# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:11:48 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: [4-[[5-chloranyl-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidin-2-yl]amino]-3-methoxy-phenyl]-morpholin-4-yl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(Nc2ccc(cc2OC)C(=O)N3CCOCC3)nc4[nH]cc(Cl)c14
#
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
 A1K  A1K  '[4-[[5-chloranyl-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidin-2-yl]amino]-3-methoxy-phenyl]-morpholin-4-yl-methanone'  ligand  50  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A1K
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
 A1K  C1   C   CH3   0  -0.515  -5.3356   2.9086   0.8634
 A1K  N1   N   NH1   0  -0.654  -5.4292   1.5025   0.5565
 A1K  O1   O   O2    0  -0.486   0.8636   3.1464   0.2718
 A1K  C2   C   CR6   0   0.514  -4.3690   0.7436   0.2635
 A1K  N2   N   NR15  0  -0.674  -3.5477  -2.5755  -0.6018
 A1K  O2   O   O     0  -0.492   5.1571   0.9257  -1.5635
 A1K  C3   C   CR56  0  -0.010  -4.4828  -0.6328  -0.0529
 A1K  N3   N   N     0  -0.526  -2.0617  -0.7249  -0.3074
 A1K  O3   O   O2    0  -0.481   7.0153  -2.0160   1.5424
 A1K  C4   C   CR5   0  -0.242  -5.5010  -1.6193  -0.1889
 A1K  C5   C   CR15  0   0.013  -4.9019  -2.7948  -0.5243
 A1K  N5   N   NT    0  -0.467   5.1630  -0.9560  -0.3089
 A1K  C6   C   CR56  0   0.529  -3.2763  -1.2816  -0.3223
 A1K  N6   N   N     0  -0.546  -3.1673   1.3066   0.2773
 A1K  C7   C   CR6   0   0.592  -2.0883   0.5572  -0.0035
 A1K  C8   C   CR6   0   0.278   0.3893   0.9020  -0.1591
 A1K  C9   C   CR16  0  -0.308   0.8291  -0.3808  -0.4719
 A1K  C10  C   CR16  0  -0.278   2.1821  -0.6457  -0.6445
 A1K  C11  C   CR6   0  -0.073   3.1242   0.3619  -0.5245
 A1K  C12  C   CR16  0  -0.412   2.6957   1.6609  -0.2409
 A1K  C13  C   CR6   0   0.333   1.3571   1.9299  -0.0382
 A1K  C14  C   CH3   0  -0.435   1.7575   4.2357   0.3877
 A1K  C15  C   C     0   0.519   4.5678   0.1416  -0.8282
 A1K  C16  C   CH2   0  -0.332   6.5036  -1.3393  -0.7204
 A1K  C17  C   CH2   0  -0.184   7.4655  -1.2447   0.4502
 A1K  C18  C   CH2   0  -0.175   5.7378  -1.5998   1.9656
 A1K  C19  C   CH2   0  -0.334   4.7039  -1.6996   0.8534
 A1K  CL1  CL  CL    0  -0.158  -7.1891  -1.3847   0.0272
 A1K  H1   H   HCH3  0   0.236  -4.9653   3.4887   0.0165
 A1K  H2   H   HCH3  0   0.251  -6.3293   3.2663   1.1168
 A1K  H3   H   HCH3  0   0.238  -4.6759   3.0906   1.7116
 A1K  H4   H   HNH1  0   0.396  -6.3442   1.0889   0.5091
 A1K  H5   H   HNR5  0   0.417  -2.8619  -3.2764  -0.8344
 A1K  H6   H   HNH1  0   0.405  -1.0718   2.2467   0.2758
