# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:34:15 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: [(2-bromo-4-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)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
 MFP  MFP  '[(2-bromo-4-methylphenyl){6-[(4-{[(2R)-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_MFP
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
 MFP  C22   C   CR16  0  -0.344   0.6590   0.9097   3.7140
 MFP  C1    C   CR16  0   0.067   1.7952   0.3262  -1.5813
 MFP  C5    C   CR6   0   0.566   0.1001  -0.6318  -0.4494
 MFP  C4    C   CR16  0  -0.508  -0.4127  -1.1308  -1.6546
 MFP  C3    C   CR6   0   0.557   0.3009  -0.8331  -2.8059
 MFP  C11   C   CR6   0   0.102   1.8738  -0.0018  -7.5701
 MFP  C10   C   CR16  0  -0.288   1.0391   0.8722  -6.8761
 MFP  C9    C   CR6   0  -0.111   0.3958   0.4625  -5.7197
 MFP  C8    C   CR6   0   0.331   0.5793  -0.8225  -5.2115
 MFP  C12   C   CR16  0  -0.306   2.0500  -1.2871  -7.0687
 MFP  C16   C   CH2   0  -0.444  -1.2152  -2.1491  -4.2027
 MFP  C13   C   CR16  0  -0.249   1.4160  -1.6867  -5.9031
 MFP  C20   C   CR6   0   0.337  -0.2534  -0.5452   2.0214
 MFP  N2    N   N     0  -0.471   1.4186  -0.0950  -2.7691
 MFP  N6    N   N     0  -0.481   1.2118   0.1067  -0.4157
 MFP  N7    N   NT    0  -0.592  -0.0829  -1.2756  -4.0449
 MFP  BR    BR  BR    0  -0.027  -0.7406   1.6710  -4.8295
 MFP  N18   N   NS    0  -0.252  -3.5166  -0.9072  -4.0542
 MFP  N19   N   NH1   0  -0.775  -0.5546  -0.9100   0.7037
 MFP  C21   C   CR16  0  -0.279   0.4511   0.6068   2.3807
 MFP  C23   C   CR6   0   0.374   0.1639   0.0911   4.7284
 MFP  C24   C   CR16  0  -0.370  -0.5464  -1.0525   4.3768
 MFP  C25   C   CR16  0  -0.336  -0.7425  -1.3606   3.0380
 MFP  O26   O   O2    0  -0.478   0.4116   0.4812   5.9966
 MFP  C27   C   CH2   0  -0.178  -0.1098  -0.2972   7.0560
 MFP  C28   C   CH1   0   0.005   0.2340   0.3822   8.3608
 MFP  C29   C   CH2   0  -0.308  -0.4355  -0.3558   9.5226
 MFP  N30   N   NT    0  -0.437   0.1177   0.1074  10.7824
 MFP  C31   C   CH3   0  -0.526  -0.4227   1.3887  11.1939
 MFP  C32   C   CH3   0  -0.515  -0.0040  -0.8770  11.8382
 MFP  O33   O   OH1   0  -0.681   1.6271   0.3875   8.5501
 MFP  H22   H   HCR6  0   0.262   1.2064   1.8068   3.9759
 MFP  H1    H   HCR6  0   0.253   2.7000   0.9254  -1.5526
 MFP  H4    H   HCR6  0   0.282  -1.3230  -1.7134  -1.6523
 MFP  H10   H   HCR6  0   0.275   0.8918   1.8775  -7.2508
 MFP  H12   H   HCR6  0   0.262   2.7000  -1.9822  -7.5849
 MFP  H161  H   HCH2  0   0.352  -1.1640  -2.6389  -5.1749
 MFP  H162  H   HCH2  0   0.331  -1.2119  -2.9480  -3.4577
 MFP  H13   H   HCR6  0   0.274   1.5743  -2.6851  -5.5147
 MFP  H151  H   HCH3  0   0.256   1.8303   0.4595  -9.6646
 MFP  H152  H   HCH3  0   0.251   2.9520   1.4466  -8.7420
 MFP  H153  H   HCH3  0   0.250   3.3528  -0.2300  -9.1162
