# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:12:47 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-methyl-5-[(3R)-3-(3,4,5-trimethoxyphenyl)pent-1-yn-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C#Cc1c(C)nc(N)nc1N)c2cc(OC)c(OC)c(OC)c2
#
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
 QLR  QLR  6-methyl-5-[(3R)-3-(3,4,5-trimethoxyphenyl)pent-1-yn-1-yl]pyrimidine-2,4-diamine  ligand  50  26  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QLR
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
 QLR  N1    N  N     0  -0.500   4.4826  -1.9663   0.0354
 QLR  C2    C  CR6   0   0.540   5.5647  -1.1838  -0.0585
 QLR  N3    N  N     0  -0.503   5.5720   0.1421  -0.1842
 QLR  C4    C  CR6   0   0.455   4.3940   0.7533  -0.2052
 QLR  C5    C  CR6   0  -0.348   3.1810   0.0248  -0.0996
 QLR  C6    C  CR6   0   0.250   3.3035  -1.3588   0.0172
 QLR  CAB   C  CH3   0  -0.438  -5.0931   1.8937  -2.1584
 QLR  CAC   C  CH3   0  -0.440  -1.5794  -2.4653   2.2877
 QLR  CAD   C  CH3   0  -0.409  -4.9292  -2.4883  -0.8363
 QLR  CAE   C  CH3   0  -0.762   2.0890  -2.2195   0.1508
 QLR  NAF   N  NH2   0  -0.819   6.7605  -1.7964  -0.0004
 QLR  NAG   N  NH2   0  -0.824   4.3853   2.0905  -0.3085
 QLR  CAH   C  CSP   0   0.101   1.9310   0.6895  -0.1020
 QLR  CAI   C  CSP   0   0.153   0.8770   1.2790  -0.1035
 QLR  CAJ   C  CR16  0  -0.487  -2.7142   1.3377  -0.7707
 QLR  CAK   C  CR16  0  -0.465  -1.5268  -0.1355   0.7240
 QLR  CAL   C  CH2   0  -0.404  -0.4782   2.9402   1.1388
 QLR  CAU   C  CR6   0   0.188  -1.5714   1.0157  -0.0513
 QLR  CAW   C  CR6   0   0.348  -3.8267   0.4989  -0.7197
 QLR  CAX   C  CR6   0   0.349  -2.6368  -0.9755   0.7795
 QLR  CAY   C  CR6   0   0.161  -3.7944  -0.6559   0.0647
 QLR  CAZ   C  CH1   0  -0.507  -0.4024   1.9814  -0.0669
 QLR  HAA   H  HCH3  0   0.238   0.5132   4.6613   1.9912
 QLR  HAAA  H  HCH3  0   0.222   1.6087   3.5356   1.1990
 QLR  HAAB  H  HCH3  0   0.223   0.5853   4.5987   0.2323
 QLR  HAB   H  HCH3  0   0.261  -6.0860   1.8719  -2.6006
 QLR  HABA  H  HCH3  0   0.229  -5.0001   2.7948  -1.5466
 QLR  HABB  H  HCH3  0   0.229  -4.3531   1.9354  -2.9614
 QLR  HAC   H  HCH3  0   0.263  -1.8399  -3.3921   2.7929
 QLR  HACA  H  HCH3  0   0.224  -0.6854  -2.6383   1.6829
 QLR  HACB  H  HCH3  0   0.231  -1.3547  -1.7039   3.0388
 QLR  HAD   H  HCH3  0   0.221  -4.0787  -3.1678  -0.7453
 QLR  HADA  H  HCH3  0   0.237  -5.8455  -3.0531  -0.6726
 QLR  HADB  H  HCH3  0   0.221  -4.9466  -2.0825  -1.8506
 QLR  HAE   H  HCH3  0   0.257   1.7077  -2.1691   1.1736
 QLR  HAEA  H  HCH3  0   0.252   1.2840  -1.8877  -0.5045
 QLR  HAEB  H  HCH3  0   0.256   2.3273  -3.2579  -0.0676
 QLR  HNAF  H  HNH2  0   0.395   6.8025  -2.7982  -0.0644
 QLR  HNAA  H  HNH2  0   0.395   7.5922  -1.2784  -0.2229
 QLR  HNAG  H  HNH2  0   0.397   5.2436   2.5682  -0.5248
 QLR  HNAB  H  HNH2  0   0.401   3.5278   2.5772  -0.5058
 QLR  HAJ   H  HCR6  0   0.275  -2.7203   2.2377  -1.3717
 QLR  HAK   H  HCR6  0   0.270  -0.6232  -0.3720   1.2707
 QLR  HAL   H  HCH2  0   0.229  -0.4421   2.3522   2.0590
