# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 00:41:37 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-(trifluoromethyl)phenyl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2ccc3N(CCc3c2)C(=O)Cc4cccc(c4)C(F)(F)F)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
 0WH  0WH  1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-(trifluoromethyl)phenyl]ethanone  ligand  53  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0WH
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
 0WH  C     C  CR56  0   0.508   6.3932  -0.9098  -0.2334
 0WH  F     F  F     0  -0.302  -7.9641  -1.6742   0.1917
 0WH  N     N  N     0  -0.462   7.2855  -1.8989  -0.1481
 0WH  O     O  O     0  -0.468  -3.0465   2.5426   0.4247
 0WH  C01   C  CH3   0  -0.527   7.9525   0.8539  -1.0418
 0WH  F01   F  F     0  -0.315  -6.6058  -1.1542   1.7769
 0WH  N01   N  NR5   0  -0.504   6.6667   0.3651  -0.6006
 0WH  C02   C  CR15  0  -0.056   5.5011   1.0851  -0.5690
 0WH  F02   F  F     0  -0.315  -6.1714  -2.8232   0.4970
 0WH  N02   N  NR5   0  -0.612  -0.8421   2.1911   0.3756
 0WH  C03   C  CR5   0  -0.010   4.4565   0.2926  -0.1753
 0WH  N03   N  NH2   0  -0.824   3.3468  -2.5148   0.9364
 0WH  C04   C  CR6   0   0.022   3.0612   0.7257  -0.0573
 0WH  N04   N  N     0  -0.474   5.4903  -3.2576   0.6236
 0WH  C05   C  CR16  0  -0.354   2.0258  -0.0158  -0.6235
 0WH  C06   C  CR16  0  -0.276   0.6957   0.3796  -0.5370
 0WH  C07   C  CR56  0   0.415   0.3877   1.5620   0.1265
 0WH  C08   C  CH2   0  -0.279  -0.6434   3.4150   1.1715
 0WH  C09   C  CH2   0  -0.509   0.8748   3.5615   1.3218
 0WH  C10   C  CR56  0  -0.009   1.4186   2.3244   0.6784
 0WH  C11   C  CR16  0  -0.373   2.7324   1.9167   0.5977
 0WH  C13   C  CH2   0  -0.740  -2.3531   0.5779  -0.7402
 0WH  C14   C  CR6   0   0.210  -3.8123   0.3564  -1.0041
 0WH  C15   C  CR16  0  -0.288  -4.4412   0.9726  -2.0827
 0WH  C16   C  CR16  0  -0.227  -5.7893   0.7692  -2.3242
 0WH  C17   C  CR16  0  -0.302  -6.5353  -0.0553  -1.4918
 0WH  C18   C  CR6   0  -0.173  -5.9139  -0.6733  -0.4168
 0WH  C19   C  CR16  0  -0.333  -4.5585  -0.4668  -0.1750
 0WH  C20   C  CT    0   1.051  -6.6693  -1.5772   0.5051
 0WH  C21   C  CR56  0  -0.112   5.0249  -1.0042   0.0534
 0WH  C22   C  CR6   0   0.393   4.6073  -2.2585   0.5464
 0WH  C23   C  CR16  0   0.035   6.7530  -3.0279   0.2708
 0WH  H01   H  HCH3  0   0.255   8.1140   0.6430  -2.0985
 0WH  H01A  H  HCH3  0   0.261   7.9990   1.9284  -0.8860
 0WH  H01B  H  HCH3  0   0.261   8.7442   0.3840  -0.4644
 0WH  H02   H  HCR5  0   0.293   5.4950   2.1269  -0.8501
 0WH  HN03  H  HNH2  0   0.407   2.7020  -1.7617   1.1030
 0WH  HN0A  H  HNH2  0   0.396   3.1674  -3.3772   1.4229
 0WH  H05   H  HCR6  0   0.265   2.2540  -0.9228  -1.1693
 0WH  H06   H  HCR6  0   0.272  -0.0455  -0.2471  -1.0037
 0WH  H08   H  HCH2  0   0.261  -1.0900   4.2664   0.6611
 0WH  H09   H  HCH2  0   0.271   1.2417   4.4583   0.8202
 0WH  H11   H  HCR6  0   0.249   3.5113   2.5146   1.0561
