# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 22:22:18 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-[2-[[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]amino]phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccccc1Nc2nc(NC3CCOCC3)ncc2Cl
#
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
 CQ3  CQ3  N-[2-[[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]amino]phenyl]propanamide  ligand  48  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CQ3
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
 CQ3  C     C   CH3   0  -0.658   7.0341   1.3296  -1.0744
 CQ3  N     N   NH1   0  -0.758   3.8117  -0.5618  -0.7528
 CQ3  O     O   O     0  -0.466   5.7435  -0.6844   0.4170
 CQ3  CL    CL  CL    0  -0.124   1.3643   3.1141   0.4936
 CQ3  C1    C   CH2   0  -0.584   5.6423   0.8479  -1.4391
 CQ3  N1    N   NH1   0  -0.765   1.4939   0.1055   0.5277
 CQ3  O1    O   O2    0  -0.483  -6.9926  -0.7343  -1.1543
 CQ3  C2    C   C     0   0.540   5.0998  -0.2025  -0.4948
 CQ3  N2    N   N     0  -0.487  -2.3033   1.6318   0.2882
 CQ3  C3    C   CR6   0   0.265   3.1086  -1.5627  -0.0506
 CQ3  N3    N   N     0  -0.512  -0.7958  -0.2059   0.3866
 CQ3  C4    C   CR16  0  -0.273   3.5944  -2.8619   0.0227
 CQ3  N4    N   NH1   0  -0.664  -3.0412  -0.5486   0.2718
 CQ3  C5    C   CR16  0  -0.274   2.8825  -3.8406   0.6965
 CQ3  C6    C   CR16  0  -0.257   1.6756  -3.5158   1.3013
 CQ3  C7    C   CR16  0  -0.294   1.1822  -2.2227   1.2430
 CQ3  C8    C   CR6   0   0.321   1.8957  -1.2318   0.5701
 CQ3  C9    C   CR6   0   0.624   0.2394   0.6082   0.4524
 CQ3  C10   C   CR6   0  -0.255   0.0371   2.0065   0.4318
 CQ3  C11   C   CR16  0   0.017  -1.2597   2.4487   0.3486
 CQ3  C12   C   CR6   0   0.610  -2.0207   0.3271   0.3111
 CQ3  C13   C   CH1   0  -0.059  -4.4221  -0.1911   0.0372
 CQ3  C14   C   CH2   0  -0.471  -5.3372  -1.3028   0.5377
 CQ3  C15   C   CH2   0  -0.184  -6.7872  -0.9670   0.2214
 CQ3  C16   C   CH2   0  -0.186  -6.2095   0.3393  -1.6301
 CQ3  C17   C   CH2   0  -0.458  -4.7228   0.0861  -1.4358
 CQ3  H     H   HCH3  0   0.236   7.3635   2.0857  -1.7861
 CQ3  HA    H   HCH3  0   0.230   7.0573   1.7772  -0.0813
 CQ3  HB    H   HCH3  0   0.230   7.7595   0.5175  -1.0948
 CQ3  HN    H   HNH1  0   0.410   3.3444  -0.1247  -1.5343
 CQ3  H1    H   HCH2  0   0.263   4.9428   1.6881  -1.4675
 CQ3  H1A   H   HCH2  0   0.274   5.6356   0.4290  -2.4499
 CQ3  HN1   H   HNH1  0   0.393   2.2443   0.7771   0.4689
 CQ3  H4    H   HCR6  0   0.267   4.5250  -3.1100  -0.4696
 CQ3  HN4   H   HNH1  0   0.389  -2.7828  -1.5190   0.1824
 CQ3  H5    H   HCR6  0   0.259   3.2646  -4.8515   0.7421
 CQ3  H6    H   HCR6  0   0.261   1.1135  -4.2717   1.8335
 CQ3  H7    H   HCR6  0   0.273   0.2508  -1.9805   1.7297
 CQ3  H11   H   HCR6  0   0.284  -1.4663   3.5138   0.3289
 CQ3  H13   H   HCH1  0   0.242  -4.6353   0.7152   0.6104
 CQ3  H14   H   HCH2  0   0.231  -5.0658  -2.2501   0.0599
 CQ3  H14A  H   HCH2  0   0.249  -5.2240  -1.4371   1.6160
