# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 06:41:34 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 1-methyl-2-(2-{[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(OC(F)(F)F)c(Nc3nccc(n3)c4cc5C(=O)NCCc5n4C)c2
#
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
 664  664  1-methyl-2-(2-{[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one  ligand  62  36  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_664
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
 664  N1    N  N     0  -0.457   0.0109   1.6276  -0.7535
 664  C2    C  CR6   0   0.588   0.4526   0.4467  -0.3448
 664  C6    C  CR16  0  -0.010   0.9504   2.5299  -1.0225
 664  N3    N  N     0  -0.495   1.7292   0.0922  -0.1933
 664  N7    N  NH1   0  -0.765  -0.4372  -0.5468  -0.0520
 664  C4    C  CR6   0   0.258   2.6579   0.9986  -0.4667
 664  C5    C  CR16  0  -0.398   2.2983   2.2845  -0.8942
 664  C26   C  CR5   0   0.326   4.0560   0.6276  -0.3484
 664  C8    C  CR6   0   0.345  -1.8194  -0.5477  -0.2037
 664  C10   C  CR16  0  -0.286  -3.8281  -1.8052  -0.6595
 664  C9    C  CR6   0   0.212  -2.4547  -1.7394  -0.5709
 664  C11   C  CR16  0  -0.385  -4.6035  -0.6789  -0.4335
 664  C13   C  CR16  0  -0.403  -2.6064   0.5645   0.0585
 664  C12   C  CR6   0   0.402  -4.0018   0.5336  -0.0744
 664  O14   O  O2    0  -0.524  -1.6793  -2.8780  -0.7836
 664  N15   N  NT    0  -0.522  -4.7409   1.6775   0.2003
 664  C16   C  CH2   0  -0.315  -6.1869   1.5878   0.1480
 664  C17   C  CH2   0  -0.279  -6.8238   2.7865   0.8264
 664  N18   N  NT    0  -0.412  -6.3591   4.0287   0.2495
 664  C19   C  CH2   0  -0.283  -4.9199   4.1127   0.3687
 664  C20   C  CH2   0  -0.306  -4.2561   2.9449  -0.3312
 664  C21   C  CH3   0  -0.519  -7.0170   5.1718   0.8390
 664  C22   C  CT    0   1.076  -1.3557  -3.1747  -2.0505
 664  F23   F  F     0  -0.298  -0.7513  -2.1669  -2.6807
 664  F24   F  F     0  -0.277  -0.5294  -4.2085  -2.0224
 664  F25   F  F     0  -0.298  -2.4164  -3.5092  -2.7878
 664  N27   N  NR5   0  -0.542   4.5322  -0.4668   0.3586
 664  C28   C  CR15  0  -0.410   5.1290   1.2399  -0.9605
 664  C29   C  CR5   0  -0.143   6.2713   0.4907  -0.6325
 664  C30   C  CR5   0   0.377   5.8638  -0.5479   0.1827
 664  C31   C  CH2   0  -0.535   6.8193  -1.5188   0.7766
 664  C32   C  CH2   0  -0.282   8.0279  -1.5908  -0.1513
 664  N33   N  NH1   0  -0.649   8.5015  -0.2694  -0.5290
 664  C34   C  C     0   0.472   7.6775   0.7186  -0.9558
 664  O35   O  O     0  -0.493   8.0832   1.7282  -1.5204
 664  C36   C  CH3   0  -0.525   3.7772  -1.3515   1.2280
 664  H6    H  HCR6  0   0.272   0.5999   3.5015  -1.3521
 664  H7    H  HNH1  0   0.402   0.0018  -1.4296   0.1600
 664  H5    H  HCR6  0   0.270   3.0283   3.0521  -1.1005
 664  H13   H  HCR6  0   0.279  -2.1162   1.4648   0.3900
 664  H10   H  HCR6  0   0.276  -4.3095  -2.7377  -0.9234
 664  HA    H  HCR6  0   0.275  -5.6727  -0.7664  -0.5536
 664  H161  H  HCH2  0   0.216  -6.5488   1.5114  -0.8884
 664  H162  H  HCH2  0   0.254  -6.5187   0.6942   0.6775
 664  H201  H  HCH2  0   0.255  -3.1808   3.0308  -0.1931
 664  H202  H  HCH2  0   0.220  -4.4502   3.0067  -1.4117
