# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:36:10 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: N~2~-{4-methoxy-3-[3-(pyrrolidin-1-yl)propoxy]phenyl}-N~4~,6-dimethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(C)nc(Nc2ccc(OC)c(OCCCN3CCCC3)c2)n1
#
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
 N47  N47  N~2~-{4-methoxy-3-[3-(pyrrolidin-1-yl)propoxy]phenyl}-N~4~,6-dimethylpyrimidine-2,4-diamine  ligand  56  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N47
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
 N47  N    N  NH1   0  -0.659   7.2094  18.2374  26.5994
 N47  C    C  CH3   0  -0.517   5.8527  17.8905  26.9402
 N47  C12  C  CH2   0  -0.269   6.0786   6.8269  26.9944
 N47  C11  C  CH2   0  -0.468   6.6753   6.7291  25.5887
 N47  C10  C  CH2   0  -0.462   8.1979   6.6400  25.8273
 N47  C9   C  CH2   0  -0.276   8.3414   6.6499  27.3501
 N47  N3   N  NT    0  -0.422   7.1605   7.3619  27.8001
 N47  C8   C  CH2   0  -0.267   6.9096   7.2946  29.2195
 N47  C7   C  CH2   0  -0.494   7.9474   8.0448  30.0468
 N47  C6   C  CH2   0  -0.182   8.1472   9.4819  29.6180
 N47  O    O  O2    0  -0.465   6.9100  10.1613  29.7572
 N47  C5   C  CR6   0   0.345   6.8044  11.4170  29.2940
 N47  C4   C  CR16  0  -0.509   7.8643  12.1709  28.8268
 N47  C13  C  CR6   0   0.277   5.5058  11.9675  29.3057
 N47  C14  C  CH3   0  -0.434   3.2172  11.6823  29.8225
 N47  C15  C  CR16  0  -0.373   5.3327  13.2546  28.8377
 N47  C16  C  CR16  0  -0.348   6.4009  14.0181  28.3611
 N47  C3   C  CR6   0   0.372   7.6801  13.4823  28.3543
 N47  C2   C  CR6   0   0.579   9.0293  15.3806  27.4043
 N47  N1   N  N     0  -0.529   7.9965  16.1956  27.2573
 N47  N4   N  N     0  -0.527  10.3030  15.6416  27.0987
 N47  C17  C  CR6   0   0.278  10.5514  16.8516  26.5938
 N47  C18  C  CH3   0  -0.736  11.9754  17.1701  26.2531
 N47  C19  C  CR16  0  -0.474   9.5554  17.7844  26.3923
 N47  C1   C  CR6   0   0.581   8.2496  17.4049  26.7496
 N47  H1   H  HNH1  0   0.401   7.3828  19.1408  26.1943
 N47  H2   H  HCH3  0   0.253   5.2187  18.7456  26.7225
 N47  H3   H  HCH3  0   0.233   5.4892  17.0386  26.3627
 N47  H4   H  HCH3  0   0.234   5.7491  17.6464  27.9987
 N47  H6   H  HCH2  0   0.186   5.7692   5.8268  27.3448
 N47  H7   H  HCH2  0   0.233   6.4268   7.6107  24.9971
 N47  H8   H  HCH2  0   0.232   6.2849   5.8640  25.0532
 N47  H9   H  HCH2  0   0.232   8.6398   5.7444  25.3917
 N47  H10  H  HCH2  0   0.233   8.7086   7.4970  25.3874
 N47  H11  H  HCH2  0   0.188   8.3618   5.6160  27.7375
 N47  H12  H  HCH2  0   0.230   9.2588   7.1383  27.6845
 N47  H14  H  HCH2  0   0.231   5.9230   7.7230  29.4103
 N47  H15  H  HCH2  0   0.197   6.8646   6.2484  29.5712
 N47  H16  H  HCH2  0   0.244   7.6527   8.0075  31.0988
 N47  H17  H  HCH2  0   0.239   8.9194   7.5480  29.9921
 N47  H18  H  HCH2  0   0.223   8.4837   9.5233  28.5771
 N47  H19  H  HCH2  0   0.228   8.9154   9.9571  30.2387
 N47  H20  H  HCR6  0   0.287   8.8640  11.7551  28.8262
 N47  H21  H  HCH3  0   0.256   2.5881  10.9017  30.2438
 N47  H22  H  HCH3  0   0.223   3.1456  12.5715  30.4555
 N47  H23  H  HCH3  0   0.223   2.8415  11.9338  28.8262
 N47  H24  H  HCR6  0   0.276   4.3489  13.7045  28.8240
 N47  H25  H  HCR6  0   0.299   6.2180  15.0170  28.0037
 N47  H27  H  HCH3  0   0.248  12.6208  16.3132  26.4328
