# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:13:41 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N~4~-(5-chloro-1,3-benzodioxol-4-yl)-N~2~-(3-morpholin-4-ylphenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2OCOc2c1Nc3ccnc(Nc4cccc(c4)N5CCOCC5)n3
#
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
 7X7  7X7  N~4~-(5-chloro-1,3-benzodioxol-4-yl)-N~2~-(3-morpholin-4-ylphenyl)pyrimidine-2,4-diamine  ligand  50  30  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7X7
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
 7X7  CL1   CL  CL    0  -0.107   8.2826   3.4497   9.8890
 7X7  C1    C   CR6   0  -0.126   8.4300   2.8641  11.5093
 7X7  C2    C   CR16  0  -0.252   7.7337   1.7352  11.8948
 7X7  C3    C   CR16  0  -0.352   7.8498   1.2308  13.1949
 7X7  C4    C   CR56  0   0.317   8.6686   1.9137  14.0577
 7X7  O1    O   O     0  -0.483   8.9420   1.6508  15.3550
 7X7  C5    C   CH2   0   0.073   9.8174   2.6746  15.8116
 7X7  O2    O   O     0  -0.469  10.0535   3.5463  14.7075
 7X7  C6    C   CR56  0   0.297   9.3435   3.0599  13.6733
 7X7  C7    C   CR6   0   0.277   9.2655   3.5700  12.3954
 7X7  N1    N   NH1   0  -0.734   9.9434   4.7312  12.0223
 7X7  C8    C   CR6   0   0.541  11.2917   4.8821  12.0178
 7X7  C9    C   CR16  0  -0.430  12.1838   3.8422  12.3088
 7X7  C10   C   CR16  0  -0.031  13.5194   4.1769  12.2563
 7X7  N2    N   N     0  -0.490  13.9725   5.3865  11.9542
 7X7  C11   C   CR6   0   0.597  13.0336   6.2990  11.6835
 7X7  N3    N   NH1   0  -0.774  13.5303   7.5294  11.3741
 7X7  C12   C   CR6   0   0.407  12.9107   8.7275  11.0350
 7X7  C13   C   CR16  0  -0.356  11.5399   8.8954  10.8504
 7X7  C14   C   CR16  0  -0.232  11.0743  10.1560  10.4949
 7X7  C15   C   CR16  0  -0.358  11.9135  11.2390  10.3268
 7X7  C16   C   CR6   0   0.396  13.2981  11.0864  10.5137
 7X7  C17   C   CR16  0  -0.499  13.7715   9.8190  10.8540
 7X7  N4    N   NT    0  -0.527  14.1517  12.1802  10.3969
 7X7  C18   C   CH2   0  -0.330  15.5653  11.9814  10.6516
 7X7  C19   C   CH2   0  -0.183  16.2651  13.3186  10.8132
 7X7  O3    O   O2    0  -0.482  16.0639  14.1626   9.7046
 7X7  C20   C   CH2   0  -0.188  14.6873  14.3931   9.5149
 7X7  C21   C   CH2   0  -0.321  13.9277  13.1010   9.2900
 7X7  N5    N   N     0  -0.521  11.7248   6.1008  11.7012
 7X7  H2    H   HCR6  0   0.286   7.0970   1.2281  11.1839
 7X7  H3    H   HCR6  0   0.287   7.3140   0.3410  13.4944
 7X7  H5C1  H   HCH2  0   0.246   9.3463   3.2319  16.6239
 7X7  H5C2  H   HCH2  0   0.247  10.7613   2.2373  16.1425
 7X7  H1    H   HNH1  0   0.404   9.4071   5.5108  11.6698
 7X7  H9    H   HCR6  0   0.277  11.8671   2.8377  12.5427
 7X7  H10   H   HCR6  0   0.270  14.2703   3.4233  12.4676
 7X7  HA    H   HNH1  0   0.405  14.5375   7.5625  11.4188
 7X7  H13   H   HCR6  0   0.278  10.8541   8.0762  10.9800
 7X7  H17   H   HCR6  0   0.277  14.8324   9.6478  10.9804
 7X7  H14   H   HCR6  0   0.251  10.0096  10.2947  10.3543
 7X7  H15   H   HCR6  0   0.258  11.4861  12.1993  10.0748
 7X7  H181  H   HCH2  0   0.256  15.7022  11.4310  11.5837
 7X7  H182  H   HCH2  0   0.221  16.0456  11.3976   9.8515
 7X7  H211  H   HCH2  0   0.223  14.2392  12.6485   8.3370
 7X7  H212  H   HCH2  0   0.259  12.8724  13.3497   9.2023
 7X7  H191  H   HCH2  0   0.205  15.9076  13.8027  11.7332