 664  H171  H  HCH2  0   0.242  -7.9075   2.7158   0.7057
 664  H172  H  HCH2  0   0.194  -6.6162   2.7372   1.9099
 664  H191  H  HCH2  0   0.242  -4.5718   5.0389  -0.0940
 664  H192  H  HCH2  0   0.194  -4.5967   4.1349   1.4244
 664  H211  H  HCH3  0   0.193  -6.8392   5.2655   1.9218
 664  H212  H  HCH3  0   0.234  -6.6683   6.0899   0.3635
 664  H213  H  HCH3  0   0.234  -8.0948   5.1025   0.6848
 664  H28   H  HCR5  0   0.262   5.0835   2.1054  -1.6024
 664  H361  H  HCH3  0   0.261   3.1526  -2.0311   0.6557
 664  H362  H  HCH3  0   0.264   4.4765  -1.9270   1.8270
 664  H363  H  HCH3  0   0.263   3.1453  -0.7779   1.8992
 664  H311  H  HCH2  0   0.274   7.1172  -1.1923   1.7782
 664  H312  H  HCH2  0   0.275   6.3962  -2.5189   0.8762
 664  H321  H  HCH2  0   0.266   8.8445  -2.1129   0.3427
 664  H322  H  HCH2  0   0.242   7.7579  -2.1703  -1.0403
 664  H33   H  HNH1  0   0.397   9.4705  -0.1915  -0.7982

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
 664  N1   C2    aromatic  1.325  0.020  1.325
 664  N1   C6    aromatic  1.330  0.020  1.330
 664  C2   N3    aromatic  1.334  0.020  1.334
 664  C2   N7    single    1.365  0.020  1.365
 664  N3   C4    aromatic  1.326  0.020  1.326
 664  C4   C5    aromatic  1.402  0.020  1.402
 664  C4   C26   single    1.451  0.020  1.451
 664  C5   C6    aromatic  1.376  0.020  1.376
 664  N7   C8    single    1.391  0.020  1.391
 664  C8   C9    aromatic  1.399  0.020  1.399
 664  C8   C13   aromatic  1.388  0.020  1.388
 664  C9   C10   aromatic  1.378  0.020  1.378
 664  C9   O14   single    1.394  0.020  1.394
 664  C10  C11   aromatic  1.386  0.020  1.386
 664  C11  C12   aromatic  1.400  0.020  1.400
 664  C12  C13   aromatic  1.402  0.020  1.402
 664  C12  N15   single    1.389  0.020  1.389
 664  O14  C22   single    1.341  0.020  1.341
 664  N15  C16   single    1.450  0.020  1.450
 664  N15  C20   single    1.457  0.020  1.457
 664  C16  C17   single    1.518  0.020  1.518
 664  C17  N18   single    1.446  0.020  1.446
 664  N18  C19   single    1.447  0.020  1.447
 664  N18  C21   single    1.445  0.020  1.445
 664  C19  C20   single    1.515  0.020  1.515
 664  C22  F23   single    1.334  0.020  1.334
 664  C22  F24   single    1.324  0.020  1.324
 664  C22  F25   single    1.334  0.020  1.334
 664  C26  N27   aromatic  1.387  0.020  1.387
 664  C26  C28   aromatic  1.379  0.020  1.379
 664  N27  C30   aromatic  1.346  0.020  1.346
 664  N27  C36   single    1.452  0.020  1.452
 664  C28  C29   aromatic  1.405  0.020  1.405
 664  C29  C30   aromatic  1.382  0.020  1.382
 664  C29  C34   single    1.461  0.020  1.461
 664  C30  C31   single    1.486  0.020  1.486
 664  C31  C32   single    1.525  0.020  1.525
 664  C32  N33   single    1.454  0.020  1.454
 664  N33  C34   single    1.355  0.020  1.355
 664  C34  O35   double    1.226  0.020  1.226
 664  C6   H6    single    0.930  0.020  1.080
 664  N7   H7    single    0.860  0.020  1.020
 664  C5   H5    single    0.930  0.020  1.080
 664  C13  H13   single    0.930  0.020  1.080
 664  C10  H10   single    0.930  0.020  1.080
 664  C11  HA    single    0.930  0.020  1.080