 QLR  HALA  H  HCH2  0   0.240  -1.4570   3.4252   1.1139
 QLR  HAZ   H  HCH1  0   0.277  -0.4806   2.5906  -0.9748
 QLR  OAO   O  O2    0  -0.464  -4.9737   0.7163  -1.3854
 QLR  CAA   C  CH3   0  -0.672   0.6193   3.9912   1.1381
 QLR  OAP   O  O2    0  -0.463  -2.6949  -2.1118   1.4961
 QLR  OAQ   O  O2    0  -0.482  -4.8890  -1.4591   0.1432

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
 QLR  C2   N1    aromatic  1.339  0.020  1.339
 QLR  N1   C6    aromatic  1.327  0.020  1.327
 QLR  NAF  C2    single    1.345  0.020  1.345
 QLR  C2   N3    aromatic  1.332  0.020  1.332
 QLR  N3   C4    aromatic  1.327  0.020  1.327
 QLR  C4   NAG   single    1.341  0.020  1.341
 QLR  C4   C5    aromatic  1.419  0.020  1.419
 QLR  C6   C5    aromatic  1.394  0.020  1.394
 QLR  C5   CAH   single    1.416  0.020  1.416
 QLR  C6   CAE   single    1.495  0.020  1.495
 QLR  CAL  CAA   single    1.520  0.020  1.520
 QLR  CAA  HAA   single    0.970  0.020  1.090
 QLR  CAA  HAAA  single    0.970  0.020  1.090
 QLR  CAA  HAAB  single    0.970  0.020  1.090
 QLR  OAO  CAB   single    1.414  0.020  1.414
 QLR  CAB  HAB   single    0.970  0.020  1.090
 QLR  CAB  HABA  single    0.970  0.020  1.090
 QLR  CAB  HABB  single    0.970  0.020  1.090
 QLR  OAP  CAC   single    1.413  0.020  1.413
 QLR  CAC  HAC   single    0.970  0.020  1.090
 QLR  CAC  HACA  single    0.970  0.020  1.090
 QLR  CAC  HACB  single    0.970  0.020  1.090
 QLR  CAD  OAQ   single    1.421  0.020  1.421
 QLR  CAD  HAD   single    0.970  0.020  1.090
 QLR  CAD  HADA  single    0.970  0.020  1.090
 QLR  CAD  HADB  single    0.970  0.020  1.090
 QLR  CAE  HAE   single    0.970  0.020  1.090
 QLR  CAE  HAEA  single    0.970  0.020  1.090
 QLR  CAE  HAEB  single    0.970  0.020  1.090
 QLR  NAF  HNAF  single    0.890  0.020  1.040
 QLR  NAF  HNAA  single    0.890  0.020  1.040
 QLR  NAG  HNAG  single    0.890  0.020  1.040
 QLR  NAG  HNAB  single    0.890  0.020  1.040
 QLR  CAH  CAI   triple    1.208  0.020  1.208
 QLR  CAI  CAZ   single    1.460  0.020  1.460
 QLR  CAU  CAJ   aromatic  1.388  0.020  1.388
 QLR  CAJ  CAW   aromatic  1.394  0.020  1.394
 QLR  CAJ  HAJ   single    0.930  0.020  1.080
 QLR  CAU  CAK   aromatic  1.389  0.020  1.389
 QLR  CAK  CAX   aromatic  1.393  0.020  1.393
 QLR  CAK  HAK   single    0.930  0.020  1.080
 QLR  CAZ  CAL   single    1.542  0.020  1.542
 QLR  CAL  HAL   single    0.970  0.020  1.090
 QLR  CAL  HALA  single    0.970  0.020  1.090
 QLR  CAW  OAO   single    1.344  0.020  1.344
 QLR  CAX  OAP   single    1.345  0.020  1.345
 QLR  CAY  OAQ   single    1.360  0.020  1.360
 QLR  CAZ  CAU   single    1.516  0.020  1.516
 QLR  CAW  CAY   aromatic  1.396  0.020  1.396
 QLR  CAX  CAY   aromatic  1.398  0.020  1.398
 QLR  CAZ  HAZ   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
 QLR  C6    N1   C2    116.73  3.000
 QLR  NAF   C2   N3    116.92  3.000
 QLR  N3    C2   N1    126.37  3.000
 QLR  NAF   C2   N1    116.71  3.000
 QLR  C4    N3   C2    117.07  3.000
 QLR  NAG   C4   C5    120.80  3.000
 QLR  C5    C4   N3    121.41  3.000
