# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 20:49:39 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-4-fluoro-1H-indol-1-yl]-2-(6-methylpyridin-2-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2ccc3n(ccc3c2F)C(=O)Cc4cccc(C)n4)c5c(N)ncnc15
#
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
 27D  27D  1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-4-fluoro-1H-indol-1-yl]-2-(6-methylpyridin-2-yl)ethanone  ligand  50  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_27D
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
 27D  C01  C  CH3   0  -0.723  -7.8855   2.4055   0.7219
 27D  C02  C  CR6   0   0.229  -7.3200   1.2167   0.0060
 27D  C03  C  CR16  0  -0.339  -7.9104   0.7311  -1.1591
 27D  C04  C  CR16  0  -0.144  -7.3370  -0.3538  -1.7987
 27D  C05  C  CR16  0  -0.346  -6.1932  -0.9231  -1.2608
 27D  C06  C  CR6   0   0.275  -5.6722  -0.3779  -0.0960
 27D  C07  C  CH2   0  -0.721  -4.4351  -0.9521   0.5294
 27D  C08  C  C     0   0.590  -3.1994  -0.2012   0.0859
 27D  O    O  O     0  -0.408  -3.2358   0.7380  -0.6695
 27D  N01  N  NR5   0  -0.632  -1.9939  -0.6594   0.5992
 27D  C09  C  CR15  0   0.003  -1.8366  -1.7502   1.4527
 27D  C10  C  CR15  0  -0.369  -0.5319  -1.9379   1.7345
 27D  C11  C  CR56  0  -0.174   0.1933  -0.9213   1.0291
 27D  C12  C  CR56  0   0.388  -0.7325  -0.1295   0.3295
 27D  C13  C  CR16  0  -0.281  -0.3229   0.9546  -0.4424
 27D  C14  C  CR16  0  -0.297   1.0343   1.2145  -0.5067
 27D  C15  C  CR6   0  -0.247   1.9950   0.4440   0.1698
 27D  C16  C  CR5   0   0.008   3.4263   0.7574   0.0898
 27D  C17  C  CR15  0  -0.051   4.0132   1.9276   0.4845
 27D  N02  N  NR5   0  -0.505   5.3673   1.8778   0.2754
 27D  C18  C  CH3   0  -0.526   6.3194   2.9034   0.6337
 27D  C19  C  CR56  0   0.510   5.6758   0.6685  -0.2527
 27D  N03  N  N     0  -0.462   6.9005   0.2512  -0.5813
 27D  C20  C  CR16  0   0.035   6.9024  -0.9623  -1.0936
 27D  N04  N  N     0  -0.474   5.8601  -1.7579  -1.3272
 27D  C21  C  CR6   0   0.396   4.6378  -1.3265  -1.0039
 27D  N05  N  NH2   0  -0.822   3.5976  -2.1380  -1.2637
 27D  C22  C  CR56  0  -0.098   4.4920  -0.0632  -0.3985
 27D  C    C  CR6   0   0.489   1.5407  -0.6113   0.9378
 27D  F    F  F     0  -0.291   2.4132  -1.3561   1.6297
 27D  N    N  N     0  -0.432  -6.2250   0.6616   0.5193
 27D  H1   H  HCH3  0   0.255  -7.4003   3.3223   0.3794
 27D  H2   H  HCH3  0   0.245  -8.9533   2.5144   0.5383
 27D  H3   H  HCH3  0   0.249  -7.7196   2.3307   1.7954
 27D  H4   H  HCR6  0   0.263  -8.8059   1.1968  -1.5488
 27D  H5   H  HCR6  0   0.271  -7.7775  -0.7545  -2.7024
 27D  H6   H  HCR6  0   0.266  -5.7191  -1.7747  -1.7306
 27D  H7   H  HCH2  0   0.315  -4.5140  -0.8999   1.6184
 27D  H8   H  HCH2  0   0.313  -4.3291  -2.0078   0.2684
 27D  H9   H  HCR5  0   0.311  -2.6858  -2.3175   1.7932
 27D  H10  H  HCR5  0   0.269  -0.1266  -2.7112   2.3660
 27D  H11  H  HCR6  0   0.281  -1.0156   1.5755  -0.9853