 MFP  H19   H   HNH1  0   0.412  -1.3242  -1.5546   0.6124
 MFP  H21   H   HCR6  0   0.273   0.8394   1.2700   1.6246
 MFP  H24   H   HCR6  0   0.281  -0.9513  -1.7224   5.1229
 MFP  H25   H   HCR6  0   0.270  -1.2930  -2.2594   2.7860
 MFP  H271  H   HCH2  0   0.224   0.3097  -1.3107   7.0372
 MFP  H272  H   HCH2  0   0.226  -1.2000  -0.3830   6.9708
 MFP  H28   H   HCH1  0   0.207  -0.1553   1.4113   8.3169
 MFP  H291  H   HCH2  0   0.241  -0.2191  -1.4243   9.4312
 MFP  H292  H   HCH2  0   0.220  -1.5285  -0.2435   9.4678
 MFP  H311  H   HCH3  0   0.240   0.0989   1.7388  12.0849
 MFP  H312  H   HCH3  0   0.241  -0.2807   2.1388  10.4160
 MFP  H313  H   HCH3  0   0.204  -1.4966   1.3417  11.4253
 MFP  H321  H   HCH3  0   0.238   0.4769  -1.8086  11.5395
 MFP  H322  H   HCH3  0   0.236   0.4955  -0.5159  12.7380
 MFP  H323  H   HCH3  0   0.200  -1.0472  -1.1021  12.1015
 MFP  H33   H   HOH1  0   0.439   1.7364   0.3934   9.5157
 MFP  C15   C   CH3   0  -0.722   2.5420   0.4414  -8.8374
 MFP  C17   C   CSP   0   0.139  -2.5032  -1.4454  -4.1200

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
 MFP  C22  C21   aromatic  1.383  0.020  1.383
 MFP  C22  C23   aromatic  1.394  0.020  1.394
 MFP  C22  H22   single    0.930  0.020  1.080
 MFP  C1   N2    aromatic  1.315  0.020  1.315
 MFP  C1   N6    aromatic  1.322  0.020  1.322
 MFP  C1   H1    single    0.930  0.020  1.080
 MFP  C5   C4    aromatic  1.402  0.020  1.402
 MFP  C5   N6    aromatic  1.335  0.020  1.335
 MFP  C5   N19   single    1.355  0.020  1.355
 MFP  C4   C3    aromatic  1.387  0.020  1.387
 MFP  C4   H4    single    0.930  0.020  1.080
 MFP  C3   N2    aromatic  1.340  0.020  1.340
 MFP  C3   N7    single    1.370  0.020  1.370
 MFP  C11  C10   aromatic  1.394  0.020  1.394
 MFP  C11  C12   aromatic  1.391  0.020  1.391
 MFP  C11  C15   single    1.500  0.020  1.500
 MFP  C10  C9    aromatic  1.385  0.020  1.385
 MFP  C10  H10   single    0.930  0.020  1.080
 MFP  C9   C8    aromatic  1.394  0.020  1.394
 MFP  C9   BR    single    1.883  0.020  1.883
 MFP  C8   C13   aromatic  1.387  0.020  1.387
 MFP  C8   N7    single    1.416  0.020  1.416
 MFP  C12  C13   aromatic  1.386  0.020  1.386
 MFP  C12  H12   single    0.930  0.020  1.080
 MFP  C17  C16   single    1.470  0.020  1.470
 MFP  C17  N18   triple    1.149  0.020  1.149
 MFP  C16  N7    single    1.439  0.020  1.439
 MFP  C16  H161  single    0.970  0.020  1.090
 MFP  C16  H162  single    0.970  0.020  1.090
 MFP  C13  H13   single    0.930  0.020  1.080
 MFP  C15  H151  single    0.970  0.020  1.090
 MFP  C15  H152  single    0.970  0.020  1.090
 MFP  C15  H153  single    0.970  0.020  1.090
 MFP  C20  N19   single    1.400  0.020  1.400
 MFP  C20  C21   aromatic  1.397  0.020  1.397
 MFP  C20  C25   aromatic  1.392  0.020  1.392
 MFP  N19  H19   single    0.860  0.020  1.020
 MFP  C21  H21   single    0.930  0.020  1.080