 7X7  H192  H   HCH2  0   0.243  17.3388  13.1556  10.9162
 7X7  H201  H   HCH2  0   0.205  14.2622  14.9189  10.3817
 7X7  H202  H   HCH2  0   0.242  14.5768  15.0382   8.6424

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
 7X7  CL1  C1    single    1.729  0.020  1.729
 7X7  C1   C2    aromatic  1.381  0.020  1.381
 7X7  C1   C7    aromatic  1.408  0.020  1.408
 7X7  C2   C3    aromatic  1.399  0.020  1.399
 7X7  C3   C4    aromatic  1.372  0.020  1.372
 7X7  C4   O1    single    1.352  0.020  1.352
 7X7  C4   C6    aromatic  1.385  0.020  1.385
 7X7  O1   C5    single    1.422  0.020  1.422
 7X7  C5   O2    single    1.426  0.020  1.426
 7X7  O2   C6    single    1.345  0.020  1.345
 7X7  C6   C7    aromatic  1.378  0.020  1.378
 7X7  C7   N1    single    1.395  0.020  1.395
 7X7  N1   C8    single    1.357  0.020  1.357
 7X7  C8   C9    aromatic  1.401  0.020  1.401
 7X7  C8   N5    aromatic  1.332  0.020  1.332
 7X7  C9   C10   aromatic  1.378  0.020  1.378
 7X7  C10  N2    aromatic  1.327  0.020  1.327
 7X7  N2   C11   aromatic  1.337  0.020  1.337
 7X7  C11  N3    single    1.362  0.020  1.362
 7X7  C11  N5    aromatic  1.324  0.020  1.324
 7X7  N3   C12   single    1.391  0.020  1.391
 7X7  C12  C13   aromatic  1.393  0.020  1.393
 7X7  C12  C17   aromatic  1.402  0.020  1.402
 7X7  C13  C14   aromatic  1.390  0.020  1.390
 7X7  C14  C15   aromatic  1.380  0.020  1.380
 7X7  C15  C16   aromatic  1.406  0.020  1.406
 7X7  C16  C17   aromatic  1.395  0.020  1.395
 7X7  C16  N4    single    1.392  0.020  1.392
 7X7  N4   C18   single    1.450  0.020  1.450
 7X7  N4   C21   single    1.457  0.020  1.457
 7X7  C18  C19   single    1.518  0.020  1.518
 7X7  C19  O3    single    1.408  0.020  1.408
 7X7  O3   C20   single    1.409  0.020  1.409
 7X7  C20  C21   single    1.516  0.020  1.516
 7X7  C2   H2    single    0.930  0.020  1.080
 7X7  C3   H3    single    0.930  0.020  1.080
 7X7  C5   H5C1  single    0.970  0.020  1.090
 7X7  C5   H5C2  single    0.970  0.020  1.090
 7X7  N1   H1    single    0.860  0.020  1.020
 7X7  C9   H9    single    0.930  0.020  1.080
 7X7  C10  H10   single    0.930  0.020  1.080
 7X7  N3   HA    single    0.860  0.020  1.020
 7X7  C13  H13   single    0.930  0.020  1.080
 7X7  C17  H17   single    0.930  0.020  1.080
 7X7  C14  H14   single    0.930  0.020  1.080
 7X7  C15  H15   single    0.930  0.020  1.080
 7X7  C18  H181  single    0.970  0.020  1.090
 7X7  C18  H182  single    0.970  0.020  1.090
 7X7  C21  H211  single    0.970  0.020  1.090
 7X7  C21  H212  single    0.970  0.020  1.090
 7X7  C19  H191  single    0.970  0.020  1.090
 7X7  C19  H192  single    0.970  0.020  1.090
 7X7  C20  H201  single    0.970  0.020  1.090
 7X7  C20  H202  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
 7X7  C7    C1   C2    122.23  3.000
 7X7  C7    C1   CL1   118.08  3.000
 7X7  C2    C1   CL1   119.69  3.000
 7X7  H2    C2   C3    119.40  3.000
 7X7  H2    C2   C1    119.80  3.000
 7X7  C3    C2   C1    120.80  3.000
 7X7  H3    C3   C4    122.11  3.000
 7X7  H3    C3   C2    120.86  3.000
 7X7  C4    C3   C2    117.03  3.000
 7X7  C6    C4   O1    109.20  3.000
 7X7  C6    C4   C3    121.91  3.000
 7X7  O1    C4   C3    128.88  3.000
 7X7  C5    O1   C4    107.02  3.000
 7X7  H5C2  C5   H5C1  110.62  3.000
