# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:18:45 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: [(2-bromo-4-methylphenyl){6-[(4-{[(2S)-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)c3ccc(C)cc3Br)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
 MFQ  MFQ  '[(2-bromo-4-methylphenyl){6-[(4-{[(2S)-3-(dimethylamino)-2-hydroxypropyl]oxy}phenyl)amino]pyrimidin-4-yl}amino]acetonitrile'  ligand  60  33  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MFQ
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
 MFQ  C22   C   CR16  0  -0.349   0.2209   1.0614   3.6561
 MFQ  C1    C   CR16  0   0.061   1.6576   0.2835  -1.4951
 MFQ  C5    C   CR6   0   0.550  -0.1117  -0.6346  -0.4484
 MFQ  C4    C   CR16  0  -0.500  -0.5918  -1.0989  -1.6796
 MFQ  C3    C   CR6   0   0.557   0.1792  -0.8108  -2.7967
 MFQ  C11   C   CR6   0   0.106   1.9968  -0.0164  -7.4811
 MFQ  C10   C   CR16  0  -0.298   1.1619   0.8835  -6.8263
 MFQ  C9    C   CR6   0  -0.111   0.4501   0.4950  -5.7000
 MFQ  C8    C   CR6   0   0.331   0.5651  -0.7937  -5.1878
 MFQ  C12   C   CR16  0  -0.298   2.1054  -1.3095  -6.9739
 MFQ  C16   C   CH2   0  -0.444  -1.3191  -2.0613  -4.2710
 MFQ  C13   C   CR16  0  -0.250   1.4048  -1.6870  -5.8424
 MFQ  C20   C   CR6   0   0.320  -0.4881  -0.5360   1.9969
 MFQ  N2    N   N     0  -0.472   1.3171  -0.1102  -2.7041
 MFQ  N6    N   N     0  -0.473   1.0215   0.0665  -0.3578
 MFQ  N7    N   NT    0  -0.592  -0.1668  -1.2268  -4.0559
 MFQ  BR    BR  BR    0  -0.027  -0.6835   1.7422  -4.8616
 MFQ  N18   N   NS    0  -0.253  -3.5813  -0.7423  -4.2147
 MFQ  N19   N   NH1   0  -0.771  -0.8109  -0.9024   0.6805
 MFQ  C21   C   CR16  0  -0.264  -0.0355   0.7402   2.3373
 MFQ  C23   C   CR6   0   0.378   0.0158   0.1290   4.6749
 MFQ  C24   C   CR16  0  -0.376  -0.4492  -1.1393   4.3432
 MFQ  C25   C   CR16  0  -0.312  -0.6878  -1.4615   3.0127
 MFQ  O26   O   O2    0  -0.477   0.2853   0.5425   5.9299
 MFQ  C27   C   CH2   0  -0.178   0.0826  -0.3597   7.0003
 MFQ  C28   C   CH1   0   0.004   0.3908   0.3589   8.2933
 MFQ  C29   C   CH2   0  -0.307   0.3402  -0.6319   9.4594
 MFQ  N30   N   NT    0  -0.437   0.3285   0.0901  10.7184
 MFQ  C31   C   CH3   0  -0.515  -0.2877  -0.6662  11.7893
 MFQ  C32   C   CH3   0  -0.525   1.6438   0.5648  11.1018
 MFQ  O33   O   OH1   0  -0.680  -0.5473   1.3843   8.5056
 MFQ  H22   H   HCR6  0   0.263   0.5720   2.0542   3.9088
 MFQ  H1L   H   HCR6  0   0.252   2.5790   0.8530  -1.4219
 MFQ  H4    H   HCR6  0   0.281  -1.5213  -1.6488  -1.7221
 MFQ  H10   H   HCR6  0   0.275   1.0661   1.8933  -7.2050
 MFQ  H12   H   HCR6  0   0.261   2.7538  -2.0268  -7.4613
 MFQ  H161  H   HCH2  0   0.351  -1.2415  -2.5455  -5.2443
 MFQ  H162  H   HCH2  0   0.331  -1.3751  -2.8645  -3.5332
 MFQ  H13   H   HCR6  0   0.273   1.5085  -2.6907  -5.4497
 MFQ  H151  H   HCH3  0   0.255   2.3444  -0.1014  -9.5964
 MFQ  H152  H   HCH3  0   0.249   2.6974   1.4664  -8.8775
