# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:26:13 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 1-(2-hydroxyethyl)-8-[[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino]-4,5-dihydropyrimido[5,4-g]indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(OC(F)(F)F)c(Nc3ncc4CCc5c(nn(CCO)c5c4n3)C(N)=O)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
 937  937  1-(2-hydroxyethyl)-8-[[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino]-4,5-dihydropyrimido[5,4-g]indazole-3-carboxamide  ligand  65  38  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_937
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
 937  N1    N  N     0  -0.450   0.1356   1.3359   0.6694
 937  C2    C  CR6   0   0.593   0.4404   0.0933   0.3239
 937  N3    N  N     0  -0.491   1.6699  -0.3705   0.0932
 937  C4    C  CR16  0  -0.048   1.1506   2.1862   0.7744
 937  C5    C  CR66  0  -0.029   2.4683   1.8387   0.5497
 937  C6    C  CR66  0   0.279   2.6635   0.4932   0.2088
 937  C7    C  C     0  -0.514   4.9107   2.1679   1.1037
 937  C8    C  C     0  -0.522   3.6179   2.8058   0.5897
 937  C9    C  CR56  0  -0.134   5.1104   0.8464   0.4393
 937  C10   C  CR56  0   0.414   4.0407   0.0792   0.0238
 937  N11   N  NR5   0  -0.362   4.5418  -1.0736  -0.4849
 937  N12   N  N     0  -0.276   5.8554  -1.0845  -0.4390
 937  C13   C  CR5   0   0.085   6.2272   0.0574   0.1302
 937  N14   N  NH1   0  -0.770  -0.5443  -0.8425   0.1997
 937  C15   C  C     0   0.469   7.6541   0.3663   0.3714
 937  O16   O  O     0  -0.479   7.9824   1.3953   0.9477
 937  C17   C  CR6   0   0.346  -1.9148  -0.6961   0.3784
 937  C18   C  CR16  0  -0.400  -2.6038   0.4566   0.0280
 937  C19   C  CR6   0   0.397  -3.9931   0.5620   0.1791
 937  C20   C  CR16  0  -0.384  -4.6939  -0.5526   0.6551
 937  C21   C  CR16  0  -0.285  -4.0183  -1.7196   0.9754
 937  C22   C  CR6   0   0.212  -2.6470  -1.7859   0.8634
 937  O23   O  O2    0  -0.524  -1.9693  -2.9650   1.1685
 937  C24   C  CT    0   1.076  -1.6569  -3.1795   2.4546
 937  F25   F  F     0  -0.299  -2.7328  -3.3894   3.2160
 937  F26   F  F     0  -0.277  -0.8962  -4.2616   2.5092
 937  F27   F  F     0  -0.298  -0.9895  -2.1641   3.0032
 937  N28   N  NH2   0  -0.811   8.5242  -0.5463  -0.0793
 937  C29   C  CH2   0  -0.336   3.8388  -2.1672  -1.1275
 937  C30   C  CH2   0  -0.151   3.4054  -1.7851  -2.5350
 937  O31   O  OH1   0  -0.666   2.7861  -2.9164  -3.0947
 937  N32   N  NT    0  -0.521  -4.6337   1.7381  -0.1950
 937  C33   C  CH2   0  -0.316  -6.0828   1.7656  -0.1507
 937  C34   C  CH2   0  -0.278  -6.6191   2.9578  -0.9207
 937  N35   N  NT    0  -0.412  -6.0642   4.1969  -0.4223
 937  C36   C  CH2   0  -0.284  -4.6215   4.1627  -0.5275
 937  C37   C  CH2   0  -0.306  -4.0548   2.9972   0.2577
 937  C38   C  CH3   0  -0.520  -6.6281   5.3448  -1.0937
 937  H4    H  HCR6  0   0.270   0.8945   3.2036   1.0535
 937  H14   H  HNH1  0   0.405  -0.1982  -1.7753   0.0360
 937  H81C  H  H     0   0.260   3.7928   3.1819  -0.4241
 937  H82C  H  H     0   0.264   3.3553   3.6713   1.1996
 937  H71C  H  H     0   0.265   5.7517   2.8332   0.9212
 937  H72C  H  H     0   0.256   4.8563   2.0230   2.1873
 937  H291  H  HCH2  0   0.279   4.5293  -3.0082  -1.1551
 937  H292  H  HCH2  0   0.274   2.9763  -2.4391  -0.5230
