# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:28:02 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-[(3R,4S)-4-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}oxolan-3-yl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(Cl)c(c1Cl)C2=Cc3cnc(N[C@@H]4COC[C@@H]4NC(=O)C=C)nc3N(C)C2=O
#
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
 QS7  QS7  N-[(3R,4S)-4-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}oxolan-3-yl]prop-2-enamide  ligand  58  35  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QS7
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
 QS7  C4    C   CR66  0   0.566  -1.1552  -1.1111  -0.5851
 QS7  C5    C   CR66  0  -0.093  -0.7712  -0.7238   0.7107
 QS7  C6    C   CR16  0  -0.034  -1.7814  -0.7608   1.6683
 QS7  N1    N   N     0  -0.452  -3.0171  -1.1104   1.3992
 QS7  N3    N   N     0  -0.494  -2.3911  -1.4769  -0.8714
 QS7  CAV   C   CH3   0  -0.444   6.0629   3.6323   0.7578
 QS7  CAO   C   CR6   0   0.528   4.5165   1.8621   0.4471
 QS7  CAN   C   CR6   0  -0.295   3.1954   1.4630   0.2306
 QS7  CLAS  CL  CL    0  -0.099   1.9845   2.6832   0.0596
 QS7  CAP   C   CR16  0  -0.572   5.5082   0.8938   0.5664
 QS7  CAL   C   CR6   0   0.526   5.1911  -0.4584   0.4714
 QS7  OAT   O   O2    0  -0.455   6.0858  -1.4449   0.5690
 QS7  CAW   C   CH3   0  -0.444   7.4446  -1.1169   0.8017
 QS7  CAM   C   CR6   0  -0.284   3.8635  -0.8312   0.2609
 QS7  CLAR  CL  CL    0  -0.103   3.4786  -2.5101   0.1505
 QS7  CAK   C   CR6   0   0.288   2.8573   0.1189   0.1432
 QS7  CAI   C   CR6   0  -0.222   1.4569  -0.3004  -0.0589
 QS7  CAJ   C   CR16  0  -0.143   0.5640  -0.3168   0.9505
 QS7  CAH   C   CR6   0   0.566   1.0796  -0.6905  -1.4108
 QS7  OAQ   O   O     0  -0.455   1.8693  -0.6640  -2.3400
 QS7  NAG   N   NR6   0  -0.587  -0.2383  -1.0978  -1.5973
 QS7  CBI   C   CH3   0  -0.538  -0.6777  -1.4990  -2.9278
 QS7  C2    C   CR6   0   0.592  -3.2774  -1.4337   0.1225
 QS7  NAX   N   NH1   0  -0.649  -4.5522  -1.7501  -0.1878
 QS7  CAY   C   CH1   0  -0.132  -5.6630  -1.3215   0.6173
 QS7  CAZ   C   CH2   0  -0.178  -6.9776  -1.9265   0.1121
 QS7  OBA   O   O2    0  -0.487  -7.9563  -0.9394   0.3360
 QS7  CBB   C   CH2   0  -0.176  -7.3634   0.2897  -0.0106
 QS7  CBC   C   CH1   0  -0.124  -5.9435   0.2267   0.5623
 QS7  NBD   N   NH1   0  -0.648  -5.0005   0.9599  -0.2295
 QS7  CBE   C   C     0   0.533  -3.9831   1.6979   0.2718
 QS7  OBH   O   O     0  -0.480  -3.8784   1.9903   1.4521
 QS7  CBF   C   C1    0  -0.328  -2.9813   2.0967  -0.7524
 QS7  CBG   C   C2    0  -0.465  -1.7948   2.5844  -0.4106
 QS7  H1    H   HCR6  0   0.281  -1.5567  -0.4900   2.6954
 QS7  H2    H   HCH3  0   0.237   6.4609   3.2585   1.7041
 QS7  H3    H   HCH3  0   0.237   6.7388   3.3484  -0.0521
 QS7  H4    H   HCH3  0   0.268   6.0059   4.7163   0.8039
 QS7  H5    H   HCR6  0   0.321   6.5325   1.1940   0.7338
 QS7  H6    H   HCH3  0   0.237   7.8577  -0.5057  -0.0039
