# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:20:04 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: [(2-chloro-5-methylphenyl){6-[(4-{[(2R)-3-(dimethylamino)-2-hydroxypropyl]oxy}phenyl)amino]pyrimidin-4-yl}amino]acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@@H](O)COc1ccc(Nc2cc(ncn2)N(CC#N)c3cc(C)ccc3Cl)cc1
#
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
 QQ2  QQ2  '[(2-chloro-5-methylphenyl){6-[(4-{[(2R)-3-(dimethylamino)-2-hydroxypropyl]oxy}phenyl)amino]pyrimidin-4-yl}amino]acetonitrile'  ligand  60  33  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQ2
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
 QQ2  C22   C   CR16  0  -0.347   3.2988   1.4213  -0.2243
 QQ2  C1    C   CR16  0   0.064  -2.0294   1.6653   0.6575
 QQ2  C5    C   CR6   0   0.556  -0.9576   0.1583  -0.6280
 QQ2  C4    C   CR16  0  -0.503  -2.1936  -0.3377  -1.0649
 QQ2  C3    C   CR6   0   0.553  -3.3266   0.2796  -0.5559
 QQ2  C11   C   CR16  0  -0.308  -7.9517   1.3185   1.1634
 QQ2  C10   C   CR6   0   0.108  -7.7263   1.7485  -0.1407
 QQ2  C9    C   CR16  0  -0.329  -6.5933   1.2769  -0.7973
 QQ2  C8    C   CR6   0   0.401  -5.7151   0.3906  -0.1923
 QQ2  C12   C   CR16  0  -0.209  -7.0856   0.4336   1.7886
 QQ2  C16   C   CH2   0  -0.445  -4.8225  -1.1179  -1.8979
 QQ2  C13   C   CR6   0  -0.091  -5.9753  -0.0350   1.1079
 QQ2  C20   C   CR6   0   0.327   1.5094  -0.1059  -0.7484
 QQ2  N2    N   N     0  -0.471  -3.2439   1.2929   0.3158
 QQ2  N6    N   N     0  -0.476  -0.8781   1.1676   0.2427
 QQ2  N7    N   NT    0  -0.589  -4.5969  -0.0901  -0.9174
 QQ2  N18   N   NS    0  -0.252  -4.5030  -3.5423  -0.9583
 QQ2  N19   N   NH1   0  -0.771   0.1831  -0.4073  -1.0913
 QQ2  C21   C   CR16  0  -0.269   1.9679   1.1930  -0.5173
 QQ2  C23   C   CR6   0   0.376   4.2158   0.3708  -0.1712
 QQ2  C24   C   CR16  0  -0.373   3.7688  -0.9227  -0.4197
 QQ2  C25   C   CR16  0  -0.322   2.4265  -1.1492  -0.6963
 QQ2  O26   O   O2    0  -0.473   5.4903   0.7014   0.1198
 QQ2  C27   C   CH2   0  -0.193   6.4800  -0.3046   0.0891
 QQ2  C28   C   CH1   0  -0.014   7.8304   0.3548   0.3413
 QQ2  C29   C   CH2   0  -0.288   8.9169  -0.7190   0.3153
 QQ2  N30   N   NT    0  -0.411  10.1594  -0.3485   0.9657
 QQ2  C31   C   CH3   0  -0.521  10.9580  -1.5261   1.2401
 QQ2  C32   C   CH3   0  -0.529  10.9410   0.6133   0.2132
 QQ2  O33   O   OH1   0  -0.653   8.0493   1.4184  -0.5568
 QQ2  CL1   CL  CL    0  -0.112  -4.9044  -1.1478   1.8800
 QQ2  H22   H   HCR6  0   0.262   3.6405   2.4333  -0.0457
 QQ2  H1    H   HCR6  0   0.253  -1.9640   2.4842   1.3671
 QQ2  H4    H   HCR6  0   0.281  -2.2274  -1.1676  -1.7559
 QQ2  H11   H   HCR6  0   0.263  -8.8156   1.6787   1.7082
 QQ2  H9    H   HCR6  0   0.266  -6.3755   1.6090  -1.8056
 QQ2  H12   H   HCR6  0   0.282  -7.2777   0.1082   2.8019
 QQ2  H161  H   HCH2  0   0.353  -5.8402  -1.0389  -2.2796
 QQ2  H162  H   HCH2  0   0.331  -4.1628  -0.9976  -2.7593
