# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:52:51 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-{[(3R,4R)-3-aminotetrahydro-2H-pyran-4-yl]amino}-4-[(4-methylphenyl)amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Nc2nc(N[C@@H]3CCOC[C@@H]3N)ncc2C(N)=O)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
 S19  S19  2-{[(3R,4R)-3-aminotetrahydro-2H-pyran-4-yl]amino}-4-[(4-methylphenyl)amino]pyrimidine-5-carboxamide  ligand  47  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S19
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
 S19  C1    C  CH3   0  -0.723  -4.2953   4.9669  -0.2386
 S19  C2    C  CR6   0   0.081  -3.7534   3.5704  -0.1478
 S19  C3    C  CR16  0  -0.281  -4.6056   2.4674  -0.0928
 S19  C4    C  CR16  0  -0.356  -4.1110   1.1790  -0.0332
 S19  C5    C  CR6   0   0.350  -2.7321   0.9314  -0.0250
 S19  N6    N  NH1   0  -0.792  -2.3562  -0.4100   0.0393
 S19  C7    C  CR6   0   0.570  -1.1471  -1.0014  -0.0079
 S19  N8    N  N     0  -0.529  -0.0607  -0.2553  -0.1082
 S19  C9    C  CR6   0   0.625   1.1281  -0.8587  -0.1715
 S19  N10   N  NH1   0  -0.647   2.1934  -0.0503  -0.2487
 S19  C11   C  CH1   0  -0.095   3.5499  -0.4850  -0.5177
 S19  C12   C  CH2   0  -0.467   4.2086  -1.1503   0.6917
 S19  C13   C  CH2   0  -0.183   4.4687  -0.1522   1.8044
 S19  O14   O  O2    0  -0.484   5.2565   0.9317   1.3539
 S19  C15   C  CH2   0  -0.167   4.6350   1.6326   0.3059
 S19  C16   C  CH1   0  -0.143   4.3792   0.7461  -0.9124
 S19  N17   N  NH2   0  -0.802   3.6804   1.5303  -1.9141
 S19  N18   N  N     0  -0.484   1.3309  -2.1832  -0.1683
 S19  C19   C  CR16  0  -0.018   0.2416  -2.9201  -0.0610
 S19  C20   C  CR6   0  -0.301  -1.0513  -2.4309   0.0464
 S19  C21   C  C     0   0.545  -2.2317  -3.3044   0.1804
 S19  N22   N  NH2   0  -0.822  -2.0358  -4.6276   0.2890
 S19  O23   O  O     0  -0.518  -3.3799  -2.8459   0.1804
 S19  C24   C  CR16  0  -0.298  -1.8694   2.0267  -0.0728
 S19  C25   C  CR16  0  -0.294  -2.3881   3.3151  -0.1329
 S19  H1    H  HCH3  0   0.244  -4.7085   5.1680  -1.2292
 S19  H1A   H  HCH3  0   0.242  -5.0967   5.1349   0.4818
 S19  H1B   H  HCH3  0   0.242  -3.5187   5.7081  -0.0531
 S19  H3    H  HCR6  0   0.248  -5.6795   2.6141  -0.0962
 S19  H4    H  HCR6  0   0.261  -4.8062   0.3482   0.0070
 S19  HN6   H  HNH1  0   0.432  -3.1155  -1.0880   0.0924
 S19  HN10  H  HNH1  0   0.391   1.9889   0.9131  -0.4745
 S19  H11   H  HCH1  0   0.257   3.5479  -1.1917  -1.3554
 S19  H12   H  HCH2  0   0.253   3.5876  -1.9679   1.0585
 S19  H12A  H  HCH2  0   0.235   5.1557  -1.5929   0.3691
 S19  H13   H  HCH2  0   0.202   3.5184   0.2125   2.2198
 S19  H13A  H  HCH2  0   0.239   5.0184  -0.6257   2.6192
 S19  H15   H  HCH2  0   0.197   3.6888   2.0848   0.6403
 S19  H15A  H  HCH2  0   0.241   5.3010   2.4545   0.0299
 S19  H16   H  HCH1  0   0.235   5.3499   0.3624  -1.2581
 S19  HN17  H  HNH2  0   0.357   4.2380   2.3349  -2.1740
 S19  HN1A  H  HNH2  0   0.356   3.5669   0.9861  -2.7607