 937  H281  H  HNH2  0   0.410   8.2168  -1.3811  -0.5488
 937  H282  H  HNH2  0   0.406   9.5131  -0.4145   0.0541
 937  H18   H  HCR6  0   0.279  -2.0454   1.2767  -0.3933
 937  H20   H  HCR6  0   0.276  -5.7643  -0.5292   0.7942
 937  H21   H  HCR6  0   0.276  -4.5750  -2.5778   1.3283
 937  H301  H  HCH2  0   0.209   2.7226  -0.9287  -2.4855
 937  H302  H  HCH2  0   0.206   4.2871  -1.4698  -3.1071
 937  H31   H  HOH1  0   0.461   2.4669  -2.6818  -3.9706
 937  H331  H  HCH2  0   0.254  -6.4802   0.8632  -0.6159
 937  H332  H  HCH2  0   0.216  -6.4540   1.7973   0.8844
 937  H371  H  HCH2  0   0.220  -4.2525   3.1463   1.3290
 937  H372  H  HCH2  0   0.254  -2.9750   2.9898   0.1271
 937  H341  H  HCH2  0   0.194  -6.4056   2.8190  -1.9951
 937  H342  H  HCH2  0   0.242  -7.7058   2.9789  -0.8106
 937  H361  H  HCH2  0   0.194  -4.2884   4.0881  -1.5776
 937  H362  H  HCH2  0   0.242  -4.2075   5.0893  -0.1234
 937  H381  H  HCH3  0   0.234  -7.7097   5.3658  -0.9513
 937  H382  H  HCH3  0   0.234  -6.2164   6.2634  -0.6732
 937  H383  H  HCH3  0   0.193  -6.4336   5.3542  -2.1776

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
 937  N1   C2    aromatic  1.325  0.020  1.325
 937  N1   C4    aromatic  1.328  0.020  1.328
 937  C2   N3    aromatic  1.334  0.020  1.334
 937  C2   N14   single    1.364  0.020  1.364
 937  N3   C6    aromatic  1.322  0.020  1.322
 937  C4   C5    aromatic  1.381  0.020  1.381
 937  C5   C6    aromatic  1.402  0.020  1.402
 937  C5   C8    single    1.503  0.020  1.503
 937  C6   C10   aromatic  1.450  0.020  1.450
 937  C7   C8    single    1.531  0.020  1.531
 937  C7   C9    single    1.492  0.020  1.492
 937  C9   C10   aromatic  1.380  0.020  1.380
 937  C9   C13   aromatic  1.402  0.020  1.402
 937  C10  N11   aromatic  1.356  0.020  1.356
 937  N11  N12   aromatic  1.314  0.020  1.314
 937  N11  C29   single    1.450  0.020  1.450
 937  N12  C13   aromatic  1.329  0.020  1.329
 937  C13  C15   single    1.480  0.020  1.480
 937  N14  C17   single    1.390  0.020  1.390
 937  C15  O16   double    1.224  0.020  1.224
 937  C15  N28   single    1.339  0.020  1.339
 937  C17  C18   aromatic  1.388  0.020  1.388
 937  C17  C22   aromatic  1.400  0.020  1.400
 937  C18  C19   aromatic  1.402  0.020  1.402
 937  C19  C20   aromatic  1.400  0.020  1.400
 937  C19  N32   single    1.391  0.020  1.391
 937  C20  C21   aromatic  1.386  0.020  1.386
 937  C21  C22   aromatic  1.378  0.020  1.378
 937  C22  O23   single    1.394  0.020  1.394
 937  O23  C24   single    1.341  0.020  1.341
 937  C24  F25   single    1.335  0.020  1.335
 937  C24  F26   single    1.324  0.020  1.324
 937  C24  F27   single    1.333  0.020  1.333
 937  C29  C30   single    1.521  0.020  1.521
 937  C30  O31   single    1.406  0.020  1.406
 937  N32  C33   single    1.450  0.020  1.450
 937  N32  C37   single    1.458  0.020  1.458
 937  C33  C34   single    1.517  0.020  1.517
 937  C34  N35   single    1.446  0.020  1.446
 937  N35  C36   single    1.447  0.020  1.447
 937  N35  C38   single    1.444  0.020  1.444
 937  C36  C37   single    1.515  0.020  1.515
 937  C4   H4    single    0.930  0.020  1.080
 937  N14  H14   single    0.860  0.020  1.020
 937  C8   H81C  single    0.970  0.020  1.090
 937  C8   H82C  single    0.970  0.020  1.090