 QS7  H7    H   HCH3  0   0.237   7.5776  -0.5948   1.7521
 QS7  H8    H   HCH3  0   0.268   7.9825  -2.0602   0.8400
 QS7  H9    H   HCR6  0   0.281   0.8551  -0.0213   1.9516
 QS7  H10   H   HCH3  0   0.271   0.1564  -1.4172  -3.6126
 QS7  H11   H   HCH3  0   0.259  -1.0319  -2.5272  -2.9139
 QS7  H12   H   HCH3  0   0.257  -1.4863  -0.8562  -3.2683
 QS7  H13   H   HNH1  0   0.393  -4.7222  -1.9015  -1.1711
 QS7  H14   H   HCH1  0   0.286  -5.4812  -1.6108   1.6503
 QS7  H15   H   HCH2  0   0.215  -6.8982  -2.1664  -0.9588
 QS7  H16   H   HCH2  0   0.255  -7.2642  -2.8345   0.6412
 QS7  H17   H   HCH2  0   0.215  -7.3249   0.4177  -1.1027
 QS7  H18   H   HCH2  0   0.252  -7.9590   1.1016   0.4057
 QS7  H19   H   HCH1  0   0.284  -5.9213   0.6293   1.5724
 QS7  H20   H   HNH1  0   0.400  -4.9958   0.7779  -1.2214
 QS7  H21   H   H     0   0.270  -3.2248   1.9312  -1.7965
 QS7  H23   H   H     0   0.256  -1.0568   2.8351  -1.1598
 QS7  H24   H   H     0   0.256  -1.5186   2.7394   0.6239
 QS7  OAU   O   O2    0  -0.454   4.7419   3.1760   0.5250

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
 QS7  CAW   OAT   single    1.417  0.020  1.417
 QS7  OAT   CAL   single    1.335  0.020  1.335
 QS7  CAL   CAP   aromatic  1.392  0.020  1.392
 QS7  CAL   CAM   aromatic  1.395  0.020  1.395
 QS7  CAP   CAO   aromatic  1.391  0.020  1.391
 QS7  CAV   OAU   single    1.417  0.020  1.417
 QS7  CLAR  CAM   single    1.726  0.020  1.726
 QS7  CAM   CAK   aromatic  1.389  0.020  1.389
 QS7  CAO   OAU   single    1.335  0.020  1.335
 QS7  CAO   CAN   aromatic  1.397  0.020  1.397
 QS7  CAK   CAN   aromatic  1.389  0.020  1.389
 QS7  CAK   CAI   single    1.476  0.020  1.476
 QS7  CAN   CLAS  single    1.728  0.020  1.728
 QS7  OAQ   CAH   double    1.220  0.020  1.220
 QS7  CAI   CAH   single    1.457  0.020  1.457
 QS7  CAI   CAJ   double    1.348  0.020  1.348
 QS7  CAH   NAG   single    1.392  0.020  1.392
 QS7  CAJ   C5    single    1.416  0.020  1.416
 QS7  NAG   CBI   single    1.457  0.020  1.457
 QS7  NAG   C4    single    1.366  0.020  1.366
 QS7  C5    C4    aromatic  1.406  0.020  1.406
 QS7  C5    C6    aromatic  1.392  0.020  1.392
 QS7  C4    N3    aromatic  1.320  0.020  1.320
 QS7  C6    N1    aromatic  1.312  0.020  1.312
 QS7  N3    C2    aromatic  1.332  0.020  1.332
 QS7  N1    C2    aromatic  1.342  0.020  1.342
 QS7  C2    NAX   single    1.350  0.020  1.350
 QS7  CAZ   OBA   single    1.408  0.020  1.408
 QS7  CAZ   CAY   single    1.533  0.020  1.533
 QS7  NAX   CAY   single    1.437  0.020  1.437
 QS7  OBA   CBB   single    1.408  0.020  1.408
 QS7  CAY   CBC   single    1.574  0.020  1.574
 QS7  CBB   CBC   single    1.532  0.020  1.532
 QS7  CBC   NBD   single    1.433  0.020  1.433
 QS7  NBD   CBE   single    1.353  0.020  1.353
 QS7  CBE   OBH   double    1.221  0.020  1.221
 QS7  CBE   CBF   single    1.487  0.020  1.487
 QS7  CBG   CBF   double    1.328  0.020  1.328