 A1K  H7   H   HCR5  0   0.304  -5.3284  -3.7651  -0.7134
 A1K  H8   H   HCR6  0   0.290   0.1109  -1.1760  -0.5806
 A1K  H9   H   HCR6  0   0.264   2.4843  -1.6552  -0.8925
 A1K  H10  H   HCR6  0   0.284   3.4299   2.4522  -0.1717
 A1K  H11  H   HCH3  0   0.232   2.2711   4.4388  -0.5553
 A1K  H12  H   HCH3  0   0.264   1.1566   5.1009   0.6550
 A1K  H13  H   HCH3  0   0.232   2.5027   4.0663   1.1688
 A1K  H14  H   HCH2  0   0.251   6.4704  -2.3704  -1.0878
 A1K  H15  H   HCH2  0   0.268   6.8403  -0.7044  -1.5360
 A1K  H16  H   HCH2  0   0.210   7.5859  -0.1920   0.7429
 A1K  H17  H   HCH2  0   0.244   8.4445  -1.6274   0.1594
 A1K  H18  H   HCH2  0   0.246   5.4418  -2.2403   2.7979
 A1K  H19  H   HCH2  0   0.207   5.7704  -0.5633   2.3313
 A1K  H20  H   HCH2  0   0.277   3.7608  -1.3044   1.2214
 A1K  H21  H   HCH2  0   0.249   4.5412  -2.7462   0.5784
 A1K  N4   N   NH1   0  -0.763  -0.9243   1.2758   0.0478

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
 A1K  CL1  C4   single    1.718  0.020  1.718
 A1K  C1   N1   single    1.442  0.020  1.442
 A1K  N1   C2   single    1.336  0.020  1.336
 A1K  C4   C5   aromatic  1.361  0.020  1.361
 A1K  C4   C3   aromatic  1.424  0.020  1.424
 A1K  C5   N2   aromatic  1.374  0.020  1.374
 A1K  C2   C3   aromatic  1.417  0.020  1.417
 A1K  C2   N6   aromatic  1.327  0.020  1.327
 A1K  C3   C6   aromatic  1.396  0.020  1.396
 A1K  N6   C7   aromatic  1.343  0.020  1.343
 A1K  N2   C6   aromatic  1.351  0.020  1.351
 A1K  C6   N3   aromatic  1.336  0.020  1.336
 A1K  C10  C9   aromatic  1.389  0.020  1.389
 A1K  C10  C11  aromatic  1.385  0.020  1.385
 A1K  C9   C8   aromatic  1.392  0.020  1.392
 A1K  C7   N3   aromatic  1.318  0.020  1.318
 A1K  C7   N4   single    1.369  0.020  1.369
 A1K  O2   C15  double    1.226  0.020  1.226
 A1K  C15  C11  single    1.492  0.020  1.492
 A1K  C15  N5   single    1.352  0.020  1.352
 A1K  C11  C12  aromatic  1.397  0.020  1.397
 A1K  C8   N4   single    1.381  0.020  1.381
 A1K  C8   C13  aromatic  1.417  0.020  1.417
 A1K  C17  C16  single    1.518  0.020  1.518
 A1K  C17  O3   single    1.411  0.020  1.411
 A1K  N5   C16  single    1.454  0.020  1.454
 A1K  N5   C19  single    1.454  0.020  1.454
 A1K  C12  C13  aromatic  1.380  0.020  1.380
 A1K  C13  O1   single    1.349  0.020  1.349
 A1K  C18  O3   single    1.409  0.020  1.409
 A1K  C18  C19  single    1.522  0.020  1.522
 A1K  O1   C14  single    1.414  0.020  1.414
 A1K  C1   H1   single    0.970  0.020  1.090
 A1K  C1   H2   single    0.970  0.020  1.090
 A1K  C1   H3   single    0.970  0.020  1.090
 A1K  N1   H4   single    0.860  0.020  1.020
 A1K  N2   H5   single    0.860  0.020  1.020