 MFQ  H153  H   HCH3  0   0.252   3.8017   0.1125  -8.6410
 MFQ  H19   H   HNH1  0   0.409  -1.5767  -1.5502   0.5817
 MFQ  H21   H   HCR6  0   0.265   0.1116   1.4900   1.5746
 MFQ  H24   H   HCR6  0   0.280  -0.6210  -1.8970   5.0952
 MFQ  H25   H   HCR6  0   0.269  -1.0380  -2.4574   2.7690
 MFQ  H271  H   HCH2  0   0.227   0.7418  -1.2306   6.9007
 MFQ  H272  H   HCH2  0   0.224  -0.9528  -0.7213   7.0152
 MFQ  H28   H   HCH1  0   0.208   1.4086   0.7727   8.2184
 MFQ  H291  H   HCH2  0   0.220   1.1701  -1.3500   9.3840
 MFQ  H292  H   HCH2  0   0.240  -0.5875  -1.2079   9.3918
 MFQ  H311  H   HCH3  0   0.236  -0.3569  -0.0476  12.6850
 MFQ  H312  H   HCH3  0   0.238  -1.2985  -0.9614  11.5069
 MFQ  H313  H   HCH3  0   0.200   0.2699  -1.5759  12.0539
 MFQ  H321  H   HCH3  0   0.240   2.0785   1.1865  10.3190
 MFQ  H322  H   HCH3  0   0.239   1.5675   1.1780  12.0000
 MFQ  H323  H   HCH3  0   0.204   2.3469  -0.2550  11.3085
 MFQ  H33   H   HOH1  0   0.438  -0.5943   1.4699   9.4724
 MFQ  C15   C   CH3   0  -0.722   2.7505   0.3917  -8.7117
 MFQ  C17   C   CSP   0   0.140  -2.5847  -1.3145  -4.2395

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
 MFQ  C22  C21   aromatic  1.381  0.020  1.381
 MFQ  C22  C23   aromatic  1.396  0.020  1.396
 MFQ  C22  H22   single    0.930  0.020  1.080
 MFQ  C1   N2    aromatic  1.316  0.020  1.316
 MFQ  C1   N6    aromatic  1.321  0.020  1.321
 MFQ  C1   H1L   single    0.930  0.020  1.080
 MFQ  C5   C4    aromatic  1.401  0.020  1.401
 MFQ  C5   N6    aromatic  1.336  0.020  1.336
 MFQ  C5   N19   single    1.355  0.020  1.355
 MFQ  C4   C3    aromatic  1.388  0.020  1.388
 MFQ  C4   H4    single    0.930  0.020  1.080
 MFQ  C3   N2    aromatic  1.339  0.020  1.339
 MFQ  C3   N7    single    1.371  0.020  1.371
 MFQ  C11  C10   aromatic  1.391  0.020  1.391
 MFQ  C11  C12   aromatic  1.393  0.020  1.393
 MFQ  C11  C15   single    1.500  0.020  1.500
 MFQ  C10  C9    aromatic  1.388  0.020  1.388
 MFQ  C10  H10   single    0.930  0.020  1.080
 MFQ  C9   C8    aromatic  1.391  0.020  1.391
 MFQ  C9   BR    single    1.882  0.020  1.882
 MFQ  C8   C13   aromatic  1.390  0.020  1.390
 MFQ  C8   N7    single    1.416  0.020  1.416
 MFQ  C12  C13   aromatic  1.383  0.020  1.383
 MFQ  C12  H12   single    0.930  0.020  1.080
 MFQ  C17  C16   single    1.470  0.020  1.470
 MFQ  C17  N18   triple    1.149  0.020  1.149
 MFQ  C16  N7    single    1.439  0.020  1.439
 MFQ  C16  H161  single    0.970  0.020  1.090
 MFQ  C16  H162  single    0.970  0.020  1.090
 MFQ  C13  H13   single    0.930  0.020  1.080
 MFQ  C15  H151  single    0.970  0.020  1.090
 MFQ  C15  H152  single    0.970  0.020  1.090
 MFQ  C15  H153  single    0.970  0.020  1.090
 MFQ  C20  N19   single    1.404  0.020  1.404
 MFQ  C20  C21   aromatic  1.396  0.020  1.396
 MFQ  C20  C25   aromatic  1.389  0.020  1.389
 MFQ  N19  H19   single    0.860  0.020  1.020