 664  C16  H161  single    0.970  0.020  1.090
 664  C16  H162  single    0.970  0.020  1.090
 664  C20  H201  single    0.970  0.020  1.090
 664  C20  H202  single    0.970  0.020  1.090
 664  C17  H171  single    0.970  0.020  1.090
 664  C17  H172  single    0.970  0.020  1.090
 664  C19  H191  single    0.970  0.020  1.090
 664  C19  H192  single    0.970  0.020  1.090
 664  C21  H211  single    0.970  0.020  1.090
 664  C21  H212  single    0.970  0.020  1.090
 664  C21  H213  single    0.970  0.020  1.090
 664  C28  H28   single    0.930  0.020  1.080
 664  C36  H361  single    0.970  0.020  1.090
 664  C36  H362  single    0.970  0.020  1.090
 664  C36  H363  single    0.970  0.020  1.090
 664  C31  H311  single    0.970  0.020  1.090
 664  C31  H312  single    0.970  0.020  1.090
 664  C32  H321  single    0.970  0.020  1.090
 664  C32  H322  single    0.970  0.020  1.090
 664  N33  H33   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
 664  C6    N1   C2    115.56  3.000
 664  N7    C2   N3    113.96  3.000
 664  N7    C2   N1    119.82  3.000
 664  N3    C2   N1    126.22  3.000
 664  H6    C6   C5    120.32  3.000
 664  H6    C6   N1    116.17  3.000
 664  C5    C6   N1    123.50  3.000
 664  C4    N3   C2    117.73  3.000
 664  H7    N7   C8    117.07  3.000
 664  H7    N7   C2    113.48  3.000
 664  C8    N7   C2    128.67  3.000
 664  C26   C4   C5    120.43  3.000
 664  C26   C4   N3    118.89  3.000
 664  C5    C4   N3    120.66  3.000
 664  H5    C5   C4    122.49  3.000
 664  H5    C5   C6    121.19  3.000
 664  C4    C5   C6    116.32  3.000
 664  C28   C26  N27   108.02  3.000
 664  C28   C26  C4    126.87  3.000
 664  N27   C26  C4    125.02  3.000
 664  C13   C8   C9    118.33  3.000
 664  C13   C8   N7    122.87  3.000
 664  C9    C8   N7    118.72  3.000
 664  H10   C10  C11   119.41  3.000
 664  H10   C10  C9    120.02  3.000
 664  C11   C10  C9    120.56  3.000
 664  O14   C9   C10   120.38  3.000
 664  O14   C9   C8    118.88  3.000
 664  C10   C9   C8    120.67  3.000
 664  HA    C11  C12   121.61  3.000
 664  HA    C11  C10   118.05  3.000
 664  C12   C11  C10   120.34  3.000
 664  H13   C13  C12   120.02  3.000
 664  H13   C13  C8    118.03  3.000
 664  C12   C13  C8    121.94  3.000
 664  N15   C12  C13   119.51  3.000
 664  N15   C12  C11   122.35  3.000
 664  C13   C12  C11   118.09  3.000
 664  C22   O14  C9    117.33  3.000
 664  C20   N15  C16   111.87  3.000
 664  C20   N15  C12   117.84  3.000
 664  C16   N15  C12   118.20  3.000
 664  H162  C16  H161  107.49  3.000
 664  H162  C16  C17   107.61  3.000
 664  H161  C16  C17   109.75  3.000
 664  H162  C16  N15   109.67  3.000
 664  H161  C16  N15   111.49  3.000
 664  C17   C16  N15   110.71  3.000
 664  H172  C17  H171  106.97  3.000
 664  H172  C17  N18   111.67  3.000
 664  H171  C17  N18   109.28  3.000
 664  H172  C17  C16   108.93  3.000
 664  H171  C17  C16   108.40  3.000
 664  N18   C17  C16   111.43  3.000
 664  C21   N18  C19   111.93  3.000
 664  C21   N18  C17   111.75  3.000
 664  C19   N18  C17   109.67  3.000
 664  H192  C19  H191  107.13  3.000
 664  H192  C19  C20   109.21  3.000