 937  C7   H71C  single    0.970  0.020  1.090
 937  C7   H72C  single    0.970  0.020  1.090
 937  C29  H291  single    0.970  0.020  1.090
 937  C29  H292  single    0.970  0.020  1.090
 937  N28  H281  single    0.860  0.020  1.020
 937  N28  H282  single    0.860  0.020  1.020
 937  C18  H18   single    0.930  0.020  1.080
 937  C20  H20   single    0.930  0.020  1.080
 937  C21  H21   single    0.930  0.020  1.080
 937  C30  H301  single    0.970  0.020  1.090
 937  C30  H302  single    0.970  0.020  1.090
 937  O31  H31   single    0.850  0.020  0.980
 937  C33  H331  single    0.970  0.020  1.090
 937  C33  H332  single    0.970  0.020  1.090
 937  C37  H371  single    0.970  0.020  1.090
 937  C37  H372  single    0.970  0.020  1.090
 937  C34  H341  single    0.970  0.020  1.090
 937  C34  H342  single    0.970  0.020  1.090
 937  C36  H361  single    0.970  0.020  1.090
 937  C36  H362  single    0.970  0.020  1.090
 937  C38  H381  single    0.970  0.020  1.090
 937  C38  H382  single    0.970  0.020  1.090
 937  C38  H383  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
 937  C4    N1   C2    116.43  3.000
 937  N14   C2   N3    114.27  3.000
 937  N14   C2   N1    120.06  3.000
 937  N3    C2   N1    125.66  3.000
 937  C6    N3   C2    116.78  3.000
 937  H4    C4   C5    120.18  3.000
 937  H4    C4   N1    116.10  3.000
 937  C5    C4   N1    123.72  3.000
 937  C8    C5   C6    121.18  3.000
 937  C8    C5   C4    124.30  3.000
 937  C6    C5   C4    114.45  3.000
 937  C10   C6   C5    115.93  3.000
 937  C10   C6   N3    121.08  3.000
 937  C5    C6   N3    122.96  3.000
 937  H72C  C7   H71C  106.58  3.000
 937  H72C  C7   C9    109.28  3.000
 937  H71C  C7   C9    111.31  3.000
 937  H72C  C7   C8    110.22  3.000
 937  H71C  C7   C8    109.99  3.000
 937  C9    C7   C8    109.43  3.000
 937  H82C  C8   H81C  106.47  3.000
 937  H82C  C8   C7    110.26  3.000
 937  H81C  C8   C7    108.60  3.000
 937  H82C  C8   C5    109.96  3.000
 937  H81C  C8   C5    108.57  3.000
 937  C7    C8   C5    112.76  3.000
 937  C13   C9   C10   103.78  3.000
 937  C13   C9   C7    134.67  3.000
 937  C10   C9   C7    121.49  3.000
 937  N11   C10  C9    107.40  3.000
 937  N11   C10  C6    129.91  3.000
 937  C9    C10  C6    122.61  3.000
 937  C29   N11  N12   119.58  3.000
 937  C29   N11  C10   128.92  3.000
 937  N12   N11  C10   111.30  3.000
 937  C13   N12  N11   106.71  3.000
 937  C15   C13  N12   121.26  3.000
 937  C15   C13  C9    127.94  3.000
 937  N12   C13  C9    110.80  3.000
 937  H14   N14  C17   117.18  3.000
 937  H14   N14  C2    113.67  3.000
 937  C17   N14  C2    128.89  3.000
 937  N28   C15  O16   123.86  3.000
 937  N28   C15  C13   115.43  3.000
 937  O16   C15  C13   120.71  3.000
 937  C22   C17  C18   118.33  3.000
 937  C22   C17  N14   118.58  3.000
 937  C18   C17  N14   122.99  3.000
 937  H18   C18  C19   119.90  3.000
 937  H18   C18  C17   118.26  3.000
 937  C19   C18  C17   121.82  3.000
 937  N32   C19  C20   122.30  3.000
 937  N32   C19  C18   119.42  3.000
 937  C20   C19  C18   118.23  3.000
 937  H20   C20  C21   118.15  3.000
 937  H20   C20  C19   121.52  3.000
 937  C21   C20  C19   120.33  3.000
 937  H21   C21  C22   120.03  3.000
 937  H21   C21  C20   119.50  3.000
 937  C22   C21  C20   120.46  3.000