 S19  H19   H  HCR6  0   0.254   0.4242  -3.9895  -0.0738
 S19  HN22  H  HNH2  0   0.412  -1.1383  -5.0475   0.4508
 S19  HN2A  H  HNH2  0   0.407  -2.8362  -5.2166   0.4510
 S19  H24   H  HCR6  0   0.284  -0.8022   1.8835  -0.0642
 S19  H25   H  HCR6  0   0.246  -1.6912   4.1444  -0.1682

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
 S19  C1   C2    single    1.501  0.020  1.501
 S19  C1   H1    single    0.970  0.020  1.090
 S19  C1   H1A   single    0.970  0.020  1.090
 S19  C1   H1B   single    0.970  0.020  1.090
 S19  C3   C2    aromatic  1.395  0.020  1.395
 S19  C2   C25   aromatic  1.389  0.020  1.389
 S19  C3   C4    aromatic  1.381  0.020  1.381
 S19  C3   H3    single    0.930  0.020  1.080
 S19  C4   C5    aromatic  1.401  0.020  1.401
 S19  C4   H4    single    0.930  0.020  1.080
 S19  C5   N6    single    1.395  0.020  1.395
 S19  C5   C24   aromatic  1.395  0.020  1.395
 S19  N6   C7    single    1.347  0.020  1.347
 S19  N6   HN6   single    0.860  0.020  1.020
 S19  C7   C20   aromatic  1.434  0.020  1.434
 S19  C7   N8    aromatic  1.322  0.020  1.322
 S19  N8   C9    aromatic  1.335  0.020  1.335
 S19  C9   N18   aromatic  1.340  0.020  1.340
 S19  C9   N10   single    1.339  0.020  1.339
 S19  N10  C11   single    1.450  0.020  1.450
 S19  N10  HN10  single    0.890  0.020  1.040
 S19  C11  C16   single    1.536  0.020  1.536
 S19  C11  C12   single    1.529  0.020  1.529
 S19  C11  H11   single    0.970  0.020  1.090
 S19  C13  C12   single    1.517  0.020  1.517
 S19  C12  H12   single    0.970  0.020  1.090
 S19  C12  H12A  single    0.970  0.020  1.090
 S19  C13  O14   single    1.414  0.020  1.414
 S19  C13  H13   single    0.970  0.020  1.090
 S19  C13  H13A  single    0.970  0.020  1.090
 S19  C15  O14   single    1.406  0.020  1.406
 S19  C16  C15   single    1.528  0.020  1.528
 S19  C15  H15   single    0.970  0.020  1.090
 S19  C15  H15A  single    0.970  0.020  1.090
 S19  C16  N17   single    1.451  0.020  1.451
 S19  C16  H16   single    0.970  0.020  1.090
 S19  N17  HN17  single    0.890  0.020  1.040
 S19  N17  HN1A  single    0.890  0.020  1.040
 S19  C19  N18   aromatic  1.320  0.020  1.320
 S19  C20  C19   aromatic  1.387  0.020  1.387
 S19  C19  H19   single    0.930  0.020  1.080
 S19  C21  C20   single    1.475  0.020  1.475
 S19  O23  C21   double    1.236  0.020  1.236
 S19  C21  N22   single    1.342  0.020  1.342
 S19  N22  HN22  single    0.860  0.020  1.020
 S19  N22  HN2A  single    0.860  0.020  1.020
 S19  C25  C24   aromatic  1.390  0.020  1.390
 S19  C24  H24   single    0.930  0.020  1.080
 S19  C25  H25   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
 S19  H1B   C1   H1A   107.85  3.000
 S19  H1B   C1   H1    107.39  3.000
 S19  H1A   C1   H1    107.03  3.000
 S19  H1B   C1   C2    111.43  3.000
 S19  H1A   C1   C2    111.63  3.000
 S19  H1    C1   C2    111.27  3.000
 S19  C25   C2   C3    117.05  3.000
 S19  C25   C2   C1    121.78  3.000