 664  H191  C19  C20   108.56  3.000
 664  H192  C19  N18   111.78  3.000
 664  H191  C19  N18   109.35  3.000
 664  C20   C19  N18   110.69  3.000
 664  H202  C20  H201  107.15  3.000
 664  H202  C20  C19   109.47  3.000
 664  H201  C20  C19   108.28  3.000
 664  H202  C20  N15   110.40  3.000
 664  H201  C20  N15   110.57  3.000
 664  C19   C20  N15   110.86  3.000
 664  H213  C21  H212  107.91  3.000
 664  H213  C21  H211  107.69  3.000
 664  H212  C21  H211  107.78  3.000
 664  H213  C21  N18   110.00  3.000
 664  H212  C21  N18   110.03  3.000
 664  H211  C21  N18   113.26  3.000
 664  F25   C22  F24   108.19  3.000
 664  F25   C22  F23   106.78  3.000
 664  F24   C22  F23   108.50  3.000
 664  F25   C22  O14   112.69  3.000
 664  F24   C22  O14   107.66  3.000
 664  F23   C22  O14   112.87  3.000
 664  C36   N27  C30   123.78  3.000
 664  C36   N27  C26   127.40  3.000
 664  C30   N27  C26   108.70  3.000
 664  H28   C28  C29   126.95  3.000
 664  H28   C28  C26   126.00  3.000
 664  C29   C28  C26   107.00  3.000
 664  C34   C29  C30   122.12  3.000
 664  C34   C29  C28   130.38  3.000
 664  C30   C29  C28   107.38  3.000
 664  C31   C30  C29   122.49  3.000
 664  C31   C30  N27   128.57  3.000
 664  C29   C30  N27   108.88  3.000
 664  H312  C31  H311  107.19  3.000
 664  H312  C31  C32   108.64  3.000
 664  H311  C31  C32   110.79  3.000
 664  H312  C31  C30   112.72  3.000
 664  H311  C31  C30   110.23  3.000
 664  C32   C31  C30   107.29  3.000
 664  H322  C32  H321  107.45  3.000
 664  H322  C32  N33   110.51  3.000
 664  H321  C32  N33   108.04  3.000
 664  H322  C32  C31   108.88  3.000
 664  H321  C32  C31   109.95  3.000
 664  N33   C32  C31   111.92  3.000
 664  H33   N33  C34   116.34  3.000
 664  H33   N33  C32   116.90  3.000
 664  C34   N33  C32   123.12  3.000
 664  O35   C34  N33   122.97  3.000
 664  O35   C34  C29   123.30  3.000
 664  N33   C34  C29   113.69  3.000
 664  H363  C36  H362  108.28  3.000
 664  H363  C36  H361  108.76  3.000
 664  H362  C36  H361  109.24  3.000
 664  H363  C36  N27   110.54  3.000
 664  H362  C36  N27   108.57  3.000
 664  H361  C36  N27   111.39  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
 664  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 664  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 664  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 664  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 664  CONST_05  C26   C4   N3   C2    180.00   0.0  0
 664  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 664  CONST_07  N3    C4   C5   C6      0.00   0.0  0
 664  CONST_08  C26   C4   C5   C6    180.00   0.0  0
 664  CONST_11  C30   N27  C26  C4    180.00   0.0  0
 664  CONST_12  C29   C28  C26  C4    180.00   0.0  0
 664  CONST_15  C29   C30  N27  C26     0.00   0.0  0
 664  CONST_16  C30   C29  C28  C26     0.00   0.0  0
 664  CONST_17  C11   C10  C9   C8      0.00   0.0  0
 664  CONST_18  C11   C12  C13  C8      0.00   0.0  0
 664  CONST_19  C13   C8   C9   C10     0.00   0.0  0
 664  CONST_20  C13   C12  C11  C10     0.00   0.0  0
 664  CONST_21  C12   C13  C8   C9      0.00   0.0  0