 MFP  C23  C24   aromatic  1.391  0.020  1.391
 MFP  C23  O26   single    1.350  0.020  1.350
 MFP  C24  C25   aromatic  1.388  0.020  1.388
 MFP  C24  H24   single    0.930  0.020  1.080
 MFP  C25  H25   single    0.930  0.020  1.080
 MFP  O26  C27   single    1.414  0.020  1.414
 MFP  C27  C28   single    1.511  0.020  1.511
 MFP  C27  H271  single    0.970  0.020  1.090
 MFP  C27  H272  single    0.970  0.020  1.090
 MFP  C28  C29   single    1.531  0.020  1.531
 MFP  C28  O33   single    1.406  0.020  1.406
 MFP  C28  H28   single    0.970  0.020  1.090
 MFP  C29  N30   single    1.452  0.020  1.452
 MFP  C29  H291  single    0.970  0.020  1.090
 MFP  C29  H292  single    0.970  0.020  1.090
 MFP  N30  C31   single    1.450  0.020  1.450
 MFP  N30  C32   single    1.449  0.020  1.449
 MFP  C31  H311  single    0.970  0.020  1.090
 MFP  C31  H312  single    0.970  0.020  1.090
 MFP  C31  H313  single    0.970  0.020  1.090
 MFP  C32  H321  single    0.970  0.020  1.090
 MFP  C32  H322  single    0.970  0.020  1.090
 MFP  C32  H323  single    0.970  0.020  1.090
 MFP  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
 MFP  H22   C22  C23   119.33  3.000
 MFP  H22   C22  C21   119.38  3.000
 MFP  C23   C22  C21   121.29  3.000
 MFP  H1    C1   N6    115.86  3.000
 MFP  H1    C1   N2    116.06  3.000
 MFP  N6    C1   N2    128.08  3.000
 MFP  N19   C5   N6    119.63  3.000
 MFP  N19   C5   C4    118.81  3.000
 MFP  N6    C5   C4    121.55  3.000
 MFP  H4    C4   C3    123.43  3.000
 MFP  H4    C4   C5    119.88  3.000
 MFP  C3    C4   C5    116.69  3.000
 MFP  N7    C3   N2    115.87  3.000
 MFP  N7    C3   C4    122.48  3.000
 MFP  N2    C3   C4    121.65  3.000
 MFP  C15   C11  C12   121.42  3.000
 MFP  C15   C11  C10   120.16  3.000
 MFP  C12   C11  C10   118.42  3.000
 MFP  H10   C10  C9    120.01  3.000
 MFP  H10   C10  C11   119.43  3.000
 MFP  C9    C10  C11   120.56  3.000
 MFP  BR    C9   C8    119.92  3.000
 MFP  BR    C9   C10   119.03  3.000
 MFP  C8    C9   C10   121.05  3.000
 MFP  N7    C8   C13   119.57  3.000
 MFP  N7    C8   C9    122.26  3.000
 MFP  C13   C8   C9    118.15  3.000
 MFP  H12   C12  C13   119.38  3.000
 MFP  H12   C12  C11   119.84  3.000
 MFP  C13   C12  C11   120.78  3.000
 MFP  H162  C16  H161  106.24  3.000
 MFP  H162  C16  N7    111.52  3.000
 MFP  H161  C16  N7    109.49  3.000
 MFP  H162  C16  C17   108.32  3.000
 MFP  H161  C16  C17   107.85  3.000
 MFP  N7    C16  C17   113.12  3.000
 MFP  H13   C13  C12   120.04  3.000
 MFP  H13   C13  C8    118.92  3.000
 MFP  C12   C13  C8    121.04  3.000
 MFP  C25   C20  C21   118.19  3.000
 MFP  C25   C20  N19   117.33  3.000
 MFP  C21   C20  N19   124.42  3.000
 MFP  C3    N2   C1    116.11  3.000
 MFP  C5    N6   C1    115.92  3.000
 MFP  C16   N7   C8    118.16  3.000
 MFP  C16   N7   C3    121.04  3.000
 MFP  C8    N7   C3    120.70  3.000
 MFP  H19   N19  C20   114.59  3.000