 QS7  C6    H1    single    0.930  0.020  1.080
 QS7  CAV   H2    single    0.970  0.020  1.090
 QS7  CAV   H3    single    0.970  0.020  1.090
 QS7  CAV   H4    single    0.970  0.020  1.090
 QS7  CAP   H5    single    0.930  0.020  1.080
 QS7  CAW   H6    single    0.970  0.020  1.090
 QS7  CAW   H7    single    0.970  0.020  1.090
 QS7  CAW   H8    single    0.970  0.020  1.090
 QS7  CAJ   H9    single    0.930  0.020  1.080
 QS7  CBI   H10   single    0.970  0.020  1.090
 QS7  CBI   H11   single    0.970  0.020  1.090
 QS7  CBI   H12   single    0.970  0.020  1.090
 QS7  NAX   H13   single    0.890  0.020  1.040
 QS7  CAY   H14   single    0.970  0.020  1.090
 QS7  CAZ   H15   single    0.970  0.020  1.090
 QS7  CAZ   H16   single    0.970  0.020  1.090
 QS7  CBB   H17   single    0.970  0.020  1.090
 QS7  CBB   H18   single    0.970  0.020  1.090
 QS7  CBC   H19   single    0.970  0.020  1.090
 QS7  NBD   H20   single    0.860  0.020  1.020
 QS7  CBF   H21   single    0.930  0.020  1.080
 QS7  CBG   H23   single    0.930  0.020  1.080
 QS7  CBG   H24   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
 QS7  NAG   C4   N3    118.06  3.000
 QS7  N3    C4   C5    122.13  3.000
 QS7  NAG   C4   C5    119.80  3.000
 QS7  CAJ   C5   C6    125.11  3.000
 QS7  C6    C5   C4    115.36  3.000
 QS7  CAJ   C5   C4    119.52  3.000
 QS7  H1    C6   N1    117.09  3.000
 QS7  H1    C6   C5    119.59  3.000
 QS7  N1    C6   C5    123.32  3.000
 QS7  C2    N1   C6    116.22  3.000
 QS7  C2    N3   C4    116.87  3.000
 QS7  H4    CAV  H3    108.85  3.000
 QS7  H4    CAV  H2    108.89  3.000
 QS7  H3    CAV  H2    109.14  3.000
 QS7  H4    CAV  OAU   106.22  3.000
 QS7  H3    CAV  OAU   111.80  3.000
 QS7  H2    CAV  OAU   111.83  3.000
 QS7  CAP   CAO  CAN   119.25  3.000
 QS7  CAN   CAO  OAU   116.73  3.000
 QS7  CAP   CAO  OAU   124.02  3.000
 QS7  CAK   CAN  CLAS  120.45  3.000
 QS7  CLAS  CAN  CAO   118.45  3.000
 QS7  CAK   CAN  CAO   121.10  3.000
 QS7  H5    CAP  CAL   119.76  3.000
 QS7  H5    CAP  CAO   119.71  3.000
 QS7  CAL   CAP  CAO   120.52  3.000
 QS7  CAM   CAL  OAT   116.82  3.000
 QS7  CAM   CAL  CAP   119.12  3.000
 QS7  OAT   CAL  CAP   124.06  3.000
 QS7  CAW   OAT  CAL   118.91  3.000
 QS7  H8    CAW  H7    108.90  3.000
 QS7  H8    CAW  H6    108.93  3.000
 QS7  H7    CAW  H6    109.16  3.000
 QS7  H8    CAW  OAT   106.24  3.000
 QS7  H7    CAW  OAT   111.73  3.000
 QS7  H6    CAW  OAT   111.78  3.000
 QS7  CAK   CAM  CLAR  119.90  3.000
 QS7  CAK   CAM  CAL   121.30  3.000
 QS7  CLAR  CAM  CAL   118.80  3.000
 QS7  CAI   CAK  CAM   120.31  3.000
 QS7  CAI   CAK  CAN   120.97  3.000
 QS7  CAM   CAK  CAN   118.71  3.000
 QS7  CAH   CAI  CAJ   121.35  3.000
 QS7  CAJ   CAI  CAK   121.97  3.000
 QS7  CAH   CAI  CAK   116.68  3.000
 QS7  H9    CAJ  CAI   120.71  3.000
 QS7  H9    CAJ  C5    119.21  3.000
 QS7  CAI   CAJ  C5    120.08  3.000
 QS7  NAG   CAH  OAQ   121.15  3.000
 QS7  NAG   CAH  CAI   116.61  3.000