 0WH  H13   H  HCH2  0   0.304  -1.8060   0.6443  -1.6844
 0WH  H13A  H  HCH2  0   0.303  -1.9400  -0.2762  -0.1982
 0WH  H15   H  HCR6  0   0.262  -3.8685   1.6126  -2.7429
 0WH  H16   H  HCR6  0   0.268  -6.2675   1.2507  -3.1663
 0WH  H17   H  HCR6  0   0.272  -7.5861  -0.2056  -1.6964
 0WH  H19   H  HCR6  0   0.270  -4.0707  -0.9498   0.6640
 0WH  H23   H  HCR6  0   0.245   7.4236  -3.8775   0.3500
 0WH  H191  H  HCH2  0   0.260  -1.1392   3.3081   2.1362
 0WH  H20   H  HCH2  0   0.271   1.1698   3.6398   2.3686
 0WH  C12   C  C     0   0.565  -2.1173   1.8407   0.0626

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
 0WH  C    N     aromatic  1.335  0.020  1.335
 0WH  F    C20   single    1.336  0.020  1.336
 0WH  C01  H01   single    0.970  0.020  1.090
 0WH  C01  H01A  single    0.970  0.020  1.090
 0WH  C01  H01B  single    0.970  0.020  1.090
 0WH  N01  C     aromatic  1.355  0.020  1.355
 0WH  N01  C01   single    1.445  0.020  1.445
 0WH  C02  N01   aromatic  1.370  0.020  1.370
 0WH  C02  H02   single    0.930  0.020  1.080
 0WH  F02  C20   single    1.342  0.020  1.342
 0WH  N02  C07   single    1.404  0.020  1.404
 0WH  C03  C02   aromatic  1.369  0.020  1.369
 0WH  C03  C21   aromatic  1.434  0.020  1.434
 0WH  N03  C22   single    1.344  0.020  1.344
 0WH  N03  HN03  single    0.890  0.020  1.040
 0WH  N03  HN0A  single    0.890  0.020  1.040
 0WH  C04  C03   single    1.466  0.020  1.466
 0WH  N04  C23   aromatic  1.331  0.020  1.331
 0WH  C05  C04   aromatic  1.394  0.020  1.394
 0WH  C05  H05   single    0.930  0.020  1.080
 0WH  C06  C05   aromatic  1.390  0.020  1.390
 0WH  C06  H06   single    0.930  0.020  1.080
 0WH  C07  C06   aromatic  1.390  0.020  1.390
 0WH  C07  C10   aromatic  1.396  0.020  1.396
 0WH  C08  N02   single    1.473  0.020  1.473
 0WH  C08  C09   single    1.533  0.020  1.533
 0WH  C08  H08   single    0.970  0.020  1.090
 0WH  C09  C10   single    1.497  0.020  1.497
 0WH  C09  H09   single    0.970  0.020  1.090
 0WH  C10  C11   aromatic  1.378  0.020  1.378
 0WH  C11  C04   aromatic  1.399  0.020  1.399
 0WH  C11  H11   single    0.930  0.020  1.080
 0WH  C12  O     double    1.219  0.020  1.219
 0WH  C12  N02   single    1.359  0.020  1.359
 0WH  C13  C12   single    1.515  0.020  1.515
 0WH  C13  H13   single    0.970  0.020  1.090
 0WH  C13  H13A  single    0.970  0.020  1.090
 0WH  C14  C13   single    1.499  0.020  1.499
 0WH  C15  C14   aromatic  1.392  0.020  1.392
 0WH  C15  H15   single    0.930  0.020  1.080
 0WH  C16  C15   aromatic  1.385  0.020  1.385
 0WH  C16  H16   single    0.930  0.020  1.080
 0WH  C17  C16   aromatic  1.389  0.020  1.389
 0WH  C17  C18   aromatic  1.387  0.020  1.387
 0WH  C17  H17   single    0.930  0.020  1.080
 0WH  C18  C19   aromatic  1.392  0.020  1.392
 0WH  C19  C14   aromatic  1.386  0.020  1.386
 0WH  C19  H19   single    0.930  0.020  1.080
 0WH  C20  F01   single    1.342  0.020  1.342
 0WH  C20  C18   single    1.496  0.020  1.496