 A1K  N4   H6   single    0.860  0.020  1.020
 A1K  C5   H7   single    0.930  0.020  1.080
 A1K  C9   H8   single    0.930  0.020  1.080
 A1K  C10  H9   single    0.930  0.020  1.080
 A1K  C12  H10  single    0.930  0.020  1.080
 A1K  C14  H11  single    0.970  0.020  1.090
 A1K  C14  H12  single    0.970  0.020  1.090
 A1K  C14  H13  single    0.970  0.020  1.090
 A1K  C16  H14  single    0.970  0.020  1.090
 A1K  C16  H15  single    0.970  0.020  1.090
 A1K  C17  H16  single    0.970  0.020  1.090
 A1K  C17  H17  single    0.970  0.020  1.090
 A1K  C18  H18  single    0.970  0.020  1.090
 A1K  C18  H19  single    0.970  0.020  1.090
 A1K  C19  H20  single    0.970  0.020  1.090
 A1K  C19  H21  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
 A1K  H3   C1   H2   108.49  3.000
 A1K  H3   C1   H1   108.05  3.000
 A1K  H2   C1   H1   108.45  3.000
 A1K  H3   C1   N1   111.58  3.000
 A1K  H2   C1   N1   108.14  3.000
 A1K  H1   C1   N1   112.03  3.000
 A1K  H4   N1   C2   118.57  3.000
 A1K  H4   N1   C1   118.05  3.000
 A1K  C2   N1   C1   123.28  3.000
 A1K  C14  O1   C13  118.84  3.000
 A1K  N6   C2   C3   119.15  3.000
 A1K  N6   C2   N1   118.38  3.000
 A1K  C3   C2   N1   122.47  3.000
 A1K  H5   N2   C6   125.24  3.000
 A1K  H5   N2   C5   124.94  3.000
 A1K  C6   N2   C5   109.82  3.000
 A1K  C6   C3   C4   106.11  3.000
 A1K  C6   C3   C2   115.15  3.000
 A1K  C4   C3   C2   138.73  3.000
 A1K  C7   N3   C6   112.93  3.000
 A1K  C18  O3   C17  111.13  3.000
 A1K  CL1  C4   C5   125.54  3.000
 A1K  C5   C4   C3   107.88  3.000
 A1K  CL1  C4   C3   126.58  3.000
 A1K  H7   C5   C4   130.33  3.000
 A1K  H7   C5   N2   121.62  3.000
 A1K  C4   C5   N2   108.05  3.000
 A1K  C19  N5   C16  112.49  3.000
 A1K  C19  N5   C15  125.67  3.000
 A1K  C16  N5   C15  120.74  3.000
 A1K  N3   C6   C3   126.14  3.000
 A1K  N3   C6   N2   125.72  3.000
 A1K  C3   C6   N2   108.14  3.000
 A1K  C7   N6   C2   119.24  3.000
 A1K  N6   C7   N4   112.48  3.000
 A1K  N4   C7   N3   120.15  3.000
 A1K  N6   C7   N3   127.38  3.000
 A1K  C13  C8   C9   118.16  3.000
 A1K  C13  C8   N4   116.13  3.000
 A1K  C9   C8   N4   125.71  3.000
 A1K  H8   C9   C10  119.74  3.000
 A1K  H8   C9   C8   119.51  3.000
 A1K  C10  C9   C8   120.76  3.000
 A1K  H9   C10  C11  120.56  3.000
 A1K  H9   C10  C9   118.56  3.000
 A1K  C11  C10  C9   120.87  3.000
 A1K  C15  C11  C12  118.39  3.000
 A1K  C12  C11  C10  119.05  3.000
 A1K  C15  C11  C10  122.24  3.000
 A1K  H10  C12  C13  120.42  3.000
 A1K  H10  C12  C11  119.01  3.000
 A1K  C13  C12  C11  120.56  3.000
 A1K  C12  C13  C8   120.56  3.000