 MFP  H19   N19  C5    115.03  3.000
 MFP  C20   N19  C5    130.06  3.000
 MFP  H21   C21  C20   120.56  3.000
 MFP  H21   C21  C22   119.16  3.000
 MFP  C20   C21  C22   120.28  3.000
 MFP  O26   C23  C24   124.66  3.000
 MFP  O26   C23  C22   116.66  3.000
 MFP  C24   C23  C22   118.69  3.000
 MFP  H24   C24  C25   118.37  3.000
 MFP  H24   C24  C23   121.74  3.000
 MFP  C25   C24  C23   119.89  3.000
 MFP  H25   C25  C24   118.70  3.000
 MFP  H25   C25  C20   119.64  3.000
 MFP  C24   C25  C20   121.66  3.000
 MFP  C27   O26  C23   118.49  3.000
 MFP  H272  C27  H271  107.85  3.000
 MFP  H272  C27  C28   109.17  3.000
 MFP  H271  C27  C28   110.07  3.000
 MFP  H272  C27  O26   110.57  3.000
 MFP  H271  C27  O26   110.78  3.000
 MFP  C28   C27  O26   108.39  3.000
 MFP  H28   C28  O33   110.62  3.000
 MFP  H28   C28  C29   109.04  3.000
 MFP  O33   C28  C29   109.46  3.000
 MFP  H28   C28  C27   107.78  3.000
 MFP  O33   C28  C27   110.09  3.000
 MFP  C29   C28  C27   109.83  3.000
 MFP  H292  C29  H291  106.98  3.000
 MFP  H292  C29  N30   112.91  3.000
 MFP  H291  C29  N30   107.98  3.000
 MFP  H292  C29  C28   110.34  3.000
 MFP  H291  C29  C28   108.73  3.000
 MFP  N30   C29  C28   109.76  3.000
 MFP  C32   N30  C31   111.24  3.000
 MFP  C32   N30  C29   112.56  3.000
 MFP  C31   N30  C29   112.72  3.000
 MFP  H313  C31  H312  107.87  3.000
 MFP  H313  C31  H311  108.00  3.000
 MFP  H312  C31  H311  107.46  3.000
 MFP  H313  C31  N30   112.70  3.000
 MFP  H312  C31  N30   110.91  3.000
 MFP  H311  C31  N30   109.71  3.000
 MFP  H323  C32  H322  107.75  3.000
 MFP  H323  C32  H321  108.02  3.000
 MFP  H322  C32  H321  107.88  3.000
 MFP  H323  C32  N30   113.17  3.000
 MFP  H322  C32  N30   109.75  3.000
 MFP  H321  C32  N30   110.12  3.000
 MFP  H33   O33  C28   104.19  3.000
 MFP  H153  C15  H152  108.12  3.000
 MFP  H153  C15  H151  107.56  3.000
 MFP  H152  C15  H151  107.24  3.000
 MFP  H153  C15  C11   111.46  3.000
 MFP  H152  C15  C11   111.48  3.000
 MFP  H151  C15  C11   110.78  3.000
 MFP  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
 MFP  CONST_01  C25   C20  C21  C22     0.00   0.0  0
 MFP  CONST_02  C25   C24  C23  C22     0.00   0.0  0
 MFP  CONST_03  C4    C3   N2   C1      0.00   0.0  0
 MFP  CONST_04  C4    C5   N6   C1      0.00   0.0  0
 MFP  CONST_05  N2    C3   C4   C5      0.00   0.0  0
 MFP  CONST_06  N2    C1   N6   C5      0.00   0.0  0
 MFP  CONST_07  N6    C5   C4   C3      0.00   0.0  0
 MFP  CONST_08  N6    C1   N2   C3      0.00   0.0  0
 MFP  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 MFP  CONST_10  C8    C13  C12  C11     0.00   0.0  0
 MFP  CONST_11  C13   C12  C11  C10     0.00   0.0  0
 MFP  CONST_12  C13   C8   C9   C10     0.00   0.0  0
 MFP  CONST_13  C12   C11  C10  C9      0.00   0.0  0
 MFP  CONST_14  C12   C13  C8   C9      0.00   0.0  0
 MFP  CONST_15  C23   C22  C21  C20     0.00   0.0  0