 QLR  NAG   C4   N3    117.78  3.000
 QLR  CAH   C5   C6    122.94  3.000
 QLR  CAH   C5   C4    120.91  3.000
 QLR  C6    C5   C4    116.15  3.000
 QLR  CAE   C6   C5    120.51  3.000
 QLR  CAE   C6   N1    117.22  3.000
 QLR  C5    C6   N1    122.27  3.000
 QLR  HABB  CAB  HABA  108.80  3.000
 QLR  HABB  CAB  HAB   108.68  3.000
 QLR  HABA  CAB  HAB   108.78  3.000
 QLR  HABB  CAB  OAO   112.11  3.000
 QLR  HABA  CAB  OAO   111.93  3.000
 QLR  HAB   CAB  OAO   106.43  3.000
 QLR  HACB  CAC  HACA  108.81  3.000
 QLR  HACB  CAC  HAC   108.89  3.000
 QLR  HACA  CAC  HAC   108.55  3.000
 QLR  HACB  CAC  OAP   111.91  3.000
 QLR  HACA  CAC  OAP   112.04  3.000
 QLR  HAC   CAC  OAP   106.52  3.000
 QLR  HADB  CAD  HADA  108.60  3.000
 QLR  HADB  CAD  HAD   108.71  3.000
 QLR  HADA  CAD  HAD   108.67  3.000
 QLR  HADB  CAD  OAQ   111.79  3.000
 QLR  HADA  CAD  OAQ   107.21  3.000
 QLR  HAD   CAD  OAQ   111.77  3.000
 QLR  HAEB  CAE  HAEA  109.38  3.000
 QLR  HAEB  CAE  HAE   107.96  3.000
 QLR  HAEA  CAE  HAE   106.93  3.000
 QLR  HAEB  CAE  C6    110.72  3.000
 QLR  HAEA  CAE  C6    111.79  3.000
 QLR  HAE   CAE  C6    109.92  3.000
 QLR  HNAA  NAF  HNAF  117.74  3.000
 QLR  HNAA  NAF  C2    119.44  3.000
 QLR  HNAF  NAF  C2    119.25  3.000
 QLR  HNAB  NAG  HNAG  117.10  3.000
 QLR  HNAB  NAG  C4    120.21  3.000
 QLR  HNAG  NAG  C4    118.99  3.000
 QLR  CAI   CAH  C5    180.00  3.000
 QLR  CAZ   CAI  CAH   180.00  3.000
 QLR  HAJ   CAJ  CAW   121.08  3.000
 QLR  HAJ   CAJ  CAU   119.03  3.000
 QLR  CAW   CAJ  CAU   119.90  3.000
 QLR  HAK   CAK  CAX   120.89  3.000
 QLR  HAK   CAK  CAU   119.34  3.000
 QLR  CAX   CAK  CAU   119.77  3.000
 QLR  HALA  CAL  HAL   106.72  3.000
 QLR  HALA  CAL  CAZ   107.59  3.000
 QLR  HAL   CAL  CAZ   108.80  3.000
 QLR  HALA  CAL  CAA   109.87  3.000
 QLR  HAL   CAL  CAA   110.41  3.000
 QLR  CAZ   CAL  CAA   113.21  3.000
 QLR  CAZ   CAU  CAK   120.60  3.000
 QLR  CAZ   CAU  CAJ   118.79  3.000
 QLR  CAK   CAU  CAJ   120.53  3.000
 QLR  CAY   CAW  OAO   115.58  3.000
 QLR  CAY   CAW  CAJ   119.98  3.000
 QLR  OAO   CAW  CAJ   124.44  3.000
 QLR  CAY   CAX  OAP   115.47  3.000
 QLR  CAY   CAX  CAK   120.11  3.000
 QLR  OAP   CAX  CAK   124.42  3.000
 QLR  CAX   CAY  CAW   119.71  3.000
 QLR  CAX   CAY  OAQ   120.14  3.000
 QLR  CAW   CAY  OAQ   120.15  3.000
 QLR  HAZ   CAZ  CAU   107.91  3.000
 QLR  HAZ   CAZ  CAL   107.37  3.000
 QLR  CAU   CAZ  CAL   110.48  3.000
 QLR  HAZ   CAZ  CAI   108.00  3.000
 QLR  CAU   CAZ  CAI   111.68  3.000
 QLR  CAL   CAZ  CAI   111.21  3.000
 QLR  CAW   OAO  CAB   118.53  3.000
 QLR  HAAB  CAA  HAAA  107.89  3.000
 QLR  HAAB  CAA  HAA   107.72  3.000
 QLR  HAAA  CAA  HAA   107.54  3.000
 QLR  HAAB  CAA  CAL   111.27  3.000
 QLR  HAAA  CAA  CAL   111.48  3.000
 QLR  HAA   CAA  CAL   110.77  3.000
 QLR  CAX   OAP  CAC   118.42  3.000
 QLR  CAY   OAQ  CAD   114.25  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