 7X7  H5C2  C5   O2    109.65  3.000
 7X7  H5C1  C5   O2    109.59  3.000
 7X7  H5C2  C5   O1    109.95  3.000
 7X7  H5C1  C5   O1    109.91  3.000
 7X7  O2    C5   O1    107.05  3.000
 7X7  C6    O2   C5    106.66  3.000
 7X7  C7    C6   O2    127.50  3.000
 7X7  C7    C6   C4    122.43  3.000
 7X7  O2    C6   C4    110.06  3.000
 7X7  N1    C7   C6    121.90  3.000
 7X7  N1    C7   C1    122.50  3.000
 7X7  C6    C7   C1    115.57  3.000
 7X7  H1    N1   C8    116.15  3.000
 7X7  H1    N1   C7    118.55  3.000
 7X7  C8    N1   C7    125.18  3.000
 7X7  N5    C8   C9    121.45  3.000
 7X7  N5    C8   N1    115.20  3.000
 7X7  C9    C8   N1    123.35  3.000
 7X7  H9    C9   C10   121.26  3.000
 7X7  H9    C9   C8    123.32  3.000
 7X7  C10   C9   C8    115.41  3.000
 7X7  H10   C10  N2    116.19  3.000
 7X7  H10   C10  C9    119.67  3.000
 7X7  N2    C10  C9    124.14  3.000
 7X7  C11   N2   C10   115.38  3.000
 7X7  N5    C11  N3    119.91  3.000
 7X7  N5    C11  N2    126.11  3.000
 7X7  N3    C11  N2    113.98  3.000
 7X7  HA    N3   C12   115.30  3.000
 7X7  HA    N3   C11   112.55  3.000
 7X7  C12   N3   C11   132.14  3.000
 7X7  C17   C12  C13   119.55  3.000
 7X7  C17   C12  N3    115.39  3.000
 7X7  C13   C12  N3    125.06  3.000
 7X7  H13   C13  C14   120.51  3.000
 7X7  H13   C13  C12   121.28  3.000
 7X7  C14   C13  C12   118.21  3.000
 7X7  H14   C14  C15   118.78  3.000
 7X7  H14   C14  C13   118.60  3.000
 7X7  C15   C14  C13   122.62  3.000
 7X7  H15   C15  C16   121.13  3.000
 7X7  H15   C15  C14   119.02  3.000
 7X7  C16   C15  C14   119.84  3.000
 7X7  N4    C16  C17   121.75  3.000
 7X7  N4    C16  C15   120.50  3.000
 7X7  C17   C16  C15   117.73  3.000
 7X7  H17   C17  C16   120.32  3.000
 7X7  H17   C17  C12   117.63  3.000
 7X7  C16   C17  C12   122.04  3.000
 7X7  C21   N4   C18   111.71  3.000
 7X7  C21   N4   C16   117.77  3.000
 7X7  C18   N4   C16   118.37  3.000
 7X7  H182  C18  H181  107.38  3.000
 7X7  H182  C18  C19   110.09  3.000
 7X7  H181  C18  C19   107.19  3.000
 7X7  H182  C18  N4    111.74  3.000
 7X7  H181  C18  N4    109.97  3.000
 7X7  C19   C18  N4    110.33  3.000
 7X7  H192  C19  H191  107.87  3.000
 7X7  H192  C19  O3    107.73  3.000
 7X7  H191  C19  O3    110.40  3.000
 7X7  H192  C19  C18   109.40  3.000
 7X7  H191  C19  C18   109.10  3.000
 7X7  O3    C19  C18   112.24  3.000
 7X7  C20   O3   C19   110.11  3.000
 7X7  H202  C20  H201  107.98  3.000
 7X7  H202  C20  C21   109.56  3.000
 7X7  H201  C20  C21   109.33  3.000
 7X7  H202  C20  O3    107.67  3.000
 7X7  H201  C20  O3    110.49  3.000
 7X7  C21   C20  O3    111.73  3.000
 7X7  H212  C21  H211  107.39  3.000
 7X7  H212  C21  C20   107.65  3.000
 7X7  H211  C21  C20   109.72  3.000
 7X7  H212  C21  N4    110.79  3.000
 7X7  H211  C21  N4    110.77  3.000
 7X7  C20   C21  N4    110.43  3.000
 7X7  C11   N5   C8    117.50  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
 7X7  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 7X7  CONST_02  C4   C6   C7   C1      0.00   0.0  0
 7X7  CONST_03  C6   C7   C1   C2      0.00   0.0  0
 7X7  CONST_04  C6   C4   C3   C2      0.00   0.0  0
 7X7  CONST_05  C7   C1   C2   C3      0.00   0.0  0
 7X7  CONST_06  C7   C6   C4   C3      0.00   0.0  0
 7X7  CONST_07  N2   C10  C9   C8      0.00   0.0  0