 27D  H12  H  HCR6  0   0.263   1.3798   2.0431  -1.1109
 27D  H13  H  HCR5  0   0.295   3.5583   2.8031   0.9206
 27D  H14  H  HCH3  0   0.255   6.8108   2.6730   1.5785
 27D  H15  H  HCH3  0   0.260   7.0756   2.9981  -0.1417
 27D  H16  H  HCH3  0   0.262   5.7995   3.8525   0.7306
 27D  H17  H  HCR6  0   0.246   7.8703  -1.3674  -1.3706
 27D  H18  H  HNH2  0   0.396   3.7638  -2.9445  -1.8427
 27D  H19  H  HNH2  0   0.402   2.6628  -1.7688  -1.2804

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
 27D  C01  C02  single    1.498  0.020  1.498
 27D  C03  C02  aromatic  1.393  0.020  1.393
 27D  C03  C04  aromatic  1.384  0.020  1.384
 27D  C02  N    aromatic  1.331  0.020  1.331
 27D  C04  C05  aromatic  1.386  0.020  1.386
 27D  N    C06  aromatic  1.328  0.020  1.328
 27D  C05  C06  aromatic  1.388  0.020  1.388
 27D  C06  C07  single    1.500  0.020  1.500
 27D  C07  C08  single    1.512  0.020  1.512
 27D  C08  O    double    1.206  0.020  1.206
 27D  C08  N01  single    1.388  0.020  1.388
 27D  C09  N01  aromatic  1.394  0.020  1.394
 27D  C09  C10  aromatic  1.348  0.020  1.348
 27D  N01  C12  aromatic  1.394  0.020  1.394
 27D  C10  C11  aromatic  1.434  0.020  1.434
 27D  C12  C11  aromatic  1.405  0.020  1.405
 27D  C12  C13  aromatic  1.392  0.020  1.392
 27D  C11  C    aromatic  1.386  0.020  1.386
 27D  C13  C14  aromatic  1.383  0.020  1.383
 27D  C    F    single    1.340  0.020  1.340
 27D  C    C15  aromatic  1.382  0.020  1.382
 27D  C14  C15  aromatic  1.405  0.020  1.405
 27D  C15  C16  single    1.467  0.020  1.467
 27D  N05  C21  single    1.345  0.020  1.345
 27D  C16  C17  aromatic  1.367  0.020  1.367
 27D  C16  C22  aromatic  1.431  0.020  1.431
 27D  C17  N02  aromatic  1.371  0.020  1.371
 27D  C22  C21  aromatic  1.408  0.020  1.408
 27D  C22  C19  aromatic  1.399  0.020  1.399
 27D  C21  N04  aromatic  1.336  0.020  1.336
 27D  N02  C19  aromatic  1.355  0.020  1.355
 27D  N02  C18  single    1.445  0.020  1.445
 27D  C19  N03  aromatic  1.335  0.020  1.335
 27D  N04  C20  aromatic  1.332  0.020  1.332
 27D  N03  C20  aromatic  1.317  0.020  1.317
 27D  C01  H1   single    0.970  0.020  1.090
 27D  C01  H2   single    0.970  0.020  1.090
 27D  C01  H3   single    0.970  0.020  1.090
 27D  C03  H4   single    0.930  0.020  1.080
 27D  C04  H5   single    0.930  0.020  1.080
 27D  C05  H6   single    0.930  0.020  1.080
 27D  C07  H7   single    0.970  0.020  1.090
 27D  C07  H8   single    0.970  0.020  1.090
 27D  C09  H9   single    0.930  0.020  1.080
 27D  C10  H10  single    0.930  0.020  1.080
 27D  C13  H11  single    0.930  0.020  1.080
 27D  C14  H12  single    0.930  0.020  1.080
 27D  C17  H13  single    0.930  0.020  1.080
 27D  C18  H14  single    0.970  0.020  1.090
 27D  C18  H15  single    0.970  0.020  1.090
 27D  C18  H16  single    0.970  0.020  1.090
 27D  C20  H17  single    0.930  0.020  1.080