 CQ3  H15   H   HCH2  0   0.200  -7.0930  -0.0873   0.8072
 CQ3  H15A  H   HCH2  0   0.240  -7.4407  -1.7925   0.5081
 CQ3  H16   H   HCH2  0   0.239  -6.4441   0.4621  -2.6885
 CQ3  H16A  H   HCH2  0   0.199  -6.4930   1.2719  -1.1198
 CQ3  H17   H   HCH2  0   0.243  -4.1577   0.9539  -1.7825
 CQ3  H17A  H   HCH2  0   0.226  -4.4086  -0.7722  -2.0374

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
 CQ3  C    C1    single    1.517  0.020  1.517
 CQ3  N    C2    single    1.362  0.020  1.362
 CQ3  N    C3    single    1.410  0.020  1.410
 CQ3  O    C2    double    1.216  0.020  1.216
 CQ3  CL   C10   single    1.730  0.020  1.730
 CQ3  C1   C2    single    1.513  0.020  1.513
 CQ3  N1   C8    single    1.397  0.020  1.397
 CQ3  N1   C9    single    1.354  0.020  1.354
 CQ3  O1   C15   single    1.410  0.020  1.410
 CQ3  O1   C16   single    1.411  0.020  1.411
 CQ3  N2   C11   aromatic  1.327  0.020  1.327
 CQ3  N2   C12   aromatic  1.335  0.020  1.335
 CQ3  C3   C4    aromatic  1.389  0.020  1.389
 CQ3  C3   C8    aromatic  1.402  0.020  1.402
 CQ3  N3   C9    aromatic  1.319  0.020  1.319
 CQ3  N3   C12   aromatic  1.338  0.020  1.338
 CQ3  C4   C5    aromatic  1.385  0.020  1.385
 CQ3  N4   C12   single    1.345  0.020  1.345
 CQ3  N4   C13   single    1.446  0.020  1.446
 CQ3  C5   C6    aromatic  1.388  0.020  1.388
 CQ3  C6   C7    aromatic  1.385  0.020  1.385
 CQ3  C7   C8    aromatic  1.394  0.020  1.394
 CQ3  C9   C10   aromatic  1.413  0.020  1.413
 CQ3  C10  C11   aromatic  1.373  0.020  1.373
 CQ3  C13  C14   single    1.524  0.020  1.524
 CQ3  C13  C17   single    1.529  0.020  1.529
 CQ3  C14  C15   single    1.522  0.020  1.522
 CQ3  C16  C17   single    1.521  0.020  1.521
 CQ3  C    H     single    0.970  0.020  1.090
 CQ3  C    HA    single    0.970  0.020  1.090
 CQ3  C    HB    single    0.970  0.020  1.090
 CQ3  N    HN    single    0.860  0.020  1.020
 CQ3  C1   H1    single    0.970  0.020  1.090
 CQ3  C1   H1A   single    0.970  0.020  1.090
 CQ3  N1   HN1   single    0.860  0.020  1.020
 CQ3  C4   H4    single    0.930  0.020  1.080
 CQ3  N4   HN4   single    0.860  0.020  1.020
 CQ3  C5   H5    single    0.930  0.020  1.080
 CQ3  C6   H6    single    0.930  0.020  1.080
 CQ3  C7   H7    single    0.930  0.020  1.080
 CQ3  C11  H11   single    0.930  0.020  1.080
 CQ3  C13  H13   single    0.970  0.020  1.090
 CQ3  C14  H14   single    0.970  0.020  1.090
 CQ3  C14  H14A  single    0.970  0.020  1.090
 CQ3  C15  H15   single    0.970  0.020  1.090
 CQ3  C15  H15A  single    0.970  0.020  1.090
 CQ3  C16  H16   single    0.970  0.020  1.090
 CQ3  C16  H16A  single    0.970  0.020  1.090
 CQ3  C17  H17   single    0.970  0.020  1.090
 CQ3  C17  H17A  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
 CQ3  HB    C    HA   108.01  3.000
 CQ3  HB    C    H    107.69  3.000
 CQ3  HA    C    H    107.69  3.000
 CQ3  HB    C    C1   111.70  3.000
 CQ3  HA    C    C1   111.66  3.000