 QS7  OAQ   CAH  CAI   122.24  3.000
 QS7  CBI   NAG  CAH   119.23  3.000
 QS7  CBI   NAG  C4    118.13  3.000
 QS7  CAH   NAG  C4    122.62  3.000
 QS7  H12   CBI  H11   108.70  3.000
 QS7  H12   CBI  H10   109.29  3.000
 QS7  H11   CBI  H10   109.30  3.000
 QS7  H12   CBI  NAG   110.31  3.000
 QS7  H11   CBI  NAG   110.29  3.000
 QS7  H10   CBI  NAG   108.93  3.000
 QS7  NAX   C2   N3    116.69  3.000
 QS7  NAX   C2   N1    117.28  3.000
 QS7  N3    C2   N1    126.03  3.000
 QS7  H13   NAX  CAY   117.41  3.000
 QS7  H13   NAX  C2    114.72  3.000
 QS7  CAY   NAX  C2    122.10  3.000
 QS7  H14   CAY  CBC   108.93  3.000
 QS7  H14   CAY  CAZ   110.57  3.000
 QS7  CBC   CAY  CAZ   102.93  3.000
 QS7  H14   CAY  NAX   108.87  3.000
 QS7  CBC   CAY  NAX   114.29  3.000
 QS7  CAZ   CAY  NAX   111.13  3.000
 QS7  H16   CAZ  H15   108.06  3.000
 QS7  H16   CAZ  OBA   108.92  3.000
 QS7  H15   CAZ  OBA   110.96  3.000
 QS7  H16   CAZ  CAY   113.24  3.000
 QS7  H15   CAZ  CAY   110.18  3.000
 QS7  OBA   CAZ  CAY   105.49  3.000
 QS7  CBB   OBA  CAZ   106.27  3.000
 QS7  H18   CBB  H17   108.17  3.000
 QS7  H18   CBB  CBC   113.22  3.000
 QS7  H17   CBB  CBC   110.09  3.000
 QS7  H18   CBB  OBA   109.04  3.000
 QS7  H17   CBB  OBA   111.14  3.000
 QS7  CBC   CBB  OBA   105.20  3.000
 QS7  H19   CBC  NBD   108.08  3.000
 QS7  H19   CBC  CBB   110.55  3.000
 QS7  NBD   CBC  CBB   112.46  3.000
 QS7  H19   CBC  CAY   109.14  3.000
 QS7  NBD   CBC  CAY   113.90  3.000
 QS7  CBB   CBC  CAY   102.63  3.000
 QS7  H20   NBD  CBE   117.34  3.000
 QS7  H20   NBD  CBC   117.01  3.000
 QS7  CBE   NBD  CBC   124.69  3.000
 QS7  CBF   CBE  OBH   122.95  3.000
 QS7  CBF   CBE  NBD   113.43  3.000
 QS7  OBH   CBE  NBD   123.60  3.000
 QS7  H21   CBF  CBG   120.30  3.000
 QS7  H21   CBF  CBE   118.08  3.000
 QS7  CBG   CBF  CBE   121.55  3.000
 QS7  H24   CBG  H23   117.07  3.000
 QS7  H24   CBG  CBF   121.80  3.000
 QS7  H23   CBG  CBF   121.12  3.000
 QS7  CAO   OAU  CAV   118.94  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
 QS7  CONST_01  N1    C6   C5   C4       0.00   0.0  0
 QS7  CONST_02  N1    C2   N3   C4       0.00   0.0  0
 QS7  CONST_03  C2    N3   C4   C5       0.00   0.0  0
 QS7  CONST_04  C2    N1   C6   C5       0.00   0.0  0
 QS7  CONST_05  N3    C4   C5   C6       0.00   0.0  0
 QS7  CONST_06  N3    C2   N1   C6       0.00   0.0  0
 QS7  CONST_07  CAM   CAL  CAP  CAO      0.00   0.0  0
 QS7  CONST_08  CAM   CAK  CAN  CAO      0.00   0.0  0
 QS7  CONST_09  CAL   CAP  CAO  CAN      0.00   0.0  0
 QS7  CONST_10  CAL   CAM  CAK  CAN      0.00   0.0  0
 QS7  CONST_11  CAK   CAM  CAL  CAP      0.00   0.0  0
 QS7  CONST_12  CAK   CAN  CAO  CAP      0.00   0.0  0
 QS7  CONST_13  CAI   CAK  CAN  CAO    180.00   0.0  0
 QS7  CONST_14  CAI   CAK  CAM  CAL    180.00   0.0  0
 QS7  CONST_15  CAI   CAH  NAG  C4       0.00   0.0  0
 QS7  CONST_16  NAX   C2   N3   C4     180.00   0.0  0