 QLR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 QLR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 QLR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 QLR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 QLR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 QLR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 QLR  CONST_07  CAX   CAK  CAU  CAJ     0.00   0.0  0
 QLR  CONST_08  CAX   CAY  CAW  CAJ     0.00   0.0  0
 QLR  CONST_09  CAW   CAJ  CAU  CAK     0.00   0.0  0
 QLR  CONST_10  CAW   CAY  CAX  CAK     0.00   0.0  0
 QLR  CONST_11  CAY   CAW  CAJ  CAU     0.00   0.0  0
 QLR  CONST_12  CAY   CAX  CAK  CAU     0.00   0.0  0
 QLR  CONST_13  CAH   C5   C6   N1    180.00   0.0  0
 QLR  CONST_14  CAE   C6   N1   C2    180.00   0.0  0
 QLR  CONST_15  NAG   C4   N3   C2    180.00   0.0  0
 QLR  CONST_16  CAH   C5   C4   N3    180.00   0.0  0
 QLR  CONST_17  NAF   C2   N3   C4    180.00   0.0  0
 QLR  CONST_18  CAE   C6   C5   C4    180.00   0.0  0
 QLR  CONST_19  NAF   C2   N1   C6    180.00   0.0  0
 QLR  CONST_20  NAG   C4   C5   C6    180.00   0.0  0
 QLR  CONST_21  OAQ   CAY  CAW  CAJ   180.00   0.0  0
 QLR  CONST_22  OAQ   CAY  CAX  CAK   180.00   0.0  0
 QLR  CONST_23  CAU   CAJ  CAW  OAO   180.00   0.0  0
 QLR  CONST_24  CAX   CAY  CAW  OAO   180.00   0.0  0
 QLR  CONST_25  CAU   CAK  CAX  OAP   180.00   0.0  0
 QLR  CONST_26  CAW   CAY  CAX  OAP   180.00   0.0  0
 QLR  CONST_27  CAZ   CAU  CAJ  CAW   180.00   0.0  0
 QLR  CONST_28  CAZ   CAU  CAK  CAX   180.00   0.0  0
 QLR  CONST_29  HAK   CAK  CAU  CAJ   180.00   0.0  0
 QLR  CONST_30  HAJ   CAJ  CAU  CAK   180.00   0.0  0
 QLR  CONST_31  HNAF  NAF  C2   N1      0.00   0.0  0
 QLR  CONST_32  HNAA  NAF  C2   N1    180.00   0.0  0
 QLR  CONST_33  HNAG  NAG  C4   N3      0.00   0.0  0
 QLR  CONST_34  HNAB  NAG  C4   N3    180.00   0.0  0
 QLR  Var_01    CAJ   CAW  OAO  CAB    -2.25  30.0  3
 QLR  Var_02    CAK   CAX  OAP  CAC     2.35  30.0  2
 QLR  Var_03    CAW   CAY  OAQ  CAD    90.35  30.0  3
 QLR  Var_04    HAE   CAE  C6   N1    101.21  30.0  2
 QLR  Var_05    HAB   CAB  OAO  CAW  -179.74  30.0  3
 QLR  Var_06    HAC   CAC  OAP  CAX   178.83  30.0  3
 QLR  Var_07    HAD   CAD  OAQ  CAY    61.28  30.0  3
 QLR  Var_08    HAA   CAA  CAL  CAZ   178.55  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
 QLR  chir_01  CAZ  CAI  CAL  CAU  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
 QLR  plan-1  N1    0.020
 QLR  plan-1  C2    0.020
 QLR  plan-1  N3    0.020
 QLR  plan-1  C4    0.020
 QLR  plan-1  C5    0.020
 QLR  plan-1  C6    0.020
 QLR  plan-1  CAE   0.020
 QLR  plan-1  NAF   0.020
 QLR  plan-1  NAG   0.020
 QLR  plan-1  CAH   0.020
 QLR  plan-1  CAI   0.020
 QLR  plan-2  CAJ   0.020
 QLR  plan-2  CAK   0.020
 QLR  plan-2  CAU   0.020
 QLR  plan-2  CAW   0.020
 QLR  plan-2  CAX   0.020
 QLR  plan-2  CAY   0.020
 QLR  plan-2  CAZ   0.020
 QLR  plan-2  HAJ   0.020
 QLR  plan-2  HAK   0.020
 QLR  plan-2  OAO   0.020
 QLR  plan-2  OAP   0.020
 QLR  plan-2  OAQ   0.020
 QLR  plan-3  C2    0.020
 QLR  plan-3  NAF   0.020
 QLR  plan-3  HNAF  0.020
 QLR  plan-3  HNAA  0.020
 QLR  plan-4  C4    0.020
 QLR  plan-4  NAG   0.020
 QLR  plan-4  HNAG  0.020
 QLR  plan-4  HNAB  0.020