 MFQ  C21  H21   single    0.930  0.020  1.080
 MFQ  C23  C24   aromatic  1.391  0.020  1.391
 MFQ  C23  O26   single    1.349  0.020  1.349
 MFQ  C24  C25   aromatic  1.390  0.020  1.390
 MFQ  C24  H24   single    0.930  0.020  1.080
 MFQ  C25  H25   single    0.930  0.020  1.080
 MFQ  O26  C27   single    1.414  0.020  1.414
 MFQ  C27  C28   single    1.511  0.020  1.511
 MFQ  C27  H271  single    0.970  0.020  1.090
 MFQ  C27  H272  single    0.970  0.020  1.090
 MFQ  C28  C29   single    1.531  0.020  1.531
 MFQ  C28  O33   single    1.406  0.020  1.406
 MFQ  C28  H28   single    0.970  0.020  1.090
 MFQ  C29  N30   single    1.451  0.020  1.451
 MFQ  C29  H291  single    0.970  0.020  1.090
 MFQ  C29  H292  single    0.970  0.020  1.090
 MFQ  N30  C31   single    1.449  0.020  1.449
 MFQ  N30  C32   single    1.450  0.020  1.450
 MFQ  C31  H311  single    0.970  0.020  1.090
 MFQ  C31  H312  single    0.970  0.020  1.090
 MFQ  C31  H313  single    0.970  0.020  1.090
 MFQ  C32  H321  single    0.970  0.020  1.090
 MFQ  C32  H322  single    0.970  0.020  1.090
 MFQ  C32  H323  single    0.970  0.020  1.090
 MFQ  O33  H33   single    0.850  0.020  0.980

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
 MFQ  H22   C22  C23   119.32  3.000
 MFQ  H22   C22  C21   119.74  3.000
 MFQ  C23   C22  C21   120.93  3.000
 MFQ  H1L   C1   N6    115.90  3.000
 MFQ  H1L   C1   N2    116.00  3.000
 MFQ  N6    C1   N2    128.10  3.000
 MFQ  N19   C5   N6    119.02  3.000
 MFQ  N19   C5   C4    119.35  3.000
 MFQ  N6    C5   C4    121.63  3.000
 MFQ  H4    C4   C3    123.50  3.000
 MFQ  H4    C4   C5    119.86  3.000
 MFQ  C3    C4   C5    116.64  3.000
 MFQ  N7    C3   N2    115.89  3.000
 MFQ  N7    C3   C4    122.44  3.000
 MFQ  N2    C3   C4    121.67  3.000
 MFQ  C15   C11  C12   120.80  3.000
 MFQ  C15   C11  C10   120.78  3.000
 MFQ  C12   C11  C10   118.41  3.000
 MFQ  H10   C10  C9    119.98  3.000
 MFQ  H10   C10  C11   119.45  3.000
 MFQ  C9    C10  C11   120.57  3.000
 MFQ  BR    C9   C8    119.96  3.000
 MFQ  BR    C9   C10   119.00  3.000
 MFQ  C8    C9   C10   121.04  3.000
 MFQ  N7    C8   C13   119.49  3.000
 MFQ  N7    C8   C9    122.33  3.000
 MFQ  C13   C8   C9    118.15  3.000
 MFQ  H12   C12  C13   119.39  3.000
 MFQ  H12   C12  C11   119.84  3.000
 MFQ  C13   C12  C11   120.76  3.000
 MFQ  H162  C16  H161  106.27  3.000
 MFQ  H162  C16  N7    111.51  3.000
 MFQ  H161  C16  N7    109.52  3.000
 MFQ  H162  C16  C17   108.37  3.000
 MFQ  H161  C16  C17   107.83  3.000
 MFQ  N7    C16  C17   113.06  3.000
 MFQ  H13   C13  C12   120.07  3.000
 MFQ  H13   C13  C8    118.87  3.000
 MFQ  C12   C13  C8    121.06  3.000
 MFQ  C25   C20  C21   118.52  3.000
 MFQ  C25   C20  N19   118.61  3.000
 MFQ  C21   C20  N19   122.80  3.000
 MFQ  C3    N2   C1    116.08  3.000
 MFQ  C5    N6   C1    115.87  3.000
 MFQ  C16   N7   C8    118.16  3.000
 MFQ  C16   N7   C3    121.03  3.000
 MFQ  C8    N7   C3    120.74  3.000