 QS7  CONST_17  NAX   C2   N1   C6     180.00   0.0  0
 QS7  CONST_18  CAL   CAP  CAO  OAU    180.00   0.0  0
 QS7  CONST_19  CAK   CAN  CAO  OAU    180.00   0.0  0
 QS7  CONST_20  OAT   CAL  CAP  CAO    180.00   0.0  0
 QS7  CONST_21  CLAR  CAM  CAK  CAN    180.00   0.0  0
 QS7  CONST_22  CAP   CAO  CAN  CLAS   180.00   0.0  0
 QS7  CONST_23  CAM   CAK  CAN  CLAS   180.00   0.0  0
 QS7  CONST_24  CAI   CAK  CAN  CLAS     0.00   0.0  0
 QS7  CONST_25  CLAR  CAM  CAL  CAP    180.00   0.0  0
 QS7  CONST_26  CAK   CAM  CAL  OAT    180.00   0.0  0
 QS7  CONST_27  CAI   CAK  CAM  CLAR     0.00   0.0  0
 QS7  CONST_30  OAQ   CAH  NAG  C4     180.00   0.0  0
 QS7  CONST_31  CBI   NAG  CAH  CAI    180.00   0.0  0
 QS7  CONST_32  H1    C6   C5   C4     180.00   0.0  0
 QS7  CONST_33  H5    CAP  CAO  CAN    180.00   0.0  0
 QS7  CONST_34  CBI   NAG  CAH  OAQ      0.00   0.0  0
 QS7  CONST_35  H13   NAX  C2   N1     180.00   0.0  0
 QS7  CONST_36  OBH   CBE  NBD  CBC      0.00   0.0  0
 QS7  CONST_37  CBF   CBE  NBD  CBC    180.00   0.0  0
 QS7  CONST_38  H20   NBD  CBE  OBH    180.00   0.0  0
 QS7  Var_01    CAH   CAI  CAK  CAN    101.25  30.0  2
 QS7  Var_02    CBC   CBB  OBA  CAZ    -42.14  30.0  1
 QS7  Var_03    H15   CAZ  OBA  CBB    -78.42  30.0  1
 QS7  Var_04    CAP   CAO  OAU  CAV     -0.74  30.0  2
 QS7  Var_05    CAM   CAL  OAT  CAW   -179.12  30.0  2
 QS7  Var_06    H10   CBI  NAG  C4     179.02  30.0  3
 QS7  Var_07    H2    CAV  OAU  CAO    -60.14  30.0  3
 QS7  Var_08    H6    CAW  OAT  CAL    -61.07  30.0  3
 QS7  Var_09    CBG   CBF  CBE  NBD   -166.29  30.0  2
 QS7  Var_10    H23   CBG  CBF  CBE    177.53   0.0  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
 QS7  chir_01  CAY  CAZ  NAX  CBC  negativ
 QS7  chir_02  CBC  NBD  CAY  CBB  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
 QS7  plan-1  CBE   0.020
 QS7  plan-1  CBF   0.020
 QS7  plan-1  CBG   0.020
 QS7  plan-1  H21   0.020
 QS7  plan-1  H23   0.020
 QS7  plan-1  H24   0.020
 QS7  plan-2  CAO   0.020
 QS7  plan-2  CAN   0.020
 QS7  plan-2  CLAS  0.020
 QS7  plan-2  CAP   0.020
 QS7  plan-2  CAL   0.020
 QS7  plan-2  OAT   0.020
 QS7  plan-2  CAM   0.020
 QS7  plan-2  CLAR  0.020
 QS7  plan-2  CAK   0.020
 QS7  plan-2  CAI   0.020
 QS7  plan-2  H5    0.020
 QS7  plan-2  OAU   0.020
 QS7  plan-3  C4    0.020
 QS7  plan-3  C5    0.020
 QS7  plan-3  C6    0.020
 QS7  plan-3  N1    0.020
 QS7  plan-3  N3    0.020
 QS7  plan-3  CAK   0.020
 QS7  plan-3  CAI   0.020
 QS7  plan-3  CAJ   0.020
 QS7  plan-3  CAH   0.020
 QS7  plan-3  OAQ   0.020
 QS7  plan-3  NAG   0.020
 QS7  plan-3  CBI   0.020
 QS7  plan-3  C2    0.020
 QS7  plan-3  NAX   0.020
 QS7  plan-3  H1    0.020
 QS7  plan-3  H9    0.020
 QS7  plan-4  C2    0.020
 QS7  plan-4  NAX   0.020
 QS7  plan-4  CAY   0.020
 QS7  plan-4  H13   0.020
 QS7  plan-5  CBC   0.020
 QS7  plan-5  NBD   0.020
 QS7  plan-5  CBE   0.020
 QS7  plan-5  OBH   0.020
 QS7  plan-5  CBF   0.020
 QS7  plan-5  H20   0.020