 CQ3  H     C    C1   109.92  3.000
 CQ3  HN    N    C3   117.50  3.000
 CQ3  HN    N    C2   118.03  3.000
 CQ3  C3    N    C2   124.36  3.000
 CQ3  H1A   C1   H1   105.44  3.000
 CQ3  H1A   C1   C2   107.98  3.000
 CQ3  H1    C1   C2   108.67  3.000
 CQ3  H1A   C1   C    110.44  3.000
 CQ3  H1    C1   C    110.42  3.000
 CQ3  C2    C1   C    113.53  3.000
 CQ3  HN1   N1   C9   116.03  3.000
 CQ3  HN1   N1   C8   115.16  3.000
 CQ3  C9    N1   C8   128.60  3.000
 CQ3  C16   O1   C15  111.94  3.000
 CQ3  C1    C2   O    123.60  3.000
 CQ3  C1    C2   N    113.83  3.000
 CQ3  O     C2   N    122.56  3.000
 CQ3  C12   N2   C11  115.75  3.000
 CQ3  C8    C3   C4   120.00  3.000
 CQ3  C8    C3   N    118.96  3.000
 CQ3  C4    C3   N    121.04  3.000
 CQ3  C12   N3   C9   118.39  3.000
 CQ3  H4    C4   C5   120.10  3.000
 CQ3  H4    C4   C3   119.44  3.000
 CQ3  C5    C4   C3   120.45  3.000
 CQ3  HN4   N4   C13  117.93  3.000
 CQ3  HN4   N4   C12  115.77  3.000
 CQ3  C13   N4   C12  124.64  3.000
 CQ3  H5    C5   C6   120.48  3.000
 CQ3  H5    C5   C4   119.95  3.000
 CQ3  C6    C5   C4   119.56  3.000
 CQ3  H6    C6   C7   119.20  3.000
 CQ3  H6    C6   C5   120.16  3.000
 CQ3  C7    C6   C5   120.64  3.000
 CQ3  H7    C7   C8   120.01  3.000
 CQ3  H7    C7   C6   119.89  3.000
 CQ3  C8    C7   C6   120.10  3.000
 CQ3  C7    C8   C3   119.25  3.000
 CQ3  C7    C8   N1   123.22  3.000
 CQ3  C3    C8   N1   117.47  3.000
 CQ3  C10   C9   N3   119.86  3.000
 CQ3  C10   C9   N1   120.07  3.000
 CQ3  N3    C9   N1   120.07  3.000
 CQ3  C11   C10  C9   117.06  3.000
 CQ3  C11   C10  CL   121.38  3.000
 CQ3  C9    C10  CL   121.55  3.000
 CQ3  H11   C11  C10  119.82  3.000
 CQ3  H11   C11  N2   116.98  3.000
 CQ3  C10   C11  N2   123.20  3.000
 CQ3  N4    C12  N3   115.90  3.000
 CQ3  N4    C12  N2   118.36  3.000
 CQ3  N3    C12  N2   125.74  3.000
 CQ3  H13   C13  C17  108.45  3.000
 CQ3  H13   C13  C14  108.38  3.000
 CQ3  C17   C13  C14  109.30  3.000
 CQ3  H13   C13  N4   107.83  3.000
 CQ3  C17   C13  N4   112.90  3.000
 CQ3  C14   C13  N4   109.87  3.000
 CQ3  H14A  C14  H14  107.38  3.000
 CQ3  H14A  C14  C15  109.34  3.000
 CQ3  H14   C14  C15  109.65  3.000
 CQ3  H14A  C14  C13  110.57  3.000
 CQ3  H14   C14  C13  109.80  3.000
 CQ3  C15   C14  C13  110.05  3.000
 CQ3  H15A  C15  H15  107.37  3.000
 CQ3  H15A  C15  C14  110.43  3.000
 CQ3  H15   C15  C14  109.30  3.000
 CQ3  H15A  C15  O1   107.10  3.000
 CQ3  H15   C15  O1   110.30  3.000
 CQ3  C14   C15  O1   112.21  3.000
 CQ3  H16A  C16  H16  107.41  3.000
 CQ3  H16A  C16  C17  109.50  3.000
 CQ3  H16   C16  C17  110.67  3.000
 CQ3  H16A  C16  O1   110.21  3.000
 CQ3  H16   C16  O1   107.06  3.000
 CQ3  C17   C16  O1   111.88  3.000
 CQ3  H17A  C17  H17  107.47  3.000
 CQ3  H17A  C17  C16  109.94  3.000
 CQ3  H17   C17  C16  109.45  3.000
 CQ3  H17A  C17  C13  109.34  3.000
 CQ3  H17   C17  C13  110.38  3.000
 CQ3  C16   C17  C13  110.22  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