 A1K  C12  C13  O1   124.35  3.000
 A1K  C8   C13  O1   115.08  3.000
 A1K  H13  C14  H12  108.95  3.000
 A1K  H13  C14  H11  108.97  3.000
 A1K  H12  C14  H11  108.91  3.000
 A1K  H13  C14  O1   111.73  3.000
 A1K  H12  C14  O1   106.50  3.000
 A1K  H11  C14  O1   111.69  3.000
 A1K  C11  C15  N5   117.88  3.000
 A1K  N5   C15  O2   122.54  3.000
 A1K  C11  C15  O2   119.54  3.000
 A1K  H15  C16  H14  107.92  3.000
 A1K  H15  C16  C17  110.24  3.000
 A1K  H14  C16  C17  109.67  3.000
 A1K  H15  C16  N5   110.12  3.000
 A1K  H14  C16  N5   108.38  3.000
 A1K  C17  C16  N5   110.46  3.000
 A1K  H17  C17  H16  107.98  3.000
 A1K  H17  C17  C16  109.96  3.000
 A1K  H16  C17  C16  109.54  3.000
 A1K  H17  C17  O3   107.52  3.000
 A1K  H16  C17  O3   110.63  3.000
 A1K  C16  C17  O3   111.15  3.000
 A1K  H19  C18  H18  107.92  3.000
 A1K  H19  C18  C19  108.97  3.000
 A1K  H18  C18  C19  109.55  3.000
 A1K  H19  C18  O3   110.58  3.000
 A1K  H18  C18  O3   107.56  3.000
 A1K  C19  C18  O3   112.16  3.000
 A1K  H21  C19  H20  107.70  3.000
 A1K  H21  C19  C18  110.33  3.000
 A1K  H20  C19  C18  108.55  3.000
 A1K  H21  C19  N5   109.58  3.000
 A1K  H20  C19  N5   111.01  3.000
 A1K  C18  C19  N5   109.64  3.000
 A1K  H6   N4   C8   115.70  3.000
 A1K  H6   N4   C7   112.93  3.000
 A1K  C8   N4   C7   131.37  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
 A1K  CONST_01  C5   C4   C3   C2   180.00   0.0  0
 A1K  CONST_02  N2   C6   C3   C2   180.00   0.0  0
 A1K  CONST_03  N3   C6   C3   C2     0.00   0.0  0
 A1K  CONST_04  N3   C7   N6   C2     0.00   0.0  0
 A1K  CONST_05  C3   C4   C5   N2     0.00   0.0  0
 A1K  CONST_06  C4   C3   C6   N2     0.00   0.0  0
 A1K  CONST_07  C7   N3   C6   N2   180.00   0.0  0
 A1K  CONST_08  C7   N6   C2   C3     0.00   0.0  0
 A1K  CONST_09  C5   N2   C6   C3     0.00   0.0  0
 A1K  CONST_10  C7   N3   C6   C3     0.00   0.0  0
 A1K  CONST_11  C4   C3   C6   N3   180.00   0.0  0
 A1K  CONST_12  C5   N2   C6   N3   180.00   0.0  0
 A1K  CONST_13  C6   N2   C5   C4     0.00   0.0  0
 A1K  CONST_14  N6   C2   C3   C4   180.00   0.0  0
 A1K  CONST_15  C6   C3   C4   C5     0.00   0.0  0
 A1K  CONST_16  N6   C2   C3   C6     0.00   0.0  0
 A1K  CONST_17  N6   C7   N3   C6     0.00   0.0  0
 A1K  CONST_18  C11  C10  C9   C8     0.00   0.0  0
 A1K  CONST_19  C11  C12  C13  C8     0.00   0.0  0
 A1K  CONST_20  C12  C11  C10  C9     0.00   0.0  0
 A1K  CONST_21  C12  C13  C8   C9     0.00   0.0  0
 A1K  CONST_22  C13  C8   C9   C10    0.00   0.0  0
 A1K  CONST_23  C13  C12  C11  C10    0.00   0.0  0
 A1K  CONST_24  C4   C3   C2   N1     0.00   0.0  0
 A1K  CONST_25  C6   C3   C2   N1   180.00   0.0  0