 S19  C3    C2   C1    121.17  3.000
 S19  H3    C3   C4    118.76  3.000
 S19  H3    C3   C2    119.88  3.000
 S19  C4    C3   C2    121.36  3.000
 S19  H4    C4   C5    119.71  3.000
 S19  H4    C4   C3    119.13  3.000
 S19  C5    C4   C3    121.17  3.000
 S19  C24   C5   N6    126.16  3.000
 S19  C24   C5   C4    118.02  3.000
 S19  N6    C5   C4    115.82  3.000
 S19  HN6   N6   C7    112.24  3.000
 S19  HN6   N6   C5    116.19  3.000
 S19  C7    N6   C5    131.51  3.000
 S19  C20   C7   N8    120.72  3.000
 S19  N8    C7   N6    119.52  3.000
 S19  C20   C7   N6    119.76  3.000
 S19  C9    N8   C7    118.72  3.000
 S19  N18   C9   N10   118.44  3.000
 S19  N10   C9   N8    115.99  3.000
 S19  N18   C9   N8    125.56  3.000
 S19  HN10  N10  C11   115.71  3.000
 S19  HN10  N10  C9    115.30  3.000
 S19  C11   N10  C9    125.02  3.000
 S19  H11   C11  C16   108.75  3.000
 S19  H11   C11  C12   108.95  3.000
 S19  C16   C11  C12   108.62  3.000
 S19  H11   C11  N10   109.48  3.000
 S19  C12   C11  N10   112.75  3.000
 S19  C16   C11  N10   108.21  3.000
 S19  H12A  C12  H12   106.80  3.000
 S19  H12A  C12  C13   109.51  3.000
 S19  H12   C12  C13   110.13  3.000
 S19  H12A  C12  C11   108.40  3.000
 S19  H12   C12  C11   110.30  3.000
 S19  C13   C12  C11   111.57  3.000
 S19  H13A  C13  H13   107.30  3.000
 S19  H13A  C13  O14   106.86  3.000
 S19  H13   C13  O14   110.35  3.000
 S19  H13A  C13  C12   110.40  3.000
 S19  H13   C13  C12   110.32  3.000
 S19  O14   C13  C12   111.48  3.000
 S19  C15   O14  C13   111.94  3.000
 S19  H15A  C15  H15   106.94  3.000
 S19  H15A  C15  C16   109.69  3.000
 S19  H15   C15  C16   109.67  3.000
 S19  H15A  C15  O14   107.08  3.000
 S19  H15   C15  O14   111.00  3.000
 S19  C16   C15  O14   112.28  3.000
 S19  H16   C16  N17   113.37  3.000
 S19  H16   C16  C15   107.77  3.000
 S19  N17   C16  C15   108.50  3.000
 S19  H16   C16  C11   106.13  3.000
 S19  N17   C16  C11   110.52  3.000
 S19  C15   C16  C11   110.52  3.000
 S19  HN1A  N17  HN17  105.91  3.000
 S19  HN1A  N17  C16   109.91  3.000
 S19  HN17  N17  C16   109.95  3.000
 S19  C19   N18  C9    115.29  3.000
 S19  H19   C19  C20   120.37  3.000
 S19  H19   C19  N18   114.24  3.000
 S19  C20   C19  N18   125.38  3.000
 S19  C21   C20  C19   122.99  3.000
 S19  C21   C20  C7    122.73  3.000
 S19  C19   C20  C7    114.28  3.000
 S19  O23   C21  N22   120.08  3.000
 S19  N22   C21  C20   118.33  3.000
 S19  O23   C21  C20   121.58  3.000
 S19  HN2A  N22  HN22  116.10  3.000
 S19  HN2A  N22  C21   118.28  3.000
 S19  HN22  N22  C21   123.78  3.000
 S19  H24   C24  C25   119.56  3.000
 S19  H24   C24  C5    120.55  3.000
 S19  C25   C24  C5    119.89  3.000
 S19  H25   C25  C24   118.08  3.000
 S19  H25   C25  C2    119.40  3.000
 S19  C24   C25  C2    122.52  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
 S19  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 S19  CONST_02  C5    C24  C25  C2      0.00   0.0  0