 7X7  CONST_08  N2   C11  N5   C8      0.00   0.0  0
 7X7  CONST_09  C11  N5   C8   C9      0.00   0.0  0
 7X7  CONST_10  C11  N2   C10  C9      0.00   0.0  0
 7X7  CONST_11  N5   C8   C9   C10     0.00   0.0  0
 7X7  CONST_12  N5   C11  N2   C10     0.00   0.0  0
 7X7  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 7X7  CONST_14  C15  C16  C17  C12     0.00   0.0  0
 7X7  CONST_15  C16  C17  C12  C13     0.00   0.0  0
 7X7  CONST_16  C16  C15  C14  C13     0.00   0.0  0
 7X7  CONST_17  C17  C12  C13  C14     0.00   0.0  0
 7X7  CONST_18  C17  C16  C15  C14     0.00   0.0  0
 7X7  CONST_19  N4   C16  C17  C12   180.00   0.0  0
 7X7  CONST_20  N4   C16  C15  C14   180.00   0.0  0
 7X7  CONST_21  C3   C2   C1   CL1   180.00   0.0  0
 7X7  CONST_22  C6   C7   C1   CL1   180.00   0.0  0
 7X7  CONST_23  N1   C7   C1   C2    180.00   0.0  0
 7X7  CONST_24  N1   C7   C6   C4    180.00   0.0  0
 7X7  CONST_25  N1   C7   C6   O2      0.00   0.0  0
 7X7  CONST_26  C10  C9   C8   N1    180.00   0.0  0
 7X7  CONST_27  C11  N5   C8   N1    180.00   0.0  0
 7X7  CONST_28  N3   C11  N5   C8    180.00   0.0  0
 7X7  CONST_29  N3   C11  N2   C10   180.00   0.0  0
 7X7  CONST_30  C14  C13  C12  N3    180.00   0.0  0
 7X7  CONST_31  C16  C17  C12  N3    180.00   0.0  0
 7X7  CONST_32  H3   C3   C2   C1    180.00   0.0  0
 7X7  CONST_33  H2   C2   C3   C4    180.00   0.0  0
 7X7  CONST_34  H10  C10  C9   C8    180.00   0.0  0
 7X7  CONST_35  H9   C9   C10  N2    180.00   0.0  0
 7X7  CONST_36  H14  C14  C13  C12   180.00   0.0  0
 7X7  CONST_37  H17  C17  C12  C13   180.00   0.0  0
 7X7  CONST_38  H15  C15  C14  C13   180.00   0.0  0
 7X7  CONST_39  H13  C13  C14  C15   180.00   0.0  0
 7X7  Var_01    O2   C5   O1   C4     -0.54  30.0  1
 7X7  Var_02    C6   C4   O1   C5      0.35  30.0  1
 7X7  Var_03    C7   C6   O2   C5   -179.79  30.0  1
 7X7  Var_04    C18  N4   C16  C15   177.56  30.0  2
 7X7  Var_05    C19  C18  N4   C16  -166.04  30.0  1
 7X7  Var_06    C20  C21  N4   C16   165.26  30.0  1
 7X7  Var_07    O3   C19  C18  N4    -55.52  30.0  1
 7X7  Var_08    O3   C20  C21  N4     56.13  30.0  1
 7X7  Var_09    C21  C20  O3   C19   -58.95  30.0  1
 7X7  Var_10    C8   N1   C7   C1   -118.98  30.0  2
 7X7  Var_11    C9   C8   N1   C7      4.42  30.0  2
 7X7  Var_12    C12  N3   C11  N2    179.84  30.0  2
 7X7  Var_13    C13  C12  N3   C11    -4.52  30.0  2

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
 7X7  plan-1  N1   0.020
 7X7  plan-1  C8   0.020
 7X7  plan-1  C9   0.020
 7X7  plan-1  C10  0.020
 7X7  plan-1  N2   0.020
 7X7  plan-1  C11  0.020
 7X7  plan-1  N3   0.020
 7X7  plan-1  N5   0.020
 7X7  plan-1  H9   0.020
 7X7  plan-1  H10  0.020
 7X7  plan-2  N3   0.020
 7X7  plan-2  C12  0.020
 7X7  plan-2  C13  0.020
 7X7  plan-2  C14  0.020
 7X7  plan-2  C15  0.020
 7X7  plan-2  C16  0.020
 7X7  plan-2  C17  0.020
 7X7  plan-2  N4   0.020
 7X7  plan-2  H13  0.020
 7X7  plan-2  H17  0.020
 7X7  plan-2  H14  0.020
 7X7  plan-2  H15  0.020
 7X7  plan-3  CL1  0.020
 7X7  plan-3  C1   0.020
 7X7  plan-3  C2   0.020
 7X7  plan-3  C3   0.020
 7X7  plan-3  C4   0.020
 7X7  plan-3  O1   0.020
 7X7  plan-3  O2   0.020
 7X7  plan-3  C6   0.020
 7X7  plan-3  C7   0.020
 7X7  plan-3  N1   0.020
 7X7  plan-3  H2   0.020
 7X7  plan-3  H3   0.020