 QQ2  H19   H   HNH1  0   0.411   0.0608  -1.2386  -1.6482
 QQ2  H21   H   HCR6  0   0.268   1.2907   2.0310  -0.5697
 QQ2  H24   H   HCR6  0   0.279   4.4384  -1.7712  -0.3921
 QQ2  H25   H   HCR6  0   0.270   2.0946  -2.1652  -0.8744
 QQ2  H271  H   HCH2  0   0.222   6.4850  -0.8158  -0.8837
 QQ2  H272  H   HCH2  0   0.230   6.2913  -1.0620   0.8583
 QQ2  H28   H   HCH1  0   0.238   7.8184   0.8023   1.3403
 QQ2  H291  H   HCH2  0   0.198   9.0772  -1.0449  -0.7301
 QQ2  H292  H   HCH2  0   0.238   8.5262  -1.5926   0.8448
 QQ2  H311  H   HCH3  0   0.233  11.8614  -1.2425   1.7819
 QQ2  H312  H   HCH3  0   0.233  10.4020  -2.2283   1.8632
 QQ2  H313  H   HCH3  0   0.191  11.2736  -2.0601   0.3294
 QQ2  H321  H   HCH3  0   0.243  10.4024   1.5486   0.0869
 QQ2  H322  H   HCH3  0   0.228  11.8650   0.8307   0.7510
 QQ2  H323  H   HCH3  0   0.187  11.2176   0.2447  -0.7879
 QQ2  H33   H   HOH1  0   0.444   8.1663   1.0532  -1.4410
 QQ2  H331  H   HCH3  0   0.254  -9.3720   2.1320  -1.4633
 QQ2  H332  H   HCH3  0   0.249  -9.2670   3.2509  -0.1122
 QQ2  H333  H   HCH3  0   0.249  -8.1471   3.3914  -1.4675
 QQ2  C33   C   CH3   0  -0.723  -8.6753   2.6837  -0.8291
 QQ2  C17   C   CSP   0   0.134  -4.6444  -2.4758  -1.3626

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
 QQ2  C22  C21   aromatic  1.382  0.020  1.382
 QQ2  C22  C23   aromatic  1.396  0.020  1.396
 QQ2  C22  H22   single    0.930  0.020  1.080
 QQ2  C1   N2    aromatic  1.315  0.020  1.315
 QQ2  C1   N6    aromatic  1.321  0.020  1.321
 QQ2  C1   H1    single    0.930  0.020  1.080
 QQ2  C5   C4    aromatic  1.402  0.020  1.402
 QQ2  C5   N6    aromatic  1.335  0.020  1.335
 QQ2  C5   N19   single    1.355  0.020  1.355
 QQ2  C4   C3    aromatic  1.387  0.020  1.387
 QQ2  C4   H4    single    0.930  0.020  1.080
 QQ2  C3   N2    aromatic  1.339  0.020  1.339
 QQ2  C3   N7    single    1.372  0.020  1.372
 QQ2  C11  C10   aromatic  1.391  0.020  1.391
 QQ2  C11  C12   aromatic  1.387  0.020  1.387
 QQ2  C11  H11   single    0.930  0.020  1.080
 QQ2  C10  C9    aromatic  1.392  0.020  1.392
 QQ2  C10  C33   single    1.500  0.020  1.500
 QQ2  C9   C8    aromatic  1.387  0.020  1.387
 QQ2  C9   H9    single    0.930  0.020  1.080
 QQ2  C8   C13   aromatic  1.393  0.020  1.393
 QQ2  C8   N7    single    1.417  0.020  1.417
 QQ2  C12  C13   aromatic  1.384  0.020  1.384
 QQ2  C12  H12   single    0.930  0.020  1.080
 QQ2  C17  C16   single    1.470  0.020  1.470
 QQ2  C17  N18   triple    1.149  0.020  1.149
 QQ2  C16  N7    single    1.438  0.020  1.438
 QQ2  C16  H161  single    0.970  0.020  1.090
 QQ2  C16  H162  single    0.970  0.020  1.090
 QQ2  C13  CL1   single    1.727  0.020  1.727
 QQ2  C20  N19   single    1.403  0.020  1.403
 QQ2  C20  C21   aromatic  1.397  0.020  1.397
 QQ2  C20  C25   aromatic  1.390  0.020  1.390
 QQ2  N19  H19   single    0.860  0.020  1.020
 QQ2  C21  H21   single    0.930  0.020  1.080
 QQ2  C23  C24   aromatic  1.391  0.020  1.391