 27D  N05  H18  single    0.890  0.020  1.040
 27D  N05  H19  single    0.890  0.020  1.040

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
 27D  H3   C01  H2   108.82  3.000
 27D  H3   C01  H1   107.41  3.000
 27D  H2   C01  H1   107.38  3.000
 27D  H3   C01  C02  111.04  3.000
 27D  H2   C01  C02  111.64  3.000
 27D  H1   C01  C02  110.39  3.000
 27D  N    C02  C03  121.72  3.000
 27D  N    C02  C01  117.21  3.000
 27D  C03  C02  C01  121.07  3.000
 27D  H4   C03  C04  120.92  3.000
 27D  H4   C03  C02  120.12  3.000
 27D  C04  C03  C02  118.96  3.000
 27D  H5   C04  C05  120.52  3.000
 27D  H5   C04  C03  120.50  3.000
 27D  C05  C04  C03  118.97  3.000
 27D  H6   C05  C06  120.61  3.000
 27D  H6   C05  C04  121.08  3.000
 27D  C06  C05  C04  118.31  3.000
 27D  N    C06  C07  116.71  3.000
 27D  C07  C06  C05  120.60  3.000
 27D  N    C06  C05  122.68  3.000
 27D  H8   C07  H7   106.92  3.000
 27D  H8   C07  C08  109.29  3.000
 27D  H7   C07  C08  109.11  3.000
 27D  H8   C07  C06  110.50  3.000
 27D  H7   C07  C06  109.73  3.000
 27D  C08  C07  C06  111.19  3.000
 27D  N01  C08  O    121.00  3.000
 27D  N01  C08  C07  115.93  3.000
 27D  O    C08  C07  123.07  3.000
 27D  C12  N01  C09  108.28  3.000
 27D  C12  N01  C08  126.06  3.000
 27D  C09  N01  C08  125.64  3.000
 27D  H9   C09  C10  128.61  3.000
 27D  H9   C09  N01  121.13  3.000
 27D  C10  C09  N01  110.25  3.000
 27D  H10  C10  C11  127.36  3.000
 27D  H10  C10  C09  125.91  3.000
 27D  C11  C10  C09  106.73  3.000
 27D  C    C11  C12  118.81  3.000
 27D  C    C11  C10  133.05  3.000
 27D  C12  C11  C10  108.13  3.000
 27D  C13  C12  C11  121.40  3.000
 27D  C13  C12  N01  132.00  3.000
 27D  C11  C12  N01  106.60  3.000
 27D  H11  C13  C14  119.95  3.000
 27D  H11  C13  C12  122.62  3.000
 27D  C14  C13  C12  117.43  3.000
 27D  H12  C14  C15  118.06  3.000
 27D  H12  C14  C13  118.89  3.000
 27D  C15  C14  C13  123.05  3.000
 27D  C    C15  C16  120.93  3.000
 27D  C16  C15  C14  121.57  3.000
 27D  C    C15  C14  117.49  3.000
 27D  C22  C16  C17  105.64  3.000
 27D  C22  C16  C15  128.50  3.000
 27D  C17  C16  C15  125.86  3.000
 27D  H13  C17  N02  120.51  3.000
 27D  H13  C17  C16  129.07  3.000
 27D  N02  C17  C16  110.42  3.000
 27D  C19  N02  C18  125.46  3.000
 27D  C18  N02  C17  125.97  3.000
 27D  C19  N02  C17  108.46  3.000
 27D  H16  C18  H15  108.69  3.000
 27D  H16  C18  H14  108.86  3.000
 27D  H15  C18  H14  108.85  3.000
 27D  H16  C18  N02  109.08  3.000
 27D  H15  C18  N02  110.08  3.000
 27D  H14  C18  N02  111.24  3.000
 27D  C22  C19  N03  125.95  3.000
 27D  N03  C19  N02  125.71  3.000
 27D  C22  C19  N02  108.34  3.000
 27D  C20  N03  C19  112.64  3.000
 27D  H17  C20  N04  115.48  3.000
 27D  H17  C20  N03  116.39  3.000
 27D  N04  C20  N03  128.13  3.000
 27D  C21  N04  C20  118.73  3.000
 27D  C22  C21  N05  122.98  3.000
 27D  C22  C21  N04  119.24  3.000
 27D  N05  C21  N04  117.78  3.000