 0WH  C21  C     aromatic  1.401  0.020  1.401
 0WH  C21  C22   aromatic  1.411  0.020  1.411
 0WH  C22  N04   aromatic  1.336  0.020  1.336
 0WH  C23  N     aromatic  1.317  0.020  1.317
 0WH  C23  H23   single    0.930  0.020  1.080
 0WH  C08  H191  single    0.970  0.020  1.090
 0WH  C09  H20   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
 0WH  C21   C    N01   108.42  3.000
 0WH  C21   C    N     126.14  3.000
 0WH  N01   C    N     125.43  3.000
 0WH  C23   N    C     112.67  3.000
 0WH  H01B  C01  H01A  108.67  3.000
 0WH  H01B  C01  H01   108.88  3.000
 0WH  H01A  C01  H01   108.91  3.000
 0WH  H01B  C01  N01   109.87  3.000
 0WH  H01A  C01  N01   109.20  3.000
 0WH  H01   C01  N01   111.26  3.000
 0WH  C02   N01  C01   125.90  3.000
 0WH  C02   N01  C     108.45  3.000
 0WH  C01   N01  C     125.52  3.000
 0WH  H02   C02  C03   129.01  3.000
 0WH  C03   C02  N01   110.58  3.000
 0WH  H02   C02  N01   120.40  3.000
 0WH  C12   N02  C08   117.71  3.000
 0WH  C12   N02  C07   131.74  3.000
 0WH  C08   N02  C07   110.49  3.000
 0WH  C21   C03  C04   129.17  3.000
 0WH  C04   C03  C02   125.34  3.000
 0WH  C21   C03  C02   105.48  3.000
 0WH  HN0A  N03  HN03  116.58  3.000
 0WH  HN0A  N03  C22   118.09  3.000
 0WH  HN03  N03  C22   120.45  3.000
 0WH  C11   C04  C05   117.95  3.000
 0WH  C11   C04  C03   120.87  3.000
 0WH  C05   C04  C03   121.15  3.000
 0WH  C23   N04  C22   118.87  3.000
 0WH  H05   C05  C06   118.11  3.000
 0WH  C06   C05  C04   122.29  3.000
 0WH  H05   C05  C04   119.59  3.000
 0WH  H06   C06  C07   123.32  3.000
 0WH  C07   C06  C05   118.91  3.000
 0WH  H06   C06  C05   117.77  3.000
 0WH  C10   C07  C06   119.31  3.000
 0WH  C10   C07  N02   109.39  3.000
 0WH  C06   C07  N02   131.29  3.000
 0WH  H191  C08  H08   107.76  3.000
 0WH  H191  C08  C09   111.91  3.000
 0WH  H08   C08  C09   112.19  3.000
 0WH  H191  C08  N02   109.59  3.000
 0WH  H08   C08  N02   109.94  3.000
 0WH  C09   C08  N02   105.42  3.000
 0WH  H20   C09  H09   106.94  3.000
 0WH  H20   C09  C10   111.95  3.000
 0WH  H09   C09  C10   111.07  3.000
 0WH  H20   C09  C08   111.66  3.000
 0WH  H09   C09  C08   111.50  3.000
 0WH  C10   C09  C08   103.81  3.000
 0WH  C11   C10  C09   128.04  3.000
 0WH  C11   C10  C07   121.29  3.000
 0WH  C09   C10  C07   110.67  3.000
 0WH  H11   C11  C10   119.82  3.000
 0WH  H11   C11  C04   119.94  3.000
 0WH  C10   C11  C04   120.23  3.000
 0WH  H13A  C13  H13   106.65  3.000
 0WH  H13A  C13  C14   109.87  3.000
 0WH  H13   C13  C14   110.12  3.000
 0WH  C14   C13  C12   111.59  3.000
 0WH  H13A  C13  C12   109.26  3.000
 0WH  H13   C13  C12   109.22  3.000
 0WH  C19   C14  C15   118.88  3.000
 0WH  C19   C14  C13   120.42  3.000
 0WH  C15   C14  C13   120.71  3.000
 0WH  H15   C15  C16   119.69  3.000
 0WH  C16   C15  C14   120.66  3.000
 0WH  H15   C15  C14   119.65  3.000
 0WH  H16   C16  C17   119.57  3.000
 0WH  C17   C16  C15   120.38  3.000
 0WH  H16   C16  C15   120.06  3.000