 937  O23   C22  C21   120.46  3.000
 937  O23   C22  C17   118.70  3.000
 937  C21   C22  C17   120.76  3.000
 937  C24   O23  C22   117.30  3.000
 937  F27   C24  F26   108.54  3.000
 937  F27   C24  F25   106.77  3.000
 937  F26   C24  F25   108.13  3.000
 937  F27   C24  O23   112.92  3.000
 937  F26   C24  O23   107.71  3.000
 937  F25   C24  O23   112.62  3.000
 937  H282  N28  H281  118.08  3.000
 937  H282  N28  C15   120.30  3.000
 937  H281  N28  C15   121.61  3.000
 937  H292  C29  H291  108.90  3.000
 937  H292  C29  C30   110.54  3.000
 937  H291  C29  C30   110.56  3.000
 937  H292  C29  N11   109.07  3.000
 937  H291  C29  N11   106.65  3.000
 937  C30   C29  N11   111.01  3.000
 937  H302  C30  H301  107.43  3.000
 937  H302  C30  O31   112.18  3.000
 937  H301  C30  O31   111.84  3.000
 937  H302  C30  C29   109.00  3.000
 937  H301  C30  C29   109.38  3.000
 937  O31   C30  C29   106.96  3.000
 937  H31   O31  C30   108.22  3.000
 937  C37   N32  C33   111.78  3.000
 937  C37   N32  C19   117.65  3.000
 937  C33   N32  C19   117.91  3.000
 937  H332  C33  H331  107.59  3.000
 937  H332  C33  C34   109.61  3.000
 937  H331  C33  C34   107.76  3.000
 937  H332  C33  N32   111.49  3.000
 937  H331  C33  N32   109.61  3.000
 937  C34   C33  N32   110.65  3.000
 937  H342  C34  H341  107.03  3.000
 937  H342  C34  N35   109.30  3.000
 937  H341  C34  N35   111.64  3.000
 937  H342  C34  C33   108.40  3.000
 937  H341  C34  C33   109.06  3.000
 937  N35   C34  C33   111.27  3.000
 937  C38   N35  C36   111.98  3.000
 937  C38   N35  C34   111.77  3.000
 937  C36   N35  C34   109.71  3.000
 937  H362  C36  H361  107.14  3.000
 937  H362  C36  C37   108.60  3.000
 937  H361  C36  C37   109.15  3.000
 937  H362  C36  N35   109.32  3.000
 937  H361  C36  N35   111.81  3.000
 937  C37   C36  N35   110.70  3.000
 937  H372  C37  H371  107.25  3.000
 937  H372  C37  C36   108.32  3.000
 937  H371  C37  C36   109.47  3.000
 937  H372  C37  N32   110.55  3.000
 937  H371  C37  N32   110.38  3.000
 937  C36   C37  N32   110.79  3.000
 937  H383  C38  H382  107.79  3.000
 937  H383  C38  H381  107.66  3.000
 937  H382  C38  H381  107.91  3.000
 937  H383  C38  N35   113.29  3.000
 937  H382  C38  N35   110.04  3.000
 937  H381  C38  N35   109.97  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
 937  CONST_01  C6    N3   C2   N1      0.00   0.0  0
 937  CONST_02  C6    C5   C4   N1      0.00   0.0  0
 937  CONST_03  C5    C4   N1   C2      0.00   0.0  0
 937  CONST_04  C5    C6   N3   C2      0.00   0.0  0
 937  CONST_05  C10   C6   N3   C2    180.00   0.0  0
 937  CONST_06  C4    N1   C2   N3      0.00   0.0  0
 937  CONST_07  C4    C5   C6   N3      0.00   0.0  0
 937  CONST_09  N11   C10  C6   N3      0.00   0.0  0
 937  CONST_10  C10   C6   C5   C4    180.00   0.0  0
 937  CONST_11  C9    C10  C6   C5      0.00   0.0  0
 937  CONST_12  N11   C10  C6   C5    180.00   0.0  0
 937  CONST_13  C13   C9   C10  C6    180.00   0.0  0
 937  CONST_14  N12   N11  C10  C6    180.00   0.0  0
 937  CONST_15  N12   N11  C10  C9      0.00   0.0  0
 937  CONST_16  N11   N12  C13  C9      0.00   0.0  0
 937  CONST_17  N12   C13  C9   C10     0.00   0.0  0
 937  CONST_18  C13   N12  N11  C10     0.00   0.0  0
 937  CONST_19  C13   C9   C10  N11     0.00   0.0  0