 27D  H19  N05  H18  115.99  3.000
 27D  H19  N05  C21  120.06  3.000
 27D  H18  N05  C21  117.84  3.000
 27D  C21  C22  C19  115.23  3.000
 27D  C19  C22  C16  107.14  3.000
 27D  C21  C22  C16  137.58  3.000
 27D  F    C    C15  119.83  3.000
 27D  C15  C    C11  121.81  3.000
 27D  F    C    C11  118.36  3.000
 27D  C06  N    C02  119.36  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
 27D  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 27D  CONST_02  C05  C06  N    C02     0.00   0.0  0
 27D  CONST_03  C06  N    C02  C03     0.00   0.0  0
 27D  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 27D  CONST_05  N    C02  C03  C04     0.00   0.0  0
 27D  CONST_06  N    C06  C05  C04     0.00   0.0  0
 27D  CONST_07  C11  C10  C09  N01     0.00   0.0  0
 27D  CONST_08  C10  C11  C12  N01     0.00   0.0  0
 27D  CONST_09  C    C11  C12  N01   180.00   0.0  0
 27D  CONST_10  C14  C13  C12  N01   180.00   0.0  0
 27D  CONST_11  C11  C12  N01  C09     0.00   0.0  0
 27D  CONST_12  C13  C12  N01  C09   180.00   0.0  0
 27D  CONST_13  C12  C11  C10  C09     0.00   0.0  0
 27D  CONST_14  C    C11  C10  C09   180.00   0.0  0
 27D  CONST_15  C12  N01  C09  C10     0.00   0.0  0
 27D  CONST_16  C13  C12  C11  C10   180.00   0.0  0
 27D  CONST_17  C15  C    C11  C10   180.00   0.0  0
 27D  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 27D  CONST_19  C14  C15  C    C11     0.00   0.0  0
 27D  CONST_20  C16  C15  C    C11   180.00   0.0  0
 27D  CONST_21  C15  C    C11  C12     0.00   0.0  0
 27D  CONST_22  C15  C14  C13  C12     0.00   0.0  0
 27D  CONST_23  C    C11  C12  C13     0.00   0.0  0
 27D  CONST_24  C    C15  C14  C13     0.00   0.0  0
 27D  CONST_25  C16  C15  C14  C13   180.00   0.0  0
 27D  CONST_28  N02  C17  C16  C15   180.00   0.0  0
 27D  CONST_29  C21  C22  C16  C15     0.00   0.0  0
 27D  CONST_30  C19  C22  C16  C15   180.00   0.0  0
 27D  CONST_31  C19  N02  C17  C16     0.00   0.0  0
 27D  CONST_32  N04  C21  C22  C16   180.00   0.0  0
 27D  CONST_33  N02  C19  C22  C16     0.00   0.0  0
 27D  CONST_34  N03  C19  C22  C16   180.00   0.0  0
 27D  CONST_36  C21  C22  C16  C17   180.00   0.0  0
 27D  CONST_37  C19  C22  C16  C17     0.00   0.0  0
 27D  CONST_38  C22  C19  N02  C17     0.00   0.0  0
 27D  CONST_39  N03  C19  N02  C17   180.00   0.0  0
 27D  CONST_40  C22  C16  C17  N02     0.00   0.0  0
 27D  CONST_41  C21  C22  C19  N02   180.00   0.0  0
 27D  CONST_42  C20  N03  C19  N02   180.00   0.0  0
 27D  CONST_43  N04  C21  C22  C19     0.00   0.0  0
 27D  CONST_44  N04  C20  N03  C19     0.00   0.0  0
 27D  CONST_45  C21  C22  C19  N03     0.00   0.0  0
 27D  CONST_46  C21  N04  C20  N03     0.00   0.0  0
 27D  CONST_47  C22  C21  N04  C20     0.00   0.0  0
 27D  CONST_48  C22  C19  N03  C20     0.00   0.0  0
 27D  CONST_50  C04  C03  C02  C01   180.00   0.0  0
 27D  CONST_51  C06  N    C02  C01   180.00   0.0  0
 27D  CONST_52  C07  C06  N    C02   180.00   0.0  0