 S19  CONST_03  C24   C25  C2   C3      0.00   0.0  0
 S19  CONST_04  C24   C5   C4   C3      0.00   0.0  0
 S19  CONST_05  C25   C2   C3   C4      0.00   0.0  0
 S19  CONST_06  C25   C24  C5   C4      0.00   0.0  0
 S19  CONST_07  N18   C19  C20  C7      0.00   0.0  0
 S19  CONST_08  N18   C9   N8   C7      0.00   0.0  0
 S19  CONST_09  C19   C20  C7   N8      0.00   0.0  0
 S19  CONST_10  C19   N18  C9   N8      0.00   0.0  0
 S19  CONST_11  C20   C7   N8   C9      0.00   0.0  0
 S19  CONST_12  C20   C19  N18  C9      0.00   0.0  0
 S19  CONST_13  C4    C3   C2   C1    180.00   0.0  0
 S19  CONST_14  C24   C25  C2   C1    180.00   0.0  0
 S19  CONST_15  N6    C5   C4   C3    180.00   0.0  0
 S19  CONST_16  C25   C24  C5   N6    180.00   0.0  0
 S19  CONST_17  C19   C20  C7   N6    180.00   0.0  0
 S19  CONST_18  C9    N8   C7   N6    180.00   0.0  0
 S19  CONST_19  N10   C9   N8   C7    180.00   0.0  0
 S19  CONST_20  C21   C20  C7   N8    180.00   0.0  0
 S19  CONST_21  C19   N18  C9   N10   180.00   0.0  0
 S19  CONST_22  C21   C20  C19  N18   180.00   0.0  0
 S19  CONST_23  C11   N10  C9   N8    180.00   0.0  0
 S19  CONST_24  N18   C9   N10  C11     0.00   0.0  0
 S19  CONST_25  H4    C4   C3   C2    180.00   0.0  0
 S19  CONST_26  H24   C24  C25  C2    180.00   0.0  0
 S19  CONST_27  H25   C25  C2   C3    180.00   0.0  0
 S19  CONST_28  H3    C3   C4   C5    180.00   0.0  0
 S19  CONST_29  H19   C19  C20  C7    180.00   0.0  0
 S19  CONST_30  HN10  N10  C9   N8      0.00   0.0  0
 S19  CONST_31  HN22  N22  C21  C20     0.00   0.0  0
 S19  CONST_32  HN2A  N22  C21  C20   180.00   0.0  0
 S19  Var_01    O14   C13  C12  C11   -56.30  30.0  1
 S19  Var_02    C16   C15  O14  C13   -60.27  30.0  1
 S19  Var_03    C7    N6   C5   C4    175.88  30.0  2
 S19  Var_04    C20   C7   N6   C5   -178.34  30.0  2
 S19  Var_05    O23   C21  C20  C7      3.98  30.0  2
 S19  Var_06    H1    C1   C2   C3    -72.67  30.0  2

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
 S19  chir_01  C11  N10  C16  C12  negativ
 S19  chir_02  C16  N17  C11  C15  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
 S19  plan-1  C1    0.020
 S19  plan-1  C2    0.020
 S19  plan-1  C3    0.020
 S19  plan-1  C4    0.020
 S19  plan-1  C5    0.020
 S19  plan-1  N6    0.020
 S19  plan-1  C24   0.020
 S19  plan-1  C25   0.020
 S19  plan-1  H3    0.020
 S19  plan-1  H4    0.020
 S19  plan-1  H24   0.020
 S19  plan-1  H25   0.020
 S19  plan-2  N6    0.020
 S19  plan-2  C7    0.020
 S19  plan-2  N8    0.020
 S19  plan-2  C9    0.020
 S19  plan-2  N10   0.020
 S19  plan-2  N18   0.020
 S19  plan-2  C19   0.020
 S19  plan-2  C20   0.020
 S19  plan-2  C21   0.020
 S19  plan-2  H19   0.020
 S19  plan-3  C20   0.020
 S19  plan-3  C21   0.020
 S19  plan-3  N22   0.020
 S19  plan-3  O23   0.020
 S19  plan-3  HN22  0.020
 S19  plan-3  HN2A  0.020
 S19  plan-4  C9    0.020
 S19  plan-4  N10   0.020
 S19  plan-4  C11   0.020
 S19  plan-4  HN10  0.020