 QQ2  C23  O26   single    1.348  0.020  1.348
 QQ2  C24  C25   aromatic  1.389  0.020  1.389
 QQ2  C24  H24   single    0.930  0.020  1.080
 QQ2  C25  H25   single    0.930  0.020  1.080
 QQ2  O26  C27   single    1.412  0.020  1.412
 QQ2  C27  C28   single    1.524  0.020  1.524
 QQ2  C27  H271  single    0.970  0.020  1.090
 QQ2  C27  H272  single    0.970  0.020  1.090
 QQ2  C28  C29   single    1.528  0.020  1.528
 QQ2  C28  O33   single    1.409  0.020  1.409
 QQ2  C28  H28   single    0.970  0.020  1.090
 QQ2  C29  N30   single    1.451  0.020  1.451
 QQ2  C29  H291  single    0.970  0.020  1.090
 QQ2  C29  H292  single    0.970  0.020  1.090
 QQ2  N30  C31   single    1.449  0.020  1.449
 QQ2  N30  C32   single    1.450  0.020  1.450
 QQ2  C31  H311  single    0.970  0.020  1.090
 QQ2  C31  H312  single    0.970  0.020  1.090
 QQ2  C31  H313  single    0.970  0.020  1.090
 QQ2  C32  H321  single    0.970  0.020  1.090
 QQ2  C32  H322  single    0.970  0.020  1.090
 QQ2  C32  H323  single    0.970  0.020  1.090
 QQ2  O33  H33   single    0.850  0.020  0.980
 QQ2  C33  H331  single    0.970  0.020  1.090
 QQ2  C33  H332  single    0.970  0.020  1.090
 QQ2  C33  H333  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
 QQ2  H22   C22  C23   119.33  3.000
 QQ2  H22   C22  C21   119.56  3.000
 QQ2  C23   C22  C21   121.10  3.000
 QQ2  H1    C1   N6    115.91  3.000
 QQ2  H1    C1   N2    116.04  3.000
 QQ2  N6    C1   N2    128.05  3.000
 QQ2  N19   C5   N6    119.24  3.000
 QQ2  N19   C5   C4    119.22  3.000
 QQ2  N6    C5   C4    121.55  3.000
 QQ2  H4    C4   C3    123.43  3.000
 QQ2  H4    C4   C5    119.92  3.000
 QQ2  C3    C4   C5    116.65  3.000
 QQ2  N7    C3   N2    115.63  3.000
 QQ2  N7    C3   C4    122.68  3.000
 QQ2  N2    C3   C4    121.68  3.000
 QQ2  H11   C11  C12   118.91  3.000
 QQ2  H11   C11  C10   119.86  3.000
 QQ2  C12   C11  C10   121.23  3.000
 QQ2  C33   C10  C9    120.65  3.000
 QQ2  C33   C10  C11   121.36  3.000
 QQ2  C9    C10  C11   117.99  3.000
 QQ2  H9    C9   C8    118.33  3.000
 QQ2  H9    C9   C10   119.91  3.000
 QQ2  C8    C9   C10   121.75  3.000
 QQ2  N7    C8   C13   121.44  3.000
 QQ2  N7    C8   C9    119.56  3.000
 QQ2  C13   C8   C9    118.97  3.000
 QQ2  H12   C12  C13   120.10  3.000
 QQ2  H12   C12  C11   120.23  3.000
 QQ2  C13   C12  C11   119.68  3.000
 QQ2  H162  C16  H161  106.26  3.000
 QQ2  H162  C16  N7    111.37  3.000
 QQ2  H161  C16  N7    109.48  3.000
 QQ2  H162  C16  C17   108.41  3.000
 QQ2  H161  C16  C17   107.92  3.000
 QQ2  N7    C16  C17   113.13  3.000
 QQ2  CL1   C13  C12   119.72  3.000
 QQ2  CL1   C13  C8    119.91  3.000
 QQ2  C12   C13  C8    120.37  3.000
 QQ2  C25   C20  C21   118.37  3.000
 QQ2  C25   C20  N19   118.15  3.000
 QQ2  C21   C20  N19   123.41  3.000
 QQ2  C3    N2   C1    116.12  3.000
 QQ2  C5    N6   C1    115.95  3.000
 QQ2  C16   N7   C8    117.88  3.000
 QQ2  C16   N7   C3    121.17  3.000