 27D  CONST_53  C07  C06  C05  C04   180.00   0.0  0
 27D  CONST_54  C10  C09  N01  C08   180.00   0.0  0
 27D  CONST_55  C11  C12  N01  C08   180.00   0.0  0
 27D  CONST_56  C13  C12  N01  C08     0.00   0.0  0
 27D  CONST_57  F    C    C11  C10     0.00   0.0  0
 27D  CONST_58  F    C    C11  C12   180.00   0.0  0
 27D  CONST_59  F    C    C15  C14   180.00   0.0  0
 27D  CONST_60  F    C    C15  C16     0.00   0.0  0
 27D  CONST_61  C18  N02  C17  C16   180.00   0.0  0
 27D  CONST_62  N05  C21  C22  C16     0.00   0.0  0
 27D  CONST_63  C22  C19  N02  C18   180.00   0.0  0
 27D  CONST_64  N03  C19  N02  C18     0.00   0.0  0
 27D  CONST_65  N05  C21  C22  C19   180.00   0.0  0
 27D  CONST_66  N05  C21  N04  C20   180.00   0.0  0
 27D  CONST_67  H5   C04  C03  C02   180.00   0.0  0
 27D  CONST_68  H6   C05  C04  C03   180.00   0.0  0
 27D  CONST_69  H4   C03  C04  C05   180.00   0.0  0
 27D  CONST_70  H10  C10  C09  N01   180.00   0.0  0
 27D  CONST_71  H11  C13  C12  N01     0.00   0.0  0
 27D  CONST_72  H9   C09  C10  C11   180.00   0.0  0
 27D  CONST_73  H12  C14  C13  C12   180.00   0.0  0
 27D  CONST_74  H13  C17  C16  C15     0.00   0.0  0
 27D  CONST_75  H17  C20  N03  C19   180.00   0.0  0
 27D  CONST_76  C09  N01  C08  C07     0.00   0.0  0
 27D  CONST_77  C12  N01  C08  C07   180.00   0.0  0
 27D  CONST_78  C09  N01  C08  O     180.00   0.0  0
 27D  CONST_79  C12  N01  C08  O       0.00   0.0  0
 27D  CONST_80  H18  N05  C21  N04     0.00   0.0  0
 27D  Var_01    C08  C07  C06  C05    95.12  30.0  2
 27D  Var_02    N01  C08  C07  C06  -179.49  30.0  3
 27D  Var_03    H1   C01  C02  C03   -92.76  30.0  2
 27D  Var_04    H14  C18  N02  C17    98.24  30.0  2

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
 27D  plan-1  C01  0.020
 27D  plan-1  C02  0.020
 27D  plan-1  C03  0.020
 27D  plan-1  C04  0.020
 27D  plan-1  C05  0.020
 27D  plan-1  C06  0.020
 27D  plan-1  C07  0.020
 27D  plan-1  N    0.020
 27D  plan-1  H4   0.020
 27D  plan-1  H5   0.020
 27D  plan-1  H6   0.020
 27D  plan-2  C07  0.020
 27D  plan-2  C08  0.020
 27D  plan-2  O    0.020
 27D  plan-2  N01  0.020
 27D  plan-2  C09  0.020
 27D  plan-2  C10  0.020
 27D  plan-2  C11  0.020
 27D  plan-2  C12  0.020
 27D  plan-2  C13  0.020
 27D  plan-2  C14  0.020
 27D  plan-2  C15  0.020
 27D  plan-2  C16  0.020
 27D  plan-2  C    0.020
 27D  plan-2  F    0.020
 27D  plan-2  H9   0.020
 27D  plan-2  H10  0.020
 27D  plan-2  H11  0.020
 27D  plan-2  H12  0.020
 27D  plan-3  C15  0.020
 27D  plan-3  C16  0.020
 27D  plan-3  C17  0.020
 27D  plan-3  N02  0.020
 27D  plan-3  C18  0.020
 27D  plan-3  C19  0.020
 27D  plan-3  N03  0.020
 27D  plan-3  C20  0.020
 27D  plan-3  N04  0.020
 27D  plan-3  C21  0.020
 27D  plan-3  N05  0.020
 27D  plan-3  C22  0.020
 27D  plan-3  H13  0.020
 27D  plan-3  H17  0.020
 27D  plan-4  C21  0.020
 27D  plan-4  N05  0.020
 27D  plan-4  H18  0.020
 27D  plan-4  H19  0.020