 N47  H28  H  HCH3  0   0.252  12.0704  17.4641  25.2073
 N47  H29  H  HCH3  0   0.254  12.3377  18.0060  26.8533
 N47  H30  H  HCR6  0   0.257   9.7700  18.7628  25.9840
 N47  N2   N  NH1   0  -0.775   8.8308  14.1330  27.9167
 N47  O1   O  O2    0  -0.466   4.5289  11.1650  29.7818
 N47  H5   H  HCH2  0   0.229   5.1997   7.4738  27.0444
 N47  H26  H  HNH1  0   0.401   9.6834  13.5990  27.9852

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
 N47  C11  C10  single    1.544  0.020  1.544
 N47  C11  C12  single    1.530  0.020  1.530
 N47  C10  C9   single    1.530  0.020  1.530
 N47  C19  C1   aromatic  1.406  0.020  1.406
 N47  C19  C17  aromatic  1.379  0.020  1.379
 N47  C18  C17  single    1.498  0.020  1.498
 N47  N    C1   single    1.341  0.020  1.341
 N47  N    C    single    1.441  0.020  1.441
 N47  C1   N1   aromatic  1.336  0.020  1.336
 N47  C17  N4   aromatic  1.334  0.020  1.334
 N47  C12  N3   single    1.451  0.020  1.451
 N47  N4   C2   aromatic  1.336  0.020  1.336
 N47  N1   C2   aromatic  1.324  0.020  1.324
 N47  C9   N3   single    1.451  0.020  1.451
 N47  C2   N2   single    1.363  0.020  1.363
 N47  N3   C8   single    1.443  0.020  1.443
 N47  N2   C3   single    1.393  0.020  1.393
 N47  C3   C16  aromatic  1.387  0.020  1.387
 N47  C3   C4   aromatic  1.406  0.020  1.406
 N47  C16  C15  aromatic  1.397  0.020  1.397
 N47  C4   C5   aromatic  1.382  0.020  1.382
 N47  C15  C13  aromatic  1.380  0.020  1.380
 N47  C8   C7   single    1.525  0.020  1.525
 N47  C5   C13  aromatic  1.411  0.020  1.411
 N47  C5   O    single    1.343  0.020  1.343
 N47  C6   O    single    1.418  0.020  1.418
 N47  C6   C7   single    1.513  0.020  1.513
 N47  C13  O1   single    1.351  0.020  1.351
 N47  O1   C14  single    1.411  0.020  1.411
 N47  N    H1   single    0.860  0.020  1.020
 N47  C    H2   single    0.970  0.020  1.090
 N47  C    H3   single    0.970  0.020  1.090
 N47  C    H4   single    0.970  0.020  1.090
 N47  C12  H5   single    0.970  0.020  1.090
 N47  C12  H6   single    0.970  0.020  1.090
 N47  C11  H7   single    0.970  0.020  1.090
 N47  C11  H8   single    0.970  0.020  1.090
 N47  C10  H9   single    0.970  0.020  1.090
 N47  C10  H10  single    0.970  0.020  1.090
 N47  C9   H11  single    0.970  0.020  1.090
 N47  C9   H12  single    0.970  0.020  1.090
 N47  C8   H14  single    0.970  0.020  1.090
 N47  C8   H15  single    0.970  0.020  1.090
 N47  C7   H16  single    0.970  0.020  1.090
 N47  C7   H17  single    0.970  0.020  1.090
 N47  C6   H18  single    0.970  0.020  1.090
 N47  C6   H19  single    0.970  0.020  1.090
 N47  C4   H20  single    0.930  0.020  1.080
 N47  C14  H21  single    0.970  0.020  1.090
 N47  C14  H22  single    0.970  0.020  1.090
 N47  C14  H23  single    0.970  0.020  1.090
 N47  C15  H24  single    0.930  0.020  1.080
 N47  C16  H25  single    0.930  0.020  1.080
 N47  N2   H26  single    0.860  0.020  1.020
 N47  C18  H27  single    0.970  0.020  1.090
 N47  C18  H28  single    0.970  0.020  1.090
 N47  C18  H29  single    0.970  0.020  1.090
 N47  C19  H30  single    0.930  0.020  1.080

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
 N47  H1   N    C1   118.00  3.000
 N47  H1   N    C    118.30  3.000
 N47  C1   N    C    123.66  3.000
 N47  H4   C    H3   107.88  3.000
 N47  H4   C    H2   108.36  3.000