 MFP  CONST_16  C23   C24  C25  C20     0.00   0.0  0
 MFP  CONST_17  C24   C23  C22  C21     0.00   0.0  0
 MFP  CONST_18  C24   C25  C20  C21     0.00   0.0  0
 MFP  CONST_19  N19   C20  C21  C22   180.00   0.0  0
 MFP  CONST_20  N7    C3   N2   C1    180.00   0.0  0
 MFP  CONST_21  N19   C5   N6   C1    180.00   0.0  0
 MFP  CONST_22  N7    C3   C4   C5    180.00   0.0  0
 MFP  CONST_23  N19   C5   C4   C3    180.00   0.0  0
 MFP  CONST_24  BR    C9   C10  C11   180.00   0.0  0
 MFP  CONST_25  N7    C8   C9   C10   180.00   0.0  0
 MFP  CONST_26  C15   C11  C10  C9    180.00   0.0  0
 MFP  CONST_27  N7    C8   C13  C12   180.00   0.0  0
 MFP  CONST_28  BR    C9   C8   C13   180.00   0.0  0
 MFP  CONST_29  C15   C11  C12  C13   180.00   0.0  0
 MFP  CONST_30  C24   C25  C20  N19   180.00   0.0  0
 MFP  CONST_31  O26   C23  C22  C21   180.00   0.0  0
 MFP  CONST_32  O26   C23  C24  C25   180.00   0.0  0
 MFP  CONST_33  H24   C24  C23  C22   180.00   0.0  0
 MFP  CONST_34  H1    C1   N6   C5    180.00   0.0  0
 MFP  CONST_35  H13   C13  C12  C11   180.00   0.0  0
 MFP  CONST_36  H12   C12  C11  C10   180.00   0.0  0
 MFP  CONST_37  H10   C10  C9   C8    180.00   0.0  0
 MFP  CONST_38  H22   C22  C21  C20   180.00   0.0  0
 MFP  CONST_39  H4    C4   C3   N2    180.00   0.0  0
 MFP  CONST_40  H25   C25  C20  C21   180.00   0.0  0
 MFP  CONST_41  H21   C21  C22  C23   180.00   0.0  0
 MFP  Var_01    C21   C20  N19  C5     27.92  30.0  1
 MFP  Var_02    C20   N19  C5   C4    179.58  30.0  2
 MFP  Var_03    C8    N7   C3   C4    172.52  30.0  2
 MFP  Var_04    C9    C8   N7   C3    -73.73  30.0  3
 MFP  Var_05    H151  C15  C11  C10   -75.54  30.0  2
 MFP  Var_06    C17   C16  N7   C3     78.10  30.0  2
 MFP  Var_07    C28   C27  O26  C23  -176.85  30.0  3
 MFP  Var_08    C31   N30  C29  C28    78.15  30.0  3
 MFP  Var_09    H311  C31  N30  C29  -174.07  30.0  3
 MFP  Var_10    H321  C32  N30  C29    56.84  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
 MFP  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
 MFP  plan-1  C22  0.020
 MFP  plan-1  C20  0.020
 MFP  plan-1  N19  0.020
 MFP  plan-1  C21  0.020
 MFP  plan-1  C23  0.020
 MFP  plan-1  C24  0.020
 MFP  plan-1  C25  0.020
 MFP  plan-1  O26  0.020
 MFP  plan-1  H22  0.020
 MFP  plan-1  H21  0.020
 MFP  plan-1  H24  0.020
 MFP  plan-1  H25  0.020
 MFP  plan-2  C1   0.020
 MFP  plan-2  C5   0.020
 MFP  plan-2  C4   0.020
 MFP  plan-2  C3   0.020
 MFP  plan-2  N2   0.020
 MFP  plan-2  N6   0.020
 MFP  plan-2  N7   0.020
 MFP  plan-2  N19  0.020
 MFP  plan-2  H1   0.020
 MFP  plan-2  H4   0.020
 MFP  plan-3  C11  0.020
 MFP  plan-3  C10  0.020
 MFP  plan-3  C9   0.020
 MFP  plan-3  C8   0.020
 MFP  plan-3  C12  0.020
 MFP  plan-3  C13  0.020
 MFP  plan-3  N7   0.020
 MFP  plan-3  BR   0.020
 MFP  plan-3  H10  0.020
 MFP  plan-3  H12  0.020
 MFP  plan-3  H13  0.020
 MFP  plan-3  C15  0.020