 QQ2  C8    N7   C3    120.31  3.000
 QQ2  H19   N19  C20   115.28  3.000
 QQ2  H19   N19  C5    115.53  3.000
 QQ2  C20   N19  C5    128.52  3.000
 QQ2  H21   C21  C20   120.55  3.000
 QQ2  H21   C21  C22   119.12  3.000
 QQ2  C20   C21  C22   120.33  3.000
 QQ2  O26   C23  C24   124.77  3.000
 QQ2  O26   C23  C22   116.40  3.000
 QQ2  C24   C23  C22   118.82  3.000
 QQ2  H24   C24  C25   118.39  3.000
 QQ2  H24   C24  C23   121.75  3.000
 QQ2  C25   C24  C23   119.85  3.000
 QQ2  H25   C25  C24   118.79  3.000
 QQ2  H25   C25  C20   119.71  3.000
 QQ2  C24   C25  C20   121.51  3.000
 QQ2  C27   O26  C23   118.90  3.000
 QQ2  H272  C27  H271  107.49  3.000
 QQ2  H272  C27  C28   109.60  3.000
 QQ2  H271  C27  C28   110.11  3.000
 QQ2  H272  C27  O26   110.89  3.000
 QQ2  H271  C27  O26   110.74  3.000
 QQ2  C28   C27  O26   108.02  3.000
 QQ2  H28   C28  O33   105.95  3.000
 QQ2  H28   C28  C29   108.10  3.000
 QQ2  O33   C28  C29   114.15  3.000
 QQ2  H28   C28  C27   108.55  3.000
 QQ2  O33   C28  C27   111.03  3.000
 QQ2  C29   C28  C27   108.86  3.000
 QQ2  H292  C29  H291  105.89  3.000
 QQ2  H292  C29  N30   107.03  3.000
 QQ2  H291  C29  N30   112.00  3.000
 QQ2  H292  C29  C28   107.41  3.000
 QQ2  H291  C29  C28   109.03  3.000
 QQ2  N30   C29  C28   114.96  3.000
 QQ2  C32   N30  C31   109.89  3.000
 QQ2  C32   N30  C29   113.48  3.000
 QQ2  C31   N30  C29   110.45  3.000
 QQ2  H313  C31  H312  107.82  3.000
 QQ2  H313  C31  H311  107.41  3.000
 QQ2  H312  C31  H311  107.80  3.000
 QQ2  H313  C31  N30   113.28  3.000
 QQ2  H312  C31  N30   110.50  3.000
 QQ2  H311  C31  N30   109.83  3.000
 QQ2  H323  C32  H322  107.57  3.000
 QQ2  H323  C32  H321  107.86  3.000
 QQ2  H322  C32  H321  107.79  3.000
 QQ2  H323  C32  N30   112.63  3.000
 QQ2  H322  C32  N30   109.45  3.000
 QQ2  H321  C32  N30   111.35  3.000
 QQ2  H33   O33  C28   108.52  3.000
 QQ2  H333  C33  H332  108.10  3.000
 QQ2  H333  C33  H331  107.29  3.000
 QQ2  H332  C33  H331  107.39  3.000
 QQ2  H333  C33  C10   111.54  3.000
 QQ2  H332  C33  C10   111.50  3.000
 QQ2  H331  C33  C10   110.82  3.000
 QQ2  N18   C17  C16   180.00  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
 QQ2  CONST_01  C25   C20  C21  C22     0.00   0.0  0
 QQ2  CONST_02  C25   C24  C23  C22     0.00   0.0  0
 QQ2  CONST_03  C4    C3   N2   C1      0.00   0.0  0
 QQ2  CONST_04  C4    C5   N6   C1      0.00   0.0  0
 QQ2  CONST_05  N2    C3   C4   C5      0.00   0.0  0
 QQ2  CONST_06  N2    C1   N6   C5      0.00   0.0  0
 QQ2  CONST_07  N6    C5   C4   C3      0.00   0.0  0
 QQ2  CONST_08  N6    C1   N2   C3      0.00   0.0  0
 QQ2  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 QQ2  CONST_10  C8    C13  C12  C11     0.00   0.0  0
 QQ2  CONST_11  C13   C12  C11  C10     0.00   0.0  0
 QQ2  CONST_12  C13   C8   C9   C10     0.00   0.0  0
 QQ2  CONST_13  C12   C11  C10  C9      0.00   0.0  0
 QQ2  CONST_14  C12   C13  C8   C9      0.00   0.0  0