 N47  H3   C    H2   108.29  3.000
 N47  H4   C    N    111.88  3.000
 N47  H3   C    N    112.10  3.000
 N47  H2   C    N    108.21  3.000
 N47  H6   C12  H5   107.24  3.000
 N47  H6   C12  N3   111.51  3.000
 N47  H5   C12  N3   110.86  3.000
 N47  H6   C12  C11  110.06  3.000
 N47  H5   C12  C11  113.18  3.000
 N47  N3   C12  C11  104.05  3.000
 N47  H8   C11  H7   107.07  3.000
 N47  H8   C11  C10  112.55  3.000
 N47  H7   C11  C10  110.81  3.000
 N47  H8   C11  C12  111.25  3.000
 N47  H7   C11  C12  110.97  3.000
 N47  C10  C11  C12  104.26  3.000
 N47  H10  C10  H9   107.14  3.000
 N47  H10  C10  C9   110.65  3.000
 N47  H9   C10  C9   111.42  3.000
 N47  H10  C10  C11  110.75  3.000
 N47  H9   C10  C11  112.69  3.000
 N47  C9   C10  C11  104.25  3.000
 N47  H12  C9   H11  107.21  3.000
 N47  H12  C9   N3   111.68  3.000
 N47  H11  C9   N3   111.45  3.000
 N47  H12  C9   C10  112.75  3.000
 N47  H11  C9   C10  110.18  3.000
 N47  N3   C9   C10  103.63  3.000
 N47  C8   N3   C9   115.08  3.000
 N47  C8   N3   C12  113.54  3.000
 N47  C9   N3   C12  104.70  3.000
 N47  H15  C8   H14  106.20  3.000
 N47  H15  C8   C7   108.73  3.000
 N47  H14  C8   C7   109.09  3.000
 N47  H15  C8   N3   111.37  3.000
 N47  H14  C8   N3   108.09  3.000
 N47  C7   C8   N3   113.11  3.000
 N47  H17  C7   H16  105.80  3.000
 N47  H17  C7   C6   107.47  3.000
 N47  H16  C7   C6   109.93  3.000
 N47  H17  C7   C8   110.77  3.000
 N47  H16  C7   C8   108.77  3.000
 N47  C6   C7   C8   113.80  3.000
 N47  H19  C6   H18  107.85  3.000
 N47  H19  C6   O    110.37  3.000
 N47  H18  C6   O    110.08  3.000
 N47  H19  C6   C7   110.11  3.000
 N47  H18  C6   C7   110.24  3.000
 N47  O    C6   C7   108.18  3.000
 N47  C5   O    C6   118.87  3.000
 N47  C13  C5   C4   119.73  3.000
 N47  C13  C5   O    115.76  3.000
 N47  C4   C5   O    124.51  3.000
 N47  H20  C4   C3   118.62  3.000
 N47  H20  C4   C5   119.92  3.000
 N47  C3   C4   C5   121.46  3.000
 N47  C15  C13  C5   118.46  3.000
 N47  C5   C13  O1   115.91  3.000
 N47  C15  C13  O1   125.63  3.000
 N47  H23  C14  H22  108.52  3.000
 N47  H23  C14  H21  108.60  3.000
 N47  H22  C14  H21  108.75  3.000
 N47  H23  C14  O1   112.17  3.000
 N47  H22  C14  O1   112.07  3.000
 N47  H21  C14  O1   106.61  3.000
 N47  H24  C15  C16  117.63  3.000
 N47  H24  C15  C13  120.41  3.000
 N47  C16  C15  C13  121.96  3.000
 N47  H25  C16  C3   120.89  3.000
 N47  H25  C16  C15  119.38  3.000
 N47  C3   C16  C15  119.73  3.000
 N47  N2   C3   C16  125.68  3.000
 N47  C16  C3   C4   118.65  3.000
 N47  N2   C3   C4   115.67  3.000
 N47  N4   C2   N1   126.75  3.000
 N47  N1   C2   N2   119.44  3.000
 N47  N4   C2   N2   113.81  3.000
 N47  C1   N1   C2   116.85  3.000
 N47  C17  N4   C2   116.19  3.000
 N47  C19  C17  C18  120.61  3.000
 N47  C18  C17  N4   117.11  3.000
 N47  C19  C17  N4   122.28  3.000
 N47  H29  C18  H28  106.98  3.000
 N47  H29  C18  H27  108.40  3.000
 N47  H28  C18  H27  108.61  3.000
 N47  H29  C18  C17  110.70  3.000
 N47  H28  C18  C17  110.98  3.000
 N47  H27  C18  C17  111.03  3.000
 N47  H30  C19  C1   121.62  3.000
 N47  H30  C19  C17  121.57  3.000
 N47  C1   C19  C17  116.80  3.000
 N47  C19  C1   N1   121.13  3.000
 N47  N1   C1   N    117.24  3.000
 N47  C19  C1   N    121.63  3.000
 N47  H26  N2   C2   112.77  3.000