 MFQ  H19   N19  C20   115.75  3.000
 MFQ  H19   N19  C5    115.94  3.000
 MFQ  C20   N19  C5    127.67  3.000
 MFQ  H21   C21  C20   120.45  3.000
 MFQ  H21   C21  C22   119.19  3.000
 MFQ  C20   C21  C22   120.37  3.000
 MFQ  O26   C23  C24   124.63  3.000
 MFQ  O26   C23  C22   116.42  3.000
 MFQ  C24   C23  C22   118.95  3.000
 MFQ  H24   C24  C25   118.43  3.000
 MFQ  H24   C24  C23   121.75  3.000
 MFQ  C25   C24  C23   119.81  3.000
 MFQ  H25   C25  C24   118.95  3.000
 MFQ  H25   C25  C20   119.64  3.000
 MFQ  C24   C25  C20   121.41  3.000
 MFQ  C27   O26  C23   118.69  3.000
 MFQ  H272  C27  H271  107.87  3.000
 MFQ  H272  C27  C28   109.73  3.000
 MFQ  H271  C27  C28   109.44  3.000
 MFQ  H272  C27  O26   110.84  3.000
 MFQ  H271  C27  O26   110.58  3.000
 MFQ  C28   C27  O26   108.36  3.000
 MFQ  H28   C28  O33   110.66  3.000
 MFQ  H28   C28  C29   109.00  3.000
 MFQ  O33   C28  C29   109.57  3.000
 MFQ  H28   C28  C27   108.00  3.000
 MFQ  O33   C28  C27   109.87  3.000
 MFQ  C29   C28  C27   109.71  3.000
 MFQ  H292  C29  H291  106.96  3.000
 MFQ  H292  C29  N30   107.98  3.000
 MFQ  H291  C29  N30   112.97  3.000
 MFQ  H292  C29  C28   108.77  3.000
 MFQ  H291  C29  C28   110.20  3.000
 MFQ  N30   C29  C28   109.82  3.000
 MFQ  C32   N30  C31   111.18  3.000
 MFQ  C32   N30  C29   112.64  3.000
 MFQ  C31   N30  C29   112.64  3.000
 MFQ  H313  C31  H312  107.98  3.000
 MFQ  H313  C31  H311  107.69  3.000
 MFQ  H312  C31  H311  107.91  3.000
 MFQ  H313  C31  N30   113.21  3.000
 MFQ  H312  C31  N30   110.13  3.000
 MFQ  H311  C31  N30   109.75  3.000
 MFQ  H323  C32  H322  108.00  3.000
 MFQ  H323  C32  H321  107.77  3.000
 MFQ  H322  C32  H321  107.38  3.000
 MFQ  H323  C32  N30   112.69  3.000
 MFQ  H322  C32  N30   109.79  3.000
 MFQ  H321  C32  N30   111.02  3.000
 MFQ  H33   O33  C28   104.29  3.000
 MFQ  H153  C15  H152  108.04  3.000
 MFQ  H153  C15  H151  107.20  3.000
 MFQ  H152  C15  H151  107.73  3.000
 MFQ  H153  C15  C11   111.20  3.000
 MFQ  H152  C15  C11   111.66  3.000
 MFQ  H151  C15  C11   110.81  3.000
 MFQ  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
 MFQ  CONST_01  C25   C20  C21  C22     0.00   0.0  0
 MFQ  CONST_02  C25   C24  C23  C22     0.00   0.0  0
 MFQ  CONST_03  C4    C3   N2   C1      0.00   0.0  0
 MFQ  CONST_04  C4    C5   N6   C1      0.00   0.0  0
 MFQ  CONST_05  N2    C3   C4   C5      0.00   0.0  0
 MFQ  CONST_06  N2    C1   N6   C5      0.00   0.0  0
 MFQ  CONST_07  N6    C5   C4   C3      0.00   0.0  0
 MFQ  CONST_08  N6    C1   N2   C3      0.00   0.0  0
 MFQ  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 MFQ  CONST_10  C8    C13  C12  C11     0.00   0.0  0
 MFQ  CONST_11  C13   C12  C11  C10     0.00   0.0  0
 MFQ  CONST_12  C13   C8   C9   C10     0.00   0.0  0
 MFQ  CONST_13  C12   C11  C10  C9      0.00   0.0  0
 MFQ  CONST_14  C12   C13  C8   C9      0.00   0.0  0
 MFQ  CONST_15  C23   C22  C21  C20     0.00   0.0  0