 QQ2  CONST_15  C23   C22  C21  C20     0.00   0.0  0
 QQ2  CONST_16  C23   C24  C25  C20     0.00   0.0  0
 QQ2  CONST_17  C24   C23  C22  C21     0.00   0.0  0
 QQ2  CONST_18  C24   C25  C20  C21     0.00   0.0  0
 QQ2  CONST_19  N19   C20  C21  C22   180.00   0.0  0
 QQ2  CONST_20  N7    C3   N2   C1    180.00   0.0  0
 QQ2  CONST_21  N19   C5   N6   C1    180.00   0.0  0
 QQ2  CONST_22  N7    C3   C4   C5    180.00   0.0  0
 QQ2  CONST_23  N19   C5   C4   C3    180.00   0.0  0
 QQ2  CONST_24  CL1   C13  C12  C11   180.00   0.0  0
 QQ2  CONST_25  N7    C8   C9   C10   180.00   0.0  0
 QQ2  CONST_26  CL1   C13  C8   C9    180.00   0.0  0
 QQ2  CONST_27  C33   C10  C9   C8    180.00   0.0  0
 QQ2  CONST_28  C33   C10  C11  C12   180.00   0.0  0
 QQ2  CONST_29  N7    C8   C13  C12   180.00   0.0  0
 QQ2  CONST_30  C24   C25  C20  N19   180.00   0.0  0
 QQ2  CONST_31  O26   C23  C22  C21   180.00   0.0  0
 QQ2  CONST_32  O26   C23  C24  C25   180.00   0.0  0
 QQ2  CONST_33  H24   C24  C23  C22   180.00   0.0  0
 QQ2  CONST_34  H1    C1   N6   C5    180.00   0.0  0
 QQ2  CONST_35  H9    C9   C10  C11   180.00   0.0  0
 QQ2  CONST_36  H12   C12  C11  C10   180.00   0.0  0
 QQ2  CONST_37  H11   C11  C10  C9    180.00   0.0  0
 QQ2  CONST_38  H22   C22  C21  C20   180.00   0.0  0
 QQ2  CONST_39  H4    C4   C3   N2    180.00   0.0  0
 QQ2  CONST_40  H25   C25  C20  C21   180.00   0.0  0
 QQ2  CONST_41  H21   C21  C22  C23   180.00   0.0  0
 QQ2  Var_01    C21   C20  N19  C5    -38.45  30.0  2
 QQ2  Var_02    C20   N19  C5   C4   -177.23  30.0  2
 QQ2  Var_03    C8    N7   C3   C4    168.10  30.0  2
 QQ2  Var_04    C9    C8   N7   C3    111.92  30.0  2
 QQ2  Var_05    H331  C33  C10  C11   -97.19  30.0  2
 QQ2  Var_06    C17   C16  N7   C3     78.08  30.0  3
 QQ2  Var_07    C28   C27  O26  C23   175.45  30.0  3
 QQ2  Var_08    C31   N30  C29  C28   163.02  30.0  3
 QQ2  Var_09    H311  C31  N30  C29  -176.64  30.0  3
 QQ2  Var_10    H321  C32  N30  C29    61.93  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
 QQ2  chir_01  C28  C27  C29  O33  negativ

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
 QQ2  plan-1  C22  0.020
 QQ2  plan-1  C20  0.020
 QQ2  plan-1  N19  0.020
 QQ2  plan-1  C21  0.020
 QQ2  plan-1  C23  0.020
 QQ2  plan-1  C24  0.020
 QQ2  plan-1  C25  0.020
 QQ2  plan-1  O26  0.020
 QQ2  plan-1  H22  0.020
 QQ2  plan-1  H21  0.020
 QQ2  plan-1  H24  0.020
 QQ2  plan-1  H25  0.020
 QQ2  plan-2  C1   0.020
 QQ2  plan-2  C5   0.020
 QQ2  plan-2  C4   0.020
 QQ2  plan-2  C3   0.020
 QQ2  plan-2  N2   0.020
 QQ2  plan-2  N6   0.020
 QQ2  plan-2  N7   0.020
 QQ2  plan-2  N19  0.020
 QQ2  plan-2  H1   0.020
 QQ2  plan-2  H4   0.020
 QQ2  plan-3  C11  0.020
 QQ2  plan-3  C10  0.020
 QQ2  plan-3  C9   0.020
 QQ2  plan-3  C8   0.020
 QQ2  plan-3  C12  0.020
 QQ2  plan-3  C13  0.020
 QQ2  plan-3  N7   0.020
 QQ2  plan-3  CL1  0.020
 QQ2  plan-3  H11  0.020
 QQ2  plan-3  H9   0.020
 QQ2  plan-3  H12  0.020
 QQ2  plan-3  C33  0.020

