# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 01:00:35 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nccc1Nc2nccc(n2)C3=CC(=O)N(C=C3)[C@H](CO)c4ccc(Cl)c(F)c4
#
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
 6QB  6QB  1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one  ligand  49  31  .  2022-07-23  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_6QB
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
 6QB  C4   C   CR15  0  -0.520   7.3194  -1.2199  -0.1957
 6QB  C5   C   CR15  0  -0.066   8.6154  -0.9747   0.2832
 6QB  C8   C   CR6   0   0.608   4.2551  -0.4763  -0.4173
 6QB  C10  C   CR16  0   0.007   3.5539  -2.0935  -1.8130
 6QB  C15  C   CR16  0  -0.433   0.4200   0.8746   0.3487
 6QB  C20  C   CR16  0  -0.532  -0.2133   0.0490  -1.8113
 6QB  C21  C   CH1   0  -0.192  -3.0621   1.9873  -0.4005
 6QB  C26  C   CR16  0  -0.323  -5.3905   1.1603  -0.8000
 6QB  C28  C   CR6   0  -0.250  -6.2324  -0.8490   0.1970
 6QB  C1   C   CH3   0  -0.559   7.0952   1.7450   1.8466
 6QB  N2   N   NR5   0  -0.343   7.4137   0.5562   1.0943
 6QB  C3   C   CR5   0   0.664   6.5690  -0.1973   0.3565
 6QB  N6   N   N     0  -0.294   8.6690   0.0901   1.0547
 6QB  N7   N   NH1   0  -0.778   5.2377   0.1478   0.2903
 6QB  N9   N   N     0  -0.450   4.5586  -1.5428  -1.1464
 6QB  C11  C   CR16  0  -0.387   2.2625  -1.6037  -1.7740
 6QB  C12  C   CR6   0   0.292   2.0568  -0.4797  -0.9773
 6QB  N13  N   N     0  -0.484   3.0474   0.0740  -0.2968
 6QB  C14  C   CR6   0   0.200   0.7254   0.1485  -0.8294
 6QB  C16  C   CR16  0   0.068  -0.8058   1.4375   0.4698
 6QB  N17  N   NR6   0  -0.544  -1.7441   1.3498  -0.5095
 6QB  C18  C   CR6   0   0.605  -1.5103   0.6570  -1.6970
 6QB  O19  O   O     0  -0.503  -2.3776   0.6011  -2.5629
 6QB  C23  C   CH2   0  -0.203  -3.1445   3.0897   0.6460
 6QB  O24  O   OH1   0  -0.658  -3.1887   2.5455   1.9404
 6QB  C25  C   CR6   0   0.180  -4.1516   0.9601  -0.2028
 6QB  C27  C   CR16  0  -0.194  -6.4300   0.2661  -0.6015
 6QB  C29  C   CR6   0   0.635  -4.9945  -1.0462   0.7850
 6QB  C30  C   CR16  0  -0.454  -3.9576  -0.1555   0.6014
 6QB  F31  F   F     0  -0.296  -4.8049  -2.1241   1.5496
 6QB  H1   H   HCR5  0   0.271   6.9828  -2.0128  -0.8357
 6QB  H2   H   HCR5  0   0.257   9.5086  -1.5483   0.0861
 6QB  H3   H   HCR6  0   0.282   3.7904  -2.9715  -2.4030
 6QB  H4   H   HCR6  0   0.274   1.1333   0.9706   1.1520
 6QB  H5   H   HCR6  0   0.274  -0.0158  -0.4743  -2.7375
 6QB  H6   H   HCH1  0   0.304  -3.2353   2.4850  -1.3565
 6QB  H7   H   HCR6  0   0.268  -5.5510   2.0210  -1.4371
 6QB  H8   H   HCH3  0   0.261   6.3195   1.5478   2.5866
 6QB  H9   H   HCH3  0   0.281   7.9935   2.0607   2.3668
 6QB  H10  H   HCH3  0   0.262   6.7688   2.5538   1.1921
 6QB  H11  H   HNH1  0   0.426   4.9281   0.9585   0.8060
 6QB  H12  H   HCR6  0   0.281   1.4661  -2.0893  -2.3161
 6QB  H13  H   HCR6  0   0.323  -1.0881   1.9646   1.3673
 6QB  H14  H   HCH2  0   0.239  -2.3004   3.7775   0.5092
 6QB  H15  H   HCH2  0   0.252  -4.0539   3.6578   0.4196
 6QB  H16  H   HOH1  0   0.468  -3.2247   3.2711   2.5709