 664  CONST_22  C12   C11  C10  C9      0.00   0.0  0
 664  CONST_23  C29   C28  C26  N27     0.00   0.0  0
 664  CONST_24  C28   C29  C30  N27     0.00   0.0  0
 664  CONST_25  C30   N27  C26  C28     0.00   0.0  0
 664  CONST_26  N15   C12  C13  C8    180.00   0.0  0
 664  CONST_27  N15   C12  C11  C10   180.00   0.0  0
 664  CONST_29  N7    C2   N1   C6    180.00   0.0  0
 664  CONST_30  C4    N3   C2   N7    180.00   0.0  0
 664  CONST_31  C10   C9   C8   N7    180.00   0.0  0
 664  CONST_32  C12   C13  C8   N7    180.00   0.0  0
 664  CONST_33  C36   N27  C26  C4      0.00   0.0  0
 664  CONST_34  O14   C9   C10  C11   180.00   0.0  0
 664  CONST_35  O14   C9   C8   C13   180.00   0.0  0
 664  CONST_36  C36   N27  C26  C28   180.00   0.0  0
 664  CONST_37  C36   N27  C30  C29   180.00   0.0  0
 664  CONST_38  C36   N27  C30  C31     0.00   0.0  0
 664  CONST_39  O35   C34  N33  C32   180.00   0.0  0
 664  CONST_40  H5    C5   C6   N1    180.00   0.0  0
 664  CONST_41  H6    C6   N1   C2    180.00   0.0  0
 664  CONST_42  H28   C28  C26  C4      0.00   0.0  0
 664  CONST_43  H10   C10  C9   C8    180.00   0.0  0
 664  CONST_44  H13   C13  C8   C9    180.00   0.0  0
 664  CONST_45  HA    C11  C10  C9    180.00   0.0  0
 664  CONST_46  H33   N33  C34  C29   180.00   0.0  0
 664  Var_01    C16   N15  C12  C11     1.86  30.0  2
 664  Var_02    C17   C16  N15  C12   164.65  30.0  1
 664  Var_03    C19   C20  N15  C12  -163.68  30.0  1
 664  Var_04    N18   C17  C16  N15    55.88  30.0  1
 664  Var_05    N18   C19  C20  N15   -56.92  30.0  1
 664  Var_06    C19   N18  C17  C16   -58.51  30.0  1
 664  Var_07    C20   C19  N18  C17    58.83  30.0  1
 664  Var_08    C32   C31  C30  N27   155.84  30.0  1
 664  Var_09    N33   C34  C29  C28  -176.40  30.0  1
 664  Var_10    N33   C32  C31  C30    47.43  30.0  1
 664  Var_11    C34   N33  C32  C31   -47.14  30.0  1
 664  Var_12    C8    N7   C2   N1      4.81  30.0  2
 664  Var_13    C9    C8   N7   C2    144.71  30.0  2
 664  Var_14    H361  C36  N27  C26    74.80  30.0  2
 664  Var_15    H211  C21  N18  C17    61.01  30.0  3
 664  Var_16    F23   C22  O14  C9     54.82  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
 664  plan-1  N1   0.020
 664  plan-1  C2   0.020
 664  plan-1  C6   0.020
 664  plan-1  N3   0.020
 664  plan-1  N7   0.020
 664  plan-1  C4   0.020
 664  plan-1  C5   0.020
 664  plan-1  C26  0.020
 664  plan-1  H6   0.020
 664  plan-1  H5   0.020
 664  plan-2  N7   0.020
 664  plan-2  C8   0.020
 664  plan-2  C10  0.020
 664  plan-2  C9   0.020
 664  plan-2  C11  0.020
 664  plan-2  C13  0.020
 664  plan-2  C12  0.020
 664  plan-2  O14  0.020
 664  plan-2  N15  0.020
 664  plan-2  H13  0.020
 664  plan-2  H10  0.020
 664  plan-2  HA   0.020
 664  plan-3  C4   0.020
 664  plan-3  C26  0.020
 664  plan-3  N27  0.020
 664  plan-3  C28  0.020
 664  plan-3  C29  0.020
 664  plan-3  C30  0.020
 664  plan-3  C31  0.020
 664  plan-3  C34  0.020
 664  plan-3  C36  0.020
 664  plan-3  H28  0.020
 664  plan-4  C29  0.020
 664  plan-4  C32  0.020
 664  plan-4  N33  0.020
 664  plan-4  C34  0.020
 664  plan-4  O35  0.020
 664  plan-4  H33  0.020