 0WH  H17   C17  C18   121.34  3.000
 0WH  H17   C17  C16   119.42  3.000
 0WH  C18   C17  C16   119.23  3.000
 0WH  C20   C18  C19   118.31  3.000
 0WH  C20   C18  C17   121.38  3.000
 0WH  C19   C18  C17   120.31  3.000
 0WH  H19   C19  C18   120.43  3.000
 0WH  H19   C19  C14   119.02  3.000
 0WH  C18   C19  C14   120.55  3.000
 0WH  C18   C20  F02   111.72  3.000
 0WH  C18   C20  F01   111.70  3.000
 0WH  F02   C20  F01   106.32  3.000
 0WH  C18   C20  F     112.87  3.000
 0WH  F01   C20  F     106.93  3.000
 0WH  F02   C20  F     106.91  3.000
 0WH  C22   C21  C03   137.92  3.000
 0WH  C22   C21  C     114.86  3.000
 0WH  C03   C21  C     107.06  3.000
 0WH  C21   C22  N04   119.31  3.000
 0WH  N04   C22  N03   117.43  3.000
 0WH  C21   C22  N03   123.26  3.000
 0WH  H23   C23  N04   115.58  3.000
 0WH  H23   C23  N     116.40  3.000
 0WH  N04   C23  N     128.02  3.000
 0WH  C13   C12  N02   118.88  3.000
 0WH  C13   C12  O     121.24  3.000
 0WH  N02   C12  O     119.88  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
 0WH  CONST_01  N04   C23  N    C       0.00   0.0  0
 0WH  CONST_02  C03   C02  N01  C       0.00   0.0  0
 0WH  CONST_03  C02   C03  C21  C       0.00   0.0  0
 0WH  CONST_04  C04   C03  C21  C     180.00   0.0  0
 0WH  CONST_05  N04   C22  C21  C       0.00   0.0  0
 0WH  CONST_06  C02   N01  C    N     180.00   0.0  0
 0WH  CONST_07  C03   C21  C    N     180.00   0.0  0
 0WH  CONST_08  C22   C21  C    N       0.00   0.0  0
 0WH  CONST_09  C22   N04  C23  N       0.00   0.0  0
 0WH  CONST_10  C23   N    C    N01   180.00   0.0  0
 0WH  CONST_11  C03   C21  C    N01     0.00   0.0  0
 0WH  CONST_12  C22   C21  C    N01   180.00   0.0  0
 0WH  CONST_13  C21   C03  C02  N01     0.00   0.0  0
 0WH  CONST_14  C04   C03  C02  N01   180.00   0.0  0
 0WH  CONST_15  C21   C    N01  C02     0.00   0.0  0
 0WH  CONST_16  C22   C21  C03  C02   180.00   0.0  0
 0WH  CONST_19  N04   C22  C21  C03   180.00   0.0  0
 0WH  CONST_20  C06   C05  C04  C03   180.00   0.0  0
 0WH  CONST_21  C10   C11  C04  C03   180.00   0.0  0
 0WH  CONST_22  C22   C21  C03  C04     0.00   0.0  0
 0WH  CONST_23  C07   C06  C05  C04     0.00   0.0  0
 0WH  CONST_24  C07   C10  C11  C04     0.00   0.0  0
 0WH  CONST_26  C10   C11  C04  C05     0.00   0.0  0
 0WH  CONST_27  C10   C07  C06  C05     0.00   0.0  0
 0WH  CONST_28  C11   C04  C05  C06     0.00   0.0  0
 0WH  CONST_29  C11   C10  C07  C06     0.00   0.0  0
 0WH  CONST_31  C17   C16  C15  C14     0.00   0.0  0
 0WH  CONST_32  C17   C18  C19  C14     0.00   0.0  0
 0WH  CONST_33  C18   C19  C14  C15     0.00   0.0  0
 0WH  CONST_34  C18   C17  C16  C15     0.00   0.0  0
 0WH  CONST_35  C19   C14  C15  C16     0.00   0.0  0
 0WH  CONST_36  C19   C18  C17  C16     0.00   0.0  0
 0WH  CONST_37  C23   N    C    C21     0.00   0.0  0
 0WH  CONST_38  C23   N04  C22  C21     0.00   0.0  0
 0WH  CONST_39  N03   C22  C21  C     180.00   0.0  0
 0WH  CONST_40  C01   N01  C    N       0.00   0.0  0