 6QB  H17  H   HCR6  0   0.290  -7.3895   0.4263  -1.0740
 6QB  H18  H   HCR6  0   0.282  -3.0084  -0.3564   1.0823
 6QB  CL1  CL  CL    0  -0.093  -7.4929  -1.9933   0.4612

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
 6QB  C1   N2   single    1.442  0.020  1.442
 6QB  N2   C3   aromatic  1.351  0.020  1.351
 6QB  N2   N6   aromatic  1.340  0.020  1.340
 6QB  N7   C3   single    1.377  0.020  1.377
 6QB  N7   C8   single    1.362  0.020  1.362
 6QB  N9   C8   aromatic  1.327  0.020  1.327
 6QB  N9   C10  aromatic  1.326  0.020  1.326
 6QB  C3   C4   aromatic  1.383  0.020  1.383
 6QB  N6   C5   aromatic  1.316  0.020  1.316
 6QB  C8   N13  aromatic  1.333  0.020  1.333
 6QB  C10  C11  aromatic  1.382  0.020  1.382
 6QB  N13  C12  aromatic  1.323  0.020  1.323
 6QB  C11  C12  aromatic  1.393  0.020  1.393
 6QB  C5   C4   aromatic  1.403  0.020  1.403
 6QB  C12  C14  single    1.480  0.020  1.480
 6QB  C14  C15  single    1.417  0.020  1.417
 6QB  C14  C20  double    1.362  0.020  1.362
 6QB  C15  C16  double    1.354  0.020  1.354
 6QB  F31  C29  single    1.335  0.020  1.335
 6QB  C20  C18  single    1.437  0.020  1.437
 6QB  C16  N17  single    1.359  0.020  1.359
 6QB  C29  C30  aromatic  1.379  0.020  1.379
 6QB  C29  C28  aromatic  1.385  0.020  1.385
 6QB  C18  N17  single    1.395  0.020  1.395
 6QB  C18  O19  double    1.227  0.020  1.227
 6QB  C30  C25  aromatic  1.389  0.020  1.389
 6QB  N17  C21  single    1.468  0.020  1.468
 6QB  CL1  C28  single    1.723  0.020  1.723
 6QB  C28  C27  aromatic  1.386  0.020  1.386
 6QB  C25  C21  single    1.510  0.020  1.510
 6QB  C25  C26  aromatic  1.390  0.020  1.390
 6QB  C21  C23  single    1.522  0.020  1.522
 6QB  C27  C26  aromatic  1.386  0.020  1.386
 6QB  C23  O24  single    1.405  0.020  1.405
 6QB  C4   H1   single    0.930  0.020  1.080
 6QB  C5   H2   single    0.930  0.020  1.080
 6QB  C10  H3   single    0.930  0.020  1.080
 6QB  C15  H4   single    0.930  0.020  1.080
 6QB  C20  H5   single    0.930  0.020  1.080
 6QB  C21  H6   single    0.970  0.020  1.090
 6QB  C26  H7   single    0.930  0.020  1.080
 6QB  C1   H8   single    0.970  0.020  1.090
 6QB  C1   H9   single    0.970  0.020  1.090
 6QB  C1   H10  single    0.970  0.020  1.090
 6QB  N7   H11  single    0.860  0.020  1.020
 6QB  C11  H12  single    0.930  0.020  1.080
 6QB  C16  H13  single    0.930  0.020  1.080
 6QB  C23  H14  single    0.970  0.020  1.090
 6QB  C23  H15  single    0.970  0.020  1.090
 6QB  O24  H16  single    0.850  0.020  0.980
 6QB  C27  H17  single    0.930  0.020  1.080
 6QB  C30  H18  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
 6QB  H1   C4   C3   127.89  3.000
 6QB  H1   C4   C5   128.49  3.000
 6QB  C3   C4   C5   103.63  3.000
 6QB  H2   C5   N6   120.21  3.000
 6QB  H2   C5   C4   127.51  3.000
 6QB  N6   C5   C4   112.28  3.000
 6QB  N13  C8   N9   126.07  3.000
 6QB  N13  C8   N7   114.68  3.000
 6QB  N9   C8   N7   119.25  3.000
 6QB  H3   C10  C11  120.43  3.000
 6QB  H3   C10  N9   116.42  3.000
 6QB  C11  C10  N9   123.15  3.000
 6QB  H4   C15  C16  119.67  3.000