 A1K  CONST_26  C7   N6   C2   N1   180.00   0.0  0
 A1K  CONST_27  C9   C8   C13  O1   180.00   0.0  0
 A1K  CONST_28  C11  C12  C13  O1   180.00   0.0  0
 A1K  CONST_29  CL1  C4   C3   C2     0.00   0.0  0
 A1K  CONST_30  N4   C7   N6   C2   180.00   0.0  0
 A1K  CONST_31  CL1  C4   C5   N2   180.00   0.0  0
 A1K  CONST_32  C6   N3   C7   N4   180.00   0.0  0
 A1K  CONST_33  C10  C9   C8   N4   180.00   0.0  0
 A1K  CONST_34  C12  C13  C8   N4   180.00   0.0  0
 A1K  CONST_35  CL1  C4   C3   C6   180.00   0.0  0
 A1K  CONST_36  C15  C11  C10  C9   180.00   0.0  0
 A1K  CONST_37  C15  C11  C12  C13  180.00   0.0  0
 A1K  CONST_38  C16  N5   C15  C11  180.00   0.0  0
 A1K  CONST_40  H7   C5   C4   C3   180.00   0.0  0
 A1K  CONST_41  H5   N2   C6   C3   180.00   0.0  0
 A1K  CONST_42  H9   C10  C9   C8   180.00   0.0  0
 A1K  CONST_43  H10  C12  C13  C8   180.00   0.0  0
 A1K  CONST_44  H8   C9   C10  C11  180.00   0.0  0
 A1K  CONST_45  C16  N5   C15  O2     0.00   0.0  0
 A1K  CONST_47  C3   C2   N1   C1   180.00   0.0  0
 A1K  CONST_48  N6   C2   N1   C1     0.00   0.0  0
 A1K  CONST_49  H4   N1   C2   C3     0.00   0.0  0
 A1K  Var_01    N5   C16  C17  O3    55.47  30.0  1
 A1K  Var_02    N5   C19  C18  O3   -54.86  30.0  1
 A1K  Var_03    C18  C19  N5   C16   52.41  30.0  1
 A1K  Var_04    C19  N5   C16  C17  -53.23  30.0  1
 A1K  Var_05    C19  C18  O3   C17   58.68  30.0  1
 A1K  Var_06    C8   N4   C7   N3    -0.72  30.0  2
 A1K  Var_07    C10  C11  C15  N5   -47.27  30.0  2
 A1K  Var_08    C9   C8   N4   C7    -0.76  30.0  2
 A1K  Var_09    H1   C1   N1   C2    63.70  30.0  3
 A1K  Var_10    H11  C14  O1   C13   62.10  30.0  3

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
 A1K  plan-1  O1   0.020
 A1K  plan-1  C8   0.020
 A1K  plan-1  C9   0.020
 A1K  plan-1  C10  0.020
 A1K  plan-1  C11  0.020
 A1K  plan-1  C12  0.020
 A1K  plan-1  C13  0.020
 A1K  plan-1  C15  0.020
 A1K  plan-1  H8   0.020
 A1K  plan-1  H9   0.020
 A1K  plan-1  H10  0.020
 A1K  plan-1  N4   0.020
 A1K  plan-2  N1   0.020
 A1K  plan-2  C2   0.020
 A1K  plan-2  N2   0.020
 A1K  plan-2  C3   0.020
 A1K  plan-2  N3   0.020
 A1K  plan-2  C4   0.020
 A1K  plan-2  C5   0.020
 A1K  plan-2  C6   0.020
 A1K  plan-2  N6   0.020
 A1K  plan-2  C7   0.020
 A1K  plan-2  CL1  0.020
 A1K  plan-2  H5   0.020
 A1K  plan-2  H7   0.020
 A1K  plan-2  N4   0.020
 A1K  plan-3  C1   0.020
 A1K  plan-3  N1   0.020
 A1K  plan-3  C2   0.020
 A1K  plan-3  H4   0.020
 A1K  plan-4  O2   0.020
 A1K  plan-4  N5   0.020
 A1K  plan-4  C11  0.020
 A1K  plan-4  C15  0.020
 A1K  plan-4  C16  0.020
 A1K  plan-4  C19  0.020

