-2  N24  0.020
 63A  plan-2  N25  0.020
 63A  plan-2  H4   0.020
 63A  plan-2  H15  0.020
 63A  plan-2  H16  0.020
 63A  plan-3  N3   0.020
 63A  plan-3  C4   0.020
 63A  plan-3  C10  0.020
 63A  plan-3  C2   0.020
 63A  plan-3  C11  0.020
 63A  plan-3  O13  0.020