 6QB  H4   C15  C14  121.48  3.000
 6QB  C16  C15  C14  118.84  3.000
 6QB  H5   C20  C18  115.94  3.000
 6QB  H5   C20  C14  121.78  3.000
 6QB  C18  C20  C14  122.26  3.000
 6QB  H6   C21  C25  108.07  3.000
 6QB  H6   C21  C23  105.27  3.000
 6QB  C25  C21  C23  111.31  3.000
 6QB  H6   C21  N17  105.99  3.000
 6QB  C23  C21  N17  114.46  3.000
 6QB  C25  C21  N17  111.22  3.000
 6QB  H7   C26  C27  119.09  3.000
 6QB  H7   C26  C25  119.97  3.000
 6QB  C27  C26  C25  120.94  3.000
 6QB  CL1  C28  C29  119.63  3.000
 6QB  CL1  C28  C27  121.24  3.000
 6QB  C29  C28  C27  119.13  3.000
 6QB  H10  C1   H9   108.65  3.000
 6QB  H10  C1   H8   109.18  3.000
 6QB  H9   C1   H8   108.44  3.000
 6QB  H10  C1   N2   111.37  3.000
 6QB  H9   C1   N2   107.88  3.000
 6QB  H8   C1   N2   111.23  3.000
 6QB  N6   N2   C3   112.06  3.000
 6QB  N6   N2   C1   120.60  3.000
 6QB  C3   N2   C1   127.33  3.000
 6QB  N7   C3   N2   119.40  3.000
 6QB  N7   C3   C4   133.67  3.000
 6QB  N2   C3   C4   106.92  3.000
 6QB  N2   N6   C5   105.11  3.000
 6QB  H11  N7   C3   118.25  3.000
 6QB  H11  N7   C8   114.33  3.000
 6QB  C3   N7   C8   127.42  3.000
 6QB  C10  N9   C8   115.90  3.000
 6QB  H12  C11  C12  122.79  3.000
 6QB  H12  C11  C10  121.08  3.000
 6QB  C12  C11  C10  116.12  3.000
 6QB  C14  C12  N13  116.40  3.000
 6QB  C14  C12  C11  122.18  3.000
 6QB  N13  C12  C11  121.41  3.000
 6QB  C12  N13  C8   117.33  3.000
 6QB  C12  C14  C20  121.13  3.000
 6QB  C20  C14  C15  119.22  3.000
 6QB  C12  C14  C15  119.64  3.000
 6QB  H13  C16  N17  116.77  3.000
 6QB  H13  C16  C15  120.96  3.000
 6QB  N17  C16  C15  122.25  3.000
 6QB  C18  N17  C16  121.99  3.000
 6QB  C18  N17  C21  115.43  3.000
 6QB  C16  N17  C21  122.57  3.000
 6QB  O19  C18  N17  120.34  3.000
 6QB  O19  C18  C20  124.24  3.000
 6QB  N17  C18  C20  115.42  3.000
 6QB  H15  C23  H14  106.72  3.000
 6QB  H15  C23  O24  111.41  3.000
 6QB  H14  C23  O24  112.45  3.000
 6QB  H15  C23  C21  106.16  3.000
 6QB  H14  C23  C21  109.05  3.000
 6QB  O24  C23  C21  110.77  3.000
 6QB  H16  O24  C23  108.23  3.000
 6QB  C30  C25  C26  119.28  3.000
 6QB  C26  C25  C21  119.26  3.000
 6QB  C30  C25  C21  121.42  3.000
 6QB  H17  C27  C28  119.84  3.000
 6QB  H17  C27  C26  120.49  3.000
 6QB  C28  C27  C26  119.67  3.000
 6QB  F31  C29  C30  119.40  3.000
 6QB  C30  C29  C28  121.58  3.000
 6QB  F31  C29  C28  119.02  3.000
 6QB  H18  C30  C29  118.70  3.000
 6QB  H18  C30  C25  121.91  3.000
 6QB  C29  C30  C25  119.39  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
 6QB  CONST_01  N6   N2   C3   C4     0.00   0.0  0
 6QB  CONST_02  N2   N6   C5   C4     0.00   0.0  0
 6QB  CONST_03  C3   N2   N6   C5     0.00   0.0  0
 6QB  CONST_04  N2   C3   C4   C5     0.00   0.0  0
 6QB  CONST_05  C11  C10  N9   C8     0.00   0.0  0
 6QB  CONST_06  C11  C12  N13  C8     0.00   0.0  0
 6QB  CONST_07  N13  C8   N9   C10    0.00   0.0  0
 6QB  CONST_08  N13  C12  C11  C10    0.00   0.0  0
 6QB  CONST_09  C29  C30  C25  C26    0.00   0.0  0
 6QB  CONST_10  C29  C28  C27  C26    0.00   0.0  0