 CQ3  CONST_01  C9   C10  C11  N2      0.00   0.0  0
 CQ3  CONST_02  C9   N3   C12  N2      0.00   0.0  0
 CQ3  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 CQ3  CONST_04  C6   C7   C8   C3      0.00   0.0  0
 CQ3  CONST_05  C11  C10  C9   N3      0.00   0.0  0
 CQ3  CONST_06  C11  N2   C12  N3      0.00   0.0  0
 CQ3  CONST_07  C7   C8   C3   C4      0.00   0.0  0
 CQ3  CONST_08  C7   C6   C5   C4      0.00   0.0  0
 CQ3  CONST_09  C8   C3   C4   C5      0.00   0.0  0
 CQ3  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 CQ3  CONST_11  C12  N3   C9   C10     0.00   0.0  0
 CQ3  CONST_12  C12  N2   C11  C10     0.00   0.0  0
 CQ3  CONST_13  C5   C4   C3   N     180.00   0.0  0
 CQ3  CONST_14  C7   C8   C3   N     180.00   0.0  0
 CQ3  CONST_15  N3   C9   C10  CL    180.00   0.0  0
 CQ3  CONST_16  N2   C11  C10  CL    180.00   0.0  0
 CQ3  CONST_17  C4   C3   C8   N1    180.00   0.0  0
 CQ3  CONST_18  C6   C7   C8   N1    180.00   0.0  0
 CQ3  CONST_19  C12  N3   C9   N1    180.00   0.0  0
 CQ3  CONST_20  C11  C10  C9   N1    180.00   0.0  0
 CQ3  CONST_21  C11  N2   C12  N4    180.00   0.0  0
 CQ3  CONST_22  C9   N3   C12  N4    180.00   0.0  0
 CQ3  CONST_23  C13  N4   C12  N2      0.00   0.0  0
 CQ3  CONST_24  C13  N4   C12  N3    180.00   0.0  0
 CQ3  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 CQ3  CONST_26  H7   C7   C8   C3    180.00   0.0  0
 CQ3  CONST_27  H6   C6   C5   C4    180.00   0.0  0
 CQ3  CONST_28  H4   C4   C5   C6    180.00   0.0  0
 CQ3  CONST_29  H11  C11  C10  C9    180.00   0.0  0
 CQ3  CONST_32  HN4  N4   C12  N2    180.00   0.0  0
 CQ3  CONST_34  C3   N    C2   O       0.00   0.0  0
 CQ3  CONST_35  C3   N    C2   C1    180.00   0.0  0
 CQ3  Var_01    C13  C14  C15  O1     56.28  30.0  1
 CQ3  Var_02    C13  C17  C16  O1    -56.35  30.0  1
 CQ3  Var_03    C17  C16  O1   C15    59.74  30.0  1
 CQ3  Var_04    C9   N1   C8   C3    146.32  30.0  3
 CQ3  Var_05    C8   N1   C9   N3     -1.14  30.0  2
 CQ3  Var_06    N    C2   C1   C     175.05  30.0  3
 CQ3  Var_07    H    C    C1   C2   -179.66  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
 CQ3  chir_01  C13  N4  C14  C17  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
 CQ3  plan-1  CL   0.020
 CQ3  plan-1  N1   0.020
 CQ3  plan-1  N2   0.020
 CQ3  plan-1  N3   0.020
 CQ3  plan-1  N4   0.020
 CQ3  plan-1  C9   0.020
 CQ3  plan-1  C10  0.020
 CQ3  plan-1  C11  0.020
 CQ3  plan-1  C12  0.020
 CQ3  plan-1  H11  0.020
 CQ3  plan-2  N    0.020
 CQ3  plan-2  N1   0.020
 CQ3  plan-2  C3   0.020
 CQ3  plan-2  C4   0.020
 CQ3  plan-2  C5   0.020
 CQ3  plan-2  C6   0.020
 CQ3  plan-2  C7   0.020
 CQ3  plan-2  C8   0.020
 CQ3  plan-2  H4   0.020
 CQ3  plan-2  H5   0.020
 CQ3  plan-2  H6   0.020
 CQ3  plan-2  H7   0.020
 CQ3  plan-3  N4   0.020
 CQ3  plan-3  C12  0.020
 CQ3  plan-3  C13  0.020
 CQ3  plan-3  HN4  0.020
 CQ3  plan-4  N    0.020
 CQ3  plan-4  O    0.020
 CQ3  plan-4  C1   0.020
 CQ3  plan-4  C2   0.020
 CQ3  plan-4  C3   0.020
 CQ3  plan-4  HN   0.020