 N47  H26  N2   C3   115.46  3.000
 N47  C2   N2   C3   131.76  3.000
 N47  C14  O1   C13  117.70  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
 N47  CONST_01  C16  C3   C4   C5      0.00   0.0  0
 N47  CONST_02  C16  C15  C13  C5      0.00   0.0  0
 N47  CONST_03  C15  C16  C3   C4      0.00   0.0  0
 N47  CONST_04  C15  C13  C5   C4      0.00   0.0  0
 N47  CONST_05  C3   C16  C15  C13     0.00   0.0  0
 N47  CONST_06  C3   C4   C5   C13     0.00   0.0  0
 N47  CONST_07  C19  C17  N4   C2      0.00   0.0  0
 N47  CONST_08  C19  C1   N1   C2      0.00   0.0  0
 N47  CONST_09  C17  C19  C1   N1      0.00   0.0  0
 N47  CONST_10  C17  N4   C2   N1      0.00   0.0  0
 N47  CONST_11  C1   C19  C17  N4      0.00   0.0  0
 N47  CONST_12  C1   N1   C2   N4      0.00   0.0  0
 N47  CONST_13  C17  C19  C1   N     180.00   0.0  0
 N47  CONST_14  C2   N1   C1   N     180.00   0.0  0
 N47  CONST_15  C16  C15  C13  O1    180.00   0.0  0
 N47  CONST_16  C4   C5   C13  O1    180.00   0.0  0
 N47  CONST_17  C3   C4   C5   O     180.00   0.0  0
 N47  CONST_18  C15  C13  C5   O     180.00   0.0  0
 N47  CONST_19  N2   C3   C4   C5    180.00   0.0  0
 N47  CONST_20  N2   C3   C16  C15   180.00   0.0  0
 N47  CONST_21  C17  N4   C2   N2    180.00   0.0  0
 N47  CONST_22  C1   N1   C2   N2    180.00   0.0  0
 N47  CONST_23  C18  C17  N4   C2    180.00   0.0  0
 N47  CONST_24  C1   C19  C17  C18   180.00   0.0  0
 N47  CONST_25  H24  C15  C13  C5    180.00   0.0  0
 N47  CONST_26  H25  C16  C3   C4    180.00   0.0  0
 N47  CONST_27  H20  C4   C5   C13   180.00   0.0  0
 N47  CONST_28  H30  C19  C1   N1    180.00   0.0  0
 N47  CONST_29  C19  C1   N    C     180.00   0.0  0
 N47  CONST_30  N1   C1   N    C       0.00   0.0  0
 N47  CONST_31  H1   N    C1   N1    180.00   0.0  0
 N47  Var_01    C9   C10  C11  C12     1.72  30.0  1
 N47  Var_02    C10  C9   N3   C12    43.23  30.0  1
 N47  Var_03    N3   C9   C10  C11   -26.72  30.0  1
 N47  Var_04    C9   N3   C12  C11   -42.17  30.0  1
 N47  Var_05    N3   C12  C11  C10    23.88  30.0  1
 N47  Var_06    C2   N2   C3   C4    179.90  30.0  2
 N47  Var_07    N4   C2   N2   C3    179.91  30.0  2
 N47  Var_08    C7   C8   N3   C12  -171.27  30.0  3
 N47  Var_09    C4   C5   O    C6     -8.16  30.0  2
 N47  Var_10    C15  C13  O1   C14    -0.75  30.0  1
 N47  Var_11    H27  C18  C17  N4      2.73  30.0  2
 N47  Var_12    C6   C7   C8   N3     53.17  30.0  3
 N47  Var_13    H18  C6   O    C5    -52.12  30.0  1
 N47  Var_14    H21  C14  O1   C13  -179.20  30.0  3
 N47  Var_15    H2   C    N    C1    179.79  30.0  3
 N47  Var_16    O    C6   C7   C8     60.30  30.0  1

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
 N47  plan-1  O    0.020
 N47  plan-1  C5   0.020
 N47  plan-1  C4   0.020
 N47  plan-1  C13  0.020
 N47  plan-1  C15  0.020
 N47  plan-1  C16  0.020
 N47  plan-1  C3   0.020
 N47  plan-1  H20  0.020
 N47  plan-1  H24  0.020
 N47  plan-1  H25  0.020
 N47  plan-1  N2   0.020
 N47  plan-1  O1   0.020
 N47  plan-2  N    0.020
 N47  plan-2  C2   0.020
 N47  plan-2  N1   0.020
 N47  plan-2  N4   0.020
 N47  plan-2  C17  0.020
 N47  plan-2  C18  0.020
 N47  plan-2  C19  0.020
 N47  plan-2  C1   0.020
 N47  plan-2  H30  0.020
 N47  plan-2  N2   0.020
 N47  plan-3  N    0.020
 N47  plan-3  C    0.020
 N47  plan-3  C1   0.020
 N47  plan-3  H1   0.020