 6QB  CONST_11  C25  C30  C29  C28    0.00   0.0  0
 6QB  CONST_12  C25  C26  C27  C28    0.00   0.0  0
 6QB  CONST_13  N6   C5   C4   C3     0.00   0.0  0
 6QB  CONST_14  C12  N13  C8   N9     0.00   0.0  0
 6QB  CONST_15  C12  C11  C10  N9     0.00   0.0  0
 6QB  CONST_16  C30  C29  C28  C27    0.00   0.0  0
 6QB  CONST_17  C30  C25  C26  C27    0.00   0.0  0
 6QB  CONST_18  C14  C12  N13  C8   180.00   0.0  0
 6QB  CONST_19  C14  C12  C11  C10  180.00   0.0  0
 6QB  CONST_20  C16  N17  C18  C20    0.00   0.0  0
 6QB  CONST_21  C1   N2   C3   C4   180.00   0.0  0
 6QB  CONST_22  C1   N2   N6   C5   180.00   0.0  0
 6QB  CONST_23  N7   C3   C4   C5   180.00   0.0  0
 6QB  CONST_24  N7   C8   N9   C10  180.00   0.0  0
 6QB  CONST_25  C29  C30  C25  C21  180.00   0.0  0
 6QB  CONST_26  C27  C26  C25  C21  180.00   0.0  0
 6QB  CONST_27  CL1  C28  C27  C26  180.00   0.0  0
 6QB  CONST_28  N7   C3   N2   N6   180.00   0.0  0
 6QB  CONST_29  C12  N13  C8   N7   180.00   0.0  0
 6QB  CONST_30  F31  C29  C30  C25  180.00   0.0  0
 6QB  CONST_31  F31  C29  C28  C27  180.00   0.0  0
 6QB  CONST_32  CL1  C28  C29  C30  180.00   0.0  0
 6QB  CONST_33  C21  N17  C18  C20  180.00   0.0  0
 6QB  CONST_34  O19  C18  N17  C16  180.00   0.0  0
 6QB  CONST_35  H3   C10  N9   C8   180.00   0.0  0
 6QB  CONST_36  H18  C30  C25  C26  180.00   0.0  0
 6QB  CONST_37  H7   C26  C27  C28  180.00   0.0  0
 6QB  CONST_38  H1   C4   C3   N2   180.00   0.0  0
 6QB  CONST_39  H2   C5   N6   N2   180.00   0.0  0
 6QB  CONST_40  H12  C11  C10  N9   180.00   0.0  0
 6QB  CONST_41  H17  C27  C26  C25  180.00   0.0  0
 6QB  CONST_42  O19  C18  N17  C21    0.00   0.0  0
 6QB  Var_01    N13  C12  C14  C15  -25.88  30.0  3
 6QB  Var_02    C8   N7   C3   C4    -1.41  30.0  1
 6QB  Var_03    N9   C8   N7   C3    -0.14  30.0  2
 6QB  Var_04    H8   C1   N2   C3    57.83  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
 6QB  chir_01  C21  N17  C25  C23  negativ

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
 6QB  plan-1  C4   0.020
 6QB  plan-1  C5   0.020
 6QB  plan-1  C1   0.020
 6QB  plan-1  N2   0.020
 6QB  plan-1  C3   0.020
 6QB  plan-1  N6   0.020
 6QB  plan-1  N7   0.020
 6QB  plan-1  H1   0.020
 6QB  plan-1  H2   0.020
 6QB  plan-2  C8   0.020
 6QB  plan-2  C10  0.020
 6QB  plan-2  N7   0.020
 6QB  plan-2  N9   0.020
 6QB  plan-2  C11  0.020
 6QB  plan-2  C12  0.020
 6QB  plan-2  N13  0.020
 6QB  plan-2  C14  0.020
 6QB  plan-2  H3   0.020
 6QB  plan-2  H12  0.020
 6QB  plan-3  C15  0.020
 6QB  plan-3  C20  0.020
 6QB  plan-3  C21  0.020
 6QB  plan-3  C12  0.020
 6QB  plan-3  C14  0.020
 6QB  plan-3  C16  0.020
 6QB  plan-3  N17  0.020
 6QB  plan-3  C18  0.020
 6QB  plan-3  O19  0.020
 6QB  plan-3  H4   0.020
 6QB  plan-3  H5   0.020
 6QB  plan-3  H13  0.020
 6QB  plan-4  C21  0.020
 6QB  plan-4  C26  0.020
 6QB  plan-4  C28  0.020
 6QB  plan-4  C25  0.020
 6QB  plan-4  C27  0.020
 6QB  plan-4  C29  0.020
 6QB  plan-4  C30  0.020
 6QB  plan-4  F31  0.020
 6QB  plan-4  H7   0.020
 6QB  plan-4  H17  0.020
 6QB  plan-4  H18  0.020
 6QB  plan-4  CL1  0.020