 937  CONST_20  C20   C19  C18  C17     0.00   0.0  0
 937  CONST_21  C20   C21  C22  C17     0.00   0.0  0
 937  CONST_22  C21   C22  C17  C18     0.00   0.0  0
 937  CONST_23  C21   C20  C19  C18     0.00   0.0  0
 937  CONST_24  C22   C17  C18  C19     0.00   0.0  0
 937  CONST_25  C22   C21  C20  C19     0.00   0.0  0
 937  CONST_26  N32   C19  C18  C17   180.00   0.0  0
 937  CONST_27  N32   C19  C20  C21   180.00   0.0  0
 937  CONST_28  N14   C2   N1   C4    180.00   0.0  0
 937  CONST_29  N14   C2   N3   C6    180.00   0.0  0
 937  CONST_30  C29   N11  C10  C6      0.00   0.0  0
 937  CONST_31  C15   C13  C9   C7      0.00   0.0  0
 937  CONST_32  C29   N11  C10  C9    180.00   0.0  0
 937  CONST_33  C15   C13  C9   C10   180.00   0.0  0
 937  CONST_34  C15   C13  N12  N11   180.00   0.0  0
 937  CONST_35  C29   N11  N12  C13   180.00   0.0  0
 937  CONST_36  C19   C18  C17  N14   180.00   0.0  0
 937  CONST_37  C21   C22  C17  N14   180.00   0.0  0
 937  CONST_38  O23   C22  C17  C18   180.00   0.0  0
 937  CONST_39  O23   C22  C21  C20   180.00   0.0  0
 937  CONST_40  H4    C4   N1   C2    180.00   0.0  0
 937  CONST_41  H21   C21  C22  C17   180.00   0.0  0
 937  CONST_42  H20   C20  C19  C18   180.00   0.0  0
 937  CONST_43  H18   C18  C19  C20   180.00   0.0  0
 937  CONST_44  H281  N28  C15  C13     0.00   0.0  0
 937  CONST_45  H282  N28  C15  C13   180.00   0.0  0
 937  Var_01    C7    C8   C5   C4    146.89  30.0  1
 937  Var_02    C9    C7   C8   C5     45.65  30.0  1
 937  Var_03    C10   C9   C7   C8    -29.81  30.0  1
 937  Var_04    C33   N32  C19  C18   173.97  30.0  2
 937  Var_05    C34   C33  N32  C19  -165.06  30.0  1
 937  Var_06    C36   C37  N32  C19   164.38  30.0  1
 937  Var_07    N35   C34  C33  N32   -56.24  30.0  1
 937  Var_08    N35   C36  C37  N32    56.85  30.0  1
 937  Var_09    C36   N35  C34  C33    58.64  30.0  1
 937  Var_10    C37   C36  N35  C34   -58.81  30.0  1
 937  Var_11    C17   N14  C2   N1      0.58  30.0  2
 937  Var_12    C18   C17  N14  C2     35.68  30.0  2
 937  Var_13    O16   C15  C13  C9      2.83  30.0  2
 937  Var_14    C30   C29  N11  C10    74.27  30.0  2
 937  Var_15    H381  C38  N35  C34    59.30  30.0  3
 937  Var_16    O31   C30  C29  N11   177.63  30.0  3
 937  Var_17    F25   C24  O23  C22    67.76  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
 937  plan-1  N14   0.020
 937  plan-1  C17   0.020
 937  plan-1  C18   0.020
 937  plan-1  C19   0.020
 937  plan-1  C20   0.020
 937  plan-1  C21   0.020
 937  plan-1  C22   0.020
 937  plan-1  O23   0.020
 937  plan-1  N32   0.020
 937  plan-1  H18   0.020
 937  plan-1  H20   0.020
 937  plan-1  H21   0.020
 937  plan-2  C6    0.020
 937  plan-2  C7    0.020
 937  plan-2  C9    0.020
 937  plan-2  C10   0.020
 937  plan-2  N11   0.020
 937  plan-2  N12   0.020
 937  plan-2  C13   0.020
 937  plan-2  C15   0.020
 937  plan-2  C29   0.020
 937  plan-3  N1    0.020
 937  plan-3  C2    0.020
 937  plan-3  N3    0.020
 937  plan-3  C4    0.020
 937  plan-3  C5    0.020
 937  plan-3  C6    0.020
 937  plan-3  C8    0.020
 937  plan-3  C10   0.020
 937  plan-3  N14   0.020
 937  plan-3  H4    0.020
 937  plan-4  C13   0.020
 937  plan-4  C15   0.020
 937  plan-4  O16   0.020
 937  plan-4  N28   0.020
 937  plan-4  H281  0.020
 937  plan-4  H282  0.020