 MFQ  CONST_16  C23   C24  C25  C20     0.00   0.0  0
 MFQ  CONST_17  C24   C23  C22  C21     0.00   0.0  0
 MFQ  CONST_18  C24   C25  C20  C21     0.00   0.0  0
 MFQ  CONST_19  N19   C20  C21  C22   180.00   0.0  0
 MFQ  CONST_20  N7    C3   N2   C1    180.00   0.0  0
 MFQ  CONST_21  N19   C5   N6   C1    180.00   0.0  0
 MFQ  CONST_22  N7    C3   C4   C5    180.00   0.0  0
 MFQ  CONST_23  N19   C5   C4   C3    180.00   0.0  0
 MFQ  CONST_24  BR    C9   C10  C11   180.00   0.0  0
 MFQ  CONST_25  N7    C8   C9   C10   180.00   0.0  0
 MFQ  CONST_26  C15   C11  C10  C9    180.00   0.0  0
 MFQ  CONST_27  N7    C8   C13  C12   180.00   0.0  0
 MFQ  CONST_28  BR    C9   C8   C13   180.00   0.0  0
 MFQ  CONST_29  C15   C11  C12  C13   180.00   0.0  0
 MFQ  CONST_30  C24   C25  C20  N19   180.00   0.0  0
 MFQ  CONST_31  O26   C23  C22  C21   180.00   0.0  0
 MFQ  CONST_32  O26   C23  C24  C25   180.00   0.0  0
 MFQ  CONST_33  H24   C24  C23  C22   180.00   0.0  0
 MFQ  CONST_34  H1L   C1   N6   C5    180.00   0.0  0
 MFQ  CONST_35  H13   C13  C12  C11   180.00   0.0  0
 MFQ  CONST_36  H12   C12  C11  C10   180.00   0.0  0
 MFQ  CONST_37  H10   C10  C9   C8    180.00   0.0  0
 MFQ  CONST_38  H22   C22  C21  C20   180.00   0.0  0
 MFQ  CONST_39  H4    C4   C3   N2    180.00   0.0  0
 MFQ  CONST_40  H25   C25  C20  C21   180.00   0.0  0
 MFQ  CONST_41  H21   C21  C22  C23   180.00   0.0  0
 MFQ  Var_01    C21   C20  N19  C5     44.35  30.0  1
 MFQ  Var_02    C20   N19  C5   C4    179.38  30.0  2
 MFQ  Var_03    C8    N7   C3   C4    173.16  30.0  2
 MFQ  Var_04    C9    C8   N7   C3    -74.39  30.0  2
 MFQ  Var_05    H151  C15  C11  C10  -109.55  30.0  2
 MFQ  Var_06    C17   C16  N7   C3     78.41  30.0  3
 MFQ  Var_07    C28   C27  O26  C23  -177.36  30.0  3
 MFQ  Var_08    C31   N30  C29  C28   154.62  30.0  3
 MFQ  Var_09    H311  C31  N30  C29  -174.67  30.0  3
 MFQ  Var_10    H321  C32  N30  C29    56.10  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
 MFQ  chir_01  C28  C27  C29  O33  positiv

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
 MFQ  plan-1  C22  0.020
 MFQ  plan-1  C20  0.020
 MFQ  plan-1  N19  0.020
 MFQ  plan-1  C21  0.020
 MFQ  plan-1  C23  0.020
 MFQ  plan-1  C24  0.020
 MFQ  plan-1  C25  0.020
 MFQ  plan-1  O26  0.020
 MFQ  plan-1  H22  0.020
 MFQ  plan-1  H21  0.020
 MFQ  plan-1  H24  0.020
 MFQ  plan-1  H25  0.020
 MFQ  plan-2  C1   0.020
 MFQ  plan-2  C5   0.020
 MFQ  plan-2  C4   0.020
 MFQ  plan-2  C3   0.020
 MFQ  plan-2  N2   0.020
 MFQ  plan-2  N6   0.020
 MFQ  plan-2  N7   0.020
 MFQ  plan-2  N19  0.020
 MFQ  plan-2  H1L  0.020
 MFQ  plan-2  H4   0.020
 MFQ  plan-3  C11  0.020
 MFQ  plan-3  C10  0.020
 MFQ  plan-3  C9   0.020
 MFQ  plan-3  C8   0.020
 MFQ  plan-3  C12  0.020
 MFQ  plan-3  C13  0.020
 MFQ  plan-3  N7   0.020
 MFQ  plan-3  BR   0.020
 MFQ  plan-3  H10  0.020
 MFQ  plan-3  H12  0.020
 MFQ  plan-3  H13  0.020
 MFQ  plan-3  C15  0.020