 0WH  CONST_41  C21   C    N01  C01   180.00   0.0  0
 0WH  CONST_42  C03   C02  N01  C01   180.00   0.0  0
 0WH  CONST_43  N03   C22  C21  C03     0.00   0.0  0
 0WH  CONST_44  C23   N04  C22  N03   180.00   0.0  0
 0WH  CONST_45  C16   C15  C14  C13   180.00   0.0  0
 0WH  CONST_46  C18   C19  C14  C13   180.00   0.0  0
 0WH  CONST_47  C20   C18  C19  C14   180.00   0.0  0
 0WH  CONST_48  C20   C18  C17  C16   180.00   0.0  0
 0WH  CONST_49  H23   C23  N    C     180.00   0.0  0
 0WH  CONST_50  H02   C02  N01  C     180.00   0.0  0
 0WH  CONST_51  H06   C06  C07  N02     0.00   0.0  0
 0WH  CONST_52  H05   C05  C04  C03     0.00   0.0  0
 0WH  CONST_53  H11   C11  C04  C03     0.00   0.0  0
 0WH  CONST_54  H16   C16  C15  C14   180.00   0.0  0
 0WH  CONST_55  H19   C19  C14  C15   180.00   0.0  0
 0WH  CONST_56  H17   C17  C16  C15   180.00   0.0  0
 0WH  CONST_57  H15   C15  C16  C17   180.00   0.0  0
 0WH  CONST_58  C07   N02  C12  O     180.00   0.0  0
 0WH  CONST_59  C08   N02  C12  O       0.00   0.0  0
 0WH  CONST_60  C13   C12  N02  C07     0.00   0.0  0
 0WH  CONST_61  C13   C12  N02  C08   180.00   0.0  0
 0WH  CONST_62  HN03  N03  C22  N04   180.00   0.0  0
 0WH  CONST_63  HN0A  N03  C22  N04     0.00   0.0  0
 0WH  Var_01    C10   C09  C08  N02    -4.43  30.0  1
 0WH  Var_02    C08   N02  C07  C06   177.90  30.0  1
 0WH  Var_03    C09   C08  N02  C07     4.07  30.0  1
 0WH  Var_04    C08   C09  C10  C07     3.53  30.0  1
 0WH  Var_05    C17   C18  C20  F      -1.68  30.0  2
 0WH  Var_06    C14   C13  C12  N02  -179.39  30.0  1
 0WH  Var_07    C15   C14  C13  C12    84.55  30.0  2
 0WH  Var_08    H01   C01  N01  C      82.42  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
 0WH  plan-1  C13   0.020
 0WH  plan-1  C14   0.020
 0WH  plan-1  C15   0.020
 0WH  plan-1  C16   0.020
 0WH  plan-1  C17   0.020
 0WH  plan-1  C18   0.020
 0WH  plan-1  C19   0.020
 0WH  plan-1  C20   0.020
 0WH  plan-1  H15   0.020
 0WH  plan-1  H16   0.020
 0WH  plan-1  H17   0.020
 0WH  plan-1  H19   0.020
 0WH  plan-2  C     0.020
 0WH  plan-2  N     0.020
 0WH  plan-2  C01   0.020
 0WH  plan-2  N01   0.020
 0WH  plan-2  C02   0.020
 0WH  plan-2  C03   0.020
 0WH  plan-2  N03   0.020
 0WH  plan-2  C04   0.020
 0WH  plan-2  N04   0.020
 0WH  plan-2  C21   0.020
 0WH  plan-2  C22   0.020
 0WH  plan-2  C23   0.020
 0WH  plan-2  H02   0.020
 0WH  plan-2  H23   0.020
 0WH  plan-3  N02   0.020
 0WH  plan-3  C03   0.020
 0WH  plan-3  C04   0.020
 0WH  plan-3  C05   0.020
 0WH  plan-3  C06   0.020
 0WH  plan-3  C07   0.020
 0WH  plan-3  C09   0.020
 0WH  plan-3  C10   0.020
 0WH  plan-3  C11   0.020
 0WH  plan-3  H05   0.020
 0WH  plan-3  H06   0.020
 0WH  plan-3  H11   0.020
 0WH  plan-4  O     0.020
 0WH  plan-4  N02   0.020
 0WH  plan-4  C07   0.020
 0WH  plan-4  C08   0.020
 0WH  plan-4  C13   0.020
 0WH  plan-4  C12   0.020
 0WH  plan-5  N03   0.020
 0WH  plan-5  C22   0.020
 0WH  plan-5  HN03  0.020
 0WH  plan-5  HN0A  0.020

